changeset 3:ff6df146c0d5

Uploaded
author marcel
date Sun, 26 Jun 2011 13:53:57 -0400
parents bbc4a2c1d276
children 02c8570cde57
files CADDSuite/AntitargetRescorer CADDSuite/AutoModel CADDSuite/BindingDBCleaner CADDSuite/CADDSuite-description.txt CADDSuite/CombiLibGenerator CADDSuite/ConstraintsFinder CADDSuite/Converter CADDSuite/DBExporter CADDSuite/DBImporter CADDSuite/DockResultMerger CADDSuite/EvenSplit CADDSuite/FeatureSelector CADDSuite/GalaxyConfigGenerator CADDSuite/GridBuilder CADDSuite/IMGDock CADDSuite/InputPartitioner CADDSuite/InputReader CADDSuite/InteractionConstraintDefiner CADDSuite/LigCheck CADDSuite/Ligand3DGenerator CADDSuite/LigandFileSplitter CADDSuite/ModelCreator CADDSuite/MolCombine CADDSuite/MolDepict CADDSuite/MolFilter CADDSuite/MolPredictor CADDSuite/PDBCutter CADDSuite/PDBDownload CADDSuite/PartialChargesCopy CADDSuite/PocketDetector CADDSuite/Predictor CADDSuite/PropertyModifier CADDSuite/PropertyPlotter CADDSuite/ProteinCheck CADDSuite/ProteinProtonator CADDSuite/QuEasyRun CADDSuite/README CADDSuite/RMSDCalculator CADDSuite/ScoreAnalyzer CADDSuite/SideChainGridBuilder CADDSuite/SimilarityAnalyzer CADDSuite/SimpleRescorer CADDSuite/SpatialConstraintDefiner CADDSuite/TaGRes CADDSuite/TaGRes-train CADDSuite/Validator CADDSuite/VendorFinder CADDSuite/WaterFinder CADDSuite/bin/AntitargetRescorer.bin CADDSuite/bin/AutoModel.bin CADDSuite/bin/BindingDBCleaner.bin CADDSuite/bin/CombiLibGenerator.bin CADDSuite/bin/ConstraintsFinder.bin CADDSuite/bin/Converter.bin CADDSuite/bin/DBExporter.bin CADDSuite/bin/DBImporter.bin CADDSuite/bin/DockResultMerger.bin CADDSuite/bin/EvenSplit.bin CADDSuite/bin/FeatureSelector.bin CADDSuite/bin/GalaxyConfigGenerator.bin CADDSuite/bin/GridBuilder.bin CADDSuite/bin/IMGDock.bin CADDSuite/bin/InputPartitioner.bin CADDSuite/bin/InputReader.bin CADDSuite/bin/InteractionConstraintDefiner.bin CADDSuite/bin/LigCheck.bin CADDSuite/bin/Ligand3DGenerator.bin CADDSuite/bin/LigandFileSplitter.bin CADDSuite/bin/ModelCreator.bin CADDSuite/bin/MolCombine.bin CADDSuite/bin/MolDepict.bin CADDSuite/bin/MolFilter.bin CADDSuite/bin/MolPredictor.bin CADDSuite/bin/PDBCutter.bin CADDSuite/bin/PDBDownload.bin CADDSuite/bin/PartialChargesCopy.bin CADDSuite/bin/PocketDetector.bin CADDSuite/bin/Predictor.bin CADDSuite/bin/PropertyModifier.bin CADDSuite/bin/PropertyPlotter.bin CADDSuite/bin/ProteinCheck.bin CADDSuite/bin/ProteinProtonator.bin CADDSuite/bin/RMSDCalculator.bin CADDSuite/bin/ScoreAnalyzer.bin CADDSuite/bin/SimilarityAnalyzer.bin CADDSuite/bin/SimpleRescorer.bin CADDSuite/bin/SpatialConstraintDefiner.bin CADDSuite/bin/TaGRes-train.bin CADDSuite/bin/TaGRes.bin CADDSuite/bin/Validator.bin CADDSuite/bin/VendorFinder.bin CADDSuite/bin/WaterFinder.bin CADDSuite/bin/gnuplot CADDSuite/changelog.txt CADDSuite/data/Amber/amber96-docking.ini CADDSuite/data/OpenBabel/CMakeLists.txt CADDSuite/data/OpenBabel/MACCS.txt CADDSuite/data/OpenBabel/Makefile CADDSuite/data/OpenBabel/SMARTS_InteLigand.txt CADDSuite/data/OpenBabel/UFF.prm CADDSuite/data/OpenBabel/aromatic.h CADDSuite/data/OpenBabel/aromatic.txt CADDSuite/data/OpenBabel/atomtyp.h CADDSuite/data/OpenBabel/atomtyp.txt CADDSuite/data/OpenBabel/babel_povray3.inc CADDSuite/data/OpenBabel/bin2hex.pl CADDSuite/data/OpenBabel/bondtyp.h CADDSuite/data/OpenBabel/bondtyp.txt CADDSuite/data/OpenBabel/cmake_install.cmake CADDSuite/data/OpenBabel/element.h CADDSuite/data/OpenBabel/element.txt CADDSuite/data/OpenBabel/fragments.txt CADDSuite/data/OpenBabel/gaff.dat CADDSuite/data/OpenBabel/gaff.prm CADDSuite/data/OpenBabel/genheaders.sh CADDSuite/data/OpenBabel/ghemical.prm CADDSuite/data/OpenBabel/isotope-small.txt CADDSuite/data/OpenBabel/isotope.h CADDSuite/data/OpenBabel/isotope.txt CADDSuite/data/OpenBabel/logp.txt CADDSuite/data/OpenBabel/mm2.prm CADDSuite/data/OpenBabel/mmff94.ff CADDSuite/data/OpenBabel/mmff94s.ff CADDSuite/data/OpenBabel/mmffang.par CADDSuite/data/OpenBabel/mmffbndk.par CADDSuite/data/OpenBabel/mmffbond.par CADDSuite/data/OpenBabel/mmffchg.par CADDSuite/data/OpenBabel/mmffdef.par CADDSuite/data/OpenBabel/mmffdfsb.par CADDSuite/data/OpenBabel/mmffoop.par CADDSuite/data/OpenBabel/mmffpbci.par CADDSuite/data/OpenBabel/mmffprop.par CADDSuite/data/OpenBabel/mmffs_oop.par CADDSuite/data/OpenBabel/mmffs_tor.par CADDSuite/data/OpenBabel/mmffstbn.par CADDSuite/data/OpenBabel/mmfftor.par CADDSuite/data/OpenBabel/mmffvdw.par CADDSuite/data/OpenBabel/mr.txt CADDSuite/data/OpenBabel/patterns.txt CADDSuite/data/OpenBabel/phmodel.txt CADDSuite/data/OpenBabel/phmodeldata.h CADDSuite/data/OpenBabel/plugindefines.txt CADDSuite/data/OpenBabel/psa.txt CADDSuite/data/OpenBabel/qeq.txt CADDSuite/data/OpenBabel/resdata.h CADDSuite/data/OpenBabel/resdata.txt CADDSuite/data/OpenBabel/ringtyp.txt CADDSuite/data/OpenBabel/space-groups.txt CADDSuite/data/OpenBabel/space-groups.xsl CADDSuite/data/OpenBabel/superatom.txt CADDSuite/data/OpenBabel/svgformat.script CADDSuite/data/OpenBabel/templates.sdf CADDSuite/data/OpenBabel/torlib.h CADDSuite/data/OpenBabel/torlib.txt CADDSuite/data/OpenBabel/types.h CADDSuite/data/OpenBabel/types.txt CADDSuite/data/QSAR/atomic_electron_affinities.data CADDSuite/data/QSAR/atomic_ionization_potentials.data CADDSuite/data/QSAR/atomic_polarizabilities.data CADDSuite/data/QSAR/dragon_descriptors.txt CADDSuite/data/XRAY/spacegroups.dat CADDSuite/data/atomtyping/AMBERTypes.dat CADDSuite/data/atomtyping/GAFFTypes.dat CADDSuite/data/atomtyping/SYBYLTypes.dat CADDSuite/data/bond_lengths/BondOrder.xml CADDSuite/data/bond_lengths/BondOrderGAFF.xml CADDSuite/data/bond_lengths/bond_lengths.db CADDSuite/data/bond_lengths/bond_lengths_mmff94.ini CADDSuite/data/fonts/FreeSans.ttf CADDSuite/data/fragments/A.db CADDSuite/data/fragments/ACE.db CADDSuite/data/fragments/ALA.db CADDSuite/data/fragments/ARG.db CADDSuite/data/fragments/ASN.db CADDSuite/data/fragments/ASP.db CADDSuite/data/fragments/Benzene-Skeleton.db CADDSuite/data/fragments/C.db CADDSuite/data/fragments/CA.db CADDSuite/data/fragments/CYS.db CADDSuite/data/fragments/Editing-Fragments.db CADDSuite/data/fragments/Fragments.db CADDSuite/data/fragments/G.db CADDSuite/data/fragments/GLN.db CADDSuite/data/fragments/GLU.db CADDSuite/data/fragments/GLY.db CADDSuite/data/fragments/HIS.db CADDSuite/data/fragments/HOH.db CADDSuite/data/fragments/ILE.db CADDSuite/data/fragments/Indole-Skeleton.db CADDSuite/data/fragments/LEU.db CADDSuite/data/fragments/LYS.db CADDSuite/data/fragments/MET.db CADDSuite/data/fragments/MG.db CADDSuite/data/fragments/MSE.db CADDSuite/data/fragments/NME.db CADDSuite/data/fragments/Names.Amber.db CADDSuite/data/fragments/Names.CHARMM.db CADDSuite/data/fragments/Names.DNA.db CADDSuite/data/fragments/Names.Discover.db CADDSuite/data/fragments/Names.Star.db CADDSuite/data/fragments/Names.XPLOR.db CADDSuite/data/fragments/PCA.db CADDSuite/data/fragments/PHE.db CADDSuite/data/fragments/PRO.db CADDSuite/data/fragments/Pyrrole-Skeleton.db CADDSuite/data/fragments/SER.db CADDSuite/data/fragments/T.db CADDSuite/data/fragments/THR.db CADDSuite/data/fragments/TRP.db CADDSuite/data/fragments/TYR.db CADDSuite/data/fragments/U.db CADDSuite/data/fragments/VAL.db CADDSuite/data/fragments/ZN.db CADDSuite/data/fragments/functionalGroups.smarts CADDSuite/galaxyconfigs/confFiles.py CADDSuite/galaxyconfigs/countResidues.sh CADDSuite/galaxyconfigs/datatypes_conf.xml CADDSuite/galaxyconfigs/molFiles.py CADDSuite/galaxyconfigs/tool_conf.xml CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml CADDSuite/galaxyconfigs/tools/AutoModel.xml CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml CADDSuite/galaxyconfigs/tools/Converter.xml CADDSuite/galaxyconfigs/tools/DBExporter.xml CADDSuite/galaxyconfigs/tools/DBImporter.xml CADDSuite/galaxyconfigs/tools/DockResultMerger.xml CADDSuite/galaxyconfigs/tools/EvenSplit.xml CADDSuite/galaxyconfigs/tools/FeatureSelector.xml CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml CADDSuite/galaxyconfigs/tools/GridBuilder.xml CADDSuite/galaxyconfigs/tools/IMGDock.xml CADDSuite/galaxyconfigs/tools/InputPartitioner.xml CADDSuite/galaxyconfigs/tools/InputReader.xml CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml CADDSuite/galaxyconfigs/tools/LigCheck.xml CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml CADDSuite/galaxyconfigs/tools/ModelCreator.xml CADDSuite/galaxyconfigs/tools/MolCombine.xml CADDSuite/galaxyconfigs/tools/MolDepict.xml CADDSuite/galaxyconfigs/tools/MolFilter.xml CADDSuite/galaxyconfigs/tools/MolPredictor.xml CADDSuite/galaxyconfigs/tools/PDBCutter.xml CADDSuite/galaxyconfigs/tools/PDBDownload.xml CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml CADDSuite/galaxyconfigs/tools/PocketDetector.xml CADDSuite/galaxyconfigs/tools/Predictor.xml CADDSuite/galaxyconfigs/tools/PropertyModifier.xml CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml CADDSuite/galaxyconfigs/tools/ProteinCheck.xml CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml CADDSuite/galaxyconfigs/tools/TaGRes-train.xml CADDSuite/galaxyconfigs/tools/TaGRes.xml CADDSuite/galaxyconfigs/tools/Validator.xml CADDSuite/galaxyconfigs/tools/VendorFinder.xml CADDSuite/galaxyconfigs/tools/WaterFinder.xml CADDSuite/galaxyconfigs/tools/upload.xml CADDSuite/install.sh CADDSuite/lib/libBALL.so.1.4 CADDSuite/lib/libQtCore.so.4 CADDSuite/lib/libQtNetwork.so.4 CADDSuite/lib/libQtSql.so.4 CADDSuite/lib/libQtXml.so.4 CADDSuite/lib/libblas.so.3 CADDSuite/lib/libboost_iostreams-mt.so CADDSuite/lib/libboost_regex-mt.so CADDSuite/lib/libboost_system-mt.so CADDSuite/lib/libboost_thread-mt.so CADDSuite/lib/libbz2.so.1 CADDSuite/lib/libdl.so.2 CADDSuite/lib/libfftw3.so.3 CADDSuite/lib/libfftw3f.so.3 CADDSuite/lib/libgfortran.so.1 CADDSuite/lib/libgsl.so.0 CADDSuite/lib/libgslcblas.so.0 CADDSuite/lib/liblapack.so.3 CADDSuite/lib/libmysqlclient_r.so.16 CADDSuite/lib/libnsl.so.1 CADDSuite/lib/libopenbabel.so.4 CADDSuite/lib/libz.so.1 CADDSuite/lib/plugin_forcefields.so CADDSuite/license.txt CADDSuite/rescoring_common CADDSuite/setPathes.sh CADDSuite/suite_config.xml
diffstat 292 files changed, 89297 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/AntitargetRescorer	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/AntitargetRescorer.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/AutoModel	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/AutoModel.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/BindingDBCleaner	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/BindingDBCleaner.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/CADDSuite-description.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,60 @@
+This package contains tools belonging to
+CADDSuite: A flexible and open framework for Computer-Aided Drug Design
+
+There are tools for the following tasks:
+
+Get Data:
+	- CombiLibGenerator: generate R-group decorated ligands
+	- DBExporter: fetch (filtered) molecules from DB
+
+Preparation of input:
+	- PDBCutter: separate ligand and receptor
+	- ProteinProtonator: protonate protein structures
+	- BindingDBCleaner: fix data from bindingdb.org
+	- EvenSplit: generate splits w/ equal property range
+	- PropertyModifier: modify property tags
+	- LigandFileSplitter: split molecule files
+	- Ligand3DGenerator: generate 3D coordinates for small molecules
+
+Structure checks and evaluations:
+	- ProteinCheck: evaluate protein quality
+	- LigCheck: chemical sanity check for ligands
+
+QuEasy (QSAR):
+	- InputReader: read molecules and generate features
+	- ModelCreator: create a QSAR model
+	- FeatureSelector: automatically select features of a QSAR model
+	- Validator: evaluate quality of a QSAR model
+	- MolPredictor: predict molecule activities with QSAR model
+	- AutoModel: automatically find best QSAR model
+
+Docking:
+	- WaterFinder: find strongly bound water molecules
+	- SpatialConstraintDefiner: define spatial constraint
+	- ConstraintsFinder: find strongly interacting residues
+	- PocketDetector: detect ligand binding pocket
+	- GridBuilder: precalculate grids for docking
+	- IMeedyDock: run Iterative Multi-Greedy Docking
+
+Rescoring:
+	- SimpleRescorer: rescore docking results 
+	- TaGRes-train: Target-specific Grid-Rescoring, training
+	- TaGRes: Target-specific Grid-Rescoring
+	- AntitargetRescoring: rescore w/ respect to antitarget
+
+Analysis:
+	- ScoreAnalyzer: generate ROC or enrichment plots
+	- SimilarityAnalyzer: analyze similarity between two molecule sets
+	- PropertyPlotter: plot molecule properties
+	- RMSDCalculator: calculate RMSD between conformations
+	- VendorFinder: search vendors for compounds
+
+Convert, combine and store:
+	- DockResultMerger: merge docking output files and/or filter them
+	- MolCombine: combine molecular files
+	- DBImporter: import molecules into DB
+	- Converter: interconvert molecular file-formats
+	- MolDepict: generate structure diagrams
+	- VendorFinder: search vendors for compounds
+
+For more information about an individual tool, please call the tool without any parameters (or with '-help').
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/CombiLibGenerator	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/CombiLibGenerator.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ConstraintsFinder	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/ConstraintsFinder.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Converter	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/Converter.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/DBExporter	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/DBExporter.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/DBImporter	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/DBImporter.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/DockResultMerger	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/DockResultMerger.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/EvenSplit	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/EvenSplit.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/FeatureSelector	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/FeatureSelector.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/GalaxyConfigGenerator	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/GalaxyConfigGenerator.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/GridBuilder	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/GridBuilder.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/IMGDock	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/IMGDock.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/InputPartitioner	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/InputPartitioner.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/InputReader	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/InputReader.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/InteractionConstraintDefiner	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/InteractionConstraintDefiner.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/LigCheck	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/LigCheck.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Ligand3DGenerator	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/Ligand3DGenerator.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/LigandFileSplitter	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/LigandFileSplitter.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ModelCreator	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/ModelCreator.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolCombine	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/MolCombine.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolDepict	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/MolDepict.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolFilter	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/MolFilter.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolPredictor	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/MolPredictor.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PDBCutter	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/PDBCutter.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PDBDownload	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/PDBDownload.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PartialChargesCopy	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/PartialChargesCopy.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PocketDetector	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/PocketDetector.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Predictor	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/Predictor.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PropertyModifier	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/PropertyModifier.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PropertyPlotter	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/PropertyPlotter.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ProteinCheck	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/ProteinCheck.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ProteinProtonator	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/ProteinProtonator.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/QuEasyRun	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/QuEasyRun.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/README	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,41 @@
+-----------------------------------------------------------------------
+   CADDSuite - A flexible and open framework and workflow system
+               for computer-aided drug design
+-----------------------------------------------------------------------
+
+This package contains all tools belonging to CADDSuite.
+For an overview over the contained tools, please see CADDSuite-description.txt.
+After extraction the package, you can directly start the applications using the startup-scripts in the base-folder.
+
+For more information about an individual tool, please call the tool without any parameters (or with '-h').
+
+
+
+--------------------------------------------------------------------
+Instructions for integration of CADDSuite into the workflow-system
+Galaxy (http://getgalaxy.org)
+--------------------------------------------------------------------
+
+
+In order to install CADDSuite into your Galaxy installation, please to the following:
+
+Let's assume $galaxybase is the base-folder of your Galaxy installation.
+If you don't have a galaxy-installation yet, download a version from http://getgalaxy.org and follow the installation instructions shown there first.
+
+
+-- Extract the CADDSuite archive into a new folder $galaxybase/tools/CADDSuite, or extract it somewhere else and create a link named $galaxybase/tools/CADDSuite that points to this destination.
+
+After this, you need to copy a few files that you find in the galaxyconfig/ subfolder of this archive to the destinations specified below:
+
+-- Copy tool_conf.xml and datatypes_conf.xml to $galaxybase if you want to setup your Galaxy instance for exclusive use of CADDSuite, or copy the contents of those files into the files already existing in $galaxybase if you want to keep using tools that came along with the Galaxy installation.
+
+-- Copy molFiles.py, confFiles.py and countResidues.sh to $galaxybase/lib/galaxy/datatypes/
+
+-- Add "#import molFiles, confFiles.py" to the beginning of the file $galaxybase/lib/galaxy/datatypes/registry.py
+
+
+
+Last but not least, restart Galaxy.
+All CADDSuite tools should now appear in your Galaxy webinterface.
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/RMSDCalculator	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/RMSDCalculator.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ScoreAnalyzer	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/ScoreAnalyzer.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/SideChainGridBuilder	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/SideChainGridBuilder.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/SimilarityAnalyzer	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/SimilarityAnalyzer.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/SimpleRescorer	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/SimpleRescorer.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/SpatialConstraintDefiner	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/SpatialConstraintDefiner.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/TaGRes	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/TaGRes.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/TaGRes-train	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/TaGRes-train.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Validator	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/Validator.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/VendorFinder	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/VendorFinder.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/WaterFinder	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/WaterFinder.bin "$@" 
Binary file CADDSuite/bin/AntitargetRescorer.bin has changed
Binary file CADDSuite/bin/AutoModel.bin has changed
Binary file CADDSuite/bin/BindingDBCleaner.bin has changed
Binary file CADDSuite/bin/CombiLibGenerator.bin has changed
Binary file CADDSuite/bin/ConstraintsFinder.bin has changed
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Binary file CADDSuite/bin/TaGRes-train.bin has changed
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Binary file CADDSuite/bin/Validator.bin has changed
Binary file CADDSuite/bin/VendorFinder.bin has changed
Binary file CADDSuite/bin/WaterFinder.bin has changed
Binary file CADDSuite/bin/gnuplot has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/changelog.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,46 @@
+Version 0.94, 06-27-2011:
+	- Fixed tool-startup script for pathes containing whitespaces
+	- New tool SpatialConstraintDefiner
+	- New tool InteractionConstraintDefiner
+	- Removed superficial pathes from startup-script
+	- Slight change in ParamFile format (i.e. the files written with -write_par)
+	- Renamed IMeedyDock to IMGDock
+
+Version 0.93, 05-30-2011:
+	- Split Rescorer into 3 tools: SimpleRescorer, TaGRes-train, TaGRes (Target-Specific Grid-Rescoring)
+	- Allow to optionally specify output filenames to LigandFileSplitter
+	- Fixed creation of galaxy-scripts for tools with inputfile-lists
+	- Fixed creation of galaxy-scripts for Converter and DockResultMerger
+	- Automatically create and add all files necessary for integration of CADDSuite into Galaxy to the makeself archive
+	- New tool MolFilter
+	- Fixed some gnuplot issues
+	- Added PDBDownload tool
+	- Slight change of format of ParamFile
+	- Added some missing tool-manuals
+	- Disable B-factor check for hydrogens in ProteinCheck
+	- Added safeguards to several tools
+	- Automatically delete existing hydrogens from BALL-system before protonation is done by ProteinProtonator
+	- Fixed reading of mulitple ScoreGridSets (for cases when no ini-file is used)
+	- Simplified use of VendorFinder by allowing to set all db-parameters on the command-line (instead of using ini-file)
+	- Enhanced several tool manuals
+	- Let tools register their category (e.g. Preparation, Docking, etc.). Write and read information about this category to/from ParamFiles.
+
+Version 0.92, 05-17-2011:
+	- Speed-up of ob-mol generation
+	- Support build on Windows
+	- ProteinCheck now generates protein-quality report as pdf
+	- Added info about mandatory parameters and parameter-restrictions to parameter xml-file
+	- Simplified use of DBImporter+DBExporter by allowing to set all db-parameters on the command-line (instead of using ini-file)
+	- Simplified use of some other tools by merging several flags into one string-parameter that has restrictions.
+	- New tool MolDepict. It generates structure diagrams for small molecules by using openbabel's svg-writer and merges them to one pdf-file (3 on 5).
+	- Allow to create makeself-archive containing CADDSuite, all necessary contrib-libs, data-files and install-script
+	- Write information about supported file-formats to parameter xml-file
+	- new tool ProteinProtonator
+	- new tool Ligand3DGenerator
+	- new tool GalaxyConfigGenerator
+	- allow to open file that do not have an extension (by searching for format-specific keywords)
+
+Version 0.91, 04-12-2011:
+	- All tools now write a manual text to cout as well as to parameter xml-file (as generated by 'write_par)
+
+Version 0.9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/Amber/amber96-docking.ini	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,1666 @@
+; This file contains parameter needed for nonbonded ScoringComponents.
+; The parameters were converted from parm96.dat using amber2ini and all sections for bonded parameters were removed since are not needed for docking.
+; Furthermore, lennard-jones and AtomType parameters for some metal ions were obtained from the sources indicated in the comment column and added to this file.
+
+[Options]
+key:0
+@SCEE=1.2
+; please check the settings for SCEE! AMBER91/89a requires a value of 2.0 here!
+
+
+
+
+[HydrophilicTypes]
+; ignored
+;
+C   H   HO  N   NA  NB  NC  N2  NT  N2  N3  N*  O   OH  OS  P   O2 
+
+
+[HydrogenBonds]
+ver:version key:I key:J value:A value:B
+@unit_A=kcal/mol*A^12
+@unit_B=kcal/mol*A^10
+;
+;
+;  Rev  I   J      A          B
+;  --- --- --- ---------- ----------
+   1.0  HW OW     0.0000     0.0000
+
+
+[AtomTypes]
+value:ver key:type value:mass value:comment
+@unit=g/mol
+;
+;
+;   Rev Type    mass      comment
+;   --- ---- ---------- ----------------------------------
+    1.0  BR    79.90000 "bromine"
+    1.0  C     12.01000 "sp2 C carbonyl group "
+    1.0  F     19.00000 "fluorine"
+    1.0  I    126.90000 "iodine"
+    1.0  H      1.00800 "H bonded to nitrogen atoms"
+    1.0  IM    35.45000 "assumed to be Cl-"
+    1.0  IP    22.99000 "assumed to be Na+"
+    1.0  IB   131.00000 "'big ion w/ waters' for vacuum (Na+, 6H2O)"
+    1.0  N     14.01000 "sp2 nitrogen in amide groups"
+    1.0  O     16.00000 "carbonyl group oxygen"
+    1.0  P     30.97000 "phosphate"
+    1.0  S     32.06000 "sulphur in disulfide linkage"
+    1.0  Cu    63.55000 "copper"
+    1.0  Fe    55.00000 "iron"
+    1.0  Li     6.94000 "lithium"
+    1.0  K     39.10000 "potassium"
+    1.0  Rb    85.47000 "rubidium"
+    1.0  Cs   132.91000 "cesium"
+    ant  Cl    35.450   "same as cl"
+    2.0  Ca    40.08000 "calcium"
+    1.0  Mg    24.30500 "magnesium"
+    ant  Zn    65.4     "Zn2+, taken from parm99.dat (antechamber)"
+
+
+[LennardJones]
+ver:version key:I value:R value:epsilon
+@unit_R=Angstrom
+@unit_epsilon=kcal/mol
+@format=RE
+;
+;
+;  Rev  I      R       epsilon    comment
+;  --- --- ---------- ---------- -------------------------
+   1.0 Ca   1.600000   0.100000 " calcium from parm91.dat"
+   1.0 H    0.600000   0.015700 " !Ferguson base pair geom."
+   1.0 O    1.661200   0.210000 " OPLS"
+   1.0 C    1.908000   0.086000 " OPLS"
+   1.0 N    1.824000   0.170000 " OPLS"
+   1.0 S    2.000000   0.250000 " W. Cornell CH3SH and CH3SCH3 FEP's"
+   1.0 P    2.100000   0.200000 " JCC,7,(1986),230;"
+   1.0 IM   2.470000   0.100000 " Cl- Smith & Dang, JCP 1994,100:5,3757"
+   1.0 IB   5.000000   0.100000 " solvated ion for vacuum approximation"
+   1.0 Li   1.137000   0.018300 " Li+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 IP   1.868000   0.002770 " Na+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 K    2.658000   0.000328 " K+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 Rb   2.956000   0.000170 " Rb+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 Cs   3.395000   0.000081 " Cs+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 I    2.350000   0.400000 " JCC,7,(1986),230;"
+   1.0 F    1.750000   0.061000 " Gough et al. JCC 13,(1992),963."
+   ant Cl   2.47       0.1      " Cl- Smith & Dang, JCP 1994,100:5,3757, taken from parm99.dat (antechamber)"
+   ant Zn   1.10       0.0125   " Zn2+, Merz,PAK, JACS,113,8262,(1991), taken from parm99.dat (antechamber)"
+   ant Mg   0.7926     0.8947   " Mg2+ Aqvist JPC 1990,94,8021.(adapted), taken from parm99.dat (antechamber)"
+;   ant Cl  1.9480  0.2650  "same as cl"
+;   1.0 Mg   1.170000   0.100000 " magnesium from parm91.dat"
+
+
+[ResidueImproperTorsions]
+key:name
+;
+;
+;    res:atom
+;  -------------
+   ALA:N
+   ALA:C
+   GLY:N
+   GLY:C
+   SER:N
+   SER:C
+   THR:N
+   THR:C
+   LEU:N
+   LEU:C
+   ILE:N
+   ILE:C
+   VAL:N
+   VAL:C
+   ASN:N
+   ASN:C
+   ASN:CG
+   ASN:ND2
+   GLN:N
+   GLN:C
+   GLN:CD
+   GLN:NE2
+   ARG:N
+   ARG:C
+   ARG:CZ
+   ARG:NE
+   ARG:NH1
+   ARG:NH2
+   HIS:N
+   HIS:C
+   HIS:ND1
+   HIS:CD2
+   HIS:CE1
+   HIS:CG
+   HIS:N
+   HIS:C
+   HIS:NE2
+   HIS:CD2
+   HIS:CE1
+   HIS:CG
+   HIS:N
+   HIS:C
+   HIS:ND1
+   HIS:NE2
+   HIS:CD2
+   HIS:CE1
+   HIS:CG
+   TRP:N
+   TRP:C
+   TRP:NE1
+   TRP:CZ2
+   TRP:CH2
+   TRP:CZ3
+   TRP:CE3
+   TRP:CD1
+   TRP:CG
+   PHE:N
+   PHE:C
+   PHE:CD2
+   PHE:CE2
+   PHE:CZ
+   PHE:CE1
+   PHE:CD1
+   PHE:CG
+   TYR:N
+   TYR:C
+   TYR:CD2
+   TYR:CE2
+   TYR:CE1
+   TYR:CD1
+   TYR:CG
+   TYR:CZ
+   GLU:N
+   GLU:C
+   GLU:CD
+   ASP:N
+   ASP:C
+   ASP:CG
+   LYS:N
+   LYS:C
+   LYN:N
+   LYN:C
+   PRO:C
+   PRO:N
+   CYS:N
+   CYS:C
+   CYM:N
+   CYM:C
+   CYS-S:N
+   CYS-S:C
+   MET:N
+   MET:C
+   ACE:C
+   NME:N
+   ASH:N
+   ASH:C
+   ASH:CG
+   GLH:N
+   GLH:C
+   GLH:CD
+   ALA-N:C
+   GLY-N:C
+   SER-N:C
+   THR-N:C
+   LEU-N:C
+   ILE-N:C
+   VAL-N:C
+   ASN-N:C
+   ASN-N:CG
+   ASN-N:ND2
+   GLN-N:C
+   GLN-N:CD
+   GLN-N:NE2
+   ARG-N:C
+   ARG-N:CZ
+   ARG-N:NE
+   ARG-N:NH1
+   ARG-N:NH2
+   HIS-N:C
+   HIS-N:ND1
+   HIS-N:CD2
+   HIS-N:CE1
+   HIS-N:CG
+   HIS-N:C
+   HIS-N:NE2
+   HIS-N:CD2
+   HIS-N:CE1
+   HIS-N:CG
+   HIS-N:C
+   HIS-N:ND1
+   HIS-N:NE2
+   HIS-N:CD2
+   HIS-N:CE1
+   HIS-N:CG
+   TRP-N:C
+   TRP-N:NE1
+   TRP-N:CZ2
+   TRP-N:CH2
+   TRP-N:CZ3
+   TRP-N:CE3
+   TRP-N:CD1
+   TRP-N:CG
+   PHE-N:C
+   PHE-N:CD2
+   PHE-N:CE2
+   PHE-N:CZ
+   PHE-N:CE1
+   PHE-N:CD1
+   PHE-N:CG
+   TYR-N:C
+   TYR-N:CD2
+   TYR-N:CE2
+   TYR-N:CE1
+   TYR-N:CD1
+   TYR-N:CG
+   TYR-N:CZ
+   GLU-N:C
+   GLU-N:CD
+   ASP-N:C
+   ASP-N:CG
+   LYS-N:C
+   PRO-N:C
+   CYS-N:C
+   CYS-NS:C
+   MET-N:C
+   ALA-C:N
+   ALA-C:C
+   GLY-C:N
+   GLY-C:C
+   SER-C:N
+   SER-C:C
+   THR-C:N
+   THR-C:C
+   LEU-C:N
+   LEU-C:C
+   ILE-C:N
+   ILE-C:C
+   VAL-C:N
+   VAL-C:C
+   ASN-C:N
+   ASN-C:C
+   ASN-C:CG
+   ASN-C:ND2
+   GLN-C:N
+   GLN-C:C
+   GLN-C:CD
+   GLN-C:NE2
+   ARG-C:N
+   ARG-C:C
+   ARG-C:CZ
+   ARG-C:NE
+   ARG-C:NH1
+   ARG-C:NH2
+   HIS-C:N
+   HIS-C:C
+   HIS-C:ND1
+   HIS-C:CD2
+   HIS-C:CE1
+   HIS-C:CG
+   HIS-C:N
+   HIS-C:C
+   HIS-C:NE2
+   HIS-C:CD2
+   HIS-C:CE1
+   HIS-C:CG
+   HIS-C:N
+   HIS-C:C
+   HIS-C:ND1
+   HIS-C:NE2
+   HIS-C:CD2
+   HIS-C:CE1
+   HIS-C:CG
+   TRP-C:N
+   TRP-C:C
+   TRP-C:NE1
+   TRP-C:CZ2
+   TRP-C:CH2
+   TRP-C:CZ3
+   TRP-C:CE3
+   TRP-C:CD1
+   TRP-C:CG
+   PHE-C:N
+   PHE-C:C
+   PHE-C:CD2
+   PHE-C:CE2
+   PHE-C:CZ
+   PHE-C:CE1
+   PHE-C:CD1
+   PHE-C:CG
+   TYR-C:N
+   TYR-C:C
+   TYR-C:CD2
+   TYR-C:CE2
+   TYR-C:CE1
+   TYR-C:CD1
+   TYR-C:CG
+   TYR-C:CZ
+   GLU-C:N
+   GLU-C:C
+   GLU-C:CD
+   ASP-C:N
+   ASP-C:C
+   ASP-C:CG
+   LYS-C:N
+   LYS-C:C
+   PRO-C:C
+   PRO-C:N
+   CYS-C:N
+   CYS-C:C
+   CYS-CS:N
+   CYS-CS:C
+   MET-C:N
+   MET-C:C
+
+[ChargesAndTypeNames]
+ver:version key:name value:q value:type
+@unit_q=e0
+   1.0 ALA:N      -0.41570 N    
+   1.0 ALA:H       0.27190 H    
+   1.0 ALA:CA      0.03370 CT   
+   1.0 ALA:HA      0.08230 H1   
+   1.0 ALA:CB     -0.18250 CT   
+   1.0 ALA:1HB     0.06030 HC   
+   1.0 ALA:2HB     0.06030 HC   
+   1.0 ALA:3HB     0.06030 HC   
+   1.0 ALA:C       0.59730 C    
+   1.0 ALA:O      -0.56790 O    
+   1.0 GLY:N      -0.41570 N    
+   1.0 GLY:H       0.27190 H    
+   1.0 GLY:CA     -0.02520 CT   
+   1.0 GLY:1HA     0.06980 H1   
+   1.0 GLY:2HA     0.06980 H1   
+   1.0 GLY:C       0.59730 C    
+   1.0 GLY:O      -0.56790 O    
+   1.0 SER:N      -0.41570 N    
+   1.0 SER:H       0.27190 H    
+   1.0 SER:CA     -0.02490 CT   
+   1.0 SER:HA      0.08430 H1   
+   1.0 SER:CB      0.21170 CT   
+   1.0 SER:1HB     0.03520 H1   
+   1.0 SER:2HB     0.03520 H1   
+   1.0 SER:OG     -0.65460 OH   
+   1.0 SER:HG      0.42750 HO   
+   1.0 SER:C       0.59730 C    
+   1.0 SER:O      -0.56790 O    
+   1.0 THR:N      -0.41570 N    
+   1.0 THR:H       0.27190 H    
+   1.0 THR:CA     -0.03890 CT   
+   1.0 THR:HA      0.10070 H1   
+   1.0 THR:CB      0.36540 CT   
+   1.0 THR:HB      0.00430 H1   
+   1.0 THR:CG2    -0.24380 CT   
+   1.0 THR:1HG2    0.06420 HC   
+   1.0 THR:2HG2    0.06420 HC   
+   1.0 THR:3HG2    0.06420 HC   
+   1.0 THR:OG1    -0.67610 OH   
+   1.0 THR:HG1     0.41020 HO   
+   1.0 THR:C       0.59730 C    
+   1.0 THR:O      -0.56790 O    
+   1.0 LEU:N      -0.41570 N    
+   1.0 LEU:H       0.27190 H    
+   1.0 LEU:CA     -0.05180 CT   
+   1.0 LEU:HA      0.09220 H1   
+   1.0 LEU:CB     -0.11020 CT   
+   1.0 LEU:1HB     0.04570 HC   
+   1.0 LEU:2HB     0.04570 HC   
+   1.0 LEU:CG      0.35310 CT   
+   1.0 LEU:HG     -0.03610 HC   
+   1.0 LEU:CD1    -0.41210 CT   
+   1.0 LEU:1HD1    0.10000 HC   
+   1.0 LEU:2HD1    0.10000 HC   
+   1.0 LEU:3HD1    0.10000 HC   
+   1.0 LEU:CD2    -0.41210 CT   
+   1.0 LEU:1HD2    0.10000 HC   
+   1.0 LEU:2HD2    0.10000 HC   
+   1.0 LEU:3HD2    0.10000 HC   
+   1.0 LEU:C       0.59730 C    
+   1.0 LEU:O      -0.56790 O    
+   1.0 ILE:N      -0.41570 N    
+   1.0 ILE:H       0.27190 H    
+   1.0 ILE:CA     -0.05970 CT   
+   1.0 ILE:HA      0.08690 H1   
+   1.0 ILE:CB      0.13030 CT   
+   1.0 ILE:HB      0.01870 HC   
+   1.0 ILE:CG2    -0.32040 CT   
+   1.0 ILE:1HG2    0.08820 HC   
+   1.0 ILE:2HG2    0.08820 HC   
+   1.0 ILE:3HG2    0.08820 HC   
+   1.0 ILE:CG1    -0.04300 CT   
+   1.0 ILE:1HG1    0.02360 HC   
+   1.0 ILE:2HG1    0.02360 HC   
+   1.0 ILE:CD1    -0.06600 CT   
+   1.0 ILE:1HD1    0.01860 HC   
+   1.0 ILE:2HD1    0.01860 HC   
+   1.0 ILE:3HD1    0.01860 HC   
+   1.0 ILE:C       0.59730 C    
+   1.0 ILE:O      -0.56790 O    
+   1.0 VAL:N      -0.41570 N    
+   1.0 VAL:H       0.27190 H    
+   1.0 VAL:CA     -0.08750 CT   
+   1.0 VAL:HA      0.09690 H1   
+   1.0 VAL:CB      0.29850 CT   
+   1.0 VAL:HB     -0.02970 HC   
+   1.0 VAL:CG1    -0.31920 CT   
+   1.0 VAL:1HG1    0.07910 HC   
+   1.0 VAL:2HG1    0.07910 HC   
+   1.0 VAL:3HG1    0.07910 HC   
+   1.0 VAL:CG2    -0.31920 CT   
+   1.0 VAL:1HG2    0.07910 HC   
+   1.0 VAL:2HG2    0.07910 HC   
+   1.0 VAL:3HG2    0.07910 HC   
+   1.0 VAL:C       0.59730 C    
+   1.0 VAL:O      -0.56790 O    
+   1.0 ASN:N      -0.41570 N    
+   1.0 ASN:H       0.27190 H    
+   1.0 ASN:CA      0.01430 CT   
+   1.0 ASN:HA      0.10480 H1   
+   1.0 ASN:CB     -0.20410 CT   
+   1.0 ASN:1HB     0.07970 HC   
+   1.0 ASN:2HB     0.07970 HC   
+   1.0 ASN:CG      0.71300 C    
+   1.0 ASN:OD1    -0.59310 O    
+   1.0 ASN:ND2    -0.91910 N    
+   1.0 ASN:1HD2    0.41960 H    
+   1.0 ASN:2HD2    0.41960 H    
+   1.0 ASN:C       0.59730 C    
+   1.0 ASN:O      -0.56790 O    
+   1.0 GLN:N      -0.41570 N    
+   1.0 GLN:H       0.27190 H    
+   1.0 GLN:CA     -0.00310 CT   
+   1.0 GLN:HA      0.08500 H1   
+   1.0 GLN:CB     -0.00360 CT   
+   1.0 GLN:1HB     0.01710 HC   
+   1.0 GLN:2HB     0.01710 HC   
+   1.0 GLN:CG     -0.06450 CT   
+   1.0 GLN:1HG     0.03520 HC   
+   1.0 GLN:2HG     0.03520 HC   
+   1.0 GLN:CD      0.69510 C    
+   1.0 GLN:OE1    -0.60860 O    
+   1.0 GLN:NE2    -0.94070 N    
+   1.0 GLN:1HE2    0.42510 H    
+   1.0 GLN:2HE2    0.42510 H    
+   1.0 GLN:C       0.59730 C    
+   1.0 GLN:O      -0.56790 O    
+   1.0 ARG:N      -0.34790 N    
+   1.0 ARG:H       0.27470 H    
+   1.0 ARG:CA     -0.26370 CT   
+   1.0 ARG:HA      0.15600 H1   
+   1.0 ARG:CB     -0.00070 CT   
+   1.0 ARG:1HB     0.03270 HC   
+   1.0 ARG:2HB     0.03270 HC   
+   1.0 ARG:CG      0.03900 CT   
+   1.0 ARG:1HG     0.02850 HC   
+   1.0 ARG:2HG     0.02850 HC   
+   1.0 ARG:CD      0.04860 CT   
+   1.0 ARG:1HD     0.06870 H1   
+   1.0 ARG:2HD     0.06870 H1   
+   1.0 ARG:NE     -0.52950 N2   
+   1.0 ARG:HE      0.34560 H    
+   1.0 ARG:CZ      0.80760 CA   
+   1.0 ARG:NH1    -0.86270 N2   
+   1.0 ARG:1HH1    0.44780 H    
+   1.0 ARG:2HH1    0.44780 H    
+   1.0 ARG:NH2    -0.86270 N2   
+   1.0 ARG:1HH2    0.44780 H    
+   1.0 ARG:2HH2    0.44780 H    
+   1.0 ARG:C       0.73410 C    
+   1.0 ARG:O      -0.58940 O    
+   1.0 HIS:N      -0.34790 N    
+   1.0 HIS:H       0.27470 H    
+   1.0 HIS:CA     -0.13540 CT   
+   1.0 HIS:HA      0.12120 H1   
+   1.0 HIS:CB     -0.04140 CT   
+   1.0 HIS:1HB     0.08100 HC   
+   1.0 HIS:2HB     0.08100 HC   
+   1.0 HIS:CG     -0.00120 CC   
+   1.0 HIS:ND1    -0.15130 NA   
+   1.0 HIS:HD1     0.38660 H    
+   1.0 HIS:CE1    -0.01700 CR   
+   1.0 HIS:HE1     0.26810 H5   
+   1.0 HIS:NE2    -0.17180 NA   
+   1.0 HIS:CD2    -0.11410 CW   
+   1.0 HIS:HD2     0.23170 H4   
+   1.0 HIS:C       0.73410 C    
+   1.0 HIS:O      -0.58940 O    
+   1.0 HIS:N      -0.34790 N    
+   1.0 HIS:H       0.27470 H    
+   1.0 HIS:CA     -0.13540 CT   
+   1.0 HIS:HA      0.12120 H1   
+   1.0 HIS:CB     -0.04140 CT   
+   1.0 HIS:1HB     0.08100 HC   
+   1.0 HIS:2HB     0.08100 HC   
+   1.0 HIS:CG     -0.00120 CC   
+   1.0 HIS:ND1    -0.15130 NA   
+   1.0 HIS:CE1    -0.01700 CR   
+   1.0 HIS:HE1     0.26810 H5   
+   1.0 HIS:NE2    -0.17180 NA   
+   1.0 HIS:HE2     0.39110 H    
+   1.0 HIS:CD2    -0.11410 CW   
+   1.0 HIS:HD2     0.23170 H4   
+   1.0 HIS:C       0.73410 C    
+   1.0 HIS:O      -0.58940 O    
+   1.0 HIS:N      -0.34790 N    
+   1.0 HIS:H       0.27470 H    
+   1.0 HIS:CA     -0.13540 CT   
+   1.0 HIS:HA      0.12120 H1   
+   1.0 HIS:CB     -0.04140 CT   
+   1.0 HIS:1HB     0.08100 HC   
+   1.0 HIS:2HB     0.08100 HC   
+   1.0 HIS:CG     -0.00120 CC   
+   1.0 HIS:ND1    -0.15130 NA   
+   1.0 HIS:HD1     0.38660 H    
+   1.0 HIS:CE1    -0.01700 CR   
+   1.0 HIS:HE1     0.26810 H5   
+   1.0 HIS:NE2    -0.17180 NA   
+   1.0 HIS:HE2     0.39110 H    
+   1.0 HIS:CD2    -0.11410 CW   
+   1.0 HIS:HD2     0.23170 H4   
+   1.0 HIS:C       0.73410 C    
+   1.0 HIS:O      -0.58940 O    
+   1.0 TRP:N      -0.41570 N    
+   1.0 TRP:H       0.27190 H    
+   1.0 TRP:CA     -0.02750 CT   
+   1.0 TRP:HA      0.11230 H1   
+   1.0 TRP:CB     -0.00500 CT   
+   1.0 TRP:1HB     0.03390 HC   
+   1.0 TRP:2HB     0.03390 HC   
+   1.0 TRP:CG     -0.14150 C*   
+   1.0 TRP:CD1    -0.16380 CW   
+   1.0 TRP:HD1     0.20620 H4   
+   1.0 TRP:NE1    -0.34180 NA   
+   1.0 TRP:HE1     0.34120 H    
+   1.0 TRP:CE2     0.13800 CN   
+   1.0 TRP:CZ2    -0.26010 CA   
+   1.0 TRP:HZ2     0.15720 HA   
+   1.0 TRP:CH2    -0.11340 CA   
+   1.0 TRP:HH2     0.14170 HA   
+   1.0 TRP:CZ3    -0.19720 CA   
+   1.0 TRP:HZ3     0.14470 HA   
+   1.0 TRP:CE3    -0.23870 CA   
+   1.0 TRP:HE3     0.17000 HA   
+   1.0 TRP:CD2     0.12430 CB   
+   1.0 TRP:C       0.59730 C    
+   1.0 TRP:O      -0.56790 O    
+   1.0 PHE:N      -0.41570 N    
+   1.0 PHE:H       0.27190 H    
+   1.0 PHE:CA     -0.00240 CT   
+   1.0 PHE:HA      0.09780 H1   
+   1.0 PHE:CB     -0.03430 CT   
+   1.0 PHE:1HB     0.02950 HC   
+   1.0 PHE:2HB     0.02950 HC   
+   1.0 PHE:CG      0.01180 CA   
+   1.0 PHE:CD1    -0.12560 CA   
+   1.0 PHE:HD1     0.13300 HA   
+   1.0 PHE:CE1    -0.17040 CA   
+   1.0 PHE:HE1     0.14300 HA   
+   1.0 PHE:CZ     -0.10720 CA   
+   1.0 PHE:HZ      0.12970 HA   
+   1.0 PHE:CE2    -0.17040 CA   
+   1.0 PHE:HE2     0.14300 HA   
+   1.0 PHE:CD2    -0.12560 CA   
+   1.0 PHE:HD2     0.13300 HA   
+   1.0 PHE:C       0.59730 C    
+   1.0 PHE:O      -0.56790 O    
+   1.0 TYR:N      -0.41570 N    
+   1.0 TYR:H       0.27190 H    
+   1.0 TYR:CA     -0.00140 CT   
+   1.0 TYR:HA      0.08760 H1   
+   1.0 TYR:CB     -0.01520 CT   
+   1.0 TYR:1HB     0.02950 HC   
+   1.0 TYR:2HB     0.02950 HC   
+   1.0 TYR:CG     -0.00110 CA   
+   1.0 TYR:CD1    -0.19060 CA   
+   1.0 TYR:HD1     0.16990 HA   
+   1.0 TYR:CE1    -0.23410 CA   
+   1.0 TYR:HE1     0.16560 HA   
+   1.0 TYR:CZ      0.32260 C    
+   1.0 TYR:OH     -0.55790 OH   
+   1.0 TYR:HH      0.39920 HO   
+   1.0 TYR:CE2    -0.23410 CA   
+   1.0 TYR:HE2     0.16560 HA   
+   1.0 TYR:CD2    -0.19060 CA   
+   1.0 TYR:HD2     0.16990 HA   
+   1.0 TYR:C       0.59730 C    
+   1.0 TYR:O      -0.56790 O    
+   1.0 GLU:N      -0.51630 N    
+   1.0 GLU:H       0.29360 H    
+   1.0 GLU:CA      0.03970 CT   
+   1.0 GLU:HA      0.11050 H1   
+   1.0 GLU:CB      0.05600 CT   
+   1.0 GLU:1HB    -0.01730 HC   
+   1.0 GLU:2HB    -0.01730 HC   
+   1.0 GLU:CG      0.01360 CT   
+   1.0 GLU:1HG    -0.04250 HC   
+   1.0 GLU:2HG    -0.04250 HC   
+   1.0 GLU:CD      0.80540 C    
+   1.0 GLU:OE1    -0.81880 O2   
+   1.0 GLU:OE2    -0.81880 O2   
+   1.0 GLU:C       0.53660 C    
+   1.0 GLU:O      -0.58190 O    
+   1.0 ASP:N      -0.51630 N    
+   1.0 ASP:H       0.29360 H    
+   1.0 ASP:CA      0.03810 CT   
+   1.0 ASP:HA      0.08800 H1   
+   1.0 ASP:CB     -0.03030 CT   
+   1.0 ASP:1HB    -0.01220 HC   
+   1.0 ASP:2HB    -0.01220 HC   
+   1.0 ASP:CG      0.79940 C    
+   1.0 ASP:OD1    -0.80140 O2   
+   1.0 ASP:OD2    -0.80140 O2   
+   1.0 ASP:C       0.53660 C    
+   1.0 ASP:O      -0.58190 O    
+   1.0 LYS:N      -0.34790 N    
+   1.0 LYS:H       0.27470 H    
+   1.0 LYS:CA     -0.24000 CT   
+   1.0 LYS:HA      0.14260 H1   
+   1.0 LYS:CB     -0.00940 CT   
+   1.0 LYS:1HB     0.03620 HC   
+   1.0 LYS:2HB     0.03620 HC   
+   1.0 LYS:CG      0.01870 CT   
+   1.0 LYS:1HG     0.01030 HC   
+   1.0 LYS:2HG     0.01030 HC   
+   1.0 LYS:CD     -0.04790 CT   
+   1.0 LYS:1HD     0.06210 HC   
+   1.0 LYS:2HD     0.06210 HC   
+   1.0 LYS:CE     -0.01430 CT   
+   1.0 LYS:1HE     0.11350 HP   
+   1.0 LYS:2HE     0.11350 HP   
+   1.0 LYS:NZ     -0.38540 N3   
+   1.0 LYS:1HZ     0.34000 H    
+   1.0 LYS:2HZ     0.34000 H    
+   1.0 LYS:3HZ     0.34000 H    
+   1.0 LYS:C       0.73410 C    
+   1.0 LYS:O      -0.58940 O    
+   1.0 LYN:N      -0.41570 N    
+   1.0 LYN:H       0.27190 H    
+   1.0 LYN:CA     -0.07206 CT   
+   1.0 LYN:HA      0.09940 H1   
+   1.0 LYN:CB     -0.04845 CT   
+   1.0 LYN:HB2     0.03400 HC   
+   1.0 LYN:HB3     0.03400 HC   
+   1.0 LYN:CG      0.06612 CT   
+   1.0 LYN:HG2     0.01041 HC   
+   1.0 LYN:HG3     0.01041 HC   
+   1.0 LYN:CD     -0.03768 CT   
+   1.0 LYN:HD2     0.01155 HC   
+   1.0 LYN:HD3     0.01155 HC   
+   1.0 LYN:CE      0.32604 CT   
+   1.0 LYN:HE2    -0.03358 HP   
+   1.0 LYN:HE3    -0.03358 HP   
+   1.0 LYN:NZ     -1.03581 N3   
+   1.0 LYN:HZ2     0.38604 H    
+   1.0 LYN:HZ3     0.38604 H    
+   1.0 LYN:C       0.59730 C    
+   1.0 LYN:O      -0.56790 O    
+   1.0 PRO:N      -0.25480 N    
+   1.0 PRO:CD      0.01920 CT   
+   1.0 PRO:1HD     0.03910 H1   
+   1.0 PRO:2HD     0.03910 H1   
+   1.0 PRO:CG      0.01890 CT   
+   1.0 PRO:1HG     0.02130 HC   
+   1.0 PRO:2HG     0.02130 HC   
+   1.0 PRO:CB     -0.00700 CT   
+   1.0 PRO:1HB     0.02530 HC   
+   1.0 PRO:2HB     0.02530 HC   
+   1.0 PRO:CA     -0.02660 CT   
+   1.0 PRO:HA      0.06410 H1   
+   1.0 PRO:C       0.58960 C    
+   1.0 PRO:O      -0.57480 O    
+   1.0 CYS:N      -0.41570 N    
+   1.0 CYS:H       0.27190 H    
+   1.0 CYS:CA      0.02130 CT   
+   1.0 CYS:HA      0.11240 H1   
+   1.0 CYS:CB     -0.12310 CT   
+   1.0 CYS:1HB     0.11120 H1   
+   1.0 CYS:2HB     0.11120 H1   
+   1.0 CYS:SG     -0.31190 SH   
+   1.0 CYS:HG      0.19330 HS   
+   1.0 CYS:C       0.59730 C    
+   1.0 CYS:O      -0.56790 O    
+   1.0 CYM:N      -0.46300 N    
+   1.0 CYM:HN      0.25200 H    
+   1.0 CYM:CA      0.03500 CT   
+   1.0 CYM:HA      0.04800 H1   
+   1.0 CYM:CB     -0.73600 CT   
+   1.0 CYM:HB3     0.24400 H1   
+   1.0 CYM:HB2     0.24400 H1   
+   1.0 CYM:SG     -0.73600 SH   
+   1.0 CYM:C       0.61600 C    
+   1.0 CYM:O      -0.50400 O    
+   1.0 CYS-S:N    -0.41570 N    
+   1.0 CYS-S:H     0.27190 H    
+   1.0 CYS-S:CA    0.04290 CT   
+   1.0 CYS-S:HA    0.07660 H1   
+   1.0 CYS-S:CB   -0.07900 CT   
+   1.0 CYS-S:1HB   0.09100 H1   
+   1.0 CYS-S:2HB   0.09100 H1   
+   1.0 CYS-S:SG   -0.10810 S    
+   1.0 CYS-S:C     0.59730 C    
+   1.0 CYS-S:O    -0.56790 O    
+   1.0 MET:N      -0.41570 N    
+   1.0 MET:H       0.27190 H    
+   1.0 MET:CA     -0.02370 CT   
+   1.0 MET:HA      0.08800 H1   
+   1.0 MET:CB      0.03420 CT   
+   1.0 MET:1HB     0.02410 HC   
+   1.0 MET:2HB     0.02410 HC   
+   1.0 MET:CG      0.00180 CT   
+   1.0 MET:1HG     0.04400 H1   
+   1.0 MET:2HG     0.04400 H1   
+   1.0 MET:SD     -0.27370 S    
+   1.0 MET:CE     -0.05360 CT   
+   1.0 MET:1HE     0.06840 H1   
+   1.0 MET:2HE     0.06840 H1   
+   1.0 MET:3HE     0.06840 H1   
+   1.0 MET:C       0.59730 C    
+   1.0 MET:O      -0.56790 O    
+   1.0 ACE:1HH3    0.11230 HC   
+   1.0 ACE:CH3    -0.36620 CT   
+   1.0 ACE:2HH3    0.11230 HC   
+   1.0 ACE:3HH3    0.11230 HC   
+   1.0 ACE:C       0.59720 C    
+   1.0 ACE:O      -0.56790 O    
+   1.0 HOH:1H      0.41700 HW   
+   1.0 HOH:O      -0.83400 OW   
+   1.0 HOH:2H      0.41700 HW   
+   1.0 HOH:H1      0.41700 HW   
+   1.0 HOH:O      -0.83400 OW   
+   1.0 HOH:H2      0.41700 HW   
+   1.0 WAT:1H      0.41700 HW   
+   1.0 WAT:O      -0.83400 OW   
+   1.0 WAT:2H      0.41700 HW   
+   1.0 ASH:N      -0.41570 N    
+   1.0 ASH:H       0.27190 H    
+   1.0 ASH:CA      0.03410 CT   
+   1.0 ASH:HA      0.08640 H1   
+   1.0 ASH:CB     -0.03160 CT   
+   1.0 ASH:HB2     0.04880 HC   
+   1.0 ASH:HB3     0.04880 HC   
+   1.0 ASH:CG      0.64620 C    
+   1.0 ASH:OD1    -0.55540 O    
+   1.0 ASH:OD2    -0.63760 OH   
+   1.0 ASH:HD2     0.47470 HO   
+   1.0 ASH:C       0.59730 C    
+   1.0 ASH:O      -0.56790 O    
+   1.0 GLH:N      -0.41570 N    
+   1.0 GLH:H       0.27190 H    
+   1.0 GLH:CA      0.01450 CT   
+   1.0 GLH:HA      0.07790 H1   
+   1.0 GLH:CB     -0.00710 CT   
+   1.0 GLH:HB2     0.02560 HC   
+   1.0 GLH:HB3     0.02560 HC   
+   1.0 GLH:CG     -0.01740 CT   
+   1.0 GLH:HG2     0.04300 HC   
+   1.0 GLH:HG3     0.04300 HC   
+   1.0 GLH:CD      0.68010 C    
+   1.0 GLH:OE1    -0.58380 O    
+   1.0 GLH:OE2    -0.65110 OH   
+   1.0 GLH:HE2     0.46410 HO   
+   1.0 GLH:C       0.59730 C    
+   1.0 GLH:O      -0.56790 O    
+   1.0 CIP:NA+     1.00000 IP   
+   1.0 CIM:CL-    -1.00000 IM   
+   1.0 ALA-N:N     0.14140 N3   
+   1.0 ALA-N:1H    0.19970 H    
+   1.0 ALA-N:2H    0.19970 H    
+   1.0 ALA-N:3H    0.19970 H    
+   1.0 ALA-N:CA    0.09620 CT   
+   1.0 ALA-N:HA    0.08890 HP   
+   1.0 ALA-N:CB   -0.05970 CT   
+   1.0 ALA-N:1HB   0.03000 HC   
+   1.0 ALA-N:2HB   0.03000 HC   
+   1.0 ALA-N:3HB   0.03000 HC   
+   1.0 ALA-N:C     0.61630 C    
+   1.0 ALA-N:O    -0.57220 O    
+   1.0 GLY-N:N     0.29430 N3   
+   1.0 GLY-N:1H    0.16420 H    
+   1.0 GLY-N:2H    0.16420 H    
+   1.0 GLY-N:3H    0.16420 H    
+   1.0 GLY-N:CA   -0.01000 CT   
+   1.0 GLY-N:1HA   0.08950 HP   
+   1.0 GLY-N:2HA   0.08950 HP   
+   1.0 GLY-N:C     0.61630 C    
+   1.0 GLY-N:O    -0.57220 O    
+   1.0 SER-N:N     0.18490 N3   
+   1.0 SER-N:1H    0.18980 H    
+   1.0 SER-N:2H    0.18980 H    
+   1.0 SER-N:3H    0.18980 H    
+   1.0 SER-N:CA    0.05670 CT   
+   1.0 SER-N:HA    0.07820 HP   
+   1.0 SER-N:CB    0.25960 CT   
+   1.0 SER-N:1HB   0.02730 H1   
+   1.0 SER-N:2HB   0.02730 H1   
+   1.0 SER-N:OG   -0.67140 OH   
+   1.0 SER-N:HG    0.42390 HO   
+   1.0 SER-N:C     0.61630 C    
+   1.0 SER-N:O    -0.57220 O    
+   1.0 THR-N:N     0.18120 N3   
+   1.0 THR-N:1H    0.19340 H    
+   1.0 THR-N:2H    0.19340 H    
+   1.0 THR-N:3H    0.19340 H    
+   1.0 THR-N:CA    0.00340 CT   
+   1.0 THR-N:HA    0.10870 HP   
+   1.0 THR-N:CB    0.45140 CT   
+   1.0 THR-N:HB   -0.03230 H1   
+   1.0 THR-N:CG2  -0.25540 CT   
+   1.0 THR-N:1HG2  0.06270 HC   
+   1.0 THR-N:2HG2  0.06270 HC   
+   1.0 THR-N:3HG2  0.06270 HC   
+   1.0 THR-N:OG1  -0.67640 OH   
+   1.0 THR-N:HG1   0.40700 HO   
+   1.0 THR-N:C     0.61630 C    
+   1.0 THR-N:O    -0.57220 O    
+   1.0 LEU-N:N     0.10100 N3   
+   1.0 LEU-N:1H    0.21480 H    
+   1.0 LEU-N:2H    0.21480 H    
+   1.0 LEU-N:3H    0.21480 H    
+   1.0 LEU-N:CA    0.01040 CT   
+   1.0 LEU-N:HA    0.10530 HP   
+   1.0 LEU-N:CB   -0.02440 CT   
+   1.0 LEU-N:1HB   0.02560 HC   
+   1.0 LEU-N:2HB   0.02560 HC   
+   1.0 LEU-N:CG    0.34210 CT   
+   1.0 LEU-N:HG   -0.03800 HC   
+   1.0 LEU-N:CD1  -0.41060 CT   
+   1.0 LEU-N:1HD1  0.09800 HC   
+   1.0 LEU-N:2HD1  0.09800 HC   
+   1.0 LEU-N:3HD1  0.09800 HC   
+   1.0 LEU-N:CD2  -0.41040 CT   
+   1.0 LEU-N:1HD2  0.09800 HC   
+   1.0 LEU-N:2HD2  0.09800 HC   
+   1.0 LEU-N:3HD2  0.09800 HC   
+   1.0 LEU-N:C     0.61230 C    
+   1.0 LEU-N:O    -0.57130 O    
+   1.0 ILE-N:N     0.03110 N3   
+   1.0 ILE-N:1H    0.23290 H    
+   1.0 ILE-N:2H    0.23290 H    
+   1.0 ILE-N:3H    0.23290 H    
+   1.0 ILE-N:CA    0.02570 CT   
+   1.0 ILE-N:HA    0.10310 HP   
+   1.0 ILE-N:CB    0.18850 CT   
+   1.0 ILE-N:HB    0.02130 HC   
+   1.0 ILE-N:CG2  -0.37200 CT   
+   1.0 ILE-N:1HG2  0.09470 HC   
+   1.0 ILE-N:2HG2  0.09470 HC   
+   1.0 ILE-N:3HG2  0.09470 HC   
+   1.0 ILE-N:CG1  -0.03870 CT   
+   1.0 ILE-N:1HG1  0.02010 HC   
+   1.0 ILE-N:2HG1  0.02010 HC   
+   1.0 ILE-N:CD1  -0.09080 CT   
+   1.0 ILE-N:1HD1  0.02260 HC   
+   1.0 ILE-N:2HD1  0.02260 HC   
+   1.0 ILE-N:3HD1  0.02260 HC   
+   1.0 ILE-N:C     0.61230 C    
+   1.0 ILE-N:O    -0.57130 O    
+   1.0 VAL-N:N     0.05770 N3   
+   1.0 VAL-N:1H    0.22720 H    
+   1.0 VAL-N:2H    0.22720 H    
+   1.0 VAL-N:3H    0.22720 H    
+   1.0 VAL-N:CA   -0.00540 CT   
+   1.0 VAL-N:HA    0.10930 HP   
+   1.0 VAL-N:CB    0.31960 CT   
+   1.0 VAL-N:HB   -0.02210 HC   
+   1.0 VAL-N:CG1  -0.31290 CT   
+   1.0 VAL-N:1HG1  0.07350 HC   
+   1.0 VAL-N:2HG1  0.07350 HC   
+   1.0 VAL-N:3HG1  0.07350 HC   
+   1.0 VAL-N:CG2  -0.31290 CT   
+   1.0 VAL-N:1HG2  0.07350 HC   
+   1.0 VAL-N:2HG2  0.07350 HC   
+   1.0 VAL-N:3HG2  0.07350 HC   
+   1.0 VAL-N:C     0.61630 C    
+   1.0 VAL-N:O    -0.57220 O    
+   1.0 ASN-N:N     0.18010 N3   
+   1.0 ASN-N:1H    0.19210 H    
+   1.0 ASN-N:2H    0.19210 H    
+   1.0 ASN-N:3H    0.19210 H    
+   1.0 ASN-N:CA    0.03680 CT   
+   1.0 ASN-N:HA    0.12310 HP   
+   1.0 ASN-N:CB   -0.02830 CT   
+   1.0 ASN-N:1HB   0.05150 HC   
+   1.0 ASN-N:2HB   0.05150 HC   
+   1.0 ASN-N:CG    0.58330 C    
+   1.0 ASN-N:OD1  -0.57440 O    
+   1.0 ASN-N:ND2  -0.86340 N    
+   1.0 ASN-N:1HD2  0.40970 H    
+   1.0 ASN-N:2HD2  0.40970 H    
+   1.0 ASN-N:C     0.61630 C    
+   1.0 ASN-N:O    -0.57220 O    
+   1.0 GLN-N:N     0.14930 N3   
+   1.0 GLN-N:1H    0.19960 H    
+   1.0 GLN-N:2H    0.19960 H    
+   1.0 GLN-N:3H    0.19960 H    
+   1.0 GLN-N:CA    0.05360 CT   
+   1.0 GLN-N:HA    0.10150 HP   
+   1.0 GLN-N:CB    0.06510 CT   
+   1.0 GLN-N:1HB   0.00500 HC   
+   1.0 GLN-N:2HB   0.00500 HC   
+   1.0 GLN-N:CG   -0.09030 CT   
+   1.0 GLN-N:1HG   0.03310 HC   
+   1.0 GLN-N:2HG   0.03310 HC   
+   1.0 GLN-N:CD    0.73540 C    
+   1.0 GLN-N:OE1  -0.61330 O    
+   1.0 GLN-N:NE2  -1.00310 N    
+   1.0 GLN-N:1HE2  0.44290 H    
+   1.0 GLN-N:2HE2  0.44290 H    
+   1.0 GLN-N:C     0.61230 C    
+   1.0 GLN-N:O    -0.57130 O    
+   1.0 ARG-N:N     0.13050 N3   
+   1.0 ARG-N:1H    0.20830 H    
+   1.0 ARG-N:2H    0.20830 H    
+   1.0 ARG-N:3H    0.20830 H    
+   1.0 ARG-N:CA   -0.02230 CT   
+   1.0 ARG-N:HA    0.12420 HP   
+   1.0 ARG-N:CB    0.01180 CT   
+   1.0 ARG-N:1HB   0.02260 HC   
+   1.0 ARG-N:2HB   0.02260 HC   
+   1.0 ARG-N:CG    0.02360 CT   
+   1.0 ARG-N:1HG   0.03090 HC   
+   1.0 ARG-N:2HG   0.03090 HC   
+   1.0 ARG-N:CD    0.09350 CT   
+   1.0 ARG-N:1HD   0.05270 H1   
+   1.0 ARG-N:2HD   0.05270 H1   
+   1.0 ARG-N:NE   -0.56500 N2   
+   1.0 ARG-N:HE    0.35920 H    
+   1.0 ARG-N:CZ    0.82810 CA   
+   1.0 ARG-N:NH1  -0.86930 N2   
+   1.0 ARG-N:1HH1  0.44940 H    
+   1.0 ARG-N:2HH1  0.44940 H    
+   1.0 ARG-N:NH2  -0.86930 N2   
+   1.0 ARG-N:1HH2  0.44940 H    
+   1.0 ARG-N:2HH2  0.44940 H    
+   1.0 ARG-N:C     0.72140 C    
+   1.0 ARG-N:O    -0.60130 O    
+   1.0 HIS-N:N     0.25600 N3   
+   1.0 HIS-N:1H    0.17040 H    
+   1.0 HIS-N:2H    0.17040 H    
+   1.0 HIS-N:3H    0.17040 H    
+   1.0 HIS-N:CA    0.05810 CT   
+   1.0 HIS-N:HA    0.10470 HP   
+   1.0 HIS-N:CB    0.04840 CT   
+   1.0 HIS-N:1HB   0.05310 HC   
+   1.0 HIS-N:2HB   0.05310 HC   
+   1.0 HIS-N:CG   -0.02360 CC   
+   1.0 HIS-N:ND1  -0.15100 NA   
+   1.0 HIS-N:HD1   0.38210 H    
+   1.0 HIS-N:CE1  -0.00110 CR   
+   1.0 HIS-N:HE1   0.26450 H5   
+   1.0 HIS-N:NE2  -0.17390 NA   
+   1.0 HIS-N:CD2  -0.14330 CW   
+   1.0 HIS-N:HD2   0.24950 H4   
+   1.0 HIS-N:C     0.72140 C    
+   1.0 HIS-N:O    -0.60130 O    
+   1.0 HIS-N:N     0.25600 N3   
+   1.0 HIS-N:1H    0.17040 H    
+   1.0 HIS-N:2H    0.17040 H    
+   1.0 HIS-N:3H    0.17040 H    
+   1.0 HIS-N:CA    0.05810 CT   
+   1.0 HIS-N:HA    0.10470 HP   
+   1.0 HIS-N:CB    0.04840 CT   
+   1.0 HIS-N:1HB   0.05310 HC   
+   1.0 HIS-N:2HB   0.05310 HC   
+   1.0 HIS-N:CG   -0.02360 CC   
+   1.0 HIS-N:ND1  -0.15100 NA   
+   1.0 HIS-N:CE1  -0.00110 CR   
+   1.0 HIS-N:HE1   0.26450 H5   
+   1.0 HIS-N:NE2  -0.17390 NA   
+   1.0 HIS-N:HE2   0.39210 H    
+   1.0 HIS-N:CD2  -0.14330 CW   
+   1.0 HIS-N:HD2   0.24950 H4   
+   1.0 HIS-N:C     0.72140 C    
+   1.0 HIS-N:O    -0.60130 O    
+   1.0 HIS-N:N     0.25600 N3   
+   1.0 HIS-N:1H    0.17040 H    
+   1.0 HIS-N:2H    0.17040 H    
+   1.0 HIS-N:3H    0.17040 H    
+   1.0 HIS-N:CA    0.05810 CT   
+   1.0 HIS-N:HA    0.10470 HP   
+   1.0 HIS-N:CB    0.04840 CT   
+   1.0 HIS-N:1HB   0.05310 HC   
+   1.0 HIS-N:2HB   0.05310 HC   
+   1.0 HIS-N:CG   -0.02360 CC   
+   1.0 HIS-N:ND1  -0.15100 NA   
+   1.0 HIS-N:HD1   0.38210 H    
+   1.0 HIS-N:CE1  -0.00110 CR   
+   1.0 HIS-N:HE1   0.26450 H5   
+   1.0 HIS-N:NE2  -0.17390 NA   
+   1.0 HIS-N:HE2   0.39210 H    
+   1.0 HIS-N:CD2  -0.14330 CW   
+   1.0 HIS-N:HD2   0.24950 H4   
+   1.0 HIS-N:C     0.72140 C    
+   1.0 HIS-N:O    -0.60130 O    
+   1.0 TRP-N:N     0.19130 N3   
+   1.0 TRP-N:1H    0.18880 H    
+   1.0 TRP-N:2H    0.18880 H    
+   1.0 TRP-N:3H    0.18880 H    
+   1.0 TRP-N:CA    0.04210 CT   
+   1.0 TRP-N:HA    0.11620 HP   
+   1.0 TRP-N:CB    0.05430 CT   
+   1.0 TRP-N:1HB   0.02220 HC   
+   1.0 TRP-N:2HB   0.02220 HC   
+   1.0 TRP-N:CG   -0.16540 C*   
+   1.0 TRP-N:CD1  -0.17880 CW   
+   1.0 TRP-N:HD1   0.21950 H4   
+   1.0 TRP-N:NE1  -0.34440 NA   
+   1.0 TRP-N:HE1   0.34120 H    
+   1.0 TRP-N:CE2   0.15750 CN   
+   1.0 TRP-N:CZ2  -0.27100 CA   
+   1.0 TRP-N:HZ2   0.15890 HA   
+   1.0 TRP-N:CH2  -0.10800 CA   
+   1.0 TRP-N:HH2   0.14110 HA   
+   1.0 TRP-N:CZ3  -0.20340 CA   
+   1.0 TRP-N:HZ3   0.14580 HA   
+   1.0 TRP-N:CE3  -0.22650 CA   
+   1.0 TRP-N:HE3   0.16460 HA   
+   1.0 TRP-N:CD2   0.11320 CB   
+   1.0 TRP-N:C     0.61230 C    
+   1.0 TRP-N:O    -0.57130 O    
+   1.0 PHE-N:N     0.17370 N3   
+   1.0 PHE-N:1H    0.19210 H    
+   1.0 PHE-N:2H    0.19210 H    
+   1.0 PHE-N:3H    0.19210 H    
+   1.0 PHE-N:CA    0.07330 CT   
+   1.0 PHE-N:HA    0.10410 HP   
+   1.0 PHE-N:CB    0.03300 CT   
+   1.0 PHE-N:1HB   0.01040 HC   
+   1.0 PHE-N:2HB   0.01040 HC   
+   1.0 PHE-N:CG    0.00310 CA   
+   1.0 PHE-N:CD1  -0.13920 CA   
+   1.0 PHE-N:HD1   0.13740 HA   
+   1.0 PHE-N:CE1  -0.16020 CA   
+   1.0 PHE-N:HE1   0.14330 HA   
+   1.0 PHE-N:CZ   -0.12080 CA   
+   1.0 PHE-N:HZ    0.13290 HA   
+   1.0 PHE-N:CE2  -0.16030 CA   
+   1.0 PHE-N:HE2   0.14330 HA   
+   1.0 PHE-N:CD2  -0.13910 CA   
+   1.0 PHE-N:HD2   0.13740 HA   
+   1.0 PHE-N:C     0.61230 C    
+   1.0 PHE-N:O    -0.57130 O    
+   1.0 TYR-N:N     0.19400 N3   
+   1.0 TYR-N:1H    0.18730 H    
+   1.0 TYR-N:2H    0.18730 H    
+   1.0 TYR-N:3H    0.18730 H    
+   1.0 TYR-N:CA    0.05700 CT   
+   1.0 TYR-N:HA    0.09830 HP   
+   1.0 TYR-N:CB    0.06590 CT   
+   1.0 TYR-N:1HB   0.01020 HC   
+   1.0 TYR-N:2HB   0.01020 HC   
+   1.0 TYR-N:CG   -0.02050 CA   
+   1.0 TYR-N:CD1  -0.20020 CA   
+   1.0 TYR-N:HD1   0.17200 HA   
+   1.0 TYR-N:CE1  -0.22390 CA   
+   1.0 TYR-N:HE1   0.16500 HA   
+   1.0 TYR-N:CZ    0.31390 C    
+   1.0 TYR-N:OH   -0.55780 OH   
+   1.0 TYR-N:HH    0.40010 HO   
+   1.0 TYR-N:CE2  -0.22390 CA   
+   1.0 TYR-N:HE2   0.16500 HA   
+   1.0 TYR-N:CD2  -0.20020 CA   
+   1.0 TYR-N:HD2   0.17200 HA   
+   1.0 TYR-N:C     0.61230 C    
+   1.0 TYR-N:O    -0.57130 O    
+   1.0 GLU-N:N     0.00170 N3   
+   1.0 GLU-N:1H    0.23910 H    
+   1.0 GLU-N:2H    0.23910 H    
+   1.0 GLU-N:3H    0.23910 H    
+   1.0 GLU-N:CA    0.05880 CT   
+   1.0 GLU-N:HA    0.12020 HP   
+   1.0 GLU-N:CB    0.09090 CT   
+   1.0 GLU-N:1HB  -0.02320 HC   
+   1.0 GLU-N:2HB  -0.02320 HC   
+   1.0 GLU-N:CG   -0.02360 CT   
+   1.0 GLU-N:1HG  -0.03150 HC   
+   1.0 GLU-N:2HG  -0.03150 HC   
+   1.0 GLU-N:CD    0.80870 C    
+   1.0 GLU-N:OE1  -0.81890 O2   
+   1.0 GLU-N:OE2  -0.81890 O2   
+   1.0 GLU-N:C     0.56210 C    
+   1.0 GLU-N:O    -0.58890 O    
+   1.0 ASP-N:N     0.07820 N3   
+   1.0 ASP-N:1H    0.22000 H    
+   1.0 ASP-N:2H    0.22000 H    
+   1.0 ASP-N:3H    0.22000 H    
+   1.0 ASP-N:CA    0.02920 CT   
+   1.0 ASP-N:HA    0.11410 HP   
+   1.0 ASP-N:CB   -0.02350 CT   
+   1.0 ASP-N:1HB  -0.01690 HC   
+   1.0 ASP-N:2HB  -0.01690 HC   
+   1.0 ASP-N:CG    0.81940 C    
+   1.0 ASP-N:OD1  -0.80840 O2   
+   1.0 ASP-N:OD2  -0.80840 O2   
+   1.0 ASP-N:C     0.56210 C    
+   1.0 ASP-N:O    -0.58890 O    
+   1.0 LYS-N:N     0.09660 N3   
+   1.0 LYS-N:1H    0.21650 H    
+   1.0 LYS-N:2H    0.21650 H    
+   1.0 LYS-N:3H    0.21650 H    
+   1.0 LYS-N:CA   -0.00150 CT   
+   1.0 LYS-N:HA    0.11800 HP   
+   1.0 LYS-N:CB    0.02120 CT   
+   1.0 LYS-N:1HB   0.02830 HC   
+   1.0 LYS-N:2HB   0.02830 HC   
+   1.0 LYS-N:CG   -0.00480 CT   
+   1.0 LYS-N:1HG   0.01210 HC   
+   1.0 LYS-N:2HG   0.01210 HC   
+   1.0 LYS-N:CD   -0.06080 CT   
+   1.0 LYS-N:1HD   0.06330 HC   
+   1.0 LYS-N:2HD   0.06330 HC   
+   1.0 LYS-N:CE   -0.01810 CT   
+   1.0 LYS-N:1HE   0.11710 HP   
+   1.0 LYS-N:2HE   0.11710 HP   
+   1.0 LYS-N:NZ   -0.37640 N3   
+   1.0 LYS-N:1HZ   0.33820 H    
+   1.0 LYS-N:2HZ   0.33820 H    
+   1.0 LYS-N:3HZ   0.33820 H    
+   1.0 LYS-N:C     0.72140 C    
+   1.0 LYS-N:O    -0.60130 O    
+   1.0 PRO-N:N    -0.20200 N3
+   1.0 PRO-N:1H    0.31200 H    
+   1.0 PRO-N:2H    0.31200 H    
+   1.0 PRO-N:3H    0.31200 H    
+   1.0 PRO-N:CD   -0.01200 CT   
+   1.0 PRO-N:1HD   0.10000 HP   
+   1.0 PRO-N:2HD   0.10000 HP   
+   1.0 PRO-N:CG   -0.12100 CT   
+   1.0 PRO-N:1HG   0.10000 HC   
+   1.0 PRO-N:2HG   0.10000 HC   
+   1.0 PRO-N:CB   -0.11500 CT   
+   1.0 PRO-N:1HB   0.10000 HC   
+   1.0 PRO-N:2HB   0.10000 HC   
+   1.0 PRO-N:CA    0.10000 CT   
+   1.0 PRO-N:HA    0.10000 HP   
+   1.0 PRO-N:C     0.52600 C    
+   1.0 PRO-N:O    -0.50000 O    
+   1.0 CYS-N:N     0.13250 N3   
+   1.0 CYS-N:1H    0.20230 H    
+   1.0 CYS-N:2H    0.20230 H    
+   1.0 CYS-N:3H    0.20230 H    
+   1.0 CYS-N:CA    0.09270 CT   
+   1.0 CYS-N:HA    0.14110 HP   
+   1.0 CYS-N:CB   -0.11950 CT   
+   1.0 CYS-N:1HB   0.11880 H1   
+   1.0 CYS-N:2HB   0.11880 H1   
+   1.0 CYS-N:SG   -0.32980 SH   
+   1.0 CYS-N:HSG   0.19750 HS   
+   1.0 CYS-N:C     0.61230 C    
+   1.0 CYS-N:O    -0.57130 O    
+   1.0 CYS-NS:N    0.20690 N3   
+   1.0 CYS-NS:1H   0.18150 H    
+   1.0 CYS-NS:2H   0.18150 H    
+   1.0 CYS-NS:3H   0.18150 H    
+   1.0 CYS-NS:CA   0.10550 CT   
+   1.0 CYS-NS:HA   0.09220 HP   
+   1.0 CYS-NS:CB  -0.02770 CT   
+   1.0 CYS-NS:1HB  0.06800 H1   
+   1.0 CYS-NS:2HB  0.06800 H1   
+   1.0 CYS-NS:SG  -0.09840 S    
+   1.0 CYS-NS:C    0.61230 C    
+   1.0 CYS-NS:O   -0.57130 O    
+   1.0 MET-N:N     0.15920 N3   
+   1.0 MET-N:1H    0.19840 H    
+   1.0 MET-N:2H    0.19840 H    
+   1.0 MET-N:3H    0.19840 H    
+   1.0 MET-N:CA    0.02210 CT   
+   1.0 MET-N:HA    0.11160 HP   
+   1.0 MET-N:CB    0.08650 CT   
+   1.0 MET-N:1HB   0.01250 HC   
+   1.0 MET-N:2HB   0.01250 HC   
+   1.0 MET-N:CG    0.03340 CT   
+   1.0 MET-N:1HG   0.02920 H1   
+   1.0 MET-N:2HG   0.02920 H1   
+   1.0 MET-N:SD   -0.27740 S    
+   1.0 MET-N:CE   -0.03410 CT   
+   1.0 MET-N:1HE   0.05970 H1   
+   1.0 MET-N:2HE   0.05970 H1   
+   1.0 MET-N:3HE   0.05970 H1   
+   1.0 MET-N:C     0.61230 C    
+   1.0 MET-N:O    -0.57130 O    
+   1.0 ALA-C:N    -0.38210 N    
+   1.0 ALA-C:H     0.26810 H    
+   1.0 ALA-C:CA   -0.17470 CT   
+   1.0 ALA-C:HA    0.10670 H1   
+   1.0 ALA-C:CB   -0.20930 CT   
+   1.0 ALA-C:1HB   0.07640 HC   
+   1.0 ALA-C:2HB   0.07640 HC   
+   1.0 ALA-C:3HB   0.07640 HC   
+   1.0 ALA-C:C     0.77310 C    
+   1.0 ALA-C:O    -0.80550 O2   
+   1.0 ALA-C:OXT  -0.80550 O2   
+   1.0 GLY-C:N    -0.38210 N    
+   1.0 GLY-C:H     0.26810 H    
+   1.0 GLY-C:CA   -0.24930 CT   
+   1.0 GLY-C:1HA   0.10560 H1   
+   1.0 GLY-C:2HA   0.10560 H1   
+   1.0 GLY-C:C     0.72310 C    
+   1.0 GLY-C:O    -0.78550 O2   
+   1.0 GLY-C:OXT  -0.78550 O2   
+   1.0 SER-C:N    -0.38210 N    
+   1.0 SER-C:H     0.26810 H    
+   1.0 SER-C:CA   -0.27220 CT   
+   1.0 SER-C:HA    0.13040 H1   
+   1.0 SER-C:CB    0.11230 CT   
+   1.0 SER-C:1HB   0.08130 H1   
+   1.0 SER-C:2HB   0.08130 H1   
+   1.0 SER-C:OG   -0.65140 OH   
+   1.0 SER-C:HG    0.44740 HO   
+   1.0 SER-C:C     0.81130 C    
+   1.0 SER-C:O    -0.81320 O2   
+   1.0 SER-C:OXT  -0.81320 O2   
+   1.0 THR-C:N    -0.38210 N    
+   1.0 THR-C:H     0.26810 H    
+   1.0 THR-C:CA   -0.24200 CT   
+   1.0 THR-C:HA    0.12070 H1   
+   1.0 THR-C:CB    0.30250 CT   
+   1.0 THR-C:HB    0.00780 H1   
+   1.0 THR-C:CG2  -0.18530 CT   
+   1.0 THR-C:1HG2  0.05860 HC   
+   1.0 THR-C:2HG2  0.05860 HC   
+   1.0 THR-C:3HG2  0.05860 HC   
+   1.0 THR-C:OG1  -0.64960 OH   
+   1.0 THR-C:HG1   0.41190 HO   
+   1.0 THR-C:C     0.78100 C    
+   1.0 THR-C:O    -0.80440 O2   
+   1.0 THR-C:OXT  -0.80440 O2   
+   1.0 LEU-C:N    -0.38210 N    
+   1.0 LEU-C:H     0.26810 H    
+   1.0 LEU-C:CA   -0.28470 CT   
+   1.0 LEU-C:HA    0.13460 H1   
+   1.0 LEU-C:CB   -0.24690 CT   
+   1.0 LEU-C:1HB   0.09740 HC   
+   1.0 LEU-C:2HB   0.09740 HC   
+   1.0 LEU-C:CG    0.37060 CT   
+   1.0 LEU-C:HG   -0.03740 HC   
+   1.0 LEU-C:CD1  -0.41630 CT   
+   1.0 LEU-C:1HD1  0.10380 HC   
+   1.0 LEU-C:2HD1  0.10380 HC   
+   1.0 LEU-C:3HD1  0.10380 HC   
+   1.0 LEU-C:CD2  -0.41630 CT   
+   1.0 LEU-C:1HD2  0.10380 HC   
+   1.0 LEU-C:2HD2  0.10380 HC   
+   1.0 LEU-C:3HD2  0.10380 HC   
+   1.0 LEU-C:C     0.83260 C    
+   1.0 LEU-C:O    -0.81990 O2   
+   1.0 LEU-C:OXT  -0.81990 O2   
+   1.0 ILE-C:N    -0.38210 N    
+   1.0 ILE-C:H     0.26810 H    
+   1.0 ILE-C:CA   -0.31000 CT   
+   1.0 ILE-C:HA    0.13750 H1   
+   1.0 ILE-C:CB    0.03630 CT   
+   1.0 ILE-C:HB    0.07660 HC   
+   1.0 ILE-C:CG2  -0.34980 CT   
+   1.0 ILE-C:1HG2  0.10210 HC   
+   1.0 ILE-C:2HG2  0.10210 HC   
+   1.0 ILE-C:3HG2  0.10210 HC   
+   1.0 ILE-C:CG1  -0.03230 CT   
+   1.0 ILE-C:1HG1  0.03210 HC   
+   1.0 ILE-C:2HG1  0.03210 HC   
+   1.0 ILE-C:CD1  -0.06990 CT   
+   1.0 ILE-C:1HD1  0.01960 HC   
+   1.0 ILE-C:2HD1  0.01960 HC   
+   1.0 ILE-C:3HD1  0.01960 HC   
+   1.0 ILE-C:C     0.83430 C    
+   1.0 ILE-C:O    -0.81900 O2   
+   1.0 ILE-C:OXT  -0.81900 O2   
+   1.0 NME-C:N      -0.41570 N    
+   1.0 NME-C:H       0.27190 H    
+   1.0 NME-C:CH3    -0.14900 CT   
+   1.0 NME-C:1HH3    0.09760 H1   
+   1.0 NME-C:2HH3    0.09760 H1   
+   1.0 NME-C:3HH3    0.09760 H1   
+   1.0 VAL-C:N    -0.38210 N    
+   1.0 VAL-C:H     0.26810 H    
+   1.0 VAL-C:CA   -0.34380 CT   
+   1.0 VAL-C:HA    0.14380 H1   
+   1.0 VAL-C:CB    0.19400 CT   
+   1.0 VAL-C:HB    0.03080 HC   
+   1.0 VAL-C:CG1  -0.30640 CT   
+   1.0 VAL-C:1HG1  0.08360 HC   
+   1.0 VAL-C:2HG1  0.08360 HC   
+   1.0 VAL-C:3HG1  0.08360 HC   
+   1.0 VAL-C:CG2  -0.30640 CT   
+   1.0 VAL-C:1HG2  0.08360 HC   
+   1.0 VAL-C:2HG2  0.08360 HC   
+   1.0 VAL-C:3HG2  0.08360 HC   
+   1.0 VAL-C:C     0.83500 C    
+   1.0 VAL-C:O    -0.81730 O2   
+   1.0 VAL-C:OXT  -0.81730 O2   
+   1.0 ASN-C:N    -0.38210 N    
+   1.0 ASN-C:H     0.26810 H    
+   1.0 ASN-C:CA   -0.20800 CT   
+   1.0 ASN-C:HA    0.13580 H1   
+   1.0 ASN-C:CB   -0.22990 CT   
+   1.0 ASN-C:1HB   0.10230 HC   
+   1.0 ASN-C:2HB   0.10230 HC   
+   1.0 ASN-C:CG    0.71530 C    
+   1.0 ASN-C:OD1  -0.60100 O    
+   1.0 ASN-C:ND2  -0.90840 N    
+   1.0 ASN-C:1HD2  0.41500 H    
+   1.0 ASN-C:2HD2  0.41500 H    
+   1.0 ASN-C:C     0.80500 C    
+   1.0 ASN-C:O    -0.81470 O2   
+   1.0 ASN-C:OXT  -0.81470 O2   
+   1.0 GLN-C:N    -0.38210 N    
+   1.0 GLN-C:H     0.26810 H    
+   1.0 GLN-C:CA   -0.22480 CT   
+   1.0 GLN-C:HA    0.12320 H1   
+   1.0 GLN-C:CB   -0.06640 CT   
+   1.0 GLN-C:1HB   0.04520 HC   
+   1.0 GLN-C:2HB   0.04520 HC   
+   1.0 GLN-C:CG   -0.02100 CT   
+   1.0 GLN-C:1HG   0.02030 HC   
+   1.0 GLN-C:2HG   0.02030 HC   
+   1.0 GLN-C:CD    0.70930 C    
+   1.0 GLN-C:OE1  -0.60980 O    
+   1.0 GLN-C:NE2  -0.95740 N    
+   1.0 GLN-C:1HE2  0.43040 H    
+   1.0 GLN-C:2HE2  0.43040 H    
+   1.0 GLN-C:C     0.77750 C    
+   1.0 GLN-C:O    -0.80420 O2   
+   1.0 GLN-C:OXT  -0.80420 O2   
+   1.0 ARG-C:N    -0.34810 N    
+   1.0 ARG-C:H     0.27640 H    
+   1.0 ARG-C:CA   -0.30680 CT   
+   1.0 ARG-C:HA    0.14470 H1   
+   1.0 ARG-C:CB   -0.03740 CT   
+   1.0 ARG-C:1HB   0.03710 HC   
+   1.0 ARG-C:2HB   0.03710 HC   
+   1.0 ARG-C:CG    0.07440 CT   
+   1.0 ARG-C:1HG   0.01850 HC   
+   1.0 ARG-C:2HG   0.01850 HC   
+   1.0 ARG-C:CD    0.11140 CT   
+   1.0 ARG-C:1HD   0.04680 H1   
+   1.0 ARG-C:2HD   0.04680 H1   
+   1.0 ARG-C:NE   -0.55640 N2   
+   1.0 ARG-C:HE    0.34790 H    
+   1.0 ARG-C:CZ    0.83680 CA   
+   1.0 ARG-C:NH1  -0.87370 N2   
+   1.0 ARG-C:1HH1  0.44930 H    
+   1.0 ARG-C:2HH1  0.44930 H    
+   1.0 ARG-C:NH2  -0.87370 N2   
+   1.0 ARG-C:1HH2  0.44930 H    
+   1.0 ARG-C:2HH2  0.44930 H    
+   1.0 ARG-C:C     0.85570 C    
+   1.0 ARG-C:O    -0.82660 O2   
+   1.0 ARG-C:OXT  -0.82660 O2   
+   1.0 HIS-C:N    -0.34810 N    
+   1.0 HIS-C:H     0.27640 H    
+   1.0 HIS-C:CA   -0.14450 CT   
+   1.0 HIS-C:HA    0.11150 H1   
+   1.0 HIS-C:CB   -0.08000 CT   
+   1.0 HIS-C:1HB   0.08680 HC   
+   1.0 HIS-C:2HB   0.08680 HC   
+   1.0 HIS-C:CG    0.02980 CC   
+   1.0 HIS-C:ND1  -0.15010 NA   
+   1.0 HIS-C:HD1   0.38830 H    
+   1.0 HIS-C:CE1  -0.02510 CR   
+   1.0 HIS-C:HE1   0.26940 H5   
+   1.0 HIS-C:NE2  -0.16830 NA   
+   1.0 HIS-C:CD2  -0.12560 CW   
+   1.0 HIS-C:HD2   0.23360 H4   
+   1.0 HIS-C:C     0.80320 C    
+   1.0 HIS-C:O    -0.81770 O2   
+   1.0 HIS-C:OXT  -0.81770 O2   
+   1.0 HIS-C:N    -0.34810 N    
+   1.0 HIS-C:H     0.27640 H    
+   1.0 HIS-C:CA   -0.14450 CT   
+   1.0 HIS-C:HA    0.11150 H1   
+   1.0 HIS-C:CB   -0.08000 CT   
+   1.0 HIS-C:1HB   0.08680 HC   
+   1.0 HIS-C:2HB   0.08680 HC   
+   1.0 HIS-C:CG    0.02980 CC   
+   1.0 HIS-C:ND1  -0.15010 NA   
+   1.0 HIS-C:CE1  -0.02510 CR   
+   1.0 HIS-C:HE1   0.26940 H5   
+   1.0 HIS-C:NE2  -0.16830 NA   
+   1.0 HIS-C:HE2   0.39130 H    
+   1.0 HIS-C:CD2  -0.12560 CW   
+   1.0 HIS-C:HD2   0.23360 H4   
+   1.0 HIS-C:C     0.80320 C    
+   1.0 HIS-C:O    -0.81770 O2   
+   1.0 HIS-C:OXT  -0.81770 O2   
+   1.0 HIS-C:N    -0.34810 N    
+   1.0 HIS-C:H     0.27640 H    
+   1.0 HIS-C:CA   -0.14450 CT   
+   1.0 HIS-C:HA    0.11150 H1   
+   1.0 HIS-C:CB   -0.08000 CT   
+   1.0 HIS-C:1HB   0.08680 HC   
+   1.0 HIS-C:2HB   0.08680 HC   
+   1.0 HIS-C:CG    0.02980 CC   
+   1.0 HIS-C:ND1  -0.15010 NA   
+   1.0 HIS-C:HD1   0.38830 H    
+   1.0 HIS-C:CE1  -0.02510 CR   
+   1.0 HIS-C:HE1   0.26940 H5   
+   1.0 HIS-C:NE2  -0.16830 NA   
+   1.0 HIS-C:HE2   0.39130 H    
+   1.0 HIS-C:CD2  -0.12560 CW   
+   1.0 HIS-C:HD2   0.23360 H4   
+   1.0 HIS-C:C     0.80320 C    
+   1.0 HIS-C:O    -0.81770 O2   
+   1.0 HIS-C:OXT  -0.81770 O2   
+   1.0 TRP-C:N    -0.38210 N    
+   1.0 TRP-C:H     0.26810 H    
+   1.0 TRP-C:CA   -0.20840 CT   
+   1.0 TRP-C:HA    0.12720 H1   
+   1.0 TRP-C:CB   -0.07420 CT   
+   1.0 TRP-C:1HB   0.04970 HC   
+   1.0 TRP-C:2HB   0.04970 HC   
+   1.0 TRP-C:CG   -0.07960 C*   
+   1.0 TRP-C:CD1  -0.18080 CW   
+   1.0 TRP-C:HD1   0.20430 H4   
+   1.0 TRP-C:NE1  -0.33160 NA   
+   1.0 TRP-C:HE1   0.34130 H    
+   1.0 TRP-C:CE2   0.12220 CN   
+   1.0 TRP-C:CZ2  -0.25940 CA   
+   1.0 TRP-C:HZ2   0.15670 HA   
+   1.0 TRP-C:CH2  -0.10200 CA   
+   1.0 TRP-C:HH2   0.14010 HA   
+   1.0 TRP-C:CZ3  -0.22870 CA   
+   1.0 TRP-C:HZ3   0.15070 HA   
+   1.0 TRP-C:CE3  -0.18370 CA   
+   1.0 TRP-C:HE3   0.14910 HA   
+   1.0 TRP-C:CD2   0.10780 CB   
+   1.0 TRP-C:C     0.76580 C    
+   1.0 TRP-C:O    -0.80110 O2   
+   1.0 TRP-C:OXT  -0.80110 O2   
+   1.0 PHE-C:N    -0.38210 N    
+   1.0 PHE-C:H     0.26810 H    
+   1.0 PHE-C:CA   -0.18250 CT   
+   1.0 PHE-C:HA    0.10980 H1   
+   1.0 PHE-C:CB   -0.09590 CT   
+   1.0 PHE-C:1HB   0.04430 HC   
+   1.0 PHE-C:2HB   0.04430 HC   
+   1.0 PHE-C:CG    0.05520 CA   
+   1.0 PHE-C:CD1  -0.13000 CA   
+   1.0 PHE-C:HD1   0.14080 HA   
+   1.0 PHE-C:CE1  -0.18470 CA   
+   1.0 PHE-C:HE1   0.14610 HA   
+   1.0 PHE-C:CZ   -0.09440 CA   
+   1.0 PHE-C:HZ    0.12800 HA   
+   1.0 PHE-C:CE2  -0.18470 CA   
+   1.0 PHE-C:HE2   0.14610 HA   
+   1.0 PHE-C:CD2  -0.13000 CA   
+   1.0 PHE-C:HD2   0.14080 HA   
+   1.0 PHE-C:C     0.76600 C    
+   1.0 PHE-C:O    -0.80260 O2   
+   1.0 PHE-C:OXT  -0.80260 O2   
+   1.0 TYR-C:N    -0.38210 N    
+   1.0 TYR-C:H     0.26810 H    
+   1.0 TYR-C:CA   -0.20150 CT   
+   1.0 TYR-C:HA    0.10920 H1   
+   1.0 TYR-C:CB   -0.07520 CT   
+   1.0 TYR-C:1HB   0.04900 HC   
+   1.0 TYR-C:2HB   0.04900 HC   
+   1.0 TYR-C:CG    0.02430 CA   
+   1.0 TYR-C:CD1  -0.19220 CA   
+   1.0 TYR-C:HD1   0.17800 HA   
+   1.0 TYR-C:CE1  -0.24580 CA   
+   1.0 TYR-C:HE1   0.16730 HA   
+   1.0 TYR-C:CZ    0.33950 C    
+   1.0 TYR-C:OH   -0.56430 OH   
+   1.0 TYR-C:HH    0.40170 HO   
+   1.0 TYR-C:CE2  -0.24580 CA   
+   1.0 TYR-C:HE2   0.16730 HA   
+   1.0 TYR-C:CD2  -0.19220 CA   
+   1.0 TYR-C:HD2   0.17800 HA   
+   1.0 TYR-C:C     0.78170 C    
+   1.0 TYR-C:O    -0.80700 O2   
+   1.0 TYR-C:OXT  -0.80700 O2   
+   1.0 GLU-C:N    -0.51920 N    
+   1.0 GLU-C:H     0.30550 H    
+   1.0 GLU-C:CA   -0.20590 CT   
+   1.0 GLU-C:HA    0.13990 H1   
+   1.0 GLU-C:CB    0.00710 CT   
+   1.0 GLU-C:1HB  -0.00780 HC   
+   1.0 GLU-C:2HB  -0.00780 HC   
+   1.0 GLU-C:CG    0.06750 CT   
+   1.0 GLU-C:1HG  -0.05480 HC   
+   1.0 GLU-C:2HG  -0.05480 HC   
+   1.0 GLU-C:CD    0.81830 C    
+   1.0 GLU-C:OE1  -0.82200 O2   
+   1.0 GLU-C:OE2  -0.82200 O2   
+   1.0 GLU-C:C     0.74200 C    
+   1.0 GLU-C:O    -0.79300 O2   
+   1.0 GLU-C:OXT  -0.79300 O2   
+   1.0 ASP-C:N    -0.51920 N    
+   1.0 ASP-C:H     0.30550 H    
+   1.0 ASP-C:CA   -0.18170 CT   
+   1.0 ASP-C:HA    0.10460 H1   
+   1.0 ASP-C:CB   -0.06770 CT   
+   1.0 ASP-C:1HB  -0.02120 HC   
+   1.0 ASP-C:2HB  -0.02120 HC   
+   1.0 ASP-C:CG    0.88510 C    
+   1.0 ASP-C:OD1  -0.81620 O2   
+   1.0 ASP-C:OD2  -0.81620 O2   
+   1.0 ASP-C:C     0.72560 C    
+   1.0 ASP-C:O    -0.78870 O2   
+   1.0 ASP-C:OXT  -0.78870 O2   
+   1.0 LYS-C:N    -0.34810 N    
+   1.0 LYS-C:H     0.27640 H    
+   1.0 LYS-C:CA   -0.29030 CT   
+   1.0 LYS-C:HA    0.14380 H1   
+   1.0 LYS-C:CB   -0.05380 CT   
+   1.0 LYS-C:1HB   0.04820 HC   
+   1.0 LYS-C:2HB   0.04820 HC   
+   1.0 LYS-C:CG    0.02270 CT   
+   1.0 LYS-C:1HG   0.01340 HC   
+   1.0 LYS-C:2HG   0.01340 HC   
+   1.0 LYS-C:CD   -0.03920 CT   
+   1.0 LYS-C:1HD   0.06110 HC   
+   1.0 LYS-C:2HD   0.06110 HC   
+   1.0 LYS-C:CE   -0.01760 CT   
+   1.0 LYS-C:1HE   0.11210 HP   
+   1.0 LYS-C:2HE   0.11210 HP   
+   1.0 LYS-C:NZ   -0.37410 N3   
+   1.0 LYS-C:1HZ   0.33740 H    
+   1.0 LYS-C:2HZ   0.33740 H    
+   1.0 LYS-C:3HZ   0.33740 H    
+   1.0 LYS-C:C     0.84880 C    
+   1.0 LYS-C:O    -0.82520 O2   
+   1.0 LYS-C:OXT  -0.82520 O2   
+   1.0 PRO-C:N    -0.28020 N    
+   1.0 PRO-C:CD    0.04340 CT   
+   1.0 PRO-C:1HD   0.03310 H1   
+   1.0 PRO-C:2HD   0.03310 H1   
+   1.0 PRO-C:CG    0.04660 CT   
+   1.0 PRO-C:1HG   0.01720 HC   
+   1.0 PRO-C:2HG   0.01720 HC   
+   1.0 PRO-C:CB   -0.05430 CT   
+   1.0 PRO-C:1HB   0.03810 HC   
+   1.0 PRO-C:2HB   0.03810 HC   
+   1.0 PRO-C:CA   -0.13360 CT   
+   1.0 PRO-C:HA    0.07760 H1   
+   1.0 PRO-C:C     0.66310 C    
+   1.0 PRO-C:O    -0.76970 O2   
+   1.0 PRO-C:OXT  -0.76970 O2   
+   1.0 CYS-C:N    -0.38210 N    
+   1.0 CYS-C:H     0.26810 H    
+   1.0 CYS-C:CA   -0.16350 CT   
+   1.0 CYS-C:HA    0.13960 H1   
+   1.0 CYS-C:CB   -0.19960 CT   
+   1.0 CYS-C:1HB   0.14370 H1   
+   1.0 CYS-C:2HB   0.14370 H1   
+   1.0 CYS-C:SG   -0.31020 SH   
+   1.0 CYS-C:HSG   0.20680 HS   
+   1.0 CYS-C:C     0.74970 C    
+   1.0 CYS-C:O    -0.79810 O2   
+   1.0 CYS-C:OXT  -0.79810 O2   
+   1.0 CYS-CS:N   -0.38210 N    
+   1.0 CYS-CS:H    0.26810 H    
+   1.0 CYS-CS:CA  -0.13180 CT   
+   1.0 CYS-CS:HA   0.09380 H1   
+   1.0 CYS-CS:CB  -0.19430 CT   
+   1.0 CYS-CS:1HB  0.12280 H1   
+   1.0 CYS-CS:2HB  0.12280 H1   
+   1.0 CYS-CS:SG  -0.05290 S    
+   1.0 CYS-CS:C    0.76180 C    
+   1.0 CYS-CS:O   -0.80410 O2   
+   1.0 CYS-CS:OXT -0.80410 O2   
+   1.0 MET-C:N    -0.38210 N    
+   1.0 MET-C:H     0.26810 H    
+   1.0 MET-C:CA   -0.25970 CT   
+   1.0 MET-C:HA    0.12770 H1   
+   1.0 MET-C:CB   -0.02360 CT   
+   1.0 MET-C:1HB   0.04800 HC   
+   1.0 MET-C:2HB   0.04800 HC   
+   1.0 MET-C:CG    0.04920 CT   
+   1.0 MET-C:1HG   0.03170 H1   
+   1.0 MET-C:2HG   0.03170 H1   
+   1.0 MET-C:SD   -0.26920 S    
+   1.0 MET-C:CE   -0.03760 CT   
+   1.0 MET-C:1HE   0.06250 H1   
+   1.0 MET-C:2HE   0.06250 H1   
+   1.0 MET-C:3HE   0.06250 H1   
+   1.0 MET-C:C     0.80130 C    
+   1.0 MET-C:O    -0.81050 O2   
+   1.0 MET-C:OXT  -0.81050 O2   
+   1.0 CA:CA       2.00000 C0
+   1.0 MG:MG       2.00000 MG
+   1.0 CH4-M:C       0.00000 CT
+   1.0 CH4-M:1H      0.00000 H1
+   1.0 CH4-M:2H      0.00000 H1
+   1.0 CH4-M:3H      0.00000 H1
+   1.0 CH4-M:4H      0.00000 H1
+   1.0 PCA:N      -0.720984 N
+   1.0 PCA:H       0.374677 H
+   1.0 PCA:CA     -0.025874 CT
+   1.0 PCA:C       0.865161 C
+   1.0 PCA:O      -0.798202 O
+   1.0 PCA:CB      0.114954 CT
+   1.0 PCA:CG     -0.126748 CT
+   1.0 PCA:CD      0.770356 C
+   1.0 PCA:OE     -0.682912 O
+   1.0 PCA:HA      0.039708 H1
+   1.0 PCA:1HB     0.000266 HC
+   1.0 PCA:2HB    -0.031861 HC
+   1.0 PCA:1HG     0.034072 HC
+   1.0 PCA:2HG     0.025655 HC
+   1.0 PCA:OXT    -0.838268 O
+   1.0 PCA-N:N      -0.720984 N
+   1.0 PCA-N:H       0.374677 H
+   1.0 PCA-N:CA     -0.025874 CT
+   1.0 PCA-N:C       0.865161 C
+   1.0 PCA-N:O      -0.798202 O
+   1.0 PCA-N:CB      0.114954 CT
+   1.0 PCA-N:CG     -0.126748 CT
+   1.0 PCA-N:CD      0.770356 C
+   1.0 PCA-N:OE     -0.682912 O
+   1.0 PCA-N:HA      0.039708 H1
+   1.0 PCA-N:1HB     0.000266 HC
+   1.0 PCA-N:2HB    -0.031861 HC
+   1.0 PCA-N:1HG     0.034072 HC
+   1.0 PCA-N:2HG     0.025655 HC
+   1.0 PCA-M:N      -0.720984 N
+   1.0 PCA-M:H       0.374677 H
+   1.0 PCA-M:CA     -0.025874 CT
+   1.0 PCA-M:C       0.865161 C
+   1.0 PCA-M:O      -0.798202 O
+   1.0 PCA-M:CB      0.114954 CT
+   1.0 PCA-M:CG     -0.126748 CT
+   1.0 PCA-M:CD      0.770356 C
+   1.0 PCA-M:OE     -0.682912 O
+   1.0 PCA-M:HA      0.039708 H1
+   1.0 PCA-M:1HB     0.000266 HC
+   1.0 PCA-M:2HB    -0.031861 HC
+   1.0 PCA-M:1HG     0.034072 HC
+   1.0 PCA-M:2HG     0.025655 HC
+   1.0 PCA-M:OXT    -0.838268 O
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/CMakeLists.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,53 @@
+# 2008-03-15
+
+set(to_install
+    aromatic.txt
+    atomtyp.txt
+    bondtyp.txt
+    element.txt
+    fragments.txt
+    gaff.dat
+    gaff.prm
+    ghemical.prm
+    isotope-small.txt
+    isotope.txt
+    logp.txt
+    MACCS.txt
+    mmff94.ff
+    mmff94s.ff
+    mmffang.par
+    mmffbndk.par
+    mmffbond.par
+    mmffchg.par
+    mmffdef.par
+    mmffdfsb.par
+    mmffoop.par
+    mmffpbci.par
+    mmffprop.par
+    mmffstbn.par
+    mmfftor.par
+    mmffvdw.par
+    mmffs_oop.par
+    mmffs_tor.par
+    mr.txt
+    patterns.txt
+    phmodel.txt
+    plugindefines.txt
+    psa.txt
+    qeq.txt
+    resdata.txt
+    ringtyp.txt
+    SMARTS_InteLigand.txt
+    space-groups.txt
+    superatom.txt
+    svgformat.script
+    torlib.txt
+    types.txt
+    UFF.prm
+)
+
+if(NOT MSVC)
+  install(FILES ${to_install} DESTINATION share/openbabel/${BABEL_VERSION})
+else(NOT MSVC)
+  install(FILES ${to_install} DESTINATION bin/data)
+endif(NOT MSVC)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/MACCS.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,205 @@
+#Comments after SMARTS
+# Extracted from RDKit Jul 2008 release (r747) Python/Chem/MACCSKeys.py
+#
+# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC
+#
+#   @@ All Rights Reserved  @@
+#
+#Redistribution and use in source and binary forms, with or without
+#modification, are permitted provided that the following conditions are
+#met: 
+#
+#    * Redistributions of source code must retain the above copyright 
+#      notice, this list of conditions and the following disclaimer.
+#    * Redistributions in binary form must reproduce the above
+#      copyright notice, this list of conditions and the following 
+#      disclaimer in the documentation and/or other materials provided 
+#      with the distribution.
+#    * Neither the name of Rational Discovery nor the names of its 
+#      contributors may be used to endorse or promote products derived 
+#      from this software without specific prior written permission.
+#
+#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+#"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+#LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+#A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+#OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+#SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+#LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+#DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+#THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+#(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+# these are SMARTS patterns corresponding to the MDL MACCS keys
+  1:('?',0), # ISOTOPE
+  #2:('[#103,#104,#105,#106,#107,#106,#109,#110,#111,#112]',0),  # ISOTOPE Not complete
+  2:('[#103,#104]',0),  # ISOTOPE Not complete
+  3:('[Ge,As,Se,Sn,Sb,Te,Tl,Pb,Bi]',0), # Group IVa,Va,VIa Periods 4-6 (Ge...)  *NOTE* spec wrong
+  4:('[Ac,Th,Pa,U,Np,Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr]',0), # actinide
+  5:('[Sc,Ti,Y,Zr,Hf]',0), # Group IIIB,IVB (Sc...)  *NOTE* spec wrong
+  6:('[La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu]',0), # Lanthanide
+  7:('[V,Cr,Mn,Nb,Mo,Tc,Ta,W,Re]',0), # Group VB,VIB,VIIB (V...) *NOTE* spec wrong
+  8:('[!C;!c;!#1]1~*~*~*~*1',0), # QAAA@1
+  9:('[Fe,Co,Ni,Ru,Rh,Pd,Os,Ir,Pt]',0), # Group VIII (Fe...)
+  10:('[Be,Mg,Ca,Sr,Ba,Ra]',0), # Group IIa (Alkaline earth)
+  11:('*1~*~*~*~*1',0), # 4M Ring *NOTE* Was '*1~*~*~*~1' This and 9 others changed by CM because OB didn't like it
+  12:('[Cu,Zn,Ag,Cd,Au,Hg]',0), # Group IB,IIB (Cu..)
+  13:('[O,o]~[N,n](~[C,c])~[C,c]',0), # ON(C)C
+  14:('[S,s]-[S,s]',0), # S-S
+  15:('[O,o]~[C,c](~[O,o])~[O,o]',0), # OC(O)O
+  16:('[!C;!c;!#1]1~*~*~*1',0), # QAA@1
+  17:('[C,c]#[C,c]',0), #CTC
+  18:('[B,Al,Ga,In,Tl]',0), # Group IIIA (B...) *NOTE* spec wrong
+  19:('*1~*~*~*~*~*~*~*1',0), # 7M Ring
+  20:('[Si]',0), #Si
+  21:('[C,c]=[C,c](~[!C;!c;!#1])~[!C;!c;!#1]',0), # C=C(Q)Q
+  22:('*1~*~*~*1',0), # 3M Ring
+  23:('[N,n]~[C,c](~[O,o])~[O,o]',0), # NC(O)O
+  24:('[N,n]-[O,o]',0), # N-O
+  25:('[N,n]~[C,c](~[N,n])~[N,n]',0), # NC(N)N
+  26:('[C,c]=;@[C,c](@*)@*',0), # C$=C($A)$A
+  27:('[I]',0), # I
+  28:('[!C;!c;!#1]~[CH2]~[!C;!c;!#1]',0), # QCH2Q
+  29:('P',0),# P
+  30:('[C,c]~[!C;!c;!#1](~[C,c])(~[C,c])~*',0), # CQ(C)(C)A
+  31:('[!C;!c;!#1]~[F,Cl,Br,I]',0), # QX
+  32:('[C,c]~[S,s]~[N,n]',0), # CSN
+  33:('[N,n]~[S,s]',0), # NS
+  34:('[CH2]=*',0), # CH2=A
+  35:('[Li,Na,K,Rb,Cs,Fr]',0), # Group IA (Alkali Metal)
+  36:('[$(S@*),$(s@*)]',0), # S Heterocycle
+  37:('[N,n]~[C,c](~[O,o])~[N,n]',0), # NC(O)N
+  38:('[N,n]~[C,c](~[C,c])~[N,n]',0), # NC(C)N
+  39:('[O,o]~[S,s](~[O,o])~[O,o]',0), # OS(O)O
+  40:('[S,s]-[O,o]',0), # S-O
+  41:('[C,c]#[N,n]',0), # CTN
+  42:('F',0), # F
+  43:('[!C;!c;!#1;H,H2,H3,H4]~*~[!C;!c;!#1;H,H2,H3,H4]',0), # QHAQH FIX: possibly incomplete
+  44:('?',0), # OTHER
+  45:('[C,c]=[C,c]~[N,n]',0), # C=CN
+  46:('Br',0), # BR
+  47:('[S,s]~*~[N,n]',0), # SAN
+  48:('[O,o]~[!C;!c;!#1](~[O,o])(~[O,o])~*',0), # OQ(O)O
+  49:('[-,-2,-3,-4,+,+2,+3,+4]',0), # CHARGE  FIX: possibly incomplete
+  50:('[C,c]=[C,c](~[C,c])~[C,c]',0), # C=C(C)C
+  51:('[C,c]~[S,s]~[O,o]',0), # CSO
+  52:('[N,n]~[N,n]',0), # NN
+  53:('[!#6;!#1;!H0]~*~*~*~[!#6;!#1;!H0]',0), # QHAAAQH FIX: possibly incomplete
+  54:('[!#6;!#1;!H0]~*~*~[!#6;!#1;!H0]',0), # QHAAQH FIX: possibly incomplete
+  55:('[O,o]~[S,s]~[O,o]',0), #OSO
+  56:('[O,o]~[N,n](~[O,o])~[C,c]',0), # ON(O)C
+  57:('[$(O@*),$(o@*)]',0), # O Heterocycle
+  58:('[!C;!c;!#1]~[S,s]~[!C;!c;!#1]',0), # QSQ
+  59:('[S,s]!:*:*',0), # Snot%A%A
+  60:('[S,s]=[O,o]',0), # S=O
+  61:('*~[S,s](~*)~*',0), # AS(A)A
+  62:('*@*!@*@*',0), # A$!A$A
+  63:('[N,n]=[O,o]',0), # N=O
+  64:('*@*!@[S,s]',0), # A$A!S
+  65:('[C,c]:[N,n]',0), # C%N
+  66:('[C,c]~[C,c](~[C,c])(~[C,c])~*',0), # CC(C)(C)A
+  67:('[!C;!c;!#1]~[S,s]',0), # QS
+  68:('[!#6;!#1;!H0]~[!#6;!#1;!H0]',0), # QHQH FIX: possibly incomplete
+  69:('[!C;!c;!#1]~[!#6;!#1;!H0]',0), # QQH FIX: possibly incomplete
+  70:('[!C;!c;!#1]~[N,n]~[!C;!c;!#1]',0), # QNQ
+  71:('[N,n]~[O,o]',0), # NO
+  72:('[O,o]~*~*~[O,o]',0), # OAAO
+  73:('[S,s]=*',0), # S=A
+  74:('[CH3]~*~[CH3]',0), # CH3ACH3
+  75:('*!@[N,n]@*',0), # A!N$A
+  76:('[C,c]=[C,c](~*)~*',0), # C=C(A)A
+  77:('[N,n]~*~[N,n]',0), # NAN
+  78:('[C,c]=[N,n]',0), # C=N
+  79:('[N,n]~*~*~[N,n]',0), # NAAN
+  80:('[N,n]~*~*~*~[N,n]',0), # NAAAN
+  81:('[S,s]~*(~*)~*',0), # SA(A)A
+  82:('*~[CH2]~[!#6;!#1;!H0]',0), # ACH2QH
+  83:('[!C;!c;!#1]1~*~*~*~*~*1',0), # QAAAA@1
+  84:('[NH2]',0), #NH2
+  85:('[C,c]~[N,n](~[C,c])~[C,c]',0), # CN(C)C
+  86:('[CH2][!C;!c;!#1][CH2]',0), # CH2QCH2
+  87:('[F,Cl,Br,I]!@*@*',0), # X!A$A
+  88:('[S,s]',0), # S
+  89:('[O,o]~*~*~*~[O,o]',0), # OAAAO
+  90:('[!#6;!#1;!H0]~*~*~[CH2]~*',0), # QHAACH2A
+  91:('[!#6;!#1;!H0]~*~*~*~[CH2]~*',0), # QHAAACH2A
+  92:('[O,o]~[C,c](~[N,n])~[C,c]',0), # OC(N)C
+  93:('[!C;!c;!#1]~[CH3]',0), # QCH3
+  94:('[!C;!c;!#1]~[N,n]',0), # QN
+  95:('[N,n]~*~*~[O,o]',0), # NAAO
+  96:('*1~*~*~*~*~*1',0), # 5 M ring
+  97:('[N,n]~*~*~*~[O,o]',0), # NAAAO
+  98:('[!C;!c;!#1]1~*~*~*~*~*~*1',0), # QAAAAA@1
+  99:('[C,c]=[C,c]',0), # C=C
+  100:('*~[CH2]~[N,n]',0), # ACH2N
+  101:('[r8,r9,r10,r11,r12]',0), # 8M Ring or larger FIX: This is not exhaustive and it appears that oelib doesn't do this right
+  102:('[!C;!c;!#1]~[O,o]',0), # QO
+  103:('Cl',0), # CL
+  104:('[!#6;!#1;!H0]~*~[CH2]~*',0), # QHACH2A
+  105:('[!C;!c;!#1]@*(@*)@*',0), # A$A($A)$A
+  106:('[!C;!c;!#1]~*(~[!C;!c;!#1])~[!C;!c;!#1]',0), # QA(Q)Q
+  107:('[F,Cl,Br,I]~*(~*)~*',0), # XA(A)A
+  108:('[CH3]~*~*~*~[CH2]~*',0), # CH3AAACH2A
+  109:('*~[CH2]~[O,o]',0), # ACH2O
+  110:('[N,n]~[C,c]~[O,o]',0), # NCO
+  111:('[N,n]~*~[CH2]~*',0), # NACH2A
+  112:('*~*(~*)(~*)~*',0), # AA(A)(A)A
+  113:('[O,o]!:*:*',0), # Onot%A%A
+  114:('[CH3]~[CH2]~*',0), # CH3CH2A
+  115:('[CH3]~*~[CH2]~*',0), # CH3ACH2A
+  116:('[CH3]~*~*~[CH2]~*',0), # CH3AACH2A
+  117:('[N,n]~*~[O,o]',0), # NAO
+  118:('*~[CH2]~[CH2]~*',1), # ACH2CH2A > 1
+  119:('[N,n]=*',0), # N=A
+  120:('[!C;!c;R]',1), # Heterocyclic atom > 1
+  121:('[$(N@*),$(n@*)]',0), # N Heterocycle
+  122:('*~[N,n](~*)~*',0), # AN(A)A
+  123:('[O,o]~[C,c]~[O,o]',0), # OCO
+  124:('[!C;!c;!#1]~[!C;!c;!#1]',0), # QQ
+  125:('?',0), # Aromatic Ring > 1
+  126:('*!@[O,o]!@*',0), # A!O!A
+  127:('*@*!@[O,o]',1), # A$A!O > 1
+  128:('*~[CH2]~*~*~*~[CH2]~*',0), # ACH2AAACH2A
+  129:('*~[CH2]~*~*~[CH2]~*',0), # ACH2AACH2A
+  130:('[!C;!c;!#1]~[!C;!c;!#1]',1), # QQ > 1 (&...)
+  131:('[!#6;!#1;!H0]',1), # QH > 1
+  132:('[O,o]~*~[CH2]~*',0), # OACH2A
+  133:('*@*!:[N,n]',0), # A$A!N
+  134:('[F,Cl,Br,I]',0), # X (HALOGEN)
+  135:('[N,n]!:*:*',0), # Nnot%A%A
+  136:('[O,o]=*',1), # O=A>1 FIX: maybe not right key
+  137:('[!C;!c;R]',0), # Heterocycle
+  138:('[!C;!c;!#1]~[CH2]~*',1), # QCH2A>1 (&...)
+  139:('[OH,OH2,OH3]',0), # OH
+  140:('[O,o]',3), # O > 3
+  141:('[CH3]',2), # CH3 > 2
+  142:('[N,n]',1), # N > 1
+  143:('*@*!@[O,o]',0), # A$A!O
+  144:('*!:*:*!:*',0), # Anot%A%Anot%A
+  145:('*1~*~*~*~*~*~*1',1), # 6M ring > 1
+  146:('[O,o]',2), # O > 2
+  147:('*~[CH2]~[CH2]~*',0), # ACH2CH2A
+  148:('*~[!C;!c;!#1](~*)~*',0), # AQ(A)A
+  149:('[CH3]',1), # CH3 > 1
+  150:('*!@*@*!@*',0), # A!A$A!A
+  151:('[N!H0]',0), # NH
+  152:('[O,o]~[C,c](~[C,c])~[C,c]',0), # OC(C)C
+  153:('[!C;!c;!#1]~[CH2]~*',0), # QCH2A
+  154:('[C,c]=[O,o]',0), # C=O
+  155:('*!@[CH2]!@*',0), # A!CH2!A
+  156:('[N,n]~*(~*)~*',0), # NA(A)A
+  157:('[C,c]-[O,o]',0), # C-O
+  158:('[C,c]-[N,n]',0), # C-N
+  159:('[O,o]',1), # O>1
+  160:('[CH3]',0), #CH3
+  161:('[N,n]',0), # N
+  162:('a',0), # Aromatic
+  163:('*1~*~*~*~*~*~*1',0), # 6M Ring
+  164:('[O,o]',0), # O
+  165:('[R]',0), # Ring
+  166:('?',0), # Fragments  FIX: this should be (*).(*), but that doesn't work properly in oelib
+
+# Output with SMILES "CNO"
+#>	24: N-O	68: QHQH 	69: QQH 	71: NO	93: QCH3	94: QN	102: QO	
+#124: QQ	131: QH > 1*2	139: OH	151: NH	158: C-N	160: CH3	161: N	164: O
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/Makefile	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,178 @@
+# CMAKE generated file: DO NOT EDIT!
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+
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+# The main all target
+all: cmake_check_build_system
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+.PHONY : depend
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+# Help Target
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+	@echo "... all (the default if no target is provided)"
+	@echo "... clean"
+	@echo "... depend"
+	@echo "... edit_cache"
+	@echo "... install"
+	@echo "... install/local"
+	@echo "... install/strip"
+	@echo "... list_install_components"
+	@echo "... rebuild_cache"
+	@echo "... test"
+.PHONY : help
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+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
+cmake_check_build_system:
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+.PHONY : cmake_check_build_system
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/SMARTS_InteLigand.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,983 @@
+#
+#              SMARTS Patterns for Functional Group Classification 
+#
+#              written by Christian Laggner 
+#              Copyright 2005 Inte:Ligand Software-Entwicklungs und Consulting GmbH
+#
+#              Released under the Lesser General Public License (LGPL license)
+#              see http://www.gnu.org/copyleft/lesser.html
+#              Modified from Version 221105
+#####################################################################################################
+
+# General Stuff:
+# These patters were written in an attempt to represent the classification of organic compounds 
+# from the viewpoint of an organic chemist.
+# They are often very restrictive. This may be generally a good thing, but it also takes some time
+# for filtering/indexing large compound sets. 
+# For filtering undesired groups (in druglike compounds) one will want to have more general patterns 
+# (e.g. you don't want *any* halide of *any* acid, *neither* aldehyde *nor* formyl esters and amides, ...). 
+#
+
+# Part I: Carbon 
+# ==============
+
+
+# I.1: Carbon-Carbon Bonds
+# ------------------------
+
+# I.1.1 Alkanes:
+
+Primary_carbon: [CX4H3][#6]
+
+Secondary_carbon: [CX4H2]([#6])[#6]
+
+Tertiary_carbon: [CX4H1]([#6])([#6])[#6]
+
+Quaternary_carbon: [CX4]([#6])([#6])([#6])[#6]
+
+
+# I.1.2 C-C double and Triple Bonds
+
+Alkene: [CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])] 
+# sp2 C may be substituted only by C or H - 
+# does not hit ketenes and allenes, nor enamines, enols and the like
+
+Alkyne: [CX2]#[CX2]
+# non-carbon substituents (e.g. alkynol ethers) are rather rare, thus no further discrimination
+
+Allene: [CX3]=[CX2]=[CX3]
+
+
+# I.2: One Carbon-Hetero Bond
+# ---------------------------
+
+
+# I.2.1 Alkyl Halogenides
+
+Alkylchloride: [ClX1][CX4]
+# will also hit chloromethylethers and the like, but no chloroalkenes, -alkynes or -aromats 
+# a more restrictive version can be obtained by modifying the Alcohol string.
+
+Alkylfluoride: [FX1][CX4]
+
+Alkylbromide: [BrX1][CX4]
+
+Alkyliodide: [IX1][CX4]
+
+
+# I.2.2 Alcohols and Ethers
+
+Alcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])]
+# nonspecific definition, no acetals, aminals, and the like
+
+Primary_alcohol: [OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])]
+
+Secondary_alcohol: [OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])]
+
+Tertiary_alcohol: [OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])]
+
+Dialkylether: [OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]
+# no acetals and the like; no enolethers
+
+Dialkylthioether: [SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]
+# no acetals and the like; no enolethers
+
+Alkylarylether: [OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]
+# no acetals and the like; no enolethers
+
+Diarylether: [c][OX2][c]
+
+Alkylarylthioether: [SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]
+
+Diarylthioether: [c][SX2][c]
+
+Oxonium: [O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])]
+# can't be aromatic, thus O and not #8
+
+# I.2.3 Amines
+
+Amine: [NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])]
+# hits all amines (prim/sec/tert/quart), including ammonium salts, also enamines, but not amides, imides, aminals, ...
+
+# the following amines include also the protonated forms 
+
+Primary_aliph_amine: [NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
+
+Secondary_aliph_amine: [NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
+
+Tertiary_aliph_amine: [NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
+
+Quaternary_aliph_ammonium: [NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
+
+Primary_arom_amine: [NX3H2+0,NX4H3+]c
+
+Secondary_arom_amine: [NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
+
+Tertiary_arom_amine: [NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
+
+Quaternary_arom_ammonium: [NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
+
+Secondary_mixed_amine: [NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])]
+
+Tertiary_mixed_amine: [NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])]
+
+Quaternary_mixed_ammonium: [NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])]
+
+Ammonium: [N+;!$([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])]
+# only C and H substituents allowed. Quaternary or protonated amines
+# NX4+ or Nv4+ is not recognized by Daylight's depictmatch if less than four C are present
+
+
+# I.2.4 Others
+
+Alkylthiol: [SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])]
+
+Dialkylthioether: [SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])]
+
+Alkylarylthioether: [SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])]
+
+Disulfide: [SX2D2][SX2D2]
+
+1,2-Aminoalcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])]
+# does not hit alpha-amino acids, enaminoalcohols, 1,2-aminoacetals, o-aminophenols, etc.
+
+1,2-Diol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H]
+# does not hit alpha-hydroxy acids, enolalcohols, 1,2-hydroxyacetals, 1,2-diphenols, etc.
+
+1,1-Diol: [OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H]
+
+Hydroperoxide: [OX2H][OX2]
+#does not neccessarily have to be connected to a carbon atom, includes also hydrotrioxides
+
+Peroxo: [OX2D2][OX2D2]
+
+Organolithium_compounds: [LiX1][#6,#14]
+
+Organomagnesium_compounds: [MgX2][#6,#14]
+# not restricted to Grignard compounds, also dialkyl Mg
+
+Organometallic_compounds: [!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-]
+# very general, includes all metals covalently bound to carbon 
+
+
+# I.3: Two Carbon-Hetero Bonds (Carbonyl and Derivatives)
+# ----------------------------
+
+# I.3.1 Double Bond to Hetero
+
+Aldehyde: [$([CX3H][#6]),$([CX3H2])]=[OX1]
+# hits aldehydes including formaldehyde
+
+Ketone: [#6][CX3](=[OX1])[#6]
+# does not include oxo-groups connected to a (hetero-) aromatic ring
+
+Thioaldehyde: [$([CX3H][#6]),$([CX3H2])]=[SX1]
+
+Thioketone: [#6][CX3](=[SX1])[#6]
+# does not include thioxo-groups connected to a (hetero-) aromatic ring
+
+Imine: [NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])]
+# nitrogen is not part of an amidelike strukture, nor of an aromatic ring, but can be part of an aminal or similar
+
+Immonium: [NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])]
+
+Oxime: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H]
+
+Oximether: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])]
+# ether, not ester or amide; does not hit isoxazole
+
+
+# I.3.2. Two Single Bonds to Hetero
+
+Acetal: [OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]
+# does not hit hydroxy-methylesters, ketenacetals, hemiacetals, orthoesters, etc.
+
+Hemiacetal: [OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]
+
+Aminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6] 
+# Ns are not part of an amide or similar. v3 ist to exclude nitro and similar groups
+
+Hemiaminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H]
+
+Thioacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])]
+
+Thiohemiacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H]
+
+Halogen_acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]
+# hits chloromethylenethers and other reactive alkylating agents
+
+Acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
+# includes all of the above and other combinations (S-C-N, hydrates, ...), but still no aminomethylenesters and similar
+
+Halogenmethylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]
+# also reactive alkylating agents. Acid does not have to be carboxylic acid, also S- and P-based acids allowed
+
+NOS_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
+# Same as above, but N,O or S instead of halogen. Ester/amide allowed only on one side 
+
+Hetero_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
+# Combination of the last two patterns
+
+Cyanhydrine: [NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H]
+
+
+# I.3.3 Single Bond to Hetero, C=C Double Bond (Enols and Similar)
+
+Chloroalkene: [ClX1][CX3]=[CX3]
+
+Fluoroalkene: [FX1][CX3]=[CX3]
+
+Bromoalkene: [BrX1][CX3]=[CX3]
+
+Iodoalkene: [IX1][CX3]=[CX3]
+
+Enol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3]
+# no phenols
+
+Endiol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H]
+# no 1,2-diphenols, ketenacetals, ...
+
+Enolether: [OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3]
+# finds also endiodiethers, but not enolesters, no aromats
+
+Enolester: [OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])]
+
+
+Enamine: [NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3]
+# does not hit amines attached to aromatic rings, nor may the nitrogen be aromatic
+
+Thioenol: [SX2H][CX3;$([H1]),$(C[#6])]=[CX3]
+
+Thioenolether: [SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3]
+
+
+# I.4: Three Carbon-Hetero Bonds (Carboxyl and Derivatives)
+# ------------------------------
+
+Acylchloride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1] 
+
+Acylfluoride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1] 
+
+Acylbromide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1] 
+
+Acyliodide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1]
+
+Acylhalide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1]
+# all of the above
+
+
+# The following contains all simple carboxylic combinations of O, N, S, & Hal -
+# - acids, esters, amides, ... as well as a few extra cases (anhydride, hydrazide...)
+# Cyclic structures (including aromats) like lactones, lactames, ... got their own  
+# definitions. Structures where both heteroatoms are part of an aromatic ring  
+# (oxazoles, imidazoles, ...) were excluded.
+
+Carboxylic_acid: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])]
+# includes carboxylate anions
+
+Carboxylic_ester:  [CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
+# does not hit anhydrides or lactones
+
+Lactone: [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
+# may also be aromatic
+
+Carboxylic_anhydride: [CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1])
+# anhydride formed by two carboxylic acids, no mixed anhydrides (e.g. between carboxylic acid and sulfuric acid); may be part of a ring, even aromatic
+
+Carboxylic_acid_derivative: [$([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6]
+# includes most of the structures of I.4 and many more, also 1,3-heteroaromatics such as isoxazole
+
+Carbothioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])]
+# hits both tautomeric forms, as well as anions
+
+Carbothioic_S_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])]
+
+Carbothioic_S_lactone: [#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])]
+# may also be aromatic
+
+Carbothioic_O_ester: [CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])]
+
+Carbothioic_O_lactone: [#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])]
+
+Carbothioic_halide: [CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1]
+
+Carbodithioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])]
+
+Carbodithioic_ester: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])]
+
+Carbodithiolactone: [#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])]
+
+
+Amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+# does not hit lactames
+
+Primary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2]
+
+Secondary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])]
+
+Tertiary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])]
+
+Lactam: [#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+# cyclic amides, may also be aromatic
+
+Alkyl_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])
+# may be part of a ring, even aromatic. only C allowed at central N. May also be triacyl amide
+
+N_hetero_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])
+# everything else than H or C at central N
+
+Imide_acidic: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1])
+# can be deprotonated
+
+Thioamide: [$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+# does not hit thiolactames
+
+Thiolactam: [#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+# cyclic thioamides, may also be aromatic
+
+
+Oximester: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])]
+# may also be part of a ring / aromatic
+
+Amidine: [NX3;!$(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])]
+# only basic amidines, not as part of aromatic ring (e.g. imidazole)
+
+Hydroxamic_acid: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])]
+
+Hydroxamic_acid_ester: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])]
+# does not hit anhydrides of carboxylic acids withs hydroxamic acids
+
+
+Imidoacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
+# not cyclic 
+
+Imidoacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]  
+# the enamide-form of lactames. may be aromatic like 2-hydroxypyridine 
+
+Imidoester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]
+# esters of the above structures. no anhydrides. 
+
+Imidolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]
+# no oxazoles and similar
+
+Imidothioacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]
+# not cyclic 
+
+Imidothioacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]  
+# the enamide-form of thiolactames. may be aromatic like 2-thiopyridine 
+
+Imidothioester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]
+# thioesters of the above structures. no anhydrides. 
+
+Imidothiolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]
+# no thioxazoles and similar
+
+Amidine: [#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])]
+# only basic amidines, not substituted by carbonyl or thiocarbonyl, not as part of a ring 
+
+Imidolactam: [#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])]  
+# one of the two C~N bonds is part of a ring (may be aromatic), but not both - thus no imidazole
+
+Imidoylhalide: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]
+# not cyclic
+
+Imidoylhalide_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]
+# may also be aromatic
+ 
+# may be ring, aromatic, substituted with carbonyls, hetero, ...
+# (everything else would get too complicated)
+
+Amidrazone: [$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])]
+# hits both tautomers. as above, it may be ring, aromatic, substituted with carbonyls, hetero, ...
+
+
+Alpha_aminoacid: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-]
+# N may be alkylated, but not part of an amide (as in peptides), ionic forms are included
+# includes also non-natural aminoacids with double-bonded or two aliph./arom. substituents at alpha-C 
+# N may not be aromatic as in 1H-pyrrole-2-carboxylic acid
+
+Alpha_hydroxyacid: [OX2H][C][CX3](=[OX1])[OX2H,OX1-]
+
+Peptide_middle: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]
+# finds peptidic structures which are neither C- nor N-terminal. Both neighbours must be amino-acids/peptides
+
+Peptide_C_term: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-]
+# finds C-terminal amino acids
+
+Peptide_N_term: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]
+# finds N-terminal amino acids. As above, N may be substituted, but not part of an amide-bond.
+
+
+Carboxylic_orthoester: [#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6] 
+# hits also anhydride like struktures (e. g. HC(OMe)2-OC=O residues)
+
+Ketene: [CX3]=[CX2]=[OX1]
+
+Ketenacetal: [#7X2,#8X3,#16X2;$(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3]
+# includes aminals, silylacetals, ketenesters, etc. C=C DB is not aromatic, everything else may be
+
+Nitrile: [NX1]#[CX2]
+# includes cyanhydrines
+
+Isonitrile: [CX1-]#[NX2+]
+
+
+Vinylogous_carbonyl_or_carboxyl_derivative: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I]
+# may be part of a ring, even aromatic
+
+Vinylogous_acid: [#6X3](=[OX1])[#6X3]=,:[#6X3][$([OX2H]),$([OX1-])]
+
+Vinylogous_ester: [#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!$(C=[O,N,S])]
+
+Vinylogous_amide: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Vinylogous_halide: [#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1]
+
+
+
+# I.5: Four Carbon-Hetero Bonds (Carbonic Acid and Derivatives)
+# -----------------------------
+
+Carbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
+# may be part of a ring, even aromatic
+
+Carbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1]
+
+Carbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])]
+# unstable
+
+Carbonic_acid_derivatives: [!#6][#6X3](=[!#6])[!#6]
+
+
+Thiocarbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])]
+# may be part of a ring, even aromatic
+
+Thiocarbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1]
+
+Thiocarbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])]
+
+
+Urea:[#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])]
+# no check whether part of imide, biuret, etc. Aromatic structures are only hit if
+# both N share no double bonds, like in the dioxo-form of uracil
+
+Thiourea: [#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])]
+
+Isourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])]
+# O may be substituted. no check whether further amide-like bonds are present. Aromatic 
+# structures are only hit if single bonded N shares no additional double bond, like in
+# the 1-hydroxy-3-oxo form of uracil
+
+Isothiourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])]
+
+Guanidine: [N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+]
+# also hits guanidinium salts. v3 and v4 to avoid nitroamidines
+
+Carbaminic_acid: [NX3]C(=[OX1])[O;X2H,X1-]
+# quite unstable, unlikely to be found. Also hits salts
+
+Urethan: [#7X3][#6](=[OX1])[#8X2][#6]
+# also hits when part of a ring, no check whether the last C is part of carbonyl
+
+Biuret: [#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3]
+
+Semicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
+
+Carbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1]
+
+Semicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
+
+Carbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1]
+
+Thiosemicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
+
+Thiocarbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1]
+
+Thiosemicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
+
+Thiocarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1]
+
+
+Isocyanate: [NX2]=[CX2]=[OX1]
+
+Cyanate: [OX2][CX2]#[NX1]
+
+Isothiocyanate: [NX2]=[CX2]=[SX1]
+
+Thiocyanate: [SX2][CX2]#[NX1]
+
+Carbodiimide: [NX2]=[CX2]=[NX2]
+
+Orthocarbonic_derivatives: [CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I]
+# halogen allowed just once, to avoid mapping to -OCF3 and similar groups (much more
+# stable as for example C(OCH3)4)
+
+
+# I.6 Aromatics
+# -------------
+
+# I know that this classification is not very logical, arylamines are found under I.2 ...
+
+Phenol: [OX2H][c]
+
+1,2-Diphenol: [OX2H][c][c][OX2H]
+
+Arylchloride: [Cl][c]
+
+Arylfluoride: [F][c]
+
+Arylbromide: [Br][c]
+
+Aryliodide: [I][c]
+
+Arylthiol: [SX2H][c]
+
+Iminoarene: [c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])]
+# N may be substituted with H or C, but not carbonyl or similar
+# aromatic atom is always C, not S or P (these are not planar when substituted)
+
+Oxoarene: [c]=[OX1]
+
+Thioarene: [c]=[SX1]
+
+Hetero_N_basic_H: [nX3H1+0]
+# as in pyrole. uncharged to exclude pyridinium ions
+
+Hetero_N_basic_no_H: [nX3H0+0]
+# as in N-methylpyrole. uncharged to exclude pyridinium ions
+
+Hetero_N_nonbasic: [nX2,nX3+]
+# as in pyridine, pyridinium
+
+Hetero_O: [o]
+
+Hetero_S: [sX2]
+# X2 because Daylight's depictmatch falsely describes C1=CS(=O)C=C1 as aromatic
+# (is not planar because of lonepair at S)
+
+Heteroaromatic: [a;!c]
+
+
+# Part II: N, S, P, Si, B 
+# =======================
+
+
+# II.1 Nitrogen
+# -------------
+
+Nitrite: [NX2](=[OX1])[O;$([X2]),$([X1-])]
+# hits nitrous acid, its anion, esters, and other O-substituted derivatives 
+
+Thionitrite: [SX2][NX2]=[OX1]
+
+Nitrate: [$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])] 
+# hits nitric acid, its anion, esters, and other O-substituted derivatives 
+
+Nitro: [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]
+# hits nitro groups attached to C,N, ... but not nitrates
+
+Nitroso: [NX2](=[OX1])[!#7;!#8]
+# no nitrites, no nitrosamines
+
+Azide: [NX1]~[NX2]~[NX2,NX1]
+# hits both mesomeric forms, also anion
+
+Acylazide: [CX3](=[OX1])[NX2]~[NX2]~[NX1]
+
+Diazo: [$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])] 
+
+Diazonium: [#6][NX2+]#[NX1]
+
+Nitrosamine: [#7;!$(N*=O)][NX2]=[OX1]
+
+Nitrosamide: [NX2](=[OX1])N-*=O
+# includes nitrososulfonamides
+
+N-Oxide: [$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])] 
+# Hits both forms. Won't hit azoxy, nitro, nitroso, or nitrate.
+
+
+Hydrazine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])]
+# no hydrazides
+
+Hydrazone: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6]
+
+Hydroxylamine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])]
+# no discrimination between O-, N-, and O,N-substitution
+
+
+# II.2 Sulfur
+# -----------
+
+Sulfon: [$([SX4](=[OX1])(=[OX1])([#6])[#6]),$([SX4+2]([OX1-])([OX1-])([#6])[#6])]
+# can't be aromatic, thus S and not #16
+
+Sulfoxide: [$([SX3](=[OX1])([#6])[#6]),$([SX3+]([OX1-])([#6])[#6])]
+
+Sulfonium: [S+;!$([S]~[!#6]);!$([S]*~[#7,#8,#15,#16])]
+# can't be aromatic, thus S and not #16
+
+Sulfuric_acid: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
+# includes anions
+
+Sulfuric_monoester: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
+
+Sulfuric_diester: [SX4](=[OX1])(=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
+
+Sulfuric_monoamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
+
+Sulfuric_diamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Sulfuric_esteramide: [SX4](=[OX1])(=[OX1])([#7X3][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
+
+Sulfuric_derivative: [SX4D4](=[!#6])(=[!#6])([!#6])[!#6]
+# everything else (would not be a "true" derivative of sulfuric acid, if one of the substituents were less electronegative 
+# than sulfur, but this should be very very rare, anyway)
+
+
+
+#### sulfurous acid and derivatives missing!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+
+
+
+Sulfonic_acid: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])]
+
+Sulfonamide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Sulfonic_ester: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])]
+
+Sulfonic_halide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1]
+
+Sulfonic_derivative: [SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6]
+# includes all of the above and many more
+# for comparison: this is what "all sulfonic derivatives but not the ones above" would look like:
+# [$([SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6;!O])[!#6]),$([SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[!$([FX1,ClX1,BrX1,IX1]);!$([#6]);!$([OX2H]);!$([OX1-]);!$([OX2][#6;!$(C=[O,N,S])]);!$([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])])]
+
+
+Sulfinic_acid: [SX3;$([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])]
+
+Sulfinic_amide: [SX3;$([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Sulfinic_ester: [SX3;$([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
+
+Sulfinic_halide: [SX3;$([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1]
+
+Sulfinic_derivative: [SX3;$([H1]),$([H0][#6])](=[!#6])[!#6]
+
+Sulfenic_acid: [SX2;$([H1]),$([H0][#6])][$([OX2H]),$([OX1-])]
+
+Sulfenic_amide: [SX2;$([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Sulfenic_ester: [SX2;$([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])]
+
+Sulfenic_halide: [SX2;$([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1]
+
+Sulfenic_derivative: [SX2;$([H1]),$([H0][#6])][!#6]
+
+
+# II.3 Phosphorous
+# ----------------
+
+Phosphine: [PX3;$([H3]),$([H2][#6]),$([H1]([#6])[#6]),$([H0]([#6])([#6])[#6])]
+# similar to amine, but less restrictive: includes also amide- and aminal-analogues 
+
+Phosphine_oxide: [PX4;$([H3]=[OX1]),$([H2](=[OX1])[#6]),$([H1](=[OX1])([#6])[#6]),$([H0](=[OX1])([#6])([#6])[#6])]
+
+Phosphonium: [P+;!$([P]~[!#6]);!$([P]*~[#7,#8,#15,#16])]
+# similar to Ammonium
+
+Phosphorylen: [PX4;$([H3]=[CX3]),$([H2](=[CX3])[#6]),$([H1](=[CX3])([#6])[#6]),$([H0](=[CX3])([#6])([#6])[#6])]
+
+
+# conventions for the following acids and derivatives: 
+# acids find protonated and deprotonated acids
+# esters do not find mixed anhydrides ( ...P-O-C(=O))
+# derivatives: subtituents which go in place of the OH and =O are not H or C (may also be O, 
+# thus including acids and esters)
+
+Phosphonic_acid: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
+# includes anions
+
+Phosphonic_monoester: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphonic_diester: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphonic_monoamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphonic_diamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphonic_esteramide: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphonic_acid_derivative: [PX4;$([H1]),$([H0][#6])](=[!#6])([!#6])[!#6]
+# all of the above and much more 
+
+
+Phosphoric_acid: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
+# includes anions
+
+Phosphoric_monoester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphoric_diester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphoric_triester: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphoric_monoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphoric_diamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphoric_triamide: [PX4D4](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphoric_monoestermonoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphoric_diestermonoamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphoric_monoesterdiamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphoric_acid_derivative: [PX4D4](=[!#6])([!#6])([!#6])[!#6]
+
+
+Phosphinic_acid: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])]
+
+Phosphinic_ester: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphinic_amide: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphinic_acid_derivative: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6]
+
+
+Phosphonous_acid: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
+
+Phosphonous_monoester: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphonous_diester: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphonous_monoamide: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphonous_diamide: [PX3;$([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphonous_esteramide: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphonous_derivatives: [PX3;$([D2]),$([D3][#6])]([!#6])[!#6]
+
+
+Phosphinous_acid: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])]
+
+Phosphinous_ester: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])]
+
+Phosphinous_amide: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphinous_derivatives: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6]
+
+
+# II.4 Silicon
+# ------------
+
+Quart_silane: [SiX4]([#6])([#6])([#6])[#6]
+# four C-substituents. non-reactive, non-toxic, in experimental phase for drug development
+
+Non-quart_silane: [SiX4;$([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])]
+# has 1-4 hydride(s), reactive. Daylight's depictmatch does not add hydrogens automatically to 
+# the free positions at Si, thus Hs had to be added implicitly
+
+Silylmonohalide: [SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6]
+# reagents for inserting protection groups
+
+Het_trialkylsilane: [SiX4]([!#6])([#6])([#6])[#6]
+# mostly acid-labile protection groups such as trimethylsilyl-ethers 
+
+Dihet_dialkylsilane: [SiX4]([!#6])([!#6])([#6])[#6]
+
+Trihet_alkylsilane: [SiX4]([!#6])([!#6])([!#6])[#6]
+
+Silicic_acid_derivative: [SiX4]([!#6])([!#6])([!#6])[!#6]
+# four substituent which are neither C nor H
+
+
+# II.5 Boron
+# ----------
+
+Trialkylborane: [BX3]([#6])([#6])[#6] 
+# also carbonyls allowed
+
+Boric_acid_derivatives: [BX3]([!#6])([!#6])[!#6]
+# includes acids, esters, amides, ... H-substituent at B is very rare.
+
+Boronic_acid_derivative: [BX3]([!#6])([!#6])[!#6]
+# # includes acids, esters, amides, ...
+
+Borohydride: [BH1,BH2,BH3,BH4]
+# at least one H attached to B
+
+Quaternary_boron: [BX4]
+# mostly borates (negative charge), in complex with Lewis-base
+
+
+
+# Part III: Some Special Patterns
+# ===============================
+
+
+# III.1 Chains
+# ------------
+
+# some simple chains
+
+
+
+# III.2 Rings
+# -----------
+
+Aromatic: a
+
+Heterocyclic: [!#6;!R0]
+# may be aromatic or not
+
+Epoxide: [OX2r3]1[#6r3][#6r3]1
+# toxic/reactive. may be annelated to aromat, but must not be aromatic itself (oxirane-2,3-dione)
+
+NH_aziridine: [NX3H1r3]1[#6r3][#6r3]1
+# toxic/reactive according to Maybridge's garbage filter
+
+Spiro: [D4R;$(*(@*)(@*)(@*)@*)]
+# at least two different rings can be found which are sharing just one atom.
+# these two rings can be connected by a third ring, so it matches also some 
+# bridged systems, like morphine
+
+Annelated_rings: [R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]
+# two different rings sharing exactly two atoms
+
+Bridged_rings: [R;$(*(@*)(@*)@*);!$([D4R;$(*(@*)(@*)(@*)@*)]);!$([R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])])]
+# part of two or more rings, not spiro, not annelated -> finds bridgehead atoms, 
+# but only if they are not annelated at the same time - otherwise impossible (?)
+# to distinguish from non-bridgehead annelated atoms
+
+# some basic ring-patterns (just size, no other information):
+
+
+
+
+
+# III.3 Sugars and Nucleosides/Nucleotides, Steroids
+# --------------------------------------------------
+
+# because of the large variety of sugar derivatives, different patterns can be applied.
+# The choice of patterns and their combinations will depend on the contents of the database
+# e.g. natural products, nucleoside analoges with modified sugars, ... as well as on the 
+# desired restriction
+
+
+Sugar_pattern_1: [OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)]
+# 5 or 6-membered ring containing one O and at least one (r5) or two (r6) oxygen-substituents. 
+
+Sugar_pattern_2: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
+# 5 or 6-membered ring containing one O and an acetal-like bond at postion 2. 
+
+Sugar_pattern_combi: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)]
+# combination of the two above
+
+Sugar_pattern_2_reducing: [OX2;$([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)]
+# 5 or 6-membered cyclic hemi-acetal
+
+Sugar_pattern_2_alpha: [OX2;$([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
+# 5 or 6-membered cyclic hemi-acetal
+
+Sugar_pattern_2_beta: [OX2;$([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
+# 5 or 6-membered cyclic hemi-acetal
+
+##Poly_sugar_1: ([OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)].[OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)])
+# pattern1 occours more than once (in same molecule, but moieties don't have to be adjacent!)
+
+##Poly_sugar_2: ([OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)].[OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)])
+# pattern2 occours more than once (in same molecule, but moieties don't have to be adjacent!)
+
+
+# III.4 Everything else...
+# ------------------------
+
+Conjugated_double_bond: *=*[*]=,#,:[*]
+
+Conjugated_tripple_bond: *#*[*]=,#,:[*]
+
+Cis_double_bond: */[D2]=[D2]\*
+# only one single-bonded substituent on each DB-atom. no aromats. 
+# only found when character of DB is explicitely stated.
+
+Trans_double_bond: */[D2]=[D2]/*
+# analog
+
+Mixed_anhydrides: [$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))]
+# should hits all combinations of two acids
+
+Halogen_on_hetero: [FX1,ClX1,BrX1,IX1][!#6]
+
+Halogen_multi_subst: [F,Cl,Br,I;!$([X1]);!$([X0-])]
+# Halogen which is not mono-substituted nor an anion, e.g. chlorate.
+# Most of these cases should be also filtered by Halogen_on_hetero.
+
+Trifluoromethyl: [FX1][CX4;!$([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1])
+# C with three F attached, connected to anything which is not another halogen
+
+C_ONS_bond: [#6]~[#7,#8,#16]
+# probably all drug-like molecules have at least one O, N, or S connected to a C -> nice filter
+
+## Mixture: (*).(*)
+# two or more seperate parts, may also be salt
+# component-level grouping is not yet supported in Open Babel Version 2.0
+
+
+Charged: [!+0]
+
+Anion: [-1,-2,-3,-4,-5,-6,-7]
+
+Kation: [+1,+2,+3,+4,+5,+6,+7]
+
+Salt: ([-1,-2,-3,-4,-5,-6,-7]).([+1,+2,+3,+4,+5,+6,+7])
+# two or more seperate components with opposite charges
+
+##Zwitterion: ([-1,-2,-3,-4,-5,-6,-7].[+1,+2,+3,+4,+5,+6,+7])
+# both negative and positive charges somewhere within the same molecule. 
+
+1,3-Tautomerizable: [$([#7X2,OX1,SX1]=*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=*),$([#7X3,OX2,SX2;!H0]*:n)]
+# 1,3 migration of H allowed. Includes keto/enol and amide/enamide. 
+# Aromatic rings must stay aromatic - no keto form of phenol 
+
+1,5-Tautomerizable: [$([#7X2,OX1,SX1]=,:**=,:*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=**=*),$([#7X3,OX2,SX2;!H0]*=,:**:n)]
+
+Rotatable_bond: [!$(*#*)&!D1]-!@[!$(*#*)&!D1]
+# taken from http://www.daylight.com/support/contrib/smarts/content.html
+
+Michael_acceptor: [CX3]=[CX3][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])]
+# the classical case: C=C near carbonyl, nitrile, nitro, or similar
+# Oxo-heteroaromats and similar are not included.
+
+Dicarbodiazene: [CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1])
+# Michael-like acceptor, see Mitsunobu reaction
+
+# H-Bond_donor:
+
+# H-Bond_acceptor:
+
+# Pos_ionizable:
+
+# Neg_ionizable:
+
+# Unlikely_ions: 
+# O+,N-,C+,C-, ...
+
+CH-acidic: [$([CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]),$([CX4;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)]
+# C-H alpha to carbony, nitro or similar, C is not double-bonded, only C, H, S,P=O and nitro substituents allowed. 
+# pentadiene is included. acids, their salts, prim./sec. amides, and imides are excluded. 
+# hits also CH-acidic_strong
+
+CH-acidic_strong: [CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])]([$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])])[$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]
+# same as above (without pentadiene), but carbonyl or similar on two or three sides
+
+Chiral_center_specified: [$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)]
+# Hits atoms with tetrahedral chirality, if chiral center is specified in the SMILES string
+# depictmach does not find oxonium, sulfonium, or sulfoxides!
+
+# Chiral_center_unspecified: [$([*@?](~*)(~*)(*)*),$([*@?H](*)(*)*),$([*@?](~*)(*)*),$([*@?H](~*)~*)]
+# Hits atoms with tetrahedral chirality, if chiral center is not specified in the SMILES string
+# "@?" (unspecified chirality) is not yet supported in Open Babel Version 2.0 
+ 
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/UFF.prm	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,274 @@
+#
+# Open Babel file: UFF.prm
+#
+# Force field parameters for UFF, the Universal Force Field
+# Used by OBForceField and OBUFFForceField
+#
+# J. Am. Chem. Soc. (1992) 114(25) p. 10024-10035.
+# The parameters in this file are taken from the UFF implementation in RDKit
+# http://rdkit.org/
+#
+# Atom typing rules are based on UFF published atom descriptions
+# atom [SMARTS] [atomtype] [description]
+# These must be sorted according to the element and complexity
+#  of the type rule (i.e., generic rules first, more specific rules later)
+#
+# Parameters follow later
+# param Atom	r1	theta0	x1	D1	zeta	Z1	Vi	Uj	Xi	Hard	Radius
+
+atom [#1]     H_          Generic hydrogen
+atom [#1D2]   H_b         Bridging hydrogen
+atom [#2]     He4+4       Helium
+atom [#3]     Li          Lithium
+atom [#4]     Be3+2       Generic Be
+atom [#5]     B_2         Trigonal planar boron
+atom [#5D4]   B_3         Tetrahedral boron
+atom [#6]     C_3         Generic sp3 C
+atom [C^2]    C_2         sp2 non-aromatic C
+atom [C^1]    C_1         sp hybridized C
+atom [c]      C_R         aromatic C
+atom [#7]     N_3         Generic sp3 N
+atom [N^2]    N_2         sp2 non-aromatic N
+atom [N^1]    N_1         sp hybridized N
+atom [n]      N_R         aromatic N
+atom [#8]     O_3         generic, sp3 hybridized O
+atom [#8][#14] O_3_z      sp3 hybridized O for zeolites
+atom [O^2]    O_2         sp2 hybridized O
+atom [O^1]    O_1         sp hybridized O
+atom [o]      O_R         aromatic O
+atom [#9]     F_          generic F
+atom [#10]    Ne4+4       
+atom [#11]    Na          
+atom [#12]    Mg3+2
+atom [#13]    Al3
+atom [#14]    Si3
+#atom [#15]   P_3+q       Organometallic phosphine ligands
+atom [#15]    P_3+3       generic phosphorus
+atom [#15D5]  P_3+5       formal charge +5
+atom [#16]    S_3+2       generic S 
+atom [#16+4]  S_3+4       S+4  ( SO2 )
+atom [#16+6]  S_3+6       S+6  ( SO3 / H2SO4 )
+atom [S^2]    S_2         non-aromatic sp2 S
+atom [s]      S_R         aromatic S
+atom [#17]    Cl
+atom [#18]    Ar4+4
+atom [#19]    K_
+atom [#20]    Ca6+2
+atom [#21]    Sc3+3
+atom [#22]    Ti6+4       generic Ti (6-valent)
+atom [#22D3]  Ti3+4
+atom [#23]    V_3+5
+atom [#24]    Cr6+3
+atom [#25]    Mn6+2
+atom [#26]    Fe6+2       generic Fe (6-valent)
+atom [#26D3]  Fe3+2
+atom [#27]    Co6+3
+atom [#28]    Ni4+2
+atom [#29]    Cu3+1
+atom [#30]    Zn3+2
+atom [#31]    Ga3+3
+atom [#32]    Ge3
+atom [#33]    As3+3
+atom [#34]    Se3+2
+atom [#35]    Br
+atom [#36]    Kr4+4
+atom [#37]    Rb
+atom [#38]    Sr6+2
+atom [#39]    Y_3+3
+atom [#40]    Zr3+4
+atom [#41]    Nb3+5
+atom [#42]    Mo6+6       generic Mo (6-valent)
+atom [#42D3]  Mo3+6       trivalent Mo
+atom [#43]    Tc6+5
+atom [#44]    Ru6+2
+atom [#45]    Rh6+3
+atom [#46]    Pd4+2
+atom [#47]    Ag1+1
+atom [#48]    Cd3+2
+atom [#49]    In3+3
+atom [#50]    Sn3
+atom [#51]    Sb3+3
+atom [#52]    Te3+2
+atom [#53]    I_
+atom [#54]    Xe4+4
+atom [#55]     Cs
+atom [#56]     Ba6+2
+atom [#57]     La3+3
+atom [#58]     Ce6+3
+atom [#59]     Pr6+3
+atom [#60]     Nd6+3
+atom [#61]     Pm6+3
+atom [#62]     Sm6+3
+atom [#63]     Eu6+3
+atom [#64]     Gd6+3
+atom [#65]     Tb6+3
+atom [#66]     Dy6+3
+atom [#67]     Ho6+3
+atom [#68]     Er6+3
+atom [#69]     Tm6+3
+atom [#70]     Yb6+3
+atom [#71]     Lu6+3
+atom [#72]     Hf3+4
+atom [#73]     Ta3+5
+atom [#74]     W_6+6       generic W (6-valent)
+atom [#74D3+4] W_3+4
+atom [#74D3+6] W_3+6
+atom [#75]     Re6+5       generic Re (6-valent)
+atom [#75D3]   Re3+7       trivalent Re
+atom [#76]     Os6+6
+atom [#77]     Ir6+3
+atom [#78]     Pt4+2
+atom [#79]     Au4+3
+atom [#80]     Hg1+2
+atom [#81]     Tl3+3
+atom [#82]     Pb3
+atom [#83]     Bi3+3
+atom [#84]     Po3+2
+atom [#85]     At
+atom [#86]     Rn4+4
+atom [#87]     Fr
+atom [#88]     Ra6+2
+atom [#89]     Ac6+3
+atom [#90]     Th6+4
+atom [#91]     Pa6+4
+atom [#92]     U_6+4
+atom [#93]     Np6+4
+atom [#94]     Pu6+4
+atom [#95]     Am6+4
+atom [#96]     Cm6+3
+atom [#97]     Bk6+3
+atom [#98]     Cf6+3
+atom [#99]     Es6+3
+atom [#100]    Fm6+3
+atom [#101]    Md6+3
+atom [#102]    No6+3
+atom [#103]    Lw6+3
+
+# Atom          r1	theta0	x1	D1	zeta	Z1	Vi	Uj	Xi	Hard	Radius
+param H_	0.354	180	2.886	0.044	12	0.712	0	0	4.528	6.9452	0.371
+param H_b	0.46	83.5	2.886	0.044	12	0.712	0	0	4.528	6.9452	0.371
+param He4+4	0.849	90	2.362	0.056	15.24	0.098	0	0	9.66	14.92	1.3
+param Li	1.336	180	2.451	0.025	12	1.026	0	2	3.006	2.386	1.557
+param Be3+2	1.074	109.47	2.745	0.085	12	1.565	0	2	4.877	4.443	1.24
+param B_3	0.838	109.47	4.083	0.18	12.052	1.755	0	2	5.11	4.75	0.822
+param B_2	0.828	120	4.083	0.18	12.052	1.755	0	2	5.11	4.75	0.822
+param C_3	0.757	109.47	3.851	0.105	12.73	1.912	2.119	2	5.343	5.063	0.759
+param C_R	0.729	120	3.851	0.105	12.73	1.912	0	2	5.343	5.063	0.759
+param C_2	0.732	120	3.851	0.105	12.73	1.912	0	2	5.343	5.063	0.759
+param C_1	0.706	180	3.851	0.105	12.73	1.912	0	2	5.343	5.063	0.759
+param N_3	0.7	106.7	3.66	0.069	13.407	2.544	0.45	2	6.899	5.88	0.715
+param N_R	0.699	120	3.66	0.069	13.407	2.544	0	2	6.899	5.88	0.715
+param N_2	0.685	111.2	3.66	0.069	13.407	2.544	0	2	6.899	5.88	0.715
+param N_1	0.656	180	3.66	0.069	13.407	2.544	0	2	6.899	5.88	0.715
+param O_3	0.658	104.51	3.5	0.06	14.085	2.3	0.018	2	8.741	6.682	0.669
+param O_3_z	0.528	146	3.5	0.06	14.085	2.3	0.018	2	8.741	6.682	0.669
+param O_R	0.68	110	3.5	0.06	14.085	2.3	0	2	8.741	6.682	0.669
+param O_2	0.634	120	3.5	0.06	14.085	2.3	0	2	8.741	6.682	0.669
+param O_1	0.639	180	3.5	0.06	14.085	2.3	0	2	8.741	6.682	0.669
+param F_	0.668	180	3.364	0.05	14.762	1.735	0	2	10.874	7.474	0.706
+param Ne4+4	0.92	90	3.243	0.042	15.44	0.194	0	2	11.04	10.55	1.768
+param Na	1.539	180	2.983	0.03	12	1.081	0	1.25	2.843	2.296	2.085
+param Mg3+2	1.421	109.47	3.021	0.111	12	1.787	0	1.25	3.951	3.693	1.5
+param Al3	1.244	109.47	4.499	0.505	11.278	1.792	0	1.25	4.06	3.59	1.201
+param Si3	1.117	109.47	4.295	0.402	12.175	2.323	1.225	1.25	4.168	3.487	1.176
+param P_3+3	1.101	93.8	4.147	0.305	13.072	2.863	2.4	1.25	5.463	4	1.102
+param P_3+5	1.056	109.47	4.147	0.305	13.072	2.863	2.4	1.25	5.463	4	1.102
+param P_3+q	1.056	109.47	4.147	0.305	13.072	2.863	2.4	1.25	5.463	4	1.102
+param S_3+2	1.064	92.1	4.035	0.274	13.969	2.703	0.484	1.25	6.928	4.486	1.047
+param S_3+4	1.049	103.2	4.035	0.274	13.969	2.703	0.484	1.25	6.928	4.486	1.047
+param S_3+6	1.027	109.47	4.035	0.274	13.969	2.703	0.484	1.25	6.928	4.486	1.047
+param S_R	1.077	92.2	4.035	0.274	13.969	2.703	0	1.25	6.928	4.486	1.047
+param S_2	0.854	120	4.035	0.274	13.969	2.703	0	1.25	6.928	4.486	1.047
+param Cl	1.044	180	3.947	0.227	14.866	2.348	0	1.25	8.564	4.946	0.994
+param Ar4+4	1.032	90	3.868	0.185	15.763	0.3	0	1.25	9.465	6.355	2.108
+param K_	1.953	180	3.812	0.035	12	1.165	0	0.7	2.421	1.92	2.586
+param Ca6+2	1.761	90	3.399	0.238	12	2.141	0	0.7	3.231	2.88	2
+param Sc3+3	1.513	109.47	3.295	0.019	12	2.592	0	0.7	3.395	3.08	1.75
+param Ti3+4	1.412	109.47	3.175	0.017	12	2.659	0	0.7	3.47	3.38	1.607
+param Ti6+4	1.412	90	3.175	0.017	12	2.659	0	0.7	3.47	3.38	1.607
+param V_3+5	1.402	109.47	3.144	0.016	12	2.679	0	0.7	3.65	3.41	1.47
+param Cr6+3	1.345	90	3.023	0.015	12	2.463	0	0.7	3.415	3.865	1.402
+param Mn6+2	1.382	90	2.961	0.013	12	2.43	0	0.7	3.325	4.105	1.533
+param Fe3+2	1.27	109.47	2.912	0.013	12	2.43	0	0.7	3.76	4.14	1.393
+param Fe6+2	1.335	90	2.912	0.013	12	2.43	0	0.7	3.76	4.14	1.393
+param Co6+3	1.241	90	2.872	0.014	12	2.43	0	0.7	4.105	4.175	1.406
+param Ni4+2	1.164	90	2.834	0.015	12	2.43	0	0.7	4.465	4.205	1.398
+param Cu3+1	1.302	109.47	3.495	0.005	12	1.756	0	0.7	4.2	4.22	1.434
+param Zn3+2	1.193	109.47	2.763	0.124	12	1.308	0	0.7	5.106	4.285	1.4
+param Ga3+3	1.26	109.47	4.383	0.415	11	1.821	0	0.7	3.641	3.16	1.211
+param Ge3	1.197	109.47	4.28	0.379	12	2.789	0.701	0.7	4.051	3.438	1.189
+param As3+3	1.211	92.1	4.23	0.309	13	2.864	1.5	0.7	5.188	3.809	1.204
+param Se3+2	1.19	90.6	4.205	0.291	14	2.764	0.335	0.7	6.428	4.131	1.224
+param Br	1.192	180	4.189	0.251	15	2.519	0	0.7	7.79	4.425	1.141
+param Kr4+4	1.147	90	4.141	0.22	16	0.452	0	0.7	8.505	5.715	2.27
+param Rb	2.26	180	4.114	0.04	12	1.592	0	0.2	2.331	1.846	2.77
+param Sr6+2	2.052	90	3.641	0.235	12	2.449	0	0.2	3.024	2.44	2.415
+param Y_3+3	1.698	109.47	3.345	0.072	12	3.257	0	0.2	3.83	2.81	1.998
+param Zr3+4	1.564	109.47	3.124	0.069	12	3.667	0	0.2	3.4	3.55	1.758
+param Nb3+5	1.473	109.47	3.165	0.059	12	3.618	0	0.2	3.55	3.38	1.603
+param Mo6+6	1.467	90	3.052	0.056	12	3.4	0	0.2	3.465	3.755	1.53
+param Mo3+6	1.484	109.47	3.052	0.056	12	3.4	0	0.2	3.465	3.755	1.53
+param Tc6+5	1.322	90	2.998	0.048	12	3.4	0	0.2	3.29	3.99	1.5
+param Ru6+2	1.478	90	2.963	0.056	12	3.4	0	0.2	3.575	4.015	1.5
+param Rh6+3	1.332	90	2.929	0.053	12	3.5	0	0.2	3.975	4.005	1.509
+param Pd4+2	1.338	90	2.899	0.048	12	3.21	0	0.2	4.32	4	1.544
+param Ag1+1	1.386	180	3.148	0.036	12	1.956	0	0.2	4.436	3.134	1.622
+param Cd3+2	1.403	109.47	2.848	0.228	12	1.65	0	0.2	5.034	3.957	1.6
+param In3+3	1.459	109.47	4.463	0.599	11	2.07	0	0.2	3.506	2.896	1.404
+param Sn3	1.398	109.47	4.392	0.567	12	2.961	0.199	0.2	3.987	3.124	1.354
+param Sb3+3	1.407	91.6	4.42	0.449	13	2.704	1.1	0.2	4.899	3.342	1.404
+param Te3+2	1.386	90.25	4.47	0.398	14	2.882	0.3	0.2	5.816	3.526	1.38
+param I_	1.382	180	4.5	0.339	15	2.65	0	0.2	6.822	3.762	1.333
+param Xe4+4	1.267	90	4.404	0.332	12	0.556	0	0.2	7.595	4.975	2.459
+param Cs	2.57	180	4.517	0.045	12	1.573	0	0.1	2.183	1.711	2.984
+param Ba6+2	2.277	90	3.703	0.364	12	2.727	0	0.1	2.814	2.396	2.442
+param La3+3	1.943	109.47	3.522	0.017	12	3.3	0	0.1	2.8355	2.7415	2.071
+param Ce6+3	1.841	90	3.556	0.013	12	3.3	0	0.1	2.774	2.692	1.925
+param Pr6+3	1.823	90	3.606	0.01	12	3.3	0	0.1	2.858	2.564	2.007
+param Nd6+3	1.816	90	3.575	0.01	12	3.3	0	0.1	2.8685	2.6205	2.007
+param Pm6+3	1.801	90	3.547	0.009	12	3.3	0	0.1	2.881	2.673	2
+param Sm6+3	1.78	90	3.52	0.008	12	3.3	0	0.1	2.9115	2.7195	1.978
+param Eu6+3	1.771	90	3.493	0.008	12	3.3	0	0.1	2.8785	2.7875	2.227
+param Gd6+3	1.735	90	3.368	0.009	12	3.3	0	0.1	3.1665	2.9745	1.968
+param Tb6+3	1.732	90	3.451	0.007	12	3.3	0	0.1	3.018	2.834	1.954
+param Dy6+3	1.71	90	3.428	0.007	12	3.3	0	0.1	3.0555	2.8715	1.934
+param Ho6+3	1.696	90	3.409	0.007	12	3.416	0	0.1	3.127	2.891	1.925
+param Er6+3	1.673	90	3.391	0.007	12	3.3	0	0.1	3.1865	2.9145	1.915
+param Tm6+3	1.66	90	3.374	0.006	12	3.3	0	0.1	3.2514	2.9329	2
+param Yb6+3	1.637	90	3.355	0.228	12	2.618	0	0.1	3.2889	2.965	2.158
+param Lu6+3	1.671	90	3.64	0.041	12	3.271	0	0.1	2.9629	2.4629	1.896
+param Hf3+4	1.611	109.47	3.141	0.072	12	3.921	0	0.1	3.7	3.4	1.759
+param Ta3+5	1.511	109.47	3.17	0.081	12	4.075	0	0.1	5.1	2.85	1.605
+param W_6+6	1.392	90	3.069	0.067	12	3.7	0	0.1	4.63	3.31	1.538
+param W_3+4	1.526	109.47	3.069	0.067	12	3.7	0	0.1	4.63	3.31	1.538
+param W_3+6	1.38	109.47	3.069	0.067	12	3.7	0	0.1	4.63	3.31	1.538
+param Re6+5	1.372	90	2.954	0.066	12	3.7	0	0.1	3.96	3.92	1.6
+param Re3+7	1.314	109.47	2.954	0.066	12	3.7	0	0.1	3.96	3.92	1.6
+param Os6+6	1.372	90	3.12	0.037	12	3.7	0	0.1	5.14	3.63	1.7
+param Ir6+3	1.371	90	2.84	0.073	12	3.731	0	0.1	5	4	1.866
+param Pt4+2	1.364	90	2.754	0.08	12	3.382	0	0.1	4.79	4.43	1.557
+param Au4+3	1.262	90	3.293	0.039	12	2.625	0	0.1	4.894	2.586	1.618
+param Hg1+2	1.34	180	2.705	0.385	12	1.75	0	0.1	6.27	4.16	1.6
+param Tl3+3	1.518	120	4.347	0.68	11	2.068	0	0.1	3.2	2.9	1.53
+param Pb3	1.459	109.47	4.297	0.663	12	2.846	0.1	0.1	3.9	3.53	1.444
+param Bi3+3	1.512	90	4.37	0.518	13	2.47	1	0.1	4.69	3.74	1.514
+param Po3+2	1.5	90	4.709	0.325	14	2.33	0.3	0.1	4.21	4.21	1.48
+param At	1.545	180	4.75	0.284	15	2.24	0	0.1	4.75	4.75	1.47
+param Rn4+4	1.42	90	4.765	0.248	16	0.583	0	0.1	5.37	5.37	2.2
+param Fr	2.88	180	4.9	0.05	12	1.847	0	0	2	2	2.3
+param Ra6+2	2.512	90	3.677	0.404	12	2.92	0	0	2.843	2.434	2.2
+param Ac6+3	1.983	90	3.478	0.033	12	3.9	0	0	2.835	2.835	2.108
+param Th6+4	1.721	90	3.396	0.026	12	4.202	0	0	3.175	2.905	2.018
+param Pa6+4	1.711	90	3.424	0.022	12	3.9	0	0	2.985	2.905	1.8
+param U_6+4	1.684	90	3.395	0.022	12	3.9	0	0	3.341	2.853	1.713
+param Np6+4	1.666	90	3.424	0.019	12	3.9	0	0	3.549	2.717	1.8
+param Pu6+4	1.657	90	3.424	0.016	12	3.9	0	0	3.243	2.819	1.84
+param Am6+4	1.66	90	3.381	0.014	12	3.9	0	0	2.9895	3.0035	1.942
+param Cm6+3	1.801	90	3.326	0.013	12	3.9	0	0	2.8315	3.1895	1.9
+param Bk6+3	1.761	90	3.339	0.013	12	3.9	0	0	3.1935	3.0355	1.9
+param Cf6+3	1.75	90	3.313	0.013	12	3.9	0	0	3.197	3.101	1.9
+param Es6+3	1.724	90	3.299	0.012	12	3.9	0	0	3.333	3.089	1.9
+param Fm6+3	1.712	90	3.286	0.012	12	3.9	0	0	3.4	3.1	1.9
+param Md6+3	1.689	90	3.274	0.011	12	3.9	0	0	3.47	3.11	1.9
+param No6+3	1.679	90	3.248	0.011	12	3.9	0	0	3.475	3.175	1.9
+param Lw6+3	1.698	90	3.236	0.011	12	3.9	0	0	3.5	3.2	1.9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/aromatic.h	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,43 @@
+/***************************************************************
+This file is part of the Open Babel project.
+This is copyright under the GNU General Public License (GPL)
+For more information, see <http://openbabel.org/>
+
+This file contains a binary representation of data tables
+ used by Open Babel. It is used as a fallback if the textual
+ data table is not found at runtime. It is not a normal header.
+***************************************************************/
+
+
+#ifndef OB_AROMATIC_H
+#define OB_AROMATIC_H
+
+namespace OpenBabel
+{
+static const char AromaticData[] = {
+ 0x5B,0x23,0x36,0x72,0x44,0x32,0x5D,0x09,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,
+ 0x23,0x36,0x72,0x44,0x33,0x5D,0x7E,0x21,0x40,0x5B,0x23,0x38,0x5D,0x09,0x09,
+ 0x30,0x09,0x31,0x0A,0x5B,0x23,0x36,0x72,0x44,0x32,0x2B,0x2C,0x23,0x36,0x72,
+ 0x44,0x33,0x2B,0x5D,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x36,0x72,0x5D,
+ 0x3D,0x40,0x2A,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x36,0x72,0x44,0x33,
+ 0x5D,0x3D,0x21,0x40,0x2A,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x36,0x72,
+ 0x44,0x33,0x5D,0x3D,0x21,0x40,0x5B,0x21,0x23,0x36,0x5D,0x09,0x09,0x30,0x09,
+ 0x30,0x0A,0x5B,0x23,0x36,0x72,0x44,0x33,0x2D,0x5D,0x09,0x09,0x32,0x09,0x32,
+ 0x0A,0x5B,0x23,0x37,0x72,0x44,0x32,0x5D,0x09,0x09,0x09,0x31,0x09,0x32,0x0A,
+ 0x5B,0x23,0x37,0x72,0x44,0x33,0x5D,0x20,0x31,0x20,0x32,0x0A,0x5B,0x23,0x37,
+ 0x72,0x5D,0x28,0x2D,0x40,0x2A,0x29,0x2D,0x40,0x2A,0x20,0x09,0x09,0x31,0x09,
+ 0x32,0x0A,0x5B,0x23,0x37,0x72,0x44,0x32,0x5D,0x3D,0x40,0x2A,0x09,0x09,0x31,
+ 0x09,0x31,0x0A,0x5B,0x23,0x37,0x72,0x44,0x33,0x2B,0x5D,0x09,0x09,0x31,0x09,
+ 0x31,0x0A,0x5B,0x23,0x37,0x72,0x44,0x33,0x5D,0x3D,0x4F,0x09,0x09,0x31,0x09,
+ 0x31,0x0A,0x5B,0x23,0x37,0x72,0x44,0x32,0x2D,0x5D,0x09,0x09,0x32,0x09,0x32,
+ 0x0A,0x5B,0x23,0x38,0x72,0x5D,0x09,0x09,0x09,0x32,0x09,0x32,0x0A,0x5B,0x23,
+ 0x38,0x72,0x2B,0x5D,0x09,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x31,0x36,
+ 0x72,0x44,0x32,0x5D,0x09,0x09,0x32,0x09,0x32,0x0A,0x5B,0x23,0x31,0x36,0x72,
+ 0x44,0x32,0x2B,0x5D,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x31,0x36,0x72,
+ 0x44,0x33,0x5D,0x3D,0x21,0x40,0x4F,0x09,0x09,0x32,0x09,0x32,0x0A,0x5B,0x23,
+ 0x31,0x35,0x72,0x44,0x33,0x5D,0x09,0x09,0x32,0x09,0x32,0x0A,0x5B,0x23,0x33,
+ 0x34,0x72,0x44,0x32,0x5D,0x09,0x09,0x32,0x09,0x32,0x0A,0x00};
+
+} // namespace OpenBabel
+#endif // OB_AROMATIC_H
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/aromatic.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,59 @@
+##############################################################################
+#                                                                            #
+#	                Open Babel file: aromatic.txt                            # #                                                                            #
+#                                                                            #
+#  Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc.              #
+#  Some portions Copyright (c) 2001-2005 Geoffrey R. Hutchison               #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+# SMARTS patterns with minimum and maximum pi-electrons contributed to an    #
+#   aromatic system (used by typer.cpp:OBAromaticTyper)                      #
+# The LAST PATTERN MATCHED is used to assign values, so that patterns should #
+#   be ordered from more general to more specific                            #
+#                                                                            #
+##############################################################################
+
+#PATTERN		MIN	MAX
+
+#carbon patterns
+[#6rD2]			1	1
+# exo ketone or alcohol -- don't know which
+[#6rD3]~!@[#8]		0	1
+[#6rD2+,#6rD3+]		1	1
+[#6r]=@*		1	1
+[#6rD3]=!@*		1	1
+# external double bonds to hetero atoms contribute no electrons to the 
+# aromatic systems -- quinoid systems are non-aromatic, e.g. 1,4-benzoquinone
+[#6rD3]=!@[!#6]		0	0
+[#6rD3-]		2	2
+
+#nitrogen patterns
+[#7rD2]			1	2
+[#7rD3]                 1       2
+[#7r](-@*)-@*  		1	2
+[#7rD2]=@*		1	1
+[#7rD3+]		1	1
+[#7rD3]=O		1	1
+[#7rD2-]		2	2
+
+#oxygen patterns
+[#8r]			2	2
+[#8r+]			1	1
+
+#sulfur patterns
+[#16rD2]		2	2
+[#16rD2+]		1	1
+[#16rD3]=!@O		2	2
+
+#other misc patterns
+# Accounts Chem Res 1978 11 p. 153
+# phosphole, phosphabenzene (not v. aromatic)
+[#15rD3]		2	2
+# selenophene
+[#34rD2]		2	2
+# arsabenzene, etc. (*really* not v. aromatic)
+#[#33rD3]		2	2
+# tellurophene, etc. (*really* not v. aromatic)
+#[#52rD2]		2	2
+# stilbabenzene, etc. (very little aromatic character)
+#[#51rD3]		2	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/atomtyp.h	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,306 @@
+/***************************************************************
+This file is part of the Open Babel project.
+This is copyright under the GNU General Public License (GPL)
+For more information, see <http://openbabel.org/>
+
+This file contains a binary representation of data tables
+ used by Open Babel. It is used as a fallback if the textual
+ data table is not found at runtime. It is not a normal header.
+***************************************************************/
+
+
+#ifndef OB_ATOMTYP_H
+#define OB_ATOMTYP_H
+
+namespace OpenBabel
+{
+static const char AtomTypeData[] = {
+ 0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x44,0x34,0x5D,0x20,0x33,0x20,0x23,
+ 0x61,0x6E,0x79,0x20,0x34,0x2D,0x76,0x61,0x6C,0x65,0x6E,0x74,0x20,0x61,0x74,
+ 0x6F,0x6D,0x20,0x2D,0x2D,0x20,0x74,0x65,0x74,0x72,0x61,0x68,0x65,0x64,0x72,
+ 0x61,0x6C,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x44,0x35,0x5D,0x20,
+ 0x35,0x20,0x23,0x61,0x6E,0x79,0x20,0x35,0x2D,0x76,0x61,0x6C,0x65,0x6E,0x74,
+ 0x20,0x61,0x74,0x6F,0x6D,0x20,0x2D,0x2D,0x20,0x74,0x72,0x69,0x67,0x62,0x69,
+ 0x70,0x79,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x44,0x36,0x5D,0x20,
+ 0x36,0x20,0x23,0x61,0x6E,0x79,0x20,0x36,0x2D,0x76,0x61,0x6C,0x65,0x6E,0x74,
+ 0x20,0x61,0x74,0x6F,0x6D,0x20,0x2D,0x2D,0x20,0x6F,0x63,0x74,0x0A,0x49,0x4E,
+ 0x54,0x48,0x59,0x42,0x20,0x5B,0x43,0x5D,0x20,0x33,0x20,0x23,0x73,0x70,0x33,
+ 0x20,0x63,0x61,0x72,0x62,0x6F,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,
+ 0x5B,0x63,0x2C,0x24,0x28,0x43,0x3D,0x2A,0x29,0x5D,0x20,0x32,0x20,0x23,0x73,
+ 0x70,0x32,0x20,0x63,0x61,0x72,0x62,0x6F,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,
+ 0x42,0x20,0x5B,0x24,0x28,0x43,0x23,0x2A,0x29,0x2C,0x24,0x28,0x43,0x28,0x3D,
+ 0x2A,0x29,0x3D,0x2A,0x29,0x5D,0x20,0x31,0x20,0x23,0x73,0x70,0x20,0x63,0x61,
+ 0x72,0x62,0x6F,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x4E,0x5D,
+ 0x20,0x33,0x20,0x23,0x73,0x70,0x33,0x20,0x6E,0x69,0x74,0x72,0x6F,0x67,0x65,
+ 0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x6E,0x2C,0x24,0x28,0x4E,
+ 0x3D,0x2A,0x29,0x2C,0x24,0x28,0x4E,0x5B,0x23,0x36,0x2C,0x23,0x37,0x2C,0x23,
+ 0x38,0x5D,0x3D,0x2C,0x3A,0x2C,0x23,0x2A,0x29,0x5D,0x20,0x32,0x20,0x23,0x73,
+ 0x70,0x32,0x20,0x6E,0x69,0x74,0x72,0x6F,0x67,0x65,0x6E,0x0A,0x49,0x4E,0x54,
+ 0x48,0x59,0x42,0x20,0x5B,0x4E,0x44,0x31,0x2C,0x4E,0x44,0x32,0x2C,0x4E,0x44,
+ 0x33,0x5D,0x61,0x20,0x32,0x20,0x23,0x73,0x70,0x32,0x20,0x6E,0x69,0x74,0x72,
+ 0x6F,0x67,0x65,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x24,0x28,
+ 0x4E,0x23,0x2A,0x29,0x2C,0x24,0x28,0x5B,0x4E,0x44,0x32,0x5D,0x28,0x3D,0x2A,
+ 0x29,0x3D,0x2A,0x29,0x5D,0x20,0x31,0x20,0x23,0x73,0x70,0x20,0x6E,0x69,0x74,
+ 0x72,0x6F,0x67,0x65,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x4F,
+ 0x5D,0x20,0x33,0x20,0x23,0x73,0x70,0x33,0x20,0x6F,0x78,0x79,0x67,0x65,0x6E,
+ 0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x6F,0x2C,0x24,0x28,0x4F,0x3D,
+ 0x2A,0x29,0x2C,0x24,0x28,0x4F,0x5B,0x23,0x36,0x2C,0x23,0x37,0x2C,0x23,0x38,
+ 0x5D,0x3D,0x2C,0x3A,0x2A,0x29,0x5D,0x20,0x32,0x20,0x23,0x73,0x70,0x32,0x20,
+ 0x6F,0x78,0x79,0x67,0x65,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,
+ 0x24,0x28,0x5B,0x23,0x38,0x44,0x31,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x38,
+ 0x44,0x31,0x5D,0x29,0x5D,0x20,0x32,0x20,0x23,0x73,0x70,0x32,0x20,0x6F,0x78,
+ 0x79,0x67,0x65,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x24,0x28,
+ 0x4F,0x23,0x2A,0x29,0x5D,0x20,0x31,0x20,0x23,0x73,0x70,0x20,0x6F,0x78,0x79,
+ 0x67,0x65,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x50,0x5D,0x20,
+ 0x33,0x20,0x23,0x73,0x70,0x33,0x20,0x70,0x68,0x6F,0x73,0x70,0x68,0x6F,0x72,
+ 0x75,0x73,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x23,0x31,0x35,0x3B,
+ 0x24,0x28,0x5B,0x50,0x44,0x31,0x5D,0x3D,0x2A,0x29,0x5D,0x20,0x32,0x20,0x23,
+ 0x73,0x70,0x32,0x20,0x70,0x68,0x6F,0x73,0x70,0x68,0x6F,0x72,0x75,0x73,0x0A,
+ 0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x50,0x44,0x35,0x5D,0x09,0x09,0x09,
+ 0x20,0x35,0x09,0x20,0x23,0x73,0x70,0x33,0x64,0x20,0x70,0x68,0x6F,0x73,0x70,
+ 0x68,0x6F,0x72,0x75,0x73,0x2C,0x20,0x61,0x73,0x20,0x69,0x6E,0x20,0x50,0x46,
+ 0x35,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x50,0x76,0x35,0x5D,0x09,
+ 0x09,0x09,0x20,0x35,0x09,0x20,0x23,0x73,0x70,0x33,0x64,0x20,0x70,0x68,0x6F,
+ 0x73,0x70,0x68,0x6F,0x72,0x75,0x73,0x2C,0x20,0x61,0x73,0x20,0x69,0x6E,0x20,
+ 0x48,0x33,0x50,0x4F,0x34,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x53,
+ 0x5D,0x20,0x33,0x20,0x23,0x73,0x70,0x33,0x20,0x73,0x75,0x6C,0x66,0x75,0x72,
+ 0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x23,0x31,0x36,0x3B,0x73,0x2C,
+ 0x24,0x28,0x5B,0x53,0x44,0x31,0x5D,0x3D,0x2A,0x29,0x5D,0x20,0x32,0x20,0x23,
+ 0x73,0x70,0x32,0x20,0x73,0x75,0x6C,0x66,0x75,0x72,0x0A,0x49,0x4E,0x54,0x48,
+ 0x59,0x42,0x20,0x5B,0x53,0x44,0x36,0x5D,0x09,0x09,0x09,0x20,0x36,0x09,0x20,
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+ 0x4F,0x0A,0x49,0x4D,0x50,0x56,0x41,0x4C,0x20,0x5B,0x23,0x31,0x36,0x44,0x31,
+ 0x2D,0x5D,0x20,0x31,0x0A,0x49,0x4D,0x50,0x56,0x41,0x4C,0x20,0x5B,0x23,0x31,
+ 0x37,0x44,0x30,0x5D,0x20,0x31,0x0A,0x49,0x4D,0x50,0x56,0x41,0x4C,0x20,0x5B,
+ 0x23,0x31,0x37,0x44,0x30,0x2D,0x5D,0x20,0x30,0x20,0x23,0x5B,0x43,0x6C,0x2D,
+ 0x5D,0x0A,0x49,0x4D,0x50,0x56,0x41,0x4C,0x20,0x5B,0x23,0x33,0x31,0x5D,0x20,
+ 0x33,0x0A,0x49,0x4D,0x50,0x56,0x41,0x4C,0x20,0x5B,0x23,0x33,0x32,0x5D,0x20,
+ 0x34,0x0A,0x49,0x4D,0x50,0x56,0x41,0x4C,0x20,0x5B,0x23,0x33,0x33,0x5D,0x20,
+ 0x33,0x0A,0x49,0x4D,0x50,0x56,0x41,0x4C,0x20,0x5B,0x61,0x73,0x5D,0x20,0x33,
+ 0x0A,0x49,0x4D,0x50,0x56,0x41,0x4C,0x20,0x5B,0x23,0x33,0x34,0x5D,0x20,0x32,
+ 0x0A,0x49,0x4D,0x50,0x56,0x41,0x4C,0x20,0x5B,0x23,0x33,0x35,0x44,0x30,0x5D,
+ 0x20,0x31,0x0A,0x49,0x4D,0x50,0x56,0x41,0x4C,0x20,0x5B,0x23,0x33,0x35,0x44,
+ 0x30,0x2D,0x5D,0x20,0x30,0x20,0x23,0x5B,0x42,0x72,0x2D,0x5D,0x0A,0x49,0x4D,
+ 0x50,0x56,0x41,0x4C,0x20,0x5B,0x23,0x35,0x32,0x5D,0x20,0x32,0x0A,0x49,0x4D,
+ 0x50,0x56,0x41,0x4C,0x20,0x5B,0x23,0x35,0x33,0x44,0x30,0x5D,0x20,0x31,0x0A,
+ 0x49,0x4D,0x50,0x56,0x41,0x4C,0x20,0x5B,0x23,0x35,0x33,0x44,0x30,0x2D,0x5D,
+ 0x20,0x30,0x20,0x23,0x5B,0x49,0x2D,0x5D,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,
+ 0x20,0x5B,0x23,0x31,0x5D,0x5B,0x23,0x38,0x5D,0x20,0x48,0x4F,0x0A,0x45,0x58,
+ 0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x37,0x5E,0x33,0x5D,0x20,0x4E,0x33,0x0A,
+ 0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x37,0x58,0x34,0x5D,0x20,0x4E,
+ 0x33,0x2B,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x37,0x5E,0x32,
+ 0x5D,0x20,0x4E,0x70,0x6C,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,
+ 0x37,0x5E,0x31,0x5D,0x20,0x4E,0x31,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,
+ 0x5B,0x24,0x28,0x4E,0x3D,0x2A,0x29,0x5D,0x20,0x4E,0x32,0x0A,0x45,0x58,0x54,
+ 0x54,0x59,0x50,0x20,0x5B,0x24,0x28,0x5B,0x4E,0x72,0x30,0x5D,0x43,0x28,0x3D,
+ 0x5B,0x4E,0x72,0x30,0x5D,0x29,0x5B,0x4E,0x72,0x30,0x5D,0x29,0x5D,0x20,0x4E,
+ 0x67,0x2B,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x24,0x28,0x5B,0x4E,
+ 0x72,0x30,0x5D,0x3D,0x43,0x28,0x5B,0x4E,0x72,0x30,0x5D,0x29,0x5B,0x4E,0x72,
+ 0x30,0x5D,0x29,0x5D,0x20,0x4E,0x67,0x2B,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,
+ 0x20,0x5B,0x24,0x28,0x5B,0x4E,0x44,0x31,0x5D,0x3D,0x43,0x5B,0x4E,0x44,0x31,
+ 0x5D,0x29,0x5D,0x20,0x4E,0x67,0x2B,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,
+ 0x5B,0x24,0x28,0x5B,0x4E,0x44,0x31,0x5D,0x43,0x3D,0x5B,0x4E,0x44,0x31,0x5D,
+ 0x29,0x5D,0x20,0x4E,0x67,0x2B,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,
+ 0x24,0x28,0x4E,0x28,0x4F,0x29,0x2A,0x29,0x5D,0x20,0x4E,0x6F,0x78,0x0A,0x45,
+ 0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x24,0x28,0x4E,0x43,0x3D,0x5B,0x4F,0x2C,
+ 0x53,0x5D,0x29,0x5D,0x20,0x4E,0x61,0x6D,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,
+ 0x20,0x5B,0x24,0x28,0x4E,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,
+ 0x4F,0x44,0x31,0x5D,0x29,0x5D,0x20,0x4E,0x74,0x72,0x0A,0x45,0x58,0x54,0x54,
+ 0x59,0x50,0x20,0x5B,0x6E,0x5D,0x20,0x4E,0x61,0x72,0x0A,0x45,0x58,0x54,0x54,
+ 0x59,0x50,0x20,0x5B,0x23,0x36,0x5E,0x33,0x5D,0x20,0x43,0x33,0x0A,0x45,0x58,
+ 0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x36,0x5E,0x32,0x5D,0x20,0x43,0x32,0x0A,
+ 0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x24,0x28,0x43,0x28,0x3D,0x4F,0x29,
+ 0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5D,0x20,0x43,0x61,0x63,0x0A,0x45,0x58,0x54,
+ 0x54,0x59,0x50,0x20,0x5B,0x63,0x5D,0x20,0x43,0x61,0x72,0x0A,0x45,0x58,0x54,
+ 0x54,0x59,0x50,0x20,0x5B,0x23,0x36,0x5E,0x31,0x5D,0x20,0x43,0x31,0x0A,0x45,
+ 0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x36,0x2B,0x5D,0x20,0x43,0x2B,0x0A,
+ 0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x36,0x2D,0x5D,0x20,0x43,0x2D,
+ 0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x38,0x5E,0x33,0x5D,0x20,
+ 0x4F,0x33,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x38,0x5E,0x32,
+ 0x5D,0x20,0x4F,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x24,0x28,
+ 0x4F,0x61,0x29,0x5D,0x20,0x4F,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,
+ 0x5B,0x24,0x28,0x5B,0x4F,0x44,0x32,0x5D,0x43,0x3D,0x5B,0x4F,0x2C,0x53,0x5D,
+ 0x29,0x5D,0x20,0x4F,0x33,0x20,0x23,0x65,0x73,0x74,0x65,0x72,0x20,0x6F,0x78,
+ 0x79,0x67,0x65,0x6E,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x24,0x28,
+ 0x4F,0x61,0x29,0x5D,0x20,0x4F,0x33,0x20,0x23,0x61,0x72,0x6F,0x6D,0x61,0x74,
+ 0x69,0x63,0x20,0x65,0x74,0x68,0x65,0x72,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,
+ 0x20,0x5B,0x23,0x38,0x2D,0x5D,0x20,0x4F,0x2D,0x0A,0x45,0x58,0x54,0x54,0x59,
+ 0x50,0x20,0x5B,0x24,0x28,0x5B,0x23,0x38,0x44,0x31,0x5D,0x7E,0x5B,0x23,0x36,
+ 0x5E,0x32,0x5D,0x7E,0x5B,0x23,0x38,0x44,0x31,0x5D,0x29,0x5D,0x20,0x4F,0x2E,
+ 0x63,0x6F,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x31,0x35,
+ 0x5D,0x20,0x50,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x31,0x35,
+ 0x58,0x34,0x2B,0x5D,0x20,0x50,0x33,0x2B,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,
+ 0x20,0x5B,0x23,0x31,0x35,0x3B,0x24,0x28,0x5B,0x23,0x31,0x35,0x44,0x34,0x5D,
+ 0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,
+ 0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5D,0x20,0x50,0x61,0x63,0x0A,0x45,
+ 0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x31,0x35,0x3B,0x24,0x28,0x5B,0x23,
+ 0x31,0x35,0x44,0x33,0x5D,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,
+ 0x4F,0x44,0x31,0x5D,0x29,0x5D,0x20,0x50,0x61,0x63,0x0A,0x45,0x58,0x54,0x54,
+ 0x59,0x50,0x20,0x5B,0x23,0x31,0x36,0x5D,0x20,0x53,0x33,0x0A,0x45,0x58,0x54,
+ 0x54,0x59,0x50,0x20,0x5B,0x23,0x31,0x36,0x44,0x33,0x2B,0x2C,0x23,0x31,0x36,
+ 0x58,0x33,0x2B,0x5D,0x20,0x53,0x33,0x2B,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,
+ 0x20,0x5B,0x23,0x31,0x36,0x3B,0x73,0x2C,0x24,0x28,0x5B,0x53,0x44,0x31,0x5D,
+ 0x3D,0x2A,0x29,0x5D,0x20,0x53,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,
+ 0x5B,0x23,0x31,0x36,0x44,0x34,0x3B,0x24,0x28,0x53,0x28,0x3D,0x4F,0x29,0x28,
+ 0x3D,0x4F,0x29,0x29,0x5D,0x20,0x53,0x6F,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,
+ 0x50,0x20,0x5B,0x23,0x31,0x36,0x44,0x33,0x3B,0x24,0x28,0x53,0x28,0x3D,0x4F,
+ 0x29,0x29,0x5D,0x20,0x53,0x6F,0x78,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,
+ 0x5B,0x23,0x31,0x36,0x3B,0x24,0x28,0x5B,0x23,0x31,0x36,0x44,0x34,0x5D,0x28,
+ 0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,
+ 0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5D,0x20,0x53,0x61,0x63,0x0A,0x45,0x58,
+ 0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x31,0x36,0x3B,0x24,0x28,0x5B,0x23,0x31,
+ 0x36,0x44,0x33,0x5D,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,0x4F,
+ 0x44,0x31,0x5D,0x29,0x5D,0x20,0x53,0x61,0x63,0x0A,0x45,0x58,0x54,0x54,0x59,
+ 0x50,0x20,0x5B,0x23,0x35,0x5D,0x20,0x42,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,
+ 0x50,0x20,0x5B,0x23,0x35,0x44,0x34,0x5D,0x20,0x42,0x33,0x0A,0x00};
+
+} // namespace OpenBabel
+#endif // OB_ATOMTYP_H
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/atomtyp.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,249 @@
+##############################################################################
+#                                                                            #
+#                   Open Babel file: atomtyp.txt                             #
+#                                                                            #
+#                                                                            #
+#  Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc.              #
+#  Some portions Copyright (c) 2001-2008 Geoffrey R. Hutchison               #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+# SMARTS patterns for atom typing (used by typer.cpp:OBAtomTyper)            #
+#                                                                            #
+# INTHYB: used to assign the internal hybridization values for atoms         #
+# IMPVAL: used to assign the implicit valence of an atom                     #
+# EXTTYP: used to assign the external type of an atom for translation to     #
+#         package specific types (i.e. Sybyl Mol2)                           #
+#        (these should correspond to INT type names in types.txt too.)       #
+#                                                                            #
+# The LAST PATTERN MATCHED is used to assign values with the corresponding   #
+# INTHYB, IMPVAL, and EXTTYP values. Additions to this file should be placed #
+# in the EXTRA DEFINITIONS section (to separate from original patterns.)     #
+#                                                                            #
+##############################################################################
+
+INTHYB  [D4]                      3       #any 4-valent atom -- tetrahedral
+INTHYB  [D5]                      5       #any 5-valent atom -- trigbipy
+INTHYB  [D6]                      6       #any 6-valent atom -- oct
+INTHYB  [C]                       3       #sp3 carbon
+INTHYB  [c,$(C=*)]                2       #sp2 carbon
+# INTHYB  [$([#6]([#8D1])[#8D1])]   2     # Commented out after PR#3089597
+INTHYB  [$(C#*),$(C(=*)=*)]       1       #sp  carbon
+
+INTHYB  [N]                       3       #sp3 nitrogen
+INTHYB  [n,$(N=*),$(N[#6,#7,#8]=,:,#*)] 2 #sp2 nitrogen
+INTHYB  [ND1,ND2,ND3]a            2       #sp2 nitrogen
+INTHYB  [$(N#*),$([ND2](=*)=*)]   1       #sp  nitrogen
+
+INTHYB  [O]                       3       #sp3 oxygen
+INTHYB  [o,$(O=*),$(O[#6,#7,#8]=,:*)] 2   #sp2 oxygen
+INTHYB  [$([#8D1][#6][#8D1])]     2       #sp2 oxygen
+INTHYB  [$(O#*)]                  1       #sp  oxygen
+
+INTHYB  [P]                       3       #sp3 phosphorus
+INTHYB  [#15;$([PD1]=*)]          2       #sp2 phosphorus
+INTHYB  [PD5]			  5	  #sp3d phosphorus, as in PF5
+INTHYB  [Pv5]			  5	  #sp3d phosphorus, as in H3PO4
+INTHYB  [S]                       3       #sp3 sulfur
+INTHYB  [#16;s,$([SD1]=*)]        2       #sp2 sulfur
+INTHYB  [SD6]			  6	  #sp3d2 sulfur, as in SF6
+INTHYB  [B]                       2       #sp2 boron
+INTHYB  [BD4]                     3       #sp3 boron
+
+INTHYB  [Al]                      2       # typical sp2 Al (and family)
+INTHYB  [Ga]                      2
+INTHYB  [In]                      2
+INTHYB  [Tl]                      2
+INTHYB  [AlD4]                    3       # sp3 Al
+INTHYB  [Si]                      3       # sp3 Si (and family)
+INTHYB  [Ge]                      3
+INTHYB  [Sn]                      3
+INTHYB  [Pb]                      3
+INTHYB  [As]                      3       # sp3 hybridization As (and family)
+INTHYB  [Sb]                      3
+INTHYB  [Bi]                      3
+
+INTHYB  [se]                      2       # aromatic sp2 Se
+INTHYB  [Se]                      3       # sp3 hybridization Se (and family)
+INTHYB  [Te]                      3
+INTHYB  [Po]                      3
+
+INTHYB  [Be]                      1       # Alkaline earth, like sp hybrids
+INTHYB  [Mg]                      1
+INTHYB  [Ca]                      1
+INTHYB  [Sr]                      1
+INTHYB  [Ba]                      1
+INTHYB  [Ra]                      1
+
+#INTHYB  [Pt]                      4 # normally square planar
+#INTHYB  [Pd]                      4
+#INTHYB  [Cu]                      4
+#INTHYB  [Ag]                      4
+#INTHYB  [Au]                      4
+
+#
+#IMPLICIT VALENCE RULES
+#
+#IMPVAL  [#3,#11,#19,#37,#55,#87]  1 # Alkali metals
+#IMPVAL  [#4,#12,#20,#38,#56,#88]  2 # Alkaline earth
+
+IMPVAL  [#5]                      3 # Generic boron
+IMPVAL [$([#6+]=*)]		          2
+IMPVAL [$([#6+]#*)]		          1 # just for InChI C2
+
+IMPVAL  [#6^3]                    4
+IMPVAL  [#6^2]                    3
+IMPVAL  [#6^1]                    2
+IMPVAL  [#6^3-]                   3
+IMPVAL  [#6^2-]                   2
+IMPVAL  [#6^1-]                   1 # isocyanides, CO (valence=1, bond order=3)
+IMPVAL  [c+]                      2
+
+IMPVAL  [N^3]                     3
+IMPVAL  [N^3+]                    4
+IMPVAL  [N^2]                     3
+#IMPVAL  [N^2-,N^3-]              2
+IMPVAL  [ND1^1]                   1
+IMPVAL  [ND2^1]                   2
+IMPVAL  [$(N([OD1])*)]            3
+IMPVAL  [$(NC=O)]                 3
+#IMPVAL  [$(n(c=O)c=O)]           3 # aromatic diimide
+IMPVAL  [$(N(~[OD1])~[OD1])]      3
+IMPVAL  [$([Nr0]C=[Nr0])]         3
+IMPVAL  [$(N=*)]                  2
+#IMPVAL [$([Nr0]=C[Nr0])]         3
+IMPVAL  [$([Nr0]=C[Nr0])]         2
+IMPVAL  [$([N+r0]=C[Nr0])]        3 # patch from Steve Constable
+IMPVAL  [$([#7D1-]=*)]            1
+IMPVAL  [N^1-]                    1 # N2O [N-]=[N+]=O (valence=1, bondorder=2)
+IMPVAL  [N-]                      2
+IMPVAL  [n]                       2
+IMPVAL  [n-]                      2
+IMPVAL  [n+]                      3
+IMPVAL  [$([#7-]=*)]              1
+IMPVAL  [$([#7+]#*)]              2
+
+IMPVAL [$([#8+]#*)] 1
+
+IMPVAL [#8]                       2 # Generic O
+IMPVAL [#8-]                      1
+IMPVAL [#8-2]                     0
+IMPVAL [#8+]                      3
+IMPVAL [$([#8]=*)]                1
+IMPVAL [#8^1+]                    1 # carbon monoxide
+
+IMPVAL  [#9D0]                    1
+IMPVAL  [#9D0-]                   0 #[F-]
+
+IMPVAL  [#13]                     3 # generic Al
+
+IMPVAL  [#14]                     4 # regular sp3 Si
+IMPVAL  [#14^2]                   2 # silylenes
+IMPVAL  [$([#14]=*)]              3 # e.g., Si=O
+IMPVAL  [$([#14](=*)=*)]          0 # e.g., Si(=O)=O
+IMPVAL  [$([#14+]#*)]		          1 # just for InChI Si2
+IMPVAL  [$([#14-]#*)]		          1 # just for InChI Si2
+
+IMPVAL  [#15D4]                   4
+IMPVAL  [#15D3]                   3
+IMPVAL  [#15D2]                   3
+IMPVAL  [#15D1^3]                 3
+IMPVAL  [#15D1^2]                 3
+IMPVAL  [#15D0]                   3
+IMPVAL  [$([#15]=[#6])]           2
+IMPVAL  [pD2]                     2
+IMPVAL  [$([#15]=[#8])]           4 # phosphinate (double bond = one valence)
+IMPVAL  [$([#15](=[#8])=[#8])]    3 # metaphosphate (double bond = one valence)
+IMPVAL  [$([#15+](=[#8])([#8]))]  0 # R-P+O2
+
+IMPVAL  [#16]                     2 #revised CM April 2008
+IMPVAL  [$([#16D1]=*)]            1
+IMPVAL  [$([#16D3](=O)(=O)-O)]    4 #e.g. O[S](=O)=O
+IMPVAL  [$([#16D2](=O)-O)]        3 # e.g. O[S]=O
+IMPVAL  [#16D1-]                  1
+
+IMPVAL  [#17D0]                   1
+IMPVAL  [#17D0-]                  0 #[Cl-]
+
+IMPVAL  [#31]                     3
+IMPVAL  [#32]                     4
+
+IMPVAL  [#33]                     3
+IMPVAL  [as]                      3
+
+IMPVAL  [#34]                     2
+
+IMPVAL  [#35D0]                   1
+IMPVAL  [#35D0-]                  0 #[Br-]
+
+#IMPVAL  [#49,#81]                 3 # In, Tl, like Ga
+#IMPVAL  [#50,#82]                 4 # Sn, Pb, like Ge
+#IMPVAL  [#51,#83]                 3 # Sb, Bi, like As
+
+IMPVAL  [#52]                     2
+IMPVAL  [#53D0]                   1
+IMPVAL  [#53D0-]                  0 #[I-]
+
+#
+#EXTERNAL TYPE RULES
+#
+
+# Tinker OH hydrogens for MM2
+# Fixes PR# 1839274
+EXTTYP  [#1][#8]        HO
+
+EXTTYP  [#7^3]          N3
+EXTTYP  [#7X4]          N3+
+EXTTYP  [#7^2]          Npl
+EXTTYP  [#7^1]          N1
+EXTTYP  [$(N=*)]        N2
+EXTTYP  [$([Nr0]C(=[Nr0])[Nr0])]    Ng+
+EXTTYP  [$([Nr0]=C([Nr0])[Nr0])]    Ng+
+EXTTYP  [$([ND1]=C[ND1])]     Ng+
+EXTTYP  [$([ND1]C=[ND1])]     Ng+
+EXTTYP  [$(N(O)*)]        Nox
+EXTTYP  [$(NC=[O,S])]       Nam
+EXTTYP  [$(N(~[OD1])~[OD1])]      Ntr
+EXTTYP  [n]         Nar
+
+EXTTYP  [#6^3]          C3
+EXTTYP  [#6^2]          C2
+EXTTYP  [$(C(=O)[OD1])]       Cac
+EXTTYP  [c]         Car
+EXTTYP  [#6^1]          C1
+EXTTYP  [#6+]         C+
+EXTTYP  [#6-]         C-
+
+EXTTYP  [#8^3]          O3
+EXTTYP  [#8^2]          O2
+EXTTYP  [$(Oa)]         O2
+#The following 2 lines used for correct Sybyl atom typing
+EXTTYP  [$([OD2]C=[O,S])]     O3  #ester oxygen
+EXTTYP  [$(Oa)]         O3      #aromatic ether
+EXTTYP  [#8-]         O-
+EXTTYP  [$([#8D1]~[#6^2]~[#8D1])]     O.co2
+
+EXTTYP  [#15]         P
+EXTTYP  [#15X4+]        P3+
+EXTTYP  [#15;$([#15D4](~[OD1])(~[OD1])~[OD1])]  Pac
+EXTTYP  [#15;$([#15D3](~[OD1])~[OD1])]    Pac
+
+EXTTYP  [#16]         S3
+EXTTYP  [#16D3+,#16X3+]       S3+
+EXTTYP  [#16;s,$([SD1]=*)]      S2
+EXTTYP  [#16D4;$(S(=O)(=O))]      So2
+EXTTYP  [#16D3;$(S(=O))]      Sox
+EXTTYP  [#16;$([#16D4](~[OD1])(~[OD1])~[OD1])]  Sac
+EXTTYP  [#16;$([#16D3](~[OD1])~[OD1])]    Sac
+
+EXTTYP  [#5]          B2
+EXTTYP  [#5D4]          B3
+
+######################## Add Extra Definitions Here ##########################
+
+#INTHYB  [U]                      3
+#INTHYB  [W]                      3
+#INTHYB  [Mo]			  6 # for development
+#INTHYB  [Cr]			  5 # for development
+
+############################# End Extra Definitions ##########################
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/babel_povray3.inc	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,1229 @@
+//Include for Babel
+//Copyright (c) by Steffen Reith and Oliver Weichold 1996-2002
+//  This program is free software; you can redistribute it and/or modify
+//  it under the terms of the GNU General Public License as published by
+//  the Free Software Foundation version 2 of the License.
+//EMail: streit@streit.cc
+//For chemical questions send mail to
+//weichold@sas.upenn.edu
+
+//$Id: babel_povray3.inc 3895 2010-07-22 10:36:05Z baoilleach $
+
+#include "colors.inc"
+#include "metals.inc"
+
+//Do a ball and sticks model as default (nothing defined)
+#ifndef (BAS)
+ #ifndef (SPF)
+  #ifndef (CST)
+   #declare BAS = true;
+   #declare SPF = false;
+   #declare CST = false;
+  #end
+ #end
+#end
+
+//Default: No Ball and Sticks-model (if undefined)
+#ifndef (BAS)
+ #declare BAS = false;
+#end
+
+//Default: No Spacefill-model (if undefined)
+#ifndef (SPF)
+ #declare SPF = false;
+#end
+
+//Default: No capped sticks-model (if undefined)
+#ifndef (CST)
+ #declare CST = false;
+#end
+
+//Is a model (BAS, SPF or CST) selected ?
+#if (!((BAS | SPF) | CST))
+
+ //Terminate parsing
+ #error "You have to select BAS (default), SPF or CST" 
+
+#end
+
+//Select only one model
+#if ((BAS & SPF) | ((BAS & CST) | (SPF & CST)))
+
+ //Terminate parsing
+ #error "You have to select only one model-type" 
+
+#end
+
+//Display copyright
+#render "\n\n"
+#render "\nbabel31.inc (C) 1996-2002 by\n"
+#render "Oliver Weichold (weichold@sas.upenn.edu)\n"
+#render "and Steffen Reith (streit@streit.cc)\n"
+#render "\n\n"
+
+//TRANS mode off by default (only needed for transparent textures)
+#ifndef (TRANS)
+#declare TRANS = false;
+#end 
+
+#if (TRANS)
+#include "glass.inc"
+#end
+
+//Finishs for atoms (Nonmetals, Transmetals, Halfmetals and Metals)
+#if (TRANS)
+
+ #declare TransFinish = finish {
+                                ambient 0.1
+                                diffuse 0.1
+                                specular 0.8
+                                reflection 0.1
+                                roughness 0.0003
+                                phong 1 phong_size 400
+                               }                      
+
+ //Transparent finishs
+ #declare MetalFinish      = finish {TransFinish}
+ #declare HalfMetalFinish  = finish {TransFinish}
+ #declare NonMetalFinish   = finish {TransFinish}
+ #declare TransMetalFinish = finish {TransFinish}
+ #declare Bond_0_Finish    = finish {TransFinish}
+ #declare Bond_1_Finish    = finish {TransFinish}
+ #declare Bond_2_Finish    = finish {TransFinish}
+ #declare Bond_3_Finish    = finish {TransFinish}
+ #declare Bond_4_Finish    = finish {TransFinish}
+ #declare Bond_5_Finish    = finish {TransFinish}
+
+ //Filter values for transparent finishs  
+ #declare MetalFilter       = 1.00;
+ #declare HalfMetalFilter   = 0.95;
+ #declare NonMetalFilter    = 1.00;
+ #declare TransMetalFilter  = 0.95;
+ #declare Bond_0_Filter     = 0.00;
+ #declare Bond_1_Filter     = 0.90;
+ #declare Bond_2_Filter     = 0.90;
+ #declare Bond_3_Filter     = 0.90;
+ #declare Bond_4_Filter     = 0.90;
+ #declare Bond_5_Filter     = 0.90;
+
+#else
+
+ //Solid finishs
+ #declare MetalFinish      = finish {F_MetalA}
+ #declare HalfMetalFinish  = finish {F_MetalD}
+ #declare NonMetalFinish   = finish {
+
+                            ambient 0.2
+                            diffuse 0.8
+                            brilliance 1.0 
+                            phong 1.0      
+                            phong_size 80
+                            reflection 0.25
+
+                           }
+ #declare TransMetalFinish = finish {F_MetalD}
+ #declare Bond_0_Finish    = finish {F_MetalC}
+ #declare Bond_1_Finish    = finish {F_MetalC}
+ #declare Bond_2_Finish    = finish {F_MetalC}
+ #declare Bond_3_Finish    = finish {F_MetalC}
+ #declare Bond_4_Finish    = finish {F_MetalC}
+ #declare Bond_5_Finish    = finish {F_MetalC}
+
+ //No additional filter (texture is not transparent)
+ #declare MetalFilter       = 0.0;
+ #declare HalfMetalFilter   = 0.0;
+ #declare NonMetalFilter    = 0.0;
+ #declare TransMetalFilter  = 0.0;
+ #declare Bond_0_Filter     = 0.0;
+ #declare Bond_1_Filter     = 0.0;
+ #declare Bond_2_Filter     = 0.0;
+ #declare Bond_3_Filter     = 0.0;
+ #declare Bond_4_Filter     = 0.0;
+ #declare Bond_5_Filter     = 0.0;
+
+#end
+
+//Thickness of Bonds (see Makro Bond_order)
+#if (CST)
+
+ // For capped-stick models you must use _one_ Bond_Thick ! 
+ #declare Bond_Thick_0 = 0.1;
+ #declare Bond_Thick_1 = Bond_Thick_0; 
+ #declare Bond_Thick_2 = Bond_Thick_0;
+ #declare Bond_Thick_3 = Bond_Thick_0;
+ #declare Bond_Thick_4 = Bond_Thick_0;
+ #declare Bond_Thick_5 = Bond_Thick_0;
+
+#else
+
+ #declare Bond_Thick_0 = 0.1;
+ #declare Bond_Thick_1 = 0.1;
+ #declare Bond_Thick_2 = 0.1;
+ #declare Bond_Thick_3 = 0.1;
+ #declare Bond_Thick_4 = 0.1;
+ #declare Bond_Thick_5 = 0.1;
+
+#end
+
+//Colors for Bonds (see Makro Bond_order)
+#declare Bond_0_Color = rgbf <1.00,0.725,0.275,Bond_0_Filter>; 
+#declare Bond_1_Color = rgbf <1.00,0.725,0.275,Bond_1_Filter>;
+#declare Bond_2_Color = rgbf <1.00,0.725,0.275,Bond_2_Filter>;
+#declare Bond_3_Color = rgbf <1.00,0.725,0.275,Bond_3_Filter>;
+#declare Bond_4_Color = rgbf <1.00,0.725,0.275,Bond_4_Filter>;
+#declare Bond_5_Color = rgbf <1.00,0.725,0.275,Bond_5_Filter>;
+
+#declare Bond_0_Color = rgbf <0.95,0.95,0.1,Bond_0_Filter>;
+#declare Bond_1_Color = rgbf <0.95,0.95,0.1,Bond_1_Filter>;
+#declare Bond_2_Color = rgbf <0.95,0.95,0.1,Bond_2_Filter>;
+#declare Bond_3_Color = rgbf <0.95,0.95,0.1,Bond_3_Filter>;
+#declare Bond_4_Color = rgbf <0.95,0.95,0.1,Bond_4_Filter>;
+#declare Bond_5_Color = rgbf <0.95,0.95,0.1,Bond_5_Filter>;
+
+//The bond declarations
+#declare bond_0 = cylinder {
+                            <0,0,0>
+                            <1,0,0>
+                            Bond_Thick_0
+                            texture {
+
+                             pigment {color Bond_0_Color}
+                             finish {Bond_0_Finish}
+
+                            }
+#if (TRANS)
+			    interior{ I_Glass}
+#end
+                           }
+#declare bond_1 = cylinder {
+                            <0,0,0>
+                            <1,0,0>
+                            Bond_Thick_1
+                            texture {
+
+                             pigment {color Bond_1_Color}
+                             finish {Bond_1_Finish}
+
+                            }
+#if (TRANS)
+			    interior{ I_Glass}
+#end
+                           }
+#declare bond_2 = cylinder {
+                            <0,0,0>
+                            <1,0,0>
+                            Bond_Thick_2
+                            texture {
+
+                             pigment {color Bond_2_Color}
+                             finish {Bond_2_Finish}
+
+                            }
+#if (TRANS)
+			    interior{ I_Glass}
+#end
+                           }
+#declare bond_3 = cylinder {
+                            <0,0,0>
+                            <1,0,0>
+                            Bond_Thick_3
+                            texture {
+
+                             pigment {color Bond_3_Color}
+                             finish {Bond_3_Finish}
+
+                            }
+#if (TRANS)
+			    interior{ I_Glass}
+#end
+                           }
+#declare bond_4 = cylinder {
+                            <0,0,0>
+                            <1,0,0>
+                            Bond_Thick_4
+                            texture {
+
+                             pigment {color Bond_4_Color}
+                             finish {Bond_4_Finish}
+
+                            }
+#if (TRANS)
+			    interior{ I_Glass}
+#end
+                           }
+#declare bond_5 = cylinder {
+                            <0,0,0>
+                            <1,0,0>
+                            Bond_Thick_5
+                            texture {
+
+                             pigment {color Bond_5_Color}
+                             finish {Bond_5_Finish}
+
+                            }
+#if (TRANS)
+			    interior{ I_Glass}
+#end
+                           }
+
+//Generic definition of an atom
+#if (BAS)
+#render "\n\nCalculate a ball and sticks model of :"
+#declare atom = sphere {<0,0,0>,0.6}
+#end
+#if (SPF)  
+#render "\n\nCalculate a spacefill model of :"
+#declare atom = sphere {<0,0,0>,1.66}
+#end
+#if (CST)  
+#render "\n\nCalculate a capped sticks model of :"
+#declare atom = sphere {<0,0,0>,1.0}
+#end
+
+//For Povray 3.1 only
+#version 3.1;
+
+//For capped sticks models we use Bond_Thick_0 for all atom radii
+#if (CST)
+
+ #declare Radius_C1 = Bond_Thick_0;
+ #declare Radius_C2 = Bond_Thick_0;
+ #declare Radius_C3 = Bond_Thick_0;
+ #declare Radius_H  = Bond_Thick_0;
+ #declare Radius_D =  Bond_Thick_0;
+ #declare Radius_O  = Bond_Thick_0;
+ #declare Radius_N  = Bond_Thick_0;
+ #declare Radius_S  = Bond_Thick_0;
+ #declare Radius_P  = Bond_Thick_0;
+ #declare Radius_F  = Bond_Thick_0;
+ #declare Radius_Cl = Bond_Thick_0;
+ #declare Radius_Br = Bond_Thick_0;
+ #declare Radius_I  = Bond_Thick_0;
+		      
+ #declare Radius_Si = Bond_Thick_0;
+ #declare Radius_B  = Bond_Thick_0;
+ #declare Radius_Ge = Bond_Thick_0;
+ #declare Radius_Se = Bond_Thick_0;
+
+ #declare Radius_Ca  = Bond_Thick_0;
+ #declare Radius_Ca2 = Bond_Thick_0;
+ #declare Radius_Sn  = Bond_Thick_0;
+ #declare Radius_Sn2 = Bond_Thick_0;
+ #declare Radius_Sn4 = Bond_Thick_0;
+ #declare Radius_Pb  = Bond_Thick_0;
+ #declare Radius_Pb2 = Bond_Thick_0;
+ #declare Radius_Pb4 = Bond_Thick_0;
+ #declare Radius_Te  = Bond_Thick_0;
+ #declare Radius_Te4 = Bond_Thick_0;
+ #declare Radius_Te6 = Bond_Thick_0;
+ #declare Radius_Na  = Bond_Thick_0;
+ #declare Radius_Na1 = Bond_Thick_0;
+ #declare Radius_K   = Bond_Thick_0;
+ #declare Radius_K1  = Bond_Thick_0;
+ #declare Radius_Li  = Bond_Thick_0;
+ #declare Radius_Li1 = Bond_Thick_0;
+ #declare Radius_Al  = Bond_Thick_0;
+ #declare Radius_Al3 = Bond_Thick_0;
+
+ #declare Radius_Mn  = Bond_Thick_0;
+ #declare Radius_Mn2 = Bond_Thick_0;
+ #declare Radius_Mn3 = Bond_Thick_0;
+ #declare Radius_Mn4 = Bond_Thick_0;
+ #declare Radius_W   = Bond_Thick_0;
+ #declare Radius_W4  = Bond_Thick_0;
+ #declare Radius_W6  = Bond_Thick_0;
+ #declare Radius_Fe  = Bond_Thick_0;
+ #declare Radius_Fe2 = Bond_Thick_0;
+ #declare Radius_Fe3 = Bond_Thick_0;
+ #declare Radius_Pd  = Bond_Thick_0;
+ #declare Radius_Pd2 = Bond_Thick_0;
+ #declare Radius_Pd4 = Bond_Thick_0;
+ #declare Radius_Ni  = Bond_Thick_0;
+ #declare Radius_Ni2 = Bond_Thick_0;
+ #declare Radius_Ni3 = Bond_Thick_0;
+ #declare Radius_Cu  = Bond_Thick_0;
+ #declare Radius_Cu1 = Bond_Thick_0;
+ #declare Radius_Cu2 = Bond_Thick_0;
+ #declare Radius_V   = Bond_Thick_0;
+ #declare Radius_V2  = Bond_Thick_0;
+ #declare Radius_V3  = Bond_Thick_0;
+ #declare Radius_V4  = Bond_Thick_0;
+ #declare Radius_V5  = Bond_Thick_0;
+ #declare Radius_Zn  = Bond_Thick_0;
+ #declare Radius_Zn2 = Bond_Thick_0;
+
+#else
+
+ //Atom radii in A as published in J. Emsley, The Elements, 
+ //Clarender Press, Oxford 1991
+
+ //All uncharged radii are kovalent. The values for Na and V are calculated 
+ //from the atomic radius (10% less).
+ //We use the kovalent radii for the description of metal atoms. If you want to
+ //use ion radii, just replace the radius in the atom description. 
+ //E.g., replace
+ //
+ //scale Radius_Zn
+ //
+ //by
+ //
+ //scale Radius_Zn2
+ //
+ //for creating a sphere with the ion radius of Zn2+.
+
+ #declare Radius_C1 = 0.770;
+ #declare Radius_C2 = 0.670;
+ #declare Radius_C3 = 0.600;
+
+ #declare Radius_H  = 0.370;
+ #declare Radius_D  = 0.370;
+ #declare Radius_O  = 0.660;
+ #declare Radius_N  = 0.700;
+ #declare Radius_S  = 1.040;
+ #declare Radius_P  = 1.100;
+ #declare Radius_F  = 0.580;
+ #declare Radius_Cl = 0.990; 
+ #declare Radius_Br = 1.142;
+ #declare Radius_I  = 1.330;
+
+ #declare Radius_Si = 1.170;
+ #declare Radius_B  = 0.880;
+ #declare Radius_Ge = 1.220;
+ #declare Radius_Se = 1.170;
+
+ #declare Radius_Ca  = 1.740;
+ #declare Radius_Ca2 = 1.060;
+ #declare Radius_Sn  = 1.400;
+ #declare Radius_Sn2 = 0.930;
+ #declare Radius_Sn4 = 0.740;
+ #declare Radius_Pb  = 1.540;
+ #declare Radius_Pb2 = 1.320;
+ #declare Radius_Pb4 = 0.890;
+ #declare Radius_Te  = 1.370;
+ #declare Radius_Te4 = 0.970;
+ #declare Radius_Te6 = 0.560;
+ #declare Radius_Na  = 1.380;
+ #declare Radius_Na1 = 0.980;
+ #declare Radius_K   = 2.030;
+ #declare Radius_K1  = 1.330;
+ #declare Radius_Li  = 1.230;
+ #declare Radius_Li1 = 0.780;
+ #declare Radius_Al  = 1.250;
+ #declare Radius_Al3 = 0.570;
+
+ #declare Radius_Mn  = 1.170;
+ #declare Radius_Mn2 = 0.910;
+ #declare Radius_Mn3 = 0.700;
+ #declare Radius_Mn4 = 0.520;
+ #declare Radius_W   = 1.300;
+ #declare Radius_W4  = 0.680;
+ #declare Radius_W6  = 0.620;
+ #declare Radius_Fe  = 1.165;
+ #declare Radius_Fe2 = 0.820;
+ #declare Radius_Fe3 = 0.670;
+ #declare Radius_Pd  = 1.280;
+ #declare Radius_Pd2 = 0.860;
+ #declare Radius_Pd4 = 0.640;
+ #declare Radius_Ni  = 1.150;
+ #declare Radius_Ni2 = 0.780;
+ #declare Radius_Ni3 = 0.620;
+ #declare Radius_Cu  = 1.170;
+ #declare Radius_Cu1 = 0.960;
+ #declare Radius_Cu2 = 0.720;
+ #declare Radius_V   = 1.188;
+ #declare Radius_V2  = 0.720;
+ #declare Radius_V3  = 0.650;
+ #declare Radius_V4  = 0.610;
+ #declare Radius_V5  = 0.590;
+ #declare Radius_Zn  = 1.250;
+ #declare Radius_Zn2 = 0.830;
+
+#end
+
+//Atom descriptions
+
+//Section: Nonmetals
+#declare Color_C1 = rgbf <0.00,0.00,0.00,NonMetalFilter>;
+#declare Atom_C1 = object { 
+                           
+                    atom
+                    scale Radius_C1
+                    texture {
+ 
+                     pigment {color Color_C1}
+                     finish {NonMetalFinish}
+ 
+                    }                           
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+
+                   }
+#declare Atom_C	   = Atom_C1
+#declare Atom_Cac  = Atom_C1
+#declare Atom_Cbl  = Atom_C1
+#declare Atom_Cmi  = Atom_C1
+#declare Atom_Crad = Atom_C1
+#declare Atom_Cx   = Atom_C1
+#declare Atom_Nr   = Atom_C1
+
+#declare Radius_Cac  = Radius_C1;
+#declare Radius_Cbl  = Radius_C1;
+#declare Radius_Cmi  = Radius_C1;
+#declare Radius_Crad = Radius_C1;
+#declare Radius_Cx   = Radius_C1;
+#declare Radius_Nr   = Radius_C1;
+
+#declare Color_C   = Color_C1;
+#declare Color_Cac  = Color_C1;
+#declare Color_Cbl  = Color_C1;
+#declare Color_Cmi  = Color_C1;
+#declare Color_Crad = Color_C1;
+#declare Color_Cx   = Color_C1;
+#declare Color_Nr   = Color_C1;
+
+#declare Color_C2 = rgbf <0.00,0.00,0.00,NonMetalFilter>;
+#declare Atom_C2  = object { 
+
+                     atom
+                     scale Radius_C2
+                     texture {
+ 
+                      pigment {color Color_C2}
+                      finish {NonMetalFinish}
+ 
+                     }                           
+#if (TRANS)
+	             interior{ I_Glass}
+#end
+                    }
+
+#declare Color_C3 = rgbf <0.00,0.00,0.00,NonMetalFilter>;
+#declare Atom_C3 = object { 
+
+                    atom
+                    scale Radius_C3
+                    texture {
+ 
+                     pigment {color Color_C3}
+                     finish {NonMetalFinish}
+
+                    }                           
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+#declare Atom_Car = Atom_C3
+#declare Atom_Cpl = Atom_C3
+#declare Atom_Cx  = Atom_C3
+
+#declare Radius_Car = Radius_C3;
+#declare Radius_Cpl = Radius_C3;
+#declare Radius_Cx  = Radius_C3;
+
+#declare Color_Car = Color_C3;
+#declare Color_Cpl = Color_C3;
+#declare Color_Cx  = Color_C3;
+
+#declare Color_H = rgbf <1.00,1.00,1.00,NonMetalFilter>;
+#declare Atom_H = object { 
+                   
+                   atom
+                   scale Radius_H
+                   texture {
+ 
+                    pigment {color Color_H}
+                    finish {NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+#declare Atom_HC  = Atom_H
+#declare Atom_HO  = Atom_H
+#declare Atom_HN  = Atom_H
+#declare Atom_Hpl = Atom_H
+
+#declare Radius_HC  = Radius_H;
+#declare Radius_HO  = Radius_H;
+#declare Radius_HN  = Radius_H;
+#declare Radius_Hpl = Radius_H;
+
+#declare Color_HC  = Color_H;
+#declare Color_HO  = Color_H;
+#declare Color_HN  = Color_H;
+#declare Color_Hpl = Color_H;
+
+#declare Color_D = rgbf <0.85,0.85,0.95,NonMetalFilter>;
+#declare Atom_D = object { 
+                          
+                   atom
+                   scale Radius_D
+                   texture {
+ 
+                    pigment {color Color_D}
+                    finish {NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+#declare Atom_DC = Atom_D
+
+#declare Radius_DC = Radius_D;
+
+#declare Color_DC = Color_D;
+
+#declare Color_O = rgbf <1.00,0.00,0.00,NonMetalFilter>;
+#declare Atom_O = object { 
+
+                   atom
+                   scale Radius_O
+                   texture {
+
+                    pigment {color Color_O}
+                    finish {NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+#declare Atom_O3   = Atom_O
+#declare Atom_O2   = Atom_O
+#declare Atom_Omi  = Atom_O
+#declare Atom_OCO2 = Atom_O
+#declare Atom_Oany = Atom_O
+#declare Atom_Oco2 = Atom_O
+
+#declare Radius_O3   = Radius_O;
+#declare Radius_O2   = Radius_O;
+#declare Radius_Omi  = Radius_O;
+#declare Radius_OCO2 = Radius_O;
+#declare Radius_Oany = Radius_O;
+#declare Radius_Oco2 = Radius_O;
+
+#declare Color_O3   = Color_O;
+#declare Color_O2   = Color_O;
+#declare Color_Omi  = Color_O;
+#declare Color_OCO2 = Color_O;
+#declare Color_Oany = Color_O;
+#declare Color_Oco2 = Color_O;
+
+#declare Color_N = rgbf <0.14,0.42,0.56,NonMetalFilter>;
+#declare Atom_N = object { 
+     
+                   atom
+                   scale Radius_N
+                   texture {
+                         
+                    pigment {color Color_N}
+                    finish {NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+#declare Atom_NPL3 = Atom_N
+#declare Atom_N2   = Atom_N
+#declare Atom_N4   = Atom_N
+#declare Atom_N3   = Atom_N
+#declare Atom_Npl  = Atom_N
+#declare Atom_N2pl = Atom_N
+#declare Atom_Naz  = Atom_N
+#declare Atom_N1   = Atom_N
+#declare Atom_Nox  = Atom_N
+#declare Atom_Ntr  = Atom_N
+#declare Atom_NC   = Atom_N
+#declare Atom_Nar  = Atom_N
+#declare Atom_Nam  = Atom_N
+#declare Atom_Ngpl = Atom_N
+#declare Atom_N3pl = Atom_N
+#declare Atom_Nany = Atom_N
+
+#declare Radius_NPL3 = Radius_N;
+#declare Radius_N2   = Radius_N;
+#declare Radius_N4   = Radius_N;
+#declare Radius_N3   = Radius_N;
+#declare Radius_Npl  = Radius_N;
+#declare Radius_N2pl = Radius_N;
+#declare Radius_Naz  = Radius_N;
+#declare Radius_N1   = Radius_N;
+#declare Radius_Nox  = Radius_N;
+#declare Radius_Ntr  = Radius_N;
+#declare Radius_NC   = Radius_N;
+#declare Radius_Nar  = Radius_N;
+#declare Radius_Nam  = Radius_N;
+#declare Radius_Ngpl = Radius_N;
+#declare Radius_N3pl = Radius_N;
+#declare Radius_Nany = Radius_N;
+
+#declare Color_NPL3 = Color_N;
+#declare Color_N2   = Color_N;
+#declare Color_N4   = Color_N;
+#declare Color_N3   = Color_N;
+#declare Color_Npl  = Color_N;
+#declare Color_N2pl = Color_N;
+#declare Color_Naz  = Color_N;
+#declare Color_N1   = Color_N;
+#declare Color_Nox  = Color_N;
+#declare Color_Ntr  = Color_N;
+#declare Color_NC   = Color_N;
+#declare Color_Nar  = Color_N;
+#declare Color_Nam  = Color_N;
+#declare Color_Ngpl = Color_N;
+#declare Color_N3pl = Color_N;
+#declare Color_Nany = Color_N;
+
+#declare Color_F = rgbf<1.00,1.00,0.88,NonMetalFilter>;
+#declare Atom_F = object {
+
+                   atom
+                   scale Radius_F
+                   texture {
+                   
+                    pigment {color Color_F}
+                    finish {NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+
+#declare Color_Cl = rgbf <0.20,0.80,0.20,NonMetalFilter>;
+#declare Atom_Cl = object {
+
+                    atom
+                    scale Radius_Cl
+                    texture {
+                
+                     pigment {color Color_Cl}
+                     finish {NonMetalFinish}
+ 
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Br = rgbf <0.65,0.16,0.16,NonMetalFilter>;
+#declare Atom_Br = object {
+
+                    atom
+                    scale Radius_Br
+                    texture {
+                    
+                     pigment {color Color_Br}
+                     finish {NonMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_I = rgbf<0.58,0.44,0.86,NonMetalFilter>;
+#declare Atom_I = object {
+
+                   atom
+                   scale Radius_I
+                   texture {
+                  
+                    pigment {color Color_I}
+                    finish {NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+
+#declare Color_P = rgbf <1.00,0.50,0.00,NonMetalFilter>;
+#declare Atom_P = object {
+
+                   atom
+                   scale Radius_P
+                   texture {
+                   
+                    pigment {color Color_P}
+                    finish{NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+#declare Atom_Pac  = Atom_P
+#declare Atom_P3   = Atom_P
+#declare Atom_Pox  = Atom_P
+#declare Atom_P3pl = Atom_P
+
+#declare Radius_Pac  = Radius_P;
+#declare Radius_P3   = Radius_P;
+#declare Radius_Pox  = Radius_P;
+#declare Radius_P3pl = Radius_P;
+
+#declare Color_Pac  = Color_P;
+#declare Color_P3   = Color_P;
+#declare Color_Pox  = Color_P;
+#declare Color_P3pl = Color_P;
+
+#declare Color_S = rgbf <1.00,1.00,0.00,NonMetalFilter>;
+#declare Atom_S = object {
+
+                   atom
+                   scale Radius_S
+                   texture {
+                         
+                    pigment {color Color_S}
+                    finish {NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+#declare Atom_S3pl = Atom_S
+#declare Atom_S3   = Atom_S
+#declare Atom_S2   = Atom_S
+#declare Atom_Sac  = Atom_S
+#declare Atom_Sox  = Atom_S
+#declare Atom_Sany = Atom_S
+#declare Atom_So   = Atom_S
+
+#declare Radius_S3pl = Radius_S;
+#declare Radius_S3   = Radius_S;
+#declare Radius_S2   = Radius_S;
+#declare Radius_Sac  = Radius_S;
+#declare Radius_Sox  = Radius_S;
+#declare Radius_Sany = Radius_S;
+#declare Radius_So   = Radius_S;
+
+#declare Color_S3pl = Color_S;
+#declare Color_S3   = Color_S;
+#declare Color_S2   = Color_S;
+#declare Color_Sac  = Color_S;
+#declare Color_Sox  = Color_S;
+#declare Color_Sany = Color_S;
+#declare Color_So   = Color_S;
+
+//A special color for halfmetals
+#declare HalfMetalColor = rgbf <0.6,0.6,0.85,HalfMetalFilter>; 
+
+//Section: HalfMetals
+#declare Color_B = rgbf <0,1.0,0,HalfMetalFilter>;
+#declare Atom_B = object {
+
+                   atom
+                   scale Radius_B
+                   texture {
+                   
+                    pigment {color Color_B}
+                    finish {HalfMetalFinish}
+                   
+                   }
+#if (TRANS)
+                   interior{ I_Glass}
+#end
+                  }
+#declare Atom_Bac = Atom_B
+#declare Atom_Box = Atom_B
+
+#declare Radius_Bac = Radius_B;
+#declare Radius_Box = Radius_B;
+
+#declare Color_Bac = Color_B;
+#declare Color_Box = Color_B;
+
+#declare Color_Si = HalfMetalColor;
+#declare Atom_Si = object {
+ 
+                    atom
+                    scale Radius_Si
+                    texture {
+
+                     pigment {color Color_Si}
+                     finish {HalfMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+
+#declare Color_Ge = HalfMetalColor;
+#declare Atom_Ge = object { 
+
+                    atom
+                    scale Radius_Ge
+                    texture {
+
+                     pigment {color Color_Ge}
+                     finish {HalfMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+#declare Color_Se = HalfMetalColor;
+#declare Atom_Se = object { 
+
+                    atom
+                    scale Radius_Se
+                    texture {
+
+                     pigment {color Color_Se}
+                     finish {HalfMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+//Metals
+#declare Color_Metal = rgbf <0.94,0.93,0.90,MetalFilter>;
+
+#declare Color_Te = rgbf <0.6,0.6,0.6,MetalFilter>;
+#declare Atom_Te = object { 
+
+                    atom
+                    scale Radius_Te
+                    texture {
+
+                     pigment {color Color_Te}
+                     finish {MetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Li = Color_Metal;
+#declare Atom_Li = object { 
+
+                    atom
+                    scale Radius_Li                          
+                    texture {
+                     
+                     pigment {color Color_Li}
+                     finish {MetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Na = Color_Metal;
+#declare Atom_Na = object { 
+
+                    atom
+                    scale Radius_Na
+                    texture {
+                      
+                     pigment {color Color_Na}
+                     finish {MetalFinish}
+   
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_K = Color_Metal;
+#declare Atom_K = object { 
+
+                   atom
+                   scale Radius_K
+                   texture {
+                           
+                    pigment {color Color_K}
+                    finish {MetalFinish}
+
+                   }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                  }
+
+#declare Color_Ca = Color_Metal;
+#declare Atom_Ca = object {
+ 
+                    atom
+                    scale Radius_Ca
+                    texture {
+                     
+                     pigment {color Color_Ca}
+                     finish {MetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Al = Color_Metal;
+#declare Atom_Al = object { 
+
+                    atom
+                    scale Radius_Al
+                    texture {
+                    
+                     pigment {color Color_Al}
+                     finish {MetalFinish}
+ 
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Sn = Color_Metal;
+#declare Atom_Sn = object { 
+
+                    atom
+                    scale Radius_Sn
+                    texture {
+                    
+                     pigment {color Color_Sn}
+                     finish {MetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Pb = Color_Metal;
+#declare Atom_Pb = object { 
+
+                    atom
+                    scale Radius_Pb
+                    texture {
+                     
+                     pigment {color Color_Pb}
+                     finish {MetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+//TransMetals
+#declare Color_TransMetal = rgbf <0.94,0.93,0.90,TransMetalFilter>;
+
+#declare Color_W = Color_TransMetal;
+#declare Atom_W = object { 
+
+                   atom
+                   scale Radius_W
+                   texture {
+
+                    pigment {color Color_W}
+                    finish {TransMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+
+#declare Color_Pd = Color_TransMetal;
+#declare Atom_Pd = object { 
+
+                    atom
+                    scale Radius_Pd
+                    texture {
+  
+                     pigment {color Color_Pd}
+                     finish {TransMetalFinish}
+ 
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Ni = Color_TransMetal;
+#declare Atom_Ni = object { 
+
+                    atom
+                    scale Radius_Ni
+                    texture {
+
+                     pigment {color Color_Ni}
+                     finish {TransMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Cu = rgbf <0.50,0.25,0.15,TransMetalFilter>;
+#declare Atom_Cu = object { 
+
+                    atom
+                    scale Radius_Cu
+
+                    texture {
+
+                     pigment {color Color_Cu}
+                     finish {TransMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Mn = Color_TransMetal;
+#declare Atom_Mn = object { 
+
+                    atom
+                    scale Radius_Mn
+                    texture {
+
+                     pigment {color Color_Mn}
+                     finish {TransMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Fe = Color_TransMetal;
+#declare Atom_Fe = object { 
+
+                    atom
+                    scale Radius_Fe
+
+                    texture {
+
+                     pigment {color Color_Fe}
+                     finish {TransMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+
+#declare Color_V = Color_TransMetal;
+#declare Atom_V = object {
+                    
+                   atom
+                   scale Radius_V
+                   texture {
+                     
+                    pigment {color Color_V}
+                    finish {TransMetalFinish}
+                     
+                   } 
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+
+#declare Atom_V2 = object {
+                    
+                   atom
+                   scale Radius_V2
+                   texture {
+                     
+                    pigment {color Color_V}
+                    finish {TransMetalFinish}
+                     
+                   } 
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }  
+
+#declare Atom_V3 = object {
+                    
+                   atom
+                   scale Radius_V3
+                   texture {
+                     
+                    pigment {color Color_V}
+                    finish {TransMetalFinish}
+                     
+                   } 
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }  
+
+#declare Atom_V4 = object {
+                    
+                   atom
+                   scale Radius_V4
+                   texture {
+                     
+                    pigment {color Color_V}
+                    finish {TransMetalFinish}
+                     
+                   } 
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  } 
+
+#declare Atom_V5 = object {
+                    
+                   atom
+                   scale Radius_V5
+                   texture {
+                     
+                    pigment {color Color_V}
+                    finish {TransMetalFinish}
+                     
+                   } 
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }  
+
+
+#declare Color_Zn = Color_TransMetal;
+#declare Atom_Zn = object {
+                    
+                    atom
+                    scale Radius_Zn
+                    texture {
+                     
+                     pigment {color Color_Zn} 
+                     finish {TransMetalFinish}
+                     
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   } 
+
+#declare Atom_Zn2 = object {
+                    
+                    atom
+                    scale Radius_Zn2
+                    texture {
+                     
+                     pigment {color Color_Zn} 
+                     finish {TransMetalFinish}
+                     
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   } 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/bin2hex.pl	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,144 @@
+#!/usr/bin/env perl
+# bin2hex.pl
+
+########################################################################
+# Copyright (C) 2001 by OpenEye Scientific Software, Inc.
+# Some portions Copyright (c) 2002 by Geoffrey R. Hutchison
+#
+# This file is part of the Open Babel project.
+# For more information, see <http://openbabel.org/>
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation version 2 of the License.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+########################################################################
+
+
+# Autoflush STDOUT
+#STDOUT->autoflush(1);
+$| = 1;
+
+$argc = @ARGV;
+if( $argc == 2 ) {
+    $filename = @ARGV[0];
+    $arrayname = @ARGV[1];
+
+    $pos = index($filename,".");
+    if( $pos > 0 ) {
+        $guard = uc(substr($filename,0,$pos));
+    } else {
+        $guard = uc($filename);
+    }
+} elsif( $argc == 3 ) {
+    $filename = @ARGV[0];
+    $arrayname = @ARGV[1];
+    $guard = @ARGV[2];
+} else {
+    print "usage:  bin2hex.pl <binaryfile> <arrayname>\n\n";
+    exit;
+}
+
+$debug = 0;
+
+open(F,$filename) || die "Error: Unable to open binary file!\n";
+
+if( !$debug ) {
+    print "/***************************************************************\n";
+    print "This file is part of the Open Babel project.\n";
+    print "This is copyright under the GNU General Public License (GPL)\n";
+    print "For more information, see <http://openbabel.org/>\n\n";
+    print "This file contains a binary representation of data tables\n";
+    print " used by Open Babel. It is used as a fallback if the textual\n";
+    print " data table is not found at runtime. It is not a normal header.\n";
+    print "***************************************************************/\n";
+    print "\n\n";
+
+    print "#ifndef OB_" . $guard . "_H\n";
+    print "#define OB_" . $guard . "_H\n\n";
+    print "namespace OpenBabel\n{\n";
+    print "static const char " . $arrayname . "[] = {\n ";
+}
+
+binmode(F);
+
+$col = 0;
+$init = 0;
+$ignore = 0;
+$newline = 1;
+$spacerun = 0; # collapse runs of spaces
+
+while( !eof(F) ) {
+    $ch = ord(getc(F));
+    if( $ch == 13 ) { # ignore \r characters
+        $ch = 0;
+    }
+
+    if ( $spacerun ) {
+        if ( $ch == 32 ) {
+            $ch = 0;
+        } else {
+            $spacerun = 0;
+        }
+    } elsif ( $ch == 32) {
+        $spacerun = 1;
+    }
+
+    if( $ignore ) {
+        if( $ch == 10 ) { # found the \n after an '#' ignore comment
+            $ignore = 0;
+        }
+        $ch = 0;
+    } elsif( $newline ) { # just saw a \n -- do we see real text
+        if( $ch == 10 ) {
+            $ch = 0;
+        } elsif ( $ch == 35 ) { # ignore anything after a '#' until a \n
+            $ignore = 1;
+            $ch = 0;
+        } elsif( $ch == 32 ) { # space
+            $ch = 0;
+        } elsif( $ch == 9 ) { # tab
+            $ch = 0;
+        } elsif( $ch ) { # something else, so clear the blank-line boolean
+            $newline = 0;
+        }
+    } elsif( $ch == 10 ) { # set the blank-line detector
+        $newline = 1;
+    }
+
+    if( $ch ) {
+        if( $debug ) {
+            print chr($ch);
+        } else {
+            if( $init ) {
+                print ",";
+            } else {
+                $init = 1;
+            }
+            if( $col >= 15 ) {
+                print "\n ";
+                $col = 0;
+            }
+            print sprintf("0x%02X",$ch);
+            $col++;
+        }
+    }
+}
+
+if( !$debug ) {
+    if( $col >= 15 ) {
+        print ",\n0x00};\n\n";
+    } else {
+        print ",0x00};\n\n";
+    }
+    print "} // namespace OpenBabel\n";
+    print "#endif // OB_" . $guard . "_H\n\n";
+}
+
+close(F);
+exit;
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/bondtyp.h	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,132 @@
+/***************************************************************
+This file is part of the Open Babel project.
+This is copyright under the GNU General Public License (GPL)
+For more information, see <http://openbabel.org/>
+
+This file contains a binary representation of data tables
+ used by Open Babel. It is used as a fallback if the textual
+ data table is not found at runtime. It is not a normal header.
+***************************************************************/
+
+
+#ifndef OB_BONDTYP_H
+#define OB_BONDTYP_H
+
+namespace OpenBabel
+{
+static const char BondTypeData[] = {
+ 0x2A,0x31,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x32,0x29,
+ 0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x32,0x2A,0x5B,
+ 0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x33,0x29,0x5B,0x23,0x36,
+ 0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x33,0x2A,0x5B,0x23,0x36,0x5D,
+ 0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x34,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,
+ 0x36,0x5D,0x5B,0x23,0x36,0x5D,0x34,0x2A,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,
+ 0x37,0x44,0x33,0x5D,0x35,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,
+ 0x23,0x36,0x5D,0x35,0x31,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,0x32,
+ 0x20,0x31,0x20,0x31,0x20,0x33,0x20,0x31,0x20,0x33,0x20,0x34,0x20,0x32,0x20,
+ 0x34,0x20,0x35,0x20,0x31,0x20,0x35,0x20,0x32,0x20,0x31,0x20,0x35,0x20,0x36,
+ 0x20,0x32,0x20,0x36,0x20,0x37,0x20,0x31,0x20,0x37,0x20,0x38,0x20,0x32,0x20,
+ 0x37,0x20,0x39,0x20,0x31,0x20,0x39,0x20,0x31,0x30,0x20,0x32,0x20,0x31,0x30,
+ 0x20,0x31,0x31,0x20,0x31,0x20,0x31,0x31,0x20,0x38,0x20,0x31,0x20,0x31,0x31,
+ 0x20,0x31,0x32,0x20,0x32,0x20,0x31,0x32,0x20,0x31,0x33,0x20,0x31,0x20,0x31,
+ 0x33,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x33,0x20,0x31,0x35,0x20,0x32,0x20,
+ 0x31,0x35,0x20,0x31,0x36,0x20,0x31,0x20,0x31,0x36,0x20,0x31,0x37,0x20,0x32,
+ 0x20,0x31,0x37,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x37,0x20,0x31,0x38,0x20,
+ 0x31,0x20,0x31,0x38,0x20,0x31,0x39,0x20,0x32,0x20,0x31,0x39,0x20,0x32,0x30,
+ 0x20,0x31,0x20,0x31,0x39,0x20,0x32,0x31,0x20,0x31,0x20,0x32,0x31,0x20,0x32,
+ 0x32,0x20,0x32,0x20,0x32,0x32,0x20,0x32,0x33,0x20,0x31,0x20,0x32,0x33,0x20,
+ 0x32,0x30,0x20,0x32,0x0A,0x2A,0x31,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,
+ 0x44,0x33,0x5D,0x32,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,
+ 0x36,0x5D,0x32,0x2A,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x5D,0x33,0x29,
+ 0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x33,0x2A,0x5B,
+ 0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x34,0x29,0x5B,0x23,0x36,
+ 0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x34,0x2A,0x5B,0x23,0x36,0x5D,
+ 0x28,0x5B,0x23,0x37,0x5D,0x35,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,
+ 0x5B,0x23,0x36,0x5D,0x35,0x31,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,
+ 0x32,0x20,0x31,0x20,0x31,0x20,0x33,0x20,0x31,0x20,0x33,0x20,0x34,0x20,0x32,
+ 0x20,0x34,0x20,0x35,0x20,0x31,0x20,0x35,0x20,0x32,0x20,0x31,0x20,0x35,0x20,
+ 0x36,0x20,0x32,0x20,0x36,0x20,0x37,0x20,0x31,0x20,0x37,0x20,0x38,0x20,0x32,
+ 0x20,0x37,0x20,0x39,0x20,0x31,0x20,0x39,0x20,0x31,0x30,0x20,0x32,0x20,0x31,
+ 0x30,0x20,0x31,0x31,0x20,0x31,0x20,0x31,0x31,0x20,0x38,0x20,0x31,0x20,0x31,
+ 0x31,0x20,0x31,0x32,0x20,0x32,0x20,0x31,0x32,0x20,0x31,0x33,0x20,0x31,0x20,
+ 0x31,0x33,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x33,0x20,0x31,0x35,0x20,0x32,
+ 0x20,0x31,0x35,0x20,0x31,0x36,0x20,0x31,0x20,0x31,0x36,0x20,0x31,0x37,0x20,
+ 0x32,0x20,0x31,0x37,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x37,0x20,0x31,0x38,
+ 0x20,0x31,0x20,0x31,0x38,0x20,0x31,0x39,0x20,0x32,0x20,0x31,0x39,0x20,0x32,
+ 0x30,0x20,0x31,0x20,0x31,0x39,0x20,0x32,0x31,0x20,0x31,0x20,0x32,0x31,0x20,
+ 0x32,0x32,0x20,0x32,0x20,0x32,0x32,0x20,0x32,0x33,0x20,0x31,0x20,0x32,0x33,
+ 0x20,0x32,0x30,0x20,0x32,0x0A,0x2A,0x31,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,
+ 0x37,0x5D,0x32,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,
+ 0x5D,0x32,0x2A,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x5D,0x33,0x29,0x5B,
+ 0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x33,0x2A,0x5B,0x23,
+ 0x36,0x5D,0x28,0x5B,0x23,0x37,0x5D,0x34,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,
+ 0x36,0x5D,0x5B,0x23,0x36,0x5D,0x34,0x2A,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,
+ 0x37,0x5D,0x35,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,
+ 0x5D,0x35,0x31,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,0x32,0x20,0x31,
+ 0x20,0x31,0x20,0x33,0x20,0x31,0x20,0x33,0x20,0x34,0x20,0x32,0x20,0x34,0x20,
+ 0x35,0x20,0x31,0x20,0x35,0x20,0x32,0x20,0x31,0x20,0x35,0x20,0x36,0x20,0x32,
+ 0x20,0x36,0x20,0x37,0x20,0x31,0x20,0x37,0x20,0x38,0x20,0x32,0x20,0x37,0x20,
+ 0x39,0x20,0x31,0x20,0x39,0x20,0x31,0x30,0x20,0x32,0x20,0x31,0x30,0x20,0x31,
+ 0x31,0x20,0x31,0x20,0x31,0x31,0x20,0x38,0x20,0x31,0x20,0x31,0x31,0x20,0x31,
+ 0x32,0x20,0x32,0x20,0x31,0x32,0x20,0x31,0x33,0x20,0x31,0x20,0x31,0x33,0x20,
+ 0x31,0x34,0x20,0x31,0x20,0x31,0x33,0x20,0x31,0x35,0x20,0x32,0x20,0x31,0x35,
+ 0x20,0x31,0x36,0x20,0x31,0x20,0x31,0x36,0x20,0x31,0x37,0x20,0x32,0x20,0x31,
+ 0x37,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x37,0x20,0x31,0x38,0x20,0x31,0x20,
+ 0x31,0x38,0x20,0x31,0x39,0x20,0x32,0x20,0x31,0x39,0x20,0x32,0x30,0x20,0x31,
+ 0x20,0x31,0x39,0x20,0x32,0x31,0x20,0x31,0x20,0x32,0x31,0x20,0x32,0x32,0x20,
+ 0x32,0x20,0x32,0x32,0x20,0x32,0x33,0x20,0x31,0x20,0x32,0x33,0x20,0x32,0x30,
+ 0x20,0x32,0x0A,0x5B,0x23,0x37,0x44,0x32,0x5D,0x5B,0x23,0x37,0x44,0x32,0x5E,
+ 0x31,0x5D,0x5B,0x23,0x37,0x44,0x31,0x5D,0x09,0x09,0x30,0x20,0x31,0x20,0x32,
+ 0x20,0x31,0x20,0x32,0x20,0x32,0x0A,0x5B,0x23,0x38,0x44,0x31,0x5D,0x5B,0x23,
+ 0x37,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x38,0x44,0x31,0x5D,0x29,0x2A,
+ 0x09,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,0x32,0x20,0x32,0x20,0x31,
+ 0x20,0x33,0x20,0x31,0x0A,0x5B,0x23,0x31,0x36,0x44,0x34,0x5D,0x28,0x5B,0x23,
+ 0x38,0x44,0x31,0x5D,0x29,0x28,0x5B,0x23,0x38,0x44,0x31,0x5D,0x29,0x28,0x2A,
+ 0x29,0x28,0x2A,0x29,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,
+ 0x32,0x20,0x30,0x20,0x33,0x20,0x31,0x20,0x30,0x20,0x34,0x20,0x31,0x0A,0x5B,
+ 0x23,0x31,0x35,0x44,0x34,0x5D,0x28,0x5B,0x23,0x38,0x44,0x31,0x5D,0x29,0x28,
+ 0x2A,0x29,0x28,0x2A,0x29,0x28,0x2A,0x29,0x09,0x30,0x20,0x31,0x20,0x32,0x20,
+ 0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,0x20,0x30,0x20,0x34,
+ 0x20,0x31,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x38,
+ 0x44,0x31,0x5D,0x29,0x28,0x5B,0x23,0x38,0x5D,0x29,0x2A,0x09,0x09,0x30,0x20,
+ 0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,
+ 0x0A,0x5B,0x23,0x38,0x44,0x31,0x5D,0x5B,0x23,0x36,0x44,0x32,0x5E,0x31,0x5D,
+ 0x5B,0x23,0x38,0x44,0x31,0x5D,0x09,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,
+ 0x20,0x32,0x20,0x32,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,
+ 0x23,0x38,0x44,0x31,0x5D,0x29,0x28,0x5B,0x23,0x37,0x5D,0x29,0x2A,0x09,0x09,
+ 0x30,0x20,0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,
+ 0x20,0x31,0x0A,0x5B,0x23,0x33,0x34,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,
+ 0x38,0x44,0x31,0x5D,0x29,0x28,0x5B,0x23,0x38,0x5D,0x29,0x2A,0x09,0x09,0x30,
+ 0x20,0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,
+ 0x31,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x38,0x44,
+ 0x31,0x5D,0x29,0x28,0x5B,0x23,0x31,0x36,0x5D,0x29,0x2A,0x09,0x09,0x30,0x20,
+ 0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,
+ 0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x31,0x36,0x44,
+ 0x31,0x5D,0x29,0x28,0x5B,0x23,0x31,0x36,0x5D,0x29,0x2A,0x09,0x09,0x30,0x20,
+ 0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,
+ 0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x31,0x36,0x44,
+ 0x31,0x5D,0x29,0x28,0x5B,0x23,0x37,0x5D,0x29,0x2A,0x09,0x09,0x30,0x20,0x31,
+ 0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,0x0A,
+ 0x5B,0x23,0x36,0x5E,0x32,0x5D,0x5B,0x23,0x36,0x44,0x32,0x5E,0x31,0x5D,0x5B,
+ 0x23,0x36,0x5E,0x32,0x5D,0x09,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,
+ 0x32,0x20,0x32,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,0x5D,
+ 0x28,0x5B,0x23,0x37,0x44,0x31,0x48,0x30,0x3B,0x21,0x52,0x5D,0x29,0x28,0x5B,
+ 0x23,0x37,0x3B,0x21,0x52,0x5D,0x29,0x2A,0x09,0x30,0x20,0x31,0x20,0x32,0x20,
+ 0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,0x0A,0x5B,0x23,0x36,
+ 0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,0x5D,0x28,0x5B,0x23,0x37,0x44,0x32,0x48,
+ 0x31,0x3B,0x21,0x52,0x5D,0x29,0x28,0x5B,0x23,0x37,0x3B,0x21,0x52,0x5D,0x29,
+ 0x2A,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,
+ 0x20,0x33,0x20,0x31,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,
+ 0x5D,0x28,0x5B,0x23,0x37,0x44,0x33,0x48,0x32,0x3B,0x21,0x52,0x5D,0x29,0x28,
+ 0x5B,0x23,0x37,0x3B,0x21,0x52,0x5D,0x29,0x2A,0x09,0x30,0x20,0x31,0x20,0x32,
+ 0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,0x0A,0x5B,0x23,
+ 0x36,0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,0x5D,0x28,0x5B,0x23,0x31,0x2C,0x23,
+ 0x36,0x5D,0x29,0x28,0x5B,0x23,0x31,0x2C,0x23,0x36,0x5D,0x29,0x5B,0x23,0x37,
+ 0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,0x5D,0x28,0x5B,0x23,0x31,0x5D,0x29,0x5B,
+ 0x23,0x36,0x5D,0x09,0x30,0x20,0x31,0x20,0x31,0x20,0x30,0x20,0x32,0x20,0x31,
+ 0x20,0x30,0x20,0x33,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x31,0x20,0x33,0x20,
+ 0x35,0x20,0x31,0x0A,0x00};
+
+} // namespace OpenBabel
+#endif // OB_BONDTYP_H
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/bondtyp.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,76 @@
+##############################################################################
+#                                                                            #
+#    Open Babel file: bondtyp.txt                                            #
+#                                                                            #
+#  Copyright (c) 2002-2005 by Geoffrey R Hutchison                           #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+# Used by bondtyper.cpp::OBBondTyper (and thus OBMol::PerceiveBondOrders()   #
+#                                                                            #
+# List of functional groups with double, triple (etc.) bond orders           #
+# Pattern       Atom1 Atom2 Bond Order (repeat as needed)                    #
+# * = Any atom (for setting non-multiple bonds)                              #
+#                                                                            #
+# NOTE: These are applied in order, first to last.                           #
+#     So it's generally better to have a long (specifc) SMARTS first.        #
+#     (all bonds must be single bonds to match)                              #
+#                                                                            #
+##############################################################################
+
+# Porphyrin / phthalocyanine (3 patterns for three separate bonding motifs)
+# this one has explicit bonds to all four nitrogens (e.g., metal bond or hydrogens)
+#0  1    2       3   4   5  6  7     8      9  10  11  12 13   14     15 16   17  18 19  20       21 22  23
+*1[#6]([#7D3]2)[#6][#6][#6]2*[#6]([#7D3]3)[#6][#6][#6]3*[#6]([#7D3]4)[#6][#6][#6]4*[#6]([#7D3]5)[#6][#6][#6]51	0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
+
+# this one has explicit bonds to two nitrogens (12 and 14)
+#0  1    2       3   4   5  6  7    8     9  10  11  12 13   14     15 16   17  18 19  20    21 22  23
+*1[#6]([#7D3]2)[#6][#6][#6]2*[#6]([#7]3)[#6][#6][#6]3*[#6]([#7D3]4)[#6][#6][#6]4*[#6]([#7]5)[#6][#6][#6]51	0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
+
+# and this one doesn't have any explicit bonds to the nitrogens
+#0  1    2     3   4   5  6  7    8     9  10  11  12 13   14   15  16  17 18 19   20    21 22  23
+*1[#6]([#7]2)[#6][#6][#6]2*[#6]([#7]3)[#6][#6][#6]3*[#6]([#7]4)[#6][#6][#6]4*[#6]([#7]5)[#6][#6][#6]51	0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
+
+# Azide
+[#7D2][#7D2^1][#7D1]		0 1 2 1 2 2
+# Nitro
+[#8D1][#7D3^2]([#8D1])*		0 1 2 1 2 2 1 3 1
+# Sulphone
+[#16D4]([#8D1])([#8D1])(*)(*)	0 1 2 0 2 2 0 3 1 0 4 1
+# Phosphone
+[#15D4]([#8D1])(*)(*)(*)	0 1 2 0 2 1 0 3 1 0 4 1
+
+# Carboxylic Acid, ester, etc.
+[#6D3^2]([#8D1])([#8])*		0 1 2 0 2 1 0 3 1
+# Carbon dioxide
+[#8D1][#6D2^1][#8D1]		0 1 2 1 2 2
+# Amide C(=O)N
+[#6D3^2]([#8D1])([#7])*		0 1 2 0 2 1 0 3 1
+# Seleninic acid Se(=O)OH
+[#34D3^2]([#8D1])([#8])*		0 1 2 0 2 1 0 3 1
+# Thioacid / Thioester C(=O)S
+[#6D3^2]([#8D1])([#16])*		0 1 2 0 2 1 0 3 1
+# dithioacid / dithioester C(=S)S
+[#6D3^2]([#16D1])([#16])*		0 1 2 0 2 1 0 3 1
+# thioamide C(=S)N
+[#6D3^2]([#16D1])([#7])*		0 1 2 0 2 1 0 3 1
+
+# allene C=C=C
+# (this is problematic -- need to make sure the center carbon is sp)
+[#6^2][#6D2^1][#6^2]		0 1 2 1 2 2
+
+# guanidinium and amidine -C(=NH)NH2 without hydrogens
+[#6D3^2;!R]([#7D1H0;!R])([#7;!R])*	0 1 2 0 2 1 0 3 1
+# and also with hydrogens
+# (this can normally be figured out, but is needed to avoid matching the next SMARTS)
+[#6D3^2;!R]([#7D2H1;!R])([#7;!R])*	0 1 2 0 2 1 0 3 1
+# and also with more hydrogens than normal (protonated)
+[#6D3^2;!R]([#7D3H2;!R])([#7;!R])*	0 1 2 0 2 1 0 3 1
+
+# Schiff base, protonated
+[#6D3^2;!R]([#1,#6])([#1,#6])[#7D3^2;!R]([#1])[#6]	0 1 1 0 2 1 0 3 2 3 4 1 3 5 1
+
+### other potential functional groups that may (or may not) be useful to add
+# imidines ( N=C/N\C=N
+# sulfoxides
+# heme / porphyrin
+# phthalocyanine
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/cmake_install.cmake	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,82 @@
+# Install script for directory: /share/opt/x86_64_sl5/openbabel-2.3.0/build/data
+
+# Set the install prefix
+IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+  SET(CMAKE_INSTALL_PREFIX "/share/opt/x86_64_sl5/openbabel-2.3.0")
+ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+  IF(BUILD_TYPE)
+    STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+           CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+  ELSE(BUILD_TYPE)
+    SET(CMAKE_INSTALL_CONFIG_NAME "Release")
+  ENDIF(BUILD_TYPE)
+  MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+
+# Set the component getting installed.
+IF(NOT CMAKE_INSTALL_COMPONENT)
+  IF(COMPONENT)
+    MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
+    SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+  ELSE(COMPONENT)
+    SET(CMAKE_INSTALL_COMPONENT)
+  ENDIF(COMPONENT)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT)
+
+# Install shared libraries without execute permission?
+IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+  SET(CMAKE_INSTALL_SO_NO_EXE "0")
+ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/openbabel/2.3.0" TYPE FILE FILES
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/aromatic.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/atomtyp.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/bondtyp.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/element.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/fragments.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/gaff.dat"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/gaff.prm"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/ghemical.prm"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/isotope-small.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/isotope.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/logp.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/MACCS.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmff94.ff"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmff94s.ff"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffang.par"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffbndk.par"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffbond.par"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffchg.par"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffdef.par"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffdfsb.par"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffoop.par"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffpbci.par"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffprop.par"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffstbn.par"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmfftor.par"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffvdw.par"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffs_oop.par"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffs_tor.par"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mr.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/patterns.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/phmodel.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/plugindefines.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/psa.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/qeq.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/resdata.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/ringtyp.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/SMARTS_InteLigand.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/space-groups.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/superatom.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/svgformat.script"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/torlib.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/types.txt"
+    "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/UFF.prm"
+    )
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/element.h	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,616 @@
+/***************************************************************
+This file is part of the Open Babel project.
+This is copyright under the GNU General Public License (GPL)
+For more information, see <http://openbabel.org/>
+
+This file contains a binary representation of data tables
+ used by Open Babel. It is used as a fallback if the textual
+ data table is not found at runtime. It is not a normal header.
+***************************************************************/
+
+
+#ifndef OB_ELEMENT_H
+#define OB_ELEMENT_H
+
+namespace OpenBabel
+{
+static const char ElementData[] = {
+ 0x30,0x09,0x58,0x78,0x09,0x30,0x2E,0x30,0x30,0x09,0x30,0x2E,0x30,0x30,0x09,
+ 0x30,0x2E,0x30,0x30,0x09,0x30,0x2E,0x30,0x30,0x09,0x30,0x09,0x30,0x09,0x30,
+ 0x2E,0x30,0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x2E,0x30,0x37,0x09,0x30,0x2E,
+ 0x35,0x30,0x09,0x30,0x2E,0x37,0x30,0x09,0x44,0x75,0x6D,0x6D,0x79,0x0A,0x31,
+ 0x09,0x48,0x09,0x32,0x2E,0x32,0x30,0x09,0x30,0x2E,0x33,0x31,0x09,0x30,0x2E,
+ 0x33,0x31,0x09,0x31,0x2E,0x31,0x30,0x09,0x31,0x09,0x31,0x2E,0x30,0x30,0x37,
+ 0x39,0x34,0x09,0x32,0x2E,0x32,0x30,0x09,0x31,0x33,0x2E,0x35,0x39,0x38,0x34,
+ 0x09,0x30,0x2E,0x37,0x35,0x34,0x32,0x30,0x33,0x37,0x35,0x09,0x30,0x2E,0x37,
+ 0x35,0x09,0x30,0x2E,0x37,0x35,0x09,0x30,0x2E,0x37,0x35,0x09,0x48,0x79,0x64,
+ 0x72,0x6F,0x67,0x65,0x6E,0x0A,0x32,0x09,0x48,0x65,0x09,0x30,0x2E,0x30,0x30,
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+ 0x09,0x30,0x09,0x34,0x2E,0x30,0x30,0x32,0x36,0x30,0x32,0x09,0x30,0x2E,0x30,
+ 0x30,0x09,0x32,0x34,0x2E,0x35,0x38,0x37,0x34,0x09,0x30,0x09,0x30,0x2E,0x38,
+ 0x35,0x09,0x31,0x2E,0x30,0x30,0x09,0x31,0x2E,0x30,0x30,0x09,0x48,0x65,0x6C,
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+ 0x2E,0x32,0x38,0x09,0x31,0x2E,0x32,0x38,0x09,0x31,0x2E,0x38,0x31,0x09,0x31,
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+ 0x39,0x31,0x37,0x09,0x30,0x2E,0x36,0x31,0x38,0x30,0x34,0x39,0x09,0x30,0x2E,
+ 0x38,0x30,0x09,0x30,0x2E,0x35,0x30,0x09,0x31,0x2E,0x30,0x30,0x09,0x4C,0x69,
+ 0x74,0x68,0x69,0x75,0x6D,0x0A,0x34,0x09,0x42,0x65,0x09,0x31,0x2E,0x34,0x37,
+ 0x09,0x30,0x2E,0x39,0x36,0x09,0x30,0x2E,0x39,0x36,0x09,0x31,0x2E,0x35,0x33,
+ 0x09,0x32,0x09,0x39,0x2E,0x30,0x31,0x32,0x31,0x38,0x32,0x09,0x31,0x2E,0x35,
+ 0x37,0x09,0x39,0x2E,0x33,0x32,0x32,0x37,0x09,0x30,0x09,0x30,0x2E,0x37,0x36,
+ 0x09,0x31,0x2E,0x30,0x30,0x09,0x30,0x2E,0x30,0x30,0x09,0x42,0x65,0x72,0x79,
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+ 0x34,0x09,0x31,0x30,0x2E,0x38,0x31,0x31,0x09,0x32,0x2E,0x30,0x34,0x09,0x38,
+ 0x2E,0x32,0x39,0x38,0x09,0x30,0x2E,0x32,0x37,0x39,0x37,0x32,0x33,0x09,0x31,
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+ 0x2E,0x30,0x30,0x09,0x36,0x09,0x32,0x39,0x34,0x09,0x30,0x2E,0x30,0x30,0x09,
+ 0x30,0x09,0x30,0x09,0x30,0x2E,0x39,0x39,0x09,0x30,0x2E,0x30,0x30,0x09,0x30,
+ 0x2E,0x30,0x36,0x09,0x55,0x6E,0x75,0x6E,0x6F,0x63,0x74,0x69,0x75,0x6D,0x0A,
+0x00};
+
+} // namespace OpenBabel
+#endif // OB_ELEMENT_H
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/element.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,153 @@
+##############################################################################
+#                                                                            #
+#	                Open Babel file: element.txt                         #
+#                                                                            #
+#  Some portions Copyright (c) 2001-2009 Geoffrey R. Hutchison               #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+#  Created from the Blue Obelisk Cheminformatics Data Repository             #
+#  Direct Source: http://www.blueobelisk.org/                                #
+#       http://www.blueobelisk.org/repos/blueobelisk/elements.xml            #
+#  (includes furhter bibliographic citation information)                     #
+#                                                                            #
+#  Allred and Rochow Electronegativity from:                                 #
+#  http://www.hull.ac.uk/chemistry/electroneg.php?type=Allred-Rochow         #
+#                                                                            #
+#  Columns represent:  (used by data.cpp:OBElementTable and OBElement)       #
+#   - atomic number (used as an index to the vector as well)                 #
+#   - elemental symbol							     #
+#   - Allred and Rochow electronegativity  0.0 if unknown		     #
+#   - covalent radii (in Angstrom)         1.6 if unknown		     #
+#       from http://dx.doi.org/10.1039/b801115j                              #
+#   - "bond order" radii -- ignored, but included for compatibility          #
+#   - van der Waals radii (in Angstrom)	   2.0 if unknown		     #
+#       from http://dx.doi.org/10.1021/jp8111556                             #
+#   - maximum bond valence		   6 if unknown			     #
+#   - IUPAC recommended atomic masses (in amu)				     #
+#   - Pauling electronegativity		   0.0 if unknown		     #
+#   - ionization potential (in eV)         0.0 if unknown                    #
+#   - electron affinity (in eV)            0.0 if unknown                    #
+#   - RGB values (defaults for visualization)				     #
+#   - element name (in English)						     #
+#                                                                            #
+##############################################################################
+#Num	Symb	ARENeg	RCov	RBO	RVdW	MaxBnd	Mass	ElNeg.	Ionization	ElAffinity	Red	Green	Blue	Name
+0	Xx	0.00	0.00	0.00	0.00	0	0	0.00	0	0	0.07	0.50	0.70	Dummy
+1	H	2.20	0.31	0.31	1.10	1	1.00794	2.20	13.5984	0.75420375	0.75	0.75	0.75	Hydrogen
+2	He	0.00	0.28	0.28	1.40	0	4.002602	0.00	24.5874	0	0.85	1.00	1.00	Helium
+3	Li	0.97	1.28	1.28	1.81	1	6.941	0.98	5.3917	0.618049	0.80	0.50	1.00	Lithium
+4	Be	1.47	0.96	0.96	1.53	2	9.012182	1.57	9.3227	0	0.76	1.00	0.00	Beryllium
+5	B	2.01	0.84	0.84	1.92	4	10.811	2.04	8.298	0.279723	1.00	0.71	0.71	Boron
+6	C	2.50	0.76	0.76	1.70	4	12.0107	2.55	11.2603	1.262118	0.40	0.40	0.40	Carbon
+7	N	3.07	0.71	0.71	1.55	4	14.0067	3.04	14.5341	-0.07	0.05	0.05	1.00	Nitrogen
+8	O	3.50	0.66	0.66	1.52	2	15.9994	3.44	13.6181	1.461112	1.00	0.05	0.05	Oxygen
+9	F	4.10	0.57	0.57	1.47	1	18.9984032	3.98	17.4228	3.4011887	0.50	0.70	1.00	Fluorine
+10	Ne	0.00	0.58	0.58	1.54	0	20.1797	0.00	21.5645	0	0.70	0.89	0.96	Neon
+11	Na	1.01	1.66	1.66	2.27	1	22.98977	0.93	5.1391	0.547926	0.67	0.36	0.95	Sodium
+12	Mg	1.23	1.41	1.41	1.73	2	24.3050	1.31	7.6462	0	0.54	1.00	0.00	Magnesium
+13	Al	1.47	1.21	1.21	1.84	6	26.981538	1.61	5.9858	0.43283	0.75	0.65	0.65	Aluminium
+14	Si	1.74	1.11	1.11	2.10	6	28.0855	1.90	8.1517	1.389521	0.50	0.60	0.60	Silicon
+15	P	2.06	1.07	1.07	1.80	6	30.973761	2.19	10.4867	0.7465	1.00	0.50	0.00	Phosphorus
+16	S	2.44	1.05	1.05	1.80	6	32.065	2.58	10.36	2.0771029	0.70	0.70	0.00	Sulfur
+17	Cl	2.83	1.02	1.02	1.75	1	35.453	3.16	12.9676	3.612724	0.12	0.94	0.12	Chlorine
+18	Ar	0.00	1.06	1.06	1.88	0	39.948	0.00	15.7596	0	0.50	0.82	0.89	Argon
+19	K	0.91	2.03	2.03	2.75	1	39.0983	0.82	4.3407	0.501459	0.56	0.25	0.83	Potassium
+20	Ca	1.04	1.76	1.76	2.31	2	40.078	1.00	6.1132	0.02455	0.24	1.00	0.00	Calcium
+21	Sc	1.20	1.70	1.70	2.30	6	44.95591	1.36	6.5615	0.188	0.90	0.90	0.90	Scandium
+22	Ti	1.32	1.60	1.60	2.15	6	47.867	1.54	6.8281	0.084	0.75	0.76	0.78	Titanium
+23	V	1.45	1.53	1.53	2.05	6	50.9415	1.63	6.7462	0.525	0.65	0.65	0.67	Vanadium
+24	Cr	1.56	1.39	1.39	2.05	6	51.9961	1.66	6.7665	0.67584	0.54	0.60	0.78	Chromium
+25	Mn	1.60	1.39	1.39	2.05	8	54.938049	1.55	7.434	0	0.61	0.48	0.78	Manganese
+26	Fe	1.64	1.32	1.32	2.05	6	55.845	1.83	7.9024	0.151	0.88	0.40	0.20	Iron
+27	Co	1.70	1.26	1.26	2.00	6	58.9332	1.88	7.881	0.6633	0.94	0.56	0.63	Cobalt
+28	Ni	1.75	1.24	1.24	2.00	6	58.6934	1.91	7.6398	1.15716	0.31	0.82	0.31	Nickel
+29	Cu	1.75	1.32	1.32	2.00	6	63.546	1.90	7.7264	1.23578	0.78	0.50	0.20	Copper
+30	Zn	1.66	1.22	1.22	2.10	6	65.38	1.65	9.3942	0	0.49	0.50	0.69	Zinc
+31	Ga	1.82	1.22	1.22	1.87	3	69.723	1.81	5.9993	0.41	0.76	0.56	0.56	Gallium
+32	Ge	2.02	1.20	1.20	2.11	4	72.64	2.01	7.8994	1.232712	0.40	0.56	0.56	Germanium
+33	As	2.20	1.19	1.19	1.85	3	74.92160	2.18	9.7886	0.814	0.74	0.50	0.89	Arsenic
+34	Se	2.48	1.20	1.20	1.90	2	78.96	2.55	9.7524	2.02067	1.00	0.63	0.00	Selenium
+35	Br	2.74	1.20	1.20	1.83	1	79.904	2.96	11.8138	3.363588	0.65	0.16	0.16	Bromine
+36	Kr	0.00	1.16	1.16	2.02	0	83.798	3.00	13.9996	0	0.36	0.72	0.82	Krypton
+37	Rb	0.89	2.20	2.20	3.03	1	85.4678	0.82	4.1771	0.485916	0.44	0.18	0.69	Rubidium
+38	Sr	0.99	1.95	1.95	2.49	2	87.62	0.95	5.6949	0.05206	0.00	1.00	0.00	Strontium
+39	Y	1.11	1.90	1.90	2.40	6	88.90585	1.22	6.2173	0.307	0.58	1.00	1.00	Yttrium
+40	Zr	1.22	1.75	1.75	2.30	6	91.224	1.33	6.6339	0.426	0.58	0.88	0.88	Zirconium
+41	Nb	1.23	1.64	1.64	2.15	6	92.90638	1.60	6.7589	0.893	0.45	0.76	0.79	Niobium
+42	Mo	1.30	1.54	1.54	2.10	6	95.96	2.16	7.0924	0.7472	0.33	0.71	0.71	Molybdenum
+43	Tc	1.36	1.47	1.47	2.05	6	98	1.90	7.28	0.55	0.23	0.62	0.62	Technetium
+44	Ru	1.42	1.46	1.46	2.05	6	101.07	2.20	7.3605	1.04638	0.14	0.56	0.56	Ruthenium
+45	Rh	1.45	1.42	1.42	2.00	6	102.90550	2.28	7.4589	1.14289	0.04	0.49	0.55	Rhodium
+46	Pd	1.35	1.39	1.39	2.05	6	106.42	2.20	8.3369	0.56214	0.00	0.41	0.52	Palladium
+47	Ag	1.42	1.45	1.45	2.10	6	107.8682	1.93	7.5762	1.30447	0.88	0.88	1.00	Silver
+48	Cd	1.46	1.44	1.44	2.20	6	112.411	1.69	8.9938	0	1.00	0.85	0.56	Cadmium
+49	In	1.49	1.42	1.42	2.20	3	114.818	1.78	5.7864	0.404	0.65	0.46	0.45	Indium
+50	Sn	1.72	1.39	1.39	1.93	4	118.701	1.96	7.3439	1.112066	0.40	0.50	0.50	Tin
+51	Sb	1.82	1.39	1.39	2.17	3	121.760	2.05	8.6084	1.047401	0.62	0.39	0.71	Antimony
+52	Te	2.01	1.38	1.38	2.06	2	127.60	2.10	9.0096	1.970875	0.83	0.48	0.00	Tellurium
+53	I	2.21	1.39	1.39	1.98	1	126.90447	2.66	10.4513	3.059038	0.58	0.00	0.58	Iodine
+54	Xe	0.00	1.40	1.40	2.16	0	131.293	2.60	12.1298	0	0.26	0.62	0.69	Xenon
+55	Cs	0.86	2.44	2.44	3.43	1	132.90545	0.79	3.8939	0.471626	0.34	0.09	0.56	Caesium
+56	Ba	0.97	2.15	2.15	2.68	2	137.327	0.89	5.2117	0.14462	0.00	0.79	0.00	Barium
+57	La	1.08	2.07	2.07	2.50	12	138.9055	1.10	5.5769	0.47	0.44	0.83	1.00	Lanthanum
+58	Ce	0.00	2.04	2.04	2.48	6	140.116	1.12	5.5387	0.5	1.00	1.00	0.78	Cerium
+59	Pr	0.00	2.03	2.03	2.47	6	140.90765	1.13	5.473	0.5	0.85	1.00	0.78	Praseodymium
+60	Nd	0.00	2.01	2.01	2.45	6	144.24	1.14	5.525	0.5	0.78	1.00	0.78	Neodymium
+61	Pm	0.00	1.99	1.99	2.43	6	145	0.00	5.582	0.5	0.64	1.00	0.78	Promethium
+62	Sm	0.00	1.98	1.98	2.42	6	150.36	1.17	5.6437	0.5	0.56	1.00	0.78	Samarium
+63	Eu	0.00	1.98	1.98	2.40	6	151.964	0.00	5.6704	0.5	0.38	1.00	0.78	Europium
+64	Gd	0.00	1.96	1.96	2.38	6	157.25	1.20	6.1498	0.5	0.27	1.00	0.78	Gadolinium
+65	Tb	0.00	1.94	1.94	2.37	6	158.92534	0.00	5.8638	0.5	0.19	1.00	0.78	Terbium
+66	Dy	0.00	1.92	1.92	2.35	6	162.500	1.22	5.9389	0.5	0.12	1.00	0.78	Dysprosium
+67	Ho	0.00	1.92	1.92	2.33	6	164.93032	1.23	6.0215	0.5	0.00	1.00	0.61	Holmium
+68	Er	0.00	1.89	1.89	2.32	6	167.259	1.24	6.1077	0.5	0.00	0.90	0.46	Erbium
+69	Tm	0.00	1.90	1.90	2.30	6	168.93421	1.25	6.1843	0.5	0.00	0.83	0.32	Thulium
+70	Yb	0.00	1.87	1.87	2.28	6	173.054	0.00	6.2542	0.5	0.00	0.75	0.22	Ytterbium
+71	Lu	0.00	1.87	1.87	2.27	6	174.9668	1.27	5.4259	0.5	0.00	0.67	0.14	Lutetium
+72	Hf	1.23	1.75	1.75	2.25	6	178.49	1.30	6.8251	0	0.30	0.76	1.00	Hafnium
+73	Ta	1.33	1.70	1.70	2.20	6	180.9479	1.50	7.5496	0.322	0.30	0.65	1.00	Tantalum
+74	W	1.40	1.62	1.62	2.10	6	183.84	2.36	7.864	0.815	0.13	0.58	0.84	Tungsten
+75	Re	1.46	1.51	1.51	2.05	6	186.207	1.90	7.8335	0.15	0.15	0.49	0.67	Rhenium
+76	Os	1.52	1.44	1.44	2.00	6	190.23	2.20	8.4382	1.0778	0.15	0.40	0.59	Osmium
+77	Ir	1.55	1.41	1.41	2.00	6	192.217	2.20	8.967	1.56436	0.09	0.33	0.53	Iridium
+78	Pt	1.44	1.36	1.36	2.05	6	195.078	2.28	8.9588	2.1251	0.96	0.93	0.82	Platinum
+79	Au	1.42	1.36	1.36	2.10	6	196.96655	2.54	9.2255	2.30861	0.80	0.82	0.12	Gold
+80	Hg	1.44	1.32	1.32	2.05	6	200.59	2.00	10.4375	0	0.71	0.71	0.76	Mercury
+81	Tl	1.44	1.45	1.45	1.96	3	204.3833	1.62	6.1082	0.377	0.65	0.33	0.30	Thallium
+82	Pb	1.55	1.46	1.46	2.02	4	207.2	2.33	7.4167	0.364	0.34	0.35	0.38	Lead
+83	Bi	1.67	1.48	1.48	2.07	3	208.98040	2.02	7.2855	0.942363	0.62	0.31	0.71	Bismuth
+84	Po	1.76	1.40	1.40	1.97	2	209	2.00	8.414	1.9	0.67	0.36	0.00	Polonium
+85	At	1.90	1.50	1.50	2.02	1	210	2.20	0	2.8	0.46	0.31	0.27	Astatine
+86	Rn	0.00	1.50	1.50	2.20	0	222	0.00	10.7485	0	0.26	0.51	0.59	Radon
+87	Fr	0.00	2.60	2.60	3.48	1	223	0.70	4.0727	0	0.26	0.00	0.40	Francium
+88	Ra	0.00	2.21	2.21	2.83	2	226	0.90	5.2784	0	0.00	0.49	0.00	Radium
+89	Ac	0.00	2.15	2.15	2.00	6	227	1.10	5.17	0	0.44	0.67	0.98	Actinium
+90	Th	0.00	2.06	2.06	2.40	6	232.0381	1.30	6.3067	0	0.00	0.73	1.00	Thorium
+91	Pa	0.00	2.00	2.00	2.00	6	231.03588	1.50	5.89	0	0.00	0.63	1.00	Protactinium
+92	U	0.00	1.96	1.96	2.30	6	238.02891	1.38	6.1941	0	0.00	0.56	1.00	Uranium
+93	Np	0.00	1.90	1.90	2.00	6	237	1.36	6.2657	0	0.00	0.50	1.00	Neptunium
+94	Pu	0.00	1.87	1.87	2.00	6	244	1.28	6.026	0	0.00	0.42	1.00	Plutonium
+95	Am	0.00	1.80	1.80	2.00	6	243	1.30	5.9738	0	0.33	0.36	0.95	Americium
+96	Cm	0.00	1.69	1.69	2.00	6	247	1.30	5.9914	0	0.47	0.36	0.89	Curium
+97	Bk	0.00	1.60	1.60	2.00	6	247	1.30	6.1979	0	0.54	0.31	0.89	Berkelium
+98	Cf	0.00	1.60	1.60	2.00	6	251	1.30	6.2817	0	0.63	0.21	0.83	Californium
+99	Es	0.00	1.60	1.60	2.00	6	252	1.30	6.42	0	0.70	0.12	0.83	Einsteinium
+100	Fm	0.00	1.60	1.60	2.00	6	257	1.30	6.5	0	0.70	0.12	0.73	Fermium
+101	Md	0.00	1.60	1.60	2.00	6	258	1.30	6.58	0	0.70	0.05	0.65	Mendelevium
+102	No	0.00	1.60	1.60	2.00	6	259	1.30	6.65	0	0.74	0.05	0.53	Nobelium
+103	Lr	0.00	1.60	1.60	2.00	6	262	0.00	4.9	0	0.78	0.00	0.40	Lawrencium
+104	Rf	0.00	1.60	1.60	2.00	6	267	0.00	6	0	0.80	0.00	0.35	Rutherfordium
+105	Db	0.00	1.60	1.60	2.00	6	268	0.00	0	0	0.82	0.00	0.31	Dubnium
+106	Sg	0.00	1.60	1.60	2.00	6	271	0.00	0	0	0.85	0.00	0.27	Seaborgium
+107	Bh	0.00	1.60	1.60	2.00	6	272	0.00	0	0	0.88	0.00	0.22	Bohrium
+108	Hs	0.00	1.60	1.60	2.00	6	270	0.00	0	0	0.90	0.00	0.18	Hassium
+109	Mt	0.00	1.60	1.60	2.00	6	268	0.00	0	0	0.92	0.00	0.15	Meitnerium
+110	Ds	0.00	1.60	1.60	2.00	6	281	0.00	0	0	0.93	0.00	0.14	Darmstadtium
+111	Rg	0.00	1.60	1.60	2.00	6	280	0.00	0	0	0.94	0.00	0.13	Roentgenium
+112	Cn	0.00	1.60	1.60	2.00	6	285	0.00	0	0	0.95	0.00	0.12	Copernicium
+113	Uut	0.00	1.60	1.60	2.00	6	284	0.00	0	0	0.96	0.00	0.11	Ununtrium
+114	Uuq	0.00	1.60	1.60	2.00	6	289	0.00	0	0	0.97	0.00	0.10	Ununquadium
+115	Uup	0.00	1.60	1.60	2.00	6	288	0.00	0	0	0.98	0.00	0.09	Ununpentium
+116	Uuh	0.00	1.60	1.60	2.00	6	293	0.00	0	0	0.99	0.00	0.08	Ununhexium
+117	Uuh	0.00	1.60	1.60	2.00	6	294	0.00	0	0	0.99	0.00	0.07	Ununseptium
+118	Uuh	0.00	1.60	1.60	2.00	6	294	0.00	0	0	0.99	0.00	0.06	Ununoctium
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/fragments.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,33785 @@
+#
+#    Open Babel file: fragments.txt
+#
+#  Copyright (c) 2007-2008 by Geoffrey R Hutchison
+#  Part of the Open Babel package, under the GNU General Public License (GPL)
+#
+# Fragments for OBBuilder coordinate generation 
+# These consist of a generic SMARTS pattern
+# followed by the 3D coordinates of all heavy atoms
+# 
+# Fragments are ordered by length of SMARTS pattern
+#  (i.e., most complicated will match first)
+#
+# This file contains ~1000 of the most common ring fragments
+# from analysis over the NCI database and ZINC
+#
+# NCI: http://cactus.nci.nih.gov/ncidb2/download.html
+# ZINC: http://zinc.docking.org/
+#
+A1AA[A@@]2(AA1)A[A@H]1[A@H](A[A@@H]3[A@@H]1AA[A@H]1[A@@H]3AA[A@H]3AAAA[A@H]13)A2
+ -6.211 -1.460 -0.030
+ -5.943 -0.593  1.206
+ -5.091  0.648  0.864
+ -3.994  0.300 -0.169
+ -4.538 -0.250 -1.367
+ -5.898 -0.674 -1.321
+ -3.111  1.535 -0.461
+ -1.792  1.261  0.318
+ -2.126  0.038  1.158
+ -0.839 -0.820  1.272
+  0.215  0.187  0.788
+ -0.505  0.862 -0.397
+  0.361  2.038 -0.842
+  1.787  1.544 -1.206
+  2.492  0.838 -0.023
+  1.643 -0.352  0.504
+  1.731 -1.601 -0.389
+  3.140 -1.884 -0.874
+  4.220 -1.079 -0.124
+  5.652 -1.521 -0.524
+  6.711 -0.431 -0.189
+  6.283  0.453  0.974
+  4.934  1.171  0.717
+  3.983  0.435 -0.283
+ -3.106 -0.636  0.409
+A1A=A2AA3AA[A@@]45[A@@H]3A[A@@H]2[A@H]2[A@@H](A1)AAA(a1aaaaa51)[A@H]42
+ -3.888  0.914  0.115
+ -3.459 -0.469  0.519
+ -2.450 -1.056 -0.087
+ -1.962 -2.361  0.428
+ -0.673 -2.830 -0.062
+  0.191 -3.047  1.144
+  0.602 -1.615  1.554
+  0.598 -0.812  0.219
+  0.084 -1.793 -0.806
+ -0.800 -1.233 -1.901
+ -1.848 -0.330 -1.263
+ -1.065  0.868 -0.767
+ -1.865  2.101 -0.431
+ -2.873  1.838  0.542
+ -0.974  3.251  0.020
+  0.403  2.844  0.453
+  0.828  1.570  0.379
+  2.076  1.022  0.182
+  3.313  1.677  0.144
+  4.435  0.913 -0.126
+  4.355 -0.449 -0.358
+  3.133 -1.117 -0.307
+  2.013 -0.363 -0.016
+ -0.183  0.472  0.416
+A1AA[A@@H]2[A@H](A1)AA[A@H]1[A@@H]2AA[A@@H]2[A@H]1AA[A@@H]1AAA[A@@H]21
+ -3.053  1.785  1.205
+ -3.252  1.888 -0.289
+ -3.572  0.529 -0.878
+ -2.734 -0.643 -0.356
+ -2.599 -0.629  1.153
+ -2.102  0.714  1.691
+ -1.649 -1.724  1.640
+ -0.276 -1.515  1.004
+ -0.364 -1.639 -0.513
+ -1.409 -0.720 -1.105
+ -0.879  0.699 -1.318
+  0.352  0.642 -2.224
+  1.470 -0.096 -1.492
+  1.030 -1.511 -1.133
+  2.052 -2.232 -0.252
+  2.597 -1.407  0.910
+  3.123 -0.085  0.382
+  3.542  0.917  1.473
+  3.414  2.288  0.758
+  2.384  2.093 -0.385
+  1.927  0.647 -0.270
+A1AA[A@@H]2[A@H](A1)AA[A@H]1[A@@H]2AA[A@@H]2[A@H]1AA[A@H]1AAA[A@@H]21
+  3.192  1.390 -1.579
+  3.326  1.929 -0.176
+  3.606  0.809  0.807
+  2.782 -0.467  0.617
+  2.739 -0.906 -0.833
+  2.271  0.207 -1.774
+  1.821 -2.114 -1.014
+  0.409 -1.749 -0.560
+  0.383 -1.369  0.915
+  1.409 -0.313  1.261
+  0.898  1.103  1.000
+ -0.408  1.331  1.764
+ -1.489  0.408  1.193
+ -1.036 -1.032  1.362
+ -2.064 -1.979  0.744
+ -2.348 -1.673 -0.709
+ -2.655 -0.233 -0.998
+ -4.130  0.114 -0.711
+ -4.114  1.655 -0.837
+ -2.743  2.073 -0.254
+ -1.849  0.815 -0.219
+A1AA[A@@H]2AA[A@@H]3[A@@H]4AA[A@@H]5AAAA[A@H]5[A@H]4AA[A@H]3[A@H]2A1
+ -4.909  1.704  0.237
+ -5.602  0.484 -0.347
+ -4.965 -0.840  0.089
+ -3.459 -0.788 -0.071
+ -2.722 -2.033  0.391
+ -1.349 -2.083 -0.288
+ -0.780 -0.715 -0.608
+  0.775 -0.747 -0.577
+  1.278 -2.064 -0.018
+  2.758 -2.058  0.366
+  3.462 -0.795 -0.085
+  4.973 -0.838  0.090
+  5.614  0.482 -0.346
+  4.916  1.704  0.231
+  3.424  1.697 -0.102
+  2.786  0.438  0.476
+  1.277  0.412  0.258
+  0.759  1.750 -0.252
+ -0.771  1.761 -0.165
+ -1.271  0.391  0.297
+ -2.784  0.440  0.505
+ -3.412  1.699 -0.083
+A1AA[A@H]2[A@H](A1)AA[A@@H]1[A@@H]2AA[A@H]2[A@H]1AA[A@H]1AAA[A@H]21
+  5.502  0.333  0.526
+  4.863  1.616  0.014
+  3.371  1.639  0.334
+  2.674  0.469 -0.391
+  3.298 -0.826  0.113
+  4.802 -0.921  0.003
+  2.574 -2.029 -0.485
+  1.135 -2.027  0.055
+  0.416 -0.753 -0.389
+  1.198  0.486  0.015
+  0.496  1.755 -0.457
+ -0.920  1.813  0.128
+ -1.706  0.560 -0.258
+ -0.984 -0.695  0.249
+ -1.764 -1.968 -0.064
+ -3.223 -1.892  0.410
+ -3.870 -0.667 -0.197
+ -5.292 -0.350  0.299
+ -5.448  1.140 -0.118
+ -4.016  1.738 -0.098
+ -3.105  0.582  0.309
+A1AA[A@H]2[A@H](A1)AA[A@@H]1[A@@H]2AA=A2[A@H]1AA[A@H]1AAAA[A@@H]21
+  5.645 -0.390 -0.794
+  5.115 -1.554  0.033
+  3.600 -1.656 -0.115
+  2.939 -0.380  0.436
+  3.480  0.820 -0.332
+  4.983  0.935 -0.414
+  2.809  2.093  0.179
+  1.325  2.024 -0.215
+  0.652  0.802  0.394
+  1.435 -0.480  0.166
+  0.807 -1.626  0.955
+ -0.683 -1.631  0.780
+ -1.380 -0.638  0.291
+ -0.760  0.634 -0.188
+ -1.604  1.865  0.021
+ -3.097  1.660  0.069
+ -3.552  0.423  0.806
+ -5.072  0.275  0.757
+ -5.544 -0.006 -0.665
+ -4.866 -1.247 -1.241
+ -3.347 -1.092 -1.175
+ -2.884 -0.829  0.253
+A1AA[A@@H]2[A@@H](A1)AA[A@@H]1[A@H]2AA=A2[A@H]1AA[A@H]1AAAA[A@H]21
+ -5.398 -0.429  1.255
+ -5.113 -1.652  0.383
+ -3.630 -1.819  0.016
+ -2.806 -0.490  0.112
+ -3.761  0.649 -0.363
+ -4.959  0.921  0.594
+ -3.018  1.920 -0.851
+ -1.604  2.032 -0.312
+ -0.688  0.829 -0.721
+ -1.534 -0.493 -0.779
+ -0.657 -1.725 -0.700
+  0.777 -1.612 -0.423
+  1.401 -0.501  0.017
+  0.564  0.771  0.239
+  1.386  2.083  0.074
+  2.809  2.010  0.601
+  3.584  0.843 -0.046
+  5.035  0.868  0.469
+  5.838 -0.343 -0.048
+  5.182 -1.682  0.293
+  3.707 -1.696 -0.163
+  2.885 -0.484  0.352
+a1aa2A[A@H]3a4[aH]a5aaaaa5a4A[A@H]4[A@@H]5[AH2+]AA[A@]34a2a(a1)A5
+  2.429 -2.657  1.644
+  1.722 -2.948  0.480
+  1.365 -1.867 -0.334
+  0.635 -1.800 -1.468
+  0.223 -0.426 -1.699
+ -1.117 -0.217 -1.044
+ -2.313 -0.750 -1.456
+ -3.314 -0.342 -0.623
+ -4.684 -0.600 -0.611
+ -5.425 -0.010  0.400
+ -4.846  0.800  1.363
+ -3.500  1.071  1.376
+ -2.728  0.488  0.366
+ -1.315  0.538  0.056
+ -0.217  1.272  0.782
+  0.884  1.622 -0.228
+  2.111  2.119  0.551
+  3.179  2.471 -0.409
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+  1.086  1.248  0.370
+  1.901 -0.001  0.031
+  1.084 -1.250  0.370
+  0.011 -1.463 -0.700
+ -1.373 -1.248 -0.085
+[a-]1aaaa1
+ -1.113 -0.229 -0.001
+ -0.569  0.995  0.002
+  0.735  0.814 -0.002
+  1.015 -0.439  0.002
+ -0.066 -1.141 -0.001
+A1AAA[A+]1
+  0.305 -1.374  0.274
+ -1.009 -0.764 -0.288
+ -1.077  0.730  0.029
+  0.305  1.408  0.096
+  1.475  0.002 -0.112
+[Aa]1AAAA1
+  1.767  0.001  0.008
+  0.137  1.335 -0.168
+ -1.011  0.703  0.349
+ -1.050 -0.700 -0.259
+  0.155 -1.338  0.072
+A1A=AAA=A1
+  1.336 -0.230  0.121
+  0.900  1.052 -0.060
+ -0.418  1.330 -0.066
+ -1.444  0.252  0.129
+ -0.838 -1.108 -0.064
+  0.463 -1.294 -0.062
+a1aaa[a+]1
+ -0.489  0.963 -0.002
+ -1.091 -0.089  0.001
+ -0.220 -1.113  0.001
+  1.016 -0.545 -0.002
+  0.784  0.784  0.002
+A1AA=AA=A1
+  0.278 -1.309  0.000
+ -1.004 -0.899  0.002
+ -1.301  0.431 -0.003
+ -0.294  1.335  0.002
+  1.039  0.873 -0.000
+  1.280 -0.431 -0.001
+A1=AA=AAA1
+ -1.351 -0.236 -0.002
+ -0.915  1.019  0.003
+  0.536  1.245 -0.002
+  1.337  0.201 -0.000
+  0.858 -0.993  0.001
+ -0.463 -1.234  0.000
+A1AAA=AAA1
+  0.074  1.446 -0.516
+  0.925  0.916  0.601
+  1.387 -0.337  0.584
+  0.929 -1.251 -0.368
+ -0.386 -1.428 -0.540
+ -1.518 -0.517  0.461
+ -1.413  1.172 -0.222
+[aH]1aaaa1
+ -1.144  0.000 -0.002
+ -0.328 -1.082  0.003
+  0.901 -0.643 -0.002
+  0.901  0.643  0.001
+ -0.328  1.082  0.001
+A1AAAA=AA1
+  1.536 -0.516  0.070
+  0.539 -1.634 -0.136
+ -0.826 -1.408  0.492
+ -1.697 -0.080 -0.367
+ -0.948  1.318  0.430
+  0.290  1.574  0.200
+  1.109  0.744 -0.692
+A1A[A-]AA1
+  0.570  1.100  0.002
+ -0.917  0.805 -0.002
+ -1.022 -0.539  0.001
+  0.179 -1.128  0.001
+  1.188 -0.238 -0.002
+[A-]1AAAA1
+ -1.179 -0.279 -0.052
+ -0.722  0.985 -0.054
+  0.779  0.995  0.133
+  1.209 -0.459 -0.168
+ -0.087 -1.241  0.140
+A1AA2AA1A2
+ -1.213  0.790  0.037
+ -1.230 -0.768  0.057
+  0.313 -1.035  0.009
+  0.993  0.015  0.975
+  0.335  1.022 -0.017
+  0.802 -0.025 -1.060
+a1aaa[a]a1
+ -0.679  1.193  0.001
+ -1.389  0.001 -0.002
+ -0.681 -1.192  0.001
+  0.700 -1.155  0.001
+  1.346 -0.001 -0.002
+  0.701  1.155  0.001
+[At]1AAAA1
+  1.635 -0.001 -0.014
+  0.191 -1.568 -0.036
+ -1.028 -0.712  0.201
+ -0.986  0.726 -0.320
+  0.187  1.555  0.171
+a1aaa[aH]1
+ -0.108  1.131  0.003
+ -1.094  0.277 -0.002
+ -0.599 -0.970  0.001
+  0.745 -0.884  0.001
+  1.057  0.448 -0.002
+A1AAA=AA1
+  0.368  1.292  0.000
+  1.330  0.353  0.001
+  1.004 -0.957  0.000
+ -0.418 -1.329 -0.002
+ -1.349 -0.330  0.003
+ -0.936  0.972 -0.002
+A1AAAAAA1
+ -1.502  0.713  0.149
+ -0.279  1.437 -0.451
+  0.904  1.202  0.450
+  1.756 -0.000  0.000
+  0.903 -1.202 -0.450
+ -0.280 -1.437  0.450
+ -1.502 -0.712 -0.148
+A1=AA=AA1
+  1.105  0.356  0.001
+  0.743 -0.916  0.001
+ -0.743 -0.916 -0.002
+ -1.105  0.356  0.002
+  0.000  1.119 -0.002
+A1AA=AAA1
+ -0.501 -1.306  0.067
+  0.972 -1.099 -0.133
+  1.352  0.339  0.069
+  0.450  1.315  0.065
+ -0.906  1.031 -0.124
+ -1.369 -0.279  0.056
+A1AAAA=A1
+ -0.796 -1.155 -0.085
+  0.528 -1.381 -0.153
+  1.659 -0.075  0.201
+  0.671  1.332 -0.380
+ -0.729  1.203  0.152
+ -1.334  0.077  0.264
+A1=AAA=A1
+ -0.218 -1.305  0.001
+  0.921 -0.631 -0.000
+  0.930  0.633 -0.002
+ -0.244  1.311  0.003
+ -1.387 -0.009 -0.001
+A1AA21AA2
+ -1.325 -0.708 -0.290
+ -1.325  0.708  0.290
+  0.000  0.000  0.000
+  1.325  0.290 -0.708
+  1.325 -0.290  0.708
+A1AA=AA1
+ -1.305  0.000 -0.163
+ -0.372  1.197  0.136
+  1.025  0.652 -0.055
+  1.024 -0.653 -0.055
+ -0.372 -1.197  0.136
+A1A=AAA1
+ -0.028  1.145  0.002
+  1.132  0.340 -0.001
+  0.653 -0.934 -0.001
+ -0.688 -0.851  0.002
+ -1.068  0.298 -0.002
+A1AAA=A1
+  0.590 -1.000 -0.001
+  1.227  0.192  0.001
+  0.124  1.233 -0.001
+ -1.148  0.410  0.000
+ -0.792 -0.834  0.000
+A1AAAAA1
+  0.703  1.247 -0.255
+  1.446 -0.001  0.233
+  0.702 -1.248 -0.255
+ -0.743 -1.199  0.247
+ -1.367  0.000 -0.216
+ -0.742  1.199  0.247
+a1aaaaa1
+  1.200 -0.692  0.003
+ -0.000 -1.381 -0.002
+ -1.200 -0.691 -0.000
+ -1.207  0.688  0.001
+  0.000  1.389 -0.000
+  1.207  0.687 -0.002
+A1AA=A1
+  0.294  0.987  0.001
+  1.011 -0.311 -0.001
+ -0.312 -0.951  0.002
+ -0.992  0.275 -0.002
+A1AAAA1
+ -0.783 -1.009 -0.200
+  0.734 -1.068  0.074
+  1.238  0.386  0.074
+  0.009  1.278 -0.200
+ -1.198  0.413  0.251
+a1aaaa1
+ -0.188 -1.354 -0.002
+  1.002 -0.639  0.003
+  0.908  0.730 -0.002
+ -0.322  1.311  0.000
+ -1.401 -0.046  0.000
+A1AAA1
+  0.334  1.006 -0.173
+ -1.007  0.333  0.173
+ -0.333 -1.005 -0.173
+  1.006 -0.334  0.173
+A1AA1
+ -0.029  0.883  0.000
+  0.779 -0.417  0.000
+ -0.751 -0.466  0.000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/gaff.dat	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,5169 @@
+AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
+c  12.01         0.616               Sp2 C carbonyl group 
+c1 12.01         0.360               Sp C
+c2 12.01         0.360               Sp2 C  
+c3 12.01         0.878               Sp3 C
+ca 12.01         0.360               Sp2 C in pure aromatic systems
+cp 12.01         0.360               Head Sp2 C that connect two rings in biphenyl sys. 
+cq 12.01         0.360               Head Sp2 C that connect two rings in biphenyl sys. identical to cp 
+cc 12.01         0.360               Sp2 carbons in non-pure aromatic systems
+cd 12.01         0.360               Sp2 carbons in non-pure aromatic systems, identical to cc
+ce 12.01         0.360               Inner Sp2 carbons in conjugated systems
+cf 12.01         0.360               Inner Sp2 carbons in conjugated systems, identical to ce
+cg 12.01         0.360               Inner Sp carbons in conjugated systems
+ch 12.01         0.360               Inner Sp carbons in conjugated systems, identical to cg
+cx 12.01         0.360               Sp3 carbons in triangle systems
+cy 12.01         0.360               Sp3 carbons in square systems
+cu 12.01         0.360               Sp2 carbons in triangle systems
+cv 12.01         0.360               Sp2 carbons in square systems
+h1 1.008         0.135               H bonded to aliphatic carbon with 1 electrwd. group  
+h2 1.008         0.135               H bonded to aliphatic carbon with 2 electrwd. group 
+h3 1.008         0.135               H bonded to aliphatic carbon with 3 electrwd. group 
+h4 1.008         0.135               H bonded to non-sp3 carbon with 1 electrwd. group 
+h5 1.008         0.135               H bonded to non-sp3 carbon with 2 electrwd. group 
+ha 1.008         0.135               H bonded to aromatic carbon  
+hc 1.008         0.135               H bonded to aliphatic carbon without electrwd. group 
+hn 1.008         0.161               H bonded to nitrogen atoms
+ho 1.008         0.135               Hydroxyl group
+hp 1.008         0.135               H bonded to phosphate 
+hs 1.008         0.135               Hydrogen bonded to sulphur 
+hw 1.008         0.135               Hydrogen in water 
+hx 1.008         0.135               H bonded to C next to positively charged group  
+f  19.00         0.320               Fluorine
+cl 35.45         1.910               Chlorine 
+br 79.90         2.880               Bromine 
+i  126.9         4.690               Iodine 
+n  14.01         0.530               Sp2 nitrogen in amide groups
+n1 14.01         0.530               Sp N  
+n2 14.01         0.530               aliphatic Sp2 N with two connected atoms 
+n3 14.01         0.530               Sp3 N with three connected atoms
+n4 14.01         0.530               Sp3 N with four connected atoms 
+na 14.01         0.530               Sp2 N with three connected atoms 
+nb 14.01         0.530               Sp2 N in pure aromatic systems 
+nc 14.01         0.530               Sp2 N in non-pure aromatic systems
+nd 14.01         0.530               Sp2 N in non-pure aromatic systems, identical to nc
+ne 14.01         0.530               Inner Sp2 N in conjugated systems
+nf 14.01         0.530               Inner Sp2 N in conjugated systems, identical to ne
+nh 14.01         0.530               Amine N connected one or more aromatic rings 
+no 14.01         0.530               Nitro N  
+o  16.00         0.434               Oxygen with one connected atom
+oh 16.00         0.465               Oxygen in hydroxyl group
+os 16.00         0.465               Ether and ester oxygen
+ow 16.00         0.465               Oxygen in water 
+p2 30.97         1.538               Phosphate with two connected atoms 
+p3 30.97         1.538               Phosphate with three connected atoms, such as PH3
+p4 30.97         1.538               Phosphate with three connected atoms, such as O=P(CH3)2
+p5 30.97         1.538               Phosphate with four connected atoms, such as O=P(OH)3
+pb 30.97         1.538               Sp2 P in pure aromatic systems 
+pc 30.97         1.538               Sp2 P in non-pure aromatic systems
+pd 30.97         1.538               Sp2 P in non-pure aromatic systems, identical to pc
+pe 30.97         1.538               Inner Sp2 P in conjugated systems
+pf 30.97         1.538               Inner Sp2 P in conjugated systems, identical to pe
+px 30.97         1.538               Special p4 in conjugated systems
+py 30.97         1.538               Special p5 in conjugated systems
+s  32.06         2.900               S with one connected atom 
+s2 32.06         2.900               S with two connected atom, involved at least one double bond  
+s4 32.06         2.900               S with three connected atoms 
+s6 32.06         2.900               S with four connected atoms 
+sh 32.06         2.900               Sp3 S connected with hydrogen 
+ss 32.06         2.900               Sp3 S in thio-ester and thio-ether
+sx 32.06         2.900               Special s4 in conjugated systems
+sy 32.06         2.900               Special s6 in conjugated systems
+
+hn  ho  hs  n   na  nc  nd  ne  nf  n2  n3  n4  o   oh  os  ow  sh  ss
+ow-hw  553.0    0.9572      TIP3P water  
+br-br  123.2    2.542        SOURCE1     4    0.0000    0.0000
+br-c   240.3    1.946        SOURCE2     2    0.0285    0.0285
+br-c1  352.7    1.787        SOURCE2     4    0.0022    0.0024
+br-c2  278.7    1.883        SOURCE1    31    0.0000    0.0000
+br-c3  229.5    1.966        SOURCE1   100    0.0000    0.0000
+br-ca  269.6    1.897        SOURCE1   127    0.0028    0.0058
+br-cx  261.4    1.910        SOURCE1     8    0.0000    0.0000
+br-i   142.4    2.671        SOURCE1     2    0.0245    0.0245
+br-n   320.2    1.873        SOURCE3     4    0.0037    0.0046
+br-n1  330.4    1.860        SOURCE0     1                    
+br-n2  219.0    2.038        SOURCE3     5    0.0956    0.1082
+br-n3  265.9    1.952        SOURCE3     2    0.0000    0.0000
+br-n4  282.4    1.926        SOURCE3     3    0.0012    0.0013
+br-na  237.3    2.002        SOURCE3     7    0.1938    0.2156
+br-nh  270.9    1.944        SOURCE3     1    0.0000    0.0000
+br-no  191.0    2.101        SOURCE3     1    0.0000    0.0000
+br-o   278.9    1.800        SOURCE0     1                    
+br-oh  237.2    1.866        SOURCE3     1    0.0000    0.0000
+br-os  225.6    1.887        SOURCE3     2    0.0000    0.0000
+br-p2  174.3    2.210        SOURCE3     9    0.0470    0.0510
+br-p3  167.0    2.231        SOURCE3     3    0.0096    0.0101
+br-p4  188.8    2.171        SOURCE0     1                    
+br-p5  179.3    2.196        SOURCE3     3    0.0094    0.0099
+br-s   170.6    2.220        SOURCE0     1                    
+br-s4  134.3    2.341        SOURCE3     1    0.0000    0.0000
+br-s6  172.7    2.214        SOURCE3     3    0.0417    0.0443
+br-sh  174.4    2.209        SOURCE3     1    0.0000    0.0000
+br-ss  176.6    2.203        SOURCE3     3    0.0033    0.0035
+c -c   290.1    1.550        SOURCE1    31    0.0080    0.0100
+c -c1  379.8    1.460        SOURCE0     1                    
+c -c2  449.9    1.406        SOURCE3     2    0.0370    0.0370
+c -c3  328.3    1.508        SOURCE1  2949    0.0049    0.0060
+c -ca  349.7    1.487        SOURCE1   480    0.0031    0.0055
+c -cc  377.4    1.462        SOURCE3   132    0.0165    0.0210
+c -cd  377.4    1.462        SOURCE3   132    0.0165    0.0210
+c -ce  363.8    1.474        SOURCE1   601    0.0091    0.0105
+c -cf  363.8    1.474        SOURCE1   601    0.0091    0.0105
+c -cg  389.3    1.452        SOURCE3     2    0.0000    0.0000
+c -ch  389.3    1.452        SOURCE3     2    same as    c -cg
+c -cl  293.5    1.766        SOURCE3     6    0.0235    0.0250
+c -cu  441.4    1.412        SOURCE2     1    0.0000    0.0000
+c -cx  350.8    1.486        SOURCE1   105    0.0000    0.0000
+c -cy  308.5    1.529        SOURCE1    18    0.0000    0.0000
+c -f   387.9    1.325        SOURCE2     6    0.0140    0.0147
+c -ha  325.1    1.101        SOURCE3    53    0.0078    0.0102
+c -i   198.9    2.209        SOURCE3     4    0.0332    0.0365
+c -n   478.2    1.345        SOURCE1  1235    0.0162    0.0215
+c -n2  374.6    1.420        SOURCE0     1                    
+c -n4  255.5    1.546        SOURCE3     4    0.0388    0.0388
+c -nc  438.8    1.371        SOURCE3     2    0.0108    0.0108
+c -nd  438.8    1.371        SOURCE3     2    same as    c -nc
+c -ne  388.0    1.409        SOURCE3     3    0.0088    0.0094
+c -nf  388.0    1.409        SOURCE3     3    same as    c -ne
+c -no  260.1    1.540        SOURCE0     1                    
+c -o   648.0    1.214        SOURCE1  3682    0.0134    0.0165
+c -oh  466.4    1.306        SOURCE1   271    0.0026    0.0041
+c -os  411.3    1.343        SOURCE1  1044    0.0114    0.0171
+c -p2  210.3    1.900        SOURCE0     1                    
+c -p3  219.0    1.883        SOURCE3     6    0.0094    0.0129
+c -p4  220.6    1.880        SOURCE0     1                    
+c -p5  225.9    1.870        SOURCE0     1                    
+c -pe  204.9    1.911        SOURCE3     3    0.0023    0.0025
+c -pf  204.9    1.911        SOURCE3     3    same as    c -pe
+c -px  208.3    1.904        SOURCE3     1    0.0000    0.0000
+c -py  227.6    1.867        SOURCE3     6    0.0141    0.0199
+c -s   328.9    1.675        SOURCE1   401    0.0077    0.0128
+c -s4  200.4    1.870        SOURCE0     1                    
+c -s6  200.4    1.870        SOURCE0     1                    
+c -sh  249.6    1.781        SOURCE3     6    0.0157    0.0171
+c -ss  261.9    1.762        SOURCE1    20    0.0000    0.0000
+c -sx  193.3    1.885        SOURCE3     5    0.0070    0.0088
+c -sy  202.8    1.865        SOURCE3     5    0.0063    0.0085
+c1-c1  986.2    1.181        SOURCE1   265    0.0022    0.0031
+c1-c2  625.0    1.307        SOURCE1    18    0.0000    0.0000
+c1-c3  368.3    1.470        SOURCE1   215    0.0013    0.0017
+c1-ca  404.1    1.440        SOURCE0     1                    
+c1-cg  845.8    1.222        SOURCE3    22    0.0074    0.0101
+c1-ch  845.8    1.222        SOURCE3    22    same as    c1-cg
+c1-cl  419.7    1.631        SOURCE2     6    0.0046    0.0050
+c1-cx  399.1    1.444        SOURCE1    38    0.0000    0.0000
+c1-f   469.4    1.270        SOURCE2     2    0.0085    0.0085
+c1-ha  375.9    1.066        SOURCE3    63    0.0022    0.0035
+c1-hc  385.6    1.060        SOURCE0     1                    
+c1-i   318.8    1.989        SOURCE2     4    0.0025    0.0032
+c1-n   503.0    1.330        SOURCE0     1                    
+c1-n1 1014.5    1.138        SOURCE1   170    0.0038    0.0055
+c1-n2  769.8    1.210        SOURCE3     5    0.0089    0.0115
+c1-n3  409.8    1.392        SOURCE2     1    0.0000    0.0000
+c1-n4  378.2    1.417        SOURCE3     3    0.0030    0.0032
+c1-na  452.0    1.362        SOURCE3     8    0.0031    0.0034
+c1-ne  741.8    1.220        SOURCE3     1    0.0000    0.0000
+c1-nf  741.8    1.220        SOURCE3     1    same as    c1-ne
+c1-ng  465.7    1.353        SOURCE3     3    0.0025    0.0027
+c1-nh  465.7    1.353        SOURCE3     3    0.0025    0.0027
+c1-no  393.0    1.405        SOURCE3     3    0.0004    0.0005
+c1-o   777.0    1.166        SOURCE2     9    0.0044    0.0052
+c1-oh  435.6    1.326        SOURCE3     1    0.0000    0.0000
+c1-os  437.1    1.325        SOURCE3     3    0.0139    0.0148
+c1-p2  289.3    1.770        SOURCE0     1                    
+c1-p3  275.1    1.790        SOURCE0     1                    
+c1-p4  275.1    1.790        SOURCE0     1                    
+c1-p5  302.2    1.753        SOURCE3     2    0.0000    0.0000
+c1-s   371.8    1.630        SOURCE1    14    0.0000    0.0000
+c1-s2  410.0    1.595        SOURCE3     1    0.0000    0.0000
+c1-s4  272.9    1.746        SOURCE3     2    0.0000    0.0000
+c1-s6  290.4    1.722        SOURCE3     2    0.0000    0.0000
+c1-sh  324.5    1.680        SOURCE0     1                    
+c1-ss  325.4    1.679        SOURCE1    10    0.0000    0.0000
+c2-c2  589.7    1.324        SOURCE1   974    0.0048    0.0096
+c2-c3  328.3    1.508        SOURCE1  2536    0.0016    0.0021
+c2-ca  357.2    1.480        SOURCE0     1                    
+c2-cc  522.6    1.360        SOURCE1   771    0.0152    0.0185
+c2-cd  522.6    1.360        SOURCE1   771    0.0152    0.0185
+c2-ce  560.5    1.339        SOURCE3    62    0.0085    0.0128
+c2-cf  560.5    1.339        SOURCE3    62    same as    c2-ce
+c2-cl  328.8    1.722        SOURCE1   163    0.0093    0.0098
+c2-cu  573.9    1.332        SOURCE2     1    0.0000    0.0000
+c2-cx  333.3    1.503        SOURCE2     1    0.0000    0.0000
+c2-cy  309.4    1.528        SOURCE2     1    0.0000    0.0000
+c2-f   368.7    1.340        SOURCE1    34    0.0000    0.0000
+c2-h4  348.6    1.084        SOURCE3    40    0.0037    0.0058
+c2-h5  357.5    1.078        SOURCE3     3    0.0061    0.0067
+c2-ha  344.3    1.087        SOURCE3   797    0.0030    0.0046
+c2-hc  344.3    1.087        SOURCE3   789    0.0030    0.0046
+c2-hx  350.1    1.083        SOURCE3     3    0.0008    0.0008
+c2-i   223.2    2.153        SOURCE3     2    0.0000    0.0000
+c2-n   390.5    1.407        SOURCE3     9    0.0109    0.0124
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+
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+c3-ss-s     59.9      101.90    SOURCE3    1   0.0000   0.0000
+c3-ss-s4    60.1       96.37    SOURCE3    3   0.0190   0.0202
+c3-ss-s6    60.9       96.76    SOURCE3    3   1.4784   1.5680
+c3-ss-sh    60.4      101.93    SOURCE3    1   0.0000   0.0000
+c3-ss-ss    59.8      104.90    SOURCE3   25   3.6163   3.9326
+ca-ss-ca    62.4       99.92    SOURCE3    1   0.0000   0.0000
+ca-ss-cc    63.9       96.98    SOURCE3    2   0.0000   0.0000
+ca-ss-cd    63.9       96.98    SOURCE3    2   0.0000   0.0000
+ca-ss-cl    56.5      101.05    SOURCE3    1   0.0000   0.0000
+ca-ss-n     65.8       97.16    SOURCE0    1                  
+ca-ss-na    64.8       99.32    SOURCE0    1                  
+ca-ss-nc    69.2       94.76    SOURCE3    1   0.0000   0.0000
+ca-ss-nd    69.2       94.76    SOURCE3    1  same as ca-ss-nc
+cc-ss-cc    67.0       89.91    SOURCE3   11   2.0978   2.2164
+cd-ss-cd    67.0       89.91    SOURCE3   11   2.0978   2.2164
+cc-ss-cd    61.2      107.91    SOURCE3    1   0.0000   0.0000
+cc-ss-nc    69.7       95.66    SOURCE3    3   0.0000   0.0000
+cd-ss-nd    69.7       95.66    SOURCE3    3   0.0000   0.0000
+cc-ss-os    66.5       98.81    SOURCE3    2   2.1583   2.1583
+cd-ss-os    66.5       98.81    SOURCE3    2  same as cc-ss-os
+cc-ss-ss    61.5      102.46    SOURCE3    2   0.0000   0.0000
+cd-ss-ss    61.5      102.46    SOURCE3    2  same as cc-ss-ss
+cd-ss-n     66.4       97.16    SOURCE3    1   0.0000   0.0000
+cc-ss-n     66.4       97.16    SOURCE3    1  same as cd-ss-n 
+cd-ss-na    65.4       99.33    SOURCE3   18   1.9415   2.5847
+cc-ss-na    65.4       99.33    SOURCE3   18  same as cd-ss-na
+cl-ss-cl    52.4      103.37    SOURCE3    1   0.0000   0.0000
+cx-ss-cx    87.5       48.30    SOURCE2    1   0.0000   0.0000
+f -ss-f     66.2       98.30    SOURCE2    1   0.0000   0.0000
+f -ss-ss    59.9      108.30    SOURCE2    1   0.0000   0.0000
+i -ss-i     58.1      106.29    SOURCE3    1   0.0000   0.0000
+n -ss-n     66.4      103.10    SOURCE3    1   0.0000   0.0000
+n2-ss-n2    71.1       96.75    SOURCE3    1   0.0000   0.0000
+n3-ss-n3    66.5      102.34    SOURCE3    1   0.0000   0.0000
+n4-ss-n4    63.6      101.19    SOURCE3    1   0.0000   0.0000
+na-ss-na    65.9      102.81    SOURCE3    1   0.0000   0.0000
+nc-ss-nc    74.4       99.50    SOURCE2    1   0.0000   0.0000
+nd-ss-nd    74.4       99.50    SOURCE2    1  same as nc-ss-nc
+nh-ss-nh    65.3      107.89    SOURCE3    1   0.0000   0.0000
+no-ss-no    61.4      106.43    SOURCE3    1   0.0000   0.0000
+o -ss-o     69.8      119.30    SOURCE2    1   0.0000   0.0000
+o -ss-p5    78.8      106.41    SOURCE3    1   0.0000   0.0000
+o -ss-s6    62.4      105.39    SOURCE0    1                  
+o -ss-ss    62.0      112.70    SOURCE2    1   0.0000   0.0000
+oh-ss-oh    68.2      104.25    SOURCE3    1   0.0000   0.0000
+os-ss-os    67.8      102.99    SOURCE3    1   0.0000   0.0000
+p2-ss-p2   105.5       99.52    SOURCE3    1   0.0000   0.0000
+p3-ss-p3    96.8      101.67    SOURCE0    1                  
+p5-ss-p5   103.5       89.83    SOURCE3    1   0.0000   0.0000
+s -ss-s     57.7      115.04    SOURCE0    1                  
+s4-ss-s4    60.9       96.08    SOURCE3    1   0.0000   0.0000
+s4-ss-s6    59.9      101.26    SOURCE0    1                  
+s6-ss-s6    60.5      101.81    SOURCE3    1   0.0000   0.0000
+sh-ss-sh    60.3      107.54    SOURCE3    1   0.0000   0.0000
+sh-ss-ss    60.8      106.53    SOURCE0    1                  
+ss-ss-ss    60.4      108.71    SOURCE3    1   0.0000   0.0000
+c -sx-c     62.8       86.85    SOURCE3    1   0.0000   0.0000
+c -sx-c3    62.0       92.71    SOURCE3    3   0.2918   0.3095
+c -sx-o     63.5      106.17    SOURCE3    5   0.8807   0.9477
+c3-sx-ca    62.6       95.00    SOURCE3    1   0.0000   0.0000
+c3-sx-ce    62.8       94.95    SOURCE3    3   0.0006   0.0007
+c3-sx-cf    62.8       94.95    SOURCE3    3  same as c3-sx-ce
+c3-sx-ne    65.3       90.06    SOURCE3    5   1.4630   1.9627
+c3-sx-nf    65.3       90.06    SOURCE3    5  same as c3-sx-ne
+c3-sx-o     64.9      107.88    SOURCE3   30   0.7662   0.8721
+c3-sx-pe    77.0       94.32    SOURCE3    7   0.5270   0.5547
+c3-sx-pf    77.0       94.32    SOURCE3    7  same as c3-sx-pe
+c3-sx-px    74.3       96.46    SOURCE3    3   1.2587   1.3351
+c3-sx-py    74.1       95.67    SOURCE3    1   0.0000   0.0000
+c3-sx-sx    57.2       91.47    SOURCE3    4   1.9919   1.9919
+c3-sx-sy    58.7       95.47    SOURCE3    3   2.6797   2.8422
+ca-sx-ca    62.6       95.21    SOURCE3    1   0.0000   0.0000
+ca-sx-o     65.3      106.92    SOURCE3    3   0.3800   0.4031
+ce-sx-ce    63.0       94.96    SOURCE3    1   0.0000   0.0000
+cf-sx-cf    63.0       94.96    SOURCE3    1  same as ce-sx-ce
+ce-sx-o     65.4      107.47    SOURCE3    5   0.3064   0.3128
+cf-sx-o     65.4      107.47    SOURCE3    5  same as ce-sx-o 
+ne-sx-ne    66.4       90.17    SOURCE3    1   0.0000   0.0000
+nf-sx-nf    66.4       90.17    SOURCE3    1  same as ne-sx-ne
+ne-sx-o     65.4      109.20    SOURCE3    7   1.3979   1.4542
+nf-sx-o     65.4      109.20    SOURCE3    7  same as ne-sx-o 
+o -sx-pe    77.0      106.43    SOURCE3    9   2.1093   2.8345
+o -sx-pf    77.0      106.43    SOURCE3    9  same as o -sx-pe
+o -sx-px    75.2      104.77    SOURCE3    3   1.8677   1.9810
+o -sx-py    73.1      109.13    SOURCE3    7   5.2928   5.6840
+o -sx-sx    55.7      104.65    SOURCE3    6   2.8778   3.0524
+o -sx-sy    59.4      103.41    SOURCE3    5   0.7671   0.9618
+pe-sx-pe    99.2       92.62    SOURCE3    1   0.0000   0.0000
+pf-sx-pf    99.2       92.62    SOURCE3    1  same as pe-sx-pe
+py-sx-py   110.1       69.23    SOURCE3    3  16.4184  17.4143
+sx-sx-sx    58.6       84.90    SOURCE3    1   0.0000   0.0000
+sy-sx-sy    59.2       93.52    SOURCE3    1   0.0000   0.0000
+c -sy-c     59.2       99.81    SOURCE3    1   0.0000   0.0000
+c -sy-c3    60.1      101.25    SOURCE3    3   1.1172   1.1850
+c -sy-o     64.1      107.23    SOURCE3   10   0.8191   0.8425
+c3-sy-ca    60.9      103.17    SOURCE3    1   0.0000   0.0000
+c3-sy-ce    60.8      103.81    SOURCE3    3   0.3175   0.3368
+c3-sy-cf    60.8      103.81    SOURCE3    3  same as c3-sy-ce
+c3-sy-ne    63.0      103.12    SOURCE3    5   3.6732   4.1882
+c3-sy-nf    63.0      103.12    SOURCE3    5  same as c3-sy-ne
+c3-sy-o     66.0      108.48    SOURCE3   62   0.7297   0.8576
+c3-sy-pe    71.8      106.03    SOURCE3    6   2.3845   2.6117
+c3-sy-pf    71.8      106.03    SOURCE3    6  same as c3-sy-pe
+c3-sy-px    71.7      103.62    SOURCE3    3   0.6673   0.7078
+c3-sy-py    73.5      103.39    SOURCE3    3   0.4302   0.4563
+c3-sy-sx    56.3      104.64    SOURCE3    3   4.3630   4.6276
+c3-sy-sy    57.4      100.78    SOURCE3    4   1.1633   1.1633
+ca-sy-ca    62.1       99.34    SOURCE3    3   4.9868   5.2893
+ca-sy-nh    65.2      100.83    SOURCE3    1   0.0000   0.0000
+ca-sy-o     65.8      108.73    SOURCE3   26   1.1018   1.2638
+ca-sy-oh    65.7      101.84    SOURCE3    4   0.9524   1.1069
+ca-sy-os    67.6       92.98    SOURCE3    1   0.0000   0.0000
+ce-sy-ce    61.1      102.78    SOURCE3    1   0.0000   0.0000
+cf-sy-cf    61.1      102.78    SOURCE3    1  same as ce-sy-ce
+ce-sy-o     66.4      107.25    SOURCE3   10   0.5364   0.5477
+cf-sy-o     66.4      107.25    SOURCE3   10  same as ce-sy-o 
+na-sy-na    67.7       98.04    SOURCE0    1                  
+nc-sy-nc    75.2       98.04    SOURCE0    2                  
+nd-sy-nd    75.2       98.04    SOURCE0    2                  
+ne-sy-ne    66.6       98.62    SOURCE3    1   0.0000   0.0000
+nf-sy-nf    66.6       98.62    SOURCE3    1  same as ne-sy-ne
+ne-sy-o     68.9      107.06    SOURCE3   14   2.1834   2.2705
+nf-sy-o     68.9      107.06    SOURCE3   14  same as ne-sy-o 
+nh-sy-o     70.9      108.46    SOURCE3    2   0.0000   0.0000
+o -sy-o     72.4      121.88    SOURCE3   46   0.7319   0.9495
+o -sy-oh    72.7      106.93    SOURCE3    8   0.6101   0.7424
+o -sy-os    70.6      107.62    SOURCE3    2   0.0000   0.0000
+o -sy-pe    75.4      106.90    SOURCE3   12   1.4233   1.4524
+o -sy-pf    75.4      106.90    SOURCE3   12  same as o -sy-pe
+o -sy-px    74.4      106.17    SOURCE3    6   0.6656   0.7059
+o -sy-py    76.5      106.67    SOURCE3   10   0.6188   0.6478
+o -sy-sx    58.6      106.33    SOURCE3   10   1.9984   2.0456
+o -sy-sy    58.8      106.19    SOURCE3   12   0.1653   0.1754
+py-sy-py    92.8      104.49    SOURCE3    1   0.0000   0.0000
+sx-sy-sx    56.7      101.99    SOURCE3    1   0.0000   0.0000
+sy-sy-sy    56.5      103.29    SOURCE3    1   0.0000   0.0000
+br-n1-c1    51.1      180.00    HF/6-31G*
+c1-n1-c1    64.9      179.92    HF/6-31G*
+c1-n1-c2    60.2      177.73    HF/6-31G*
+c1-n1-c3    59.9      180.00    HF/6-31G*
+c1-n1-ca    59.9      179.99    HF/6-31G*
+c1-n1-cl    50.1      179.95    HF/6-31G*
+c1-n1-f     55.9      179.96    HF/6-31G*
+c1-n1-hn    45.6      179.98    HF/6-31G*
+c1-n1-i     46.2      179.95    HF/6-31G*
+c1-n1-n1    66.9      180.00    HF/6-31G*
+c1-n1-n2    65.7      171.56    HF/6-31G*
+c1-n1-n3    60.7      175.59    HF/6-31G*
+c1-n1-n4    59.7      179.69    HF/6-31G*
+c1-n1-na    59.9      180.00    HF/6-31G*
+c1-n1-nh    60.9      176.35    HF/6-31G*
+c1-n1-o     62.6      179.95    HF/6-31G*
+c1-n1-oh    62.9      174.31    HF/6-31G*
+c1-n1-os    62.2      176.61    HF/6-31G*
+c1-n1-p2    83.5      172.83    HF/6-31G*
+c1-n1-p3    68.7      173.51    HF/6-31G*
+c1-n1-p4    68.7      173.64    HF/6-31G*
+c1-n1-p5    71.5      177.28    HF/6-31G*
+c1-n1-s     53.3      179.99    HF/6-31G*
+c1-n1-s2    60.3      178.11    HF/6-31G*
+c1-n1-s4    55.2      169.60    HF/6-31G*
+c1-n1-s6    61.8      175.92    HF/6-31G*
+c1-n1-sh    55.7      174.25    HF/6-31G*
+c1-n1-ss    55.4      176.06    HF/6-31G*
+c1-ng-ng    51.9      179.97    HF/6-31G*
+c2-c1-n1    63.1      180.00    HF/6-31G*
+c2-c2-n1    71.7      122.98    HF/6-31G*
+c2-n1-n1    61.6      180.00    HF/6-31G*
+c2-n2-n1    75.5      115.09    HF/6-31G*
+c2-na-n1    66.3      124.81    HF/6-31G*
+c3-n1-n1    58.8      180.00    HF/6-31G*
+c3-os-n1    66.3      113.50    HF/6-31G*
+c3-ss-n1    65.9       98.44    HF/6-31G*
+ca-ca-n1    63.4      118.50    HF/6-31G*
+ca-n1-n1    59.0      180.00    HF/6-31G*
+ca-nh-n1    69.4      117.13    HF/6-31G*
+cl-n1-n1    51.4      179.94    HF/6-31G*
+f -n1-n1    57.4      179.93    HF/6-31G*
+h1-c3-n1    60.3      107.31    HF/6-31G*
+hn-n1-n1    47.1      179.91    HF/6-31G*
+hn-n3-n1    52.0      110.17    HF/6-31G*
+hn-n4-n1    51.8      109.39    HF/6-31G*
+hn-nh-n1    52.3      110.57    HF/6-31G*
+ho-oh-n1    52.5      107.81    HF/6-31G*
+hp-p3-n1    31.3       92.98    HF/6-31G*
+hp-p4-n1    30.5       99.91    HF/6-31G*
+hp-p5-n1    31.1      101.32    HF/6-31G*
+hs-s4-n1    51.2       90.51    HF/6-31G*
+hs-s6-n1    54.7       97.27    HF/6-31G*
+hs-sh-n1    51.7       93.51    HF/6-31G*
+i -n1-n1    47.3      179.94    HF/6-31G*
+n1-n1-n1    69.0      179.97    HF/6-31G*
+n1-n1-n2    67.7      171.57    HF/6-31G*
+n1-n1-n3    62.5      175.09    HF/6-31G*
+n1-n1-n4    61.3      179.91    HF/6-31G*
+n1-n1-na    61.6      179.97    HF/6-31G*
+n1-n1-nh    62.7      176.00    HF/6-31G*
+n1-n1-o     64.4      179.94    HF/6-31G*
+n1-n1-oh    64.8      173.77    HF/6-31G*
+n1-n1-os    64.0      176.12    HF/6-31G*
+n1-n1-p2    69.4      174.71    HF/6-31G*
+n1-n1-p3    70.2      174.27    HF/6-31G*
+n1-n1-s     54.6      179.96    HF/6-31G*
+n1-n1-sh    57.0      175.07    HF/6-31G*
+n1-n1-ss    56.9      175.61    HF/6-31G*
+n1-p4-o     49.7      114.59    HF/6-31G*
+n1-p5-o     44.7      113.78    HF/6-31G*
+n1-s2-o     73.1      108.46    HF/6-31G*
+n1-s4-o     70.2      110.09    HF/6-31G*
+n1-s6-o     78.8      107.52    HF/6-31G*
+n1-c1-n1    70.2      180.00    HF/6-31G*
+n1-c2-n1    73.6      124.15    HF/6-31G*
+n1-c3-n1    80.0      105.07    HF/6-31G*
+n1-ca-n1    75.8      117.03    HF/6-31G*
+n1-n2-n1    80.8      112.00    HF/6-31G*
+n1-n3-n1    72.4      113.21    HF/6-31G*
+n1-n4-n1    72.7      110.67    HF/6-31G*
+n1-no-o     73.8      115.00    HF/6-31G* 
+n1-nh-n1    75.1      106.71    HF/6-31G*
+n1-os-n1    70.3      117.79    HF/6-31G*
+n1-ss-n1    73.1       96.96    HF/6-31G*
+n1-s4-n1    72.4       94.02    HF/6-31G*
+n1-s6-n1    83.7       95.52    HF/6-31G*
+n1-p2-n1    46.5       86.22    HF/6-31G*
+n1-p3-n1    45.9       90.44    HF/6-31G*
+n1-p4-n1    43.5      100.61    HF/6-31G*
+n1-p5-n1    45.8      101.55    HF/6-31G*
+o -c1-o     69.3      180.00    Guess
+c3-c1-c3    51.7      180.00    Guess
+ca-c1-ca    52.8      180.00    Guess
+f -c1-f     58.2      180.00    Guess
+cl-c1-cl    46.6      180.00    Guess
+br-c1-br    57.8      180.00    Guess
+i -c1-i     53.4      180.00    Guess
+s -c1-s     54.6      180.00    Guess
+s2-c1-s2    55.8      180.00    Guess
+s4-c1-s4    51.0      180.00    Guess
+s6-c1-s6    51.7      180.00    Guess
+sh-c1-sh    53.0      180.00    Guess
+ss-c1-ss    53.0      180.00    Guess
+oh-c1-oh    60.9      180.00    Guess
+os-c1-os    61.0      180.00    Guess
+p2-c1-p2    80.6      180.00    Guess
+p3-c1-p3    79.7      180.00    Guess
+p4-c1-p4    79.7      180.00    Guess
+p5-c1-p5    81.4      180.00    Guess
+n -c1-n     60.0      180.00    Guess
+n2-c1-n2    66.0      180.00    Guess
+n3-c1-n3    57.4      180.00    Guess
+n4-c1-n4    56.3      180.00    Guess
+nh-c1-nh    59.0      180.00    Guess
+no-c1-no    56.8      180.00    Guess
+na-c1-na    58.6      180.00    Guess
+na-c1-na    58.6      180.00    Guess
+na-c1-na    58.6      180.00    Guess
+
+X -c -c -X    4    1.200       180.000           2.000
+X -c -c1-X    2    0.000       180.000           2.000     
+X -c -cg-X    2    0.000       180.000           2.000      same as X-c-c1-X 
+X -c -ch-X    2    0.000       180.000           2.000     
+X -c -c2-X    4    8.700       180.000           2.000      intrpol.bsd.on C6H6
+X -c -cu-X    4    8.700       180.000           2.000      intrpol.bsd.on C6H6
+X -c -cv-X    4    8.700       180.000           2.000      intrpol.bsd.on C6H6
+X -c -ce-X    4    8.700       180.000           2.000      intrpol.bsd.on C6H6
+X -c -cf-X    4    8.700       180.000           2.000      intrpol.bsd.on C6H6
+X -c -c3-X    6    0.000       180.000           2.000      JCC, 7, (1986), 230
+X -c -cx-X    6    0.000       180.000           2.000      JCC, 7, (1986), 230
+X -c -cy-X    6    0.000       180.000           2.000      JCC, 7, (1986), 230
+X -c -ca-X    4   14.500       180.000           2.000      intrpol.bsd.on C6H6
+X -c -cc-X    4   11.500       180.000           2.000      statistic value 
+X -c -cd-X    4   11.500       180.000           2.000      statistic value 
+X -c -n -X    4   10.000       180.000           2.000      AA,NMA (no c-n3, c-n4, c-nh)
+X -c -n2-X    2    8.300       180.000           2.000      double bond, same as X-c2-n2-X
+X -c -nc-X    2    8.00        180.000           2.000      same as X-C-NC-X 
+X -c -nd-X    2    8.00        180.000           2.000      same as X-C-NC-X 
+X -c -ne-X    2    0.400       180.000           2.000      single bond
+X -c -nf-X    2    0.400       180.000           2.000      single bond
+X -c -na-X    4    5.800       180.000          -2.000
+X -c -na-X    4    1.400       180.000           4.000
+X -c -no-X    4    1.800       180.000           2.000      
+X -c -oh-X    2    4.600       180.000           2.000      Junmei et al, 1999
+X -c -os-X    2    5.400       180.000           2.000      Junmei et al, 1999
+X -c -pc-X    2    4.000       180.000           2.000      estimated   
+X -c -p2-X    2   13.300       180.000           2.000      double bond, same as X-c2-p2-X 
+X -c -pc-X    2    4.000       180.000           2.000      estimated   
+X -c -pd-X    2    4.000       180.000           2.000      estimated 
+X -c -pe-X    2    0.000       180.000           2.000      single bond
+X -c -pf-X    2    0.000       180.000           2.000      single bond
+X -c -p3-X    4    6.200       180.000           2.000
+X -c -p4-X    4    5.400       180.000           2.000
+X -c -px-X    4    5.400       180.000           2.000     
+X -c -p5-X    4    4.000         0.000           2.000
+X -c -py-X    4    4.000         0.000           2.000      
+X -c -sh-X    2    4.500       180.000           2.000
+X -c -ss-X    2    6.200       180.000           2.000
+X -c -s4-X    4    0.800       180.000           2.000
+X -c -sx-X    4    0.800       180.000           2.000     
+X -c -s6-X    6    3.000         0.000           2.000
+X -c -sy-X    6    3.000         0.000           2.000    
+X -c1-c1-X    1    0.000       180.000           2.000      for both triple and single bonds
+X -c1-cg-X    1    0.000       180.000           2.000      for both triple and single bonds
+X -c1-ch-X    1    0.000       180.000           2.000      for both triple and single bonds
+X -cg-cg-X    1    0.000       180.000           2.000      for both triple and single bonds
+X -ch-ch-X    1    0.000       180.000           2.000      for both triple and single bonds
+X -cg-ch-X    1    0.000       180.000           2.000      for both triple and single bonds
+X -c1-c2-X    2    0.000       180.000           2.000     
+X -c1-c3-X    3    0.000       180.000           2.000     
+X -c1-ca-X    2    0.000       180.000           2.000     
+X -c1-cb-X    2    0.000       180.000           2.000     
+X -c1-cc-X    2    0.000       180.000           2.000     
+X -c1-cd-X    2    0.000       180.000           2.000     
+X -c1-ce-X    2    0.000       180.000           2.000     
+X -c1-cf-X    2    0.000       180.000           2.000     
+X -c1-cu-X    2    0.000       180.000           2.000     
+X -c1-cv-X    2    0.000       180.000           2.000     
+X -c1-cx-X    3    0.000       180.000           2.000     
+X -c1-cy-X    3    0.000       180.000           2.000     
+X -c1-n -X    2    0.000       180.000           2.000     
+X -c1-n2-X    1    0.000       180.000           2.000     
+X -c1-n3-X    2    0.000       180.000           2.000     
+X -c1-n4-X    3    0.000       180.000           2.000     
+X -c1-na-X    2    0.000       180.000           2.000     
+X -c1-nb-X    2    0.000       180.000           2.000     
+X -c1-nc-X    2    0.000       180.000           2.000     
+X -c1-nd-X    2    0.000       180.000           2.000     
+X -c1-ne-X    2    0.000       180.000           2.000     
+X -c1-nf-X    2    0.000       180.000           2.000     
+X -c1-nh-X    2    0.000       180.000           2.000     
+X -c1-no-X    2    0.000       180.000           2.000     
+X -c1-oh-X    1    0.000       180.000           2.000     
+X -c1-os-X    1    0.000       180.000           2.000     
+X -c1-p2-X    1    0.000       180.000           2.000     
+X -c1-pb-X    1    0.000       180.000           2.000     
+X -c1-pc-X    1    0.000       180.000           2.000     
+X -c1-pd-X    1    0.000       180.000           2.000     
+X -c1-pe-X    1    0.000       180.000           2.000     
+X -c1-pf-X    1    0.000       180.000           2.000     
+X -c1-p3-X    2    0.000       180.000           2.000     
+X -c1-p4-X    2    0.000       180.000           2.000     
+X -c1-px-X    2    0.000       180.000           2.000     
+X -c1-p5-X    3    0.000       180.000           2.000     
+X -c1-py-X    3    0.000       180.000           2.000     
+X -c1-s2-X    1    0.000       180.000           2.000     
+X -c1-sh-X    1    0.000       180.000           2.000     
+X -c1-ss-X    1    0.000       180.000           2.000     
+X -c1-s4-X    2    0.000       180.000           2.000     
+X -c1-sx-X    2    0.000       180.000           2.000     
+X -c1-s6-X    3    0.000       180.000           2.000     
+X -c1-sy-X    3    0.000       180.000           2.000     
+X -c2-c2-X    4   26.600       180.000           2.000      c2=c2 double bond, intrpol.bsd.on C6H6
+X -c2-ce-X    4   26.600       180.000           2.000      c2=c2 double bond, intrpol.bsd.on C6H6
+X -c2-cf-X    4   26.600       180.000           2.000      c2=c2 double bond, intrpol.bsd.on C6H6
+X -ce-cf-X    4   26.600       180.000           2.000      c2=c2 double bond, intrpol.bsd.on C6H6
+X -ce-ce-X    4    4.000       180.000           2.000      c2-c2 single bond, parm99 
+X -cf-cf-X    4    4.000       180.000           2.000      c2-c2 single bond, parm99 
+X -cc-cd-X    4   16.000       180.000           2.000      statistic value of parm94
+X -cc-cc-X    4   16.000       180.000           2.000      statistic value of parm94
+X -cd-cd-X    4   16.000       180.000           2.000      statistic value of parm94
+X -c2-c3-X    6    0.000         0.000           2.000      JCC,7,(1986),230
+X -c2-ca-X    4   10.200       180.000           2.000      intrpol.bsd.on C6H6
+X -c2-n -X    4    2.600       180.000           2.000
+X -c2-n2-X    2    8.300       180.000           2.000      double bond, parm99
+X -c2-ne-X    2    8.300       180.000           2.000      double bond, parm99
+X -c2-nf-X    2    8.300       180.000           2.000      double bond, parm99
+X -ce-ne-X    2    1.600       180.000           2.000      single bond
+X -cf-nf-X    2    1.600       180.000           2.000      single bond
+X -c2-nc-X    2    9.500       180.000           2.000      statistic value from parm94
+X -c2-nd-X    2    9.500       180.000           2.000      statistic value from parm94
+X -cc-nd-X    2    9.500       180.000           2.000      statistic value from parm94
+X -cd-nc-X    2    9.500       180.000           2.000      statistiv value from parm94
+X -cc-nc-X    2    9.500       180.000           2.000      statistic value from parm94
+X -cd-nd-X    2    9.500       180.000           2.000      statistiv value from parm94
+X -c2-n3-X    4    1.200       180.000           2.000      intrpol.  
+X -c2-n4-X    6    0.000       180.000           3.000      intrpol. 
+X -c2-na-X    4    2.500       180.000           2.000
+X -cc-na-X    4    6.800       180.000           2.000      statistic value from parm94
+X -cd-na-X    4    6.800       180.000           2.000      statistic value from parm94
+X -c2-nh-X    4    2.700       180.000           2.000
+X -c2-no-X    4    3.000       180.000           2.000
+X -c2-oh-X    2    2.100       180.000           2.000      parm99 
+X -c2-os-X    2    2.100       180.000           2.000      parm99 
+X -c2-p2-X    2   13.300       180.000           2.000      double bond
+X -c2-pe-X    2   13.300       180.000           2.000      double bond
+X -c2-pf-X    2   13.300       180.000           2.000      double bond
+X -ce-pf-X    2   13.300       180.000           2.000      double bond
+X -ce-pe-X    2    1.900       180.000           2.000      single bond
+X -cf-pf-X    2    1.900       180.000           2.000      single bond
+X -c2-pc-X    2    9.500       180.000           2.000      estimated 
+X -c2-pd-X    2    9.500       180.000           2.000      estimated 
+X -cc-pc-X    2    9.500       180.000           2.000      estimated 
+X -cc-pd-X    2    9.500       180.000           2.000      estimated 
+X -cd-pc-X    2    9.500       180.000           2.000      estimated 
+X -cd-pd-X    2    9.500       180.000           2.000      estimated
+X -c2-p3-X    4    1.800       180.000           2.000
+X -c2-p4-X    4   26.600       180.000           2.000      c2=p4 double bond !!!  
+X -ce-p4-X    4   26.600       180.000           2.000      c2=p4 double bond !!!  
+X -cf-p4-X    4   26.600       180.000           2.000      c2=p4 double bond !!!  
+X -c2-px-X    4    1.300         0.000           2.000
+X -ce-px-X    4    1.300         0.000           2.000
+X -cf-px-X    4    1.300         0.000           2.000
+X -c2-p5-X    6   39.900       180.000           2.000      c2=p5 double bond !!!
+X -ce-p5-X    6   39.900       180.000           2.000      c2=p5 double bond !!!
+X -cf-p5-X    6   39.900       180.000           2.000      c2=p5 double bond !!!
+X -c2-py-X    6    8.600       180.000           2.000
+X -ce-py-X    6    8.600       180.000           2.000
+X -cf-py-X    6    8.600       180.000           2.000
+X -c2-sh-X    2    1.000       180.000           2.000
+X -c2-ss-X    2    2.200       180.000           2.000
+X -c2-s4-X    4   26.600       180.000           2.000      c2=s4 double bond  !!!
+X -ce-s4-X    4   26.600       180.000           2.000      c2=s4 double bond  !!!
+X -cf-s4-X    4   26.600       180.000           2.000      c2=s4 double bond  !!!
+X -c2-sx-X    4    2.400         0.000           2.000
+X -ce-sx-X    4    2.400         0.000           2.000
+X -cf-sx-X    4    2.400         0.000           2.000
+X -c2-s6-X    6   39.900       180.000           2.000      c2=s6 double bond  !!!
+X -ce-s6-X    6   39.900       180.000           2.000      c2=s6 double bond  !!!
+X -cf-s6-X    6   39.900       180.000           2.000      c2=s6 double bond  !!!
+X -c2-sy-X    6    7.600       180.000           2.000
+X -ce-sy-X    6    7.600       180.000           2.000
+X -cf-sy-X    6    7.600       180.000           2.000
+X -c3-c3-X    9    1.400         0.000           3.000      JCC,7,(1986),230
+X -cx-cx-X    9    1.400         0.000           3.000      same as X-c3-c3-X 
+X -cy-cy-X    9    1.400         0.000           3.000      same as X-c3-c3-X 
+X -c3-ca-X    6    0.000         0.000           2.000      JCC,7,(1986),230
+X -c3-n -X    6    0.000         0.000           2.000      JCC,7,(1986),230
+X -cx-n -X    6    0.000         0.000           2.000      same as X-c3-n-X 
+X -cy-n -X    6    0.000         0.000           2.000      same as X-c3-n-X
+X -c3-n2-X    6    0.000         0.000           3.000      JCC,7,(1986),230
+X -c3-ne-X    6    0.000         0.000           3.000      JCC,7,(1986),230
+X -c3-nf-X    6    0.000         0.000           3.000      JCC,7,(1986),230
+X -c3-n3-X    6    1.800         0.000           3.000      Junmei et al, 1999 
+X -c3-n4-X    9    1.400         0.000           3.000      JCC,7,(1986),230
+X -c3-na-X    6    0.000         0.000           2.000      JCC,7,(1986),230
+X -c3-nh-X    6    0.000         0.000           2.000      JCC,7,(1986),230
+X -c3-no-X    6    0.000         0.000           2.000      JCC,7,(1986),230
+X -c3-oh-X    3    0.500         0.000           3.000      JCC,7,(1986),230
+X -c3-os-X    3    1.150         0.000           3.000      JCC,7,(1986),230
+X -c3-p2-X    3    0.800       180.000           2.000
+X -c3-pe-X    3    0.800       180.000           2.000
+X -c3-pf-X    3    0.800       180.000           2.000
+X -c3-p3-X    6    0.800         0.000           3.000
+X -c3-p4-X    6    0.800         0.000           3.000
+X -c3-px-X    6    0.800         0.000           3.000
+X -c3-p5-X    9    0.200         0.000           3.000
+X -c3-py-X    9    0.200         0.000           3.000
+X -c3-sh-X    3    0.750         0.000           3.000      JCC,7,(1986),230
+X -c3-ss-X    3    1.000         0.000           3.000      JCC,7,(1986),230
+X -c3-s4-X    6    1.200         0.000           3.000      
+X -c3-sx-X    6    1.200         0.000           3.000      
+X -c3-s6-X    9    1.300         0.000           3.000     
+X -c3-sy-X    9    1.300         0.000           3.000     
+X -c3-cc-X    6    0.000         0.000           3.000      same as X-c3-ca-X
+X -c3-cd-X    6    0.000         0.000           3.000      same as X-c3-ca-X
+X -ca-ca-X    4   14.500       180.000           2.000      intrpol.bsd.on C6H6
+X -ca-cc-X    4   14.500       180.000           2.000      added by EAJF Peters
+X -ca-cp-X    4   14.500       180.000           2.000      intrpol.bsd.on C6H6
+X -ca-cq-X    4   14.500       180.000           2.000      intrpol.bsd.on C6H6
+X -cp-cp-X    4    4.000       180.000           2.000      estimated, intrpol. 
+X -cq-cq-X    4    4.000       180.000           2.000      estimated, intrpol. 
+X -ca-n -X    4    1.800       180.000           2.000
+X -ca-n2-X    2    0.000       180.000           3.000
+X -ca-ne-X    2    0.000       180.000           3.000
+X -ca-nf-X    2    0.000       180.000           3.000
+X -ca-n4-X    4    7.000         0.000           2.000
+X -ca-na-X    4    1.200       180.000           2.000
+X -ca-nb-X    2    9.60        180.0             2.000      same as X-CA-NC-X
+X -ca-nc-X    2    9.60        180.0             2.000      same as X-CA-NC-X
+X -ca-nd-X    2    9.60        180.0             2.000      same as X-CA-NC-X
+X -ca-nh-X    4    4.200       180.000           2.000
+X -cc-nh-X    4    4.200       180.000           2.000      same as X-ca-nh-X
+X -cd-nh-X    4    4.200       180.000           2.000      same as X-ca-nh-X
+X -ca-no-X    4    2.400       180.000           2.000
+X -ca-oh-X    2    1.800       180.000           2.000      Junmei et al, 99
+X -ca-os-X    2    1.800       180.000           2.000      same as X-ca-oh-X 
+X -ca-p2-X    2    1.200       180.000           2.000
+X -ca-pe-X    2    1.200       180.000           2.000      same as X-ca-p2-X
+X -ca-pf-X    2    1.200       180.000           2.000      same as X-ca-p2-X
+X -ca-pc-X    2    9.600       180.000           2.000      estimated, intrpol 
+X -ca-pd-X    2    9.600       180.000           2.000      estimated, intrpol 
+X -ca-p3-X    4    0.000       180.000           2.000
+X -ca-p4-X    4    2.100       180.000           2.000
+X -ca-px-X    4    2.100       180.000           2.000      estimated, same as X-ca-p4-X
+X -ca-p5-X    6    8.800       180.000           2.000
+X -ca-py-X    6    8.800       180.000           2.000      estimated, same as X-ca-p5-X
+X -ca-sh-X    2    0.000       180.000           2.000
+X -ca-ss-X    2    0.800       180.000           2.000
+X -ca-s4-X    4    1.200         0.000           2.000
+X -ca-sx-X    4    1.200         0.000           2.000      estimated, same as X-ca-s4-X
+X -ca-s6-X    6    7.800       180.000           2.000
+X -ca-sy-X    6    7.800       180.000           2.000      estimated, same as X-ca-s6-X
+X -n -cc-X    4    6.600       180.000           2.000      statistic value from parm94
+X -n -cd-X    4    6.600       180.000           2.000      statistic value from parm94
+X -n -n -X    4    4.600         0.000           2.000
+X -n -n2-X    2    0.800         0.000           2.000
+X -n -ne-X    2    0.800         0.000           2.000
+X -n -nf-X    2    0.800         0.000           2.000
+X -n -n3-X    4    4.300         0.000           2.000
+X -n -n4-X    4    3.800         0.000           2.000
+X -n -na-X    4    2.800         0.000           2.000
+X -n -nc-X    2    9.600       180.000           2.000      estimated, intrpol.
+X -n -nd-X    2    9.600       180.000           2.000      estimated, intrpol.
+X -n -nh-X    4    4.400         0.000           2.000
+X -n -no-X    4    5.500       180.000           2.000
+X -n -oh-X    2    3.000         0.000           2.000
+X -n -os-X    2    2.200         0.000           2.000
+X -n -p2-X    2    2.000       180.000           2.000
+X -n -pe-X    2    2.000       180.000           2.000
+X -n -pf-X    2    9.600       180.000           2.000      estimated, intrpol.
+X -n -pc-X    2    9.600       180.000           2.000      estimated, intrpol.
+X -n -pd-X    2    2.000       180.000           2.000
+X -n -p3-X    4    9.000         0.000           2.000
+X -n -p4-X    4    1.300         0.000           2.000
+X -n -px-X    4    1.300         0.000           2.000
+X -n -p5-X    6   13.200       180.000           2.000
+X -n -py-X    6   13.200       180.000           2.000
+X -n -sh-X    2    2.200         0.000           2.000
+X -n -ss-X    2    3.000         0.000           2.000
+X -n -s4-X    4    6.000         0.000           3.000
+X -n -sx-X    4    6.000         0.000           3.000
+X -n -s6-X    6    6.600       180.000           2.000
+X -n -sy-X    6    6.600       180.000           2.000
+X -n1-c2-X    2    0.000       180.000           2.000     
+X -n1-c3-X    3    0.000       180.000           2.000     
+X -n1-ca-X    2    0.000       180.000           2.000     
+X -n1-cb-X    2    0.000       180.000           2.000     
+X -n1-cc-X    2    0.000       180.000           2.000     
+X -n1-cd-X    2    0.000       180.000           2.000     
+X -n1-ce-X    2    0.000       180.000           2.000     
+X -n1-cf-X    2    0.000       180.000           2.000     
+X -n1-cu-X    2    0.000       180.000           2.000     
+X -n1-cv-X    2    0.000       180.000           2.000     
+X -n1-cx-X    3    0.000       180.000           2.000     
+X -n1-cy-X    3    0.000       180.000           2.000     
+X -n1-n -X    2    0.000       180.000           2.000     
+X -n1-n1-X    1    0.000       180.000           2.000     
+X -n1-n2-X    1    0.000       180.000           2.000     
+X -n1-n3-X    2    0.000       180.000           2.000     
+X -n1-n4-X    3    0.000       180.000           2.000     
+X -n1-na-X    2    0.000       180.000           2.000     
+X -n1-nb-X    2    0.000       180.000           2.000     
+X -n1-nc-X    2    0.000       180.000           2.000     
+X -n1-nd-X    2    0.000       180.000           2.000     
+X -n1-ne-X    2    0.000       180.000           2.000     
+X -n1-nf-X    2    0.000       180.000           2.000     
+X -n1-nh-X    2    0.000       180.000           2.000     
+X -n1-no-X    2    0.000       180.000           2.000     
+X -n1-oh-X    1    0.000       180.000           2.000     
+X -n1-os-X    1    0.000       180.000           2.000     
+X -n1-p2-X    1    0.000       180.000           2.000     
+X -n1-pb-X    1    0.000       180.000           2.000     
+X -n1-pc-X    1    0.000       180.000           2.000     
+X -n1-pd-X    1    0.000       180.000           2.000     
+X -n1-pe-X    1    0.000       180.000           2.000     
+X -n1-pf-X    1    0.000       180.000           2.000     
+X -n1-p3-X    2    0.000       180.000           2.000     
+X -n1-p4-X    2    0.000       180.000           2.000     
+X -n1-px-X    2    0.000       180.000           2.000     
+X -n1-p5-X    3    0.000       180.000           2.000     
+X -n1-py-X    3    0.000       180.000           2.000     
+X -n1-s2-X    1    0.000       180.000           2.000     
+X -n1-sh-X    1    0.000       180.000           2.000     
+X -n1-ss-X    1    0.000       180.000           2.000     
+X -n1-s4-X    2    0.000       180.000           2.000     
+X -n1-sx-X    2    0.000       180.000           2.000     
+X -n1-s6-X    3    0.000       180.000           2.000     
+X -n1-sy-X    3    0.000       180.000           2.000     
+X -n2-n2-X    1    3.000       180.000          -2.000      double bond
+X -n2-n2-X    1    2.800         0.000           1.000      double bond
+X -n2-ne-X    1    3.000       180.000          -2.000      double bond
+X -n2-ne-X    1    2.800         0.000           1.000      double bond
+X -n2-nf-X    1    3.000       180.000          -2.000      double bond
+X -n2-nf-X    1    2.800         0.000           1.000      double bond
+X -ne-nf-X    1    3.000       180.000          -2.000      double bond
+X -ne-nf-X    1    2.800         0.000           1.000      double bond
+X -ne-ne-X    1    1.200       180.000           2.000      single bond, intrpol
+X -nf-nf-X    1    1.200       180.000           2.000      single bond, intrpol
+X -nc-nc-X    1    4.000       180.000           2.000      estimated, intrpol 
+X -nd-nd-X    1    4.000       180.000           2.000      estimated, intrpol  
+X -nc-nd-X    1    4.000       180.000           2.000      estimated, intrpol 
+X -n2-nc-X    1    3.000       180.000          -2.000      same as X-n2-n2-X
+X -n2-nc-X    1    2.800         0.000           1.000      
+X -n2-nd-X    1    3.000       180.000          -2.000      same as X-n2-n2-X 
+X -n2-nd-X    1    2.800         0.000           1.000      
+X -n2-n3-X    2   12.200       180.000           2.000
+X -ne-n3-X    2   12.200       180.000           2.000
+X -nf-n3-X    2   12.200       180.000           2.000
+X -n2-n4-X    3   24.000       180.000           2.000
+X -ne-n4-X    3   24.000       180.000           2.000
+X -nf-n4-X    3   24.000       180.000           2.000
+X -n2-na-X    2    3.400       180.000           2.000
+X -ne-na-X    2    3.400       180.000           2.000
+X -nf-na-X    2    3.400       180.000           2.000
+X -na-nc-X    2    9.600       180.000           2.000      estimated, intrpol.
+X -na-nd-X    2    9.600       180.000           2.000      estimated, intrpol.
+X -n2-nh-X    2    5.600       180.000           2.000
+X -ne-nh-X    2    5.600       180.000           2.000
+X -nf-nh-X    2    5.600       180.000           2.000
+X -n2-no-X    2    1.500       180.000           2.000
+X -ne-no-X    2    1.500       180.000           2.000
+X -nf-no-X    2    1.500       180.000           2.000
+X -n2-oh-X    1    3.200       180.000           2.000
+X -ne-oh-X    1    3.200       180.000           2.000
+X -nf-oh-X    1    3.200       180.000           2.000
+X -n2-os-X    1    3.000       180.000           2.000
+X -ne-os-X    1    3.000       180.000           2.000
+X -nf-os-X    1    3.000       180.000           2.000
+X -nc-os-X    1    4.800       180.000           2.000      estimated, intrpol.
+X -nc-ss-X    1    4.800       180.000           2.000      estimated, intrpol.
+X -n2-p2-X    1    5.400       180.000           2.000      estimated, intrpol.
+X -n2-pe-X    1    5.400       180.000           2.000      estimated, intrpol.
+X -n2-pf-X    1    5.400       180.000           2.000      estimated, intrpol.
+X -ne-pf-X    1    5.400       180.000           2.000      estimated, intrpol.
+X -n2-pc-X    1    5.400       180.000           2.000      estimated, intrpol.
+X -n2-pd-X    1    5.400       180.000           2.000      estimated, intrpol.
+X -nc-p2-X    1    5.400       180.000           2.000      estimated, intrpol.
+X -nd-p2-X    1    5.400       180.000           2.000      estimated, intrpol.
+X -nc-pc-X    1    6.600       180.000           2.000      estimated, intrpol.
+X -nd-pd-X    1    6.600       180.000           2.000      estimated, intrpol.
+X -nd-pc-X    1    6.600       180.000           2.000      estimated, intrpol. 
+X -nc-pd-X    1    6.600       180.000           2.000      estimated, intrpol. 
+X -ne-pe-X    1    0.600         0.000           1.000      single bond
+X -nf-pf-X    1    0.600         0.000           1.000      single bond
+X -n2-p3-X    2    4.200       180.000           2.000
+X -n2-p4-X    2   13.300       180.000           2.000      estimated  !!!
+X -ne-p4-X    2   13.300       180.000           2.000      estimated  !!!
+X -nf-p4-X    2   13.300       180.000           2.000      estimated  !!!
+X -n2-p5-X    3   20.000       180.000           2.000      estimated  !!!
+X -ne-p5-X    3    3.000       180.000           3.000
+X -nf-p5-X    3    3.000       180.000           3.000
+X -ne-px-X    3    3.000       180.000           3.000
+X -nf-px-X    3    3.000       180.000           3.000
+X -n2-sh-X    1    2.100       180.000           2.000
+X -ne-sh-X    1    2.100       180.000           2.000
+X -nf-sh-X    1    2.100       180.000           2.000
+X -n2-ss-X    1    2.800       180.000          -2.000
+X -n2-ss-X    1    1.300       180.000           1.000
+X -ne-ss-X    1    2.800       180.000          -2.000
+X -ne-ss-X    1    1.300       180.000           1.000
+X -nf-ss-X    1    2.800       180.000          -2.000
+X -nf-ss-X    1    1.300       180.000           1.000
+X -n2-s4-X    2   13.300       180.000           2.000      estimated !!!
+X -ne-sx-X    2    3.000       180.000           3.000
+X -nf-sx-X    2    3.000       180.000           3.000
+X -n2-s6-X    3   20.000       180.000           2.000      estimated  !!!
+X -ne-sy-X    3    1.500       180.000          -3.000
+X -ne-sy-X    3   20.400       180.000           1.000
+X -nf-sy-X    3    1.500       180.000          -3.000
+X -nf-sy-X    3   20.400       180.000           1.000
+X -n3-n3-X    4    9.000         0.000           2.000
+X -n3-n4-X    6    1.500         0.000           3.000
+X -n3-na-X    4    6.400         0.000           2.000
+X -n3-nh-X    4    7.600         0.000           2.000
+X -n3-no-X    4   16.000       180.000           2.000
+X -n3-oh-X    1    2.200         0.000           2.000
+X -n3-os-X    1    1.800         0.000           2.000
+X -n3-p2-X    2    6.400       180.000           2.000
+X -n3-pe-X    2    6.400       180.000           2.000
+X -n3-pf-X    2    6.400       180.000           2.000
+X -n3-p3-X    4    9.400         0.000           2.000
+X -n3-p4-X    4    8.400       180.000           2.000
+X -n3-px-X    4    8.400       180.000           2.000
+X -n3-p5-X    6   18.000       180.000           2.000
+X -n3-py-X    6   18.000       180.000           2.000
+X -n3-sh-X    1    3.100         0.000           2.000
+X -n3-ss-X    1    2.600         0.000           2.000
+X -n3-s4-X    4   15.000         0.000           2.000
+X -n3-sx-X    4   15.000         0.000           2.000
+X -n3-s6-X    6   18.800         0.000           2.000
+X -n3-sy-X    6   18.800         0.000           2.000
+X -n4-n4-X    9    1.700         0.000           3.000
+X -n4-na-X    6    1.400         0.000           3.000
+X -n4-nh-X    6    1.100         0.000           3.000
+X -n4-no-X    6    0.500       180.000           3.000
+X -n4-oh-X    3    1.000         0.000           3.000
+X -n4-os-X    3    1.700         0.000           3.000
+X -n4-p2-X    3    0.500       180.000           3.000
+X -n4-pe-X    3    0.500       180.000           3.000
+X -n4-pf-X    3    0.500       180.000           3.000
+X -n4-p3-X    6    0.900         0.000           3.000
+X -n4-p4-X    4    0.200         0.000           3.000
+X -n4-px-X    4    0.200         0.000           3.000
+X -n4-p5-X    9    0.800         0.000           3.000
+X -n4-py-X    9    0.800         0.000           3.000
+X -n4-sh-X    3    2.000         0.000           3.000
+X -n4-ss-X    3    1.000         0.000           3.000
+X -n4-s4-X    6    1.700         0.000           3.000
+X -n4-sx-X    6    1.700         0.000           3.000
+X -n4-s6-X    9    1.200         0.000           3.000
+X -n4-sy-X    9    1.200         0.000           3.000
+X -na-na-X    4    3.600         0.000           2.000
+X -na-nh-X    4    4.800         0.000           2.000
+X -na-no-X    4   24.000       180.000           2.000
+X -na-oh-X    2    2.000         0.000           2.000
+X -na-os-X    2    1.300         0.000           2.000
+X -na-p2-X    1    1.000       180.000           2.000
+X -na-pe-X    1    1.000       180.000           2.000
+X -na-pf-X    1    1.000       180.000           2.000
+X -na-p3-X    4    5.800         0.000           2.000
+X -na-p4-X    4    4.400         0.000           3.000
+X -na-px-X    4    4.400         0.000           3.000
+X -na-p5-X    6    5.000       180.000           2.000
+X -na-py-X    6    5.000       180.000           2.000
+X -na-sh-X    2    3.600         0.000           2.000
+X -na-ss-X    2   15.600         0.000           2.000
+X -na-s4-X    4    4.200         0.000           2.000
+X -na-sx-X    4    4.200         0.000           2.000
+X -na-s6-X    6   22.000       180.000           2.000
+X -na-sy-X    6   22.000       180.000           2.000
+X -nh-nh-X    4    7.200       180.000           3.000
+X -nh-no-X    4   10.200       180.000           2.000
+X -nh-oh-X    2    3.000         0.000           2.000
+X -nh-os-X    2    3.000         0.000           1.000
+X -nh-p2-X    2    2.800       180.000           2.000
+X -nh-pe-X    2    2.800       180.000           2.000
+X -nh-pf-X    2    2.800       180.000           2.000
+X -nh-p3-X    4    9.400         0.000           2.000
+X -nh-p4-X    4    4.700         0.000           3.000
+X -nh-px-X    4    4.700         0.000           3.000
+X -nh-p5-X    6    4.800         0.000           2.000
+X -nh-py-X    6    4.800         0.000           2.000
+X -nh-sh-X    2    3.200         0.000           2.000
+X -nh-ss-X    2    4.200         0.000           2.000
+X -nh-s4-X    4    3.000         0.000          -2.000
+X -nh-s4-X    4    0.400       180.000           3.000
+X -nh-sx-X    4    3.000         0.000          -2.000
+X -nh-sx-X    4    0.400       180.000           3.000
+X -nh-s6-X    6    0.600       180.000           2.000
+X -nh-sy-X    6    0.600       180.000           2.000
+X -no-no-X    4    1.600       180.000          -4.000
+X -no-no-X    4    7.200       180.000           2.000
+X -no-oh-X    2    7.800       180.000           2.000
+X -no-os-X    2    6.000       180.000           2.000
+X -no-p2-X    1    0.300       180.000           2.000
+X -no-pe-X    1    0.300       180.000           2.000
+X -no-pf-X    1    0.300       180.000           2.000
+X -no-p3-X    4    7.600       180.000           2.000
+X -no-p4-X    4    2.300       180.000           2.000
+X -no-px-X    4    2.300       180.000           2.000
+X -no-p5-X    6   14.400         0.000          -2.000
+X -no-p5-X    6    2.400         0.000           3.000
+X -no-py-X    6   14.400         0.000          -2.000
+X -no-py-X    6    2.400         0.000           3.000
+X -no-sh-X    2    4.600       180.000           2.000
+X -no-ss-X    2    5.400       180.000           2.000
+X -no-s4-X    4   10.400       180.000           2.000
+X -no-sx-X    4   10.400       180.000           2.000
+X -no-s6-X    6    2.000         0.000           2.000
+X -no-sy-X    6    2.000         0.000           2.000
+X -oh-oh-X    1    1.600         0.000           2.000
+X -oh-os-X    1    1.600         0.000           2.000
+X -oh-p2-X    1    1.500       180.000           2.000
+X -oh-pe-X    1    1.500       180.000           2.000
+X -oh-pf-X    1    1.500       180.000           2.000
+X -oh-p3-X    2    0.800       180.000           3.000
+X -oh-p4-X    2    1.400         0.000           1.000
+X -oh-px-X    2    1.400         0.000           1.000
+X -oh-p5-X    3    1.600         0.000           3.000
+X -oh-py-X    3    1.600         0.000           3.000
+X -oh-sh-X    1    2.400         0.000           2.000
+X -oh-ss-X    1    2.400         0.000           2.000
+X -oh-s4-X    2   10.000         0.000           1.000
+X -oh-sx-X    2   10.000         0.000           1.000
+X -oh-s6-X    3   28.500       180.000           1.000
+X -oh-sy-X    3   28.500       180.000           1.000
+X -os-os-X    1    1.000         0.000           1.000
+X -os-ss-X    1    2.200         0.000           2.000
+X -os-sh-X    1    1.800         0.000           2.000
+X -os-s4-X    2    3.300         0.000           3.000
+X -os-sx-X    2    3.300         0.000           3.000
+X -os-s6-X    3    3.600       180.000           2.000
+X -os-sy-X    3    3.600       180.000           2.000
+X -os-p2-X    1    3.000       180.000          -2.000
+X -os-p2-X    1    2.000       180.000           1.000
+X -os-pe-X    1    3.000       180.000          -2.000
+X -os-pe-X    1    2.000       180.000           1.000
+X -os-pf-X    1    3.000       180.000          -2.000
+X -os-pf-X    1    2.000       180.000           1.000
+X -os-p3-X    2    4.400         0.000           2.000
+X -os-p4-X    2    2.100       180.000           2.000
+X -os-px-X    2    2.100       180.000           2.000
+X -os-p5-X    3    2.400         0.000           2.000
+X -os-py-X    3    2.400         0.000           2.000
+X -p2-p2-X    1    6.600       180.000           2.000      estimated, intrpol.
+X -p2-pe-X    1    6.600       180.000           2.000      estimated, intrpol.
+X -p2-pf-X    1    6.600       180.000           2.000      estimated, intrpol.
+X -p2-pc-X    1    6.600       180.000           2.000      estimated, intrpol.
+X -p2-pd-X    1    6.600       180.000           2.000      estimated, intrpol.
+X -pe-pe-X    1    1.200       180.000           2.000      single bond
+X -pf-pf-X    1    1.200       180.000           2.000      single bond
+X -pc-pc-X    1    7.200       180.000           2.000      estimated, intrpol. 
+X -pd-pd-X    1    7.200       180.000           2.000      estimated, intrpol.  
+X -pc-pd-X    1    7.200       180.000           2.000      estimated, intrpol. 
+X -p2-p3-X    2    2.400         0.000           1.000
+X -pe-p3-X    2    2.400         0.000           1.000
+X -pf-p3-X    2    2.400         0.000           1.000
+X -p2-p4-X    2   13.300       180.000           2.000      estimated  !!!
+X -pe-px-X    2    4.900         0.000           2.000
+X -pf-px-X    2    4.900         0.000           2.000
+X -p2-p5-X    3   20.000       180.000           2.000      estimated  !!!
+X -pe-py-X    3    5.700         0.000           1.000
+X -pf-py-X    3    5.700         0.000           1.000
+X -p2-sh-X    1    1.400       180.000           2.000
+X -pe-sh-X    1    1.400       180.000           2.000
+X -pf-sh-X    1    1.400       180.000           2.000
+X -p2-ss-X    1    1.400       180.000           2.000
+X -pe-ss-X    1    1.400       180.000           2.000
+X -pf-ss-X    1    1.400       180.000           2.000
+X -p2-s4-X    2   13.300       180.000           2.000       estimated !!!
+X -pe-sx-X    2    3.000         0.000           2.000
+X -pf-sx-X    2    3.000         0.000           2.000
+X -p2-s6-X    3   20.000       180.000           2.000       estimated !!!
+X -pe-sy-X    3    1.200       180.000           3.000
+X -pf-sy-X    3    1.200       180.000           3.000
+X -p3-p3-X    4    2.000         0.000           3.000
+X -p3-p4-X    4    3.600         0.000           1.000
+X -p3-px-X    4    3.600         0.000           1.000
+X -p3-p5-X    6   11.000       180.000           2.000
+X -p3-py-X    6   11.000       180.000           2.000
+X -p3-sh-X    2    9.200         0.000           2.000
+X -p3-ss-X    2    2.300         0.000           3.000
+X -p3-ss-X    2    2.300         0.000           3.000
+X -p3-s4-X    4   15.400         0.000           2.000
+X -p3-sx-X    4   15.400         0.000           2.000
+X -p3-s6-X    6    1.600         0.000           3.000
+X -p3-sy-X    6    1.600         0.000           3.000
+X -p4-p4-X    4   26.600       180.000           2.000      estimated   !!!
+X -px-px-X    4    5.800       180.000           2.000
+X -p4-p5-X    6   39.900       180.000           2.000      estimated   !!!
+X -px-py-X    6    1.900       180.000           2.000
+X -p4-s4-X    4   26.600       180.000           2.000      estimated   !!!
+X -px-sx-X    4    3.400         0.000           1.000
+X -p4-s6-X    6   39.900       180.000           2.000      estimated   !!!
+X -px-sy-X    6    0.700         0.000           3.000
+X -p4-sh-X    2    0.500       180.000           1.000
+X -px-sh-X    2    0.500       180.000           1.000
+X -p4-ss-X    2    1.200       180.000           2.000
+X -px-ss-X    2    1.200       180.000           2.000
+X -p5-p5-X    9   60.000       180.000           2.000      estimated   !!!
+X -py-py-X    9    5.400         0.000           2.000
+X -p5-sh-X    3    0.900         0.000           3.000
+X -py-sh-X    3    0.900         0.000           3.000
+X -p5-ss-X    3   11.400       180.000           2.000
+X -py-ss-X    3   11.400       180.000           2.000
+X -p5-s4-X    6   40.000       180.000           2.000      estimated  !!!
+X -py-sx-X    6    1.600         0.000           3.000
+X -p5-s6-X    9   60.000       180.000           2.000      estimated  !!!
+X -py-sy-X    9    2.500         0.000           3.000
+X -sh-sh-X    1    5.600         0.000           3.000
+X -sh-ss-X    1    5.300         0.000           3.000
+X -sh-s4-X    2    1.400         0.000           3.000
+X -sh-sx-X    2    1.400         0.000           3.000
+X -sh-s6-X    3   14.000       180.000           2.000
+X -sh-sy-X    3   14.000       180.000           2.000
+X -ss-ss-X    1    0.000         0.000           3.000
+X -ss-s4-X    2    0.600         0.000           3.000
+X -ss-sx-X    2    0.600         0.000           3.000
+X -ss-s6-X    3    9.200       180.000           2.000
+X -ss-sy-X    3    9.200       180.000           2.000
+X -s4-s4-X    4   26.600       180.000           2.000       estimated !!!
+X -sx-sx-X    4    2.500         0.000           3.000
+X -s4-s6-X    6   40.000       180.000           2.000       estimated !!!
+X -sx-sy-X    6   26.000       180.000           2.000
+X -s6-s6-X    9   60.000       180.000           2.000       estimated !!!
+X -sy-sy-X    9    1.400       180.000           2.000
+c3-c -sh-hs   1    2.250       180.000          -2.000
+c3-c -sh-hs   1    1.300       180.000           1.000
+c2-c2-ss-c3   1    1.100       180.000          -2.000
+c2-c2-ss-c3   1    0.700       180.000           3.000
+c2-c2-n -c    1    0.650       180.000          -2.000
+c2-c2-n -c    1    1.200       180.000           1.000
+c -n -p2-c2   1    1.000       180.000          -2.000
+c -n -p2-c2   1    1.900       180.000           1.000
+n -c3-c -n    1    1.700       180.000          -1.
+n -c3-c -n    1    2.000       180.000           2.
+c -n -c3-c    1    0.850       180.000          -2.
+c -n -c3-c    1    0.800         0.000           1.
+c3-c3-n -c    1    0.50        180.0            -4.         phi,psi,parm94
+c3-c3-n -c    1    0.15        180.0            -3.         phi,psi,parm94
+c3-c3-n -c    1    0.53          0.0             1.         phi,psi,parm94
+c3-c3-c -n    1    0.100         0.0            -4.         phi,psi,parm94
+c3-c3-c -n    1    0.07          0.0             2.         phi,psi,parm94
+c2-ne-p5-o    1    2.30          0.0             1.         phi,psi,parm94
+c2-nf-p5-o    1    2.30          0.0             1.         phi,psi,parm94
+ce-ne-p5-o    1    2.30          0.0             1.         phi,psi,parm94
+ce-nf-p5-o    1    2.30          0.0             1.         phi,psi,parm94
+cf-ne-p5-o    1    2.30          0.0             1.         phi,psi,parm94
+cf-nf-p5-o    1    2.30          0.0             1.         phi,psi,parm94
+hn-n -c -o    1    2.50        180.0            -2.         JCC,7,(1986),230
+hn-n -c -o    1    2.00          0.0             1.         J.C.cistrans-NMA DE
+c3-ss-ss-c3   1    3.50          0.0            -2.         JCC,7,(1986),230
+c3-ss-ss-c3   1    0.60          0.0             3.         JCC,7,(1986),230
+c3-n3-nh-ca   1    1.90          0.0            -2.
+c3-n3-nh-ca   1    1.90          0.0             3.
+c3-n3-p5-o    1    3.00        180.0            -2.
+c3-n3-p5-o    1    2.30          0.0             3.
+ca-nh-oh-ho   1    1.20          0.0            -1.
+ca-nh-oh-ho   2    3.00          0.0             2.
+oh-p5-os-c3   1    0.25          0.0            -3.         JCC,7,(1986),230
+oh-p5-os-c3   1    1.20          0.0             2.         gg&gt ene.631g*/mp2
+os-p5-os-c3   1    0.25          0.0            -3.         JCC,7,(1986),230
+os-p5-os-c3   1    1.20          0.0             2.         gg&gt ene.631g*/mp2
+h1-c3-c -o    1    0.80          0.0            -1.         Junmei et al, 1999
+h1-c3-c -o    1    0.08        180.0             3.         Junmei et al, 1999
+hc-c3-c -o    1    0.80          0.0            -1.         Junmei et al, 1999
+hc-c3-c -o    1    0.08        180.0             3.         Junmei et al, 1999
+hc-c3-c3-hc   1    0.15          0.0             3.         Junmei et al, 1999
+hc-c3-c3-c3   1    0.16          0.0             3.         Junmei et al, 1999
+hc-c3-c2-c2   1    0.38        180.0            -3.         Junmei et al, 1999
+hc-c3-c2-c2   1    1.15          0.0             1.         Junmei et al, 1999
+ho-oh-c3-c3   1    0.16          0.0            -3.         Junmei et al, 1999
+ho-oh-c3-c3   1    0.25          0.0             1.         Junmei et al, 1999
+ho-oh-c -o    1    2.30        180.0            -2.         Junmei et al, 1999
+ho-oh-c -o    1    1.90          0.0             1.         Junmei et al, 1999
+c2-c2-c -o    1    2.175       180.0            -2.         Junmei et al, 1999
+c2-c2-c -o    1    0.30          0.0             3.         Junmei et al, 1999
+c3-c2-c2-c3   1    6.65        180.0            -2.         Junmei et al, 1999
+c3-c2-c2-c3   1    1.90        180.0             1.         Junmei et al, 1999
+c3-c3-c3-c3   1    0.18          0.0            -3.         Junmei et al, 1999
+c3-c3-c3-c3   1    0.25        180.0            -2.         Junmei et al, 1999
+c3-c3-c3-c3   1    0.20        180.0             1.         Junmei et al, 1999
+c3-c3-n3-c3   1    0.30          0.0            -3.         Junmei et al, 1999
+c3-c3-n3-c3   1    0.48        180.0             2.         Junmei et al, 1999
+c3-c3-os-c3   1    0.383         0.0            -3.
+c3-c3-os-c3   1    0.1         180.0             2.
+c3-c3-os-c    1    0.383         0.0            -3.         Junmei et al, 1999
+c3-c3-os-c    1    0.80        180.0             1.         Junmei et al, 1999
+c3-os-c3-os   1    0.10          0.0            -3.         Junmei et al, 1999
+c3-os-c3-os   1    0.85        180.0            -2.         Junmei et al, 1999
+c3-os-c3-os   1    1.35        180.0             1.         Junmei et al, 1999
+c3-os-c3-na   1    0.383         0.0            -3.         parm98.dat, TC,PC,PAK
+c3-os-c3-na   1    0.65          0.0             2.         Piotr et al.
+o -c -os-c3   1    2.70        180.0            -2.         Junmei et al, 1999
+o -c -os-c3   1    1.40        180.0             1.         Junmei et al, 1999
+os-c3-na-c2   1    0.00        000.0            -2.         parm98, TC,PC,PAK
+os-c3-na-c2   1    2.50          0.0             1.         parm98, TC,PC,PAK
+os-c3-c3-os   1    0.144         0.0            -3.         parm98, TC,PC,PAK
+os-c3-c3-os   1    1.175         0.0             2.         Piotr et al.
+os-c3-c3-oh   1    0.144         0.0            -3.         parm98, TC,PC,PAK
+os-c3-c3-oh   1    1.175         0.0             2.         parm98, TC,PC,PAK
+oh-c3-c3-oh   1    0.144         0.0            -3.         parm98, TC,PC,PAK
+oh-c3-c3-oh   1    1.175         0.0             2.         parm98, TC,PC,PAK
+f -c3-c3-f    1    1.20        180.0             1.         Junmei et al, 1999
+cl-c3-c3-cl   1    0.45        180.0             1.         Junmei et al, 1999
+br-c3-c3-br   1    0.00        180.0             1.         Junmei et al, 1999
+h1-c3-c3-os   1    0.25          0.0             1.         Junmei et al, 1999
+h1-c3-c3-oh   1    0.25          0.0             1.         Junmei et al, 1999
+h1-c3-c3-f    1    0.19          0.0             1.         Junmei et al, 1999
+h1-c3-c3-cl   1    0.25          0.0             1.         Junmei et al, 1999
+h1-c3-c3-br   1    0.55          0.0             1.         Junmei et al, 1999
+hc-c3-c3-os   1    0.25          0.0             1.         Junmei et al, 1999
+hc-c3-c3-oh   1    0.25          0.0             1.         Junmei et al, 1999
+hc-c3-c3-f    1    0.19          0.0             1.         Junmei et al, 1999
+hc-c3-c3-cl   1    0.25          0.0             1.         Junmei et al, 1999
+hc-c3-c3-br   1    0.55          0.0             1.         Junmei et al, 1999
+
+X -o -c -o          1.1          180.          2.           JCC,7,(1986),230
+X -X -c -o          10.5         180.          2.           JCC,7,(1986),230
+X -X -ca-ha         1.1          180.          2.           bsd.on C6H6 nmodes
+X -X -n -hn         1.1          180.          2.           JCC,7,(1986),230
+X -X -n2-hn         1.1          180.          2.           JCC,7,(1986),230
+X -X -na-hn         1.1          180.          2.           JCC,7,(1986),230
+X -c3-n -c3         1.1          180.          2.           JCC,7,(1986),230
+X -n2-ca-n2         10.5         180.          2.           JCC,7,(1986),230
+c -c2-c2-c3         1.1          180.          2.           dac guess, 9/94
+c -ca-ca-c3         1.1          180.          2.           dac guess, 9/94
+c -c3-n -hn         1.1          180.          2.           Junmei et al.1999
+c -c3-n -o          1.1          180.          2.           Junmei et al.1999
+c2-c2-na-c3         1.1          180.          2. 
+c2-c -c2-c3         1.1          180.          2. 
+c3-o -c -oh         1.1          180.          2. 
+c2-c3-c2-hc         1.1          180.          2.           Junmei et al.1999
+c2-c3-ca-hc         1.1          180.          2.           Junmei et al.1999
+c2-hc-c -o          1.1          180.          2.           Junmei et al.1999
+c3-o -c -oh         1.1          180.          2.
+c3-c2-c2-n2         1.1          180.          2.
+c3-c2-c2-na         1.1          180.          2.
+c3-ca-ca-n2         1.1          180.          2.
+c3-ca-ca-na         1.1          180.          2.
+ca-ca-ca-c2         1.1          180.          2. 
+ca-ca-ca-c3         1.1          180.          2. 
+ca-ca-ca-f          1.1          180.          2.           Junmei et al.1999
+ca-ca-ca-cl         1.1          180.          2.           Junmei et al.1999
+ca-ca-ca-br         1.1          180.          2.           Junmei et al.1999
+ca-ca-ca-i          1.1          180.          2.           Junmei et al.1999
+ca-ca-c -oh         1.1          180.          2.           (not used in tyr!)
+ca-ca-na-c3         1.1          180.          2.
+ca-c -ca-c3         1.1          180.          2. 
+ca-hc-c -o          1.1          180.          2.           Junmei et al.1999
+ca-n2-ca-n2         1.1          180.          2.           dac, 10/94
+hc-o -c -oh         1.1          180.          2.           Junmei et al.1999
+hc-o -c -os         1.1          180.          2.           
+n2-c2-ca-n2         1.1          180.          2.           dac guess, 9/94
+n2-ca-ca-c3         1.1          180.          2. 
+n2-ca-ca-n2         1.1          180.          2.           dac guess, 9/94
+na-ca-ca-c3         1.1          180.          2. 
+na-n2-ca-n2         1.1          180.          2.           dac, 10/94
+
+  hw  ow  0000.     0000.                                4.  flag for fast water
+
+n na n2 
+
+MOD4      RE
+  h1          1.3870  0.0157             Veenstra et al JCC,8,(1992),963 
+  h2          1.2870  0.0157             Veenstra et al JCC,8,(1992),963 
+  h3          1.1870  0.0157             Veenstra et al JCC,8,(1992),963 
+  h4          1.4090  0.0150             Spellmeyer, one electrowithdr. neighbor
+  h5          1.3590  0.0150             Spellmeyer, two electrowithdr. neighbor
+  ha          1.4590  0.0150             Spellmeyer 
+  hc          1.4870  0.0157             OPLS
+  hn          0.6000  0.0157            !Ferguson base pair geom.
+  ho          0.0000  0.0000             OPLS Jorgensen, JACS,110,(1988),1657
+  hp          0.6000  0.0157             same to hs (be careful !) 
+  hs          0.6000  0.0157             W. Cornell CH3SH --> CH3OH FEP
+  hw          0.0000  0.0000             OPLS Jorgensen, JACS,110,(1988),1657
+  hx          1.1000  0.0157             Veenstra et al JCC,8,(1992),963
+  o           1.6612  0.2100             OPLS
+  oh          1.7210  0.2104             OPLS 
+  os          1.6837  0.1700             OPLS ether
+  ow          1.7683  0.1520             TIP3P water model
+  c           1.9080  0.0860             OPLS
+  c1          1.9080  0.0860             cp C 
+  c2          1.9080  0.0860             sp2 atom in the middle of C=CD-CD=C
+  c3          1.9080  0.1094             OPLS
+  ca          1.9080  0.0860             OPLS
+  cc          1.9080  0.0860             OPLS
+  cd          1.9080  0.0860             OPLS
+  ce          1.9080  0.0860             OPLS
+  cf          1.9080  0.0860             OPLS
+  cg          1.9080  0.0860             OPLS
+  ch          1.9080  0.0860             OPLS
+  cp          1.9080  0.0860             OPLS
+  cq          1.9080  0.0860             OPLS
+  cu          1.9080  0.0860             OPLS
+  cv          1.9080  0.0860             OPLS
+  cx          1.9080  0.0860             OPLS
+  cy          1.9080  0.0860             OPLS
+  n           1.8240  0.1700             OPLS
+  n1          1.8240  0.1700             OPLS
+  n2          1.8240  0.1700             OPLS
+  n3          1.8240  0.1700             OPLS
+  n4          1.8240  0.1700             OPLS
+  na          1.8240  0.1700             OPLS
+  nb          1.8240  0.1700             OPLS
+  nc          1.8240  0.1700             OPLS
+  nd          1.8240  0.1700             OPLS
+  ne          1.8240  0.1700             OPLS
+  nf          1.8240  0.1700             OPLS
+  nh          1.8240  0.1700             OPLS
+  no          1.8240  0.1700             OPLS
+  s           2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
+  s2          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
+  s4          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
+  s6          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
+  sx          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
+  sy          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
+  sh          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
+  ss          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
+  p2          2.1000  0.2000             JCC,7,(1986),230; 
+  p3          2.1000  0.2000             JCC,7,(1986),230; 
+  p4          2.1000  0.2000             JCC,7,(1986),230; 
+  p5          2.1000  0.2000             JCC,7,(1986),230; 
+  pb          2.1000  0.2000             JCC,7,(1986),230; 
+  px          2.1000  0.2000             JCC,7,(1986),230; 
+  py          2.1000  0.2000             JCC,7,(1986),230; 
+  f           1.75    0.061              Gough et al. JCC 13,(1992),963.
+  cl          1.948   0.265              Fox, JPCB,102,8070,(98),flex.mdl CHCl3
+  br          2.22    0.320              Junmei
+  i           2.35    0.40               JCC,7,(1986),230;  
+
+END
+
+
+
+----------------------------------------------------------------------------
+		Miscellaneous 
+	!!!! gaff is still in development, for some molecules, the current version 
+	may have some problems. Please find the latest parameter file from 
+	www.amber.ucsf.edu/antechamber.html
+
+(1)	Parameters for p4 are not enough
+(2)     For bond lengty, bond angle and torsional angle parameters, hc and ha 
+        are the generic names of aliphatic and aromatic hydrogen connected 
+        to carbon, respectively.
+(3) 	Defination priority of nitrogen: n>n3, n>n4, n>nh, n2>n, no>n, na>n
+        n4>nh
+(5)     Although the four atom types are same, maybe there are several different
+        parameters correspond to different bond types. You may need to use 
+        additional atom types to apply them correctly (with antechamber package,
+        you can easily do this). 
+(4) 	Polarizabilities: mg2+ 0.120, f- 0.9743
+----------------------------------------------------------------------------
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/gaff.prm	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,222 @@
+//
+// Copyright (C) 2009 by Frank Peters <e.a.j.f.peters@tue.nl>
+// 
+// This is a SMARTS template-file for GAFF-atom types
+//
+// It is attempted to obey the typing given in the "ATOMTYPE_GFF.DEF"
+// file included with the antechamber package of amber10.
+// There is no 1-to-1 correspondence between the ATD format and SMARTS.
+// Therefore the current definitions need to be tested and possibly changed
+//
+//
+//
+// GAFF atomtypes defined using SMARTS 
+// [SMARTS] [atomtype id number] [description]
+// must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE!
+//
+// Be careful lines do not exceed the maximum length of 80!
+
+atom [*]                X
+atom [#1X1]             ha    "other hydrogen e.g. on aromatic C"
+atom [#1X1][CX4]        hc    "hydrogen on aliphatic C"
+// "hydrogen on aliphatic C with 1 ewd"
+atom [#1X1][CX4][#7,#8,#16,#17,#35,#53]        h1  
+// "hydrogen on aliphatic C with 2 ewd"
+atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53]  h2  
+// "hydrogen on aliphatic C with 3 ewd"
+atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#7,#8] h3
+atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#16,#17] h3
+atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#35,#53] h3
+// "hydrogen on sp2 C with 1 ewd"
+atom [#1X1][#6X3][#7,#8,#16,#17,#35,#53]                            h4  
+// "hydrogen on sp2 C with 2 ewd"
+atom [#1X1][#6X3]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53]   h5  
+atom [#1X1][#6](N)(N)(N)N hx  ""
+atom [#1X1]O            ho    "hydrogen on oxygen"
+atom [#1X1][Oh1]        hw    "hydrogen on water"
+atom [#1X1]N            hn    "nitrogen"
+atom [#1X1]S            hs    "sulphur"
+atom [#1X1]P            hp    "phosphor"
+atom [#6X4]             c3    "other sp3 C"
+atom [#6X4r3]           cx    "3-membered ring atom"
+atom [#6X4r4]           cy    "4-membered ring atom"
+atom [#6X3]             c2    "other sp2 C"
+atom [#6X3]=[O,S]       c     "C=O or C=S"
+atom [#6X3](N)(N)N      cz    ""
+atom [#6X3;R](=*)-*=*   cc    "inner sp2 C of conjugated ring systems"
+atom [#6X3;R](=*)-*#*   cc    "inner sp2 C of conjugated ring systems"
+atom [#6X3;R](#*)-*#*   cc    "inner sp2 C of conjugated ring systems"
+atom [#6X3;!R](=*)-*=*  ce    "inner sp2 C of conjugated ring systems"
+atom [#6X3;!R](#*)-*=*  ce    "inner sp2 C of conjugated ring systems"
+atom [#6X3;!R](#*)-*#*  ce    "inner sp2 C of conjugated ring systems"
+atom [cr6](c)(c)c       cp    "bridge aromatic c in byphenyl system"
+atom [#6X3r3]           cu    "sp2 carbon in a 3-membered ring"
+atom [#6X3r4]           cv    "sp2 carbon in a 4-membered ring"
+atom [c]                ca    "pure aromatic atom"
+atom [#6X2]             c1    "other sp C"
+atom [#6X2](=*)-*=*     cg    "sp C of conjugated system"
+atom [#6X2](#*)-*=*     cg    "sp C of conjugated system"
+atom [#6X2](#*)-*#*     cg    "sp C of conjugated system"
+atom [#6X1]             c1    "other sp C"
+
+atom [F]*               f    (-*) "general fluorine"
+atom [Cl]*              cl   (-*) "general chlorine"
+atom [Br]*              br   (-*) "general bromine"
+atom [I]*               i    (-*) "general iodine"
+
+atom [#15X1]            p2    "other sp2 P"
+atom [#15X2]            p2    "other sp2 P"
+atom [#15X2;R](=*)-*=*  pc    "inner sp2 P of conjugated ring systems"
+atom [#15X2;R](=*)-*#*  pc    "inner sp2 P of conjugated ring systems"
+atom [#15X2;R](#*)-*#*  pc    "inner sp2 P of conjugated ring systems"
+atom [#15X2;!R](=*)-*=* pe    "inner sp2 P of conjugated chain system"
+atom [#15X2;!R](=*)-*#* pe    "inner sp2 P of conjugated chain system"
+atom [#15X2;!R](#*)-*#* pe    "inner sp2 P of conjugated chain system"
+atom [#15;a]            pb    "aromatic P"
+atom [#15X3]            p3    "other sp3 P"
+atom [#15X3](=*)-*=*    px    "sp2 P of conjugated system"
+atom [#15X3](=*)-*#*    px    "sp2 P of conjugated system"
+atom [#15X3]=[O,S]      p4    "hypervalent P"
+atom [#15X4]            p5    "hypervalent P"
+atom [#15X4](=*)-*=*    py    "P of conjugated system"
+atom [#15X4](=*)-*#*    py    "P of conjugated system"
+atom [#15X5]            p5    "hypervalent P"
+atom [#15X6]            p5    "hypervalent P"
+
+atom [#7X1]             n1    "sp1 N"
+
+atom [#7X2]             n2    "sp2 N"
+atom [#7X2](=*)=*       n1    "sp1 N"
+atom [#7X2](-*)#*       n1    "sp1 N"
+atom [#7X2;R](=*)-*=*   nc    "inner sp2 N of conjugated ring systems"
+atom [#7X2;R](=*)-*#*   nc    "inner sp2 N of conjugated ring systems"
+atom [#7X2;R](#*)-*#*   nc    "inner sp2 N of conjugated ring systems"
+atom [#7X2;!R](=*)-*=*  ne    "inner sp2 N of conjugated chain system"
+atom [#7X2;!R](=*)-*#*  ne    "inner sp2 N of conjugated chain system"
+atom [#7X2;!R](#*)-*#*  ne    "inner sp2 N of conjugated chain system"
+atom [nX2]              nb    "aromatic N"
+
+atom [#7X3]             n3    "sp3 N"
+atom [#7X3]a            nh    "amine N connected to aromatic ring"
+atom [#7X3]=[CX3]       nh    ""
+atom [#7X3]=[N2]        nh    ""
+atom [#7X3]=[P2]        nh    ""
+atom [#7X3]-[CX3]=[O,S] n     "sp2 N in amides"
+atom [#7X3](O)O         no    "N in nitro group"
+atom [nX3]              na    "aromatic N"
+
+atom [#7X4]             n4    "sp3 N"
+
+atom [OX1]              o     "sp2 O"
+atom [OX2]              os    "sp3 O in esters and ethers"
+atom [OX3]              os    "sp3 O in esters and ethers"
+atom [OX2H]             oh    "sp3 O in hydroxyl group"
+atom [OX3H]             oh    "sp3 O in hydroxyl group"
+
+atom [SX1]              s     ""
+atom [SX2]              ss    "sp3 sulphur"
+atom [SX2]=*            s2    "sp2 sulphur"
+atom [SX2]#*            s2    "sp2 sulphur"
+atom [SX2H]            sh    "sp3 S in thiol"
+atom [SX3]              s4    "hypervalent S"
+atom [SX3](=*)-*=*      sx    "conjugated S"
+atom [SX3](=*)-*#*      sx    "conjugated S"
+atom [SX4]              s6    "hypervalent S"
+atom [SX4](=*)-*=*      sy    "conjugated S"
+atom [SX4](=*)-*#*      sy    "conjugated S"
+atom [SX5]              s6    "hypervalent S"
+atom [SX6]              s6    "hypervalent S"
+
+atom [He]               He    ""
+atom [Li]               Li    ""
+atom [Be]               Be    ""
+atom [B]                B     ""
+atom [Ne]               Ne    ""
+atom [Na]               Na    ""
+atom [Mg]               Mg    ""
+atom [Al]               Al    ""
+atom [Si]               Si    ""
+atom [Ar]               Ar    ""
+atom [K]                K     ""
+atom [Ca]               Ca    ""
+atom [Sc]               Sc    ""
+atom [Ti]               Ti    ""
+atom [V]                V     ""
+atom [Cr]               Cr    ""
+atom [Mn]               Mn    ""
+atom [Fe]               Fe    ""
+atom [Co]               Co    ""
+atom [Ni]               Ni    ""
+atom [Cu]               Cu    ""
+atom [Zn]               Zn    ""
+atom [Ga]               Ga    ""
+atom [Ge]               Ge    ""
+atom [As]               As    ""
+atom [Se]               Se    ""
+atom [Kr]               Kr    ""
+atom [Rb]               Rb    ""
+atom [Sr]               Sr    ""
+atom [Y]                Y     ""
+atom [Zr]               Zr    ""
+atom [Nb]               Nb    ""
+atom [Mo]               Mo    ""
+atom [Tc]               Tc    ""
+atom [Ru]               Ru    ""
+atom [Rh]               Rh    ""
+atom [Pd]               Pd    ""
+atom [Ag]               Ag    ""
+atom [Cd]               Cd    ""
+atom [In]               In    ""
+atom [Sn]               Sn    ""
+atom [Sb]               Sb    ""
+atom [Te]               Te    ""
+atom [Xe]               Xe    ""
+atom [Cs]               Cs    ""
+atom [Ba]               Ba    ""
+atom [La]               La    ""
+atom [Ce]               Ce    ""
+atom [Pr]               Pr    ""
+atom [Nd]               Nd    ""
+atom [Pm]               Pm    ""
+atom [Sm]               Sm    ""
+atom [Eu]               Eu    ""
+atom [Gd]               Gd    ""
+atom [Tb]               Tb    ""
+atom [Dy]               Dy    ""
+atom [Ho]               Ho    ""
+atom [Er]               Er    ""
+atom [Tm]               Tm    ""
+atom [Yb]               Yb    ""
+atom [Lu]               Lu    ""
+atom [Hf]               Hf    ""
+atom [Ta]               Ta    ""
+atom [W]                W     ""
+atom [Re]               Re    ""
+atom [Os]               Os    ""
+atom [Ir]               Ir    ""
+atom [Pt]               Pt    ""
+atom [Au]               Au    ""
+atom [Hg]               Hg    ""
+atom [Tl]               Tl    ""
+atom [Pb]               Pb    ""
+atom [Bi]               Bi    ""
+atom [Po]               Po    ""
+atom [At]               At    ""
+atom [Rn]               Rn    ""
+atom [Fr]               Fr    ""
+atom [Ra]               Ra    ""
+atom [Ac]               Ac    ""
+atom [Th]               Th    ""
+atom [Pa]               Pa    ""
+atom [U]                U     ""
+atom [Np]               Np    ""
+atom [Pu]               Pu    ""
+atom [Am]               Am    ""
+atom [Cm]               Cm    ""
+atom [Bk]               Bk    ""
+atom [Cf]               Cf    ""
+atom [Es]               Es    ""
+atom [Fm]               Fm    ""
+atom [Md]               Md    ""
+atom [No]               No    ""
+atom [Lr]               Lr    ""
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/genheaders.sh	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+./bin2hex.pl aromatic.txt AromaticData >aromatic.h
+./bin2hex.pl atomtyp.txt AtomTypeData >atomtyp.h
+./bin2hex.pl bondtyp.txt BondTypeData >bondtyp.h
+./bin2hex.pl element.txt ElementData >element.h
+./bin2hex.pl isotope-small.txt IsotopeData ISOTOPE >isotope.h
+./bin2hex.pl phmodel.txt PhModelData PHMODELDATA >phmodeldata.h
+./bin2hex.pl resdata.txt ResidueData >resdata.h
+./bin2hex.pl torlib.txt TorsionDefaults >torlib.h
+./bin2hex.pl types.txt TypesData >types.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/ghemical.prm	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,476 @@
+//
+// The parameters int his file are taken from ghemical.
+//
+
+// atomtypes and typerules 09.05.2000 (based on Tripos 5.2 and MMFF94)
+// [SMARTS] [atomtype id number] [typerule] [description]
+//
+// must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE!!!
+
+atom [*]         FFFF
+atom [#1]        0100 (-*) "general hydrogen"
+atom [#6]        0600 (-*) "general sp3 carbon"
+atom [#6]=*      0601 (=*) "general sp2 carbon"
+atom [#6]#*      0602 (#*) "general sp carbon"
+atom [#6](=*)=*  0602 (=*,=*) "allenic sp carbon"
+atom [c]         0603 (~*,~*) "aromatic sp2 carbon"
+//atom [#6^3r3]  0604 ([-*?*-]) "sp3 carbon in a 3-membered ring"
+//atom [#6^3r4]  0605 ([-*?*?*-]) "sp3 carbon in a 4-membered ring"
+atom [N]         0700 (-*) "general sp3 nitrogen"
+atom [N]=*       0701 (=*) "general sp2 nitrogen"
+atom [N]#*       0702 (#*) "general sp nitrogen"
+atom [n]         0703 (~*,~*) "aromatic sp2 nitrogen"
+atom [ND4]       0704 (-*,-*,-*,-*) "ammonium nitrogen"
+atom [#7][C]=O   0705 (-C(=O)) "amide nitrogen"
+atom [O]         0800 (-*) "general sp3 oxygen"
+atom [O]=*       0801 (=*) "general sp2 oxygen"
+atom [F]*        0900 (-*) "general fluorine"
+atom [P]         0F00 (-*) "general sp3 phosphorus"
+atom [S]         1000 (-*) "general sp3 sulphur"
+atom [S]=*       1001 (=*) "general sp2 sulphur"
+atom [S]=[#8]    1002 (=O) "sulfoxide sulphur"
+atom [S](=O)=O   1003 (=O,=O) "sulfone sulphur"
+atom [Cl]*       1100 (-*) "general chlorine"
+atom [Br]*       2300 (-*) "general bromine"
+atom [I]*        3500 (-*) "general iodine"
+
+// bond stretching parameters 09.05.2000 (based on Tripos 5.2 and MMFF94)
+// [id #1] [id #2] [bondtype] [opt] [fc]
+//
+// wildcard atomtype is FFFF !!!!!!!!!!!!!!!!!!!!!!!!!!!
+// wildcard atomtype is FFFF !!!!!!!!!!!!!!!!!!!!!!!!!!!
+// wildcard atomtype is FFFF !!!!!!!!!!!!!!!!!!!!!!!!!!!
+//
+// parameters containing those should be left last since the first matching
+// one is chosen. that is, choose normal parameters if there is any matching
+// one, and take wildcarded one only if there is no better choice...
+//
+// [opt] = Å
+// [fc] = kcal/(mol * Å^2)
+
+bond 	0602 0602 T 1.204 1400.0
+bond 	0602 0602 S 1.380  700.0
+bond	2300 0601 S 1.890  500.0
+bond	0602 0601 S 1.440 1340.0
+bond	0602 0601 D 1.440 1340.0
+bond	0601 0601 D 1.335 1340.0
+bond	0601 0601 S 1.470  700.0
+bond	0602 0600 S 1.458  640.0
+bond	0601 0600 S 1.501  639.0
+bond	0600 0600 S 1.540  633.6
+bond	2300 0603 S 1.850  500.0
+bond	0602 0603 S 1.440 1340.0
+bond	0601 0603 S 1.510 1340.0
+bond	0600 0603 S 1.525  640.0
+bond	0603 0603 C 1.395 1400.0
+bond	0603 0603 S 1.480 1000.0
+bond	0601 1100 S 1.750  520.0
+bond	0600 1100 S 1.767  600.0
+bond	0603 1100 S 1.750  513.4
+bond	0601 2300 S 1.850  520.0
+bond	0600 2300 S 1.867  600.0
+bond	0603 2300 S 1.850  513.4
+bond	0601 0900 S 1.330 1200.0
+bond	0600 0900 S 1.360  600.0
+bond	0603 0900 S 1.330  500.0
+bond	0602 0100 S 1.056  700.0
+bond	0601 0100 S 1.089  692.0
+bond	0600 0100 S 1.100  662.4
+bond	0603 0100 S 1.084  692.0
+bond	0600 3500 S 2.050  490.0	//added 20050225
+bond	0601 3500 S 2.050  490.0	//added 20050225
+bond	0602 3500 S 2.050  490.0	//added 20050225
+bond	0603 3500 S 2.050  490.0
+bond	0602 0702 T 1.158 1600.0
+bond	0602 0701 S 1.330 1300.0
+bond	0602 0701 D 1.330 1300.0
+bond	0601 0701 D 1.270 1305.9
+bond	0601 0701 S 1.444 1300.0
+bond	0600 0701 S 1.440  760.2
+bond	0603 0701 S 1.346 1305.9
+bond	0701 0701 D 1.346 1305.9
+bond	0701 0701 S 1.418 1300.0
+bond	0601 0700 S 1.330 1300.0
+bond	0600 0700 S 1.470  760.0
+bond	0603 0700 S 1.410  720.0
+bond	0100 0700 S 1.080  692.0
+bond	0601 0704 S 1.330 1300.0
+bond	0600 0704 S 1.470  760.0
+bond	0603 0704 S 1.410  720.0
+bond	0601 0705 S 1.345  870.1
+bond	0600 0705 S 1.450  677.6
+bond	0603 0705 S 1.416 1090.1
+bond	0100 0705 S 1.000  700.0
+bond	0701 0705 S 1.440  667.6
+bond	0705 0705 S 1.450  744.5
+bond	0603 0703 C 1.346 1305.9
+bond	0703 0703 C 1.330 1400.0
+bond	0601 0801 D 1.220 1555.2
+bond	0705 0801 S 1.240 1120.0
+bond	0705 0801 D 1.210  680.0
+bond	0601 0800 S 1.330  699.8
+bond	0600 0800 S 1.430  618.9
+bond	0603 0800 S 1.390  700.0
+bond	0100 0800 S 0.950 1007.5
+bond	0701 0800 S 1.405 1200.0
+bond	0705 0800 S 1.400  620.0
+bond	0800 0800 S 1.480 1172.2
+bond	0600 0F00 S 1.830  407.6
+bond	0801 0F00 S 1.490 1400.0
+bond	0801 0F00 D 1.490 1400.0
+bond	0800 0F00 S 1.600  800.0
+bond	0601 1001 D 1.710  400.0
+bond	0600 1001 S 1.800  381.6
+bond	0603 1001 S 1.740  700.0
+bond	0601 1000 S 1.780  360.0
+bond	0600 1000 S 1.817  381.6
+bond	0603 1000 S 1.770  360.0
+bond	0700 1000 S 1.625  360.0
+bond	0704 1000 S 1.625  360.0
+bond	0801 1000 D 1.450  600.0
+bond	1000 1000 S 2.030  600.0
+bond	0601 1002 S 1.710  360.0
+bond	0600 1002 S 1.800  381.6
+bond	0801 1002 D 1.450  600.0
+bond	0800 1002 S 1.500  600.0
+bond	0600 1003 S 1.800  381.6
+bond	0801 1003 D 1.450  600.0
+bond	0800 1003 S 1.500  600.0
+bond	FFFF 0100 S 1.008  700.0
+
+// angle bending parameters 09.05.2000 (based on Tripos 5.2 and MMFF94)
+// [id #1] [id #2] [id #3] [bt12][bt23] [opt] [fc]
+//
+// ordering should be made similarly as in parameters1.txt!!!!!!!
+// original Tripos 5.2 did not contain the bond types here at all...
+//
+// [opt] = deg
+// [fc] = kcal/(mol * deg^2)
+
+angle	0602 0602 0601 ?? 180.0 0.040
+angle	0601 0602 0702 ?? 180.0 0.040
+angle	0600 0602 0702 ?? 180.0 0.040
+angle	0603 0602 0702 ?? 180.0 0.040
+angle	0702 0602 0800 ?? 180.0 0.040
+angle	2300 0601 2300 ?? 120.0 0.020
+angle	2300 0601 0601 ?? 120.0 0.036
+angle	0601 0601 0601 ?? 121.7 0.018
+angle	0602 0601 0600 ?? 120.0 0.024
+angle	0601 0601 0600 ?? 121.0 0.024
+angle	0600 0601 0600 ?? 116.4 0.046
+angle	0602 0601 0603 ?? 120.0 0.024
+angle	0601 0601 0603 ?? 120.0 0.026
+angle	0600 0601 0603 ?? 120.0 0.024
+angle	0603 0601 0603 ?? 120.0 0.024
+angle	0601 0601 1100 ?? 120.0 0.036
+angle	0603 0601 1100 ?? 120.0 0.036
+angle	1100 0601 1100 ?? 122.0 0.030
+angle	0601 0601 2300 ?? 120.0 0.036
+angle	0603 0601 2300 ?? 120.0 0.036
+angle	2300 0601 2300 ?? 122.0 0.030
+angle	0602 0601 0701 ?? 123.0 0.070
+angle	0601 0601 0701 ?? 120.0 0.024
+angle	0600 0601 0701 ?? 118.0 0.020
+angle	0603 0601 0701 ?? 120.0 0.040
+angle	0601 0601 0700 ?? 120.0 0.024
+angle	0600 0601 0700 ?? 118.0 0.040
+angle	0701 0601 0700 ?? 121.8 0.030
+angle	0700 0601 0700 ?? 116.4 0.030
+angle	0601 0601 0705 ?? 120.0 0.024
+angle	0600 0601 0705 ?? 117.0 0.020
+angle	0603 0601 0705 ?? 120.0 0.040
+angle	0701 0601 0705 ?? 123.0 0.070
+angle	0705 0601 0705 ?? 120.0 0.030
+angle	0602 0601 0801 ?? 120.0 0.060
+angle	0601 0601 0801 ?? 120.0 0.026
+angle	0600 0601 0801 ?? 120.0 0.026
+angle	0603 0601 0801 ?? 120.0 0.026
+angle	0700 0601 0801 ?? 120.0 0.026
+angle	0705 0601 0801 ?? 123.0 0.030
+angle	0601 0601 0800 ?? 120.0 0.072
+angle	0600 0601 0800 ?? 114.0 0.030
+angle	0603 0601 0800 ?? 120.0 0.030
+angle	0705 0601 0800 ?? 110.5 0.014
+angle	0801 0601 0800 ?? 120.0 0.030
+angle	0701 0601 1000 ?? 125.6 0.028
+angle	0705 0601 1000 ?? 111.5 0.030
+angle	0801 0601 1000 ?? 125.0 0.016
+angle	0601 0600 0601 ?? 109.5 0.018
+angle	0602 0600 0600 ?? 109.5 0.024
+angle	0601 0600 0600 ?? 109.5 0.018
+angle	0600 0600 0600 ?? 109.5 0.024
+angle	0601 0600 0603 ?? 109.5 0.018
+angle	0600 0600 0603 ?? 109.5 0.024
+angle	0603 0600 0603 ?? 109.5 0.018
+angle	0600 0600 1100 ?? 109.5 0.020
+angle	1100 0600 1100 ?? 109.5 0.020
+angle	0600 0600 2300 ?? 109.5 0.020
+angle	2300 0600 2300 ?? 109.5 0.020
+angle	0603 0600 0900 ?? 110.0 0.024
+angle	0900 0600 0900 ?? 109.5 0.040
+angle	0601 0600 0100 ?? 110.0 0.016
+angle	0100 0600 0100 ?? 109.5 0.024
+angle	0600 0600 0701 ?? 109.5 0.018
+angle	0601 0600 0700 ?? 109.5 0.018
+angle	0600 0600 0700 ?? 109.5 0.024
+angle	0603 0600 0700 ?? 109.5 0.018
+angle	0601 0600 0705 ?? 109.5 0.022
+angle	0600 0600 0705 ?? 109.5 0.018
+angle	0603 0600 0705 ?? 109.5 0.020
+angle	0100 0600 0705 ?? 110.0 0.020
+angle	0701 0600 0705 ?? 109.5 0.020
+angle	0705 0600 0705 ?? 109.5 0.040
+angle	0900 0600 0703 ?? 109.5 0.040
+angle	0601 0600 0800 ?? 109.5 0.022
+angle	0600 0600 0800 ?? 109.5 0.022
+angle	0603 0600 0800 ?? 109.5 0.018
+angle	0705 0600 0800 ?? 109.5 0.020
+angle	0800 0600 0800 ?? 109.5 0.020
+angle	0600 0600 0F00 ?? 112.0 0.014
+angle	0601 0600 1001 ?? 109.5 0.018
+angle	0600 0600 1001 ?? 109.5 0.018
+angle	0705 0600 1001 ?? 109.5 0.040
+angle	0601 0600 1000 ?? 107.8 0.018
+angle	0600 0600 1000 ?? 107.8 0.018
+angle	0603 0600 1000 ?? 107.8 0.018
+angle	0705 0600 1000 ?? 109.5 0.024
+angle	0800 0600 1000 ?? 107.8 0.020
+angle	2300 0603 0603 ?? 120.0 0.036
+angle	0601 0603 0603 ?? 120.0 0.024
+angle	0600 0603 0603 ?? 120.0 0.024
+angle	0603 0603 0603 ?? 120.0 0.024
+angle	0603 0603 1100 ?? 120.0 0.036
+angle	0603 0603 2300 ?? 120.0 0.036
+angle	0603 0603 0900 ?? 120.0 0.036
+angle	0603 0603 3500 ?? 120.0 0.036
+angle	0600 0603 0701 ?? 120.0 0.040
+angle	0603 0603 0701 ?? 120.0 0.040
+angle	0701 0603 0701 ?? 120.0 0.040
+angle	0603 0603 0700 ?? 120.0 0.062
+angle	0600 0603 0705 ?? 120.0 0.040
+angle	0603 0603 0705 ?? 120.0 0.062
+angle	0701 0603 0705 ?? 118.0 0.040
+angle	0705 0603 0705 ?? 120.0 0.030
+angle	0601 0603 0703 ?? 120.0 0.040
+angle	0600 0603 0703 ?? 120.0 0.040
+angle	0603 0603 0703 ?? 120.0 0.024
+angle	0705 0603 0703 ?? 118.0 0.040
+angle	0600 0603 0800 ?? 120.0 0.040
+angle	0603 0603 0800 ?? 120.0 0.062
+angle	0603 0603 1001 ?? 120.0 0.062
+angle	0603 0603 1000 ?? 120.0 0.062
+angle	0602 0701 0601 ?? 120.0 0.040
+angle	0601 0701 0601 ?? 123.0 0.080
+angle	0601 0701 0600 ?? 110.0 0.082
+angle	0601 0701 0603 ?? 123.0 0.080
+angle	0600 0701 0603 ?? 110.0 0.082
+angle	0603 0701 0603 ?? 120.0 0.040
+angle	0601 0701 0701 ?? 112.0 0.044
+angle	0600 0701 0701 ?? 118.0 0.040
+angle	0603 0701 0701 ?? 118.0 0.040
+angle	0601 0701 0705 ?? 120.0 0.044
+angle	0601 0701 0800 ?? 105.0 0.044
+angle	0601 0700 0600 ?? 110.0 0.040
+angle	0600 0700 0600 ?? 109.5 0.018
+angle	0600 0700 0603 ?? 118.0 0.040
+angle	0603 0700 0603 ?? 118.0 0.040
+angle	0600 0700 1001 ?? 109.5 0.040
+angle	0600 0704 0600 ?? 109.5 0.018
+angle	0601 0705 0601 ?? 120.0 0.018
+angle	0601 0705 0600 ?? 118.0 0.044
+angle	0600 0705 0600 ?? 122.0 0.040
+angle	0601 0705 0603 ?? 120.0 0.052
+angle	0600 0705 0603 ?? 118.0 0.044
+angle	0603 0705 0603 ?? 120.0 0.044
+angle	0601 0705 0100 ?? 119.0 0.016
+angle	0600 0705 0100 ?? 117.0 0.020
+angle	0601 0705 0701 ?? 120.0 0.018
+angle	0600 0705 0701 ?? 120.0 0.024
+angle	0603 0705 0701 ?? 109.5 0.044
+angle	0601 0705 0705 ?? 120.0 0.018
+angle	0600 0705 0705 ?? 120.0 0.024
+angle	0603 0705 0705 ?? 120.0 0.052
+angle	0601 0705 0801 ?? 120.0 0.024
+angle	0600 0705 0801 ?? 120.0 0.020
+angle	0603 0705 0801 ?? 120.0 0.024
+angle	0801 0705 0801 ?? 120.0 0.020
+angle	0603 0703 0603 ?? 120.0 0.040
+angle	0601 0800 0601 ?? 110.0 0.020
+angle	0601 0800 0600 ?? 109.5 0.044
+angle	0600 0800 0600 ?? 109.5 0.044
+angle	0601 0800 0603 ?? 110.0 0.020
+angle	0600 0800 0603 ?? 110.0 0.020
+angle	0603 0800 0603 ?? 110.0 0.020
+angle	0601 0800 0701 ?? 108.5 0.044
+angle	0600 0800 0800 ?? 103.9 0.094
+angle	0600 0800 0F00 ?? 120.0 0.010
+angle	0801 0F00 0801 ?? 109.5 0.020
+angle	0801 0F00 0800 ?? 109.5 0.020
+angle	0800 0F00 0800 ?? 109.5 0.020
+angle	0600 1001 0700 ?? 111.0 0.040
+angle	0603 1001 0700 ?? 111.0 0.040
+angle	0601 1000 0600 ??  94.3 0.022
+angle	0600 1000 0600 ??  98.0 0.020
+angle	0603 1000 0603 ??  97.5 0.062
+angle	0603 1000 1000 ?? 102.9 0.060
+angle	0801 1003 0801 ?? 118.0 0.040
+angle	FFFF 0601 0100 ?? 120.0 0.012
+angle	FFFF 0600 0100 ?? 109.5 0.016
+angle	FFFF 1002 0801 ?? 107.0 0.040
+angle	FFFF 1003 0801 ?? 107.0 0.040
+angle	FFFF 0602 FFFF ?? 180.0 0.040
+angle	FFFF 0601 FFFF ?? 120.0 0.024
+angle	FFFF 0600 FFFF ?? 109.5 0.020
+angle	FFFF 0603 FFFF ?? 120.0 0.024
+angle	FFFF 0702 FFFF ?? 180.0 0.080
+angle	FFFF 0701 FFFF ?? 120.0 0.040
+angle	FFFF 0700 FFFF ?? 109.5 0.040
+angle	FFFF 0704 FFFF ?? 109.5 0.010
+angle	FFFF 0705 FFFF ?? 120.0 0.020
+angle	FFFF 0703 FFFF ?? 120.0 0.020
+angle	FFFF 0800 FFFF ?? 109.5 0.020
+angle	FFFF 0F00 FFFF ?? 109.5 0.020
+angle	FFFF 1001 FFFF ?? 110.5 0.040
+angle	FFFF 1000 FFFF ??  97.0 0.020
+
+// torsion parameters 09.05.2000 (based on Tripos 5.2 and MMFF94)
+// [id #1] [id #2] [id #3] [id #4] [bt12][bt23][bt34] [k] [n] [s]
+//
+// ordering should be made similarly as in parameters1.txt!!!!!!!
+// original Tripos 5.2 did not contain all these bond types here...
+//
+// [k] = kcal/mol (rotational barrier ???)
+
+torsion	0801 0601 0600 0600 ?S?  0.700 - 3.0
+torsion	0601 0600 0600 0601 ?S?  0.040 + 3.0
+torsion	0601 0600 0600 0600 ?S?  0.126 + 3.0
+torsion	0600 0600 0600 0600 ?S?  0.500 + 3.0
+torsion	0601 0601 0600 0601 ?S?  0.126 - 3.0
+torsion	0601 0601 0600 0100 ?S?  0.273 - 3.0
+torsion	0600 0601 0600 0601 ?S?  0.126 + 3.0
+torsion	0600 0601 0600 0600 ?S?  0.126 + 3.0
+torsion	0600 0601 0600 0100 ?S?  0.274 + 3.0
+torsion	0100 0601 0600 0601 ?S?  0.274 + 3.0
+torsion	0100 0601 0600 0600 ?S?  0.274 + 3.0
+torsion	0100 0601 0600 0100 ?S?  0.274 + 3.0
+torsion	0601 0601 0600 0600 ?S?  0.126 - 3.0
+torsion	FFFF 0601 0600 0601 ?S?  0.126 + 3.0
+torsion	FFFF 0601 0600 0600 ?S?  0.126 + 3.0
+torsion	FFFF 0601 0600 0100 ?S?  0.274 + 3.0
+torsion	FFFF 0600 0600 0100 ?S?  0.320 + 3.0
+torsion	0601 0601 0600 FFFF ?S?  0.126 - 3.0
+torsion	0600 0601 0600 FFFF ?S?  0.126 + 3.0
+torsion	0100 0601 0600 FFFF ?S?  0.274 + 3.0
+torsion	FFFF 0602 0602 FFFF ?T?  0.000 + 1.0
+torsion	FFFF 0602 0602 FFFF ?S?  0.000 + 1.0
+torsion	FFFF 0602 0601 FFFF ?S?  0.000 + 1.0
+torsion	FFFF 0602 0601 FFFF ?D?  0.000 + 1.0
+torsion	FFFF 0601 0601 FFFF ?D? 12.500 - 2.0
+torsion	FFFF 0601 0601 FFFF ?S?  1.424 - 2.0
+torsion	FFFF 0602 0600 FFFF ?S?  0.000 + 1.0
+torsion	FFFF 0601 0600 FFFF ?S?  0.120 - 3.0
+torsion	FFFF 0600 0600 FFFF ?S?  0.200 + 3.0
+torsion	FFFF 0602 0603 FFFF ?S?  0.000 + 1.0
+torsion	FFFF 0601 0603 FFFF ?S?  1.600 - 2.0
+torsion	FFFF 0600 0603 FFFF ?S?  0.120 - 3.0
+torsion	FFFF 0603 0603 FFFF ?C?  2.000 - 2.0
+torsion	FFFF 0603 0603 FFFF ?S?  0.600 - 2.0
+torsion	FFFF 0602 0701 FFFF ?S?  0.000 + 1.0
+torsion	FFFF 0602 0701 FFFF ?D?  0.000 + 1.0
+torsion	FFFF 0601 0701 FFFF ?D? 12.000 - 2.0
+torsion	FFFF 0601 0701 FFFF ?S? 12.000 - 2.0
+torsion	FFFF 0600 0701 FFFF ?S?  0.400 - 3.0
+torsion	FFFF 0603 0701 FFFF ?S?  1.600 - 2.0
+torsion	FFFF 0701 0701 FFFF ?D?  1.600 - 2.0
+torsion	FFFF 0701 0701 FFFF ?S?  1.600 - 2.0
+torsion	FFFF 0601 0700 FFFF ?S?  0.120 - 3.0
+torsion	FFFF 0600 0700 FFFF ?S?  0.200 + 3.0
+torsion	FFFF 0603 0700 FFFF ?S?  0.120 - 3.0
+torsion	FFFF 0700 0700 FFFF ?S?  0.200 + 3.0
+torsion	FFFF 0601 0705 FFFF ?S?  6.460 - 2.0
+torsion	FFFF 0600 0705 FFFF ?S?  0.200 + 3.0
+torsion	FFFF 0603 0705 FFFF ?S?  1.600 - 2.0
+torsion	FFFF 0701 0705 FFFF ?S?  1.600 - 2.0
+torsion	FFFF 0700 0705 FFFF ?S?  0.120 - 3.0
+torsion	FFFF 0705 0705 FFFF ?S?  1.600 - 2.0
+torsion	FFFF 0603 0703 FFFF ?C?  1.600 - 2.0
+torsion	FFFF 0601 0800 FFFF ?S?  5.800 - 2.0
+torsion	FFFF 0600 0800 FFFF ?S?  1.200 + 3.0
+torsion	FFFF 0603 0800 FFFF ?S?  1.200 - 2.0
+torsion	FFFF 0701 0800 FFFF ?S?  1.000 + 2.0
+torsion	FFFF 0700 0800 FFFF ?S?  0.200 + 3.0
+torsion	FFFF 0601 0F00 FFFF ?S?  1.000 - 2.0
+torsion	FFFF 0600 0F00 FFFF ?S?  0.400 + 3.0
+torsion	FFFF 0603 0F00 FFFF ?S?  1.000 + 3.0
+torsion	FFFF 0800 0F00 FFFF ?S?  0.400 + 3.0
+torsion	FFFF 0601 1001 FFFF ?D?  1.000 - 2.0
+torsion	FFFF 0600 1001 FFFF ?S?  0.400 + 3.0
+torsion	FFFF 0603 1001 FFFF ?S?  1.000 + 3.0
+torsion	FFFF 0700 1001 FFFF ?S?  0.400 + 3.0
+torsion	FFFF 0601 1000 FFFF ?S?  1.000 - 2.0
+torsion	FFFF 0600 1000 FFFF ?S?  0.400 + 3.0
+torsion	FFFF 0603 1000 FFFF ?S?  1.000 + 3.0
+torsion	FFFF 1000 1000 FFFF ?S?  4.000 + 3.0
+
+// lenjon-parameters 09.05.2000 (based on Tripos 5.2 and MMFF94)
+// [id] [r] [k]
+//
+// [r] = Å
+// [k] = kcal/mol
+
+vdw	0100 1.50 0.042
+vdw	0600 1.70 0.107
+vdw	0601 1.70 0.107
+vdw	0602 1.70 0.107
+vdw	0603 1.70 0.107
+vdw	0604 1.70 0.107
+vdw	0605 1.70 0.107
+vdw	0700 1.55 0.095
+vdw	0701 1.55 0.095
+vdw	0702 1.55 0.095
+vdw	0703 1.55 0.095
+vdw	0704 1.55 0.095
+vdw	0705 1.55 0.095
+vdw	0800 1.52 0.116
+vdw	0801 1.52 0.116
+vdw	0900 1.47 0.109
+vdw	0F00 1.80 0.314
+vdw	1000 1.80 0.314
+vdw	1001 1.80 0.314
+vdw	1002 1.80 0.314
+vdw	1003 1.80 0.314
+vdw	1100 1.75 0.314
+vdw	2300 1.85 0.434
+vdw	3500 1.98 0.623
+vdw	FFFF 1.50 0.042
+
+// atomic charge parameters 09.05.2000 (based on Tripos 5.2 and MMFF94)
+// [id #1] [id #2] [delta]
+//
+// THE NUMERICAL VALUES HERE ARE NOT PROPERLY CHECKED!!!
+//
+// sign of [delta] is inverted if order of atoms is switched...
+// sign of [delta] is inverted if order of atoms is switched...
+// sign of [delta] is inverted if order of atoms is switched...
+
+charge  0601 0100 S +0.100
+charge  0602 0100 S +0.200
+charge  0603 0100 S +0.100
+charge  0604 0100 S +0.050
+charge  0700 0100 S +0.100
+charge  0701 0100 S +0.200
+charge  0702 0100 S +0.250
+charge  0703 0100 S +0.250
+charge  0704 0100 S +0.200
+charge  0705 0100 S +0.150
+charge  0800 0100 S +0.250
+charge  0801 0601 D +0.100
+charge  0900 0100 S +0.500
+charge  0900 0600 S +0.125
+charge  1002 0801 D +0.200
+charge  1003 0801 D +0.200
+charge  1100 0600 S +0.150
+charge  2300 0600 S +0.175
+charge  3500 0600 S +0.200
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/isotope-small.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,141 @@
+##############################################################################
+#                                                                            #
+#	                Open Babel file: isotope-small.txt                       #
+#                                                                            #
+#  Copyright (c) 2002-2003 by Geoffrey R. Hutchison                          #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+#  Small isotope table with most frequently-used isotopes (as default data)  #
+#  (GRH currently trimmed up to atomic # 40 and #100+)                       #
+#   Note that this is only used when data files are not available            #
+#   and hence is not as likely to be updated frequently--it is hand-edited!  #
+#                                                                            #
+#  This file has a series of lines, one for each element                     #
+#   (i.e. line 0 = neutron, line 1 = hydrogen, line 2 = helium, etc.)        #
+#  Each line: Atomic #, 0 then exact mass of most abundant isotope           #
+#     then a list of isotopes as int, float pairs corresponding to masses    #
+#                                                                            #
+#  CAUTION: Masses have been zero-padded to 6 decimal places                 #
+#   (we don't currently have a math package that can deal with sig. fig.)    #
+#   so trailing zeros may not be significant and/or useful                   #
+#                                                                            #
+#  Values are compiled from "The 1995 update to the atomic mass evaluation"  #
+#                    by G.Audi and A.H.Wapstra                               #
+#           Nuclear Physics A595 vol. 4 p.409-480, December 25, 1995.        #
+#  as made available in the mass_rmd.mas95 file                              #
+#                                                                            #
+#  Currently: 110 lines (neutron, H to Mt)                                   #
+#  (note that since element 0 often represents a dummy atom, the default     #
+#   mass is 0 amu, *not* the mass of a neutron, accessible as isotope 1)     #
+#                                                                            #
+##############################################################################
+0 0 0.000000 1 1.008664
+1 0 1.007825 1 1.007825 2 2.014101 3 3.016049
+2 0 4.002603 3 3.016029 4 4.002603 5 5.012220 6 6.018888 7 7.028030 8 8.033922 9 9.043820 10 10.052400
+3 0 7.016004 5 5.012540 6 6.015122 7 7.016004 8 8.022486 9 9.026789 10 10.035481 11 11.043796
+4 0 9.012182 6 6.019726 7 7.016929 8 8.005305 9 9.012182 10 10.013533 11 11.021658 12 12.026921 14 14.042820
+5 0 11.009305 7 7.029920 8 8.024606 9 9.013328 10 10.012937 11 11.009305 12 12.014352 13 13.017780 14 14.025404 15 15.031097 17 17.046930 19 19.063730
+6 0 12.000000 8 8.037675 9 9.031040 10 10.016853 11 11.011433 12 12.000000 13 13.003354 14 14.003241 15 15.010599 16 16.014701 17 17.022584 18 18.026760 19 19.035250 20 20.040320
+7 0 14.003074 12 12.018613 13 13.005738 14 14.003074 15 15.000108 16 16.006101 17 17.008450 18 18.014082 19 19.017027 20 20.023370 21 21.027090 22 22.034440 23 23.040510
+8 0 15.994914 12 12.034405 13 13.024810 14 14.008595 15 15.003065 16 15.994914 17 16.999131 18 17.999160 19 19.003579 20 20.004076 21 21.008655 22 22.009970 23 23.015690 24 24.020370
+9 0 18.998403 15 15.018010 16 16.011466 17 17.002095 18 18.000937 19 18.998403 20 19.999981 21 20.999948 22 22.002999 23 23.003570 24 24.008100 25 25.012090 26 26.019630 27 27.026890
+10 0 19.992440 16 16.025757 17 17.017700 18 18.005697 19 19.001879 20 19.992440 21 20.993846 22 21.991385 23 22.994467 24 23.993615 25 24.997790 26 26.000460 27 27.007620 28 28.012110 29 29.019350
+11 0 22.989769 19 19.013879 20 20.007348 21 20.997655 22 21.994436 23 22.989769 24 23.990963 25 24.989954 26 25.992590 27 26.994010 28 27.998890 29 29.002810 30 30.009230 31 31.013600 32 32.019650 33 33.027390 34 34.034900 35 35.044180
+12 0 23.985041 20 20.018863 21 21.011714 22 21.999574 23 22.994124 24 23.985041 25 24.985837 26 25.982593 27 26.984340 28 27.983876 29 28.988550 30 29.990460 31 30.996550 32 31.999150 33 33.005590
+13 0 26.981538 22 22.019520 23 23.007265 24 23.999941 25 24.990428 26 25.986891 27 26.981538 28 27.981910 29 28.980444 30 29.982960 31 30.983946 32 31.988120 33 32.990870 34 33.996930 35 34.999940 36 36.006350
+14 0 27.976926 22 22.034530 24 24.011546 25 25.004107 26 25.992330 27 26.986704 28 27.976926 29 28.976494 30 29.973770 31 30.975363 32 31.974148 33 32.978001 34 33.978576 35 34.984580 36 35.986690 37 36.993000 38 37.995980 39 39.002300
+15 0 30.973761 26 26.011780 27 26.999190 28 27.992312 29 28.981801 30 29.978313 31 30.973761 32 31.973907 33 32.971725 34 33.973636 35 34.973314 36 35.978260 37 36.979610 38 37.984470 39 38.986420 40 39.991050 41 40.994800 42 42.000090
+16 0 31.972070 27 27.018800 28 28.004370 29 28.996610 30 29.984903 31 30.979554 32 31.972070 33 32.971458 34 33.967866 35 34.969032 36 35.967080 37 36.971125 38 37.971163 39 38.975140 40 39.975470 41 40.980030 42 41.981490 43 42.986600 44 43.988320
+17 0 34.968852 31 30.992420 32 31.985689 33 32.977451 34 33.973761 35 34.968852 36 35.968306 37 36.965902 38 37.968010 39 38.968007 40 39.970420 41 40.970650 42 41.973170 43 42.974200 44 43.978540 45 44.979700 46 45.984120 47 46.987950
+18 0 39.962383 31 31.012130 32 31.997660 33 32.989930 34 33.980270 35 34.975256 36 35.967546 37 36.966775 38 37.962732 39 38.964313 40 39.962383 41 40.964500 42 41.963050 43 42.965670 44 43.965365 45 44.968090 46 45.968090 47 46.972190
+19 0 38.963706 35 34.988012 36 35.981293 37 36.973376 38 37.969080 39 38.963706 40 39.963998 41 40.961825 42 41.962403 43 42.960716 44 43.961560 45 44.960700 46 45.961976 47 46.961678 48 47.965513 49 48.967450 50 49.972780 51 50.976380 52 51.982610 53 52.987120 54 53.993990
+20 0 39.962591 35 35.004770 36 35.993090 37 36.985872 38 37.976319 39 38.970717 40 39.962591 41 40.962278 42 41.958618 43 42.958766 44 43.955481 45 44.956185 46 45.953692 47 46.954546 48 47.952534 49 48.955673 50 49.957518 51 50.961470 52 51.965100 53 52.970050
+21 0 44.955910 40 39.977964 41 40.969251 42 41.965516 43 42.961151 44 43.959403 45 44.955910 46 45.955170 47 46.952408 48 47.952235 49 48.950024 50 49.952187 51 50.953603 52 51.956650 53 52.959240 54 53.963000 55 54.967430
+22 0 47.947947 39 39.001320 40 39.990500 41 40.983130 42 41.973032 43 42.968523 44 43.959690 45 44.958124 46 45.952629 47 46.951763 48 47.947947 49 48.947870 50 49.944792 51 50.946616 52 51.946898 53 52.949730 54 53.950870 55 54.955120 56 55.957990 57 56.962900 58 57.966110
+23 0 50.943963 43 42.980650 44 43.974400 45 44.965782 46 45.960199 47 46.954906 48 47.952254 49 48.948516 50 49.947162 51 50.943963 52 51.944779 53 52.944343 54 53.946444 55 54.947240 56 55.950360 57 56.952360 58 57.956650 59 58.959300 60 59.964500 61 60.967410
+24 0 51.940511 43 42.997710 44 43.985470 45 44.979160 46 45.968362 47 46.962907 48 47.954036 49 48.951341 50 49.946049 51 50.944771 52 51.940511 53 52.940653 54 53.938884 55 54.940844 56 55.940645 57 56.943750 58 57.944250 59 58.948630 60 59.949730 61 60.954090 62 61.955800 63 62.961860
+25 0 54.938049 46 45.986720 47 46.976100 48 47.968870 49 48.959623 50 49.954244 51 50.948215 52 51.945570 53 52.941294 54 53.940363 55 54.938049 56 55.938909 57 56.938287 58 57.939990 59 58.940450 60 59.943190 61 60.944460 62 61.947970 63 62.949810 64 63.953730 65 64.956100 66 65.960820
+26 0 55.934942 46 46.000810 47 46.992890 48 47.980560 49 48.973610 50 49.962990 51 50.956825 52 51.948117 53 52.945312 54 53.939614 55 54.938298 56 55.934942 57 56.935398 58 57.933280 59 58.934880 60 59.934077 61 60.936749 62 61.936770 63 62.940120 64 63.940870 65 64.944940 66 65.945980 67 66.950000 68 67.952510 69 68.957700
+27 0 58.933200 50 49.981540 51 50.970720 52 51.963590 53 52.954225 54 53.948464 55 54.942003 56 55.939843 57 56.936296 58 57.935757 59 58.933200 60 59.933822 61 60.932479 62 61.934054 63 62.933615 64 63.935814 65 64.936485 66 65.939830 67 66.940610 68 67.944360 69 68.945200 70 69.949810 71 70.951730
+28 0 57.935347 51 50.987720 52 51.975680 53 52.968460 54 53.957910 55 54.951336 56 55.942136 57 56.939800 58 57.935347 59 58.934351 60 59.930790 61 60.931060 62 61.928348 63 62.929672 64 63.927969 65 64.930088 66 65.929115 67 66.931570 68 67.931845 69 68.935180 70 69.936140 71 70.940000 72 71.941300 73 72.946080 74 73.947910
+29 0 62.929601 55 54.966050 56 55.958560 57 56.949216 58 57.944540 59 58.939504 60 59.937368 61 60.933462 62 61.932587 63 62.929601 64 63.929767 65 64.927793 66 65.928873 67 66.927750 68 67.929640 69 68.929425 70 69.932409 71 70.932620 72 71.935520 73 72.936490 74 73.940200 75 74.941700 76 75.945990 77 76.947950 78 77.952810 79 78.955280
+30 0 63.929146 57 56.964910 58 57.954600 59 58.949270 60 59.941832 61 60.939514 62 61.934334 63 62.933215 64 63.929146 65 64.929245 66 65.926036 67 66.927130 68 67.924847 69 68.926553 70 69.925325 71 70.927727 72 71.926861 73 72.929780 74 73.929460 75 74.932940 76 75.933390 77 76.937090 78 77.938570 79 78.942680 80 79.944410 81 80.950480
+31 0 68.925581 61 60.949170 62 61.944180 63 62.939140 64 63.936838 65 64.932739 66 65.931592 67 66.928204 68 67.927983 69 68.925581 70 69.926028 71 70.924705 72 71.926369 73 72.925170 74 73.926940 75 74.926501 76 75.928930 77 76.929280 78 77.931660 79 78.932920 80 79.936590 81 80.937750 82 81.943160 83 82.946870 84 83.952340
+32 0 73.921178 61 60.963790 62 61.954650 63 62.949640 64 63.941570 65 64.939440 66 65.933850 67 66.932738 68 67.928097 69 68.927972 70 69.924250 71 70.924954 72 71.922076 73 72.923459 74 73.921178 75 74.922859 76 75.921402 77 76.923548 78 77.922853 79 78.925400 80 79.925445 81 80.928820 82 81.929550 83 82.934510 84 83.937310 85 84.942690
+33 0 74.921596 65 64.949480 66 65.944370 67 66.939190 68 67.936790 69 68.932280 70 69.930930 71 70.927115 72 71.926753 73 72.923825 74 73.923929 75 74.921596 76 75.922393 77 76.920647 78 77.921829 79 78.920948 80 79.922578 81 80.922133 82 81.924500 83 82.924980 84 83.929060 85 84.931810 86 85.936230 87 86.939580
+34 0 79.916521 65 64.964660 67 66.950090 68 67.941870 69 68.939560 70 69.933500 71 70.932270 72 71.927112 73 72.926767 74 73.922476 75 74.922523 76 75.919214 77 76.919914 78 77.917309 79 78.918499 80 79.916521 81 80.917992 82 81.916700 83 82.919119 84 83.918465 85 84.922240 86 85.924271 87 86.928520 88 87.931420 89 88.936020 90 89.939420 91 90.945370
+35 0 78.918337 69 68.950180 70 69.944620 71 70.939250 72 71.936500 73 72.931790 74 73.929891 75 74.925776 76 75.924542 77 76.921380 78 77.921146 79 78.918337 80 79.918530 81 80.916291 82 81.916805 83 82.915180 84 83.916504 85 84.915608 86 85.918797 87 86.920711 88 87.924070 89 88.926390 90 89.930630 91 90.933970 92 91.939260 93 92.943100 94 93.948680
+36 0 83.911507 71 70.950510 72 71.941910 73 72.938930 74 73.933260 75 74.931034 76 75.925948 77 76.924668 78 77.920386 79 78.920083 80 79.916378 81 80.916592 82 81.913484 83 82.914136 84 83.911507 85 84.912527 86 85.910610 87 86.913354 88 87.914447 89 88.917630 90 89.919524 91 90.923440 92 91.926153 93 92.931270 94 93.934360 95 94.939840 97 96.948560
+37 0 84.911789 74 73.944470 75 74.938569 76 75.935071 77 76.930407 78 77.928141 79 78.923997 80 79.922519 81 80.918994 82 81.918208 83 82.915112 84 83.914385 85 84.911789 86 85.911167 87 86.909183 88 87.911319 89 88.912280 90 89.914809 91 90.916534 92 91.919725 93 92.922033 94 93.926407 95 94.929319 96 95.934284 97 96.937340 98 97.941700 99 98.945420 100 99.949870 101 100.953200 102 101.959210
+38 0 87.905614 76 75.941610 77 76.937760 78 77.932179 79 78.929707 80 79.924525 81 80.923213 82 81.918401 83 82.917555 84 83.913425 85 84.912933 86 85.909262 87 86.908879 88 87.905614 89 88.907452 90 89.907737 91 90.910210 92 91.911030 93 92.914022 94 93.915360 95 94.919358 96 95.921680 97 96.926149 98 97.928471 99 98.933320 100 99.935350 101 100.940520 102 101.943020
+39 0 88.905847 78 77.943500 79 78.937350 80 79.934340 81 80.929130 82 81.926790 83 82.922350 84 83.920390 85 84.916427 86 85.914888 87 86.910877 88 87.909503 89 88.905847 90 89.907151 91 90.907303 92 91.908947 93 92.909582 94 93.911594 95 94.912824 96 95.915898 97 96.918131 98 97.922220 99 98.924635 100 99.927760 101 100.930310 102 101.933560
+40 0 89.904703 80 79.940550 81 80.936820 82 81.931090 83 82.928650 84 83.923250 85 84.921470 86 85.916470 87 86.914817 88 87.910226 89 88.908889 90 89.904703 91 90.905645 92 91.905040 93 92.906475 94 93.906315 95 94.908042 96 95.908276 97 96.910951 98 97.912746 99 98.916511 100 99.917760 101 100.921140 102 101.922980 103 102.926600 104 103.928780 105 104.933050
+41 0 92.906377 82 81.943130 83 82.936700 84 83.933570 85 84.927910 86 85.925040 87 86.920360 88 87.917960 89 88.913500 90 89.911264 91 90.906991 92 91.907193 93 92.906377 94 93.907283 95 94.906835 96 95.908100 97 96.908097 98 97.910331 99 98.911618 100 99.914181 101 100.915252 102 101.918040 103 102.919140 104 103.922460 105 104.923930 106 105.928190 107 106.930310
+42 0 97.905407 84 83.940090 85 84.936590 86 85.930700 87 86.927330 88 87.921953 89 88.919481 90 89.913936 91 90.911751 92 91.906810 93 92.906812 94 93.905087 95 94.905841 96 95.904678 97 96.906021 98 97.905407 99 98.907711 100 99.907477 101 100.910347 102 101.910297 103 102.913200 104 103.913760 105 104.916970 106 105.918134 107 106.921690 108 107.923580 109 108.927810 110 109.929730
+43 0 97.907216 86 85.942880 87 86.936530 88 87.932830 89 88.927540 90 89.923560 91 90.918430 92 91.915260 93 92.910248 94 93.909656 95 94.907656 96 95.907871 97 96.906365 98 97.907216 99 98.906254 100 99.907657 101 100.907314 102 101.909213 103 102.909179 104 103.911440 105 104.911660 106 105.914355 107 106.915080 108 107.918480 109 108.919630 110 109.923390 111 110.925050 112 111.929240 113 112.931330
+44 0 101.904349 88 87.940420 89 88.936110 90 89.929780 91 90.926380 92 91.920120 93 92.917050 94 93.911360 95 94.910413 96 95.907598 97 96.907555 98 97.905287 99 98.905939 100 99.904219 101 100.905582 102 101.904349 103 102.906323 104 103.905430 105 104.907750 106 105.907327 107 106.909910 108 107.910190 109 108.913200 110 109.913970 111 110.917560 112 111.918550 113 112.922540 114 113.924000 115 114.928310
+45 0 102.905504 90 89.942870 91 90.936550 92 91.931980 93 92.925740 94 93.921700 95 94.915900 96 95.914518 97 96.911340 98 97.910716 99 98.908132 100 99.908117 101 100.906164 102 101.906843 103 102.905504 104 103.906655 105 104.905692 106 105.907285 107 106.906751 108 107.908730 109 108.908736 110 109.910950 111 110.911660 112 111.914610 113 112.915420 114 113.918850 115 114.920120 116 115.923710 117 116.925350
+46 0 105.903483 92 91.940420 93 92.935910 94 93.928770 95 94.924690 96 95.918220 97 96.916480 98 97.912721 99 98.911768 100 99.908505 101 100.908289 102 101.905608 103 102.906087 104 103.904035 105 104.905084 106 105.903483 107 106.905128 108 107.903894 109 108.905954 110 109.905152 111 110.907640 112 111.907313 113 112.910150 114 113.910365 115 114.913680 116 115.914160 117 116.917840 118 117.918980 119 118.922680 120 119.924030
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+89 0 227.027747 207 207.012090 208 208.011490 209 209.009570 210 210.009260 211 211.007650 212 212.007810 213 213.006570 214 214.006890 215 215.006450 216 216.008721 217 217.009333 218 218.011630 219 219.012400 220 220.014750 221 221.015580 222 222.017829 223 223.019126 224 224.021708 225 225.023221 226 226.026090 227 227.027747 228 228.031014 229 229.032930 230 230.036030 231 231.038550 232 232.042020 233 233.044550 234 234.048420
+90 0 232.038050 212 212.012920 213 213.012960 214 214.011450 215 215.011730 216 216.011051 217 217.013070 218 218.013268 219 219.015520 220 220.015733 221 221.018171 222 222.018454 223 223.020795 224 224.021459 225 225.023941 226 226.024891 227 227.027699 228 228.028731 229 229.031755 230 230.033126 231 231.036297 232 232.038050 233 233.041576 234 234.043595 235 235.047500 236 236.049710 237 237.053890
+91 0 231.035878 215 215.019100 216 216.019110 217 217.018290 218 218.020010 219 219.019880 220 220.021880 221 221.021860 222 222.023730 223 223.023960 224 224.025610 225 225.026120 226 226.027933 227 227.028793 228 228.031037 229 229.032089 230 230.034533 231 231.035878 232 232.038582 233 233.040240 234 234.043302 235 235.045440 236 236.048680 237 237.051140 238 238.054500
+92 0 238.050782 218 218.023490 219 219.024920 220 220.024710 221 221.026350 222 222.026070 223 223.027720 224 224.027590 225 225.029380 226 226.029340 227 227.031140 228 228.031366 229 229.033496 230 230.033927 231 231.036289 232 232.037146 233 233.039628 234 234.040945 235 235.043923 236 236.045561 237 237.048724 238 238.050782 239 239.054287 240 240.056586 241 241.060330 242 242.062930
+93 0 237.048167 226 226.035130 227 227.034960 228 228.036180 229 229.036250 230 230.037810 231 231.038230 232 232.040100 233 233.040730 234 234.042889 235 235.044055 236 236.046560 237 237.048167 238 238.050940 239 239.052931 240 240.056169 241 241.058250 242 242.061640
+94 0 244.064198 228 228.038730 229 229.040140 230 230.039646 231 231.041260 232 232.041179 233 233.042990 234 234.043305 235 235.045282 236 236.046048 237 237.048403 238 238.049553 239 239.052156 240 240.053807 241 241.056845 242 242.058736 243 243.061997 244 244.064198 245 245.067739 246 246.070198
+95 0 243.061372 232 232.046590 234 234.047790 237 237.049970 238 238.051980 239 239.053018 240 240.055288 241 241.056822 242 242.059543 243 243.061372 244 244.064279 245 245.066445 246 246.069768 247 247.072090
+96 0 247.070347 236 236.051410 237 237.052890 238 238.053020 239 239.054950 240 240.055519 241 241.057646 242 242.058829 243 243.061382 244 244.062746 245 245.065485 246 246.067217 247 247.070347 248 248.072342 249 249.075947 250 250.078351 251 251.082278
+97 0 247.070299 238 238.058270 242 242.062050 243 243.063002 244 244.065168 245 245.066355 246 246.068670 247 247.070299 248 248.073080 249 249.074980 250 250.078311 251 251.080753
+98 0 251.079580 239 239.062580 240 240.062300 241 241.063720 242 242.063690 243 243.065420 244 244.065990 245 245.068040 246 246.068798 247 247.070992 248 248.072178 249 249.074847 250 250.076400 251 251.079580 252 252.081620 253 253.085127 254 254.087316 255 255.091040
+99 0 252.082970 243 243.069630 244 244.070970 245 245.071320 246 246.072970 247 247.073650 248 248.075460 249 249.076410 250 250.078650 251 251.079984 252 252.082970 253 253.084818 254 254.088016 255 255.090266 256 256.093590
+100 0 257.095099 242 242.073430 243 243.074510 244 244.074080 245 245.075380 246 246.075280 247 247.076820 248 248.077184 249 249.079020 250 250.079515 251 251.081566 252 252.082460 253 253.085176 254 254.086848 255 255.089955 256 256.091767 257 257.095099 258 258.097070 259 259.100590
+101 0 258.098425 247 247.081800 248 248.082910 249 249.083000 250 250.084490 251 251.084920 252 252.086630 253 253.087280 254 254.089730 255 255.091075 256 256.094050 257 257.095535 258 258.098425 259 259.100500 260 260.103650
+102 0 259.101020 250 250.087490 251 251.088960 252 252.088966 253 253.090650 254 254.090949 255 255.093232 256 256.094276 257 257.096850 258 258.098200 259 259.101020 262 262.107520
+103 0 262.109690 253 253.095260 254 254.096590 255 255.096770 256 256.098760 257 257.099610 258 258.101880 259 259.102990 260 260.105570 261 261.106940 262 262.109690
+104 0 261.108750 253 253.100680 254 254.100170 255 255.101490 256 256.101180 257 257.103070 258 258.103570 259 259.105630 260 260.106430 261 261.108750 262 262.109920 263 263.112540
+105 0 262.114150 255 255.107400 257 257.107860 258 258.109440 259 259.109720 260 260.111430 261 261.112110 262 262.114150 263 263.115080
+106 0 263.118310 259 259.114650 260 260.114440 261 261.116200 263 263.118310 265 265.121070 266 266.121930
+107 0 264.124730 261 261.121800 262 262.123010 264 264.124730
+108 0 265.130000 263 263.128710 264 264.128410 265 265.130000
+109 0 268.138820 266 266.137940 268 268.138820
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/isotope.h	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,2551 @@
+/***************************************************************
+This file is part of the Open Babel project.
+This is copyright under the GNU General Public License (GPL)
+For more information, see <http://openbabel.org/>
+
+This file contains a binary representation of data tables
+ used by Open Babel. It is used as a fallback if the textual
+ data table is not found at runtime. It is not a normal header.
+***************************************************************/
+
+
+#ifndef OB_ISOTOPE_H
+#define OB_ISOTOPE_H
+
+namespace OpenBabel
+{
+static const char IsotopeData[] = {
+ 0x30,0x20,0x30,0x20,0x30,0x2E,0x30,0x30,0x30,0x30,0x30,0x30,0x20,0x31,0x20,
+ 0x31,0x2E,0x30,0x30,0x38,0x36,0x36,0x34,0x0A,0x31,0x20,0x30,0x20,0x31,0x2E,
+ 0x30,0x30,0x37,0x38,0x32,0x35,0x20,0x31,0x20,0x31,0x2E,0x30,0x30,0x37,0x38,
+ 0x32,0x35,0x20,0x32,0x20,0x32,0x2E,0x30,0x31,0x34,0x31,0x30,0x31,0x20,0x33,
+ 0x20,0x33,0x2E,0x30,0x31,0x36,0x30,0x34,0x39,0x0A,0x32,0x20,0x30,0x20,0x34,
+ 0x2E,0x30,0x30,0x32,0x36,0x30,0x33,0x20,0x33,0x20,0x33,0x2E,0x30,0x31,0x36,
+ 0x30,0x32,0x39,0x20,0x34,0x20,0x34,0x2E,0x30,0x30,0x32,0x36,0x30,0x33,0x20,
+ 0x35,0x20,0x35,0x2E,0x30,0x31,0x32,0x32,0x32,0x30,0x20,0x36,0x20,0x36,0x2E,
+ 0x30,0x31,0x38,0x38,0x38,0x38,0x20,0x37,0x20,0x37,0x2E,0x30,0x32,0x38,0x30,
+ 0x33,0x30,0x20,0x38,0x20,0x38,0x2E,0x30,0x33,0x33,0x39,0x32,0x32,0x20,0x39,
+ 0x20,0x39,0x2E,0x30,0x34,0x33,0x38,0x32,0x30,0x20,0x31,0x30,0x20,0x31,0x30,
+ 0x2E,0x30,0x35,0x32,0x34,0x30,0x30,0x0A,0x33,0x20,0x30,0x20,0x37,0x2E,0x30,
+ 0x31,0x36,0x30,0x30,0x34,0x20,0x35,0x20,0x35,0x2E,0x30,0x31,0x32,0x35,0x34,
+ 0x30,0x20,0x36,0x20,0x36,0x2E,0x30,0x31,0x35,0x31,0x32,0x32,0x20,0x37,0x20,
+ 0x37,0x2E,0x30,0x31,0x36,0x30,0x30,0x34,0x20,0x38,0x20,0x38,0x2E,0x30,0x32,
+ 0x32,0x34,0x38,0x36,0x20,0x39,0x20,0x39,0x2E,0x30,0x32,0x36,0x37,0x38,0x39,
+ 0x20,0x31,0x30,0x20,0x31,0x30,0x2E,0x30,0x33,0x35,0x34,0x38,0x31,0x20,0x31,
+ 0x31,0x20,0x31,0x31,0x2E,0x30,0x34,0x33,0x37,0x39,0x36,0x0A,0x34,0x20,0x30,
+ 0x20,0x39,0x2E,0x30,0x31,0x32,0x31,0x38,0x32,0x20,0x36,0x20,0x36,0x2E,0x30,
+ 0x31,0x39,0x37,0x32,0x36,0x20,0x37,0x20,0x37,0x2E,0x30,0x31,0x36,0x39,0x32,
+ 0x39,0x20,0x38,0x20,0x38,0x2E,0x30,0x30,0x35,0x33,0x30,0x35,0x20,0x39,0x20,
+ 0x39,0x2E,0x30,0x31,0x32,0x31,0x38,0x32,0x20,0x31,0x30,0x20,0x31,0x30,0x2E,
+ 0x30,0x31,0x33,0x35,0x33,0x33,0x20,0x31,0x31,0x20,0x31,0x31,0x2E,0x30,0x32,
+ 0x31,0x36,0x35,0x38,0x20,0x31,0x32,0x20,0x31,0x32,0x2E,0x30,0x32,0x36,0x39,
+ 0x32,0x31,0x20,0x31,0x34,0x20,0x31,0x34,0x2E,0x30,0x34,0x32,0x38,0x32,0x30,
+ 0x0A,0x35,0x20,0x30,0x20,0x31,0x31,0x2E,0x30,0x30,0x39,0x33,0x30,0x35,0x20,
+ 0x37,0x20,0x37,0x2E,0x30,0x32,0x39,0x39,0x32,0x30,0x20,0x38,0x20,0x38,0x2E,
+ 0x30,0x32,0x34,0x36,0x30,0x36,0x20,0x39,0x20,0x39,0x2E,0x30,0x31,0x33,0x33,
+ 0x32,0x38,0x20,0x31,0x30,0x20,0x31,0x30,0x2E,0x30,0x31,0x32,0x39,0x33,0x37,
+ 0x20,0x31,0x31,0x20,0x31,0x31,0x2E,0x30,0x30,0x39,0x33,0x30,0x35,0x20,0x31,
+ 0x32,0x20,0x31,0x32,0x2E,0x30,0x31,0x34,0x33,0x35,0x32,0x20,0x31,0x33,0x20,
+ 0x31,0x33,0x2E,0x30,0x31,0x37,0x37,0x38,0x30,0x20,0x31,0x34,0x20,0x31,0x34,
+ 0x2E,0x30,0x32,0x35,0x34,0x30,0x34,0x20,0x31,0x35,0x20,0x31,0x35,0x2E,0x30,
+ 0x33,0x31,0x30,0x39,0x37,0x20,0x31,0x37,0x20,0x31,0x37,0x2E,0x30,0x34,0x36,
+ 0x39,0x33,0x30,0x20,0x31,0x39,0x20,0x31,0x39,0x2E,0x30,0x36,0x33,0x37,0x33,
+ 0x30,0x0A,0x36,0x20,0x30,0x20,0x31,0x32,0x2E,0x30,0x30,0x30,0x30,0x30,0x30,
+ 0x20,0x38,0x20,0x38,0x2E,0x30,0x33,0x37,0x36,0x37,0x35,0x20,0x39,0x20,0x39,
+ 0x2E,0x30,0x33,0x31,0x30,0x34,0x30,0x20,0x31,0x30,0x20,0x31,0x30,0x2E,0x30,
+ 0x31,0x36,0x38,0x35,0x33,0x20,0x31,0x31,0x20,0x31,0x31,0x2E,0x30,0x31,0x31,
+ 0x34,0x33,0x33,0x20,0x31,0x32,0x20,0x31,0x32,0x2E,0x30,0x30,0x30,0x30,0x30,
+ 0x30,0x20,0x31,0x33,0x20,0x31,0x33,0x2E,0x30,0x30,0x33,0x33,0x35,0x34,0x20,
+ 0x31,0x34,0x20,0x31,0x34,0x2E,0x30,0x30,0x33,0x32,0x34,0x31,0x20,0x31,0x35,
+ 0x20,0x31,0x35,0x2E,0x30,0x31,0x30,0x35,0x39,0x39,0x20,0x31,0x36,0x20,0x31,
+ 0x36,0x2E,0x30,0x31,0x34,0x37,0x30,0x31,0x20,0x31,0x37,0x20,0x31,0x37,0x2E,
+ 0x30,0x32,0x32,0x35,0x38,0x34,0x20,0x31,0x38,0x20,0x31,0x38,0x2E,0x30,0x32,
+ 0x36,0x37,0x36,0x30,0x20,0x31,0x39,0x20,0x31,0x39,0x2E,0x30,0x33,0x35,0x32,
+ 0x35,0x30,0x20,0x32,0x30,0x20,0x32,0x30,0x2E,0x30,0x34,0x30,0x33,0x32,0x30,
+ 0x0A,0x37,0x20,0x30,0x20,0x31,0x34,0x2E,0x30,0x30,0x33,0x30,0x37,0x34,0x20,
+ 0x31,0x32,0x20,0x31,0x32,0x2E,0x30,0x31,0x38,0x36,0x31,0x33,0x20,0x31,0x33,
+ 0x20,0x31,0x33,0x2E,0x30,0x30,0x35,0x37,0x33,0x38,0x20,0x31,0x34,0x20,0x31,
+ 0x34,0x2E,0x30,0x30,0x33,0x30,0x37,0x34,0x20,0x31,0x35,0x20,0x31,0x35,0x2E,
+ 0x30,0x30,0x30,0x31,0x30,0x38,0x20,0x31,0x36,0x20,0x31,0x36,0x2E,0x30,0x30,
+ 0x36,0x31,0x30,0x31,0x20,0x31,0x37,0x20,0x31,0x37,0x2E,0x30,0x30,0x38,0x34,
+ 0x35,0x30,0x20,0x31,0x38,0x20,0x31,0x38,0x2E,0x30,0x31,0x34,0x30,0x38,0x32,
+ 0x20,0x31,0x39,0x20,0x31,0x39,0x2E,0x30,0x31,0x37,0x30,0x32,0x37,0x20,0x32,
+ 0x30,0x20,0x32,0x30,0x2E,0x30,0x32,0x33,0x33,0x37,0x30,0x20,0x32,0x31,0x20,
+ 0x32,0x31,0x2E,0x30,0x32,0x37,0x30,0x39,0x30,0x20,0x32,0x32,0x20,0x32,0x32,
+ 0x2E,0x30,0x33,0x34,0x34,0x34,0x30,0x20,0x32,0x33,0x20,0x32,0x33,0x2E,0x30,
+ 0x34,0x30,0x35,0x31,0x30,0x0A,0x38,0x20,0x30,0x20,0x31,0x35,0x2E,0x39,0x39,
+ 0x34,0x39,0x31,0x34,0x20,0x31,0x32,0x20,0x31,0x32,0x2E,0x30,0x33,0x34,0x34,
+ 0x30,0x35,0x20,0x31,0x33,0x20,0x31,0x33,0x2E,0x30,0x32,0x34,0x38,0x31,0x30,
+ 0x20,0x31,0x34,0x20,0x31,0x34,0x2E,0x30,0x30,0x38,0x35,0x39,0x35,0x20,0x31,
+ 0x35,0x20,0x31,0x35,0x2E,0x30,0x30,0x33,0x30,0x36,0x35,0x20,0x31,0x36,0x20,
+ 0x31,0x35,0x2E,0x39,0x39,0x34,0x39,0x31,0x34,0x20,0x31,0x37,0x20,0x31,0x36,
+ 0x2E,0x39,0x39,0x39,0x31,0x33,0x31,0x20,0x31,0x38,0x20,0x31,0x37,0x2E,0x39,
+ 0x39,0x39,0x31,0x36,0x30,0x20,0x31,0x39,0x20,0x31,0x39,0x2E,0x30,0x30,0x33,
+ 0x35,0x37,0x39,0x20,0x32,0x30,0x20,0x32,0x30,0x2E,0x30,0x30,0x34,0x30,0x37,
+ 0x36,0x20,0x32,0x31,0x20,0x32,0x31,0x2E,0x30,0x30,0x38,0x36,0x35,0x35,0x20,
+ 0x32,0x32,0x20,0x32,0x32,0x2E,0x30,0x30,0x39,0x39,0x37,0x30,0x20,0x32,0x33,
+ 0x20,0x32,0x33,0x2E,0x30,0x31,0x35,0x36,0x39,0x30,0x20,0x32,0x34,0x20,0x32,
+ 0x34,0x2E,0x30,0x32,0x30,0x33,0x37,0x30,0x0A,0x39,0x20,0x30,0x20,0x31,0x38,
+ 0x2E,0x39,0x39,0x38,0x34,0x30,0x33,0x20,0x31,0x35,0x20,0x31,0x35,0x2E,0x30,
+ 0x31,0x38,0x30,0x31,0x30,0x20,0x31,0x36,0x20,0x31,0x36,0x2E,0x30,0x31,0x31,
+ 0x34,0x36,0x36,0x20,0x31,0x37,0x20,0x31,0x37,0x2E,0x30,0x30,0x32,0x30,0x39,
+ 0x35,0x20,0x31,0x38,0x20,0x31,0x38,0x2E,0x30,0x30,0x30,0x39,0x33,0x37,0x20,
+ 0x31,0x39,0x20,0x31,0x38,0x2E,0x39,0x39,0x38,0x34,0x30,0x33,0x20,0x32,0x30,
+ 0x20,0x31,0x39,0x2E,0x39,0x39,0x39,0x39,0x38,0x31,0x20,0x32,0x31,0x20,0x32,
+ 0x30,0x2E,0x39,0x39,0x39,0x39,0x34,0x38,0x20,0x32,0x32,0x20,0x32,0x32,0x2E,
+ 0x30,0x30,0x32,0x39,0x39,0x39,0x20,0x32,0x33,0x20,0x32,0x33,0x2E,0x30,0x30,
+ 0x33,0x35,0x37,0x30,0x20,0x32,0x34,0x20,0x32,0x34,0x2E,0x30,0x30,0x38,0x31,
+ 0x30,0x30,0x20,0x32,0x35,0x20,0x32,0x35,0x2E,0x30,0x31,0x32,0x30,0x39,0x30,
+ 0x20,0x32,0x36,0x20,0x32,0x36,0x2E,0x30,0x31,0x39,0x36,0x33,0x30,0x20,0x32,
+ 0x37,0x20,0x32,0x37,0x2E,0x30,0x32,0x36,0x38,0x39,0x30,0x0A,0x31,0x30,0x20,
+ 0x30,0x20,0x31,0x39,0x2E,0x39,0x39,0x32,0x34,0x34,0x30,0x20,0x31,0x36,0x20,
+ 0x31,0x36,0x2E,0x30,0x32,0x35,0x37,0x35,0x37,0x20,0x31,0x37,0x20,0x31,0x37,
+ 0x2E,0x30,0x31,0x37,0x37,0x30,0x30,0x20,0x31,0x38,0x20,0x31,0x38,0x2E,0x30,
+ 0x30,0x35,0x36,0x39,0x37,0x20,0x31,0x39,0x20,0x31,0x39,0x2E,0x30,0x30,0x31,
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+ 0x30,0x35,0x30,0x20,0x32,0x35,0x37,0x20,0x32,0x35,0x37,0x2E,0x30,0x39,0x35,
+ 0x35,0x33,0x35,0x20,0x32,0x35,0x38,0x20,0x32,0x35,0x38,0x2E,0x30,0x39,0x38,
+ 0x34,0x32,0x35,0x20,0x32,0x35,0x39,0x20,0x32,0x35,0x39,0x2E,0x31,0x30,0x30,
+ 0x35,0x30,0x30,0x20,0x32,0x36,0x30,0x20,0x32,0x36,0x30,0x2E,0x31,0x30,0x33,
+ 0x36,0x35,0x30,0x0A,0x31,0x30,0x32,0x20,0x30,0x20,0x32,0x35,0x39,0x2E,0x31,
+ 0x30,0x31,0x30,0x32,0x30,0x20,0x32,0x35,0x30,0x20,0x32,0x35,0x30,0x2E,0x30,
+ 0x38,0x37,0x34,0x39,0x30,0x20,0x32,0x35,0x31,0x20,0x32,0x35,0x31,0x2E,0x30,
+ 0x38,0x38,0x39,0x36,0x30,0x20,0x32,0x35,0x32,0x20,0x32,0x35,0x32,0x2E,0x30,
+ 0x38,0x38,0x39,0x36,0x36,0x20,0x32,0x35,0x33,0x20,0x32,0x35,0x33,0x2E,0x30,
+ 0x39,0x30,0x36,0x35,0x30,0x20,0x32,0x35,0x34,0x20,0x32,0x35,0x34,0x2E,0x30,
+ 0x39,0x30,0x39,0x34,0x39,0x20,0x32,0x35,0x35,0x20,0x32,0x35,0x35,0x2E,0x30,
+ 0x39,0x33,0x32,0x33,0x32,0x20,0x32,0x35,0x36,0x20,0x32,0x35,0x36,0x2E,0x30,
+ 0x39,0x34,0x32,0x37,0x36,0x20,0x32,0x35,0x37,0x20,0x32,0x35,0x37,0x2E,0x30,
+ 0x39,0x36,0x38,0x35,0x30,0x20,0x32,0x35,0x38,0x20,0x32,0x35,0x38,0x2E,0x30,
+ 0x39,0x38,0x32,0x30,0x30,0x20,0x32,0x35,0x39,0x20,0x32,0x35,0x39,0x2E,0x31,
+ 0x30,0x31,0x30,0x32,0x30,0x20,0x32,0x36,0x32,0x20,0x32,0x36,0x32,0x2E,0x31,
+ 0x30,0x37,0x35,0x32,0x30,0x0A,0x31,0x30,0x33,0x20,0x30,0x20,0x32,0x36,0x32,
+ 0x2E,0x31,0x30,0x39,0x36,0x39,0x30,0x20,0x32,0x35,0x33,0x20,0x32,0x35,0x33,
+ 0x2E,0x30,0x39,0x35,0x32,0x36,0x30,0x20,0x32,0x35,0x34,0x20,0x32,0x35,0x34,
+ 0x2E,0x30,0x39,0x36,0x35,0x39,0x30,0x20,0x32,0x35,0x35,0x20,0x32,0x35,0x35,
+ 0x2E,0x30,0x39,0x36,0x37,0x37,0x30,0x20,0x32,0x35,0x36,0x20,0x32,0x35,0x36,
+ 0x2E,0x30,0x39,0x38,0x37,0x36,0x30,0x20,0x32,0x35,0x37,0x20,0x32,0x35,0x37,
+ 0x2E,0x30,0x39,0x39,0x36,0x31,0x30,0x20,0x32,0x35,0x38,0x20,0x32,0x35,0x38,
+ 0x2E,0x31,0x30,0x31,0x38,0x38,0x30,0x20,0x32,0x35,0x39,0x20,0x32,0x35,0x39,
+ 0x2E,0x31,0x30,0x32,0x39,0x39,0x30,0x20,0x32,0x36,0x30,0x20,0x32,0x36,0x30,
+ 0x2E,0x31,0x30,0x35,0x35,0x37,0x30,0x20,0x32,0x36,0x31,0x20,0x32,0x36,0x31,
+ 0x2E,0x31,0x30,0x36,0x39,0x34,0x30,0x20,0x32,0x36,0x32,0x20,0x32,0x36,0x32,
+ 0x2E,0x31,0x30,0x39,0x36,0x39,0x30,0x0A,0x31,0x30,0x34,0x20,0x30,0x20,0x32,
+ 0x36,0x31,0x2E,0x31,0x30,0x38,0x37,0x35,0x30,0x20,0x32,0x35,0x33,0x20,0x32,
+ 0x35,0x33,0x2E,0x31,0x30,0x30,0x36,0x38,0x30,0x20,0x32,0x35,0x34,0x20,0x32,
+ 0x35,0x34,0x2E,0x31,0x30,0x30,0x31,0x37,0x30,0x20,0x32,0x35,0x35,0x20,0x32,
+ 0x35,0x35,0x2E,0x31,0x30,0x31,0x34,0x39,0x30,0x20,0x32,0x35,0x36,0x20,0x32,
+ 0x35,0x36,0x2E,0x31,0x30,0x31,0x31,0x38,0x30,0x20,0x32,0x35,0x37,0x20,0x32,
+ 0x35,0x37,0x2E,0x31,0x30,0x33,0x30,0x37,0x30,0x20,0x32,0x35,0x38,0x20,0x32,
+ 0x35,0x38,0x2E,0x31,0x30,0x33,0x35,0x37,0x30,0x20,0x32,0x35,0x39,0x20,0x32,
+ 0x35,0x39,0x2E,0x31,0x30,0x35,0x36,0x33,0x30,0x20,0x32,0x36,0x30,0x20,0x32,
+ 0x36,0x30,0x2E,0x31,0x30,0x36,0x34,0x33,0x30,0x20,0x32,0x36,0x31,0x20,0x32,
+ 0x36,0x31,0x2E,0x31,0x30,0x38,0x37,0x35,0x30,0x20,0x32,0x36,0x32,0x20,0x32,
+ 0x36,0x32,0x2E,0x31,0x30,0x39,0x39,0x32,0x30,0x20,0x32,0x36,0x33,0x20,0x32,
+ 0x36,0x33,0x2E,0x31,0x31,0x32,0x35,0x34,0x30,0x0A,0x31,0x30,0x35,0x20,0x30,
+ 0x20,0x32,0x36,0x32,0x2E,0x31,0x31,0x34,0x31,0x35,0x30,0x20,0x32,0x35,0x35,
+ 0x20,0x32,0x35,0x35,0x2E,0x31,0x30,0x37,0x34,0x30,0x30,0x20,0x32,0x35,0x37,
+ 0x20,0x32,0x35,0x37,0x2E,0x31,0x30,0x37,0x38,0x36,0x30,0x20,0x32,0x35,0x38,
+ 0x20,0x32,0x35,0x38,0x2E,0x31,0x30,0x39,0x34,0x34,0x30,0x20,0x32,0x35,0x39,
+ 0x20,0x32,0x35,0x39,0x2E,0x31,0x30,0x39,0x37,0x32,0x30,0x20,0x32,0x36,0x30,
+ 0x20,0x32,0x36,0x30,0x2E,0x31,0x31,0x31,0x34,0x33,0x30,0x20,0x32,0x36,0x31,
+ 0x20,0x32,0x36,0x31,0x2E,0x31,0x31,0x32,0x31,0x31,0x30,0x20,0x32,0x36,0x32,
+ 0x20,0x32,0x36,0x32,0x2E,0x31,0x31,0x34,0x31,0x35,0x30,0x20,0x32,0x36,0x33,
+ 0x20,0x32,0x36,0x33,0x2E,0x31,0x31,0x35,0x30,0x38,0x30,0x0A,0x31,0x30,0x36,
+ 0x20,0x30,0x20,0x32,0x36,0x33,0x2E,0x31,0x31,0x38,0x33,0x31,0x30,0x20,0x32,
+ 0x35,0x39,0x20,0x32,0x35,0x39,0x2E,0x31,0x31,0x34,0x36,0x35,0x30,0x20,0x32,
+ 0x36,0x30,0x20,0x32,0x36,0x30,0x2E,0x31,0x31,0x34,0x34,0x34,0x30,0x20,0x32,
+ 0x36,0x31,0x20,0x32,0x36,0x31,0x2E,0x31,0x31,0x36,0x32,0x30,0x30,0x20,0x32,
+ 0x36,0x33,0x20,0x32,0x36,0x33,0x2E,0x31,0x31,0x38,0x33,0x31,0x30,0x20,0x32,
+ 0x36,0x35,0x20,0x32,0x36,0x35,0x2E,0x31,0x32,0x31,0x30,0x37,0x30,0x20,0x32,
+ 0x36,0x36,0x20,0x32,0x36,0x36,0x2E,0x31,0x32,0x31,0x39,0x33,0x30,0x0A,0x31,
+ 0x30,0x37,0x20,0x30,0x20,0x32,0x36,0x34,0x2E,0x31,0x32,0x34,0x37,0x33,0x30,
+ 0x20,0x32,0x36,0x31,0x20,0x32,0x36,0x31,0x2E,0x31,0x32,0x31,0x38,0x30,0x30,
+ 0x20,0x32,0x36,0x32,0x20,0x32,0x36,0x32,0x2E,0x31,0x32,0x33,0x30,0x31,0x30,
+ 0x20,0x32,0x36,0x34,0x20,0x32,0x36,0x34,0x2E,0x31,0x32,0x34,0x37,0x33,0x30,
+ 0x0A,0x31,0x30,0x38,0x20,0x30,0x20,0x32,0x36,0x35,0x2E,0x31,0x33,0x30,0x30,
+ 0x30,0x30,0x20,0x32,0x36,0x33,0x20,0x32,0x36,0x33,0x2E,0x31,0x32,0x38,0x37,
+ 0x31,0x30,0x20,0x32,0x36,0x34,0x20,0x32,0x36,0x34,0x2E,0x31,0x32,0x38,0x34,
+ 0x31,0x30,0x20,0x32,0x36,0x35,0x20,0x32,0x36,0x35,0x2E,0x31,0x33,0x30,0x30,
+ 0x30,0x30,0x0A,0x31,0x30,0x39,0x20,0x30,0x20,0x32,0x36,0x38,0x2E,0x31,0x33,
+ 0x38,0x38,0x32,0x30,0x20,0x32,0x36,0x36,0x20,0x32,0x36,0x36,0x2E,0x31,0x33,
+ 0x37,0x39,0x34,0x30,0x20,0x32,0x36,0x38,0x20,0x32,0x36,0x38,0x2E,0x31,0x33,
+ 0x38,0x38,0x32,0x30,0x0A,0x00};
+
+} // namespace OpenBabel
+#endif // OB_ISOTOPE_H
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/isotope.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,147 @@
+##############################################################################
+#                                                                            #
+#                   Open Babel file: isotope.txt                             #
+#                                                                            #
+#  Copyright (c) 2002-2004 by Geoffrey R. Hutchison                          #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+#  This file has a series of lines, one for each element                     #
+#   (i.e. line 0 = neutron, line 1 = hydrogen, line 2 = helium, etc.)        #
+#  Each line: Atomic #, 0 then exact mass of most abundant isotope           #
+#     then a list of isotopes as int, float pairs corresponding to masses    #
+#                                                                            #
+#  CAUTION: Masses have been zero-padded to 9 decimal places                 #
+#   (we don't currently have a math package that can deal with sig. fig.)    #
+#   so trailing zeros may not be significant and/or useful                   #
+#                                                                            #
+#  Values are compiled from:                                                 #
+#      "The Ame2003 atomic mass evaluation (II)"                             #
+#        by G.Audi, A.H.Wapstra and C.Thibault                               #
+#          Nuclear Physics A729 p. 337-676, December 22, 2003.               #
+#  as made available in the mass.mas03round file                             #
+#  (these are values for publication)                                        #
+#                                                                            #
+#  Currently: 110 lines (neutron, H to Mt)                                   #
+#  (note that since element 0 often represents a dummy atom, the default     #
+#   mass is 0 amu, *not* the mass of a neutron, accessible as isotope 1)     #
+#                                                                            #
+##############################################################################
+0 0 0.000000000 1 1.008664915
+1 0 1.007825032 1 1.007825032 2 2.014101778 3 3.016049278 4 4.027810000 5 5.035310000 6 6.044940000 7 7.052750000
+2 0 4.002603254 3 3.016029319 4 4.002603254 5 5.012220000 6 6.018889100 7 7.028021000 8 8.033922000 9 9.043950000 10 10.052400000
+3 0 7.016004550 3 3.030780000 4 4.027190000 5 5.012540000 6 6.015122795 7 7.016004550 8 8.022487360 9 9.026789500 10 10.035481000 11 11.043798000 12 12.053780000
+4 0 9.012182200 5 5.040790000 6 6.019726000 7 7.016929830 8 8.005305100 9 9.012182200 10 10.013533800 11 11.021658000 12 12.026921000 13 13.035690000 14 14.042890000 15 15.053460000 16 16.061920000
+5 0 11.009305400 6 6.046810000 7 7.029920000 8 8.024607200 9 9.013328800 10 10.012937000 11 11.009305400 12 12.014352100 13 13.017780200 14 14.025404000 15 15.031103000 16 16.039810000 17 17.046990000 18 18.056170000 19 19.063730000
+6 0 12.000000000 8 8.037675000 9 9.031036700 10 10.016853200 11 11.011433600 12 12.000000000 13 13.003354838 14 14.003241989 15 15.010599300 16 16.014701000 17 17.022586000 18 18.026760000 19 19.034810000 20 20.040320000 21 21.049340000 22 22.057200000
+7 0 14.003074005 10 10.041650000 11 11.026090000 12 12.018613200 13 13.005738610 14 14.003074005 15 15.000108898 16 16.006101700 17 17.008450000 18 18.014079000 19 19.017029000 20 20.023370000 21 21.027110000 22 22.034390000 23 23.041220000 24 24.051040000 25 25.060660000
+8 0 15.994914620 12 12.034405000 13 13.024812000 14 14.008596250 15 15.003065600 16 15.994914620 17 16.999131700 18 17.999161000 19 19.003580000 20 20.004076700 21 21.008656000 22 22.009970000 23 23.015690000 24 24.020470000 25 25.029460000 26 26.038340000 27 27.048260000 28 28.057810000
+9 0 18.998403220 14 14.035060000 15 15.018010000 16 16.011466000 17 17.002095240 18 18.000938000 19 18.998403220 20 19.999981320 21 20.999949000 22 22.002999000 23 23.003570000 24 24.008120000 25 25.012100000 26 26.019620000 27 27.026760000 28 28.035670000 29 29.043260000 30 30.052500000 31 31.060430000
+10 0 19.992440175 16 16.025761000 17 17.017672000 18 18.005708200 19 19.001880200 20 19.992440175 21 20.993846680 22 21.991385114 23 22.994466900 24 23.993610800 25 24.997737000 26 26.000461000 27 27.007590000 28 28.012070000 29 29.019390000 30 30.024800000 31 31.033110000 32 32.040020000 33 33.049380000 34 34.057030000
+11 0 22.989769281 18 18.025970000 19 19.013877000 20 20.007351000 21 20.997655200 22 21.994436400 23 22.989769281 24 23.990962780 25 24.989954000 26 25.992633000 27 26.994077000 28 27.998938000 29 29.002861000 30 30.008976000 31 31.013590000 32 32.020470000 33 33.026720000 34 34.035170000 35 35.042490000 36 36.051480000 37 37.059340000
+12 0 23.985041700 19 19.035470000 20 20.018863000 21 21.011713000 22 21.999573800 23 22.994123700 24 23.985041700 25 24.985836920 26 25.982592929 27 26.984340590 28 27.983876800 29 28.988600000 30 29.990434000 31 30.996546000 32 31.998975000 33 33.005254000 34 34.009460000 35 35.017340000 36 36.023000000 37 37.031400000 38 38.037570000 39 39.046770000 40 40.053930000
+13 0 26.981538630 21 21.028040000 22 22.019520000 23 23.007267000 24 23.999938900 25 24.990428100 26 25.986891690 27 26.981538630 28 27.981910310 29 28.980445000 30 29.982960000 31 30.983947000 32 31.988120000 33 32.990840000 34 33.996850000 35 34.999860000 36 36.006210000 37 37.010680000 38 38.017230000 39 39.022970000 40 40.031450000 41 41.038330000 42 42.046890000
+14 0 27.976926532 22 22.034530000 23 23.025520000 24 24.011546000 25 25.004106000 26 25.992330000 27 26.986704910 28 27.976926532 29 28.976494700 30 29.973770170 31 30.975363230 32 31.974148080 33 32.978000000 34 33.978576000 35 34.984580000 36 35.986600000 37 36.992940000 38 37.995630000 39 39.002070000 40 40.005870000 41 41.014560000 42 42.019790000 43 43.028660000 44 44.035260000
+15 0 30.973761630 24 24.034350000 25 25.020260000 26 26.011780000 27 26.999230000 28 27.992315000 29 28.981800600 30 29.978313800 31 30.973761630 32 31.973907270 33 32.971725500 34 33.973636000 35 34.973314100 36 35.978260000 37 36.979610000 38 37.984160000 39 38.986180000 40 39.991300000 41 40.994340000 42 42.001010000 43 43.006190000 44 44.012990000 45 45.019220000 46 46.027380000
+16 0 31.972071000 26 26.027880000 27 27.018830000 28 28.004370000 29 28.996610000 30 29.984903000 31 30.979554700 32 31.972071000 33 32.971458760 34 33.967866900 35 34.969032160 36 35.967080760 37 36.971125570 38 37.971163000 39 38.975130000 40 39.975450000 41 40.979580000 42 41.981020000 43 42.987150000 44 43.990210000 45 44.996510000 46 46.000750000 47 47.008590000 48 48.014170000 49 49.023620000
+17 0 34.968852680 28 28.028510000 29 29.014110000 30 30.004770000 31 30.992410000 32 31.985690000 33 32.977451900 34 33.973762820 35 34.968852680 36 35.968306980 37 36.965902590 38 37.968010430 39 38.968008200 40 39.970420000 41 40.970680000 42 41.973250000 43 42.974050000 44 43.978280000 45 44.980290000 46 45.984210000 47 46.988710000 48 47.994950000 49 49.000320000 50 50.007840000 51 51.014490000
+18 0 39.962383123 30 30.021560000 31 31.012120000 32 31.997638000 33 32.989925700 34 33.980271200 35 34.975257600 36 35.967545106 37 36.966776320 38 37.962732400 39 38.964313000 40 39.962383123 41 40.964500600 42 41.963046000 43 42.965636000 44 43.964924000 45 44.968040000 46 45.968090000 47 46.972190000 48 47.974540000 49 48.980520000 50 49.984430000 51 50.991630000 52 51.996780000 53 53.004940000
+19 0 38.963706680 32 32.021920000 33 33.007260000 34 33.998410000 35 34.988010000 36 35.981292000 37 36.973375890 38 37.969081200 39 38.963706680 40 39.963998480 41 40.961825760 42 41.962402810 43 42.960716000 44 43.961560000 45 44.960699000 46 45.961977000 47 46.961678000 48 47.965514000 49 48.967450000 50 49.972780000 51 50.976380000 52 51.982610000 53 52.987120000 54 53.994200000 55 54.999710000
+20 0 39.962590980 34 34.014120000 35 35.004940000 36 35.993090000 37 36.985870000 38 37.976318000 39 38.970719700 40 39.962590980 41 40.962278060 42 41.958618010 43 42.958766600 44 43.955481800 45 44.956186600 46 45.953692600 47 46.954546000 48 47.952534000 49 48.955674000 50 49.957519000 51 50.961500000 52 51.965100000 53 52.970050000 54 53.974350000 55 54.980550000 56 55.985570000 57 56.992360000
+21 0 44.955911900 36 36.014920000 37 37.003050000 38 37.994700000 39 38.984790000 40 39.977967000 41 40.969251130 42 41.965516430 43 42.961150700 44 43.959402800 45 44.955911900 46 45.955171900 47 46.952407500 48 47.952231000 49 48.950024000 50 49.952188000 51 50.953603000 52 51.956680000 53 52.959610000 54 53.963260000 55 54.968240000 56 55.972870000 57 56.977790000 58 57.983710000 59 58.989220000 60 59.995710000
+22 0 47.947946300 38 38.009770000 39 39.001610000 40 39.990500000 41 40.983150000 42 41.973031000 43 42.968522000 44 43.959690100 45 44.958125600 46 45.952631600 47 46.951763100 48 47.947946300 49 48.947870000 50 49.944791200 51 50.946615000 52 51.946897000 53 52.949730000 54 53.951050000 55 54.955270000 56 55.958200000 57 56.963990000 58 57.966970000 59 58.972930000 60 59.976760000 61 60.983200000 62 61.987490000 63 62.994420000
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+89 0 227.027752000 206 206.014500000 207 207.011950000 208 208.011550000 209 209.009490000 210 210.009440000 211 211.007730000 212 212.007810000 213 213.006610000 214 214.006902000 215 215.006454000 216 216.008720000 217 217.009347000 218 218.011640000 219 219.012420000 220 220.014763000 221 221.015590000 222 222.017844000 223 223.019137000 224 224.021723000 225 225.023230000 226 226.026098000 227 227.027752000 228 228.031021000 229 229.033020000 230 230.036290000 231 231.038560000 232 232.042030000 233 233.044550000 234 234.048420000 235 235.051230000 236 236.055300000
+90 0 232.038055000 209 209.017720000 210 210.015075000 211 211.014930000 212 212.012980000 213 213.013010000 214 214.011500000 215 215.011730000 216 216.011062000 217 217.013114000 218 218.013284000 219 219.015540000 220 220.015748000 221 221.018184000 222 222.018468000 223 223.020811000 224 224.021467000 225 225.023951000 226 226.024903000 227 227.027704000 228 228.028741000 229 229.031762000 230 230.033133000 231 231.036304000 232 232.038055000 233 233.041581000 234 234.043601000 235 235.047510000 236 236.049870000 237 237.053890000 238 238.056500000
+91 0 231.035884000 212 212.023200000 213 213.021110000 214 214.020920000 215 215.019190000 216 216.019110000 217 217.018320000 218 218.020042000 219 219.019880000 220 220.021880000 221 221.021880000 222 222.023740000 223 223.023960000 224 224.025626000 225 225.026130000 226 226.027948000 227 227.028805000 228 228.031051000 229 229.032096000 230 230.034541000 231 231.035884000 232 232.038592000 233 233.040247000 234 234.043308000 235 235.045440000 236 236.048680000 237 237.051150000 238 238.054500000 239 239.057260000 240 240.060980000
+92 0 238.050788000 217 217.024370000 218 218.023540000 219 219.024920000 220 220.024720000 221 221.026400000 222 222.026090000 223 223.027740000 224 224.027605000 225 225.029391000 226 226.029339000 227 227.031156000 228 228.031374000 229 229.033506000 230 230.033940000 231 231.036294000 232 232.037156000 233 233.039635000 234 234.040952000 235 235.043929000 236 236.045568000 237 237.048730000 238 238.050788000 239 239.054293000 240 240.056592000 241 241.060330000 242 242.062930000
+93 0 237.048173000 225 225.033910000 226 226.035150000 227 227.034960000 228 228.036180000 229 229.036260000 230 230.037830000 231 231.038250000 232 232.040110000 233 233.040740000 234 234.042895000 235 235.044063000 236 236.046570000 237 237.048173000 238 238.050946000 239 239.052939000 240 240.056162000 241 241.058250000 242 242.061640000 243 243.064280000 244 244.067850000
+94 0 244.064204000 228 228.038740000 229 229.040150000 230 230.039650000 231 231.041101000 232 232.041187000 233 233.043000000 234 234.043317000 235 235.045286000 236 236.046058000 237 237.048409000 238 238.049559000 239 239.052163000 240 240.053813000 241 241.056851000 242 242.058742000 243 243.062003000 244 244.064204000 245 245.067747000 246 246.070205000 247 247.074070000
+95 0 243.061381000 231 231.045560000 232 232.046590000 233 233.046350000 234 234.047810000 235 235.047950000 236 236.049580000 237 237.050000000 238 238.051980000 239 239.053024000 240 240.055300000 241 241.056829000 242 242.059549000 243 243.061381000 244 244.064284000 245 245.066452000 246 246.069775000 247 247.072090000 248 248.075750000 249 249.078480000
+96 0 247.070354000 233 233.050770000 234 234.050160000 235 235.051430000 236 236.051410000 237 237.052900000 238 238.053030000 239 239.054960000 240 240.055529000 241 241.057653000 242 242.058835000 243 243.061389000 244 244.062752000 245 245.065491000 246 246.067223000 247 247.070354000 248 248.072349000 249 249.075953000 250 250.078357000 251 251.082285000 252 252.084870000
+97 0 247.070307000 235 235.056580000 236 236.057330000 237 237.057000000 238 238.058280000 239 239.058280000 240 240.059760000 241 241.060230000 242 242.061980000 243 243.063008000 244 244.065181000 245 245.066361000 246 246.068670000 247 247.070307000 248 248.073090000 249 249.074986000 250 250.078317000 251 251.080760000 252 252.084310000 253 253.086880000 254 254.090600000
+98 0 251.079587000 237 237.062070000 238 238.061410000 239 239.062420000 240 240.062300000 241 241.063730000 242 242.063700000 243 243.065430000 244 244.066001000 245 245.068049000 246 246.068805000 247 247.071001000 248 248.072185000 249 249.074853000 250 250.076406000 251 251.079587000 252 252.081626000 253 253.085133000 254 254.087323000 255 255.091050000 256 256.093440000
+99 0 252.082980000 240 240.068920000 241 241.068540000 242 242.069750000 243 243.069550000 244 244.070880000 245 245.071320000 246 246.072900000 247 247.073660000 248 248.075470000 249 249.076410000 250 250.078610000 251 251.079992000 252 252.082980000 253 253.084824000 254 254.088022000 255 255.090273000 256 256.093600000 257 257.095980000 258 258.099520000
+100 0 257.095105000 242 242.073430000 243 243.074350000 244 244.074080000 245 245.075390000 246 246.075300000 247 247.076850000 248 248.077195000 249 249.079030000 250 250.079521000 251 251.081575000 252 252.082467000 253 253.085185000 254 254.086854000 255 255.089962000 256 256.091773000 257 257.095105000 258 258.097080000 259 259.100600000 260 260.102680000
+101 0 258.098431000 245 245.080830000 246 246.081890000 247 247.081640000 248 248.082820000 249 249.083010000 250 250.084420000 251 251.084840000 252 252.086560000 253 253.087280000 254 254.089660000 255 255.091083000 256 256.094060000 257 257.095541000 258 258.098431000 259 259.100510000 260 260.103650000 261 261.105720000 262 262.108870000
+102 0 259.101030000 248 248.086600000 249 249.087830000 250 250.087510000 251 251.089010000 252 252.088977000 253 253.090680000 254 254.090955000 255 255.093241000 256 256.094283000 257 257.096877000 258 258.098210000 259 259.101030000 260 260.102640000 261 261.105750000 262 262.107300000 263 263.110550000 264 264.112350000
+103 0 262.109630000 251 251.094360000 252 252.095370000 253 253.095210000 254 254.096450000 255 255.096680000 256 256.098630000 257 257.099560000 258 258.101810000 259 259.102900000 260 260.105500000 261 261.106880000 262 262.109630000 263 263.111290000 264 264.114040000 265 265.115840000 266 266.119310000
+104 0 261.108770000 253 253.100690000 254 254.100180000 255 255.101340000 256 256.101166000 257 257.102990000 258 258.103490000 259 259.105640000 260 260.106440000 261 261.108770000 262 262.109930000 263 263.112550000 264 264.113990000 265 265.116700000 266 266.117960000 267 267.121530000 268 268.123640000
+105 0 262.114080000 255 255.107400000 256 256.108130000 257 257.107720000 258 258.109230000 259 259.109610000 260 260.111300000 261 261.112060000 262 262.114080000 263 263.114990000 264 264.117400000 265 265.118600000 266 266.121030000 267 267.122380000 268 268.125450000 269 269.127460000 270 270.130710000
+106 0 263.118320000 258 258.113170000 259 259.114500000 260 260.114420000 261 261.116120000 262 262.116400000 263 263.118320000 264 264.118930000 265 265.121110000 266 266.122070000 267 267.124430000 268 268.125610000 269 269.128760000 270 270.130330000 271 271.133470000 272 272.135160000 273 273.138220000
+107 0 264.124600000 260 260.121970000 261 261.121660000 262 262.122890000 263 263.123040000 264 264.124600000 265 265.125150000 266 266.126940000 267 267.127650000 268 268.129760000 269 269.130690000 270 270.133620000 271 271.135180000 272 272.138030000 273 273.139620000 274 274.142440000 275 275.144250000
+108 0 265.130090000 263 263.128560000 264 264.128390000 265 265.130090000 266 266.130100000 267 267.131790000 268 268.132160000 269 269.134060000 270 270.134650000 271 271.137660000 272 272.139050000 273 273.141990000 274 274.143130000 275 275.145950000 276 276.147210000 277 277.149840000
+109 0 268.138730000 265 265.136150000 266 266.137300000 267 267.137310000 268 268.138730000 269 269.139060000 270 270.140660000 271 271.141140000 272 272.143740000 273 273.144910000 274 274.147490000 275 275.148650000 276 276.151160000 277 277.152420000 278 278.154810000 279 279.156190000
+110 0 281.162061 281 281.162061
+111 0 280.164473 280 280.164473
+112 0 285.174105 285 285.174105
+113 0 284.178080 284 284.178080
+114 0 289.187279 289 289.187279
+115 0 288.192492 288 288.192492
+116 0 292.199786 292 292.199786
+117 0 292.207550 291 291.206560 292 292.207550
+118 0 293.214670 293 293.214670
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/logp.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,169 @@
+######################################################################
+# Copyright OELIB:          OpenEye Scientific Software, Santa Fe,      
+#                           U.S.A., 1999,2000,2001                      
+# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of  
+#                           Tuebingen, Germany, 2001,2002,2003,2004,2005
+# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany,        
+#                           2003,2004,2005                              
+#                                                                       
+# Authors: Stephen Jelfs                                                                       
+#          Joerg Kurt Wegner, me@cheminformatics.eu         
+#                                                                       
+# This program is free software; you can redistribute it and/or modify  
+# it under the terms of the GNU General Public License as published by  
+# the Free Software Foundation version 2 of the License.                
+#                                                                       
+# This program is distributed in the hope that it will be useful,       
+# but WITHOUT ANY WARRANTY; without even the implied warranty of        
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         
+# GNU General Public License for more details.                          
+######################################################################
+# LopP Atomic Contributions
+# ref. Wildman, S.A. and Crippen, G.M., J. Chem. Inf. Comput. Sci., 
+#   1999, 39, 868-873.
+# Table below is adapted from above ref.
+######################################################################
+;hydrogen
+[*]	0.1125
+[#6]	0.123
+[#1]	0.123
+[O][CX4]	-0.2677
+[O]c	-0.2677
+[O][#5]	-0.2677
+[O][#14]	-0.2677
+[O][#15]	-0.2677
+[O][#33]	-0.2677
+[O][#50]	-0.2677
+[#5]	-0.2677
+[#14]	-0.2677
+[#15]	-0.2677
+[#16]	-0.2677
+[#50]	-0.2677
+[#7]	0.2142
+[O][#7]	0.2142
+[O]C=[#6]	0.298
+[O]C=[#7]	0.298
+[O]C=O	0.298
+[O]C=S	0.298
+[O]O	0.298
+[O]S	0.298
+;heavy
+[*]	0
+[#6]	0.0813
+[CH4]	0.1441
+[CH3]C	0.1441
+[CH2](C)C	0.1441
+[CH](C)(C)C	0
+[C](C)(C)(C)C	0
+[CH3][O,N,F,Cl,Br,#15,#16,#53;!a]	-0.2035
+[CH2X4][O,N,F,Cl,Br,#15,#16,#53;!a]	-0.2035
+[CHX4][O,N,F,Cl,Br,#15,#16,#53;!a]	-0.2051
+[CH0X4][O,N,F,Cl,Br,#15,#16,#53;!a]	-0.2051
+[C]=[A!#6]	-0.2783
+[CH2]=C	0.1551
+[CH1](=C)A	0.1551
+[CH0](=C)(A)A	0.1551
+[C](=C)=C	0.1551
+[CX2]#A	0.0017
+[CH3]c	0.0845
+[CH3][a!#6]	-0.1444
+[CH2X4]a	-0.0516
+[CHX4]a	0.1193
+[CH0X4]a	-0.0967
+[c][#5,#14,#15,#33,#34,#50,#80]	-0.5443
+[c][#9]	0
+[c][#17]	0.245
+[c][#35]	0.198
+[c][#53]	0
+[cH]	0.1581
+[c](:a)(:a):a	0.2955
+[c](:a)(:a)-a	0.2713
+[c](:a)(:a)-C	0.136
+[c](:a)(:a)-N	0.4619
+[c](:a)(:a)-O	0.5437
+[c](:a)(:a)-S	0.1893
+[c](:a)(:a)=C	-0.8186
+[c](:a)(:a)=N	-0.8186
+[c](:a)(:a)=O	-0.8186
+[C](=C)(a)A	0.264
+[C](=C)(c)a	0.264
+[CH](=C)a	0.264
+[C]=c	0.264
+[CX4][!#6;!#7;!#8;!#9;!#15;!#16;!#17;!#35;!#53;!#1] 0.2148
+[#7]	-0.4806
+[NH2+0]A	-1.019
+[NH+0](A)A	-0.7096
+[NH2+0]a	-1.027
+[NH+0](A)a	-0.5188
+[NH+0](a)a	-0.5188
+[NH+0]=A	0.0839
+[NH+0]=a	0.0839
+[N+0](=A)A	0.1836
+[N+0](=A)a	0.1836
+[N+0](=a)A	0.1836
+[N+0](=a)a	0.1836
+[N+0](A)(A)A	-0.3187
+[N+0](a)(A)A	-0.4458
+[N+0](a)(a)A	-0.4458
+[N+0](a)(a)a	-0.4458
+[N+0]#A	0.01508
+[NH3+*]	-1.95
+[NH2+*]	-1.95
+[NH+*]	-1.95
+[n+0]	-0.3239
+[n+*]	-1.119
+[NH0+*](A)(A)(A)A	-0.3396
+[NH0+*](=A)(A)A	-0.3396
+[NH0+*](=A)(A)a	-0.3396
+[NH0+*](=[#6])=[#7]	-0.3396
+[N+*]#A	0.2887
+[N-*]	0.2887
+[N+*](=[N-*])=N	0.2887
+[#8]	-0.1188
+[o]	0.1552
+[OH]	-0.2893
+[OH2]	-0.2893
+[O](C)C	-0.0684
+[OH0](C)[A!#6]	-0.0684
+[OH0]([A!#6])[A!#6]	-0.0684
+[O]([A;!#1])a	-0.4195
+[O](a)a	-0.4195
+[O]=[#8]	0.0335
+[O]=[#7]	0.0335
+[OX1-*][#7]	0.0335
+[OX1-*][#16]	-0.3339
+[OX1-*][#15;#33;#43;#53]	-1.189
+[O]=c	0.1788
+[O]=[CH]C	-0.1526
+[O]=C(C)C	-0.1526
+[O]=[CH0](C)[A;!6]	-0.1526
+[O]=[CH]N	-0.1526
+[O]=[CH]O	-0.1526
+[O]=[CH2]	-0.1526
+[O]=[CX2]=O	-0.1526
+[O]=[CH]c	0.1129
+[O]=C(C)c	0.1129
+[O]=C(c)c	0.1129
+[O]=[CH0](c)[a!#6]	0.1129
+[O]=[CH0](c)[A!#6]	0.1129
+[O]=[CH0](C)[a!#6]	0.1129
+[O]=C([A!#6])[A!#6]	0.4833
+[O]=C([A!#6])[a!#6]	0.4833
+[O]=C([a!#6])[a!#6]	0.4833
+[O-1]C(=O)	-1.326
+[#9-0]	0.4202
+[#17-0]	0.6895
+[#35-0]	0.8456
+[#53-0]	0.8857
+[#9-*]	-2.996
+[#17-*]	-2.996
+[#35-*]	-2.996
+[#53-*]	-2.996
+[#53+*]	-2.996
+[#15]	0.8612
+[S-0]	0.6482
+[S-*]	-0.0024
+[S+*]	-0.0024
+[s]	0.6237
+[B,Si,Ga,Ge,As,Se,Sn,Te,Pb,Nc,Nr,Kr,Xe,Rn]	-0.3808
+[Fe,Cu,Zn,Tc,Cd,Pt,Au,Hg]	-0.0025
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mm2.prm	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,2028 @@
+
+      ##############################
+      ##                          ##
+      ##  Force Field Definition  ##
+      ##                          ##
+      ##############################
+
+
+forcefield              MM2-1991
+
+bondunit                71.94
+bond-cubic              -2.0
+bond-quartic            1.25       !! keeps Ebond positive; not in "real" MM2
+angleunit               0.02191418
+angle-sextic            0.00000007
+strbndunit              2.51118
+mm2-strbnd
+opbendunit              0.02191418
+torsionunit             0.5
+vdwtype                 BUCKINGHAM
+radiusrule              ARITHMETIC
+radiustype              R-MIN
+radiussize              RADIUS
+epsilonrule             GEOMETRIC
+a-expterm               290000.0
+b-expterm               12.5
+c-expterm               2.25
+vdw-14-scale            1.0
+chg-14-scale            1.0
+dielectric              1.5
+
+
+      #############################
+      ##                         ##
+      ##  Literature References  ##
+      ##                         ##
+      #############################
+
+
+N. L. Allinger, "Conformational Analysis. 130. MM2. A Hydrocarbon
+Force Field Utilizing V1 and V2 Torsional Terms", J. Am. Chem. Soc.,
+99, 8127-8134 (1977)
+
+J. T. Sprague, J. C. Tai, Y. Yuh and N. L. Allinger, "The MMP2
+Calculational Method", J. Comput. Chem., 8, 581-603 (1987)
+
+N. L. Allinger, R. A. Kok and M. R. Imam, "Hydrogen Bonding in MM2",
+J. Comput. Chem., 9, 591-595 (1988)
+
+All parameters in this file are from the "MM2 (1991) Parameter Set",
+as provided by Prof. N. L. Allinger, University of Georgia
+
+
+      #############################
+      ##                         ##
+      ##  Atom Type Definitions  ##
+      ##                         ##
+      #############################
+
+
+atom      1    C     "CSP3 ALKANE"             6     12.000     4
+atom      2    C     "CSP2 ALKENE"             6     12.000     3
+atom      3    C     "CSP2 CARBONYL"           6     12.000     3
+atom      4    C     "CSP ALKYNE, C=C=O"       6     12.000     2
+atom      5    H     "NONPOLAR HYDROGEN"       1      1.008     1
+atom      6    O     "-O- ALCOHOL, ETHER"      8     15.995     4
+atom      7    O     "=O CARBONYL"             8     15.995     1
+atom      8    N     "NSP3"                    7     14.003     4
+atom      9    N     "NSP2 AMIDE"              7     14.003     3
+atom     10    N     "NSP"                     7     14.003     1
+atom     11    F     "FLUORIDE"                9     18.998     1
+atom     12    Cl    "CHLORIDE"               17     34.969     1
+atom     13    Br    "BROMIDE"                35     78.918     1
+atom     14    I     "IODIDE"                 53    126.900     1
+atom     15    S     "-S- SULFIDE"            16     31.972     2
+atom     16    S+    ">S+ SULFONIUM"          16     31.972     2
+atom     17    S     ">S=O SULFOXIDE"         16     31.972     3
+atom     18    S     ">SO2 SULFONE"           16     31.972     4
+atom     19    Si    "SILANE"                 14     27.977     4
+atom     20    Lp    "LONE PAIR"               0      0.000     1
+atom     21    H     "-OH ALCOHOL"             1      1.008     1
+atom     22    C     "CYCLOPROPANE"            6     12.000     4
+atom     23    H     "NH AMINE"                1      1.008     1
+atom     24    H     "COOH CARBOXYL"           1      1.008     1
+atom     25    P     ">P- PHOSPHINE"          15     30.994     3
+atom     26    B     ">B- TRIGONAL"            5     11.009     3
+atom     27    B     ">B< TETRAHEDRAL"         5     11.009     4
+atom     28    H     "-H AMIDE, ENOL"          1      1.008     1
+atom     29    C*    "CARBON RADICAL"          6     12.000     3
+atom     30    C+    "CARBONIUM ION"           6     12.000     3
+atom     31    Ge    "GERMANIUM"              32     73.922     2
+atom     32    Sn    "TIN"                    50    117.902     2
+atom     33    Pb    "LEAD (IV)"              82    207.977     4
+atom     34    Se    "SELENIUM"               34     79.917     2
+atom     35    Te    "TELLURIUM"              52    129.907     2
+atom     36    D     "DEUTERIUM"               1      2.014     1
+atom     37    N     "-N= AZO,PYRIDINE"        7     14.003     3
+atom     38    C     "CSP2 CYCLOPROPENE"       6     12.000     3
+atom     39    N+    "NSP3 AMMONIUM"           7     14.003     4
+atom     40    N     "NSP2 PYRROLE"            7     14.003     3
+atom     41    O     "OSP2 FURAN"              8     15.995     3
+atom     42    S     "SSP2 THIOPHENE"         16     31.972     2
+atom     43    N     "-N=N-O AZOXY"            7     14.003     2
+atom     44    H     "-SH THIOL"               1      1.008     1
+atom     45    N     "AZIDE (CENTER-N)"        7     14.003     2
+atom     46    N     "NO2 NITRO"               7     14.003     3
+atom     47    O     "CARBOXYLATE"             8     15.995     1
+atom     48    H     "AMMONIUM"                1      1.008     1
+atom     49    O     "EPOXY"                   8     15.995     4
+atom     50    C     "BENZENE"                 6     12.000     3
+atom     51    He    "HELIUM"                  2      4.003     0
+atom     52    Ne    "NEON"                   10     20.179     0
+atom     53    Ar    "ARGON"                  18     39.948     0
+atom     54    Kr    "KRYPTON"                36     83.800     0
+atom     55    Xe    "XENON"                  54    131.300     0
+atom     59    Mg    "MAGNESIUM"              12     24.301     0
+atom     60    P     "PHOSPHORUS (V)"         15     30.994     4
+atom     61    Fe    "IRON (II)"              26     55.847     0
+atom     62    Fe    "IRON (III)"             26     55.847     0
+atom     63    Ni    "NICKEL (II)"            27     58.710     0
+atom     64    Ni    "NICKEL (III)"           27     58.710     0
+atom     65    Co    "COBALT (II)"            28     58.933     0
+atom     66    Co    "COBALT (III)"           28     58.933     0
+atom     69    O     "AMINE OXIDE"             8     15.995     1
+atom     70    O     "KETONIUM OXYGEN"         8     15.995     1
+atom     71    C     "KETONIUM CARBON"         6     12.000     2
+atom     72    N     "=N- IMINE, OXIME"        7     14.003     3
+atom     73    N+    "=N(+)- PYRIDINIUM"       7     14.003     3
+atom     74    N+    "=N(+)- IMMINIUM"         7     14.003     3
+atom     75    N     "N-OH OXIME"              7     14.003     3
+
+
+      ################################
+      ##                            ##
+      ##  Van der Waals Parameters  ##
+      ##                            ##
+      ################################
+
+
+vdw           1               1.900      0.044
+vdw           2               1.940      0.044
+vdw           3               1.940      0.044
+vdw           4               1.940      0.044
+vdw           5               1.500      0.047      0.915
+vdw           6               1.740      0.050
+vdw           7               1.740      0.066
+vdw           8               1.820      0.055
+vdw           9               1.820      0.055
+vdw          10               1.820      0.055
+vdw          11               1.650      0.078
+vdw          12               2.030      0.240
+vdw          13               2.180      0.320
+vdw          14               2.320      0.424
+vdw          15               2.110      0.202
+vdw          16               2.110      0.202
+vdw          17               2.110      0.202
+vdw          18               2.110      0.202
+vdw          19               2.250      0.140
+vdw          20               1.200      0.016
+vdw          21               0.950      0.036
+vdw          22               1.900      0.044
+vdw          23               1.050      0.034
+vdw          24               0.900      0.015
+vdw          25               2.180      0.168
+vdw          26               1.980      0.034
+vdw          27               1.980      0.034
+vdw          28               0.900      0.015
+vdw          29               1.940      0.044
+vdw          30               1.940      0.044
+vdw          31               2.400      0.200
+vdw          32               2.550      0.270
+vdw          33               2.700      0.340
+vdw          34               2.250      0.276
+vdw          35               2.400      0.368
+vdw          36               1.497      0.047      0.915
+vdw          37               1.820      0.055
+vdw          38               1.940      0.044
+vdw          39               1.820      0.055
+vdw          40               1.820      0.055
+vdw          41               1.740      0.050
+vdw          42               2.110      0.202
+vdw          43               1.820      0.055
+vdw          44               0.000      0.000
+vdw          45               1.820      0.055
+vdw          46               1.820      0.055
+vdw          47               1.740      0.050
+vdw          48               0.900      0.015
+vdw          49               1.740      0.050
+vdw          50               1.940      0.044
+vdw          51               1.530      0.026
+vdw          52               1.600      0.090
+vdw          53               1.990      0.268
+vdw          54               2.150      0.358
+vdw          55               2.280      0.495
+vdw          59               2.200      0.015
+vdw          60               2.200      0.168
+vdw          61               2.200      0.020
+vdw          62               2.200      0.020
+vdw          63               2.200      0.020
+vdw          64               2.200      0.020
+vdw          65               2.200      0.020
+vdw          66               2.200      0.020
+vdw          69               1.820      0.059
+vdw          70               1.740      0.066
+vdw          71               1.940      0.056
+vdw          72               1.820      0.055
+vdw          73               1.820      0.055
+vdw          74               1.820      0.055
+vdw          75               1.820      0.055
+
+
+      #####################################
+      ##                                 ##
+      ##  Van der Waals Pair Parameters  ##
+      ##                                 ##
+      #####################################
+
+
+vdwpr         1    5          3.340      0.046
+vdwpr         1   36          3.337      0.046
+vdwpr         2   21          2.340      1.100
+vdwpr         2   23          2.340      0.400
+vdwpr         2   24          2.340      1.000
+vdwpr         2   28          2.340      1.000
+vdwpr         6   21          1.830      1.300
+vdwpr         6   23          1.830      0.600
+vdwpr         6   24          2.140      2.200
+vdwpr         6   28          2.140      2.400
+vdwpr         7   21          2.140      2.950
+vdwpr         7   23          2.140      0.400
+vdwpr         7   24          2.030      3.000
+vdwpr         7   28          2.030      3.000
+vdwpr         8   21          2.220      2.000
+vdwpr         8   23          2.220      0.400
+vdwpr         8   24          2.220      1.400
+vdwpr         8   28          2.220      1.000
+vdwpr        11   21          2.050      0.800
+vdwpr        11   23          2.050      0.200
+vdwpr        11   24          2.050      0.600
+vdwpr        11   28          2.050      0.400
+vdwpr        12   21          2.430      3.600
+vdwpr        12   23          2.430      0.200
+vdwpr        12   24          2.430      0.600
+vdwpr        12   28          2.430      0.400
+vdwpr        13   21          2.580      0.800
+vdwpr        13   23          2.580      0.200
+vdwpr        13   24          2.580      0.600
+vdwpr        13   28          2.580      0.400
+vdwpr        14   21          2.720      0.600
+vdwpr        14   23          2.720      0.400
+vdwpr        14   24          2.720      0.400
+vdwpr        14   28          2.720      0.200
+vdwpr        15   21          2.510      0.400
+vdwpr        15   23          2.510      0.200
+vdwpr        15   24          2.510      0.400
+vdwpr        15   28          2.510      0.200
+
+
+      ##################################
+      ##                              ##
+      ##  Bond Stretching Parameters  ##
+      ##                              ##
+      ##################################
+
+
+bond          1    1          4.400      1.523
+bond          1    2          4.400      1.497
+bond          1    3          4.400      1.509
+bond          1    4          5.200      1.470
+bond          1    5          4.600      1.113
+bond          1    6          5.360      1.402
+bond          1    8          5.100      1.438
+bond          1    9          3.520      1.437
+bond          1   11          5.100      1.392
+bond          1   12          3.230      1.795
+bond          1   13          2.300      1.949
+bond          1   14          2.200      2.149
+bond          1   15          3.213      1.815
+bond          1   16          3.213      1.816
+bond          1   17          3.213      1.805
+bond          1   18          3.213      1.784
+bond          1   19          2.970      1.880
+bond          1   22          4.400      1.502
+bond          1   25          2.910      1.856
+bond          1   29          4.400      1.497
+bond          1   31          2.700      1.950
+bond          1   32          2.124      2.147
+bond          1   33          1.900      2.242
+bond          1   34          2.680      1.948
+bond          1   35          2.700      2.140
+bond          1   36          4.600      1.108
+bond          1   37          3.950      1.470
+bond          1   38          4.400      1.497
+bond          1   39          5.100      1.499
+bond          1   41          5.360      1.414
+bond          1   43          3.950      1.488
+bond          1   46          7.000      1.498
+bond          1   50          4.400      1.497
+bond          1   70          3.000      1.480
+bond          1   71          4.400      1.509
+bond          1   72          3.950      1.470
+bond          2    2          9.600      1.337
+bond          2    3          9.600      1.351
+bond          2    4          9.900      1.313
+bond          2    5          4.600      1.101
+bond          2    6          6.000      1.355
+bond          2    8          6.320      1.377
+bond          2    9          5.000      1.410
+bond          2   11          5.400      1.320
+bond          2   12          3.400      1.719
+bond          2   13          2.500      1.881
+bond          2   14          2.480      2.075
+bond          2   19          3.500      1.865
+bond          2   22          4.400      1.467
+bond          2   25          2.910      1.828
+bond          2   37         11.090      1.260
+bond          2   38          9.600      1.336
+bond          2   40         11.090      1.266
+bond          2   41         10.000      1.225
+bond          2   42          6.471      1.459
+bond          2   46          5.050      1.463
+bond          2   72         11.090      1.260
+bond          3    3          9.600      1.415
+bond          3    5          4.600      1.113
+bond          3    6          5.050      1.338
+bond          3    7         10.800      1.208
+bond          3    9          6.400      1.385
+bond          3   22          4.400      1.447
+bond          3   36          4.600      1.130
+bond          3   72         11.090      1.280
+bond          4    4         15.600      1.212
+bond          4    5          5.900      1.090
+bond          4   10         17.730      1.158
+bond          5   15          3.800      1.345
+bond          5   16          3.800      1.346
+bond          5   17          3.800      1.346
+bond          5   18          3.800      1.346
+bond          5   19          2.720      1.489
+bond          5   22          4.600      1.086
+bond          5   25          3.330      1.437
+bond          5   29          4.600      1.101
+bond          5   31          2.570      1.530
+bond          5   32          2.229      1.696
+bond          5   33          1.894      1.775
+bond          5   34          3.170      1.472
+bond          5   35          2.850      1.670
+bond          5   38          4.600      1.072
+bond          5   71          4.600      1.113
+bond          6    6          3.950      1.428
+bond          6   19          5.500      1.626
+bond          6   20          4.600      0.600
+bond          6   21          4.600      0.942
+bond          6   24          7.200      0.972
+bond          6   25          2.900      1.615
+bond          6   28          7.200      0.972
+bond          7   17          5.000      1.480
+bond          7   18          8.412      1.450
+bond          7   43         10.800      1.268
+bond          7   46          7.500      1.220
+bond          8    8          5.600      1.381
+bond          8   20          6.100      0.600
+bond          8   23          6.100      1.020
+bond          9   18          6.100      1.660
+bond          9   28          5.900      1.022
+bond         15   15          3.100      2.024
+bond         19   19          1.850      2.332
+bond         19   22          3.500      1.860
+bond         20   37          6.100      0.600
+bond         20   41          4.600      0.600
+bond         20   72          6.100      0.600
+bond         22   22          4.400      1.474
+bond         22   38          4.400      1.488
+bond         22   46          4.350      1.477
+bond         23   37          5.240      1.022
+bond         23   40          6.100      1.050
+bond         23   72          5.240      1.022
+bond         28   41          7.200      0.972
+bond         33   33          0.980      2.891
+bond         37   37         10.720      1.248
+bond         37   40         11.000      1.230
+bond         37   43         10.720      1.257
+bond         38   38          9.600      1.303
+bond         39   48          6.100      1.045
+bond         50   50          8.065      1.392
+bond         70   71         10.000      1.236
+
+
+      ###########################################
+      ##                                       ##
+      ##  Bond Stretching Parameters (4-Ring)  ##
+      ##                                       ##
+      ###########################################
+
+
+bond4        22   22          4.400      1.528
+
+
+      ###########################################
+      ##                                       ##
+      ##  Bond Stretching Parameters (3-Ring)  ##
+      ##                                       ##
+      ###########################################
+
+
+bond3        22   22          4.400      1.503
+bond3        22   49          5.360      1.435
+
+
+      ################################
+      ##                            ##
+      ##  Angle Bending Parameters  ##
+      ##                            ##
+      ################################
+
+
+angle         1    1    1     0.450    109.470    109.510    109.500
+angle         1    1    2     0.450    109.470    109.510    109.500
+angle         1    1    3     0.450    107.800    109.900    110.000
+angle         1    1    4     0.450    109.470    112.400    109.000
+angle         1    1    5     0.360    109.390    109.410    110.000
+angle         1    1    6     0.700    107.500    107.700    107.400
+angle         1    1    8     0.570    109.470    108.800    109.500
+angle         1    1    9     0.500    109.280    110.780    109.280
+angle         1    1   11     0.650    109.500    107.500    109.500
+angle         1    1   12     0.560    108.200      0.000      0.000
+angle         1    1   13     0.630    108.200      0.000      0.000
+angle         1    1   14     0.490    108.900      0.000      0.000
+angle         1    1   15     0.550    109.000    107.000    106.500
+angle         1    1   16     0.420    107.800      0.000      0.000
+angle         1    1   17     0.420    106.000      0.000      0.000
+angle         1    1   18     0.420    102.000      0.000      0.000
+angle         1    1   19     0.400    109.000    110.900    112.700
+angle         1    1   22     0.450    112.400    112.400    112.400
+angle         1    1   25     0.480    111.500      0.000      0.000
+angle         1    1   29     0.450    110.000      0.000      0.000
+angle         1    1   31     0.640    110.500      0.000      0.000
+angle         1    1   32     0.560    110.200      0.000      0.000
+angle         1    1   33     0.300    110.200      0.000      0.000
+angle         1    1   34     0.500    108.200      0.000      0.000
+angle         1    1   35     0.450    108.200      0.000      0.000
+angle         1    1   36     0.360    109.390    109.410    110.000
+angle         1    1   37     0.380    110.740      0.000      0.000
+angle         1    1   39     0.570    103.500    102.700    103.900
+angle         1    1   41     0.700    107.500      0.000      0.000
+angle         1    1   43     0.380    104.640      0.000      0.000
+angle         1    1   46     0.600    106.000    106.800    106.800
+angle         1    1   50     0.450    109.470    109.510    109.500
+angle         1    1   70     0.700    104.000      0.000      0.000
+angle         1    1   71     0.450    107.800    109.900    110.000
+angle         2    1    2     0.450    109.470    109.510    109.500
+angle         2    1    3     0.470    109.470    110.510    110.200
+angle         2    1    4     0.470    109.470    110.510    110.200
+angle         2    1    5     0.360    109.390    109.410    110.000
+angle         2    1    6     0.700    109.500      0.000      0.000
+angle         2    1    8     1.045    110.740      0.000      0.000
+angle         2    1    9     0.500    109.800      0.000      0.000
+angle         2    1   11     0.650    109.000      0.000      0.000
+angle         2    1   12     0.560    109.500      0.000      0.000
+angle         2    1   15     0.420    107.800    107.800    109.500
+angle         2    1   16     0.420    107.800      0.000      0.000
+angle         2    1   19     0.500    109.500    110.500    113.000
+angle         2    1   22     0.450    112.400      0.000      0.000
+angle         2    1   36     0.360    109.390    109.410    110.000
+angle         2    1   37     0.380    110.510      0.000      0.000
+angle         2    1   39     1.045    110.740      0.000      0.000
+angle         2    1   43     0.380    110.510      0.000      0.000
+angle         3    1    3     0.470    109.470    110.510    110.200
+angle         3    1    5     0.370    107.900    108.800    109.470
+angle         3    1    6     0.700    109.500      0.000      0.000
+angle         3    1    8     1.045    110.740      0.000      0.000
+angle         3    1    9     0.820    109.800    111.100    109.800
+angle         3    1   11     0.650    109.200      0.000      0.000
+angle         3    1   12     0.560    109.800      0.000      0.000
+angle         3    1   13     0.630    109.100      0.000      0.000
+angle         3    1   14     0.490    108.900      0.000      0.000
+angle         3    1   15     0.420    107.800      0.000      0.000
+angle         3    1   16     0.420    107.800      0.000      0.000
+angle         3    1   36     0.370    108.800    108.800    109.470
+angle         4    1    4     0.470    109.470    110.510    110.200
+angle         4    1    5     0.360    109.390    109.410    110.000
+angle         5    1    5     0.320    109.400    109.000    109.470
+angle         5    1    6     0.540    106.700    106.700    106.700
+angle         5    1    8     0.500    108.800      0.000      0.000
+angle         5    1    9     0.420    109.000      0.000      0.000
+angle         5    1   11     0.490    110.500      0.000      0.000
+angle         5    1   12     0.530    106.900      0.000      0.000
+angle         5    1   13     0.440    106.500      0.000      0.000
+angle         5    1   14     0.540    106.400      0.000      0.000
+angle         5    1   15     0.360    112.000    112.000    109.300
+angle         5    1   16     0.300    108.200      0.000      0.000
+angle         5    1   17     0.384    108.600      0.000      0.000
+angle         5    1   18     0.384    108.600      0.000      0.000
+angle         5    1   19     0.320    108.600    110.800    107.000
+angle         5    1   22     0.360    109.410    109.410    109.410
+angle         5    1   25     0.360    111.000      0.000      0.000
+angle         5    1   29     0.360    110.000      0.000      0.000
+angle         5    1   31     0.449    110.400      0.000      0.000
+angle         5    1   32     0.350    112.000      0.000      0.000
+angle         5    1   33     0.100    109.500      0.000      0.000
+angle         5    1   34     0.330    110.500      0.000      0.000
+angle         5    1   35     0.300    110.500      0.000      0.000
+angle         5    1   36     0.320    109.400    109.000    109.470
+angle         5    1   37     0.480    107.500      0.000      0.000
+angle         5    1   39     0.500    108.800      0.000      0.000
+angle         5    1   41     0.540    106.700      0.000      0.000
+angle         5    1   43     0.480    107.500      0.000      0.000
+angle         5    1   46     0.480    109.000      0.000      0.000
+angle         5    1   50     0.360    109.390    109.410    110.000
+angle         5    1   70     0.350    102.800      0.000      0.000
+angle         5    1   71     0.370    107.900    108.800    109.500
+angle         5    1   72     0.480    107.500      0.000      0.000
+angle         6    1    6     0.460     99.900     97.000    102.200
+angle         6    1   12     0.560    108.500      0.000      0.000
+angle         6    1   71     0.700    103.000      0.000      0.000
+angle         8    1    8     1.045    110.740      0.000      0.000
+angle         8    1   39     1.045    110.740      0.000      0.000
+angle         9    1   15     0.580    107.000    108.000    114.800
+angle         9    1   36     0.420    109.000      0.000      0.000
+angle        11    1   11     1.070    107.100      0.000      0.000
+angle        11    1   12     1.075    110.400      0.000      0.000
+angle        11    1   13     1.024    109.400      0.000      0.000
+angle        12    1   12     1.080    111.700      0.000      0.000
+angle        12    1   13     1.030    110.700      0.000      0.000
+angle        13    1   13     0.980    109.700      0.000      0.000
+angle        15    1   15     0.420    116.200      0.000      0.000
+angle        19    1   19     0.400    115.500      0.000      0.000
+angle        22    1   22     0.450    112.000      0.000    105.000
+angle        22    1   37     0.380    110.200      0.000      0.000
+angle        22    1   43     0.380    110.200      0.000      0.000
+angle        36    1   36     0.320    109.400    109.000    109.470
+angle        36    1   50     0.360    109.390    109.410    110.000
+angle        50    1   50     0.450    109.470    109.510    109.500
+angle         1    2    1     0.450    117.200      0.000      0.000
+angle         1    2    2     0.550    121.400    122.000      0.000
+angle         1    2    3     0.380    121.000      0.000      0.000
+angle         1    2    4     0.470    122.000      0.000      0.000
+angle         1    2    5     0.360    118.200      0.000      0.000
+angle         1    2    6     0.500    120.000      0.000      0.000
+angle         1    2   19     0.400    120.000      0.000      0.000
+angle         1    2   37     0.550    115.100    125.300      0.000
+angle         2    2    2     0.430    120.000      0.000      0.000
+angle         2    2    3     0.600    114.600    117.600      0.000
+angle         2    2    5     0.360    120.000    120.500      0.000
+angle         2    2    6     0.700    124.300      0.000      0.000
+angle         2    2    8     0.616    123.000    124.000      0.000
+angle         2    2    9     0.500    118.000      0.000      0.000
+angle         2    2   11     0.650    121.000      0.000      0.000
+angle         2    2   12     0.550    118.800      0.000      0.000
+angle         2    2   13     0.450    118.100      0.000      0.000
+angle         2    2   14     0.410    118.800      0.000      0.000
+angle         2    2   19     0.400    122.500    120.500      0.000
+angle         2    2   22     0.550    121.000      0.000      0.000
+angle         2    2   25     0.380    120.000      0.000      0.000
+angle         2    2   37     0.430    120.000    123.500      0.000
+angle         2    2   40     0.430    120.000    119.000      0.000
+angle         2    2   41     0.600    120.000    118.100      0.000
+angle         2    2   42     0.380    119.000      0.000      0.000
+angle         2    2   46     0.600    113.500      0.000      0.000
+angle         2    2   72     0.430    120.000    123.500      0.000
+angle         3    2    5     0.240    120.000      0.000      0.000
+angle         4    2    5     0.360    121.100    121.600      0.000
+angle         5    2    5     0.320    119.000      0.000      0.000
+angle         5    2    6     0.540    116.400      0.000      0.000
+angle         5    2    8     0.540    119.000      0.000      0.000
+angle         5    2    9     0.300    109.000      0.000      0.000
+angle         5    2   11     0.450    120.000      0.000      0.000
+angle         5    2   12     0.450    112.600      0.000      0.000
+angle         5    2   13     0.460    112.100      0.000      0.000
+angle         5    2   14     0.450    112.600      0.000      0.000
+angle         5    2   19     0.240    118.400      0.000      0.000
+angle         5    2   22     0.360    118.200      0.000      0.000
+angle         5    2   37     0.360    116.500    120.500      0.000
+angle         5    2   38     0.360    120.000      0.000      0.000
+angle         5    2   40     0.400    113.500      0.000      0.000
+angle         5    2   41     0.450    108.000      0.000      0.000
+angle         5    2   42     0.400    120.000      0.000      0.000
+angle         5    2   46     0.260    119.000      0.000      0.000
+angle         5    2   72     0.360    116.500    120.500      0.000
+angle         9    2    9     0.400    120.000      0.000      0.000
+angle        12    2   41     0.500    105.000      0.000      0.000
+angle        13    2   41     0.500    104.000      0.000      0.000
+angle        14    2   41     0.500    107.000      0.000      0.000
+angle        19    2   19     0.400    120.000      0.000      0.000
+angle        37    2   37     0.400    120.000    127.000      0.000
+angle        37    2   40     0.400    126.000    126.000      0.000
+angle         1    3    1     0.400    116.600      0.000      0.000
+angle         1    3    2     0.400    115.000      0.000      0.000
+angle         1    3    3     0.600    114.000      0.000      0.000
+angle         1    3    5     0.370    116.400      0.000      0.000
+angle         1    3    6     0.650    107.100      0.000      0.000
+angle         1    3    7     0.460    122.500      0.000      0.000
+angle         1    3    9     0.660    116.500      0.000      0.000
+angle         1    3   72     0.550    116.800      0.000      0.000
+angle         2    3    2     0.600    112.000      0.000      0.000
+angle         2    3    3     0.480    120.000      0.000      0.000
+angle         2    3    5     0.400    113.500      0.000      0.000
+angle         2    3    6     0.700    124.300      0.000      0.000
+angle         2    3    7     0.460    123.000      0.000      0.000
+angle         2    3    9    99.000    120.000      0.000      0.000
+angle         2    3   72     0.690    120.400      0.000      0.000
+angle         3    3    5     0.400    112.000      0.000      0.000
+angle         3    3    7     0.430    119.000      0.000      0.000
+angle         3    3   36     0.400    112.500      0.000      0.000
+angle         5    3    5     0.360    118.200      0.000      0.000
+angle         5    3    6     0.650    105.900      0.000      0.000
+angle         5    3    7     0.370    120.300      0.000      0.000
+angle         5    3    9     0.300    109.000      0.000      0.000
+angle         5    3   72     0.660    119.500      0.000      0.000
+angle         6    3    7     0.800    122.000      0.000      0.000
+angle         7    3    9     0.670    124.300      0.000      0.000
+angle         7    3   22     0.460    122.500      0.000      0.000
+angle         7    3   36     0.370    120.000      0.000      0.000
+angle         9    3    9     0.500    120.000      0.000      0.000
+angle         1    4    4     0.200    180.000      0.000      0.000
+angle         1    4   10     0.325    180.000      0.000      0.000
+angle         2    4    2     0.400    180.000      0.000      0.000
+angle         2    4    4     0.470    180.000      0.000      0.000
+angle         4    4    5     0.360    180.000      0.000      0.000
+angle         1    6    1     0.770    106.800      0.000      0.000
+angle         1    6    2     0.770    110.800      0.000      0.000
+angle         1    6    3     0.600    109.900      0.000      0.000
+angle         1    6    6     0.635     98.700      0.000      0.000
+angle         1    6   19     0.400    114.600      0.000      0.000
+angle         1    6   20     0.350    105.160      0.000      0.000
+angle         1    6   21     0.350    106.900      0.000      0.000
+angle         1    6   25     0.770    116.000      0.000      0.000
+angle         2    6   20     0.350    103.260      0.000      0.000
+angle         2    6   25     0.800    118.000      0.000      0.000
+angle         2    6   28     0.350    108.000      0.000      0.000
+angle         3    6   20     0.350    105.160      0.000      0.000
+angle         3    6   24     0.300    106.100      0.000      0.000
+angle         6    6   20     0.350    103.260      0.000      0.000
+angle         6    6   21     0.511     98.440      0.000      0.000
+angle        19    6   19     0.150    145.700      0.000      0.000
+angle        19    6   20     0.350     97.500      0.000      0.000
+angle        20    6   20     0.240    131.000      0.000      0.000
+angle        20    6   21     0.240    101.010      0.000      0.000
+angle        20    6   24     0.240    101.000      0.000      0.000
+angle        20    6   25     0.350    105.000      0.000      0.000
+angle        20    6   28     0.240    101.100      0.000      0.000
+angle        21    6   21     0.400    104.500      0.000      0.000
+angle        21    6   21     0.630    105.000      0.000      0.000
+angle         1    8    1     0.630    107.700      0.000      0.000
+angle         1    8    2     0.698    107.000      0.000      0.000
+angle         1    8    8     0.740    105.500      0.000      0.000
+angle         1    8   20     0.500    109.200      0.000      0.000
+angle         1    8   23     0.500    109.470      0.000      0.000
+angle         2    8   20     0.350     87.000      0.000      0.000
+angle         2    8   23     0.527    109.500      0.000      0.000
+angle         8    8   20     0.350    109.000      0.000      0.000
+angle         8    8   23     0.430    103.200      0.000      0.000
+angle        20    8   20     0.587    106.820      0.000      0.000
+angle        20    8   23     0.500    108.000      0.000      0.000
+angle        23    8   23     0.500    104.500      0.000      0.000
+angle         1    9    1     0.760    126.000      0.000      0.000
+angle         1    9    2     0.630    119.900      0.000      0.000
+angle         1    9    3     0.760    119.900      0.000      0.000
+angle         1    9   18     0.300    110.000      0.000      0.000
+angle         1    9   28     0.440    124.000      0.000      0.000
+angle         2    9    2     0.400    107.000      0.000      0.000
+angle         2    9    3     0.600    115.000      0.000      0.000
+angle         2    9   28     0.500    110.000      0.000      0.000
+angle         3    9    3     0.500    125.000      0.000      0.000
+angle         3    9   28     0.420    119.000      0.000      0.000
+angle        18    9   28     0.300    122.000      0.000      0.000
+angle        28    9   28     0.320    123.000      0.000      0.000
+angle         1   15    1     0.720     96.300      0.000      0.000
+angle         1   15    5     0.480     96.000      0.000      0.000
+angle         1   15   15     1.168    102.900      0.000      0.000
+angle         5   15   15     0.400     91.200      0.000      0.000
+angle         1   16    1     0.500     94.300      0.000      0.000
+angle         1   16    5     0.400     94.000      0.000      0.000
+angle         1   17    1     0.720     93.000      0.000      0.000
+angle         1   17    7     0.597    106.000      0.000      0.000
+angle         1   18    1     0.720    102.000      0.000      0.000
+angle         1   18    7     0.597    107.700      0.000      0.000
+angle         1   18    9     0.800    103.000      0.000      0.000
+angle         5   18    7     0.560    101.500      0.000      0.000
+angle         5   18    9     0.600     98.000      0.000      0.000
+angle         7   18    7     0.900    116.600      0.000      0.000
+angle         7   18    9     1.700    108.000      0.000      0.000
+angle         1   19    1     0.480    110.800    110.400    108.500
+angle         1   19    2     0.400    110.200      0.000      0.000
+angle         1   19    5     0.460    109.300    107.000    110.200
+angle         1   19    6     0.350    108.500      0.000      0.000
+angle         1   19   19     0.750    110.000      0.000      0.000
+angle         2   19    2     0.600    109.500      0.000      0.000
+angle         2   19    5     0.240    109.500      0.000      0.000
+angle         2   19   19     0.400    110.200      0.000      0.000
+angle         5   19    5     0.380    104.500    108.700    109.500
+angle         5   19    6     0.350    109.500      0.000      0.000
+angle         5   19   19     0.378    111.000    111.000    111.000
+angle         5   19   22     0.460    110.200      0.000      0.000
+angle         6   19    6     0.450    113.500      0.000      0.000
+angle        19   19   19     0.350    111.300    110.800    110.000
+angle         1   22    1     0.450    120.000      0.000      0.000
+angle         1   22    5     0.360    123.500      0.000      0.000
+angle         1   22   22     0.600    118.200    118.200      0.000
+angle         1   22   49     0.560    115.000      0.000      0.000
+angle         2   22    2     0.450    120.000      0.000      0.000
+angle         2   22    5     0.360    123.500      0.000      0.000
+angle         2   22   22     0.600    118.200      0.000      0.000
+angle         2   22   49     0.560    115.000      0.000      0.000
+angle         3   22    5     0.360    123.500    123.500    123.500
+angle         5   22    5     0.320    120.600      0.000      0.000
+angle         5   22   19     0.240    123.500      0.000      0.000
+angle         5   22   22     0.360    124.500    119.700      0.000
+angle         5   22   38     0.360    124.500    119.700      0.000
+angle         5   22   46     0.050    114.000      0.000      0.000
+angle         5   22   49     0.430    113.000      0.000      0.000
+angle        19   22   22     0.530    117.500      0.000      0.000
+angle        22   22   22     0.350    119.140    120.700      0.000
+angle        22   22   46     0.700    117.000    117.000    117.000
+angle         1   25    1     0.576     96.000      0.000      0.000
+angle         1   25    2     0.480     92.500      0.000      0.000
+angle         1   25    5     0.480     95.000      0.000      0.000
+angle         2   25    2     0.480     93.200      0.000      0.000
+angle         5   25    5     0.438     93.400      0.000      0.000
+angle         6   25    6     0.450     99.500      0.000      0.000
+angle         1   29    1     0.450    120.000      0.000      0.000
+angle         1   29    5     0.360    120.000      0.000      0.000
+angle         5   29    5     0.320    120.000      0.000      0.000
+angle         1   31    1     0.490    110.000      0.000      0.000
+angle         1   31    5     0.352    109.500      0.000      0.000
+angle         5   31    5     0.216    109.000      0.000      0.000
+angle         1   32    1     0.320    107.000      0.000      0.000
+angle         1   32    5     0.227    110.500      0.000      0.000
+angle         5   32    5     0.132    109.500      0.000      0.000
+angle         1   33    1     0.100    109.500      0.000      0.000
+angle         1   33    5     0.100    109.500      0.000      0.000
+angle         1   33   33     0.100    109.500      0.000      0.000
+angle         5   33    5     0.100    109.500      0.000      0.000
+angle         1   34    1     0.500     94.800      0.000      0.000
+angle         1   34    5     0.430     94.500      0.000      0.000
+angle         1   35    1     0.590     95.050      0.000      0.000
+angle         1   35    5     0.390     94.600      0.000      0.000
+angle         1   37    2     0.550    108.000      0.000      0.000
+angle         1   37   20     0.350    120.000      0.000      0.000
+angle         1   37   37     0.690    106.500      0.000      0.000
+angle         1   37   43     0.570     99.100      0.000      0.000
+angle         2   37    2     0.430    115.000      0.000      0.000
+angle         2   37   20     0.500    122.500      0.000      0.000
+angle         2   37   23     0.500    110.000      0.000      0.000
+angle         2   37   37     0.400    107.500      0.000      0.000
+angle         2   37   40     0.430    115.000      0.000      0.000
+angle        20   37   23     0.500    127.500      0.000      0.000
+angle        20   37   37     0.350    120.000      0.000      0.000
+angle        20   37   40     0.500    122.500      0.000      0.000
+angle        20   37   43     0.350    120.000      0.000      0.000
+angle        23   37   37     0.400    103.500      0.000      0.000
+angle         1   38   22     0.450    117.200      0.000      0.000
+angle         2   38   22     0.550    137.000      0.000      0.000
+angle         5   38   22     0.360    146.000      0.000      0.000
+angle         5   38   38     0.360    146.000      0.000      0.000
+angle         1   39    1     0.630    108.600    111.200    115.400
+angle         1   39   48     0.500    109.470      0.000      0.000
+angle        48   39   48     0.500    104.500      0.000      0.000
+angle         2   40    2     0.430    124.000    124.000      0.000
+angle         2   40   23     0.360    118.000      0.000      0.000
+angle         2   40   37     0.430    124.000    124.000      0.000
+angle        23   40   37     0.360    113.000      0.000      0.000
+angle         1   41    2     0.770    113.600      0.000      0.000
+angle         1   41   20     0.350    124.200      0.000      0.000
+angle         2   41    2     0.870    113.950      0.000      0.000
+angle         2   41   20     0.350    122.200      0.000      0.000
+angle         2   41   28     0.360    109.000      0.000      0.000
+angle        20   41   28     0.360    128.800      0.000      0.000
+angle         2   42    2     0.680     98.500      0.000      0.000
+angle         1   43    7     0.570    120.400      0.000      0.000
+angle         1   43   37     0.380    114.000      0.000      0.000
+angle         7   43   37     0.380    125.000      0.000      0.000
+angle         1   46    7     0.594    115.830      0.000      0.000
+angle         2   46    7     0.800    115.000      0.000      0.000
+angle         7   46    7     0.600    128.600      0.000      0.000
+angle         7   46   22     0.594    111.000      0.000      0.000
+angle        20   49   20     0.240    131.000      0.000      0.000
+angle        20   49   22     0.350    103.000      0.000      0.000
+angle         1   50    1     0.450    117.200      0.000      0.000
+angle         1   50    5     0.360    118.200      0.000      0.000
+angle         1   50   50     0.550    121.400    122.000    120.000
+angle         5   50    5     0.320    119.000      0.000      0.000
+angle         5   50   50     0.360    120.000    120.500      0.000
+angle        50   50   50     0.430    120.000      0.000      0.000
+angle         1   70   71     0.800    116.000      0.000      0.000
+angle         1   71    1     0.400    116.600      0.000      0.000
+angle         1   71    5     0.370    116.400      0.000      0.000
+angle         1   71   70     0.520    113.000    116.500      0.000
+angle         5   71    5     0.440    122.400      0.000      0.000
+angle         5   71   70     0.360    111.000    117.000      0.000
+angle         1   72    3     0.550    111.000      0.000      0.000
+angle         1   72   20     0.350    120.000      0.000      0.000
+angle         2   72    3     0.570    115.000      0.000      0.000
+angle         2   72   20     0.500    122.500      0.000      0.000
+angle         3   72   20     0.550    112.500      0.000      0.000
+angle         3   72   23     0.550    110.000      0.000      0.000
+angle        20   72   23     0.500    127.500      0.000      0.000
+
+
+      #########################################
+      ##                                     ##
+      ##  Angle Bending Parameters (4-Ring)  ##
+      ##                                     ##
+      #########################################
+
+
+angle4        1    1    1     0.340    109.470      0.000    109.500
+angle4        1    1    1     0.290      0.000    109.510      0.000
+angle4        1    1    2     0.360    109.470    109.510    109.500
+angle4        1    1    3     0.340    107.800    109.900    111.000
+angle4        1    1    6     0.530    107.400      0.000      0.000
+angle4        1    1    8     0.320    108.800      0.000      0.000
+angle4        1    1    9     0.550    106.500      0.000      0.000
+angle4        1    1   15     0.500    106.500    106.500    105.800
+angle4        1    1   19     0.300     94.500      0.000     94.500
+angle4        1    1   22     0.340      0.000    112.300    112.300
+angle4        1    1   31     0.640     92.000      0.000      0.000
+angle4        1    1   37     0.350    110.740      0.000      0.000
+angle4        1    1   39     0.450    108.800      0.000      0.000
+angle4        1    1   43     0.350    110.740      0.000      0.000
+angle4        2    1    2     0.340    109.470    109.510    109.500
+angle4        1    2    1     0.220    117.200      0.000      0.000
+angle4        1    2    2     0.340    121.400    122.000    120.000
+angle4        2    2    2     0.340    120.000      0.000      0.000
+angle4        1    3    1     0.300    116.600      0.000      0.000
+angle4        1    3    6     0.480    106.500      0.000      0.000
+angle4        1    3    9     0.660    113.000      0.000      0.000
+angle4        1    3   11     0.490     88.000      0.000      0.000
+angle4       22    3   22     0.300    116.600      0.000      0.000
+angle4        1    6    1     0.580    106.800      0.000      0.000
+angle4        1    6    3     0.450    109.900      0.000      0.000
+angle4        1    8    1     0.470    107.700      0.000      0.000
+angle4        1    9    3     0.600    119.800      0.000      0.000
+angle4        1   15    1     0.650     96.500      0.000      0.000
+angle4        1   19    1     0.450     90.500      0.000     90.500
+angle4        1   22   22     0.340      0.000    119.300      0.000
+angle4        3   22   22     0.340    119.300    119.300    119.300
+angle4       22   22   22     0.450    112.500     98.000      0.000
+angle4        1   31    1     0.490     88.000      0.000      0.000
+angle4        1   37   37     0.620    106.500      0.000      0.000
+angle4        1   37   43     0.480     99.100      0.000      0.000
+angle4        1   39    1     0.380    107.700      0.000      0.000
+angle4        1   43   37     0.350    114.000      0.000      0.000
+
+
+      #########################################
+      ##                                     ##
+      ##  Angle Bending Parameters (3-Ring)  ##
+      ##                                     ##
+      #########################################
+
+
+angle3       22   22   22     0.450     55.800     60.000     60.000
+angle3       22   22   38     0.450     48.000      0.000      0.000
+angle3       22   22   49     0.560     59.300      0.000      0.000
+angle3       38   22   38     0.450     53.000      0.000      0.000
+angle3       22   38   22     0.400     67.000      0.000      0.000
+angle3       22   38   38     0.550     80.000      0.000      0.000
+angle3       22   49   22     0.620     61.400      0.000      0.000
+
+
+      ###############################
+      ##                           ##
+      ##  Stretch-Bend Parameters  ##
+      ##                           ##
+      ###############################
+
+
+strbnd        1       0.120     0.090     0.000
+strbnd        2       0.120     0.090     0.000
+strbnd        3       0.120     0.090     0.000
+strbnd        4       0.120     0.090     0.000
+strbnd        6       0.120     0.090     0.000
+strbnd        8       0.120     0.090     0.000
+strbnd        9       0.120     0.090     0.000
+strbnd       15       0.250    -0.400     0.000
+strbnd       16       0.250    -0.400     0.000
+strbnd       17       0.250    -0.400     0.000
+strbnd       18       0.250    -0.400     0.000
+strbnd       19       0.200     0.060     0.000
+strbnd       22       0.120     0.090     0.000
+strbnd       25       0.200     0.060     0.000
+strbnd       26       0.120     0.090     0.000
+strbnd       27       0.120     0.090     0.000
+strbnd       29       0.120     0.090     0.000
+strbnd       30       0.120     0.090     0.000
+strbnd       34       0.450     0.000     0.000
+strbnd       37       0.120     0.090     0.000
+strbnd       38       0.120     0.090     0.000
+strbnd       39       0.120     0.090     0.000
+strbnd       40       0.120     0.090     0.000
+strbnd       41       0.120     0.090     0.000
+strbnd       42       0.250    -0.400     0.000
+strbnd       43       0.120     0.090     0.000
+strbnd       45       0.120     0.090     0.000
+strbnd       46       0.120     0.090     0.000
+strbnd       49       0.120     0.090     0.000
+strbnd       50       0.120     0.090     0.000
+strbnd       60       0.200     0.060     0.000
+strbnd       71       0.120     0.090     0.000
+strbnd       72       0.120     0.090     0.000
+
+
+      ####################################
+      ##                                ##
+      ##  Out-of-Plane Bend Parameters  ##
+      ##                                ##
+      ####################################
+
+
+opbend        2    1          0.050
+opbend        2    2          0.050
+opbend        2    3          0.050
+opbend        2    4          0.050
+opbend        2    5          0.050
+opbend        2    6          0.050
+opbend        2    7          0.050
+opbend        2    8          0.050
+opbend        2    9          0.050
+opbend        2   11          0.050
+opbend        2   12          0.050
+opbend        2   13          0.050
+opbend        2   14          0.050
+opbend        2   19          0.050
+opbend        2   22          0.050
+opbend        2   25          0.500
+opbend        2   37          0.050
+opbend        2   38          0.050
+opbend        2   40          0.050
+opbend        2   41          0.050
+opbend        2   42          0.050
+opbend        2   46          0.200
+opbend        2   72          0.050
+opbend        3    1          0.800
+opbend        3    2          0.800
+opbend        3    3          0.900
+opbend        3    4          0.800
+opbend        3    5          0.800
+opbend        3    6          0.800
+opbend        3    7          0.800
+opbend        3    8          0.800
+opbend        3    9          0.800
+opbend        3   22          0.800
+opbend        3   36          0.800
+opbend        3   72          0.050
+opbend        9    1          0.050
+opbend        9    2          0.050
+opbend        9    3          0.050
+opbend        9    4          0.050
+opbend        9    6          0.050
+opbend        9    7          0.050
+opbend        9    8          0.050
+opbend        9    9          0.050
+opbend        9   18          0.050
+opbend        9   28          0.010
+opbend       29    1          0.150
+opbend       29    5          0.150
+opbend       30    1          0.050
+opbend       30    5          0.050
+opbend       37    1          0.050
+opbend       37    1          0.050
+opbend       37    2          0.050
+opbend       37   20          0.050
+opbend       37   20          0.050
+opbend       37   23          0.050
+opbend       37   23          0.050
+opbend       37   37          0.050
+opbend       37   37          0.050
+opbend       37   40          0.050
+opbend       37   43          0.050
+opbend       38    2          0.050
+opbend       38    5          0.050
+opbend       38   22          0.050
+opbend       38   38          0.050
+opbend       40    2          0.050
+opbend       40   23          0.050
+opbend       40   37          0.050
+opbend       41    1          0.050
+opbend       41    2          0.050
+opbend       41   20          0.050
+opbend       41   28          0.050
+opbend       43    1          0.050
+opbend       43    7          0.050
+opbend       43   37          0.050
+opbend       46    1          0.200
+opbend       46    2          0.200
+opbend       46    7          0.200
+opbend       46   22          0.200
+opbend       50    1          0.050
+opbend       50    5          0.050
+opbend       50   50          0.050
+opbend       71    1          0.800
+opbend       71    5          0.800
+opbend       71   70          1.569
+opbend       72    1          0.050
+opbend       72    2          0.050
+opbend       72    3          0.050
+opbend       72   20          0.050
+opbend       72   23          0.050
+
+
+      ############################
+      ##                        ##
+      ##  Torsional Parameters  ##
+      ##                        ##
+      ############################
+
+
+torsion      1    1    1    1      0.200 0.0 1    0.270 180.0 2    0.093 0.0 3
+torsion      1    1    1    2      0.170 0.0 1    0.270 180.0 2    0.093 0.0 3
+torsion      1    1    1    3      0.050 0.0 1    0.370 180.0 2    0.000 0.0 3
+torsion      1    1    1    4      0.200 0.0 1   -0.260 180.0 2    0.093 0.0 3
+torsion      1    1    1    5      0.000 0.0 1    0.000 180.0 2    0.267 0.0 3
+torsion      1    1    1    6      0.100 0.0 1    0.100 180.0 2    0.180 0.0 3
+torsion      1    1    1    8      0.100 0.0 1    0.400 180.0 2    0.500 0.0 3
+torsion      1    1    1    9      0.000 0.0 1    0.000 180.0 2    0.400 0.0 3
+torsion      1    1    1   11      0.000 0.0 1   -0.086 180.0 2    0.930 0.0 3
+torsion      1    1    1   12      0.000 0.0 1   -0.250 180.0 2    0.550 0.0 3
+torsion      1    1    1   13      0.000 0.0 1   -0.410 180.0 2    1.060 0.0 3
+torsion      1    1    1   14      0.000 0.0 1   -0.500 180.0 2    0.267 0.0 3
+torsion      1    1    1   15      0.140 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      1    1    1   16      0.000 0.0 1    0.000 180.0 2    0.483 0.0 3
+torsion      1    1    1   17      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      1    1    1   18      0.200 0.0 1    0.270 180.0 2    0.093 0.0 3
+torsion      1    1    1   19      0.000 0.0 1    0.000 180.0 2    0.500 0.0 3
+torsion      1    1    1   22      0.200 0.0 1   -0.200 180.0 2    0.600 0.0 3
+torsion      1    1    1   25      0.000 0.0 1    0.000 180.0 2    0.400 0.0 3
+torsion      1    1    1   29      0.170 0.0 1    0.270 180.0 2    0.093 0.0 3
+torsion      1    1    1   31      0.000 0.0 1    0.000 180.0 2   -0.065 0.0 3
+torsion      1    1    1   32     -0.083 0.0 1   -0.083 180.0 2    0.050 0.0 3
+torsion      1    1    1   33      0.000 0.0 1   -0.008 180.0 2    0.110 0.0 3
+torsion      1    1    1   34      0.140 0.0 1    0.000 180.0 2    0.100 0.0 3
+torsion      1    1    1   35      0.000 0.0 1    0.200 180.0 2    0.400 0.0 3
+torsion      1    1    1   36      0.000 0.0 1    0.000 180.0 2    0.267 0.0 3
+torsion      1    1    1   37      0.000 0.0 1    0.000 180.0 2    0.100 0.0 3
+torsion      1    1    1   39      0.100 0.0 1    0.400 180.0 2    0.500 0.0 3
+torsion      1    1    1   43      0.000 0.0 1    0.000 180.0 2    0.100 0.0 3
+torsion      1    1    1   46      0.000 0.0 1    0.000 180.0 2    0.800 0.0 3
+torsion      1    1    1   50      0.170 0.0 1    0.270 180.0 2    0.093 0.0 3
+torsion      1    1    1   70      0.129 0.0 1   -0.650 180.0 2    0.817 0.0 3
+torsion      1    1    1   71      0.050 0.0 1    0.370 180.0 2    0.000 0.0 3
+torsion      2    1    1    2      2.100 0.0 1    0.270 180.0 2    0.093 0.0 3
+torsion      2    1    1    3      0.000 0.0 1    0.000 180.0 2    0.180 0.0 3
+torsion      2    1    1    4      0.000 0.0 1    0.000 180.0 2    0.093 0.0 3
+torsion      2    1    1    5      0.000 0.0 1    0.000 180.0 2    0.500 0.0 3
+torsion      2    1    1    6      0.000 0.0 1    0.000 180.0 2    0.180 0.0 3
+torsion      2    1    1    8      0.000 0.0 1    0.000 180.0 2    0.180 0.0 3
+torsion      2    1    1    9      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      2    1    1   15      0.000 0.0 1    0.000 180.0 2    0.483 0.0 3
+torsion      2    1    1   16      0.000 0.0 1    0.000 180.0 2    0.483 0.0 3
+torsion      2    1    1   19      0.000 0.0 1    0.000 180.0 2    0.167 0.0 3
+torsion      2    1    1   36      0.000 0.0 1    0.000 180.0 2    0.500 0.0 3
+torsion      2    1    1   39      0.000 0.0 1    0.000 180.0 2    0.180 0.0 3
+torsion      3    1    1    3      0.000 0.0 1    0.000 180.0 2    0.180 0.0 3
+torsion      3    1    1    5      0.000 0.0 1    0.000 180.0 2    0.180 0.0 3
+torsion      3    1    1    6      0.000 0.0 1    0.000 180.0 2    0.180 0.0 3
+torsion      3    1    1    8      0.000 0.0 1    0.400 180.0 2    0.500 0.0 3
+torsion      3    1    1    9      0.000 0.0 1    0.000 180.0 2    0.180 0.0 3
+torsion      3    1    1   11     -1.000 0.0 1    0.000 180.0 2    0.200 0.0 3
+torsion      3    1    1   12     -0.585 0.0 1    0.000 180.0 2    0.200 0.0 3
+torsion      3    1    1   13     -0.465 0.0 1    0.000 180.0 2    0.200 0.0 3
+torsion      3    1    1   15      0.000 0.0 1    0.000 180.0 2    0.483 0.0 3
+torsion      3    1    1   16      0.000 0.0 1    0.000 180.0 2    0.483 0.0 3
+torsion      3    1    1   25      0.000 0.0 1    0.000 180.0 2    0.400 0.0 3
+torsion      3    1    1   36      0.000 0.0 1    0.000 180.0 2    0.180 0.0 3
+torsion      3    1    1   39      0.000 0.0 1    0.400 180.0 2    0.500 0.0 3
+torsion      4    1    1    4      1.000 0.0 1    0.000 180.0 2    0.093 0.0 3
+torsion      4    1    1    5      0.000 0.0 1    0.000 180.0 2    0.400 0.0 3
+torsion      4    1    1    6      0.000 0.0 1   -0.400 180.0 2    0.180 0.0 3
+torsion      5    1    1    5      0.000 0.0 1    0.000 180.0 2    0.237 0.0 3
+torsion      5    1    1    6      0.000 0.0 1    0.000 180.0 2    0.180 0.0 3
+torsion      5    1    1    8     -0.150 0.0 1    0.000 180.0 2    0.150 0.0 3
+torsion      5    1    1    9      0.000 0.0 1    0.000 180.0 2    0.400 0.0 3
+torsion      5    1    1   11      0.000 0.0 1    0.000 180.0 2    0.351 0.0 3
+torsion      5    1    1   12      0.000 0.0 1    0.000 180.0 2    0.406 0.0 3
+torsion      5    1    1   13      0.000 0.0 1    0.000 180.0 2    0.385 0.0 3
+torsion      5    1    1   14      0.000 0.0 1    0.000 180.0 2    0.267 0.0 3
+torsion      5    1    1   15      0.000 0.0 1    0.000 180.0 2    0.330 0.0 3
+torsion      5    1    1   16      0.000 0.0 1    0.000 180.0 2    0.483 0.0 3
+torsion      5    1    1   17      0.000 0.0 1    0.000 180.0 2    0.125 0.0 3
+torsion      5    1    1   18      0.000 0.0 1    0.000 180.0 2    0.125 0.0 3
+torsion      5    1    1   19      0.000 0.0 1    0.000 180.0 2    0.105 0.0 3
+torsion      5    1    1   22      0.000 0.0 1    0.000 180.0 2    0.167 0.0 3
+torsion      5    1    1   25      0.000 0.0 1    0.000 180.0 2    0.330 0.0 3
+torsion      5    1    1   29      0.000 0.0 1    0.000 180.0 2    0.100 0.0 3
+torsion      5    1    1   31      0.000 0.0 1    0.000 180.0 2   -0.065 0.0 3
+torsion      5    1    1   32      0.000 0.0 1    0.000 180.0 2   -0.155 0.0 3
+torsion      5    1    1   33      0.000 0.0 1    0.000 180.0 2    0.040 0.0 3
+torsion      5    1    1   34      0.000 0.0 1    0.000 180.0 2    0.280 0.0 3
+torsion      5    1    1   35      0.000 0.0 1    0.000 180.0 2    0.540 0.0 3
+torsion      5    1    1   36      0.000 0.0 1    0.000 180.0 2    0.237 0.0 3
+torsion      5    1    1   37      0.000 0.0 1    0.000 180.0 2    0.500 0.0 3
+torsion      5    1    1   39     -0.150 0.0 1    0.000 180.0 2    0.150 0.0 3
+torsion      5    1    1   41      0.000 0.0 1    0.000 180.0 2    0.180 0.0 3
+torsion      5    1    1   43      0.000 0.0 1    0.000 180.0 2    0.500 0.0 3
+torsion      5    1    1   46      0.000 0.0 1    0.000 180.0 2    0.300 0.0 3
+torsion      5    1    1   50      0.000 0.0 1    0.000 180.0 2    0.500 0.0 3
+torsion      5    1    1   70      0.004 0.0 1    0.000 180.0 2    0.427 0.0 3
+torsion      5    1    1   71      0.000 0.0 1    0.000 180.0 2    0.180 0.0 3
+torsion      6    1    1    6      0.000 0.0 1   -0.600 180.0 2    0.300 0.0 3
+torsion      6    1    1    8      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      6    1    1    9      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      6    1    1   11      0.000 0.0 1   -1.400 180.0 2    0.180 0.0 3
+torsion      6    1    1   12      0.000 0.0 1   -1.400 180.0 2    0.180 0.0 3
+torsion      6    1    1   13      0.000 0.0 1   -1.400 180.0 2    0.180 0.0 3
+torsion      6    1    1   14      0.000 0.0 1   -1.400 180.0 2    0.180 0.0 3
+torsion      6    1    1   15     -0.800 0.0 1    0.900 180.0 2   -0.300 0.0 3
+torsion      6    1    1   17     -0.800 0.0 1    0.900 180.0 2   -0.300 0.0 3
+torsion      6    1    1   18     -0.800 0.0 1    0.000 180.0 2   -0.300 0.0 3
+torsion      6    1    1   39      0.000 0.0 1   -0.600 180.0 2    0.300 0.0 3
+torsion      6    1    1   70     -5.500 0.0 1   -2.500 180.0 2    2.000 0.0 3
+torsion      6    1    1   71     -7.225 0.0 1    0.000 180.0 2    0.740 0.0 3
+torsion      8    1    1    8     -0.400 0.0 1   -1.100 180.0 2    1.200 0.0 3
+torsion      8    1    1    9      1.170 0.0 1   -1.263 180.0 2    2.064 0.0 3
+torsion      9    1    1    9      0.000 0.0 1    0.000 180.0 2   -0.500 0.0 3
+torsion      9    1    1   15     -1.000 0.0 1   -0.300 180.0 2    0.400 0.0 3
+torsion      9    1    1   15      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     11    1    1   11     -0.100 0.0 1   -2.000 180.0 2    0.200 0.0 3
+torsion     11    1    1   12      0.000 0.0 1    0.000 180.0 2    0.253 0.0 3
+torsion     11    1    1   13      0.000 0.0 1    0.000 180.0 2    0.253 0.0 3
+torsion     12    1    1   12     -0.240 0.0 1    0.620 180.0 2    0.540 0.0 3
+torsion     12    1    1   13      0.000 0.0 1    0.000 180.0 2    0.267 0.0 3
+torsion     13    1    1   13      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     15    1    1   15     -0.800 0.0 1    0.900 180.0 2   -0.300 0.0 3
+torsion     15    1    1   17      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     17    1    1   17      0.000 0.0 1    0.000 180.0 2    0.125 0.0 3
+torsion     19    1    1   19      0.000 0.0 1    0.000 180.0 2    0.167 0.0 3
+torsion     22    1    1   22      0.200 0.0 1    0.270 180.0 2    0.093 0.0 3
+torsion     29    1    1   29      2.100 0.0 1    0.270 180.0 2    0.093 0.0 3
+torsion     36    1    1   36      0.000 0.0 1    0.000 180.0 2    0.237 0.0 3
+torsion     41    1    1   41      0.000 0.0 1   -0.600 180.0 2    0.300 0.0 3
+torsion      1    1    2    1      0.400 0.0 1    0.030 180.0 2    0.500 0.0 3
+torsion      1    1    2    2     -0.440 0.0 1    0.240 180.0 2    0.060 0.0 3
+torsion      1    1    2    3      0.000 0.0 1    0.000 180.0 2    0.457 0.0 3
+torsion      1    1    2    4     -0.440 0.0 1    0.240 180.0 2    0.060 0.0 3
+torsion      1    1    2    5      0.000 0.0 1    0.000 180.0 2    0.010 0.0 3
+torsion      1    1    2    6      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      1    1    2   19      0.000 0.0 1    0.000 180.0 2    0.350 0.0 3
+torsion      2    1    2    1      0.000 0.0 1    0.000 180.0 2    0.300 0.0 3
+torsion      2    1    2    2      0.100 0.0 1    0.000 180.0 2    0.500 0.0 3
+torsion      2    1    2    5      0.000 0.0 1    0.000 180.0 2    0.600 0.0 3
+torsion      2    1    2    6      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      3    1    2    1      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      3    1    2    2      0.000 0.0 1    0.000 180.0 2    0.100 0.0 3
+torsion      3    1    2    5      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      4    1    2    1      0.000 0.0 1    0.000 180.0 2    0.780 0.0 3
+torsion      4    1    2    2      0.000 0.0 1    0.000 180.0 2    0.100 0.0 3
+torsion      4    1    2    5      0.000 0.0 1    0.000 180.0 2    0.780 0.0 3
+torsion      5    1    2    1      0.000 0.0 1    0.000 180.0 2    0.540 0.0 3
+torsion      5    1    2    2      0.000 0.0 1    0.000 180.0 2   -0.240 0.0 3
+torsion      5    1    2    3      0.000 0.0 1    0.000 180.0 2    0.200 0.0 3
+torsion      5    1    2    4      0.000 0.0 1    0.000 180.0 2   -0.240 0.0 3
+torsion      5    1    2    5      0.000 0.0 1    0.000 180.0 2    0.520 0.0 3
+torsion      5    1    2    6      0.000 0.0 1    0.000 180.0 2    0.540 0.0 3
+torsion      5    1    2   37      0.000 0.0 1    0.000 180.0 2   -0.240 0.0 3
+torsion      6    1    2    1      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      6    1    2    2      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      6    1    2    5      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      8    1    2    1      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      8    1    2    2      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      8    1    2    5      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     11    1    2    2      1.243 0.0 1    1.445 180.0 2   -1.243 0.0 3
+torsion     11    1    2    5      0.848 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     12    1    2    2      0.500 0.0 1    0.300 180.0 2   -0.500 0.0 3
+torsion     12    1    2    5      1.500 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     15    1    2    1      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     15    1    2    2      0.000 0.0 1    0.000 180.0 2    0.100 0.0 3
+torsion     15    1    2    5      0.000 0.0 1    0.000 180.0 2    0.100 0.0 3
+torsion     16    1    2    1      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     16    1    2    2      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     16    1    2    5      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     19    1    2    2      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     19    1    2    5      0.000 0.0 1    0.000 180.0 2    0.717 0.0 3
+torsion     22    1    2    1      0.400 0.0 1    0.030 180.0 2    0.500 0.0 3
+torsion     22    1    2    2     -0.440 0.0 1    0.240 180.0 2    0.060 0.0 3
+torsion     22    1    2    5      0.000 0.0 1    0.000 180.0 2    0.010 0.0 3
+torsion     36    1    2    2      0.000 0.0 1    0.000 180.0 2   -0.240 0.0 3
+torsion     37    1    2    2     -0.440 0.0 1    0.000 180.0 2    0.100 0.0 3
+torsion     37    1    2    5      0.000 0.0 1    0.000 180.0 2    0.500 0.0 3
+torsion     39    1    2    2      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     43    1    2    2     -0.440 0.0 1    0.000 180.0 2    0.100 0.0 3
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+torsion      5    1   33    1      0.000 0.0 1    0.000 180.0 2    0.021 0.0 3
+torsion      5    1   33    5      0.000 0.0 1    0.000 180.0 2    0.021 0.0 3
+torsion      5    1   33   33      0.000 0.0 1    0.000 180.0 2    0.021 0.0 3
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+torsion      1    1   34    5      0.000 0.0 1   -0.200 180.0 2    0.300 0.0 3
+torsion      5    1   34    1      0.000 0.0 1    0.000 180.0 2    0.360 0.0 3
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+torsion      5    1   35    5      0.000 0.0 1    0.000 180.0 2    0.270 0.0 3
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+torsion      1    1   37   37      0.340 0.0 1    0.000 180.0 2   -0.900 0.0 3
+torsion      1    1   37   43      0.340 0.0 1    0.000 180.0 2   -0.600 0.0 3
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+torsion      2    1   37   43     -0.440 0.0 1    0.000 180.0 2    0.100 0.0 3
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+torsion      5    1   37   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      5    1   37   37      0.000 0.0 1    0.000 180.0 2   -0.316 0.0 3
+torsion      5    1   37   43      0.000 0.0 1    0.000 180.0 2   -0.316 0.0 3
+torsion     22    1   37   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     22    1   37   43      0.000 0.0 1    0.000 180.0 2    0.100 0.0 3
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+torsion      1    1   39   48      0.000 0.0 1    0.120 180.0 2    0.100 0.0 3
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+torsion      2    1   39   48      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
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+torsion      5    1   39   48      0.000 0.0 1    0.000 180.0 2    0.250 0.0 3
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+torsion      5    1   43   37      0.000 0.0 1    0.000 180.0 2   -0.316 0.0 3
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+torsion     22    1   43   37      0.000 0.0 1    0.000 180.0 2    0.700 0.0 3
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+torsion     50    1   50   50      0.100 0.0 1    0.000 180.0 2    0.500 0.0 3
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+torsion      1    1   71    5      0.730 0.0 1    0.270 180.0 2    0.680 0.0 3
+torsion      1    1   71   70     -0.250 0.0 1    0.200 180.0 2    0.000 0.0 3
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+torsion      5    1   71    5      0.180 0.0 1    0.000 180.0 2    0.275 0.0 3
+torsion      5    1   71   70      0.000 0.0 1    0.000 180.0 2   -0.270 0.0 3
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+torsion      6    1   71    5      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      6    1   71   70     -3.870 0.0 1    5.700 180.0 2    0.000 0.0 3
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+torsion      5    2    2   72      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
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+torsion      6    2    2   14      0.000 0.0 1    5.250 180.0 2    0.000 0.0 3
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+torsion     12    2    2   12     -1.600 0.0 1   15.500 180.0 2    0.000 0.0 3
+torsion     13    2    2   13     -0.800 0.0 1   15.500 180.0 2    0.000 0.0 3
+torsion     14    2    2   14     -3.840 0.0 1   15.500 180.0 2    0.000 0.0 3
+torsion     14    2    2   41     -1.000 0.0 1   15.500 180.0 2    0.000 0.0 3
+torsion     19    2    2   19      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
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+torsion     37    2    2   40      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion     40    2    2   40      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion     41    2    2   41     -2.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion     42    2    2   42      3.000 0.0 1   15.000 180.0 2    0.500 0.0 3
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+torsion      1    2    3    5      3.300 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion      1    2    3    7      2.750 0.0 1   15.000 180.0 2    0.000 0.0 3
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+torsion      5    2    3   72      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
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+torsion      5    2    6    2      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      5    2    6   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      5    2    6   25     -0.100 0.0 1    2.000 180.0 2    0.000 0.0 3
+torsion      5    2    6   28      2.940 0.0 1    1.500 180.0 2   -1.100 0.0 3
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+torsion      2    2    8   20      0.000 0.0 1    0.000 180.0 2    0.010 0.0 3
+torsion      2    2    8   23      0.000 0.0 1    2.000 180.0 2    0.000 0.0 3
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+torsion      5    2    8   20      0.000 0.0 1    0.000 180.0 2    0.010 0.0 3
+torsion      5    2    8   23      0.000 0.0 1    1.690 180.0 2    0.000 0.0 3
+torsion      2    2    9    1      0.000 0.0 1    2.000 180.0 2    0.000 0.0 3
+torsion      2    2    9    2      0.000 0.0 1    0.000 180.0 2    1.490 0.0 3
+torsion      2    2    9    3      0.000 0.0 1    2.000 180.0 2    0.000 0.0 3
+torsion      2    2    9   28      0.000 0.0 1    2.000 180.0 2    0.000 0.0 3
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+torsion      5    2    9   28      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      9    2    9    1      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      9    2    9   28      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
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+torsion      2    2   19    2      0.000 0.0 1    0.000 180.0 2    0.400 0.0 3
+torsion      2    2   19    5      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
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+torsion      5    2   19    2      0.000 0.0 1    0.000 180.0 2    0.600 0.0 3
+torsion      5    2   19    5      0.000 0.0 1    0.000 180.0 2    0.520 0.0 3
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+torsion      2    2   22   49      0.001 0.0 1    0.000 180.0 2    0.000 0.0 3
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+torsion      5    2   22    5      0.000 0.0 1    0.000 180.0 2    0.520 0.0 3
+torsion      5    2   22   22      0.000 0.0 1    0.000 180.0 2    0.010 0.0 3
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+torsion      2    2   25    2      0.000 0.0 1    0.000 180.0 2    0.330 0.0 3
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+torsion      1    2   37   20      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      1    2   37   23      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
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+torsion      2    2   37   23      0.750 0.0 1   10.000 180.0 2    0.000 0.0 3
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+torsion      2    2   37   40      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
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+torsion      5    2   37    2      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      5    2   37   20      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      5    2   37   23      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      5    2   37   37      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      5    2   37   40      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion     37    2   37    2      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion     37    2   37   20      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion     37    2   37   37      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion     37    2   37   40      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion     40    2   37    2      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion     40    2   37   20      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      5    2   38   22      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion      2    2   40    2      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion      2    2   40   23      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion      2    2   40   37      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion      5    2   40    2      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion      5    2   40   23      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion      5    2   40   37      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion     37    2   40    2      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion     37    2   40   23      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion     37    2   40   37      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion      2    2   41    1      0.000 0.0 1    9.200 180.0 2    0.000 0.0 3
+torsion      2    2   41    2      0.000 0.0 1    8.300 180.0 2   -0.800 0.0 3
+torsion      2    2   41   20      0.000 0.0 1    0.000 180.0 2    0.250 0.0 3
+torsion      2    2   41   28      1.000 0.0 1    7.000 180.0 2    0.000 0.0 3
+torsion      5    2   41    1     -0.820 0.0 1    9.200 180.0 2    3.700 0.0 3
+torsion      5    2   41    2     -0.460 0.0 1    2.700 180.0 2    0.700 0.0 3
+torsion      5    2   41   20      0.000 0.0 1    7.500 180.0 2    0.000 0.0 3
+torsion      5    2   41   28      1.250 0.0 1    0.000 180.0 2    0.500 0.0 3
+torsion     12    2   41    2      0.000 0.0 1   15.500 180.0 2    0.000 0.0 3
+torsion     12    2   41   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     13    2   41    2      0.000 0.0 1   15.500 180.0 2    0.000 0.0 3
+torsion     13    2   41   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     14    2   41    2      0.000 0.0 1   15.500 180.0 2    0.000 0.0 3
+torsion     14    2   41   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      2    2   42    2      0.000 0.0 1    1.700 180.0 2    0.400 0.0 3
+torsion      5    2   42    2      0.000 0.0 1    1.700 180.0 2    0.000 0.0 3
+torsion      2    2   46    7      0.000 0.0 1    1.500 180.0 2    0.000 0.0 3
+torsion      5    2   46    7      0.000 0.0 1    1.300 180.0 2    0.000 0.0 3
+torsion      2    2   72    3      1.581 0.0 1    3.430 180.0 2    3.010 0.0 3
+torsion      2    2   72   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      5    2   72    3      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      5    2   72   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      1    3    3    1      1.000 0.0 1    6.500 180.0 2    0.000 0.0 3
+torsion      1    3    3    5      0.000 0.0 1    5.200 180.0 2    0.000 0.0 3
+torsion      1    3    3    7     -1.000 0.0 1    6.500 180.0 2    0.000 0.0 3
+torsion      2    3    3    2      1.000 0.0 1   12.500 180.0 2    0.000 0.0 3
+torsion      2    3    3    5      0.000 0.0 1    5.000 180.0 2    0.000 0.0 3
+torsion      2    3    3    7     -0.700 0.0 1   12.500 180.0 2    0.000 0.0 3
+torsion      5    3    3    5      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      5    3    3    7     -0.120 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      5    3    3   36      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      7    3    3    7      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      7    3    3   36     -0.120 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion     36    3    3   36      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      1    3    6    1     -2.500 0.0 1    1.390 180.0 2    0.000 0.0 3
+torsion      1    3    6   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      1    3    6   24      0.000 0.0 1    0.500 180.0 2    0.000 0.0 3
+torsion      2    3    6    1      3.530 0.0 1    2.300 180.0 2   -3.530 0.0 3
+torsion      5    3    6    1      0.000 0.0 1    0.880 180.0 2    0.000 0.0 3
+torsion      5    3    6   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      5    3    6   24     -0.770 0.0 1    0.850 180.0 2    0.000 0.0 3
+torsion      7    3    6    1     -1.660 0.0 1    8.980 180.0 2    0.000 0.0 3
+torsion      7    3    6   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      7    3    6   24     -3.285 0.0 1    5.600 180.0 2    0.000 0.0 3
+torsion      1    3    9    1      1.100 0.0 1    5.000 180.0 2    0.000 0.0 3
+torsion      1    3    9    2     -4.000 0.0 1    2.700 180.0 2    0.500 0.0 3
+torsion      1    3    9    3     -0.900 0.0 1    1.600 180.0 2    0.000 0.0 3
+torsion      1    3    9   28      0.000 0.0 1    5.000 180.0 2    0.000 0.0 3
+torsion      2    3    9    1      0.000 0.0 1    5.000 180.0 2    0.000 0.0 3
+torsion      5    3    9    1      0.000 0.0 1    5.000 180.0 2    0.000 0.0 3
+torsion      5    3    9    3      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      5    3    9   28      0.000 0.0 1    5.000 180.0 2    0.000 0.0 3
+torsion      7    3    9    1      0.000 0.0 1    5.000 180.0 2    0.000 0.0 3
+torsion      7    3    9    2     -0.600 0.0 1    4.200 180.0 2    0.000 0.0 3
+torsion      7    3    9    2     -3.100 0.0 1    2.900 180.0 2    0.000 0.0 3
+torsion      7    3    9    3      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      7    3    9    3      0.600 0.0 1    1.300 180.0 2    0.000 0.0 3
+torsion      7    3    9   28      1.100 0.0 1    5.000 180.0 2    0.000 0.0 3
+torsion      9    3    9    1      0.000 0.0 1    0.000 180.0 2    0.010 0.0 3
+torsion      9    3    9    2      2.400 0.0 1    2.500 180.0 2    0.000 0.0 3
+torsion      9    3    9    3      0.800 0.0 1    1.300 180.0 2    0.000 0.0 3
+torsion      9    3    9   28      0.000 0.0 1    1.000 180.0 2    0.000 0.0 3
+torsion      7    3   22    5     -0.167 0.0 1    0.000 180.0 2   -0.100 0.0 3
+torsion      7    3   22   22     -0.300 0.0 1    1.200 180.0 2   -0.350 0.0 3
+torsion     22    3   22    5      0.000 0.0 1    0.000 180.0 2    0.130 0.0 3
+torsion      1    3   72    1     -1.900 0.0 1   17.800 180.0 2    0.000 0.0 3
+torsion      1    3   72   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      1    3   72   23     -0.950 0.0 1   17.950 180.0 2    1.110 0.0 3
+torsion      2    3   72    1     -1.090 0.0 1   17.950 180.0 2    0.000 0.0 3
+torsion      2    3   72    2      1.150 0.0 1   15.250 180.0 2    0.000 0.0 3
+torsion      2    3   72   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      5    3   72    1      0.000 0.0 1   16.900 180.0 2    1.600 0.0 3
+torsion      5    3   72    2      0.000 0.0 1   14.150 180.0 2   -0.990 0.0 3
+torsion      5    3   72    5      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      5    3   72    5      0.000 0.0 1   16.000 180.0 2    1.600 0.0 3
+torsion      5    3   72   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      5    3   72   23      0.000 0.0 1   16.800 180.0 2    0.000 0.0 3
+torsion      1    4    4    2      0.000 0.0 1    0.001 180.0 2    0.000 0.0 3
+torsion      1    4    4    4      0.000 0.0 1    0.001 180.0 2    0.000 0.0 3
+torsion      2    4    4    2      0.000 0.0 1    0.001 180.0 2    0.000 0.0 3
+torsion      2    4    4    4      0.000 0.0 1    0.001 180.0 2    0.000 0.0 3
+torsion      2    4    4    5      0.000 0.0 1    0.001 180.0 2    0.000 0.0 3
+torsion      4    4    4    4      0.000 0.0 1    0.001 180.0 2    0.000 0.0 3
+torsion      1    6    6    1      2.095 0.0 1   -2.155 180.0 2   -0.113 0.0 3
+torsion      1    6    6   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      1    6    6   21      2.865 0.0 1   -2.305 180.0 2    0.505 0.0 3
+torsion     20    6    6   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     20    6    6   21      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     21    6    6   21      0.753 0.0 1   -1.202 180.0 2   -0.250 0.0 3
+torsion      1    6   19    1      0.000 0.0 1    0.000 180.0 2    0.230 0.0 3
+torsion      1    6   19    5      0.000 0.0 1    0.000 180.0 2    0.320 0.0 3
+torsion      1    6   19    6      0.000 0.0 1    0.000 180.0 2    0.150 0.0 3
+torsion     19    6   19    1      0.000 0.0 1    0.000 180.0 2    0.100 0.0 3
+torsion     19    6   19    5      0.000 0.0 1    0.000 180.0 2    0.100 0.0 3
+torsion     19    6   19    6      0.000 0.0 1    0.000 180.0 2    0.100 0.0 3
+torsion     20    6   19    1      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     20    6   19    5      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     20    6   19    6      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      1    6   25    6      0.000 0.0 1    0.000 180.0 2    0.400 0.0 3
+torsion      2    6   25    6      0.200 0.0 1    0.000 180.0 2   -0.300 0.0 3
+torsion     20    6   25    6     -0.300 0.0 1    1.200 180.0 2   -0.350 0.0 3
+torsion      1    8    8    1      0.900 0.0 1   -6.800 180.0 2    0.210 0.0 3
+torsion      1    8    8   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      1    8    8   23      2.000 0.0 1   -8.500 180.0 2    0.800 0.0 3
+torsion      8    8    8   23      0.025 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     20    8    8   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     20    8    8   23      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     23    8    8   23      1.800 0.0 1   -9.680 180.0 2    0.210 0.0 3
+torsion      1    9   18    1     -4.000 0.0 1   -3.000 180.0 2   -2.100 0.0 3
+torsion      1    9   18    7     -0.500 0.0 1   -1.000 180.0 2    0.000 0.0 3
+torsion     28    9   18    1     -0.500 0.0 1   -2.000 180.0 2   -4.000 0.0 3
+torsion     28    9   18    5      0.000 0.0 1    0.000 180.0 2    0.030 0.0 3
+torsion     28    9   18    7      0.000 0.0 1    0.000 180.0 2    0.060 0.0 3
+torsion      1   15   15    1      0.000 0.0 1   -7.000 180.0 2    0.467 0.0 3
+torsion      5   15   15    5      0.000 0.0 1   -7.000 180.0 2    0.000 0.0 3
+torsion      1   19   19    1      0.000 0.0 1    0.000 180.0 2    0.633 0.0 3
+torsion      1   19   19    2      0.170 0.0 1    0.270 180.0 2    0.093 0.0 3
+torsion      1   19   19   19      0.000 0.0 1    0.000 180.0 2    0.300 0.0 3
+torsion      2   19   19    2      0.000 0.0 1    0.000 180.0 2    0.400 0.0 3
+torsion      2   19   19    5      0.000 0.0 1    0.000 180.0 2    0.450 0.0 3
+torsion      5   19   19    5      0.000 0.0 1    0.000 180.0 2    0.136 0.0 3
+torsion      5   19   19   19      0.000 0.0 1    0.000 180.0 2    0.070 0.0 3
+torsion     19   19   19   19      0.000 0.0 1    0.000 180.0 2    0.100 0.0 3
+torsion      5   19   22    5      0.000 0.0 1    0.000 180.0 2    0.500 0.0 3
+torsion      5   19   22   22      0.000 0.0 1    0.000 180.0 2    0.083 0.0 3
+torsion      1   22   22    1      0.200 0.0 1    0.270 180.0 2    0.240 0.0 3
+torsion      1   22   22    3      0.200 0.0 1    0.200 180.0 2    0.000 0.0 3
+torsion      1   22   22    5      0.000 0.0 1    0.000 180.0 2    0.120 0.0 3
+torsion      1   22   22   22      0.200 0.0 1    0.270 180.0 2    0.093 0.0 3
+torsion      1   22   22   49      0.000 0.0 1    0.000 180.0 2    0.530 0.0 3
+torsion      2   22   22    2      0.200 0.0 1    0.270 180.0 2    0.093 0.0 3
+torsion      2   22   22    5      0.000 0.0 1    0.000 180.0 2    0.120 0.0 3
+torsion      2   22   22   22      0.170 0.0 1    0.270 180.0 2    0.093 0.0 3
+torsion      2   22   22   49      0.000 0.0 1    0.000 180.0 2    0.530 0.0 3
+torsion      3   22   22    5      0.000 0.0 1    0.000 180.0 2    0.120 0.0 3
+torsion      3   22   22   22      0.200 0.0 1    0.200 180.0 2    0.000 0.0 3
+torsion      5   22   22    5      0.000 0.0 1    0.000 180.0 2    0.137 0.0 3
+torsion      5   22   22   19      0.000 0.0 1    0.000 180.0 2    0.120 0.0 3
+torsion      5   22   22   22      0.000 0.0 1    0.000 180.0 2    0.167 0.0 3
+torsion      5   22   22   38      0.000 0.0 1    2.000 180.0 2    0.500 0.0 3
+torsion      5   22   22   46      0.000 0.0 1    0.000 180.0 2    0.200 0.0 3
+torsion      5   22   22   49      0.000 0.0 1    0.000 180.0 2    0.530 0.0 3
+torsion     19   22   22   22      0.220 0.0 1    0.270 180.0 2    0.093 0.0 3
+torsion     22   22   22   22     -0.520 0.0 1    0.000 180.0 2    0.160 0.0 3
+torsion     22   22   22   46      0.000 0.0 1    0.000 180.0 2    0.167 0.0 3
+torsion      5   22   38    1      0.000 0.0 1    0.000 180.0 2    0.540 0.0 3
+torsion      5   22   38    2      0.000 0.0 1    0.000 180.0 2   -0.240 0.0 3
+torsion      5   22   38    5      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      5   22   38   22      0.000 0.0 1    2.000 180.0 2    0.540 0.0 3
+torsion      5   22   38   38      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     22   22   38    2      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     22   22   38    5      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion     38   22   38    1      0.000 0.0 1    0.000 180.0 2    0.300 0.0 3
+torsion     38   22   38    2      0.100 0.0 1    0.000 180.0 2    0.500 0.0 3
+torsion     38   22   38    5      0.000 0.0 1    0.000 180.0 2    0.600 0.0 3
+torsion      5   22   46    7      0.000 0.0 1    1.000 180.0 2    0.000 0.0 3
+torsion     22   22   46    7      0.000 0.0 1    2.000 180.0 2    0.000 0.0 3
+torsion      1   22   49   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      1   22   49   22      0.000 0.0 1    0.000 180.0 2    1.210 0.0 3
+torsion      2   22   49   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      2   22   49   22      0.000 0.0 1    0.000 180.0 2    1.210 0.0 3
+torsion      5   22   49   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      5   22   49   22      0.000 0.0 1    0.000 180.0 2    1.210 0.0 3
+torsion     22   22   49   20      0.000 0.0 1    0.000 180.0 2    0.000 0.0 3
+torsion      1   33   33    1      0.000 0.0 1    0.000 180.0 2    0.021 0.0 3
+torsion      1   37   37    1     -1.900 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      1   37   37   20      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      2   37   37    2      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      2   37   37   20      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion     20   37   37   20      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion     20   37   37   23      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion     23   37   37   23      2.400 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion      2   37   40    2      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      2   37   40   23      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion     20   37   40    2      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion     20   37   40   23      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      1   37   43    1     -1.900 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      1   37   43    7     -5.400 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion     20   37   43    1      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion     20   37   43    7      0.000 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion      1   38   38   22     -0.100 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion      5   38   38    5      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion      5   38   38   22      0.000 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion      1   50   50    1     -0.100 0.0 1    9.000 180.0 2    0.000 0.0 3
+torsion      1   50   50    5      0.000 0.0 1    9.000 180.0 2    0.000 0.0 3
+torsion      1   50   50   50     -0.270 0.0 1    9.000 180.0 2    0.000 0.0 3
+torsion      5   50   50    5      0.000 0.0 1    9.000 180.0 2    0.000 0.0 3
+torsion      5   50   50   50      0.000 0.0 1    5.405 180.0 2   -1.060 0.0 3
+torsion     50   50   50   50     -0.930 0.0 1    4.800 180.0 2    0.000 0.0 3
+torsion      1   70   71    1      0.000 0.0 1   10.560 180.0 2    0.000 0.0 3
+torsion      1   70   71    5      0.000 0.0 1    9.070 180.0 2    0.000 0.0 3
+
+
+      #####################################
+      ##                                 ##
+      ##  Torsional Parameters (4-Ring)  ##
+      ##                                 ##
+      #####################################
+
+
+torsion4     1    1    1    1      0.200 0.0 1    0.270 180.0 2    1.533 0.0 3
+torsion4     1    1    1    2      0.000 0.0 1    0.000 180.0 2    1.900 0.0 3
+torsion4     1    1    1    3      0.200 0.0 1    0.270 180.0 2    1.533 0.0 3
+torsion4     1    1    1    6      0.130 0.0 1    0.000 180.0 2    1.500 0.0 3
+torsion4     1    1    1    8      0.100 0.0 1    0.400 180.0 2    2.500 0.0 3
+torsion4     1    1    1   15      0.000 0.0 1   -0.100 180.0 2    1.100 0.0 3
+torsion4     1    1    1   19      0.100 0.0 1    0.000 180.0 2    0.900 0.0 3
+torsion4     1    1    1   31      0.000 0.0 1    0.000 180.0 2   -0.065 0.0 3
+torsion4     1    1    1   39      0.100 0.0 1    0.400 180.0 2    2.500 0.0 3
+torsion4     2    1    1    2      0.200 0.0 1    0.270 180.0 2    1.530 0.0 3
+torsion4     3    1    1    6      0.100 0.0 1    0.000 180.0 2    1.500 0.0 3
+torsion4     3    1    1    9      0.000 0.0 1    0.000 180.0 2    0.250 0.0 3
+torsion4    22    1    1   22      0.200 0.0 1    0.270 180.0 2    1.533 0.0 3
+torsion4    37    1    1   37      0.000 0.0 1    0.000 180.0 2    1.533 0.0 3
+torsion4    37    1    1   43      0.000 0.0 1    0.000 180.0 2    1.533 0.0 3
+torsion4     1    1    2    1      0.000 0.0 1    0.030 180.0 2    0.900 0.0 3
+torsion4     1    1    2    2     -0.700 0.0 1    0.240 180.0 2    0.060 0.0 3
+torsion4     2    1    2    1      0.000 0.0 1    0.000 180.0 2    0.300 0.0 3
+torsion4     2    1    2    2      0.000 0.0 1    0.000 180.0 2    0.600 0.0 3
+torsion4     1    1    3    1      0.550 0.0 1   -0.180 180.0 2    0.400 0.0 3
+torsion4     1    1    3    6      0.100 0.0 1    0.000 180.0 2    1.500 0.0 3
+torsion4     1    1    3    9      0.000 0.0 1    0.000 180.0 2    0.250 0.0 3
+torsion4     1    1    6    1      0.130 0.0 1    0.000 180.0 2    1.500 0.0 3
+torsion4     1    1    6    3      0.100 0.0 1    0.000 180.0 2    1.500 0.0 3
+torsion4     1    1    8    1     -0.200 0.0 1    0.730 180.0 2    2.500 0.0 3
+torsion4     1    1    9    3      0.000 0.0 1    0.000 180.0 2    0.250 0.0 3
+torsion4     1    1   15    1      0.000 0.0 1   -0.100 180.0 2    1.100 0.0 3
+torsion4     1    1   19    1      0.100 0.0 1    0.000 180.0 2    0.900 0.0 3
+torsion4     1    1   22   22      0.200 0.0 1    0.270 180.0 2    1.533 0.0 3
+torsion4     1    1   31    1      0.000 0.0 1    0.000 180.0 2    0.152 0.0 3
+torsion4     1    1   37   37      0.000 0.0 1    0.000 180.0 2    0.060 0.0 3
+torsion4     1    1   37   43      0.000 0.0 1    0.000 180.0 2    0.060 0.0 3
+torsion4     1    1   39    1     -0.200 0.0 1    0.730 180.0 2    2.500 0.0 3
+torsion4     1    2    2    1     -0.100 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion4     2    2    2    2     -0.930 0.0 1   15.000 180.0 2    0.000 0.0 3
+torsion4     1    3    6    1     -2.500 0.0 1    1.390 180.0 2    0.000 0.0 3
+torsion4     1    3    9    1      0.000 0.0 1    0.000 180.0 2    0.250 0.0 3
+torsion4    22    3   22   22      0.550 0.0 1   -0.180 180.0 2    0.400 0.0 3
+torsion4     1   22   22    1      0.200 0.0 1    0.270 180.0 2    2.500 0.0 3
+torsion4     1   22   22   22      0.200 0.0 1    0.270 180.0 2    1.533 0.0 3
+torsion4     3   22   22   22      0.200 0.0 1    0.270 180.0 2    1.533 0.0 3
+torsion4    22   22   22   22      6.070 0.0 1    0.000 180.0 2   -0.880 0.0 3
+torsion4     1   37   37    1     -1.900 0.0 1   10.000 180.0 2    0.000 0.0 3
+torsion4     1   37   43    1     -1.900 0.0 1   10.000 180.0 2    0.000 0.0 3
+
+
+      ######################################
+      ##                                  ##
+      ##  Torsional Parameters (Allenes)  ##
+      ##                                  ##
+      ######################################
+
+
+#torsion     1    2    2    1      0.000 0.0 1  -11.500 180.0 2    0.000 0.0 3
+#torsion     1    2    2    5      0.000 0.0 1  -11.500 180.0 2    0.000 0.0 3
+#torsion     5    2    2    5      0.050 0.0 1  -12.100 180.0 2    0.000 0.0 3
+
+
+      ########################################
+      ##                                    ##
+      ##  Atomic Partial Charge Parameters  ##
+      ##                                    ##
+      ########################################
+
+
+charge       16               1.000
+charge       30               1.000
+charge       39               1.000
+charge       47              -0.500
+
+
+      #####################################
+      ##                                 ##
+      ##  Bond Dipole Moment Parameters  ##
+      ##                                 ##
+      #####################################
+
+
+dipole        1    2          0.300      0.500
+dipole        1    3          0.300      0.500
+dipole        1    4          0.750      0.500
+dipole        1    6          0.440      0.500
+dipole        1    8          0.040      0.500
+dipole        1    9          1.470      0.500
+dipole        1   11          1.820      0.500
+dipole        1   12          1.940      0.500
+dipole        1   13          1.790      0.500
+dipole        1   14          1.300      0.500
+dipole        1   15          1.200      0.500
+dipole        1   16          1.200      0.500
+dipole        1   17          1.200      0.500
+dipole        1   18          1.200      0.500
+dipole        1   19         -0.600      0.500
+dipole        1   22          0.150      0.500
+dipole        1   25          0.830      0.500
+dipole        1   31         -0.550      0.500
+dipole        1   32         -0.650      0.500
+dipole        1   33         -0.500      0.500
+dipole        1   34         -1.100      0.500
+dipole        1   35         -1.000      0.500
+dipole        1   37          1.260      0.500
+dipole        1   38          0.300      0.500
+dipole        1   41          0.220      0.500
+dipole        1   43          1.260      0.500
+dipole        1   46          1.350      0.500
+dipole        1   50          0.300      0.500
+dipole        1   70          1.900      0.500
+dipole        1   71          0.300      0.500
+dipole        1   72          1.260      0.500
+dipole        2    6          0.001      0.500
+dipole        2    8         -0.400      0.500
+dipole        2    9          1.300      0.500
+dipole        2   11          1.480      0.500
+dipole        2   12          1.580      0.500
+dipole        2   13          1.560      0.500
+dipole        2   14          1.400      0.500
+dipole        2   19         -0.650      0.500
+dipole        2   22         -0.150      0.500
+dipole        2   25          1.040      0.500
+dipole        2   37          0.583      0.500
+dipole        2   40          0.870      0.500
+dipole        2   41          0.950      0.500
+dipole        2   42          1.925      0.500
+dipole        2   46          1.700      0.500
+dipole        2   72          0.583      0.500
+dipole        3    6         -0.200      0.500
+dipole        3    7          2.600      0.500
+dipole        3    9         -0.290      0.500
+dipole        3   11          1.480      0.500
+dipole        3   12          1.580      0.500
+dipole        3   13          1.560      0.500
+dipole        3   14          1.400      0.500
+dipole        3   22          0.300      0.500
+dipole        3   72          0.583      0.500
+dipole        4   10          3.400      0.500
+dipole        5   15          0.900      0.500
+dipole        5   25          0.500      0.500
+dipole        5   34          0.700      0.500
+dipole        5   35          0.800      0.500
+dipole        6   19         -0.400      0.500
+dipole        6   20          0.900      0.500
+dipole        6   21         -1.115      0.500
+dipole        6   24         -0.700      0.500
+dipole        6   25          0.970      0.500
+dipole        6   28         -0.700      0.500
+dipole        7   17         -3.030      0.500
+dipole        7   18         -2.930      0.500
+dipole        7   43         -2.600      0.500
+dipole        7   46         -2.530      0.500
+dipole        8   20          0.600      0.500
+dipole        8   23         -0.760      0.500
+dipole        9   18          0.800      0.500
+dipole        9   28         -1.310      0.500
+dipole       20   37         -0.600      0.500
+dipole       20   41         -0.750      0.500
+dipole       20   72         -0.600      0.500
+dipole       22   46          1.700      0.500
+dipole       23   37          0.600      0.500
+dipole       23   40          0.550      0.500
+dipole       23   72          0.600      0.500
+dipole       28   41          0.700      0.500
+dipole       37   40          0.300      0.500
+dipole       70   71         -2.800      0.500
+
+
+      ##############################################
+      ##                                          ##
+      ##  Bond Dipole Moment Parameters (3-Ring)  ##
+      ##                                          ##
+      ##############################################
+
+
+dipole3      22   49         0.735      0.500
+
+
+      ###########################################
+      ##                                       ##
+      ##  Conjugated Pisystem Atom Parameters  ##
+      ##                                       ##
+      ###########################################
+
+
+piatom        2         1.0      -11.160     11.134
+piatom        3         1.0      -11.160     11.134
+piatom        4         1.0      -11.160     11.134
+piatom        6         2.0      -17.600     19.342
+piatom        7         1.0      -17.210     14.520
+piatom        9         2.0      -13.145     17.210
+piatom       10         1.0      -14.120     12.340
+piatom       37         1.0      -14.120     12.340
+piatom       40         2.0      -13.145     17.210
+piatom       41         2.0      -17.600     19.342
+piatom       42         2.0      -15.800     11.920
+piatom       72         1.0      -14.120     12.340
+
+
+      ###########################################
+      ##                                       ##
+      ##  Conjugated Pisystem Bond Parameters  ##
+      ##                                       ##
+      ###########################################
+
+
+pibond        2    2          4.600      0.166
+pibond        2    3          4.600      0.166
+pibond        2    4          7.790      0.156
+pibond        2   37         10.880      0.196
+pibond        2   40         10.880      0.196
+pibond        2   41          5.440      0.196
+pibond        2   42          4.861      0.397
+pibond        2   72         10.880      0.196
+pibond        3    3          4.600      0.140
+pibond        3    4          4.600      0.166
+pibond        3    7          4.600      0.105
+pibond        3   72         10.880      0.196
+pibond        4    4          4.600      0.238
+pibond       37   37         10.500      0.170
+pibond       37   40         10.880      0.196
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmff94.ff	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,28 @@
+#
+# MMFF94 paremeter files
+#
+
+# atom properties
+prop	mmffprop.par
+# fallback defs
+def	mmffdef.par
+# bond stretching parameters
+bond	mmffbond.par
+# angle bending parameters
+ang	mmffang.par
+# empirical rule parameters (bond stretching)
+bndk	mmffbndk.par
+# charge parameters
+chg	mmffchg.par
+# empirical rule parameters (bend-stretch)
+dfsb	mmffdfsb.par
+# out-of-plane parameters
+oop	mmffoop.par
+# partial bond charge increments
+pbci	mmffpbci.par
+# strech-bend parameters
+stbn	mmffstbn.par
+# torsion parameters
+tor	mmfftor.par
+# van der waals parameters
+vdw	mmffvdw.par
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmff94s.ff	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,28 @@
+#
+# MMFF94 paremeter files
+#
+
+# atom properties
+prop	mmffprop.par
+# fallback defs
+def	mmffdef.par
+# bond stretching parameters
+bond	mmffbond.par
+# angle bending parameters
+ang	mmffang.par
+# empirical rule parameters (bond stretching)
+bndk	mmffbndk.par
+# charge parameters
+chg	mmffchg.par
+# empirical rule parameters (bend-stretch)
+dfsb	mmffdfsb.par
+# out-of-plane parameters
+oop	mmffs_oop.par
+# partial bond charge increments
+pbci	mmffpbci.par
+# strech-bend parameters
+stbn	mmffstbn.par
+# torsion parameters
+tor	mmffs_tor.par
+# van der waals parameters
+vdw	mmffvdw.par
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffang.par	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,2354 @@
+*
+*                 Copyright (c) Merck and Co., Inc., 1994
+*                           All Rights Reserved
+*
+* MMFF ANGLE PARAMETERS- Rev:  26-Oct-94  Source: MMFF94
+* C94  = CORE MMFF94 parameter - obtained from ab initio data
+* X94  = EXTD MMFF94 parameter - fit to additional ab initio data
+* E94  = theta0 from fit to X-ray data, ka from empirical rule
+* #E94 = theta0 and ka both from empirical rules
+*
+*      types         ka     theta0    Comment/origin
+0   0    1    0     0.000   108.900   0:*-1-* MMFF94 DEF
+0   1    1    1     0.851   109.608   C94
+0   1    1    2     0.736   109.445   C94
+0   1    1    3     0.777   107.517   C94
+0   1    1    4     1.006   110.265   E94
+0   1    1    5     0.636   110.549   C94
+0   1    1    6     0.992   108.133   C94
+0   1    1    8     0.777   108.290   C94
+0   1    1    9     1.136   108.194   E94
+0   1    1   10     1.050   109.960   C94
+0   1    1   11     1.225   108.313   C94
+0   1    1   12     1.056   108.679   C94
+0   1    1   13     1.078   106.820   E94
+0   1    1   14     0.980   109.945   E94
+0   1    1   15     0.743   107.397   C94
+0   1    1   17     1.089   108.578   E94
+0   1    1   18     1.093   109.315   E94
+0   1    1   19     0.755   115.436   E94
+0   1    1   20     1.021   108.659   E94
+0   1    1   22     1.001   110.125   E94
+0   1    1   25     0.803   112.356   X94
+0   1    1   26     0.833   109.879   E94
+0   1    1   34     1.179   106.493   C94
+0   1    1   37     0.756   108.617   C94
+0   1    1   39     0.927   109.170   C94
+0   1    1   40     1.130   108.678   E94
+0   1    1   41     0.330    98.422   C94
+0   1    1   43     1.135   108.019   E94
+0   1    1   45     1.197   105.028   E94
+0   1    1   54     1.173   106.424   E94
+0   1    1   55     1.150   107.604   E94
+0   1    1   56     1.199   110.371   C94
+0   1    1   57     1.012   109.900   E94
+0   1    1   58     1.179   106.327   E94
+0   1    1   61     1.125   109.311   E94
+0   1    1   63     1.006   110.058   E94
+0   1    1   64     0.988   111.064   E94
+0   1    1   67     1.216   104.557   E94
+0   1    1   68     1.018   107.195   C94
+0   1    1   73     1.160   104.658   E94
+0   1    1   78     1.012   109.850   E94
+0   1    1   80     0.947   113.327   E94
+0   1    1   81     1.108   109.837   E94
+0   2    1    2     1.113   111.453   C94
+0   2    1    3     0.667   104.829   C94
+0   2    1    4     1.022   109.873   E94
+0   2    1    5     0.632   110.292   C94
+0   2    1    6     1.074   108.699   C94
+0   2    1    8     0.884   111.553   C94
+0   2    1    9     1.118   109.577   E94
+0   2    1   10     1.160   107.963   E94
+0   2    1   11     1.192   110.419   E94
+0   2    1   12     1.070   109.410   E94
+0   2    1   15     1.078   109.560   E94
+0   2    1   17     1.077   109.434   E94
+0   2    1   18     1.188   105.110   E94
+0   2    1   20     1.053   107.448   E94
+0   2    1   22     0.942   114.020   E94
+0   2    1   25     0.893   106.815   E94
+0   2    1   26     1.029    99.065   E94
+0   2    1   34     1.066   111.817   E94
+0   2    1   37     0.985   111.446   E94
+0   2    1   39     1.124   109.513   E94
+0   2    1   40     1.149   108.270   E94
+0   2    1   45     1.232   103.978   E94
+0   2    1   63     0.935   114.692   E94
+0   2    1   67     1.224   104.687   E94
+0   3    1    3     0.974   111.746   E94
+0   3    1    4     1.019   109.850   E94
+0   3    1    5     0.650   108.385   C94
+0   3    1    6     0.528   104.112   C94
+0   3    1    8     1.197   105.837   E94
+0   3    1    9     1.201   105.535   E94
+0   3    1   10     0.634   102.655   C94
+0   3    1   11     1.189   110.328   E94
+0   3    1   12     1.136   106.064   E94
+0   3    1   13     1.147   103.645   E94
+0   3    1   14     1.048   106.404   E94
+0   3    1   15     1.125   107.192   E94
+0   3    1   17     1.092   108.602   E94
+0   3    1   18     1.120   108.119   E94
+0   3    1   20     0.969   111.830   E94
+0   3    1   22     0.999   110.522   E94
+0   3    1   26     0.742   116.555   E94
+0   3    1   34     1.141   107.871   E94
+0   3    1   37     1.011   109.833   E94
+0   3    1   39     1.136   108.751   E94
+0   3    1   40     1.174   106.941   E94
+0   3    1   41     1.033   108.216   E94
+0   3    1   45     1.221   104.281   E94
+0   3    1   63     1.069   107.077   E94
+0   3    1   64     1.028   109.186   E94
+0   3    1   81     1.167   107.327   E94
+0   4    1    4     0.954   114.186   E94
+0   4    1    5     0.615   111.417   X94
+0   4    1    6     1.273   109.977   E94
+0   4    1    8     1.099   111.063   E94
+0   4    1    9     1.187   106.750   E94
+0   4    1   10     1.117   110.488   E94
+0   4    1   13     1.021   110.047   E94
+0   4    1   15     1.028   112.432   E94
+0   4    1   18     1.187   105.351   E94
+0   4    1   22     1.174   102.556   E94
+0   4    1   26     0.853   108.999   E94
+0   4    1   34     1.148   108.160   E94
+0   4    1   37     0.993   111.424   E94
+0   5    1    5     0.516   108.836   C94
+0   5    1    6     0.781   108.577   C94
+0   5    1    8     0.653   110.297   C94
+0   5    1    9     0.733   109.894   C94
+0   5    1   10     0.740   107.646   C94
+0   5    1   11     0.875   107.897   C94
+0   5    1   12     0.698   108.162   C94
+0   5    1   13     0.613   106.049   E94
+0   5    1   14     0.508   113.019   E94
+0   5    1   15     0.576   109.609   C94
+0   5    1   17     0.634   107.944   X94
+0   5    1   18     0.663   106.855   X94
+0   5    1   19     0.450   113.195   X94
+0   5    1   20     0.706   111.000   C94
+0   5    1   22     0.618   110.380   E94
+0   5    1   25     0.487   109.486   X94
+0   5    1   26     0.466   111.172   X94
+0   5    1   34     0.872   106.224   C94
+0   5    1   35     0.644   125.663   X94
+0   5    1   37     0.627   109.491   C94
+0   5    1   39     0.811   106.299   C94
+0   5    1   40     0.719   109.870   C94
+0   5    1   41     0.525   108.904   C94
+0   5    1   43     0.692   109.083   X94
+0   5    1   45     0.741   105.197   X94
+0   5    1   46     0.719   106.735   X94
+0   5    1   54     0.874   106.973   C94
+0   5    1   55     0.861   108.507   C94
+0   5    1   56     0.814   108.223   C94
+0   5    1   57     0.626   110.420   E94
+0   5    1   58     0.750   105.481   E94
+0   5    1   61     0.710   109.227   X94
+0   5    1   62     0.655   113.035   X94
+0   5    1   63     0.621   110.467   E94
+0   5    1   64     0.622   110.457   E94
+0   5    1   67     0.732   106.474   E94
+0   5    1   68     0.748   103.817   C94
+0   5    1   72     0.547   116.576   X94
+0   5    1   73     0.633   107.153   X94
+0   5    1   78     0.640   109.078   E94
+0   5    1   80     0.684   105.144   E94
+0   5    1   81     0.721   107.870   E94
+0   6    1    6     1.156   111.368   C94
+0   6    1    8     1.333   112.223   E94
+0   6    1    9     1.224   116.950   E94
+0   6    1   10     1.432   108.568   E94
+0   6    1   11     1.593   106.900   E94
+0   6    1   15     1.273   112.012   E94
+0   6    1   17     1.348   108.655   E94
+0   6    1   19     0.906   117.214   E94
+0   6    1   20     1.293   108.202   E94
+0   6    1   22     1.287   108.913   E94
+0   6    1   25     1.171   103.598   E94
+0   6    1   26     0.888   118.433   E94
+0   6    1   34     1.257   114.975   E94
+0   6    1   37     0.878   107.978   C94
+0   6    1   39     1.485   106.464   E94
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+0  63   39   64     1.004   120.577   E94
+1  63   39   64     0.899   126.936   E94
+0  63   39   65     1.284   112.087   C94
+1  63   39   65     1.146   117.990   E94
+0  63   39   78     1.300   105.800   E94
+0  64   39   65     1.007   126.117   E94
+0  65   39   65     1.462   116.898   C94
+0   0   40    0     0.000   115.000   0:*-40-* MMFF94 DEF
+3   0   40    0     0.000    57.800   3::*-40-* MMFF94 DEF
+0   1   40    1     1.064   113.703   E94
+0   1   40    2     0.998   118.873   E94
+0   1   40    3     1.007   118.319   E94
+0   1   40    6     1.421   109.742   E94
+0   1   40    9     1.203   113.198   E94
+0   1   40   10     1.232   111.320   E94
+0   1   40   11     1.436   104.665   E94
+0   1   40   12     1.202   109.320   E94
+0   1   40   20     1.047   114.970   E94
+0   1   40   25     0.912   114.483   E94
+0   1   40   28     0.689   112.374   C94
+0   1   40   30     1.024   118.604   E94
+0   1   40   37     0.835   107.349   C94
+0   1   40   39     1.254   110.622   E94
+0   1   40   40     1.183   114.011   E94
+0   1   40   45     1.223   112.226   E94
+0   1   40   46     1.025   122.982   E94
+0   1   40   63     1.084   114.473   E94
+0   1   40   64     1.064   115.483   E94
+0   2   40    2     0.997   120.651   E94
+0   2   40    3     0.981   121.660   E94
+0   2   40    6     1.316   115.626   E94
+0   2   40    9     1.118   119.196   E94
+0   2   40   10     1.142   117.260   E94
+0   2   40   19     0.732   128.087   E94
+0   2   40   28     0.767   111.053   C94
+0   2   40   37     1.049   117.022   E94
+0   2   40   39     1.192   115.106   E94
+0   2   40   40     1.060   122.253   E94
+0   2   40   63     1.008   120.447   E94
+0   3   40    3     0.883   128.240   E94
+0   3   40    8     1.259   111.557   E94
+0   3   40    9     1.106   119.822   E94
+0   3   40   10     1.269   111.261   E94
+0   3   40   12     1.146   112.718   E94
+0   3   40   15     1.105   117.871   E94
+0   3   40   20     1.130   112.139   E94
+0   3   40   22     1.072   114.420   E94
+0   3   40   25     0.820   121.724   E94
+0   3   40   28     0.700   114.808   C94
+0   3   40   37     1.056   116.655   E94
+0   3   40   40     1.147   117.511   E94
+0   3   40   64     1.132   113.602   E94
+0   6   40   28     0.889   110.000   #E94
+0   8   40   28     0.764   111.915   E94
+0   8   40   37     1.216   112.920   E94
+0   8   40   63     1.351   108.085   E94
+0   9   40   28     0.774   112.549   E94
+0   9   40   37     1.236   112.751   E94
+0  10   40   28     0.799   109.725   E94
+0  10   40   37     1.316   108.686   E94
+0  11   40   37     1.546   101.687   E94
+0  15   40   15     1.154   121.497   E94
+3  22   40   22     0.204    57.777   E94
+0  22   40   37     1.066   114.220   E94
+0  22   40   63     1.126   112.006   E94
+0  25   40   28     0.485   120.000   #E94
+0  25   40   37     0.868   117.977   E94
+0  26   40   28     0.506   118.000   #E94
+0  26   40   37     0.812   122.336   E94
+0  28   40   28     0.560   109.160   C94
+0  28   40   30     0.656   119.230   E94
+0  28   40   37     0.662   110.288   C94
+0  28   40   39     0.789   110.951   E94
+0  28   40   40     0.782   111.731   E94
+0  28   40   45     0.674   120.000   #E94
+0  28   40   54     0.738   118.714   E94
+0  28   40   63     0.670   116.188   E94
+0  28   40   64     0.659   117.057   E94
+0  28   40   78     0.618   119.829   E94
+0  37   40   37     1.004   119.018   E94
+0  37   40   45     1.376   106.579   E94
+0  37   40   54     1.394   107.777   E94
+0  37   40   63     1.060   116.867   E94
+0  45   40   64     1.283   111.332   E94
+0  45   40   78     1.410   105.678   E94
+0  46   40   64     1.189   116.345   E94
+0   0   41    0     0.000   118.300   0:*-41-* MMFF94 DEF
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+0   1   41   72     1.024   114.936   X94
+0   2   41   32     1.309   115.461   C94
+0   3   41   32     1.210   114.810   E94
+0   5   41   32     0.912   113.960   C94
+0   6   41   72     1.319   113.899   E94
+0   9   41   72     1.089   117.795   E94
+0  10   41   72     1.039   121.240   E94
+0  20   41   32     1.090   120.965   E94
+0  22   41   32     1.079   122.748   E94
+0  32   41   32     1.181   130.600   C94
+0  32   41   37     1.136   118.871   E94
+0  32   41   41     1.401   107.694   E94
+0  37   41   72     1.035   114.919   E94
+0  55   41   72     0.982   123.972   E94
+0  62   41   72     1.052   120.425   E94
+0  72   41   72     0.912   130.128   X94
+0  72   41   80     1.094   112.175   E94
+0   0   43    0     0.000   113.300   0:*-43-* MMFF94 DEF
+0   1   43    1     1.109   110.353   E94
+0   1   43    2     1.052   114.321   E94
+0   1   43    3     0.938   121.050   E94
+0   1   43    4     0.927   123.204   E94
+0   1   43   18     1.116   115.011   X94
+0   1   43   25     0.853   115.637   X94
+0   1   43   28     0.646   113.739   X94
+0   1   43   37     1.083   112.511   E94
+0   1   43   45     1.140   115.034   E94
+0   1   43   64     1.025   116.188   E94
+0   2   43   18     1.227   110.268   E94
+0   3   43   18     1.011   121.488   X94
+0   3   43   20     1.053   113.913   E94
+4   3   43   20     1.327    93.575   E94
+0   3   43   28     0.626   117.464   X94
+0   4   43   28     0.616   122.000   E94
+0   4   43   45     1.253   112.373   E94
+0   6   43   18     1.673   104.311   E94
+3   6   43   22     0.279    54.827   E94
+0   6   43   28     0.868   110.000   #E94
+0   6   43   37     1.519   105.833   E94
+0   6   43   43     1.603   108.652   E94
+0   8   43   18     1.511   104.036   E94
+0   8   43   28     0.794   110.320   E94
+0  15   43   15     1.558   103.008   E94
+0  15   43   18     1.409   108.458   E94
+0  17   43   18     1.367   111.904   E94
+0  18   43   18     1.144   120.463   E94
+0  18   43   20     0.961   123.768   E94
+4  18   43   20     1.451    92.867   E94
+0  18   43   22     1.171   112.379   E94
+0  18   43   28     0.628   116.881   X94
+0  18   43   34     1.324   111.347   E94
+0  18   43   37     1.185   112.132   X94
+0  18   43   43     1.379   109.036   E94
+0  18   43   64     1.108   116.279   E94
+0  20   43   28     0.626   115.000   #E94
+3  22   43   22     0.209    57.032   E94
+0  25   43   28     0.468   118.274   X94
+0  28   43   28     0.477   112.596   X94
+0  28   43   34     0.810   110.000   #E94
+0  28   43   37     0.669   113.350   X94
+0  28   43   64     0.658   115.293   E94
+0   0   44    0     0.000    91.600   0:*-44-* MMFF94 DEF
+0  63   44   63     1.962    88.495   C94
+0  63   44   65     2.261    94.137   C94
+0  63   44   78     1.738    86.270   E94
+0  63   44   80     1.748    86.194   E94
+0  65   44   65     1.530   101.147   E94
+0  65   44   80     1.629    93.534   E94
+0  78   44   78     0.903   119.401   E94
+0   0   45    0     0.000   116.700   0:*-45-* MMFF94 DEF
+0   1   45   32     1.260   118.182   X94
+0   2   45   32     1.294   118.082   X94
+0   3   45   32     1.343   115.589   E94
+0   6   45   32     1.787   111.682   X94
+0   8   45   32     1.515   115.695   E94
+0   9   45   32     1.339   123.850   E94
+0  10   45   32     1.578   112.194   E94
+0  20   45   32     1.245   118.893   E94
+0  22   45   32     1.293   117.503   E94
+0  32   45   32     1.467   128.036   X94
+0  32   45   37     1.298   117.857   E94
+0  32   45   39     1.715   107.633   E94
+0  32   45   40     1.497   116.432   E94
+0  32   45   43     1.545   113.711   E94
+0  32   45   63     1.335   116.765   E94
+0  32   45   64     1.330   116.908   E94
+0  32   45   78     1.394   114.962   E94
+0   0   46    0     0.000   111.000   0:*-46-* MMFF94 DEF
+0   1   46    7     1.440   110.492   X94
+0   2   46    7     1.489   112.709   E94
+0   7   46    8     1.724   109.817   E94
+0   7   46   37     1.519   110.569   E94
+0   7   46   40     1.650   111.405   E94
+0   0   48    0     0.000   118.400   0:*-48-* MMFF94 DEF
+0   3   48   18     1.065   122.928   E94
+0  18   48   28     0.736   113.969   X94
+0   0   49    0     0.000   111.400   0:*-49-* MMFF94 DEF
+0  50   49   50     0.522   111.433   C94
+0   0   51    0     0.000   111.400   0:*-51-* MMFF94 DEF
+0   3   51   52     0.913   111.360   X94
+0   0   53    0     0.000   180.000   0:*-53-* MMFF94 DEF
+0   3   53   47     0.574   180.000   E94
+0   9   53   47     0.649   180.000   E94
+0   0   54    0     0.000   119.500   0:*-54-* MMFF94 DEF
+1   0   54    0     0.000   115.700   1:*-54-* MMFF94 DEF
+0   1   54    1     0.923   121.439   E94
+0   1   54    3     0.707   124.083   C94
+0   1   54   36     0.294   122.881   C94
+0   3   54    6     1.376   115.398   E94
+1   3   54    9     1.128   114.457   E94
+0   3   54   36     0.685   119.698   C94
+1   3   54   40     1.105   116.439   E94
+0   6   54   36     0.826   115.000   #E94
+0   9   54   40     1.195   123.403   E94
+0  36   54   36     0.300   113.943   C94
+0   0   55    0     0.000   120.800   0:*-55-* MMFF94 DEF
+0   1   55    1     0.951   119.946   E94
+0   1   55   36     0.307   126.448   C94
+0   1   55   37     1.032   117.035   E94
+0   1   55   57     0.751   120.606   C94
+0   1   55   80     0.972   121.082   E94
+0   2   55    3     1.041   116.994   E94
+0   2   55   36     0.621   120.000   #E94
+0   2   55   57     1.047   118.847   E94
+0   3   55    9     1.053   121.298   E94
+0   3   55   36     0.567   124.000   #E94
+0   3   55   57     0.953   123.573   E94
+0   3   55   62     1.041   122.163   E94
+0   6   55   36     0.833   114.000   #E94
+0   6   55   57     1.408   112.958   E94
+0   8   55   36     0.656   122.000   #E94
+0   8   55   57     1.259   113.209   E94
+0   9   55   57     1.001   126.373   E94
+0  18   55   36     0.578   125.000   #E94
+0  18   55   57     1.054   122.320   E94
+0  36   55   36     0.355   117.729   C94
+0  36   55   37     0.623   120.405   E94
+0  36   55   41     0.485   134.689   E94
+0  36   55   57     0.663   119.499   C94
+0  36   55   64     0.632   118.000   #E94
+0  36   55   80     0.684   115.880   E94
+0  37   55   57     1.110   115.816   E94
+0  41   55   57     0.911   126.801   E94
+0  57   55   62     1.054   123.366   E94
+0  57   55   64     1.026   119.465   E94
+0   0   56    0     0.000   119.100   0:*-56-* MMFF94 DEF
+0   1   56   36     0.472   123.585   C94
+0   1   56   57     0.774   119.267   C94
+0   2   56    9     1.181   116.311   E94
+0   2   56   36     0.582   124.037   E94
+0   2   56   57     1.029   118.607   E94
+0   3   56   36     0.585   121.521   E94
+0   3   56   57     0.885   126.567   E94
+0   8   56   36     0.785   111.009   E94
+0   8   56   57     1.288   110.357   E94
+0   9   56   36     0.683   120.258   E94
+0   9   56   57     1.186   115.661   E94
+0  36   56   36     0.450   117.534   C94
+0  36   56   37     0.602   120.000   #E94
+0  36   56   57     0.646   120.649   C94
+0  36   56   63     0.579   123.766   E94
+0  36   56   80     0.625   120.000   #E94
+0  37   56   57     1.058   115.912   E94
+0  57   56   63     1.019   118.915   E94
+0   0   57    0     0.000   120.900   0:*-57-* MMFF94 DEF
+1   0   57    0     0.000   118.100   1:*-57-* MMFF94 DEF
+0   1   57   55     1.017   117.865   E94
+1   3   57   55     1.085   115.034   E94
+0   5   57   55     0.674   116.747   C94
+0   6   57   55     1.279   119.257   E94
+1   9   57   55     0.980   128.143   E94
+0  12   57   55     1.058   118.327   E94
+0  15   57   55     0.983   123.646   E94
+0  25   57   55     0.790   122.889   E94
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+0  55   57   55     0.855   126.476   C94
+1  55   57   63     1.016   118.800   E94
+1  55   57   64     1.039   117.166   E94
+0  56   57   56     1.342   120.010   C94
+0   0   58    0     0.000   119.000   0:*-58-* MMFF94 DEF
+1   0   58    0     0.000   119.900   1:*-58-* MMFF94 DEF
+0   1   58   37     1.003   119.236   E94
+0   1   58   64     0.961   121.070   E94
+1   3   58   37     0.983   121.506   E94
+0   6   58   37     1.371   114.370   E94
+0  18   58   37     1.005   120.665   E94
+0  36   58   37     0.650   118.713   E94
+0  36   58   63     0.650   118.000   #E94
+0  36   58   64     0.620   120.051   E94
+0  37   58   37     0.996   122.710   E94
+1  37   58   37     1.036   118.260   E94
+0  37   58   63     1.087   116.989   E94
+0  37   58   64     1.061   117.942   E94
+0   0   59    0     0.000   105.600   0:*-59-* MMFF94 DEF
+0  63   59   63     1.273   106.313   C94
+0  63   59   65     1.750   107.755   C94
+0  63   59   78     1.713   101.179   E94
+0  63   59   80     1.599   105.341   E94
+0  65   59   65     1.754   107.683   E94
+0  65   59   78     1.644   107.142   E94
+0  65   59   82     1.864   103.624   E94
+0   0   61    0     0.000   180.000   0:*-61-* MMFF94 DEF
+0   1   61   60     0.475   180.000   E94
+0  37   61   42     0.536   180.000   E94
+0  37   61   60     0.484   180.000   E94
+0   0   62    0     0.000   108.300   0:*-62-* MMFF94 DEF
+0   1   62   18     1.316   109.273   X94
+0   2   62   23     0.817   105.542   X94
+0   3   62    3     1.318   106.821   E94
+0   3   62   18     1.311   111.144   E94
+0   3   62   55     1.528   102.414   E94
+0   9   62   18     1.515   107.660   E94
+0  18   62   37     1.229   114.618   E94
+0  18   62   41     1.366   108.722   E94
+0  18   62   63     1.427   106.284   E94
+0  18   62   64     1.317   110.366   E94
+0   0   63    0     0.000   123.300   0:*-63-* MMFF94 DEF
+1   0   63    0     0.000   124.300   1:*-63-* MMFF94 DEF
+0   1   63   39     0.935   121.832   E94
+0   1   63   44     0.902   122.101   E94
+0   1   63   59     1.175   115.253   E94
+0   1   63   64     0.737   131.378   E94
+0   1   63   66     0.865   127.610   E94
+1   2   63   39     1.027   117.864   E94
+1   2   63   59     0.987   127.524   E94
+1   2   63   64     0.730   133.818   E94
+1   2   63   66     0.828   132.383   E94
+1   3   63   39     0.900   125.395   E94
+1   3   63   44     0.935   120.481   E94
+1   3   63   59     1.158   117.219   E94
+1   3   63   64     0.766   130.065   E94
+1   3   63   66     0.950   123.049   E94
+1   4   63   44     0.848   126.602   E94
+1   4   63   59     1.211   114.804   E94
+1   4   63   64     0.795   127.817   E94
+0   5   63   39     0.617   121.127   C94
+0   5   63   44     0.393   126.141   C94
+0   5   63   59     0.784   114.076   C94
+0   5   63   64     0.577   131.721   C94
+0   5   63   66     0.643   125.134   C94
+0   5   63   78     0.482   130.000   #E94
+0   5   63   81     0.588   124.000   #E94
+0   6   63   39     1.234   120.509   E94
+0   6   63   59     1.564   113.514   E94
+0   6   63   64     0.951   131.301   E94
+1   9   63   39     1.068   121.741   E94
+1   9   63   44     0.963   124.598   E94
+1   9   63   64     0.804   134.237   E94
+1   9   63   66     0.912   133.020   E94
+0  10   63   39     1.084   120.356   E94
+0  10   63   44     1.112   115.732   E94
+0  10   63   59     1.307   116.218   E94
+0  10   63   64     0.867   128.750   E94
+0  10   63   66     0.981   127.617   E94
+0  12   63   39     1.111   114.439   E94
+0  12   63   44     1.035   119.321   E94
+0  12   63   64     0.838   126.226   E94
+0  12   63   66     0.980   122.280   E94
+0  15   63   39     1.064   117.958   E94
+0  15   63   44     0.952   125.654   E94
+0  15   63   64     0.813   129.284   E94
+0  15   63   66     0.962   124.490   E94
+0  18   63   44     1.110   116.077   E94
+0  18   63   64     0.740   135.028   E94
+0  19   63   39     0.647   132.369   E94
+0  19   63   64     0.517   141.986   E94
+0  25   63   39     0.597   139.439   E94
+0  25   63   66     0.776   122.699   E94
+0  35   63   59     1.351   124.475   E94
+0  35   63   64     0.808   145.098   E94
+0  37   63   39     1.011   132.046   C94
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+0  37   63   44     0.764   133.930   E94
+1  37   63   44     0.915   121.637   E94
+0  37   63   59     1.041   124.836   E94
+1  37   63   59     1.214   114.211   E94
+0  37   63   64     0.679   122.881   C94
+1  37   63   64     0.742   131.784   E94
+0  37   63   66     0.742   140.668   E94
+1  37   63   66     0.871   128.130   E94
+0  38   63   39     1.022   124.814   E94
+0  38   63   64     0.910   126.513   E94
+0  39   63   39     0.910   131.461   E94
+1  39   63   39     1.105   119.174   E94
+0  39   63   40     1.112   119.261   E94
+1  39   63   44     1.144   114.126   E94
+0  39   63   45     1.166   115.115   E94
+1  39   63   57     0.931   123.222   E94
+0  39   63   58     1.042   123.231   E94
+1  39   63   63     0.949   122.353   E94
+0  39   63   64     0.813   107.255   C94
+1  39   63   64     0.943   123.441   E94
+0  39   63   66     1.012   110.865   C94
+1  39   63   66     1.095   120.834   E94
+0  40   63   44     0.943   125.881   E94
+0  40   63   59     1.298   117.078   E94
+0  40   63   64     0.845   130.865   E94
+0  40   63   66     0.940   130.926   E94
+0  44   63   45     1.125   114.633   E94
+0  44   63   56     1.030   120.178   E94
+0  44   63   62     0.991   122.899   E94
+1  44   63   63     0.894   123.341   E94
+0  44   63   64     0.853   108.480   C94
+0  44   63   66     0.854   114.516   C94
+0  44   63   72     0.915   129.129   E94
+0  44   63   78     1.217   106.254   E94
+0  44   63   81     1.278   108.400   E94
+0  45   63   59     1.467   108.824   E94
+0  45   63   64     0.940   122.725   E94
+0  45   63   66     1.164   116.157   E94
+0  56   63   66     0.875   134.888   E94
+1  57   63   66     0.945   123.246   E94
+0  58   63   64     0.965   122.522   E94
+0  59   63   64     1.035   110.108   C94
+0  59   63   66     1.181   115.592   C94
+0  62   63   66     0.976   128.662   E94
+1  63   63   64     0.776   129.499   E94
+1  63   63   66     0.929   124.689   E94
+0  66   63   72     0.911   129.610   E94
+0   0   64    0     0.000   121.400   0:*-64-* MMFF94 DEF
+1   0   64    0     0.000   121.700   1:*-64-* MMFF94 DEF
+0   1   64   63     0.776   128.041   E94
+0   1   64   64     0.766   128.061   E94
+0   1   64   65     0.963   120.640   E94
+0   1   64   66     0.952   120.685   E94
+0   1   64   81     1.050   114.735   E94
+0   1   64   82     1.013   117.414   E94
+1   2   64   63     0.861   122.947   E94
+1   2   64   64     0.816   125.433   E94
+1   2   64   65     0.907   125.781   E94
+1   2   64   66     1.010   118.540   E94
+1   2   64   82     0.923   124.473   E94
+1   3   64   63     0.828   124.890   E94
+1   3   64   64     0.774   128.286   E94
+1   3   64   65     0.973   120.954   E94
+1   3   64   66     0.949   121.821   E94
+1   3   64   81     0.995   118.754   E94
+1   4   64   63     0.845   123.889   E94
+1   4   64   64     0.804   126.131   E94
+1   4   64   65     1.036   117.401   E94
+1   4   64   66     1.010   118.254   E94
+0   5   64   63     0.501   126.170   C94
+0   5   64   64     0.546   127.405   C94
+0   5   64   65     0.664   118.412   C94
+0   5   64   66     0.699   120.478   C94
+0   5   64   78     0.482   127.331   E94
+0   5   64   81     0.605   120.000   #E94
+0   5   64   82     0.597   122.000   #E94
+0   6   64   63     1.112   120.985   E94
+0   6   64   64     1.043   123.922   E94
+0   6   64   65     1.348   115.506   E94
+0   6   64   66     1.156   123.890   E94
+1   9   64   64     0.959   120.924   E94
+1   9   64   65     1.098   119.529   E94
+1   9   64   66     1.013   123.743   E94
+0  10   64   63     0.937   123.695   E94
+0  10   64   64     0.893   125.735   E94
+0  10   64   65     1.016   124.788   E94
+0  10   64   66     1.065   121.125   E94
+0  12   64   63     0.845   126.259   E94
+0  12   64   64     0.869   124.058   E94
+0  12   64   65     1.020   120.198   E94
+0  12   64   66     0.971   122.900   E94
+0  13   64   63     0.845   123.004   E94
+0  13   64   64     0.883   120.111   E94
+0  15   64   63     0.870   124.581   E94
+0  15   64   64     0.882   123.309   E94
+0  15   64   65     1.008   121.049   E94
+0  15   64   66     0.990   121.826   E94
+0  18   64   65     1.065   118.404   E94
+0  18   64   66     1.067   118.002   E94
+0  37   64   63     0.906   117.966   C94
+0  37   64   64     0.854   136.087   C94
+1  37   64   64     0.772   128.673   E94
+0  37   64   65     0.799   134.844   E94
+1  37   64   65     0.942   122.866   E94
+0  37   64   66     0.845   130.337   E94
+0  37   64   78     0.706   135.432   E94
+0  37   64   81     0.917   124.856   E94
+0  37   64   82     0.946   123.684   E94
+1  37   64   82     1.000   119.086   E94
+0  38   64   63     0.988   121.242   E94
+0  38   64   64     0.858   129.014   E94
+0  38   64   65     0.989   127.335   E94
+0  38   64   66     1.022   124.454   E94
+0  39   64   64     1.086   114.312   E94
+0  39   64   65     1.060   122.481   E94
+1  39   64   65     1.204   114.188   E94
+1  39   64   66     1.170   115.157   E94
+0  40   64   63     0.948   123.538   E94
+0  40   64   64     0.928   123.853   E94
+0  40   64   65     0.958   129.125   E94
+0  40   64   81     1.035   123.154   E94
+0  40   64   82     1.183   115.934   E94
+0  43   64   63     0.885   126.749   E94
+0  43   64   64     0.898   124.876   E94
+0  43   64   65     1.024   123.706   E94
+0  43   64   66     1.017   123.409   E94
+0  45   64   63     0.981   120.063   E94
+0  45   64   64     0.921   123.014   E94
+0  45   64   65     1.276   110.521   E94
+0  45   64   66     1.199   113.371   E94
+0  55   64   64     0.907   124.405   E94
+0  55   64   65     1.002   125.220   E94
+1  57   64   65     1.020   117.950   E94
+1  57   64   66     0.959   121.017   E94
+0  58   64   63     1.075   115.646   E94
+0  58   64   64     0.815   131.812   E94
+0  58   64   66     0.978   126.562   E94
+0  62   64   64     0.885   126.560   E94
+0  62   64   65     1.073   121.703   E94
+0  63   64   64     0.866   108.239   C94
+1  63   64   64     0.827   124.584   E94
+0  63   64   66     1.038   111.621   C94
+0  63   64   78     1.172   105.176   E94
+0  63   64   81     1.164   110.895   E94
+0  63   64   82     1.395   101.902   E94
+0  64   64   64     0.967   115.037   E94
+0  64   64   65     0.916   113.570   C94
+1  64   64   66     1.003   118.067   E94
+0  64   64   78     1.194   103.479   E94
+0  64   64   82     1.210   108.553   E94
+0  65   64   66     1.055   115.369   C94
+0  65   64   81     1.168   116.240   E94
+0  66   64   66     0.932   129.624   E94
+0   0   65    0     0.000   104.500   0:*-65-* MMFF94 DEF
+0  39   65   64     1.738   101.550   C94
+0  39   65   66     1.589   106.360   C94
+0  39   65   82     1.740   101.208   E94
+0  44   65   64     1.430   103.829   C94
+0  44   65   66     1.366   110.552   E94
+0  44   65   78     1.419   104.213   E94
+0  59   65   64     1.788   103.452   C94
+0  59   65   81     1.774   104.872   E94
+0   0   66    0     0.000   106.900   0:*-66-* MMFF94 DEF
+0  63   66   64     1.206   103.779   C94
+0  63   66   66     1.406   106.735   C94
+0  63   66   78     1.339   105.365   E94
+0  63   66   81     1.408   106.806   E94
+0  64   66   65     1.709   107.658   C94
+0  65   66   66     1.932   111.306   C94
+0   0   67    0     0.000   119.900   0:*-67-* MMFF94 DEF
+1   0   67    0     0.000   116.600   1:*-67-* MMFF94 DEF
+0   1   67    3     0.982   120.683   E94
+0   1   67    9     1.178   115.581   E94
+0   1   67   32     1.233   119.589   E94
+0   1   67   67     1.257   111.574   E94
+1   2   67   32     1.118   126.320   E94
+1   2   67   67     1.231   113.438   E94
+0   3   67   23     0.567   128.000   #E94
+0   3   67   32     1.290   120.945   E94
+1   3   67   37     1.122   113.631   E94
+1   9   67   30     1.142   118.899   E94
+0   9   67   32     1.325   125.531   E94
+1   9   67   37     1.186   115.979   E94
+0  23   67   32     0.805   120.000   #E94
+1  30   67   32     1.370   114.854   E94
+1  32   67   37     1.240   120.019   E94
+0  32   67   67     1.504   117.327   E94
+1  37   67   67     1.310   110.017   E94
+0   0   68    0     0.000   108.800   0:*-68-* MMFF94 DEF
+0   1   68    1     1.159   108.238   C94
+0   1   68   23     0.772   107.200   C94
+0   1   68   32     0.958   110.757   C94
+0  23   68   23     0.650   104.892   C94
+0  23   68   32     0.659   112.977   C94
+0   0   69    0     0.000   120.300   0:*-69-* MMFF94 DEF
+0  32   69   37     1.123   121.777   C94
+0  32   69   38     1.486   117.217   E94
+0  37   69   37     1.223   116.447   C94
+0  38   69   38     1.122   125.930   E94
+0  31   70   31     0.658   103.978   C94
+0   0   73    0     0.000   106.600   0:*-73-* MMFF94 DEF
+0   1   73   32     1.590   100.180   X94
+0   1   73   72     1.481    96.166   X94
+0  32   73   32     1.665   115.012   X94
+0  32   73   72     1.326   115.134   X94
+0   0   74    0     0.000   113.000   0:*-74-* MMFF94 DEF
+0   3   74    7     1.357   113.010   X94
+0   0   75    0     0.000    94.900   0:*-75-* MMFF94 DEF
+0   1   75    3     1.138    96.779   E94
+0   3   75   19     1.044    91.970   E94
+0   3   75   71     0.729    95.899   X94
+0   0   76    0     0.000   107.600   0:*-76-* MMFF94 DEF
+0  76   76   76     1.434   109.889   X94
+0  76   76   78     1.493   103.519   X94
+0  78   76   78     1.235   109.421   E94
+0   0   77    0     0.000   109.500   0:*-77-* MMFF94 DEF
+0  32   77   32     1.652   109.472   X94
+0   0   78    0     0.000   121.900   0:*-78-* MMFF94 DEF
+1   0   78    0     0.000   126.100   1:*-78-* MMFF94 DEF
+0   1   78   78     0.744   130.960   E94
+0   1   78   81     0.938   121.477   E94
+1   3   78   78     0.827   125.468   E94
+1   3   78   81     0.922   123.748   E94
+0   5   78   76     0.584   123.407   X94
+0   5   78   78     0.546   128.000   C94
+0   5   78   79     0.617   122.000   #E94
+0   5   78   81     0.542   109.881   C94
+1   9   78   78     0.863   129.501   E94
+1   9   78   81     0.991   125.857   E94
+0  37   78   76     0.770   137.282   E94
+0  37   78   78     0.803   128.249   E94
+0  37   78   81     0.864   128.714   E94
+0  38   78   78     0.844   130.617   E94
+0  38   78   81     1.023   123.532   E94
+0  39   78   64     0.734   138.714   E94
+0  39   78   78     1.202   109.426   E94
+0  40   78   76     0.930   130.150   E94
+0  40   78   78     0.778   135.746   E94
+0  40   78   81     1.058   121.251   E94
+0  44   78   63     0.677   141.902   E94
+0  44   78   64     0.663   142.589   E94
+0  44   78   66     0.816   134.701   E94
+0  44   78   78     1.089   111.702   E94
+0  45   78   76     1.199   114.467   E94
+0  45   78   78     0.915   125.050   E94
+0  45   78   81     1.216   112.926   E94
+0  59   78   64     0.963   128.471   E94
+0  59   78   65     1.097   128.375   E94
+0  59   78   78     1.443   105.916   E94
+0  63   78   64     0.942   117.779   E94
+0  64   78   65     0.835   131.530   E94
+0  64   78   78     1.038   111.834   E94
+0  66   78   78     1.030   118.376   E94
+0  76   78   76     1.245   113.179   X94
+0  76   78   78     1.159   111.900   E94
+0  78   78   78     1.336    99.459   E94
+0  78   78   81     1.302   105.130   C94
+0  79   78   81     1.217   114.792   E94
+0   0   79    0     0.000   103.400   0:*-79-* MMFF94 DEF
+0  78   79   81     1.569   102.043   E94
+0  79   79   81     1.625   104.857   E94
+0   0   80    0     0.000   121.900   0:*-80-* MMFF94 DEF
+1   0   80    0     0.000   128.200   1:*-80-* MMFF94 DEF
+0   1   80   81     0.864   127.147   E94
+1   3   80   81     0.886   128.181   E94
+0   5   80   81     0.651   125.682   C94
+0  18   80   81     1.032   120.869   E94
+0  41   80   81     0.909   125.057   E94
+0  44   80   55     0.918   127.755   E94
+0  44   80   81     1.184   112.411   E94
+0  55   80   59     1.254   120.263   E94
+0  55   80   81     0.991   127.612   E94
+0  56   80   81     1.003   126.038   E94
+0  59   80   81     1.439   112.030   E94
+0  81   80   81     1.205   108.609   C94
+0   0   81    0     0.000   119.500   0:*-81-* MMFF94 DEF
+0   1   81   63     0.996   120.129   E94
+0   1   81   64     0.978   119.970   E94
+0   1   81   78     0.879   126.535   E94
+0   1   81   79     1.144   116.113   E94
+0   1   81   80     0.895   126.324   E94
+1   2   81   78     0.927   125.080   E94
+1   2   81   80     0.895   128.399   E94
+1   9   81   78     1.015   124.270   E94
+1   9   81   80     1.106   120.028   E94
+0  36   81   64     0.522   130.295   E94
+0  36   81   66     0.583   128.738   E94
+0  36   81   78     0.578   124.658   C94
+0  36   81   80     0.575   124.787   C94
+0  37   81   64     0.929   122.408   E94
+1  37   81   64     0.983   119.722   E94
+0  37   81   65     1.184   114.158   E94
+1  37   81   65     1.281   110.477   E94
+1  37   81   78     0.884   126.208   E94
+1  37   81   80     0.940   123.333   E94
+0  63   81   64     1.115   114.945   E94
+0  64   81   65     1.075   122.099   E94
+0  64   81   80     1.143   113.176   E94
+0  66   81   80     1.067   122.250   E94
+0  78   81   80     0.957   110.556   C94
+0  79   81   80     1.379   107.936   E94
+0  32   82   59     1.666   114.660   E94
+0  32   82   64     1.075   131.706   E94
+0  32   82   65     1.238   129.293   E94
+0  59   82   64     1.563   105.660   E94
+0  64   82   65     1.281   112.955   E94
+$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffbndk.par	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,68 @@
+*
+*                Copyright (c) Merck and Co., Inc., 1994
+*                         All Rights Reserved
+*
+* MMFF BOND LENGTH, FORCE CONSTANT DEFAULT-RULE PARAMETERS
+* C94 =  Fitted to ab-initio derived core MMFF94 force constants
+* E94 =  Based on Herschberg/Laurie parameterization of Badger's rule
+*
+*   species r0-ref  kb-ref    Source
+    1    6   1.084   5.15     C94
+    1    7   1.001   7.35     C94
+    1    8   0.947   9.10     C94
+    1    9   0.92   10.6      E94
+    1   14   1.48    2.3      E94
+    1   15   1.415   2.95     C94
+    1   16   1.326   4.30     C94
+    1   17   1.28    4.3      E94
+    1   35   1.41    4.2      E94
+    1   53   1.60    2.7      E94
+    6    6   1.512   3.80     C94
+    6    7   1.439   4.55     C94
+    6    8   1.393   5.40     C94
+    6    9   1.353   6.20     C94
+    6   14   1.86    2.6      E94
+    6   15   1.84    2.7      E94
+    6   16   1.812   2.85     C94
+    6   17   1.781   2.75     C94
+    6   35   1.94    2.6      E94
+    6   53   2.16    1.4      E94
+    7    7   1.283   6.00     C94
+    7    8   1.333   5.90     C94
+    7    9   1.36    5.9      E94
+    7   14   1.74    3.7      E94
+    7   15   1.65    4.8      E94
+    7   16   1.674   3.75     C94
+    7   17   1.75    3.5      E94
+    7   35   1.90    2.9      E94
+    7   53   2.10    1.6      E94
+    8    8   1.48    3.6      E94
+    8    9   1.42    4.6      E94
+    8   14   1.63    5.2      E94
+    8   15   1.66    4.7      E94
+    8   16   1.470   9.90     C94
+    8   17   1.70    4.1      E94
+    8   35   1.85    3.4      E94
+    8   53   2.05    1.6      E94
+    9   14   1.57    6.4      E94
+    9   15   1.54    7.1      E94
+    9   16   1.55    6.9      E94
+   14   14   2.32    1.3      E94
+   14   15   2.25    1.5      E94
+   14   16   2.15    2.0      E94
+   14   17   2.02    3.1      E94
+   14   35   2.19    2.1      E94
+   14   53   2.44    1.5      E94
+   15   15   2.21    1.7      E94
+   15   16   2.10    2.4      E94
+   15   17   2.03    3.0      E94
+   15   35   2.21    2.0      E94
+   15   53   2.47    1.4      E94
+   16   16   2.052   2.50     C94
+   16   17   2.04    2.9      E94
+   16   35   2.24    1.9      E94
+   16   53   2.40    1.7      E94
+   17   17   1.99    3.5      E94
+   35   35   2.28    2.4      E94
+   53   53   2.67    1.6      E94
+$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffbond.par	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,507 @@
+*
+*                 Copyright (c) Merck and Co., Inc., 1994
+*                           All Rights Reserved
+*
+* MMFF BOND PARAMETERS- Rev: 26-OCT-94  Source: MMFF94
+* C94  = CORE MMFF94 parameter - obtained from ab initio data
+* X94  = EXTD MMFF94 parameter - fit to additional ab initio data
+* E94  = r0 from fit to X-ray data, kb from empirical rule
+* #C94 = r0 lies between C94 and E94 values, kb from empirical rule
+* #X94 = r0 lies between X94 and E94 values, kb from empirical rule
+* #E94  = r0 and k both from empirical rules
+*
+*   types       kb         r0    Source
+0   1    1     4.258     1.508   C94
+0   1    2     4.539     1.482   C94
+0   1    3     4.190     1.492   C94
+0   1    4     4.707     1.459   X94
+0   1    5     4.766     1.093   C94
+0   1    6     5.047     1.418   C94
+0   1    8     5.084     1.451   C94
+0   1    9     4.763     1.458   C94
+0   1   10     4.664     1.436   C94
+0   1   11     6.011     1.360   #C94
+0   1   12     2.974     1.773   C94
+0   1   13     2.529     1.949   E94
+0   1   14     1.706     2.090   E94
+0   1   15     2.893     1.805   C94
+0   1   17     2.841     1.813   X94
+0   1   18     3.258     1.772   X94
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+0  45   63     5.119     1.411   E94
+0  45   64     5.076     1.413   E94
+0  45   78     5.724     1.385   E94
+0  47   53    12.192     1.140   #X94
+0  49   50     6.812     0.991   C94
+0  51   52     7.100     0.987   X94
+0  55   57     7.227     1.319   C94
+0  55   62     3.977     1.374   E94
+0  55   64     5.529     1.393   E94
+0  55   80     7.500     1.324   E94
+0  56   57     4.137     1.383   C94
+0  56   63     5.900     1.378   E94
+0  56   80     6.470     1.357   E94
+1  57   63     5.400     1.426   E94
+1  57   64     5.135     1.438   E94
+0  58   63     6.794     1.346   E94
+0  58   64     6.164     1.368   E94
+0  59   63     5.787     1.360   C94
+0  59   65     4.756     1.388   C94
+0  59   78     6.127     1.364   E94
+0  59   80     7.064     1.332   E94
+0  59   82     3.855     1.431   E94
+0  60   61    15.749     1.170   #X94
+0  62   63     6.947     1.341   E94
+0  62   64     6.273     1.364   E94
+1  63   63     5.729     1.412   E94
+0  63   64     7.118     1.377   C94
+0  63   66     8.326     1.313   C94
+0  63   72     4.503     1.679   E94
+0  63   78     7.434     1.352   E94
+0  63   81     7.778     1.316   E94
+0  64   64     4.313     1.418   C94
+1  64   64     4.926     1.448   E94
+0  64   65     8.258     1.335   C94
+0  64   66     4.456     1.369   C94
+0  64   78     5.492     1.422   E94
+0  64   81     5.824     1.381   E94
+0  64   82     6.794     1.346   E94
+0  65   66     7.243     1.323   C94
+0  65   78     8.447     1.298   E94
+0  65   81     5.223     1.313   E94
+0  65   82     5.622     1.297   E94
+0  66   66     3.874     1.368   C94
+0  66   78     6.385     1.360   E94
+0  66   81     3.960     1.375   E94
+0  67   67     6.085     1.280   E94
+0  71   75     2.852     1.423   X94
+0  72   73     2.628     2.035   X94
+0  76   76     4.286     1.357   X94
+0  76   78     6.824     1.345   X94
+0  78   78     5.573     1.374   C94
+0  78   79     8.890     1.287   E94
+0  78   81     5.046     1.381   C94
+0  79   79     6.408     1.269   E94
+0  79   81     4.305     1.356   E94
+0  80   81     8.237     1.335   C94
+$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffchg.par	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,512 @@
+*
+*                Copyright (c) Merck and Co., Inc., 1994
+*                         All Rights Reserved
+*
+* MMFF BOND-CHARGE INCREMENTS - Rev: 26-OCT-94  Source: MMFF94
+* C94  - CORE MMFF94 parameter, obtained from fit to dipole moments
+* #C94 - CORE MMFF94 parameter, either fixed or adjusted to fit 
+*        HF/6-31G* interaction energies
+* X94  - EXTD MMFF94 parameter, obtained from fit to dipole moments
+* #X94 - EXTD MMFF94 parameter, fixed in the fit to dipole moments
+* E94  - derived from partial bond charge increments (empirical rule)
+*
+*  types       bci     Source
+0   1    1    0.0000   #C94
+0   1    2   -0.1382   C94
+0   1    3   -0.0610   #C94
+0   1    4   -0.2000   #X94
+0   1    5    0.0000   #C94
+0   1    6   -0.2800   #C94
+0   1    8   -0.2700   #C94
+0   1    9   -0.2460   #C94
+0   1   10   -0.3001   C94
+0   1   11   -0.3400   #C94
+0   1   12   -0.2900   #C94
+0   1   13   -0.2300   #X94
+0   1   14   -0.1900   #X94
+0   1   15   -0.2300   #C94
+0   1   17   -0.1935   X94
+0   1   18   -0.1052   X94
+0   1   19    0.0805   X94
+0   1   20    0.0000   #C94
+0   1   22   -0.0950   E94
+0   1   25    0.0000   #X94
+0   1   26   -0.1669   X94
+0   1   34   -0.5030   C94
+0   1   35   -0.4274   X94
+0   1   37   -0.1435   C94
+0   1   39   -0.2556   C94
+0   1   40   -0.3691   C94
+0   1   41    0.1060   #C94
+0   1   43   -0.3557   X94
+0   1   45   -0.2402   X94
+0   1   46   -0.3332   X94
+0   1   54   -0.3461   C94
+0   1   55   -0.4895   C94
+0   1   56   -0.3276   C94
+0   1   57   -0.1050   E94
+0   1   58   -0.4880   E94
+0   1   61   -0.2657   X94
+0   1   62   -0.2000   #X94
+0   1   63   -0.1800   E94
+0   1   64   -0.1810   E94
+0   1   67   -0.0990   E94
+0   1   68   -0.2560   #C94
+0   1   72   -0.5500   #X94
+0   1   73   -0.0877   X94
+0   1   75   -0.2550   E94
+0   1   78   -0.1680   E94
+0   1   80   -0.1440   E94
+0   1   81   -0.5140   E94
+0   2    2    0.0000   #C94
+1   2    2    0.0000   #C94
+1   2    3   -0.0144   C94
+0   2    4   -0.0650   E94
+1   2    4   -0.0650   E94
+0   2    5    0.1500   #C94
+0   2    6   -0.0767   C94
+1   2    9   -0.1710   E94
+0   2   10   -0.1090   E94
+0   2   11   -0.1495   X94
+0   2   12   -0.1400   #X94
+0   2   13   -0.1100   #X94
+0   2   14   -0.0900   #X94
+0   2   15   -0.1010   E94
+0   2   17   -0.0560   E94
+0   2   18    0.0170   E94
+0   2   19    0.2290   E94
+0   2   20    0.1160   E94
+0   2   22    0.0400   E94
+0   2   25    0.1470   E94
+0   2   30   -0.0310   E94
+0   2   34   -0.3560   E94
+0   2   35   -0.3500   #X94
+1   2   37    0.0284   C94
+1   2   39    0.0310   E94
+0   2   40   -0.1000   #C94
+0   2   41    0.2500   #C94
+0   2   43   -0.1910   E94
+0   2   45   -0.2044   X94
+0   2   46   -0.2940   E94
+0   2   55   -0.3410   E94
+0   2   56   -0.3030   E94
+0   2   62   -0.0500   #X94
+1   2   63   -0.0450   E94
+1   2   64   -0.0460   E94
+1   2   67    0.0360   E94
+0   2   72   -0.4500   #X94
+1   2   81   -0.3790   E94
+1   3    3    0.0000   #C94
+1   3    4   -0.1050   E94
+0   3    5    0.0600   #C94
+0   3    6   -0.1500   #C94
+0   3    7   -0.5700   #C94
+0   3    9   -0.4500   #C94
+1   3    9   -0.2110   E94
+0   3   10   -0.0600   C94
+0   3   11   -0.2220   E94
+0   3   12   -0.2090   E94
+0   3   15   -0.1410   E94
+0   3   16   -0.3800   #X94
+0   3   17   -0.0960   E94
+0   3   18   -0.0230   E94
+0   3   20    0.0530   #C94
+0   3   22    0.0000   E94
+0   3   25    0.1070   E94
+1   3   30   -0.0710   E94
+0   3   35   -0.3610   E94
+1   3   37    0.0862   C94
+1   3   39   -0.0090   E94
+0   3   40   -0.0500   #C94
+0   3   41    0.1470   E94
+0   3   43   -0.2363   X94
+0   3   45   -0.1650   E94
+0   3   48   -0.4300   E94
+0   3   51   -0.9500   #X94
+0   3   53   -0.0134   X94
+0   3   54   -0.4000   #C94
+1   3   54   -0.3290   E94
+0   3   55   -0.3810   E94
+0   3   56   -0.3430   E94
+1   3   57   -0.0100   E94
+1   3   58   -0.3930   E94
+0   3   62   -0.0300   E94
+1   3   63   -0.0850   E94
+1   3   64   -0.0860   E94
+0   3   67   -0.0040   E94
+0   3   74   -0.3190   X94
+0   3   75   -0.2474   X94
+1   3   78   -0.0730   E94
+1   3   80   -0.0490   E94
+0   4    5    0.1770   E94
+0   4    6   -0.0430   E94
+0   4    7   -0.4870   E94
+0   4    9   -0.3000   E94
+1   4    9   -0.1060   E94
+0   4   10   -0.0440   E94
+0   4   15   -0.0360   E94
+0   4   20    0.1810   E94
+0   4   22    0.1050   E94
+0   4   30    0.0340   E94
+1   4   37    0.0730   E94
+0   4   40   -0.0640   E94
+0   4   42   -0.5571   X94
+0   4   43   -0.1260   E94
+1   4   63    0.0200   E94
+1   4   64    0.0190   E94
+0   5   19    0.2000   #X94
+0   5   20    0.0000   #C94
+0   5   22   -0.1000   #C94
+0   5   30   -0.1500   #C94
+0   5   37   -0.1500   #C94
+0   5   41    0.2203   C94
+0   5   57   -0.1500   #C94
+0   5   63   -0.1500   #C94
+0   5   64   -0.1500   #C94
+0   5   78   -0.1500   #C94
+0   5   80   -0.1500   #C94
+0   6    6    0.0000   #C94
+0   6    8   -0.1000   #C94
+0   6    9   -0.0630   E94
+0   6   10    0.0355   C94
+0   6   15    0.0070   E94
+0   6   17    0.0520   E94
+0   6   18    0.1837   X94
+0   6   19    0.2974   X94
+0   6   20    0.2579   C94
+0   6   21    0.4000   #C94
+0   6   22    0.1480   E94
+0   6   24    0.5000   #C94
+0   6   25    0.2712   X94
+0   6   26    0.1010   E94
+0   6   29    0.4500   #C94
+0   6   30    0.0770   E94
+0   6   33    0.5000   #X94
+0   6   37    0.0825   C94
+0   6   39    0.1390   E94
+0   6   40   -0.0210   E94
+0   6   41    0.2950   E94
+0   6   43   -0.0830   E94
+0   6   45   -0.0090   X94
+0   6   54   -0.1810   E94
+0   6   55   -0.2330   E94
+0   6   57    0.1380   E94
+0   6   58   -0.2450   E94
+0   6   63    0.0630   E94
+0   6   64    0.0620   E94
+0   7   17    0.5000   #X94
+0   7   46    0.1618   X94
+0   7   74    0.5000   #X94
+0   8    8    0.0000   #C94
+0   8    9   -0.0530   E94
+0   8   10    0.0090   E94
+0   8   12   -0.0510   E94
+0   8   15    0.0170   E94
+0   8   17    0.0620   E94
+0   8   19    0.3470   E94
+0   8   20    0.2096   C94
+0   8   22    0.1580   E94
+0   8   23    0.3600   #C94
+0   8   25    0.2679   X94
+0   8   26    0.1110   E94
+0   8   34   -0.2380   E94
+0   8   39    0.1490   E94
+0   8   40   -0.0110   E94
+0   8   43   -0.0730   E94
+0   8   45   -0.0070   E94
+0   8   46   -0.1760   E94
+0   8   55   -0.2230   E94
+0   8   56   -0.1850   E94
+0   9    9    0.0000   #C94
+0   9   10    0.0620   E94
+0   9   12    0.0020   E94
+0   9   15    0.0700   E94
+0   9   18    0.1880   E94
+0   9   19    0.4000   E94
+0   9   20    0.2870   E94
+0   9   25    0.3180   E94
+0   9   27    0.4000   #C94
+0   9   34   -0.1850   E94
+0   9   35   -0.1500   E94
+1   9   37    0.1790   E94
+1   9   39    0.2020   E94
+0   9   40    0.0420   E94
+0   9   41    0.3580   E94
+0   9   45    0.0460   E94
+0   9   53    0.3179   X94
+0   9   54   -0.1180   E94
+0   9   55   -0.1700   E94
+0   9   56   -0.1320   E94
+1   9   57    0.2010   E94
+0   9   62    0.1810   E94
+1   9   63    0.1260   E94
+1   9   64    0.1250   E94
+0   9   67    0.2070   E94
+1   9   78    0.1380   E94
+1   9   81   -0.2080   E94
+0  10   10    0.0000   #C94
+0  10   13    0.0060   E94
+0  10   14    0.0360   E94
+0  10   15    0.0080   E94
+0  10   17    0.0530   E94
+0  10   20    0.2250   E94
+0  10   22    0.1490   E94
+0  10   25    0.2560   E94
+0  10   26    0.1020   E94
+0  10   28    0.3700   #C94
+0  10   34   -0.2470   E94
+0  10   35   -0.2120   E94
+0  10   37    0.1170   E94
+0  10   39    0.1400   E94
+0  10   40   -0.0200   E94
+0  10   41    0.2960   E94
+0  10   45   -0.0160   E94
+0  10   63    0.0640   E94
+0  10   64    0.0630   E94
+0  11   20    0.2980   E94
+0  11   22    0.2317   X94
+0  11   25    0.3290   E94
+0  11   26    0.1750   E94
+0  11   37    0.1900   E94
+0  11   40    0.0530   E94
+0  12   15    0.0680   E94
+0  12   18    0.1860   E94
+0  12   19    0.3701   X94
+0  12   20    0.2900   #C94
+0  12   22    0.2273   X94
+0  12   25    0.3160   E94
+0  12   26    0.2112   X94
+0  12   37    0.1770   E94
+0  12   40    0.0400   E94
+0  12   57    0.1990   E94
+0  12   63    0.1240   E94
+0  12   64    0.1230   E94
+0  13   20    0.2190   E94
+0  13   22    0.1430   E94
+0  13   37    0.1110   E94
+0  13   64    0.0570   E94
+0  14   20    0.1890   E94
+0  14   37    0.0810   E94
+0  15   15    0.0000   #C94
+0  15   18    0.1180   E94
+0  15   19    0.3300   E94
+0  15   20    0.2170   E94
+0  15   22    0.1410   E94
+0  15   25    0.2480   E94
+0  15   26    0.0940   E94
+0  15   30    0.0700   E94
+0  15   37    0.1015   C94
+0  15   40   -0.0280   E94
+0  15   43   -0.0900   E94
+0  15   57    0.1310   E94
+0  15   63    0.0560   E94
+0  15   64    0.0550   E94
+0  15   71    0.1800   #C94
+0  16   16    0.0000   #C94
+0  17   17    0.0000   #X94
+0  17   20    0.1720   E94
+0  17   22    0.0960   E94
+0  17   37    0.0640   E94
+0  17   43   -0.1350   E94
+0  18   18    0.0000   #X94
+0  18   20    0.0990   E94
+0  18   22    0.0230   E94
+0  18   32   -0.6500   #X94
+0  18   37   -0.0090   E94
+0  18   39    0.0140   E94
+0  18   43   -0.1380   X94
+0  18   48   -0.5895   X94
+0  18   55   -0.3580   E94
+0  18   58   -0.3700   E94
+0  18   62    0.2099   X94
+0  18   63   -0.0620   E94
+0  18   64   -0.0630   E94
+0  18   80   -0.0260   E94
+0  19   19    0.0000   #X94
+0  19   20   -0.1130   E94
+0  19   37   -0.2210   E94
+0  19   40   -0.3580   E94
+0  19   63   -0.2740   E94
+0  19   75   -0.3490   E94
+0  20   20    0.0000   #C94
+0  20   22   -0.0760   E94
+0  20   25    0.0310   E94
+0  20   26   -0.1230   E94
+0  20   30   -0.1380   #C94
+0  20   34   -0.4720   E94
+0  20   37   -0.1080   E94
+0  20   40   -0.2450   E94
+0  20   41    0.0710   E94
+0  20   43   -0.3070   E94
+0  20   45   -0.2410   E94
+0  22   22    0.0000   #C94
+0  22   30   -0.0710   E94
+0  22   34   -0.3960   E94
+0  22   37   -0.0320   E94
+0  22   40   -0.1690   E94
+0  22   41    0.1470   E94
+0  22   43   -0.2310   E94
+0  22   45   -0.1650   E94
+0  23   39   -0.2700   #C94
+0  23   62   -0.4000   #X94
+0  23   67   -0.2920   E94
+0  23   68   -0.3600   #C94
+0  25   25    0.0000   #X94
+0  25   32   -0.7000   #X94
+0  25   37   -0.1390   E94
+0  25   39   -0.1160   E94
+0  25   40   -0.2760   E94
+0  25   43   -0.3380   E94
+0  25   57   -0.1170   E94
+0  25   63   -0.1920   E94
+0  25   71   -0.0362   X94
+0  25   72   -0.6773   X94
+0  26   26    0.0000   #X94
+0  26   34   -0.3490   E94
+0  26   37    0.0150   E94
+0  26   40   -0.1220   E94
+0  26   71    0.0960   X94
+0  28   40   -0.4000   #C94
+0  28   43   -0.4200   #X94
+0  28   48   -0.4000   #X94
+0  30   30    0.0000   #C94
+0  30   40   -0.0980   E94
+1  30   67    0.0670   E94
+0  31   70   -0.4300   #C94
+0  32   41    0.6500   #C94
+0  32   45    0.5200   #X94
+0  32   67    0.6330   E94
+0  32   68    0.7500   #C94
+0  32   69    0.7500   #C94
+0  32   73    0.3500   #X94
+0  32   77    0.4500   #X94
+0  32   82    0.6330   E94
+0  34   36    0.4500   #C94
+0  34   37    0.3640   E94
+0  34   43    0.1650   E94
+0  35   37    0.3290   E94
+0  35   63    0.2760   E94
+0  36   54   -0.4000   #C94
+0  36   55   -0.4500   #C94
+0  36   56   -0.4500   #C94
+0  36   58   -0.4570   E94
+4  36   58   -0.4500   #C94
+0  36   81   -0.4500   #C94
+0  37   37    0.0000   #C94
+1  37   37    0.0000   #C94
+0  37   38   -0.3100   #C94
+0  37   39    0.0230   E94
+1  37   39    0.0230   E94
+0  37   40   -0.1000   #C94
+0  37   41    0.1790   E94
+0  37   43   -0.1990   E94
+0  37   45   -0.1330   E94
+0  37   46   -0.3020   E94
+0  37   55   -0.3490   E94
+0  37   56   -0.3110   E94
+1  37   57    0.0220   E94
+0  37   58   -0.3610   E94
+1  37   58   -0.3610   E94
+4  37   58   -0.3500   #C94
+0  37   61   -0.1380   E94
+0  37   62    0.0020   E94
+0  37   63    0.0000   #C94
+1  37   63   -0.0530   E94
+0  37   64    0.0000   #C94
+1  37   64   -0.0540   E94
+1  37   67    0.0280   E94
+0  37   69   -0.0895   C94
+0  37   78   -0.0410   E94
+0  37   81   -0.3870   E94
+1  37   81   -0.3870   E94
+0  38   38    0.0000   #C94
+0  38   63    0.2570   E94
+0  38   64    0.2560   E94
+0  38   69    0.3380   E94
+0  38   78    0.2690   E94
+1  39   39    0.0000   #C94
+0  39   40   -0.1600   E94
+0  39   45   -0.1560   E94
+0  39   63   -0.1516   C94
+1  39   63   -0.0760   E94
+0  39   64   -0.0770   E94
+1  39   64   -0.0770   E94
+0  39   65   -0.4180   C94
+0  39   78   -0.0640   E94
+0  40   40    0.0000   #C94
+0  40   45    0.0040   E94
+0  40   46   -0.1650   E94
+0  40   54   -0.1600   E94
+0  40   63    0.0840   E94
+0  40   64    0.0830   E94
+0  40   78    0.0960   E94
+0  41   41    0.0000   #C94
+0  41   55   -0.5280   E94
+0  41   62   -0.1770   E94
+0  41   72   -0.5000   #X94
+0  41   80   -0.1960   E94
+0  42   61    0.4920   E94
+0  43   43    0.0000   #X94
+0  43   45    0.0660   E94
+0  43   64    0.1450   E94
+0  44   63    0.0400   #C94
+0  44   65   -0.2207   C94
+0  44   78    0.0690   E94
+0  44   80    0.0930   E94
+0  45   63    0.0800   E94
+0  45   64    0.0790   E94
+0  45   78    0.0920   E94
+0  47   53    0.3700   #X94
+0  49   50    0.5673   C94
+0  51   52    0.5000   #X94
+0  55   57    0.3544   C94
+0  55   62    0.3510   E94
+0  55   64    0.2950   E94
+0  55   80    0.3320   E94
+0  56   57    0.4000   #C94
+0  56   63    0.2580   E94
+0  56   80    0.2700   E94
+4  57   58   -0.4000   #C94
+1  57   63   -0.0750   E94
+1  57   64   -0.0760   E94
+0  58   63    0.3080   E94
+0  58   64    0.3070   E94
+0  59   63    0.1400   #C94
+0  59   65   -0.1209   C94
+0  59   78    0.1690   E94
+0  59   80    0.1930   E94
+0  59   82    0.2380   E94
+0  60   61    0.3700   #X94
+0  62   63   -0.0550   E94
+0  62   64   -0.0560   E94
+0  63   63    0.0000   #C94
+1  63   63    0.0000   #C94
+0  63   64    0.0000   #C94
+0  63   66   -0.3381   C94
+0  63   72   -0.4000   E94
+0  63   78    0.0120   E94
+0  63   81   -0.3340   E94
+0  64   64    0.0000   #C94
+0  64   65   -0.2888   C94
+0  64   66   -0.2272   C94
+0  64   78    0.0130   E94
+0  64   81   -0.3330   E94
+0  64   82    0.0820   E94
+0  65   66    0.0000   #C94
+0  65   78    0.3070   E94
+0  65   81   -0.0390   E94
+0  65   82    0.3760   E94
+0  66   66    0.0000   #C94
+0  66   78    0.2990   E94
+0  66   81   -0.0470   E94
+0  71   75   -0.0958   X94
+0  72   73    0.4500   #X94
+0  76   76    0.0000   #X94
+0  76   78    0.4000   #X94
+0  78   78    0.0000   #C94
+1  78   78    0.0000   #C94
+0  78   79   -0.3030   E94
+0  78   81   -0.3500   #C94
+0  79   81   -0.0430   E94
+0  80   81   -0.4000   #C94
+$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffdef.par	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,192 @@
+*
+*                Copyright (c) Merck and Co., Inc., 1994
+*                         All Rights Reserved
+*
+*      PRIMARY
+* MMFF   MMFF                                 
+*SYMBOL  TYPE   DEFAULT TYPES       DEFINITION           
+*
+   CR      1    1    1    1    0    ALKYL CARBON           
+   C=C     2    2    2    1    0    VINYLIC                
+*  CSP2    2    2    2    1    0    GENERIC CSP2           
+*  CGD     2    2    2    1    0    GUANIDINE CARBON       
+   C=O     3    3    3    1    0    GENERAL CARBONYL C     
+*  C=N     3    3    3    1    0    C=N                    
+*  C=OR    3    3    3    1    0    KETONE OR ALDEHYDE CO  
+*  C=ON    3    3    3    1    0    AMIDE CARBONYL         
+*  COO     3    3    3    1    0    CARBOXYLIC ACID OF EST 
+*  COON    3    3    3    1    0    CARBAMATE CARBONYL     
+*  COOO    3    3    3    1    0    CARBONIC ACID OR ESTER 
+*  C=OS    3    3    3    1    0    THIOESTER, C=O         
+*  C=S     3    3    3    1    0    THIOESTER, C=S         
+*  C=SN    3    3    3    1    0    THIOAMIDE              
+*  CSO2    3    3    3    1    0    CARBON IN >C=SO2       
+   CSP     4    4    4    1    0    ACETYLENIC C           
+*  =C=     4    4    4    1    0    ALLENIC C              
+   HC      5    5    5    5    0    H-C                    
+*  HSI     5    5    5    5    0    H-SI                   
+*  HP      5    5    5    5    0    H-P                    
+   OR      6    6    6    6    0    O-CSP3                 
+*  OH2     6    6    6    6    0    OXYGEN IN H2O          
+*  OC=O    6    6    6    6    0    ESTER OR ACID -O-      
+*  OC=C    6    6    6    6    0    ENOL OR PHEMOLIC O     
+*  OC=N    6    6    6    6    0    OXYGEN IN -O-C=N MOIETY
+*  OSO3    6    6    6    6    0    DIVALENT O IN SULFATE
+*  OSO2    6    6    6    6    0    DIVALENT O IN SULFITE
+*  OSO     6    6    6    6    0    PAIR OF DIVALENT O ON S
+*  -OS     6    6    6    6    0    OTHER DIVALENT O ON S
+*  OPO3    6    6    6    6    0    DIVALENT O IN PHOSPHATE
+*  OPO2    6    6    6    6    0    DIVALENT O IN PHOSPHITE
+*  OPO     6    6    6    6    0    PAIR OF DIVALENT O ON P
+*  -OP     6    6    6    6    0    OTHER DIVALENT O ON P
+*  -O-     6    6    6    6    0    GENERAL DIVALENT OX    
+   O=C     7    7    7    6    0    O=C, GENERIC           
+*  O=CN    7    7    7    6    0    O=C IN AMIDES          
+*  O=CR    7    7    7    6    0    O=C IN KET, ALD        
+*  O=CO    7    7    7    6    0    O=C IN ACIDS, ESTERS   
+*  O=S     7    7    7    6    0    TERMINAL O SULFOXIDES  
+*  O=N     7    7    7    6    0    NITROSO-GROUP OXYGEN   
+   NR      8    8    8    8    0    AMINE N                
+   N=C     9    9    9    8    0    N=C, IMINES            
+*  N=N     9    9    9    8    0    N=N, AZO COMPOUNDS     
+   NC=O   10   10   10    8    0    N-C=O, AMIDES          
+*  NC=S   10   10   10    8    0    N-C=S (DELOC LP)       
+*  NN=C   10   10   10    8    0    N-N=C (DELOC LP)       
+*  NN=N   10   10   10    8    0    N-N=N (DELOC LP)       
+   F      11   11   11   11    0    FLUORINE               
+   CL     12   12   12   12    0    CHLORINE               
+   BR     13   13   13   13    0    BROMINE                
+   I      14   14   14   14    0    IODINE                 
+   S      15   15   15   15    0    THIOL, SULFIDE         
+   S=C    16   16   16   15    0    S DOUBLY BONDED TO C   
+   S=O    17   17   17   15    0    SULFOXIDE S            
+   SO2    18   18   18   15    0    SULFONE S              
+*  SO2N   18   18   18   15    0    SULFONAMIDE S          
+*  SO3    18   18   18   15    0    SULFONATE S            
+*  =SO2   18   18   18   15    0    OXYGENATED SULFONE S   
+*  SNO    18   18   18   15    0    NITROGEN ANALOG OF SO2 
+   SI     19   19   19   19    0    SILICON                
+   CR4R   20   20    1    1    0    C IN CYCLOBUTYL        
+   HOR    21   21   21    5    0    H-O, ALCOHOLS          
+*  HO     21   21   21    5    0    GENERAL H ON O         
+   CR3R   22   22   22    1    0    C IN CYCLOPROPLY       
+   HNR    23   23   23    5    0    H-N, AMINES            
+*  H3N    23   23   23    5    0    H, AMMONIA             
+*  HPYL   23   23   23    5    0    H-N IN PYRROLE         
+*  HN     23   23   23    5    0    GENERAL H-N            
+   HOCO   24   24   24    5    0    H-O, ACIDS             
+*  HOP    24   21   21    5    0    H-O-P, PHOS ACIDS      
+   PO4    25   25   25   25    0    PHOSPHODIESTER         
+*  PO3    25   25   25   25    0    TETRACRD P, 3 OXYGENS  
+*  PO2    25   25   25   25    0    TETRACRD P, 2 OXYGENS  
+*  PO     25   25   25   25    0    TETRACRD P, 2 OXYGENS  
+*  PTET   25   25   25   25    0    GENERAL TETRACRD P     
+   P      26   26   26   25    0    TRICOORDINATE P        
+   HN=C   27   27   28    5    0    IMINE N-H              
+*  HN=N   27   27   28    5    0    AZO N-H                
+   HNCO   28   28   28    5    0    H-N, AMIDES            
+*  HNCC   28   28   28    5    0    H-N, ENAMINES          
+*  HNCS   28   28   28    5    0    H-N, THIOAMIDES        
+*  HNCN   28   28   28    5    0    H-N, HN-C=N            
+*  HNNC   28   28   28    5    0    H-N, HN-N=C            
+*  HNNN   28   28   28    5    0    H-N, HN-N=N            
+*  HSP2   28   28   28    5    0    GENERAL H ON SP2 N     
+   HOCC   29   29   29    5    0    H-O, ENOLS, PHENOLS    
+*  HOCN   29   29   29    5    0    H-O IN HO-C=N          
+   CE4R   30   30    2    1    0    C=C IN 4-RING          
+   HOH    31   31   31   31    0    H-OH                   
+   O2CM   32   32    7    6    0    O, CARBOXYLATE ANION   
+*  OXN    32   32    7    6    0    OXIDE ON NITROHGEN     
+*  O2N    32   32    7    6    0    NITRO-GROUP OXYGEN     
+*  O2NO   32   32    7    6    0    NITRO-GROUP IN NITRATE 
+*  O3N    32   32    7    6    0    NITRATE ANION OXYGEN   
+*  O-S    32   32    7    6    0    SINGLE TERM O ON TET S 
+*  O2S    32   32    7    6    0    SULFONES, SULFONAMIDES 
+*  O3S    32   32    7    6    0    SULFONATES, TERM OX    
+*  O4S    32   32    7    6    0    SO4(3-)                
+*  OSMS   32   32    7    6    0    THIOSULFINATE O (-1/2) 
+*  OP     32   32    7    6    0    TERMINAL O, O-P        
+*  O2P    32   32    7    6    0    TERMINAL O, O2P GROUP  
+*  O3P    32   32    7    6    0    TERMINAL O, O3P GROUP  
+*  O4P    32   32    7    6    0    TERMINAL O, PO4(-3)    
+*  O4CL   32   32    7    6    0    TERMINAL O IN CLO4(-)  
+   HOS    33   33   21    5    0    H-O-S, SULF ACIDS      
+   NR+    34   34    8    8    0    N+, QUATERNARY N       
+   OM     35   35    6    6    0    OXIDE OXYGEN ON SP3 C  
+*  OM2    35   35    6    6    0    OXIDE OXYGEN ON SP2 C  
+   HNR+   36   36   36    5    0    H-N+                   
+*  HNN+   36   36   36    5    0    H ON IMIDAZOLIUM N     
+*  HNC+   36   36   36    5    0    H ON PROTONATED N+=C-N 
+*  HGD+   36   36   36    5    0    H ON GUANIDINIUM N     
+   CB     37   37    2    1    0    AROMATIC C             
+   NPYD   38   38    9    8    0    AROMATIC N, PYRIDINE   
+   NPYL   39   39   10    8    0    AROMATIC N, PYRROLE    
+   NC=C   40   40   10    8    0    N-C=C (DELOC LP)       
+*  NC=N   40   40   10    8    0    N-C=N (DELOC LP)       
+   CO2M   41   41    3    1    0    C IN CO2- ANION        
+*  CS2M   41   41    3    1    0    THIOCARBOXYLATE C      
+   NSP    42   42   42    8    0    N TRIPLE BONDED        
+   NSO2   43   43   10    8    0    N, SULFONAMIDES        
+   STHI   44   44   16   15    0    S IN THIOPHENE         
+   NO2    45   45   10    8    0    NITRO GROUP N          
+*  NO3    45   45   10    8    0    NITRATE GROUP N        
+   N=O    46   46    9    8    0    NITROSO GROUP N        
+   NAZT   47   47   42    8    0    TERMINAL N, AZIDE      
+   NSO    48   48    9    8    0    DIVAL. N IN S(N)(O) GP 
+   O+     49   49    6    6    0    OXONIUM (TRICOORD) O   
+   HO+    50   50   21    5    0    H ON OXONIUM OXYGEN    
+   O=+    51   51    7    6    0    OXENIUM OXYGEN+        
+   HO=+   52   52   21    5    0    H ON OXENIUM O+        
+   =N=    53   53   42    8    0    N TWICE DOUBLE BONDED  
+   N+=C   54   54    9    8    0    IMINIUM NITROGEN       
+*  N+=N   54   54    9    8    0    AZONIUM NITROGEN       
+   NCN+   55   55   10    8    0    N IN +N=C-N: ; Q=1/2   
+   NGD+   56   56   10    8    0    GUANIDINIUM N; Q=1/3   
+   CGD+   57   57    2    1    0    GUANIDINIUM CARBON     
+*  CNN+   57   57    2    1    0    C IN +N=C-N RESONANCE  
+   NPD+   58   58   10    8    0    N PYRIDINIUM ION       
+   OFUR   59   59    6    6    0    AROMATIC O, FURAN      
+   C%     60   60    4    1    0    ISONITRILE CARBON      
+   NR%    61   61   42    8    0    ISONITRILE N           
+   NM     62   62   10    8    0    SULFONAMIDE N-         
+   C5A    63   63    2    1    0    ALPHA AROM 5-RING  C   
+   C5B    64   64    2    1    0    BETA AROM 5-RING  C    
+   N5A    65   65    9    8    0    ALPHA AROM 5-RING N    
+   N5B    66   66    9    8    0    ALPHA AROM 5-RING N    
+   N2OX   67   67    9    8    0    NITROGEN IN N-OXIDE    
+   N3OX   68   68    8    8    0    NITROGEN IN N-OXIDE    
+   NPOX   69   69    9    8    0    NITROGEN IN N-OXIDE    
+   OH2    70   70   70   70   70    OXYGEN IN WATER        
+   HS     71   71    5    5    0    H-S                    
+   S2CM   72   72   16   15    0    THIOCARBOXYLATE S      
+*  S-P    72   72   16   15    0    TERMINAL SULFUR ON P   
+*  SM     72   72   16   15    0    TERMINAL SULFUR ON C   
+*  SSMO   72   72   16   15    0    TERM S, THIOSULFINATE  
+   SO2M   73   73   18   15    0    SULFUR IN SULFINATE    
+*  SSOM   73   73   18   15    0    SULFUR, THIOSULFINATE  
+   =S=O   74   74   17   15    0    SULFINYL SULFUR, C=S=O 
+   -P=C   75   75   26   25    0    P DOUBLY BONDED TO C
+   N5M    76   76    9    8    0    NEG N IN TETRAZOLE AN  
+   CLO4   77   77   12   12    0    CHLORINE IN CLO4(-)     
+   C5     78   78    2    1    0    GENERAL AROM 5-RING C  
+   N5     79   79    9    8    0    GENERAL AROM 5-RING N  
+   CIM+   80   80    2    1    0    C IN N-C-N, IM+ ION    
+   NIM+   81   81   10    8    0    N IN N-C-N, IM+ ION    
+   N5AX   82   82    9    8    0    5R NITROGEN IN N-OXIDE 
+*  N5BX   82   82    9    8    0    5R NITROGEN IN N-OXIDE 
+*  N5OX   82   82    9    8    0    5R NITROGEN IN N-OXIDE 
+   FE+2   87   87   87   87   87    IRON +2 CATION
+   FE+3   88   88   88   88   88    IRON +3 CATION
+   F-     89   89   89   89   89    FLUORIDE ANION
+   CL-    90   90   90   90   90    CHLORIDE ANION
+   BR-    91   91   91   91   91    BROMIDE ANION
+   LI+    92   92   92   92   92    LITHIUM CATION         
+   NA+    93   93   93   93   93    SODIUM CATION          
+   K+     94   94   94   94   94    POTASSIUM CATION       
+   ZN+2   95   95   95   95   95    DIPOSITIVE ZINC CATION 
+*  ZINC   95   95   95   95   95    DIPOSITIVE ZINC CATION 
+   CA+2   96   96   96   96   96    DIPOSITIVE CALCIUM CATION
+   CU+1   97   97   97   97   97    MONOPOSITIVE COPPER CATION
+   CU+2   98   98   98   98   98    DIPOSITIVE COPPER CATION
+   MG+2   99   99   99   99   99    DIPOSITIVE MAGNESIUM CATION
+$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffdfsb.par	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,39 @@
+*
+*                Copyright (c) Merck and Co., Inc., 1994
+*                         All Rights Reserved
+*
+* MMFF Default Stretch-Bend Parameters
+*      Row in 
+*  Periodic Table         
+*   IR   JR   KR   F(I_J,K)  F(K_J,I)
+    0    1    0      0.15      0.15
+    0    1    1      0.10      0.30
+    0    1    2      0.05      0.35
+    0    1    3      0.05      0.35
+    0    1    4      0.05      0.35
+    0    2    0      0.00      0.00
+    0    2    1      0.00      0.15
+    0    2    2      0.00      0.15
+    0    2    3      0.00      0.15
+    0    2    4      0.00      0.15
+    1    1    1      0.30      0.30
+    1    1    2      0.30      0.50
+    1    1    3      0.30      0.50
+    1    1    4      0.30      0.50
+    2    1    2      0.50      0.50
+    2    1    3      0.50      0.50
+    2    1    4      0.50      0.50
+    3    1    3      0.50      0.50
+    3    1    4      0.50      0.50
+    4    1    4      0.50      0.50
+    1    2    1      0.30      0.30
+    1    2    2      0.25      0.25
+    1    2    3      0.25      0.25
+    1    2    4      0.25      0.25
+    2    2    2      0.25      0.25
+    2    2    3      0.25      0.25
+    2    2    4      0.25      0.25
+    3    2    3      0.25      0.25
+    3    2    4      0.25      0.25
+    4    2    4      0.25      0.25
+$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffoop.par	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,127 @@
+*
+*                Copyright (c) Merck and Co., Inc., 1994
+*                         All Rights Reserved
+*
+* MMFF OUT-OF-PLANE PARAMETERS- Rev: 15-OCT-93  Source: MMFF94
+* C94  - CORE MMFF94 parameter, from fits to HF/6-31G* 2nd D's
+* #C94 - Value adjusted from CORE MMFF93 value
+*
+*   MMFF  atom types     koop    Source
+    1    2    1    2     0.030   C94
+    1    2    2    2     0.027   C94
+    1    2    2    3     0.026   C94
+    1    2    2    5     0.013   C94
+    1    2    2   37     0.032   C94
+    2    2    2    5     0.013   C94
+    2    2    3    5     0.012   C94
+    2    2    5    5     0.006   C94
+    2    2    5    6     0.027   C94
+    2    2    5   37     0.017   C94
+    2    2    5   40     0.012   C94
+    2    2    5   41     0.008   C94
+    0    2    0    0     0.020   *-2-*-* C94 DEF
+    1    3    1    7     0.146   C94
+    1    3    2    7     0.138   C94
+    1    3    3    7     0.134   C94
+    1    3    5    7     0.122   C94
+    1    3    6    7     0.141   C94
+    1    3    7   10     0.129   C94
+    1    3    7   37     0.138   C94
+    2    3    5    7     0.113   C94
+    2    3    5    9     0.081   C94
+    2    3    6    7     0.127   C94
+    2    3    7   10     0.116   C94
+    3    3    5    7     0.113   C94
+    3    3    6    7     0.127   C94
+    5    3    5    7     0.103   C94
+    5    3    5    9     0.074   C94
+    5    3    5   54     0.078   C94
+    5    3    6    7     0.119   C94
+    5    3    7   10     0.102   C94
+    5    3    9   40     0.067   C94
+    6    3    7   37     0.127   C94
+    7    3   10   10     0.113   C94
+    7    3   20   20     0.151   C94
+    9    3   40   40     0.057   C94
+    0    3    0    0     0.130   *-3-*-* C94 DEF
+    0    8    0    0     0.000   *-8-*-* C94 DEF
+    1   10    1    3    -0.02    #C94 (C93=-0.034)
+    1   10    3    6    -0.033   C94
+    1   10    3   28    -0.02    #C94 (C93=-0.030)
+    3   10    3   28    -0.030   C94
+    3   10   28   28    -0.019   C94
+    0   10    0    0    -0.020   *-10-*-* C94 DEF
+    0   17    0    0     0.000   *-17-*-* E94 DEF
+    0   26    0    0     0.000   *-26-*-* CE4 DEF
+    5   30   20   30     0.008   C94
+    0   30    0    0     0.010   *-30-*-* C94 DEF
+    1   37   37   37     0.040   C94
+    2   37   37   37     0.031   C94
+    3   37   37   37     0.027   C94
+    5   37   37   37     0.015   C94
+    5   37   37   38     0.046   C94
+    5   37   37   63     0.008   C94
+    5   37   37   64     0.012   C94
+    5   37   37   69     0.016   C94
+    5   37   38   38     0.084   C94
+    6   37   37   37     0.048   C94
+   15   37   37   37     0.025   C94
+   37   37   37   40     0.046   C94
+    0   37    0    0     0.035   *-37-*-* C94 DEF
+    1   39   63   63     0.012   C94
+   23   39   63   63    -0.014   C94
+   23   39   63   65     0.021   C94
+   23   39   65   65     0.062   C94
+    0   39    0    0     0.020   *-39-*-* C94 DEF
+    1   40   28   37    -0.006   C94
+    2   40   28   28    -0.007   C94
+    3   40   28   28    -0.007   C94
+   28   40   28   37     0.004   C94
+    0   40    0    0    -0.005   *-40-*-* C94 DEF
+    1   41   32   32     0.178   C94
+    2   41   32   32     0.161   C94
+    5   41   32   32     0.158   C94
+    0   41    0    0     0.180   *-41-*-* C94 DEF
+    0   43    0    0     0.000   *-43-*-* E94 DEF
+    0   45    0    0     0.150   *-45-*-* E94 DEF
+   50   49   50   50     0.000   #C94
+    0   49    0    0     0.000   *-49-*-* E94 DEF
+    1   54    3   36     0.016   C94
+    3   54   36   36     0.018   C94
+    0   54    0    0     0.020   *-54-*-* C94 DEF
+    1   55   36   57     0.020   #C94
+   36   55   36   57     0.020   #C94
+    0   55    0    0     0.020   *-55-*-* C94 DEF
+    1   56   36   57     0.020   #C94
+   36   56   36   57     0.020   #C94
+    0   56    0    0     0.020   *-56-*-* C94 DEF
+    5   57   55   55     0.038   C94
+   56   57   56   56     0.158   C94
+    0   57    0    0     0.080   *-57-*-* C94 DEF
+    0   58    0    0     0.025   *-58-*-* E94 DEF
+    5   63   39   64     0.019   C94
+    5   63   39   66     0.068   C94
+    5   63   44   64     0.014   C94
+    5   63   44   66     0.055   C94
+    5   63   59   64     0.033   C94
+    5   63   59   66     0.085   C94
+   37   63   39   64     0.010   C94
+    0   63    0    0     0.050   *-63-*-* C94 DEF
+    5   64   63   64     0.006   C94
+    5   64   63   66     0.043   C94
+    5   64   64   65     0.052   C94
+    5   64   65   66     0.094   C94
+   37   64   63   64    -0.011   C94
+    0   64    0    0     0.040   *-64-*-* C94 DEF
+    0   67    0    0     0.070   *-67-*-* E94 DEF
+   32   69   37   37     0.067   C94
+    0   69    0    0     0.070   *-69-*-* C94 DEF
+    0   73    0    0     0.000   *-73-*-* E94 DEF
+    5   78   78   81     0.046   C94
+    0   78    0    0     0.045   *-78-*-* C94 DEF
+    5   80   81   81     0.057   C94
+    0   80    0    0     0.080   *-80-*-* C94 DEF
+   36   81   78   80     0.016   C94
+    0   81    0    0     0.025   *-81-*-* C94 DEF
+    0   82    0    0     0.000   *-82-*-* E94 DEF
+$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffpbci.par	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,106 @@
+*
+*                Copyright (c) Merck and Co., Inc., 1994
+*                         All Rights Reserved
+*
+* MMFF Partial Bond Charge Incs and Formal-Charge Adj. Factors: 19-MAY-1994
+*
+* type    pbci      fcadj   Origin/Comment
+0   1     0.000     0.000   Fitted default
+0   2    -0.135     0.000   Fitted default
+0   3    -0.095     0.000   Fitted default
+0   4    -0.200     0.000   Fitted default
+0   5    -0.023     0.000   Fitted default
+0   6    -0.243     0.000   Fitted default
+0   7    -0.687     0.000   Fitted default
+0   8    -0.253     0.000   Fitted default
+0   9    -0.306     0.000   Fitted default
+0  10    -0.244     0.000   Fitted default
+0  11    -0.317     0.000   Fitted default
+0  12    -0.304     0.000   Fitted default
+0  13    -0.238     0.000   Fitted default
+0  14    -0.208     0.000   Fitted default
+0  15    -0.236     0.000   Fitted default
+0  16    -0.475     0.000   Fitted default
+0  17    -0.191     0.000   Fitted default
+0  18    -0.118     0.000   Fitted default
+0  19     0.094     0.000   Fitted default
+0  20    -0.019     0.000   Fitted default
+0  21     0.157     0.000   Fitted default
+0  22    -0.095     0.000   Fitted default
+0  23     0.193     0.000   Fitted default
+0  24     0.257     0.000   Fitted default
+0  25     0.012     0.000   Fitted default
+0  26    -0.142     0.000   Fitted default
+0  27     0.094     0.000   Fitted default
+0  28     0.058     0.000   Fitted default
+0  29     0.207     0.000   Fitted default
+0  30    -0.166     0.000   Fitted default
+0  31     0.161     0.000   Fitted default
+0  32    -0.732     0.500   Fitted default
+0  33     0.257     0.000   Fitted default
+0  34    -0.491     0.000   Fitted default
+0  35    -0.456     0.500   Fitted default
+0  36    -0.031     0.000   Fitted default
+0  37    -0.127     0.000   Fitted default
+0  38    -0.437     0.000   Fitted default
+0  39    -0.104     0.000   Fitted default
+0  40    -0.264     0.000   Fitted default
+0  41     0.052     0.000   Fitted default
+0  42    -0.757     0.000   Fitted default
+0  43    -0.326     0.000   Fitted default
+0  44    -0.237     0.000   Fitted default
+0  45    -0.260     0.000   Fitted default
+0  46    -0.429     0.000   Fitted default
+0  47    -0.418     0.000   Fitted default
+0  48    -0.525     0.000   Fitted default
+0  49    -0.283     0.000   Fitted default
+0  50     0.284     0.000   Fitted default
+0  51    -1.046     0.000   Fitted default
+0  52    -0.546     0.000   Fitted default
+0  53    -0.048     0.000   Fitted default
+0  54    -0.424     0.000   Fitted default
+0  55    -0.476     0.000   Fitted default
+0  56    -0.438     0.000   Fitted default
+0  57    -0.105     0.000   Fitted default
+0  58    -0.488     0.000   Fitted default
+0  59    -0.337     0.000   Fitted default
+0  60    -0.635     0.000   Fitted default
+0  61    -0.265     0.000   Fitted default
+0  62    -0.125     0.250   Fitted default
+0  63    -0.180     0.000   Fitted default
+0  64    -0.181     0.000   Fitted default
+0  65    -0.475     0.000   Fitted default
+0  66    -0.467     0.000   Fitted default
+0  67    -0.099     0.000   == 69
+0  68    -0.135     0.000   Fitted default
+0  69    -0.099     0.000   Fitted default
+0  70    -0.269     0.000   Fitted default
+0  71    -0.071     0.000   Fitted default
+0  72    -0.580     0.500   Fitted default
+0  73    -0.200     0.000   Fitted default
+0  74    -0.301     0.000   Fitted default
+0  75    -0.255     0.000   Fitted default
+0  76    -0.568     0.250   Fitted default
+0  77    -0.282     0.000   Fitted default
+0  78    -0.168     0.000   Fitted default
+0  79    -0.471     0.000   == (65+66)/2
+0  80    -0.144     0.000   Fitted default
+0  81    -0.514     0.000   Fitted default
+0  82    -0.099     0.000   == 69
+0  83     0.000     0.000  Unused
+0  84     0.000     0.000  Unused
+0  85     0.000     0.000  Unused
+0  86     0.000     0.000  Unused
+0  87     0.000     0.000  Unused
+0  88     0.000     0.000  Unused
+0  89     0.000     0.000  Unused
+0  90     0.000     0.000  Unused
+0  91     0.000     0.000  Unused
+0  92     1.000     0.000  Ionic charge
+0  93     1.000     0.000  Ionic charge
+0  94     1.000     0.000  Ionic charge
+0  95     2.000     0.000  Ionic charge
+0  96     2.000     0.000  Ionic charge
+0  97     1.000     0.000  Ionic charge
+0  98     2.000     0.000  Ionic charge
+$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffprop.par	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,103 @@
+*
+*                Copyright (c) Merck and Co., Inc., 1993
+*                         All Rights Reserved
+*
+* MMFFPROP - MMFF atom-type properties
+*
+* atype aspec crd val  pilp mltb arom lin sbmb
+    1    6    4    4    0    0    0    0    0
+    2    6    3    4    0    2    0    0    1
+    3    6    3    4    0    2    0    0    1
+    4    6    2    4    0    3    0    1    1
+    5    1    1    1    0    0    0    0    0
+    6    8    2    2    1    0    0    0    0
+    7    8    1    2    0    2    0    0    0
+    8    7    3    3    1    0    0    0    0
+    9    7    2    3    0    2    0    0    1
+   10    7    3    3    1    1    0    0    0
+   11    9    1    1    1    0    0    0    0
+   12   17    1    1    1    0    0    0    0
+   13   35    1    1    1    0    0    0    0
+   14   53    1    1    1    0    0    0    0
+   15   16    2    2    1    0    0    0    0
+   16   16    1    2    0    2    0    0    0
+   17   16    3    4    0    2    0    0    0
+   18   16    4    4    0    0    0    0    0
+   19   14    4    4    0    0    0    0    0
+   20    6    4    4    0    0    0    0    0
+   21    1    1    1    0    0    0    0    0
+   22    6    4    4    0    0    0    0    0
+   23    1    1    1    0    0    0    0    0
+   24    1    1    1    0    0    0    0    0
+   25   15    4    4    0    0    0    0    0
+   26   15    3    3    1    0    0    0    0
+   27    1    1    1    0    0    0    0    0
+   28    1    1    1    0    0    0    0    0
+   29    1    1    1    0    0    0    0    0
+   30    6    3    4    0    2    0    0    1
+   31    1    1    1    0    0    0    0    0
+   32    8    1   12    1    1    0    0    0
+   33    1    1    1    0    0    0    0    0
+   34    7    4    4    0    0    0    0    0
+   35    8    1    1    1    1    0    0    0
+   36    1    1    1    0    0    0    0    0
+   37    6    3    4    0    2    1    0    1
+   38    7    2    3    0    2    1    0    0
+   39    7    3    3    1    1    1    0    1
+   40    7    3    3    1    0    0    0    0
+   41    6    3    4    0    1    0    0    0
+   42    7    1    3    0    3    0    0    0
+   43    7    3    3    1    0    0    0    0
+   44   16    2    2    1    1    1    0    0
+   45    7    3    4    0    2    0    0    0
+   46    7    2    3    0    2    0    0    0
+   47    7    1    2    0    2    0    0    0
+   48    7    2    2    0    0    0    0    0
+   49    8    3    3    0    0    0    0    0
+   50    1    1    1    0    0    0    0    0
+   51    8    2    3    0    2    0    0    0
+   52    1    1    1    0    0    0    0    0
+   53    7    2    4    0    2    0    1    0
+   54    7    3    4    0    2    0    0    1
+   55    7    3   34    0    1    0    0    0
+   56    7    3   34    0    1    0    0    0
+   57    6    3    4    0    2    0    0    1
+   58    7    3    4    0    1    1    0    1
+   59    8    2    2    1    1    1    0    0
+   60    6    1    3    0    3    0    0    0
+   61    7    2    4    0    3    0    1    0
+   62    7    2    2    1    0    0    0    0
+   63    6    3    4    0    2    1    0    1
+   64    6    3    4    0    2    1    0    1
+   65    7    2    3    0    2    1    0    0
+   66    7    2    3    0    2    1    0    0
+   67    7    3    4    0    2    0    0    1
+   68    7    4    4    0    0    0    0    0
+   69    7    3    4    0    1    1    0    0
+   70    8    2    2    1    0    0    0    0
+   71    1    1    1    0    0    0    0    0
+   72   16    1    1    1    1    0    0    0
+   73   16    3    3    0    0    0    0    0
+   74   16    2    4    0    2    0    0    0
+   75   15    2    3    0    2    0    0    1
+   76    7    2    2    1    0    0    0    0
+   77   17    4    4    0    0    0    0    0
+   78    6    3    4    0    2    1    0    1
+   79    7    2    3    0    2    1    0    0
+   80    6    3    4    0    2    0    0    1
+   81    7    3    4    0    1    1    0    1
+   82    7    3    4    0    1    1    0    0
+   87   26    0    0    0    0    0    0    0
+   88   26    0    0    0    0    0    0    0
+   89    9    0    0    0    0    0    0    0
+   90   17    0    0    0    0    0    0    0
+   91   35    0    0    0    0    0    0    0
+   92    3    0    0    0    0    0    0    0
+   93   11    0    0    0    0    0    0    0
+   94   19    0    0    0    0    0    0    0
+   95   30    0    0    0    0    0    0    0
+   96   20    0    0    0    0    0    0    0
+   97   29    0    0    0    0    0    0    0
+   98   29    0    0    0    0    0    0    0
+   99   12    0    0    0    0    0    0    0
+$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffs_oop.par	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,128 @@
+*
+*   Copyright (c) Merck and Co., Inc., 1994,1995,1996,1997,1998,1999
+*                         All Rights Reserved
+*
+* MMFF94s OUT-OF-PLANE PARAMETERS
+* C94  - CORE MMFF94 parameter, from fits to HF/6-31G* 2nd D's
+* C94S - CORE MMFF94s parameter,adjusted to promote planarity
+* #C94 - Value adjusted from CORE MMFF94 value
+*
+*   MMFF  atom types     koop    Source
+    0    2    0    0     0.020   *-2-*-* C94 DEF
+    1    2    1    2     0.030   C94
+    1    2    2    2     0.027   C94
+    1    2    2    3     0.026   C94
+    1    2    2    5     0.013   C94
+    1    2    2   37     0.032   C94
+    2    2    2    5     0.013   C94
+    2    2    3    5     0.012   C94
+    2    2    5    5     0.006   C94
+    2    2    5    6     0.027   C94
+    2    2    5   37     0.017   C94
+    2    2    5   40     0.012   C94
+    2    2    5   41     0.008   C94
+    0    3    0    0     0.130   *-3-*-* C94 DEF
+    1    3    1    7     0.146   C94
+    1    3    2    7     0.138   C94
+    1    3    3    7     0.134   C94
+    1    3    5    7     0.122   C94
+    1    3    6    7     0.141   C94
+    1    3    7   10     0.129   C94
+    1    3    7   37     0.138   C94
+    2    3    5    7     0.113   C94
+    2    3    5    9     0.081   C94
+    2    3    6    7     0.127   C94
+    2    3    7   10     0.116   C94
+    3    3    5    7     0.113   C94
+    3    3    6    7     0.127   C94
+    5    3    5    7     0.103   C94
+    5    3    5    9     0.074   C94
+    5    3    5   54     0.078   C94
+    5    3    6    7     0.119   C94
+    5    3    7   10     0.102   C94
+    5    3    9   40     0.067   C94
+    6    3    7   37     0.127   C94
+    7    3   10   10     0.113   C94
+    7    3   20   20     0.151   C94
+    9    3   40   40     0.057   C94
+    0    8    0    0     0.000   *-8-*-* C94 DEF
+    0   10    0    0     0.015   *-10-*-* C94S DEF
+    1   10    1    3     0.015   C94S
+    1   10    3    6     0.015   C94
+    1   10    3   28     0.015   C94S
+    3   10    3   28     0.015   C94S
+    3   10   28   28     0.015   C94S
+    0   17    0    0     0.000   *-17-*-* E94 DEF
+    0   26    0    0     0.000   *-26-*-* CE4 DEF
+    0   30    0    0     0.010   *-30-*-* C94 DEF
+    5   30   20   30     0.008   C94
+    0   37    0    0     0.035   *-37-*-* C94 DEF
+    1   37   37   37     0.040   C94
+    2   37   37   37     0.031   C94
+    3   37   37   37     0.027   C94
+    5   37   37   37     0.015   C94
+    5   37   37   38     0.046   C94
+    5   37   37   63     0.008   C94
+    5   37   37   64     0.012   C94
+    5   37   37   69     0.016   C94
+    5   37   38   38     0.084   C94
+    6   37   37   37     0.048   C94
+   15   37   37   37     0.025   C94
+   37   37   37   40     0.046   C94
+    0   39    0    0     0.020   *-39-*-* C94 DEF
+    1   39   63   63     0.012   C94
+   23   39   63   63    -0.014   C94
+   23   39   63   65     0.021   C94
+   23   39   65   65     0.062   C94
+    0   40    0    0     0.030   *-40-*-* C94S DEF
+    1   40   28   37     0.030   C94S
+    2   40   28   28     0.030   C94S
+    3   40   28   28     0.030   C94S
+   28   40   28   37     0.030   C94S
+    0   41    0    0     0.180   *-41-*-* C94 DEF
+    1   41   32   32     0.178   C94
+    2   41   32   32     0.161   C94
+    5   41   32   32     0.158   C94
+    0   43    0    0     0.000   *-43-*-* E94 DEF
+    0   45    0    0     0.150   *-45-*-* E94 DEF
+    0   49    0    0     0.000   *-49-*-* E94 DEF
+   50   49   50   50     0.000   #C94
+    0   54    0    0     0.020   *-54-*-* C94 DEF
+    1   54    3   36     0.016   C94
+    3   54   36   36     0.018   C94
+    0   55    0    0     0.020   *-55-*-* C94 DEF
+    1   55   36   57     0.020   #C94
+   36   55   36   57     0.020   #C94
+    0   56    0    0     0.020   *-56-*-* C94 DEF
+    1   56   36   57     0.020   #C94
+   36   56   36   57     0.020   #C94
+    0   57    0    0     0.080   *-57-*-* C94 DEF
+    5   57   55   55     0.038   C94
+   56   57   56   56     0.158   C94
+    0   58    0    0     0.025   *-58-*-* E94 DEF
+    0   63    0    0     0.050   *-63-*-* C94 DEF
+    5   63   39   64     0.019   C94
+    5   63   39   66     0.068   C94
+    5   63   44   64     0.014   C94
+    5   63   44   66     0.055   C94
+    5   63   59   64     0.033   C94
+    5   63   59   66     0.085   C94
+   37   63   39   64     0.010   C94
+    0   64    0    0     0.040   *-64-*-* C94 DEF
+    5   64   63   64     0.006   C94
+    5   64   63   66     0.043   C94
+    5   64   64   65     0.052   C94
+    5   64   65   66     0.094   C94
+   37   64   63   64    -0.011   C94
+    0   67    0    0     0.070   *-67-*-* E94 DEF
+    0   69    0    0     0.070   *-69-*-* C94 DEF
+   32   69   37   37     0.067   C94
+    0   73    0    0     0.000   *-73-*-* E94 DEF
+    0   78    0    0     0.045   *-78-*-* C94 DEF
+    5   78   78   81     0.046   C94
+    0   80    0    0     0.080   *-80-*-* C94 DEF
+    5   80   81   81     0.057   C94
+    0   81    0    0     0.025   *-81-*-* C94 DEF
+   36   81   78   80     0.016   C94
+    0   82    0    0     0.000   *-82-*-* E94 DEF
+$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffs_tor.par	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,939 @@
+*
+*   Copyright (c) Merck and Co., Inc., 1994,1995,1996,1997,1998,1999
+*                         All Rights Reserved
+*
+* MMFF94s TORSION PARAMETERS
+* C94  - CORE MMFF94 parameter - from fits to conformational energies
+* C94S - CORE MMFF94s parameter - from fits to conformational energies
+* X94  - EXTD MMFF94 parameter - also from fits to conformational E's
+* E94  - EXTD MMFF94 parameter - from empirical rule
+* #E94 - Adjusted from empirical rule value
+*
+*      atom types       V1      V2      V3     Source
+0   0    1    1    0   0.000   0.000   0.300   C94 0:*-1-1-* Def
+5   0    1    1    0   0.200  -0.800   1.500   C94 5:*-1-1-* Def
+0   1    1    1    1   0.103   0.681   0.332   C94
+5   1    1    1    1   0.144  -0.547   1.126   C94
+0   1    1    1    2  -0.295   0.438   0.584   C94
+0   1    1    1    3   0.066  -0.156   0.143   C94
+0   1    1    1    5   0.639  -0.630   0.264   C94
+0   1    1    1    6  -0.688   1.757   0.477   C94
+5   1    1    1    6   0.000   0.000   0.054   C94
+0   1    1    1    8  -1.420  -0.092   1.101   C94
+5   1    1    1    8   0.000  -0.158   0.323   C94
+0   1    1    1   11   0.593   0.662   1.120   C94
+0   1    1    1   12  -0.678   0.417   0.624   C94
+0   1    1    1   15  -0.714   0.698   0.000   C94
+0   1    1    1   34  -0.647   0.550   0.590   C94
+0   2    1    1    5   0.321  -0.411   0.144   C94
+0   3    1    1    3   0.443   0.000  -1.140   C94
+0   3    1    1    5  -0.256   0.058   0.000   C94
+0   3    1    1    6  -0.679  -0.029   0.000   C94
+0   5    1    1    5   0.284  -1.386   0.314   C94
+0   5    1    1    6  -0.654   1.072   0.279   C94
+0   5    1    1    8  -0.744  -1.235   0.337   C94
+0   5    1    1   10   0.000   0.000   0.418   C94S
+0   5    1    1   11   0.000   0.516   0.291   C94
+0   5    1    1   12   0.678  -0.602   0.398   C94
+0   5    1    1   15   1.142  -0.644   0.367   C94
+0   5    1    1   25   0.000   0.000   0.295   X94
+0   5    1    1   34   0.692  -0.530   0.278   C94
+0   5    1    1   37   0.000   0.000   0.389   C94
+0   5    1    1   39   0.000   0.000   0.278   C94
+0   5    1    1   41   0.000   0.000  -0.141   C94
+0   5    1    1   56   0.000   0.000   0.324   C94
+0   5    1    1   68   0.000   0.000   0.136   C94
+0   6    1    1    6   0.408   1.397   0.961   C94
+5   6    1    1    6   0.313  -1.035   1.631   C94
+0   8    1    1    8   1.055   0.834   0.000   C94
+0  11    1    1   11  -0.387  -0.543   1.405   C94
+0  12    1    1   12   0.000   0.000   0.893   C94
+0  15    1    1   15  -0.177   0.000   0.049   C94
+0   0    1    2    0   0.000   0.000   0.000   C94 0:*-1-2-* Def
+2   0    1    2    0   0.000   0.000   0.000   E94 2:*1-2-* Def
+5   0    1    2    0   0.000   0.000   0.000   C94 5:*-1-2-*  Def
+0   0    1    2    2   0.000   0.000  -0.650   C94 0:*-1-2=2 Def
+5   0    1    2    2   0.000   0.000  -0.650   C94 5:*-1-2=2  Def
+0   1    1    2    1   0.419   0.296   0.282   C94
+0   1    1    2    2  -0.494   0.274  -0.630   C94
+0   1    1    2    5   0.075   0.000   0.358   C94
+0   2    1    2    2  -0.293   0.115  -0.508   C94
+0   2    1    2    5   0.301   0.104   0.507   C94
+0   3    1    2    1   0.565  -0.554   0.234   C94
+0   3    1    2    2  -0.577  -0.482  -0.427   C94
+0   3    1    2    5   0.082   0.000   0.123   C94
+0   5    1    2    1   0.000  -0.184   0.220   C94
+0   5    1    2    2   0.501  -0.410  -0.535   C94
+2   5    1    2    2   0.000   0.000   0.055   C94
+2   5    1    2    3   0.000   0.000  -0.108   C94
+0   5    1    2    5  -0.523  -0.228   0.208   C94
+2   5    1    2   37   0.000   0.000   0.000   C94
+0   6    1    2    1  -0.467   0.000   0.490   C94
+0   6    1    2    2   0.425   0.168  -0.875   C94
+0   6    1    2    5   0.000   0.136   0.396   C94
+0   8    1    2    1  -0.504   0.371   0.557   C94
+0   8    1    2    2   0.541   0.539  -1.009   C94
+0   8    1    2    5   0.000   0.204   0.464   C94
+0   0    1    3    0   0.000   0.400   0.300   C94 0:*-1-3-* Def
+2   0    1    3    0   0.000   0.500   0.350   C94 2:*-1-3-*  Def
+5   0    1    3    0   0.000   0.000   0.000   E94 5:*1-3-* Def
+0   0    1    3    1   0.000   0.000   0.550   C94 0:*-1-3-1 Def
+0   0    1    3    5   0.000   0.200   0.700   C94 0:*-1-3-5 Def
+0   0    1    3    7   0.000   0.400   0.400   C94 0:*-1-3-7 Def
+0   1    1    3    1   0.103   0.177   0.545   C94
+0   1    1    3    5  -0.072   0.316   0.674   C94
+0   1    1    3    6  -0.117  -0.333   0.202   C94
+0   1    1    3    7   0.825   0.139   0.325   C94
+0   1    1    3   10  -0.763   1.244   0.986   C94S
+0   2    1    3    5   0.663  -0.167   0.426   C94
+0   2    1    3    7  -0.758   0.112   0.563   C94
+0   5    1    3    1  -0.073   0.085   0.531   C94
+2   5    1    3    2   0.000   0.000   0.115   C94
+2   5    1    3    3   0.000   0.000   0.446   C94
+0   5    1    3    5  -0.822   0.501   1.008   C94
+0   5    1    3    6   0.000  -0.624   0.330   C94
+0   5    1    3    7   0.659  -1.407   0.308   C94
+0   5    1    3   10  -0.687   1.244   0.136   C94S
+2   5    1    3   37   0.000   0.000   0.056   C94
+0   5    1    3   43   0.000   1.027   0.360   X94
+0   5    1    3   51   0.000   1.543   0.350   X94
+0   5    1    3   53   0.000   0.501   0.000   X94
+0   5    1    3   74   0.000   0.513  -0.344   X94
+0   5    1    3   75   0.000   0.511  -0.186   X94
+0   6    1    3    6   0.447   0.652   0.318   C94
+0   6    1    3    7  -0.395   0.730  -0.139   C94
+0  10    1    3    7   0.530   2.905   2.756   C94S
+0  10    1    3   10   0.465  -0.241   1.850   C94S
+0   0    1    4    0   0.000   0.000   0.000   C94 0:*-1-4-* Def
+0   0    1    6    0   0.000   0.000   0.200   C94 0:*-1-6-* Def
+5   0    1    6    0   0.000  -0.200   0.400   C94 5:*-1-6-*  Def
+0   1    1    6    1  -0.681   0.755   0.755   C94
+5   1    1    6    1   0.000   0.243  -0.596   C94
+0   1    1    6    3  -0.547   0.000   0.320   C94
+0   1    1    6   21   0.000   0.270   0.237   C94
+0   2    1    6   21   0.102   0.460  -0.128   C94
+0   3    1    6   21  -1.652  -1.660   0.283   C94
+0   5    1    6    1   0.571   0.319   0.570   C94
+0   5    1    6    2   0.000   0.000   0.306   C94
+0   5    1    6    3   0.572   0.000  -0.304   C94
+0   5    1    6   21   0.596  -0.276   0.346   C94
+0   5    1    6   25   0.000   0.000   0.061   X94
+0   5    1    6   37   0.000   0.000   0.106   C94
+0   5    1    6   45   0.000   0.000  -0.174   X94
+0   6    1    6    1   0.229  -0.710   0.722   C94
+5   6    1    6    1   0.000   0.000   0.040   C94
+0   6    1    6   21   1.488  -3.401  -0.320   C94
+0  37    1    6   21   0.712   1.320  -0.507   C94
+0   0    1    8    0   0.000  -0.300   0.500   C94 0:*-1-8-* Def
+5   0    1    8    0   0.000   0.000   0.297   E94 5:*1-8-* Def
+0   1    1    8    1  -0.439   0.786   0.272   C94
+5   1    1    8    1   0.115  -0.390   0.658   C94
+0   1    1    8    6  -0.608   0.339   1.496   C94
+0   1    1    8   23  -0.428   0.323   0.280   C94
+0   2    1    8   23   0.594  -0.409   0.155   C94
+0   5    1    8    1   0.393  -0.385   0.562   C94
+0   5    1    8    6   0.598  -0.158   0.399   C94
+0   5    1    8   23  -0.152  -0.440   0.357   C94
+0   0    1    9    0   0.000   0.000   0.000   C94 0:*-1-9-* Def
+5   0    1    9    0   0.000   0.000   0.000   E94 5:*1-9-* Def
+0   5    1    9    3   0.204  -0.335  -0.352   C94
+0   5    1    9   53   0.000   0.000   0.097   X94
+0   0    1   10    0   0.000   0.000   0.300   C94 0:*-1-10-* Def
+5   0    1   10    0   0.000   0.000   0.000   E94 5:*1-10-* Def
+0   0    1   10    3   0.000   0.000   1.000   C94 0:*-1-10-3 Def
+0   1    1   10    3  -0.884   0.578   0.818   C94S
+0   1    1   10    6   0.000  -0.379   0.565   C94S
+0   1    1   10   28   0.750  -0.404   0.369   C94S
+0   3    1   10    3   3.219  -2.699   1.875   C94S
+0   3    1   10   28   0.207   0.461   0.324   C94S
+0   5    1   10    1   0.000   0.000   0.706   C94S
+0   5    1   10    3  -2.334   1.517  -0.065   C94S
+0   5    1   10    6   0.000   0.688   0.665   C94S
+0   5    1   10   28  -0.982  -0.207   0.166   C94S
+0   0    1   15    0   0.000   0.000   0.400   C94 0:*-1-15-* Def
+5   0    1   15    0   0.000   0.000   0.336   E94 5:*1-15-* Def
+0   1    1   15    1  -1.047   0.170   0.398   C94
+0   1    1   15   15  -1.438   0.263   0.501   C94
+0   1    1   15   71  -0.376  -0.133   0.288   C94
+0   5    1   15    1   1.143  -0.231   0.447   C94
+0   5    1   15   15   1.555  -0.323   0.456   C94
+0   5    1   15   37   0.000   0.000   0.459   C94
+0   5    1   15   71   0.229   0.203   0.440   C94
+0   0    1   17    0   0.000   0.000   0.350   C94 0:*-1-17-* Def
+5   0    1   17    0   0.000   0.000   0.000   E94 5:*1-17-* Def
+0   5    1   17    1   0.000   0.000   0.536   X94
+0   5    1   17    7   0.000   0.000   0.212   X94
+0   0    1   18    0   0.000   0.000   0.100   C94 0:*-1-18-* Def
+5   0    1   18    0   0.000   0.000   0.112   E94 5:*1-18-* Def
+0   5    1   18    1   0.000   0.000   0.000   X94
+0   5    1   18    6   0.000   0.000   0.099   X94
+0   5    1   18   32   0.000   0.585   0.388   X94
+0   5    1   18   43   0.000  -0.412   0.121   X94
+0   5    1   18   48   0.000   0.000   0.195   X94
+0   5    1   18   62   0.000   0.000  -0.088   X94
+0   0    1   19    0   0.000   0.000   0.150   C94 0:*-1-19-* Def
+5   0    1   19    0   0.000   0.000   0.179   E94 5:*1-19-* Def
+0   5    1   19    5   0.000   0.000   0.196   X94
+0   5    1   19    6   0.000   0.000   0.176   X94
+0   5    1   19   12   0.000   0.000   0.152   X94
+0   0    1   20    0   0.000   0.000   0.350   C94 0:*-1-20-* Def
+5   0    1   20    0   0.000   0.000   0.350   C94 5:*-1-20-*  Def
+0   5    1   20    5   0.000   0.000   0.344   C94
+0   5    1   20   20   0.000   0.000   0.361   C94
+0   0    1   22    0   0.000   0.000   0.236   E94 0:*1-22-* Def
+5   0    1   22    0   0.000   0.000   0.236   E94 5:*1-22-* Def
+0   0    1   25    0   0.000   0.000   0.300   C94 0:*-1-25-* Def
+5   0    1   25    0   0.000   0.000   0.251   E94 5:*1-25-* Def
+0   1    1   25    1   0.000  -0.207   0.232   X94
+0   1    1   25   32   0.000   0.288   0.218   X94
+0   5    1   25    1   0.000   0.152   0.235   X94
+0   5    1   25    6   0.000   0.000   0.495   X94
+0   5    1   25   32   0.000  -0.130   0.214   X94
+0   5    1   25   43   0.000   0.000   0.466   X94
+0   5    1   25   72   0.000   0.000   0.243   X94
+0   0    1   26    0   0.000   0.000   0.450   C94 0:*-1-26-* Def
+5   0    1   26    0   0.000   0.000   0.376   E94 5:*1-26-* Def
+0   5    1   26   12   0.000   0.000   0.439   X94
+0   5    1   26   71   0.000   0.000   0.472   X94
+0   0    1   34    0   0.000   0.000   0.250   C94 0:*-1-34-* Def
+5   0    1   34    0   0.000   0.000   0.198   E94 5:*1-34-* Def
+0   1    1   34   36   0.000   0.000   0.187   C94
+0   5    1   34    1   0.000   0.000   0.247   C94
+0   5    1   34   36   0.000   0.000   0.259   C94
+0   0    1   37    0   0.000   0.000   0.200   C94 0:*-1-37-* Def
+5   0    1   37    0   0.000   0.000   0.000   E94 5:*1-37-* Def
+0   1    1   37   37   0.000   0.449   0.000   C94
+0   5    1   37   37   0.000  -0.420   0.391   C94
+0   6    1   37   37   0.000   0.000   0.150   C94
+0   0    1   39    0   0.000   0.000   0.000   C94 0:*-1-39-* Def
+5   0    1   39    0   0.000   0.000   0.000   E94 5:*1-39-* Def
+0   1    1   39   63   0.000  -0.080  -0.056   C94
+0   5    1   39   63   0.000   0.000  -0.113   C94
+0   0    1   40    0   0.000   0.000   0.250   C94 0:*-1-40-* Def
+5   0    1   40    0   0.000   0.000   0.297   E94 5:*1-40-* Def
+0   5    1   40   28   0.000  -0.105   0.000   C94S
+0   5    1   40   37   0.000   0.000   0.468   C94S
+0   0    1   41    0   0.000   0.600   0.000   C94 0:*-1-41-* Def
+0   1    1   41   32   0.000   1.263   0.000   C94
+0   5    1   41   32   0.000   0.000  -0.106   C94
+0   5    1   41   72   0.000   0.632   0.000   X94
+0   0    1   43    0   0.000   0.000   0.150   C94 0:*-1-43-* Def
+5   0    1   43    0   0.000   0.000   0.297   E94 5:*1-43-* Def
+0   5    1   43   18   0.357  -0.918   0.000   X94
+0   5    1   43   25   0.000   0.000   0.061   X94
+0   5    1   43   28  -0.249   0.382   0.343   X94
+0   0    1   45    0   0.000   0.000   0.100   C94 0:*-1-45-* Def
+0   5    1   45   32   0.000   0.000   0.125   X94
+0   0    1   46    0   0.000   0.000  -0.500   C94 0:*-1-46-* Def
+0   5    1   46    7   0.000   0.000  -0.540   X94
+0   0    1   54    0   0.000   0.000   0.000   C94 0:*-1-54-* Def
+2   0    1   54    0   0.000   0.000   0.000   E94 2:*1-54-* Def
+5   0    1   54    0   0.000   0.000   0.000   E94 5:*1-54-* Def
+0   5    1   54    3   0.000   0.000  -0.315   C94
+0   5    1   54   36   0.000   0.000   0.315   C94
+0   0    1   55    0   0.000   0.000   0.000   C94 0:*-1-55-* Def
+5   0    1   55    0   0.000   0.000   0.000   E94 5:*1-55-* Def
+0   5    1   55   36   0.000  -0.058   0.084   C94
+0   5    1   55   57   0.000  -0.058  -0.092   C94
+0   0    1   56    0   0.000   0.000  -0.300   C94 0:*-1-56-* Def
+0   1    1   56   36   0.875   0.668  -0.015   C94
+0   1    1   56   57  -0.870   0.775  -0.406   C94
+0   5    1   56   36  -0.958  -0.629  -0.372   C94
+0   5    1   56   57   0.952  -0.715  -0.483   C94
+0   0    1   57    0   0.000   0.000   0.000   E94 0:*1-57-* Def
+5   0    1   57    0   0.000   0.000   0.000   E94 5:*1-57-* Def
+0   0    1   58    0   0.000   0.000   0.000   E94 0:*1-58-* Def
+0   0    1   62    0   0.000   0.000   0.250   C94 0:*-1-62-* Def
+0   5    1   62   18   0.000   0.000   0.270   X94
+0   0    1   63    0   0.000   0.000   0.000   E94 0:*1-63-* Def
+5   0    1   63    0   0.000   0.000   0.000   E94 5:*1-63-* Def
+0   0    1   64    0   0.000   0.000   0.000   E94 0:*1-64-* Def
+5   0    1   64    0   0.000   0.000   0.000   E94 5:*1-64-* Def
+0   0    1   67    0   0.000   0.000   0.000   E94 0:*1-67-* Def
+5   0    1   67    0   0.000   0.000   0.000   E94 5:*1-67-* Def
+0   0    1   68    0   0.000   0.000   0.400   C94 0:*-1-68-* Def
+0   1    1   68    1  -0.117   0.090   0.751   C94
+0   1    1   68   23   0.373   0.153   0.635   C94
+0   1    1   68   32  -0.090  -0.169   0.075   C94
+0   5    1   68    1   0.134  -0.112   0.329   C94
+0   5    1   68   23  -0.361  -0.202   0.560   C94
+0   5    1   68   32   0.072   0.218   0.093   C94
+0   0    1   73    0   0.000   0.000   0.500   C94 0:*-1-73-* Def
+0   5    1   73   32   0.000   0.000   0.509   X94
+0   5    1   73   72   0.000   0.000   0.443   X94
+0   0    1   75    0   0.000   0.000   0.000   E94 0:*1-75-* Def
+0   0    1   78    0   0.000   0.000   0.000   E94 0:*1-78-* Def
+0   0    1   80    0   0.000   0.000   0.000   E94 0:*1-80-* Def
+0   0    1   81    0   0.000   0.000   0.000   E94 0:*1-81-* Def
+0   0    2    2    0   0.000  12.000   0.000   C94 0:*-2=2-* Def
+1   0    2    2    0   0.000   1.800   0.000   C94 1:*=2-2=*  Def
+5   0    2    2    0   0.000  12.000   0.000   C94 5:*-2=2-*  Def
+0   1    2    2    1  -0.403  12.000   0.000   C94
+0   1    2    2    2   0.000  12.000   0.000   C94
+1   1    2    2    2  -0.418   2.089  -0.310   C94
+0   1    2    2    5   0.000  12.000   0.000   C94
+1   1    2    2    5   0.412   2.120   0.269   C94
+1   2    2    2    2   0.094   1.621   0.877   C94
+0   2    2    2    5   0.000  12.000   0.000   C94
+1   2    2    2    5   0.317   1.421  -0.870   C94
+0   3    2    2    5   0.000  12.000   0.000   C94
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+0   0   30   40    0   0.000   3.600   0.000   E94 0:*-30-40-* Def
+1   0   30   67    0   0.000   1.800   0.000   E94 1:*-30-67-* Def
+0   0   34   37    0   0.000   0.000   0.000   E94 0:*-34-37-* Def
+0   0   34   43    0   0.000   0.000   0.250   E94 0:*-34-43-* Def
+0   0   37   37    0   0.000   7.000   0.000   C94 0:*-37-37-* Def
+1   0   37   37    0   0.000   2.000   0.000   #E94 1:*-37-37-* Def
+4   0   37   37    0   0.000   6.000   0.000   E94 4:*-37-37-* Def
+5   0   37   37    0   0.000   6.000   0.000   E94 5:*-37-37-* Def
+0   1   37   37    5   0.000   7.000   0.000   C94
+0   1   37   37   37   0.000   7.000   0.000   C94
+0   2   37   37    5   0.000   7.000   0.000   C94
+0   2   37   37   37   0.000   7.000   0.000   C94
+0   3   37   37    5   0.000   7.000   0.000   C94
+0   3   37   37   37   0.000   7.000   0.000   C94
+0   5   37   37    5   0.000   7.000   0.000   C94
+0   5   37   37    6   0.000   7.000   0.000   C94
+0   5   37   37   15   0.000   7.000   0.000   C94
+0   5   37   37   18   0.000   7.000   0.000   X94
+0   5   37   37   37   0.000   7.000   0.000   C94
+0   5   37   37   40   0.000   7.000   0.000   C94
+0   5   37   37   43   0.000   7.000   0.000   X94
+0   6   37   37   37   0.000   7.000   0.000   C94
+0  15   37   37   37   0.000   7.000   0.000   C94
+0  18   37   37   37   0.000   7.000   0.000   X94
+0  37   37   37   37   0.000   7.000   0.000   C94
+0  37   37   37   40   0.000   7.000   0.000   C94
+0  37   37   37   43   0.000   7.000   0.000   X94
+0   0   37   38    0   0.000   7.000   0.000   C94 0:*-37-38-* Def
+0   0   37   39    0   0.000   3.600   0.000   E94 0:*-37-39-* Def
+1   0   37   39    0   0.000   6.000   0.000   E94 1:*-37-39-* Def
+0   0   37   40    0   0.000   4.000   0.000   C94 0:*-37-40-* Def
+5   0   37   40    0   0.000   3.600   0.000   E94 5:*-37-40-* Def
+0  37   37   40    1   0.000   4.095   0.382   C94S
+0  37   37   40   28   0.698   2.542   3.072   C94S
+0   0   37   41    0   0.000   1.800   0.000   E94 0:*-37-41-* Def
+0   0   37   43    0   0.000   2.000   1.800   C94 0:*-37-43-* Def
+5   0   37   43    0   0.000   3.600   0.000   E94 5:*-37-43-* Def
+0  37   37   43   18   0.372   2.284   2.034   X94
+0  37   37   43   28   0.000   1.694   1.508   X94
+0   0   37   45    0   0.000   1.800   0.000   E94 0:*-37-45-* Def
+0   0   37   46    0   0.000   1.800   0.000   E94 0:*-37-46-* Def
+0   0   37   55    0   0.000   4.800   0.000   E94 0:*-37-55-* Def
+0   0   37   56    0   0.000   4.800   0.000   E94 0:*-37-56-* Def
+1   0   37   57    0   0.000   1.800   0.000   E94 1:*-37-57-* Def
+0   0   37   58    0   0.000   6.000   0.000   E94 0:*-37-58-* Def
+1   0   37   58    0   0.000   4.800   0.000   E94 1:*-37-58-* Def
+0   0   37   62    0   0.000   3.600   0.000   E94 0:*-37-62-* Def
+0   0   37   63    0   0.000   7.000   0.000   C94 0:*-37-63-* Def
+1   0   37   63    0   0.000   1.800   0.000   E94 1:*-37-63-* Def
+0   0   37   64    0   0.000   7.000   0.000   C94 0:*-37-64-* Def
+1   0   37   64    0   0.000   1.800   0.000   E94 1:*-37-64-* Def
+1   0   37   67    0   0.000   1.800   0.000   E94 1:*-37-67-* Def
+0   0   37   69    0   0.000   7.000   0.000   C94 0:*-37-69-* Def
+0   0   37   78    0   0.000   6.000   0.000   E94 0:*-37-78-* Def
+0   0   37   81    0   0.000   6.000   0.000   E94 0:*-37-81-* Def
+1   0   37   81    0   0.000   4.800   0.000   E94 1:*-37-81-* Def
+0   0   38   38    0   0.000   7.000   0.000   C94 0:*-38-38-* Def
+0   0   38   58    0   0.000   7.000   0.000   C94 0:*-38-58-* Def
+0   0   38   63    0   0.000   7.000   0.000   C94 0:*-38-63-* Def
+0   0   38   64    0   0.000   7.000   0.000   C94 0:*-38-64-* Def
+0   0   38   69    0   0.000   6.000   0.000   E94 0:*-38-69-* Def
+0   0   38   78    0   0.000   6.000   0.000   E94 0:*-38-78-* Def
+0   0   39   40    0   0.000   0.000   0.000   E94 0:*-39-40-* Def
+0   0   39   45    0   0.000   6.000   0.000   E94 0:*-39-45-* Def
+0   0   39   63    0   0.000   4.000   0.000   C94 0:*-39-63-* Def
+1   0   39   63    0   0.000   6.000   0.000   E94 1:*-39-63-* Def
+5   0   39   63    0   0.000   3.600   0.000   E94 5:*-39-63-* Def
+0   1   39   63    5   0.000   4.000   0.000   C94
+0   1   39   63   64   0.000   4.000   0.000   C94
+0  18   39   63    5   0.000   4.000   0.000   X94
+0  18   39   63   64   0.000   4.000   0.000   X94
+0  63   39   63    5   0.000   4.000   0.000   C94
+0  63   39   63   64   0.000   4.000   0.000   C94
+0   0   39   64    0   0.000   3.600   0.000   E94 0:*-39-64-* Def
+1   0   39   64    0   0.000   6.000   0.000   E94 1:*-39-64-* Def
+0   0   39   65    0   0.000   4.000   0.000   C94 0:*-39-65-* Def
+0   0   39   78    0   0.000   3.600   0.000   E94 0:*-39-78-* Def
+0   0   40   40    0   0.000   0.000   0.375   E94 0:*-40-40-* Def
+0   0   40   45    0   0.000   3.600   0.000   E94 0:*-40-45-* Def
+0   0   40   46    0   0.000   3.600   0.000   E94 0:*-40-46-* Def
+0   0   40   54    0   0.000   3.600   0.000   E94 0:*-40-54-* Def
+2   0   40   54    0   0.000   3.600   0.000   E94 2:*-40-54-* Def
+0   0   40   63    0   0.000   3.600   0.000   E94 0:*-40-63-* Def
+0   0   40   64    0   0.000   3.600   0.000   E94 0:*-40-64-* Def
+0   0   40   78    0   0.000   3.600   0.000   E94 0:*-40-78-* Def
+0   0   41   41    0   0.000   1.800   0.000   E94 0:*-41-41-* Def
+0   0   41   55    0   0.000   4.800   0.000   E94 0:*-41-55-* Def
+0   0   41   62    0   0.000   3.600   0.000   E94 0:*-41-62-* Def
+0   0   41   80    0   0.000   1.800   0.000   E94 0:*-41-80-* Def
+0   0   43   43    0   0.000   0.000   0.375   E94 0:*-43-43-* Def
+0   0   43   45    0   0.000   3.600   0.000   E94 0:*-43-45-* Def
+0   0   43   64    0   0.000   3.600   0.000   E94 0:*-43-64-* Def
+0   0   44   57    0   0.000   7.000   0.000   C94 0:*-44-57-* Def
+0   0   44   63    0   0.000   7.000   0.000   C94 0:*-44-63-* Def
+0   0   44   65    0   0.000   7.000   0.000   C94 0:*-44-65-* Def
+0   0   44   78    0   0.000   2.846   0.000   E94 0:*-44-78-* Def
+0   0   44   80    0   0.000   2.846   0.000   E94 0:*-44-80-* Def
+0   0   45   63    0   0.000   1.800   0.000   E94 0:*-45-63-* Def
+0   0   45   64    0   0.000   1.800   0.000   E94 0:*-45-64-* Def
+0   0   45   78    0   0.000   1.800   0.000   E94 0:*-45-78-* Def
+0   0   55   57    0   0.000  10.000   0.000   C94 0:*-55-57-* Def
+2   0   55   57    0   0.000   4.800   0.000   E94 2:*-55-57-* Def
+5   0   55   57    0   0.000   4.800   0.000   E94 5:*-55-57-* Def
+0   1   55   57    5   0.423  12.064   0.090   C94
+0   1   55   57   55  -0.428  12.044   0.000   C94
+0  36   55   57    5  -0.268   8.077  -0.806   C94
+0  36   55   57   55   0.273   8.025   0.692   C94
+0   0   55   62    0   0.000   3.600   0.000   E94 0:*-55-62-* Def
+0   0   55   64    0   0.000   4.800   0.000   E94 0:*-55-64-* Def
+0   0   55   80    0   0.000   4.800   0.000   E94 0:*-55-80-* Def
+0   0   56   57    0   0.000   6.000   0.000   C94 0:*-56-57-* Def
+0   1   56   57   56   0.000   6.886  -0.161   C94
+0  36   56   57   56   0.000   4.688   0.107   C94
+0   0   56   63    0   0.000   4.800   0.000   E94 0:*-56-63-* Def
+0   0   56   80    0   0.000   4.800   0.000   E94 0:*-56-80-* Def
+1   0   57   63    0   0.000   1.800   0.000   E94 1:*-57-63-* Def
+1   0   57   64    0   0.000   1.800   0.000   E94 1:*-57-64-* Def
+0   0   58   63    0   0.000   6.000   0.000   E94 0:*-58-63-* Def
+0   0   58   64    0   0.000   6.000   0.000   E94 0:*-58-64-* Def
+0   0   59   63    0   0.000   7.000   0.000   C94 0:*-59-63-* Def
+0   0   59   65    0   0.000   7.000   0.000   C94 0:*-59-65-* Def
+0   0   59   78    0   0.000   3.600   0.000   E94 0:*-59-78-* Def
+0   0   59   80    0   0.000   3.600   0.000   E94 0:*-59-80-* Def
+0   0   59   82    0   0.000   3.600   0.000   E94 0:*-59-82-* Def
+0   0   62   63    0   0.000   3.600   0.000   E94 0:*-62-63-* Def
+0   0   62   64    0   0.000   3.600   0.000   E94 0:*-62-64-* Def
+1   0   63   63    0   0.000   1.800   0.000   E94 1:*-63-63-* Def
+0   0   63   64    0   0.000   7.000   0.000   C94 0:*-63-64-* Def
+0   5   63   64    5   0.000   7.000   0.000   C94
+0   5   63   64   64   0.000   7.000   0.000   C94
+0  39   63   64    5   0.000   7.000   0.000   C94
+0  39   63   64   64   0.000   7.000   0.000   C94
+0   0   63   66    0   0.000   7.000   0.000   C94 0:*-63-66-* Def
+0   0   63   78    0   0.000   6.000   0.000   E94 0:*-63-78-* Def
+0   0   63   81    0   0.000   6.000   0.000   E94 0:*-63-81-* Def
+0   0   64   64    0   0.000   7.000   0.000   C94 0:*-64-64-* Def
+1   0   64   64    0   0.000   1.800   0.000   E94 1:*-64-64-* Def
+0   5   64   64    5   0.000   7.000   0.000   C94
+0   5   64   64   63   0.000   7.000   0.000   C94
+0  63   64   64   63   0.000   7.000   0.000   C94
+0   0   64   65    0   0.000   7.000   0.000   C94 0:*-64-65-* Def
+0   0   64   66    0   0.000   7.000   0.000   C94 0:*-64-66-* Def
+0   0   64   78    0   0.000   6.000   0.000   E94 0:*-64-78-* Def
+0   0   64   81    0   0.000   6.000   0.000   E94 0:*-64-81-* Def
+5   0   64   81    0   0.000   6.000   0.000   E94 5:*-64-81-* Def
+0   0   64   82    0   0.000   6.000   0.000   E94 0:*-64-82-* Def
+0   0   65   66    0   0.000   7.000   0.000   C94 0:*-65-66-* Def
+0   0   65   78    0   0.000   6.000   0.000   E94 0:*-65-78-* Def
+0   0   65   81    0   0.000   6.000   0.000   E94 0:*-65-81-* Def
+0   0   65   82    0   0.000   6.000   0.000   E94 0:*-65-82-* Def
+0   0   66   66    0   0.000   7.000   0.000   C94 0:*-66-66-* Def
+0   0   66   78    0   0.000   6.000   0.000   E94 0:*-66-78-* Def
+0   0   66   81    0   0.000   6.000   0.000   E94 0:*-66-81-* Def
+0   0   67   67    0   0.000  12.000   0.000   E94 0:*-67-67-* Def
+5   0   67   67    0   0.000  12.000   0.000   E94 5:*-67-67-* Def
+0   0   76   76    0   0.000   3.600   0.000   E94 0:*-76-76-* Def
+0   0   76   78    0   0.000   3.600   0.000   E94 0:*-76-78-* Def
+0   0   78   78    0   0.000   7.000   0.000   C94 0:*-78-78-* Def
+0   0   78   79    0   0.000   6.000   0.000   E94 0:*-78-79-* Def
+0   0   78   81    0   0.000   4.000   0.000   C94 0:*-78-81-* Def
+0   0   79   79    0   0.000   6.000   0.000   E94 0:*-79-79-* Def
+0   0   79   81    0   0.000   6.000   0.000   E94 0:*-79-81-* Def
+0   0   80   81    0   0.000   4.000   0.000   C94 0:*-80-81-* Def
+$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffstbn.par	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,292 @@
+*
+*                Copyright (c) Merck and Co., Inc., 1994
+*                         All Rights Reserved
+*
+* MMFF STRETCH-BEND PARAMETERS- Rev: 23-FEB-93  Source: MMFF94
+* C94 - CORE MMFF94 parameter, from fits to HF/6-31G* 2nd D's
+* X94 - EXTD MMFF94 parameter, also from fits to HF/6-31G* 2nd D's
+*
+* types I, J, K    kbaIJK    kbaKJI   Source
+0   1    1    1     0.206     0.206   C94
+0   1    1    2     0.136     0.197   C94
+0   1    1    3     0.211     0.092   C94
+0   1    1    5     0.227     0.070   C94
+0   1    1    6     0.173     0.417   C94
+0   1    1    8     0.136     0.282   C94
+0   1    1   10     0.187     0.338   C94
+0   1    1   11     0.209     0.633   C94
+0   1    1   12     0.176     0.386   C94
+0   1    1   15     0.139     0.217   C94
+0   1    1   34     0.236     0.436   C94
+0   1    1   37     0.152     0.260   C94
+0   1    1   39     0.144     0.595   C94
+0   1    1   41     0.122     0.051   C94
+0   1    1   56     0.262     0.451   C94
+0   1    1   68     0.186     0.125   C94
+0   2    1    2     0.282     0.282   C94
+0   2    1    3     0.206     0.022   C94
+0   2    1    5     0.234     0.088   C94
+0   2    1    6     0.183     0.387   C94
+0   2    1    8     0.214     0.363   C94
+0   3    1    5     0.157     0.115   C94
+0   3    1    6    -0.036     0.456   C94
+0   3    1   10     0.038     0.195   C94
+0   5    1    5     0.115     0.115   C94
+0   5    1    6     0.013     0.436   C94
+0   5    1    8     0.027     0.358   C94
+0   5    1    9     0.040     0.418   C94
+0   5    1   10     0.043     0.261   C94
+0   5    1   11     0.003     0.452   C94
+0   5    1   12    -0.018     0.380   C94
+0   5    1   15     0.018     0.255   C94
+0   5    1   18     0.121     0.218   X94
+0   5    1   20     0.069     0.327   C94
+0   5    1   22     0.055     0.267   X94
+0   5    1   34    -0.003     0.342   C94
+0   5    1   37     0.074     0.287   C94
+0   5    1   39     0.092     0.607   C94
+0   5    1   40     0.023     0.335   C94
+0   5    1   41     0.093     0.118   C94
+0   5    1   54     0.016     0.343   C94
+0   5    1   55     0.030     0.397   C94
+0   5    1   56     0.031     0.384   C94
+0   5    1   68     0.041     0.216   C94
+0   6    1    6     0.320     0.320   C94
+0   6    1   37     0.310     0.160   C94
+0  11    1   11     0.586     0.586   C94
+0  12    1   12     0.508     0.508   C94
+0   1    2    1     0.250     0.250   C94
+0   1    2    2     0.203     0.207   C94
+2   1    2    2     0.222     0.269   C94
+2   1    2    3     0.244     0.292   C94
+0   1    2    5     0.215     0.128   C94
+2   1    2   37     0.246     0.260   C94
+1   2    2    2     0.250     0.219   C94
+2   2    2    3     0.155     0.112   C94
+0   2    2    5     0.207     0.157   C94
+1   2    2    5     0.267     0.159   C94
+0   2    2    6     0.118     0.576   C94
+2   2    2   37     0.143     0.172   C94
+0   2    2   40     0.289     0.390   C94
+0   2    2   41     0.191    -0.047   C94
+1   3    2    5     0.264     0.156   C94
+0   5    2    5     0.140     0.140   C94
+0   5    2    6     0.213     0.502   C94
+2   5    2   37     0.153     0.288   C94
+0   5    2   40     0.070     0.463   C94
+0   5    2   41     0.191     0.005   C94
+0   1    3    1     0.358     0.358   C94
+2   1    3    2     0.246     0.409   C94
+2   1    3    3     0.303     0.145   C94
+0   1    3    5     0.321     0.183   C94
+0   1    3    6     0.338     0.732   C94
+0   1    3    7     0.154     0.856   C94
+0   1    3   10     0.223     0.732   C94
+2   1    3   37     0.217     0.207   C94
+1   2    3    5     0.407     0.159   C94
+1   2    3    6     0.429     0.473   C94
+1   2    3    7     0.214     0.794   C94
+1   2    3    9     0.227     0.610   C94
+1   2    3   10     0.298     0.600   C94
+1   3    3    5     0.251     0.133   C94
+1   3    3    6     0.066     0.668   C94
+1   3    3    7    -0.093     0.866   C94
+0   5    3    5     0.126     0.126   C94
+0   5    3    6     0.174     0.734   C94
+0   5    3    7     0.032     0.805   C94
+0   5    3    9     0.037     0.669   C94
+0   5    3   10     0.169     0.619   C94
+0   5    3   40     0.087     0.685   C94
+0   5    3   54     0.098     0.210   C94
+0   6    3    7     0.494     0.578   C94
+4   6    3   20     1.179     0.752   X94
+2   6    3   37     0.350     0.175   C94
+0   7    3   10     0.771     0.353   C94
+0   7    3   20     0.865    -0.181   C94
+2   7    3   37     0.707     0.007   C94
+0   9    3   40     0.680     0.260   C94
+0  10    3   10     1.050     1.050   C94
+4  20    3   20     0.536     0.536   C94
+0  40    3   40     0.482     0.482   C94
+0   1    6    1     0.309     0.309   C94
+0   1    6    2     0.157     0.375   C94
+0   1    6    3    -0.153     0.252   C94
+0   1    6   21     0.256     0.143   C94
+0   1    6   37     0.163     0.375   C94
+0   2    6    3    -0.228     0.052   C94
+0   2    6   29     0.259     0.163   C94
+4   3    6   20     0.456     0.379   X94
+0   3    6   24     0.215     0.064   C94
+0   3    6   37    -0.225    -0.320   C94
+0   8    6   21     0.304     0.055   C94
+0  10    6   21     0.419     0.158   C94
+0  18    6   33     0.309     0.120   X94
+4  20    6   20     0.739     0.739   C94
+0  29    6   37     0.130     0.241   C94
+0  31    6   31     0.227     0.227   X94
+0   1    8    1     0.312     0.312   C94
+0   1    8    6     0.212     0.354   C94
+0   1    8   23     0.309     0.135   C94
+0   6    8   23     0.418     0.020   C94
+4  20    8   20     0.653     0.653   C94
+0  20    8   23     0.128     0.122   C94
+0  23    8   23     0.190     0.190   C94
+0   1    9    3     0.326     0.580   C94
+0   3    9   27     0.464     0.222   C94
+0   1   10    1     0.063     0.063   C94
+0   1   10    3    -0.021     0.340   C94
+0   1   10    6    -0.024     0.374   C94
+0   1   10   28     0.155    -0.051   C94
+0   3   10    3    -0.219    -0.219   C94
+0   3   10    6     0.497     0.513   C94
+0   3   10   28     0.137     0.066   C94
+0  28   10   28     0.081     0.081   C94
+0   1   15    1     0.125     0.125   C94
+0   1   15   15     0.012     0.238   C94
+0   1   15   37     0.048     0.229   C94
+0   1   15   71     0.080    -0.012   C94
+0  15   15   71     0.172    -0.068   C94
+0  37   15   71     0.187    -0.027   C94
+0  71   15   71     0.045     0.045   C94
+0   1   18    1     0.023     0.023   X94
+0   1   18    6     0.003     0.213   X94
+0   1   18   32    -0.091     0.390   X94
+0   1   18   43    -0.008     0.607   X94
+0   6   18    6     0.088     0.088   X94
+0   6   18   32     0.123     0.369   X94
+0  32   18   32     0.404     0.404   X94
+0  32   18   43     0.384     0.281   X94
+0  43   18   43     0.428     0.428   X94
+0   1   20    5     0.290     0.098   C94
+0   1   20   20     0.179     0.004   C94
+0   3   20    5    -0.049     0.171   C94
+4   3   20   20     0.607     0.437   C94
+0   5   20    5     0.182     0.182   C94
+0   5   20    6     0.051     0.312   C94
+0   5   20    8     0.072     0.226   C94
+0   5   20   12     0.014     0.597   C94
+0   5   20   20     0.101     0.079   C94
+0   5   20   30     0.108     0.123   C94
+4   6   20   20     0.823     0.396   C94
+4   8   20   20     0.701     0.369   C94
+0  12   20   20     0.310     0.000   C94
+4  20   20   20     0.283     0.283   C94
+4  20   20   30     0.340     0.529   C94
+0   1   22    5     0.067     0.174   X94
+0   1   22   22     0.199     0.039   X94
+0   5   22    5     0.254     0.254   C94
+0   5   22   22     0.181     0.108   C94
+5  22   22   22     0.000     0.000   C94
+0   5   26    5    -0.121    -0.121   X94
+0   5   30   20     0.251     0.007   C94
+0   5   30   30     0.267     0.054   C94
+4  20   30   30     0.413     0.705   C94
+0   1   34    1     0.202     0.202   C94
+0   1   34   36     0.160    -0.009   C94
+0  36   34   36     0.087     0.087   C94
+0   1   37   37     0.485     0.311   C94
+1   2   37   37     0.321     0.235   C94
+1   3   37   37     0.179     0.217   C94
+0   5   37   37     0.279     0.250   C94
+0   5   37   38     0.267     0.389   C94
+0   5   37   63     0.216     0.434   C94
+0   5   37   64     0.167     0.364   C94
+0   5   37   69     0.273     0.391   C94
+0   6   37   37     0.830     0.339   C94
+0  15   37   37     0.650     0.259   C94
+0  37   37   37    -0.411    -0.411   C94
+0  37   37   38    -0.424    -0.466   C94
+0  37   37   40     0.429     0.901   C94
+0  37   37   63    -0.173    -0.215   C94
+0  37   37   64    -0.229    -0.229   C94
+0  37   37   69    -0.244    -0.555   C94
+0  38   37   38    -0.516    -0.516   C94
+0  37   38   37    -0.342    -0.342   C94
+0  37   38   38    -0.164    -1.130   C94
+0   1   39   63     0.313     0.500   C94
+0  23   39   63    -0.131     0.422   C94
+0  23   39   65    -0.122     0.281   C94
+0  63   39   63     0.469     0.469   C94
+0  63   39   65     0.741     0.506   C94
+0  65   39   65     0.706     0.706   C94
+0   1   40   28     0.238     0.091   C94
+0   1   40   37     0.153     0.590   C94
+0   2   40   28     0.342     0.156   C94
+0   3   40   28     0.228     0.104   C94
+0  28   40   28     0.094     0.094   C94
+0  28   40   37     0.186     0.423   C94
+0   1   41   32     0.503     0.943   C94
+0   2   41   32     0.594     0.969   C94
+0   5   41   32     0.276     0.852   C94
+0  32   41   32     0.652     0.652   C94
+0  18   43   23     0.377     0.057   X94
+0  23   43   23     0.082     0.082   X94
+0  63   44   63     0.591     0.591   C94
+0  63   44   65     0.857     0.978   C94
+0  50   49   50     0.072     0.072   C94
+0   1   54    3     0.192    -0.051   C94
+0   1   54   36     0.240     0.079   C94
+0   3   54   36     0.005     0.127   C94
+0  36   54   36     0.148     0.148   C94
+0   1   55   36     0.189     0.033   C94
+0   1   55   57     0.166     0.211   C94
+0  36   55   36     0.106     0.106   C94
+0  36   55   57     0.093     0.080   C94
+0   1   56   36     0.211    -0.040   C94
+0   1   56   57     0.026     0.386   C94
+0  36   56   36     0.101     0.101   C94
+0  36   56   57     0.108     0.068   C94
+0   5   57   55     0.043     0.420   C94
+0  55   57   55     0.125     0.125   C94
+0  56   57   56     0.431     0.431   C94
+0  58   57   58     0.732     0.732   C94
+0  63   59   63     0.497     0.497   C94
+0  63   59   65     0.723     0.874   C94
+0   5   63   39     0.009     0.654   C94
+0   5   63   44    -0.015     0.446   C94
+0   5   63   59     0.067     0.588   C94
+0   5   63   64     0.055     0.370   C94
+0   5   63   66     0.110     0.464   C94
+0  37   63   39     0.178     0.523   C94
+0  37   63   64    -0.045     0.497   C94
+0  39   63   64     0.422     0.409   C94
+0  39   63   66     0.436     0.525   C94
+0  44   63   64     0.581     0.426   C94
+0  44   63   66     0.542     0.365   C94
+0  59   63   64     0.852     0.332   C94
+0  59   63   66     0.775     0.300   C94
+0   5   64   63     0.086     0.345   C94
+0   5   64   64     0.085     0.369   C94
+0   5   64   65     0.051     0.436   C94
+0   5   64   66     0.113     0.452   C94
+0  37   64   63     0.059     0.299   C94
+0  37   64   64     0.277     0.377   C94
+0  63   64   64     0.206     0.030   C94
+0  63   64   66     0.171     0.078   C94
+0  64   64   65     0.079     0.403   C94
+0  65   64   66     0.406     0.066   C94
+0  39   65   64     0.528     0.644   C94
+0  39   65   66     0.397     0.258   C94
+0  44   65   64     0.816     0.543   C94
+0  59   65   64     1.177     0.594   C94
+0  63   66   64     0.213    -0.173   C94
+0  63   66   66     0.234     0.077   C94
+0  64   66   65    -0.149     0.383   C94
+0  65   66   66     0.199     0.101   C94
+0   1   68    1     0.217     0.217   C94
+0   1   68   23     0.285     0.050   C94
+0   1   68   32    -0.047     0.503   C94
+0  23   68   23     0.145     0.145   C94
+0  23   68   32    -0.182     0.504   C94
+0  32   69   37     1.018     0.418   C94
+0  37   69   37    -0.169    -0.169   C94
+0  31   70   31     0.210     0.210   C94
+0   5   78   78     0.279     0.250   C94
+0   5   78   81     0.083     0.250   C94
+0  78   78   81    -0.398     0.314   C94
+0   5   80   81    -0.101     0.691   C94
+0  81   80   81     0.732     0.732   C94
+0  36   81   78     0.021     0.368   C94
+0  36   81   80     0.018     0.422   C94
+0  78   81   80     0.366     0.419   C94
+$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmfftor.par	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,938 @@
+*
+*                 Copyright (c) Merck and Co., Inc., 1994
+*                           All Rights Reserved
+*
+* MMFF TORSION PARAMETERS- Rev:  26-OCT-94  Source: MMFF94
+* C94  - CORE MMFF94 parameter - from fits to conformational energies
+* X94  - EXTD MMFF94 parameter - also from fits to conformational E's
+* E94  - EXTD MMFF94 parameter - from empirical rule
+* #E94 - Adjusted from empirical rule value
+*
+*      atom types       V1      V2      V3     Source
+0   0    1    1    0   0.000   0.000   0.300   C94 0:*-1-1-* Def
+5   0    1    1    0   0.200  -0.800   1.500   C94 5:*-1-1-* Def
+0   1    1    1    1   0.103   0.681   0.332   C94
+5   1    1    1    1   0.144  -0.547   1.126   C94
+0   1    1    1    2  -0.295   0.438   0.584   C94
+0   1    1    1    3   0.066  -0.156   0.143   C94
+0   1    1    1    5   0.639  -0.630   0.264   C94
+0   1    1    1    6  -0.688   1.757   0.477   C94
+5   1    1    1    6   0.000   0.000   0.054   C94
+0   1    1    1    8  -1.420  -0.092   1.101   C94
+5   1    1    1    8   0.000  -0.158   0.323   C94
+0   1    1    1   11   0.593   0.662   1.120   C94
+0   1    1    1   12  -0.678   0.417   0.624   C94
+0   1    1    1   15  -0.714   0.698   0.000   C94
+0   1    1    1   34  -0.647   0.550   0.590   C94
+0   2    1    1    5   0.321  -0.411   0.144   C94
+0   3    1    1    3   0.443   0.000  -1.140   C94
+0   3    1    1    5  -0.256   0.058   0.000   C94
+0   3    1    1    6  -0.679  -0.029   0.000   C94
+0   5    1    1    5   0.284  -1.386   0.314   C94
+0   5    1    1    6  -0.654   1.072   0.279   C94
+0   5    1    1    8  -0.744  -1.235   0.337   C94
+0   5    1    1   10   0.000   0.000   0.427   C94
+0   5    1    1   11   0.000   0.516   0.291   C94
+0   5    1    1   12   0.678  -0.602   0.398   C94
+0   5    1    1   15   1.142  -0.644   0.367   C94
+0   5    1    1   25   0.000   0.000   0.295   X94
+0   5    1    1   34   0.692  -0.530   0.278   C94
+0   5    1    1   37   0.000   0.000   0.389   C94
+0   5    1    1   39   0.000   0.000   0.278   C94
+0   5    1    1   41   0.000   0.000  -0.141   C94
+0   5    1    1   56   0.000   0.000   0.324   C94
+0   5    1    1   68   0.000   0.000   0.136   C94
+0   6    1    1    6   0.408   1.397   0.961   C94
+5   6    1    1    6   0.313  -1.035   1.631   C94
+0   8    1    1    8   1.055   0.834   0.000   C94
+0  11    1    1   11  -0.387  -0.543   1.405   C94
+0  12    1    1   12   0.000   0.000   0.893   C94
+0  15    1    1   15  -0.177   0.000   0.049   C94
+0   0    1    2    0   0.000   0.000   0.000   C94 0:*-1-2-* Def
+2   0    1    2    0   0.000   0.000   0.000   E94 2:*-1-2-* Def
+5   0    1    2    0   0.000   0.000   0.000   C94 5:*-1-2-*  Def
+0   0    1    2    2   0.000   0.000  -0.650   C94 0:*-1-2=2 Def
+5   0    1    2    2   0.000   0.000  -0.650   C94 5:*-1-2=2  Def
+0   1    1    2    1   0.419   0.296   0.282   C94
+0   1    1    2    2  -0.494   0.274  -0.630   C94
+0   1    1    2    5   0.075   0.000   0.358   C94
+0   2    1    2    2  -0.293   0.115  -0.508   C94
+0   2    1    2    5   0.301   0.104   0.507   C94
+0   3    1    2    1   0.565  -0.554   0.234   C94
+0   3    1    2    2  -0.577  -0.482  -0.427   C94
+0   3    1    2    5   0.082   0.000   0.123   C94
+0   5    1    2    1   0.000  -0.184   0.220   C94
+0   5    1    2    2   0.501  -0.410  -0.535   C94
+2   5    1    2    2   0.000   0.000   0.055   C94
+2   5    1    2    3   0.000   0.000  -0.108   C94
+0   5    1    2    5  -0.523  -0.228   0.208   C94
+2   5    1    2   37   0.000   0.000   0.000   C94
+0   6    1    2    1  -0.467   0.000   0.490   C94
+0   6    1    2    2   0.425   0.168  -0.875   C94
+0   6    1    2    5   0.000   0.136   0.396   C94
+0   8    1    2    1  -0.504   0.371   0.557   C94
+0   8    1    2    2   0.541   0.539  -1.009   C94
+0   8    1    2    5   0.000   0.204   0.464   C94
+0   0    1    3    0   0.000   0.400   0.300   C94 0:*-1-3-* Def
+2   0    1    3    0   0.000   0.500   0.350   C94 2:*-1-3-*  Def
+5   0    1    3    0   0.000   0.000   0.000   E94 5:*-1-3-* Def
+0   0    1    3    1   0.000   0.000   0.550   C94 0:*-1-3-1 Def
+0   0    1    3    5   0.000   0.200   0.700   C94 0:*-1-3-5 Def
+0   0    1    3    7   0.000   0.400   0.400   C94 0:*-1-3-7 Def
+0   1    1    3    1   0.103   0.177   0.545   C94
+0   1    1    3    5  -0.072   0.316   0.674   C94
+0   1    1    3    6  -0.117  -0.333   0.202   C94
+0   1    1    3    7   0.825   0.139   0.325   C94
+0   1    1    3   10  -0.927   1.112   1.388   C94
+0   2    1    3    5   0.663  -0.167   0.426   C94
+0   2    1    3    7  -0.758   0.112   0.563   C94
+0   5    1    3    1  -0.073   0.085   0.531   C94
+2   5    1    3    2   0.000   0.000   0.115   C94
+2   5    1    3    3   0.000   0.000   0.446   C94
+0   5    1    3    5  -0.822   0.501   1.008   C94
+0   5    1    3    6   0.000  -0.624   0.330   C94
+0   5    1    3    7   0.659  -1.407   0.308   C94
+0   5    1    3   10  -0.412   0.693   0.087   C94
+2   5    1    3   37   0.000   0.000   0.056   C94
+0   5    1    3   43   0.000   1.027   0.360   X94
+0   5    1    3   51   0.000   1.543   0.350   X94
+0   5    1    3   53   0.000   0.501   0.000   X94
+0   5    1    3   74   0.000   0.513  -0.344   X94
+0   5    1    3   75   0.000   0.511  -0.186   X94
+0   6    1    3    6   0.447   0.652   0.318   C94
+0   6    1    3    7  -0.395   0.730  -0.139   C94
+0  10    1    3    7   0.338   2.772   2.145   C94
+0  10    1    3   10   0.548   0.000   1.795   C94
+0   0    1    4    0   0.000   0.000   0.000   C94 0:*-1-4-* Def
+0   0    1    6    0   0.000   0.000   0.200   C94 0:*-1-6-* Def
+5   0    1    6    0   0.000  -0.200   0.400   C94 5:*-1-6-*  Def
+0   1    1    6    1  -0.681   0.755   0.755   C94
+5   1    1    6    1   0.000   0.243  -0.596   C94
+0   1    1    6    3  -0.547   0.000   0.320   C94
+0   1    1    6   21   0.000   0.270   0.237   C94
+0   2    1    6   21   0.102   0.460  -0.128   C94
+0   3    1    6   21  -1.652  -1.660   0.283   C94
+0   5    1    6    1   0.571   0.319   0.570   C94
+0   5    1    6    2   0.000   0.000   0.306   C94
+0   5    1    6    3   0.572   0.000  -0.304   C94
+0   5    1    6   21   0.596  -0.276   0.346   C94
+0   5    1    6   25   0.000   0.000   0.061   X94
+0   5    1    6   37   0.000   0.000   0.106   C94
+0   5    1    6   45   0.000   0.000  -0.174   X94
+0   6    1    6    1   0.229  -0.710   0.722   C94
+5   6    1    6    1   0.000   0.000   0.040   C94
+0   6    1    6   21   1.488  -3.401  -0.320   C94
+0  37    1    6   21   0.712   1.320  -0.507   C94
+0   0    1    8    0   0.000  -0.300   0.500   C94 0:*-1-8-* Def
+5   0    1    8    0   0.000   0.000   0.297   E94 5:*-1-8-* Def
+0   1    1    8    1  -0.439   0.786   0.272   C94
+5   1    1    8    1   0.115  -0.390   0.658   C94
+0   1    1    8    6  -0.608   0.339   1.496   C94
+0   1    1    8   23  -0.428   0.323   0.280   C94
+0   2    1    8   23   0.594  -0.409   0.155   C94
+0   5    1    8    1   0.393  -0.385   0.562   C94
+0   5    1    8    6   0.598  -0.158   0.399   C94
+0   5    1    8   23  -0.152  -0.440   0.357   C94
+0   0    1    9    0   0.000   0.000   0.000   C94 0:*-1-9-* Def
+5   0    1    9    0   0.000   0.000   0.000   E94 5:*-1-9-* Def
+0   5    1    9    3   0.204  -0.335  -0.352   C94
+0   5    1    9   53   0.000   0.000   0.097   X94
+0   0    1   10    0   0.000   0.000   0.300   C94 0:*-1-10-* Def
+5   0    1   10    0   0.000   0.000   0.000   E94 5:*-1-10-* Def
+0   0    1   10    3   0.000   0.000   1.000   C94 0:*-1-10-3 Def
+0   1    1   10    3  -1.027   0.694   0.948   C94
+0   1    1   10    6   0.159  -0.552   0.198   C94
+0   1    1   10   28   0.552  -0.380   0.326   C94
+0   3    1   10    3   3.100  -2.529   1.494   C94
+0   3    1   10   28   0.079   0.280   0.402   C94
+0   5    1   10    1   0.000   0.000   0.779   C94
+0   5    1   10    3  -2.099   1.363   0.021   C94
+0   5    1   10    6  -0.162   0.832   0.552   C94
+0   5    1   10   28  -0.616   0.000   0.274   C94
+0   0    1   15    0   0.000   0.000   0.400   C94 0:*-1-15-* Def
+5   0    1   15    0   0.000   0.000   0.336   E94 5:*-1-15-* Def
+0   1    1   15    1  -1.047   0.170   0.398   C94
+0   1    1   15   15  -1.438   0.263   0.501   C94
+0   1    1   15   71  -0.376  -0.133   0.288   C94
+0   5    1   15    1   1.143  -0.231   0.447   C94
+0   5    1   15   15   1.555  -0.323   0.456   C94
+0   5    1   15   37   0.000   0.000   0.459   C94
+0   5    1   15   71   0.229   0.203   0.440   C94
+0   0    1   17    0   0.000   0.000   0.350   C94 0:*-1-17-* Def
+5   0    1   17    0   0.000   0.000   0.000   E94 5:*-1-17-* Def
+0   5    1   17    1   0.000   0.000   0.536   X94
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+0   5   64   64   63   0.000   7.000   0.000   C94
+0  63   64   64   63   0.000   7.000   0.000   C94
+0   0   64   65    0   0.000   7.000   0.000   C94 0:*-64-65-* Def
+0   0   64   66    0   0.000   7.000   0.000   C94 0:*-64-66-* Def
+0   0   64   78    0   0.000   6.000   0.000   E94 0:*-64-78-* Def
+0   0   64   81    0   0.000   6.000   0.000   E94 0:*-64-81-* Def
+5   0   64   81    0   0.000   6.000   0.000   E94 5:*-64-81-* Def
+0   0   64   82    0   0.000   6.000   0.000   E94 0:*-64-82-* Def
+0   0   65   66    0   0.000   7.000   0.000   C94 0:*-65-66-* Def
+0   0   65   78    0   0.000   6.000   0.000   E94 0:*-65-78-* Def
+0   0   65   81    0   0.000   6.000   0.000   E94 0:*-65-81-* Def
+0   0   65   82    0   0.000   6.000   0.000   E94 0:*-65-82-* Def
+0   0   66   66    0   0.000   7.000   0.000   C94 0:*-66-66-* Def
+0   0   66   78    0   0.000   6.000   0.000   E94 0:*-66-78-* Def
+0   0   66   81    0   0.000   6.000   0.000   E94 0:*-66-81-* Def
+0   0   67   67    0   0.000  12.000   0.000   E94 0:*-67-67-* Def
+5   0   67   67    0   0.000  12.000   0.000   E94 5:*-67-67-* Def
+0   0   76   76    0   0.000   3.600   0.000   E94 0:*-76-76-* Def
+0   0   76   78    0   0.000   3.600   0.000   E94 0:*-76-78-* Def
+0   0   78   78    0   0.000   7.000   0.000   C94 0:*-78-78-* Def
+0   0   78   79    0   0.000   6.000   0.000   E94 0:*-78-79-* Def
+0   0   78   81    0   0.000   4.000   0.000   C94 0:*-78-81-* Def
+0   0   79   79    0   0.000   6.000   0.000   E94 0:*-79-79-* Def
+0   0   79   81    0   0.000   6.000   0.000   E94 0:*-79-81-* Def
+0   0   80   81    0   0.000   4.000   0.000   C94 0:*-80-81-* Def
+$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffvdw.par	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,105 @@
+*
+*                Copyright (c) Merck and Co., Inc., 1994
+*                         All Rights Reserved
+*
+*  power      B       Beta     DARAD      DAEPS
+*  0.25      0.2       12.       0.8        0.5      
+*
+*  type  alpha-i     N-i       A-i       G-i DA Symb   Origin
+*------------------------------------------------------------
+    1     1.050     2.490     3.890     1.282 - CR     E94
+    2     1.350     2.490     3.890     1.282 - C=C    E94
+    3     1.100     2.490     3.890     1.282 - C=O    E94
+    4     1.300     2.490     3.890     1.282 - CSP    E94
+    5     0.250     0.800     4.200     1.209 - HC     C94
+    6     0.70      3.150     3.890     1.282 A OR     C94
+    7     0.65      3.150     3.890     1.282 A O=C    C94
+    8     1.15      2.820     3.890     1.282 A NR     C94
+    9     0.90      2.820     3.890     1.282 A N=C    C94
+   10     1.000     2.820     3.890     1.282 A NC=O   E94
+   11     0.35      3.480     3.890     1.282 A F      C94
+   12     2.300     5.100     3.320     1.345 A CL     E94
+   13     3.400     6.000     3.190     1.359 A BR     E94
+   14     5.500     6.950     3.080     1.404 A I      E94
+   15     3.00      4.800     3.320     1.345 A S      C94
+   16     3.900     4.800     3.320     1.345 A S=C    E94
+   17     2.700     4.800     3.320     1.345 - SO     E94
+   18     2.100     4.800     3.320     1.345 - SO2    E94
+   19     4.500     4.200     3.320     1.345 - SI     E94
+   20     1.050     2.490     3.890     1.282 - CR3R   E94
+   21     0.150     0.800     4.200     1.209 D HOR    C94
+   22     1.100     2.490     3.890     1.282 - CR3R   E94
+   23     0.150     0.800     4.200     1.209 D HNR    C94
+   24     0.150     0.800     4.200     1.209 D HOCO   C94
+   25     1.600     4.500     3.320     1.345 - PO4    E94
+   26     3.600     4.500     3.320     1.345 A P      E94
+   27     0.150     0.800     4.200     1.209 D HN=C   C94
+   28     0.150     0.800     4.200     1.209 D HNCO   C94
+   29     0.150     0.800     4.200     1.209 D HOCC   C94
+   30     1.350     2.490     3.890     1.282 - CE4R   E94
+   31     0.150     0.800     4.200     1.209 D HOH    C94
+   32     0.75      3.150     3.890     1.282 A O2CM   C94
+   33     0.150     0.800     4.200     1.209 D HOS    C94
+   34     1.00      2.820     3.890     1.282 - NR+    C94
+   35     1.50      3.150     3.890     1.282 A OM     X94
+   36     0.150     0.800     4.200     1.209 D HNR+   C94
+   37     1.350     2.490     3.890     1.282 - CB     E94
+   38     0.85      2.820     3.890     1.282 A NPYD   C94
+   39     1.10      2.820     3.890     1.282 - NPYL   C94
+   40     1.00      2.820     3.890     1.282 A NC=C   E94
+   41     1.100     2.490     3.890     1.282 - CO2M   C94
+   42     1.000     2.820     3.890     1.282 A NSP    E94
+   43     1.000     2.820     3.890     1.282 A NSO2   E94
+   44     3.00      4.800     3.320     1.345 A STHI   C94
+   45     1.150     2.820     3.890     1.282 - NO2    E94
+   46     1.300     2.820     3.890     1.282 - N=O    E94
+   47     1.000     2.820     3.890     1.282 A NAZT   X94
+   48     1.200     2.820     3.890     1.282 A NSO    X94
+   49     1.00      3.150     3.890     1.282 - O+     X94
+   50     0.150     0.800     4.200     1.209 D HO+    C94
+   51     0.400     3.150     3.890     1.282 - O=+    E94
+   52     0.150     0.800     4.200     1.209 D HO=+   C94
+   53     1.000     2.820     3.890     1.282 - =N=    X94
+   54     1.30      2.820     3.890     1.282 - N+=C   C94
+   55     0.80      2.820     3.890     1.282 - NCN+   E94
+   56     0.80      2.820     3.890     1.282 - NGD+   E94
+   57     1.000     2.490     3.890     1.282 - CNN+   E94
+   58     0.80      2.820     3.890     1.282 - NPD+   E94
+   59     0.65      3.150     3.890     1.282 A OFUR   C94
+   60     1.800     2.490     3.890     1.282 A C%-    E94
+   61     0.800     2.820     3.890     1.282 A NR%    E94
+   62     1.300     2.820     3.890     1.282 A NM     X94
+   63     1.350     2.490     3.890     1.282 - C5A    E94
+   64     1.350     2.490     3.890     1.282 - C5B    E94
+   65     1.000     2.820     3.890     1.282 A N5A    E94
+   66     0.75      2.820     3.890     1.282 A N5B    C94
+   67     0.950     2.82      3.890     1.282 A N2OX   X94
+   68     0.90      2.82      3.890     1.282 A N3OX   C94
+   69     0.950     2.82      3.890     1.282 A NPOX   C94
+   70     0.87      3.150     3.890     1.282 A OH2    C94
+   71     0.150     0.800     4.200     1.209 D HS     C94
+   72     4.000     4.800     3.320     1.345 A SM     X94
+   73     3.000     4.800     3.320     1.345 - SMO2   X94
+   74     3.000     4.800     3.320     1.345 - =S=O   X94
+   75     4.000     4.500     3.320     1.345 A -P=C   X94
+   76     1.200     2.820     3.890     1.282 A N5M    X94
+   77     1.500     5.100     3.320     1.345 A CLO4   X94
+   78     1.350     2.490     3.890     1.282 - C5     X94
+   79     1.000     2.820     3.890     1.282 A N5     X94
+   80     1.000     2.490     3.890     1.282 - CIM+   C94
+   81     0.80      2.820     3.890     1.282 - NIM+   C94
+   82     0.950     2.82      3.890     1.282 A N5OX   X94
+   87     0.45      6.        4.        1.4   - FE+2   X94
+   88     0.55      6.        4.        1.4   - FE+3   X94
+   89     1.4       3.48      3.890     1.282 A F-     X94
+   90     4.5       5.100     3.320     1.345 A CL-    X94
+   91     6.0       6.000     3.190     1.359 A BR-    X94
+   92     0.15      2.        4.        1.3   - LI+    X94
+   93     0.4       3.5       4.        1.3   - NA+    X94
+   94     1.0       5.        4.        1.3   - K+     X94
+   95     0.43      6.        4.        1.4   - ZN+2   X94
+   96     0.9       5.        4.        1.4   - CA+2   X94
+   97     0.35      6.        4.        1.4   - CU+1   X94
+   98     0.40      6.        4.        1.4   - CU+2   X94
+   99     0.35      3.5       4.        1.3   - MG+2   X94
+$
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mr.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,168 @@
+######################################################################
+# Copyright OELIB:          OpenEye Scientific Software, Santa Fe,      
+#                           U.S.A., 1999,2000,2001                      
+# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of  
+#                           Tuebingen, Germany, 2001,2002,2003,2004,2005
+# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany,        
+#                           2003,2004,2005                              
+#                                                                       
+# Authors: Stephen Jelfs                                                                       
+#          Joerg Kurt Wegner, me@cheminformatics.eu         
+#                                                                       
+# This program is free software; you can redistribute it and/or modify  
+# it under the terms of the GNU General Public License as published by  
+# the Free Software Foundation version 2 of the License.                
+#                                                                       
+# This program is distributed in the hope that it will be useful,       
+# but WITHOUT ANY WARRANTY; without even the implied warranty of        
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         
+# GNU General Public License for more details.                          
+######################################################################
+# MR Atomic Contributions
+# ref. Wildman, S.A. and Crippen, G.M., J. Chem. Inf. Comput. 
+#   Sci., 1999, 39, 868-873.
+# Table below is adapted from above ref. 
+######################################################################
+;hydrogen
+[*]	1.112
+[#6]	1.057
+[#1]	1.057
+[O][CX4]	1.395
+[O]c	1.395
+[O][#5]	1.395
+[O][#14]	1.395
+[O][#15]	1.395
+[O][#33]	1.395
+[O][#50]	1.395
+[#5]	1.395
+[#14]	1.395
+[#15]	1.395
+[#16]	1.395
+[#50]	1.395
+[#7]	0.9627
+[O][#7]	0.9627
+[O]C=[#6]	1.805
+[O]C=[#7]	1.805
+[O]C=O	1.805
+[O]C=S	1.805
+[O]O	1.805
+[O]S	1.805
+;heavy
+[*]	0
+[#6]	3.243
+[CH4]	2.503
+[CH3]C	2.503
+[CH2](C)C	2.503
+[CH](C)(C)C	2.433
+[C](C)(C)(C)C	2.433
+[CH3][O,N,F,Cl,Br,#15,#16,#53;!a]	2.753
+[CH2X4][O,N,F,Cl,Br,#15,#16,#53;!a]	2.753
+[CHX4][O,N,F,Cl,Br,#15,#16,#53;!a]	2.731
+[CH0X4][O,N,F,Cl,Br,#15,#16,#53;!a]	2.731
+[C]=[A!#6]	5.007
+[CH2]=C	3.513
+[CH1](=C)A	3.513
+[CH0](=C)(A)A	3.513
+[C](=C)=C	3.513
+[CX2]#A	3.888
+[CH3]c	2.464
+[CH3][a!#6]	2.412
+[CH2X4]a	2.488
+[CHX4]a	2.582
+[CH0X4]a	2.576
+[c][#5,#14,#15,#33,#34,#50,#80]	4.041
+[c][#9]	3.257
+[c][#17]	3.564
+[c][#35]	3.18
+[c][#53]	3.104
+[cH]	3.35
+[c](:a)(:a):a	4.346
+[c](:a)(:a)-a	3.904
+[c](:a)(:a)-C	3.509
+[c](:a)(:a)-N	4.067
+[c](:a)(:a)-O	3.853
+[c](:a)(:a)-S	2.673
+[c](:a)(:a)=C	3.135
+[c](:a)(:a)=N	3.135
+[c](:a)(:a)=O	3.135
+[C](=C)(a)A	4.305
+[C](=C)(c)a	4.305
+[CH](=C)a	4.305
+[C]=c	4.305
+[CX4][!#6;!#7;!#8;!#9;!#15;!#16;!#17;!#35;!#53]	2.693
+[#7]	2.134
+[NH2+0]A	2.262
+[NH+0](A)A	2.173
+[NH2+0]a	2.827
+[NH+0](A)a	3
+[NH+0](a)a	3
+[NH+0]=A	1.757
+[NH+0]=a	1.757
+[N+0](=A)A	2.428
+[N+0](=A)a	2.428
+[N+0](=a)A	2.428
+[N+0](=a)a	2.428
+[N+0](A)(A)A	1.839
+[N+0](a)(A)A	2.819
+[N+0](a)(a)A	2.819
+[N+0](a)(a)a	2.819
+[N+0]#A	1.725
+[NH3+*]	2.134
+[NH2+*]	2.134
+[NH+*]	2.134
+[n+0]	2.202
+[n+*]	2.134
+[NH0+*](A)(A)(A)A	0.2604
+[NH0+*](=A)(A)A	0.2604
+[NH0+*](=A)(A)a	0.2604
+[NH0+*](=[#6])=[#7]	0.2604
+[N+*]#A	3.359
+[N-*]	3.359
+[N+*](=[N-*])=N	3.359
+[#8]	0.6865
+[o]	1.08
+[OH]	0.8238
+[OH2]	0.8238
+[O](C)C	1.085
+[OH0](C)[A!#6]	1.085
+[OH0]([A!#6])[A!#6]	1.085
+[O](A)a	1.182
+[O](a)a	1.182
+[O]=[#8]	3.367
+[O]=[#7]	3.367
+[OX1-*][#7]	3.367
+[OX1-*][#16]	0.7774
+[OX1-*][#15;#33;#43;#53]	0
+[O]=c	3.135
+[O]=[CH]C	0
+[O]=C(C)C	0
+[O]=[CH0](C)[A;!6]	0
+[O]=[CH]N	0
+[O]=[CH]O	0
+[O]=[CH2]	0
+[O]=[CX2]=O	0
+[O]=[CH]c	0.2215
+[O]=C(C)c	0.2215
+[O]=C(c)c	0.2215
+[O]=[CH0](c)[a!#6]	0.2215
+[O]=[CH0](c)[A!#6]	0.2215
+[O]=[CH0](C)[a!#6]	0.2215
+[O]=C([A!#6])[A!#6]	0.389
+[O]=C([A!#6])[a!#6]	0.389
+[O]=C([a!#6])[a!#6]	0.389
+[O-1]C(=O)	0.6865
+[#9-0]	1.108
+[#17-0]	5.853
+[#35-0]	8.927
+[#53-0]	14.02
+[#9-*]	1.108
+[#17-*]	5.853
+[#35-*]	8.927
+[#53-*]	14.02
+[#53+*]	14.02
+[#15]	6.920
+[S-0]	7.591
+[S-*]	7.365
+[S+*]	7.365
+[s]	6.691
+[B,Si,Ga,Ge,As,Se,Sn,Te,Pb,Nc,Nr,Kr,Xe,Rn]	5.754
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/patterns.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,76 @@
+#Comments after SMARTS
+##############################################################################
+#                                                                            #
+#                       Open Babel file: patterns.txt                        #
+#                                                                            #
+#  Copyright (c) 2005 Chris Morley                                           #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+# Functional groups for molecular fingerprinting based on Checkmol:          #
+#   http://merian.pch.univie.ac.at/~nhaider/cheminf/fgtable.pdf              #
+# (Numbers 200+ are from Chris Swain)                                        #
+# SMARTS Patterns are used by finger3.cpp:PatternFP                          #
+# Format of each line is a SMARTS pattern, then optionally                   #
+#   followed by a tab character and a pattern number and/or description      #
+#   (everything after the tab will be ignored by the code)                   #
+# A file of this format needs the same first line as this one.               #
+# An alternative format, as in SMARTS_InteLigand.txt, can also be used       #
+#                                                                            #
+#  INCOMPLETE!! Really only useful to test the fingerprint FP3               #
+##############################################################################
+[+]	1	cation
+[-]	2	anion
+[#6][CX3](=O)	3 aldehyde or ketone
+[CX3H1](=O)[#6]	4 aldehyde
+[#6][CX3](=O)[#6]	5 ketone
+[#6][CX3](=S)	6 thioaldehyde or thioketone
+[CX3H1](=S)	7 thioaldehyde
+[#6]C(=[S])[#6]	8 thioketone
+[CX3]=N([#6,#1])[#6,#1]	9 imine
+[#6,#1]C([#6,#1])=[N][N]([#6,#1])[#6,#1]	10 hydrazone
+[#6,#1]C([#6,#1])=[N][N]([#6,#1])C(=[O])[N]([#6,#1])[#6,#1]	11 semicarbazone
+[#6,#1]C([#6,#1])=[N][N]([#6,#1])C(=[S])[N]([#6,#1])[#6,#1]	12 thiosemicarbazone
+[#6,#1]C([#6,#1])=[N][OH]	13 oxime
+[#6,#1]C([#6,#1])=[N][O][#6]	14 oxime ether
+[CX3]=C=O	15 ketene
+[CX3]=C=O	16 keten acetyl derivative***
+[#6,#1]C([#6,#1])([OH])([OH])	17 carbonyl hydrate
+[#6,#1]C([#6,#1])([OH])(O[#6])	18 hemiacetal
+[#6,#1]C([#6,#1])(O[#6])(O[#6])	19 acetal
+[#6,#1]C([#6,#1])(N([#6,#1])[#6,#1])(O[#6])	20 hemiaminal	
+[#6,#1]C([#6,#1])(N([#6,#1])[#6,#1])(N([#6,#1])[#6,#1])	21 aminal	
+[#6,#1]C([#6,#1])(N([#6,#1])[#6,#1])([S][#6])	22 thiohemiaminal	
+[#6,#1]C([#6,#1])([S][#6])([S][#6])	23 thioacetal
+[#6,#1]C([#6,#1])=C([#6,#1])N([#6,#1])[#6,#1]	24 enamine
+[#6,#1]C([#6,#1])=C([#6,#1])[OH]	25 enol
+[#6,#1]C([#6,#1])=C([#6,#1])O[#6]	26 enol ether
+[#6][OH]	27 hydroxy compound
+C[OH]	28 alcohol
+[#6][CH2][OH]	29 primary alcohol   
+[#6][CH]([#6])[OH]	30 secondary alcohol   
+[#6][C]([#6])([#6])[OH]	31 tertiary alcohol   
+[#6,#1]C([#6,#1])([OH])C([#6,#1])([#6,#1])[OH]	32 1,2-diol
+[#6,#1]C([#6,#1])([OH])C([#6,#1])([#6,#1])[NH2]	33 1,2-aminoalcohol
+c[OH]	34 phenol
+[OH]cc[OH]	35 1,2-diphenol
+[OH]C=C[OH]	36 enediol
+[#6]O[#6]	37 ether
+COC	38 dialkyl ether
+cOC	39 alkylaryl ether
+cOc	40 diaryl ether
+[#6]S[#6]	41 thioether
+[#6]SS[#6]	42 disulfide
+[#6]OO[#6]	43 peroxide
+[#6]O[OH]	44 hydroperoxide
+[a]	200 aryl
+[!#6;$([N,O,S,F,Cl,Br,I,P])]	201 heteroatom
+[!#6;!$([+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])]	202 HBA
+[$([N,O;!H0]),$(N(C)(C)C)]	203 HBD
+[R]	204 Ring
+[$([$([C;$(C=[$([O;D1;$(O=C)])])]);$(C[$([O;$([H1&-0,H0&-1])])]);$(C[#6,#1])])]	205 carboxylic acid
+[$([$([C;$(C=[$([O;D1;$(O=C)])])]);$(C(=O)O[#6]);$(C[#6,#1])])]	206 ester
+[$([N;+0,+1;$(N(=O)~[O;H0;-0,-1])])]	207 nitro
+[$([C;$(C#[N;D1])])]	208 nitrile
+[$([N;!$(N*=[!#6])]);$(N[$([a])]);!$(N~[!#6])]	209 aniline
+[$([N;$(N[$([$([C;$(C=[$([O;D1;$(O=C)])])]);$(C(=O)(N)N)])])])]	210 urea
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/phmodel.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,169 @@
+##############################################################################
+#                                                                            #
+#                   Open Babel file: phmodel.txt                             #
+#                                                                            #
+#  Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc.              #
+#  Some portions Copyright (c) 2001-2003 by Geoffrey R. Hutchison            #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+#  pH model data (used by phmodel.cpp:OBPhModel)                             #
+#                                                                            #
+# TRANSFORM: chemical transforms can be used to modify formal charges, bond  #
+#            orders, and to delete atoms (i.e hydrogens). Changes are applied#
+#        to vector bound atoms (use the [:#] SMARTS notation) and bonds      #
+#            between vector bound atoms.                                     #
+# SEEDCHARGE: used to seed partial charges.  Seed partial charges            #
+#             are used as initial values in Gasteiger charge calculation     #
+#                                                                            #
+##############################################################################
+
+#carboxylic acid							# pKa
+#TRANSFORM O=CO[#1:1] >> O=CO						4.0 # pKa from acid (AH)
+TRANSFORM O=C[OD1-0:1] >> O=C[O-:1]					4.0 # pKa from acid (AH)
+
+#uncomment for vinylogous carboxylic acids (e.g. ascorbic acid)
+TRANSFORM [O:1]=[C:2][C:3]=[C:4][O:5] >> [O-:1][C:2]=[C:3][C:4]=[O:5]	4.0 # pKa from acid (AH)
+
+#charged amine
+TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1]				10.0 # pKa from conjugated acid (BH+)
+
+#imidazole: note pKa=7.0
+#if you uncomment this, also uncomment the seedcharge statement below
+TRANSFORM [nD2:1]1c[nH]cc1 >> [n+:1]1c[nH]cc1				7.0
+
+#imine
+TRANSFORM [ND3+0:1]=[#6] >> [ND3+:1]=[#6]				4.0 # pKa from conjugated acid (BH+)
+
+#tetrazole
+TRANSFORM [nD2:1]([#1:2])1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1	4.89 #pKa from acid (AH)
+TRANSFORM [nD2-0]1[nD2:1]([#1:2])[nD2-0][nD2-0]c1 >> n1[n-:1]nnc1	4.89 #pKa from acid (AH)
+TRANSFORM [nD2-0:1]1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1		4.89 #pKa from acid (AH)
+
+#azide
+TRANSFORM [ND1:1]=[ND2:2]=A >> [N-:1]=[N+:2]=A				1E+10 # always apply transformation
+TRANSFORM [ND2:1]=[ND2:2]=A >> N=[N+:2]=A				1E+10 # always apply this transformation
+
+#hydroxamic acid
+#TRANSFORM O=CN[OD1-0:1][#1:2] >> O=CN[O-:1]				8.0
+TRANSFORM O=CN[OD1-0:1]     >> O=CN[O-:1]				8.0
+
+#sulfinic acid
+TRANSFORM [SD3](=O)[OD1:1]   >> [SD3](=O)[O-:1]				2.0
+TRANSFORM [SD3](=O)[O:1][#1:2] >> [SD3](=O)[O-:1]			2.0
+
+#sulfonic acid
+TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1]	-2.6
+TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1]	-2.6
+#sulfuric acid (same as sulfonic acid...)
+#TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1]
+#TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1]
+
+#guanidine or amidine
+TRANSFORM [#6^2+0:1](~[N^2])(~[N^2])* >> [#6+:1](~N)(~N)*		12.5
+
+#phosphate ester
+TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1] >> [PD4](=O)([OD2])([OD2])[O-:1]	2.0
+#TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1][#1:2] >> [PD4](=O)([OD2])([OD2])[O-:1]	2.0
+
+#phosphoric acid
+#TRANSFORM O=P([!D1])([O:1][#1:2])[O:3][#1:4] >> O=P([*D2,*D3])([O:1])[O:3]	2.12
+TRANSFORM O=P([!D1])([O:1][#1:2])[OD1]       >> O=P([!D1])([O:1])O		2.12
+TRANSFORM O=P([*D2,*D3])([OD1:1])[OD1:2] >> O=P([*D2,*D3])([O-:1])[O-:2]	2.12
+#phosphate
+
+#
+#	Amino acids
+#									pKa sidechain
+# aspartic acid
+#TRANSFORM O=CC(N)CC(=O)O[#1:1] >> O=CC(N)CC(=O)O			3.8
+TRANSFORM O=C(O)C(N)CC(=O)[OD1:1] >> O=C(O)C(N)CC(=O)[O-:1]		3.8 
+TRANSFORM O=C(NCC=O)C(N)CC(=O)[OD1:1] >> O=C(NCC=O)C(N)CC(=O)[O-:1]     3.8 
+
+# glutamic acid
+#TRANSFORM O=CC(N)CCC(=O)O[#1:1] >> O=CC(N)CCC(=O)O		        4.3
+TRANSFORM O=C(O)C(N)CCC(=O)[OD1:1] >> O=C(O)C(N)CCC(=O)[O-:1]		5.0
+TRANSFORM O=C(NCC=O)C(N)CCC(=O)[OD1:1] >> O=C(NCC=O)C(N)CCC(=O)[O-:1]	5.0
+
+# arginine
+TRANSFORM O=C(O)C(N)CCCNC(N)=[N:1] >> O=C(O)C(N)CCCNC(N)=[N+:1] 	12.0
+TRANSFORM O=C(NCC=O)C(N)CCCNC(N)=[N:1] >> O=C(NCC=O)C(N)CCCNC(N)=[N+:1] 12.0
+
+# lysine
+TRANSFORM O=C(O)C(N)CCCC[N:1] >> O=C(O)C(N)CCCC[N+:1] 			10.5
+TRANSFORM O=C(NCC=O)C(N)CCCC[N:1] >> O=C(NCC=O)C(N)CCCC[N+:1] 	        10.5
+
+# histidine
+TRANSFORM O=C(O)C(N)Cc1nc[n:1]c1  >> O=C(O)C(N)Cc1nc[n+:1]c1            6.08
+TRANSFORM O=C(NCC=O)C(N)Cc1nc[n:1]c1  >> O=C(NCC=O)C(N)Cc1nc[n+:1]c1    6.08
+
+# cysteine
+TRANSFORM O=C(O)C(N)C[S:1]  >> O=C(O)C(N)C[S-:1]			 8.28
+TRANSFORM O=C(NCC=O)C(N)C[S:1]  >> O=C(NCC=O)C(N)C[S-:1]		 8.28
+
+# tyrosine
+TRANSFORM O=C(O)C(N)Cc1ccc([O:1])cc1  >> O=C(O)C(N)Cc1ccc([O-:1])cc1	        10.1
+TRANSFORM O=C(NCC=O)C(N)Cc1ccc([O:1])cc1  >> O=C(NCC=O)C(N)Cc1ccc([O-:1])cc1    10.1
+
+# old:
+# histidine
+#TRANSFORM [nD2:1]1c[nD2]cc1 >> [n+:1]1c[nD2]cc1
+# uncomment for tryptophan
+# TRANSFORM [nD2:1]1cccc1 >> [n+:1]1cccc1
+#, histidine pKa=6.0
+
+
+#
+#	Seeding partial charges for gasteiger calculation
+#
+#default charges
+SEEDCHARGE [#6+]	1.0
+SEEDCHARGE [#6-]	-1.0
+SEEDCHARGE [#7+]	1.0
+SEEDCHARGE [#7-]	-1.0
+SEEDCHARGE [#8+]	1.0
+SEEDCHARGE [#8-]	-1.0
+SEEDCHARGE [#15+]	1.0
+SEEDCHARGE [#15-]	-1.0
+SEEDCHARGE [#16+]	1.0
+SEEDCHARGE [#16-]	-1.0
+
+#charges spread over multiple atoms
+#carboxylic acid
+SEEDCHARGE	C(=O)[O-]		0.0	-0.5	-0.5
+
+#amines
+SEEDCHARGE	[N+]		1.0
+#tetrazole
+SEEDCHARGE	[nD2]1[nD2][nD2][nD2]c1	-0.2	-0.2	-0.2   -0.2    -0.2
+
+#sulfinic
+SEEDCHARGE	[SD3](=O)[O-]		0.0	-0.5	-0.5
+#sulfuric acid
+SEEDCHARGE	[SD4](=O)(=O)([O-])[OH1]	0.0	-0.33	-0.33	-0.33	0.0
+#sulfonic acid
+SEEDCHARGE	[SD4]([D2])(~[OD1])(~[OD1])~[OD1]	0.0	0.0	-0.33	-0.33	-0.33
+
+#guanidine
+SEEDCHARGE	[#7^2]~[C^2](~[N^2])~[N^2]	0.33	0.0	0.33	0.33
+
+#amidine
+SEEDCHARGE	[#6]~[C^2](~[N^2])~[N^2]	0.0	0.0	0.5	0.5
+
+#phosphoate ester
+SEEDCHARGE	[PD4](=O)([OD2])([OD2])[OD1]	0.0	-0.5	0.0	0.0	-0.5
+#phosphoric acid
+SEEDCHARGE	O=P([!D1])([O-])[O-]	-0.66	0.0	0.0	-0.66	-0.66
+
+
+#phosphuric acid
+SEEDCHARGE	P(=O)(=O)([O-])[O-]	0.0	0.0	0.0     -0.5	-0.5
+#phosphonic acid
+SEEDCHARGE	[#6]P(~[OD1])(~[OD1])~[OD1]	0.0	0.0	-0.33  -0.33 -0.33
+
+#hydroxamic acid
+SEEDCHARGE	O=C[N;!$(N(C=O)C=O)][OD1]	-0.5	0.0	0.0	-0.5
+SEEDCHARGE	O=CN([OD1])NC=O		-0.33	0.0	0.0	-0.33	0.0 0.0	-0.33
+
+#imidazole: note pKa=7.0, histidine pKa=6.0
+#if you uncomment this, also uncomment the transform statement above
+SEEDCHARGE	[n+H]1c[nH]cc1		0.5	0.0	0.5	0.0	0.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/phmodeldata.h	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,248 @@
+/***************************************************************
+This file is part of the Open Babel project.
+This is copyright under the GNU General Public License (GPL)
+For more information, see <http://openbabel.org/>
+
+This file contains a binary representation of data tables
+ used by Open Babel. It is used as a fallback if the textual
+ data table is not found at runtime. It is not a normal header.
+***************************************************************/
+
+
+#ifndef OB_PHMODELDATA_H
+#define OB_PHMODELDATA_H
+
+namespace OpenBabel
+{
+static const char PhModelData[] = {
+ 0x54,0x52,0x41,0x4E,0x53,0x46,0x4F,0x52,0x4D,0x20,0x4F,0x3D,0x43,0x5B,0x4F,
+ 0x44,0x31,0x2D,0x30,0x3A,0x31,0x5D,0x20,0x3E,0x3E,0x20,0x4F,0x3D,0x43,0x5B,
+ 0x4F,0x2D,0x3A,0x31,0x5D,0x09,0x09,0x09,0x09,0x09,0x34,0x2E,0x30,0x20,0x23,
+ 0x20,0x70,0x4B,0x61,0x20,0x66,0x72,0x6F,0x6D,0x20,0x61,0x63,0x69,0x64,0x20,
+ 0x28,0x41,0x48,0x29,0x0A,0x54,0x52,0x41,0x4E,0x53,0x46,0x4F,0x52,0x4D,0x20,
+ 0x5B,0x4F,0x3A,0x31,0x5D,0x3D,0x5B,0x43,0x3A,0x32,0x5D,0x5B,0x43,0x3A,0x33,
+ 0x5D,0x3D,0x5B,0x43,0x3A,0x34,0x5D,0x5B,0x4F,0x3A,0x35,0x5D,0x20,0x3E,0x3E,
+ 0x20,0x5B,0x4F,0x2D,0x3A,0x31,0x5D,0x5B,0x43,0x3A,0x32,0x5D,0x3D,0x5B,0x43,
+ 0x3A,0x33,0x5D,0x5B,0x43,0x3A,0x34,0x5D,0x3D,0x5B,0x4F,0x3A,0x35,0x5D,0x09,
+ 0x34,0x2E,0x30,0x20,0x23,0x20,0x70,0x4B,0x61,0x20,0x66,0x72,0x6F,0x6D,0x20,
+ 0x61,0x63,0x69,0x64,0x20,0x28,0x41,0x48,0x29,0x0A,0x54,0x52,0x41,0x4E,0x53,
+ 0x46,0x4F,0x52,0x4D,0x20,0x5B,0x4E,0x5E,0x33,0x3B,0x21,0x24,0x28,0x4E,0x7E,
+ 0x5B,0x21,0x23,0x36,0x3B,0x21,0x23,0x31,0x5D,0x29,0x3A,0x31,0x5D,0x20,0x3E,
+ 0x3E,0x20,0x5B,0x4E,0x2B,0x3A,0x31,0x5D,0x09,0x09,0x09,0x09,0x31,0x30,0x2E,
+ 0x30,0x20,0x23,0x20,0x70,0x4B,0x61,0x20,0x66,0x72,0x6F,0x6D,0x20,0x63,0x6F,
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+ 0x42,0x48,0x2B,0x29,0x0A,0x54,0x52,0x41,0x4E,0x53,0x46,0x4F,0x52,0x4D,0x20,
+ 0x5B,0x6E,0x44,0x32,0x3A,0x31,0x5D,0x31,0x63,0x5B,0x6E,0x48,0x5D,0x63,0x63,
+ 0x31,0x20,0x3E,0x3E,0x20,0x5B,0x6E,0x2B,0x3A,0x31,0x5D,0x31,0x63,0x5B,0x6E,
+ 0x48,0x5D,0x63,0x63,0x31,0x09,0x09,0x09,0x09,0x37,0x2E,0x30,0x0A,0x54,0x52,
+ 0x41,0x4E,0x53,0x46,0x4F,0x52,0x4D,0x20,0x5B,0x4E,0x44,0x33,0x2B,0x30,0x3A,
+ 0x31,0x5D,0x3D,0x5B,0x23,0x36,0x5D,0x20,0x3E,0x3E,0x20,0x5B,0x4E,0x44,0x33,
+ 0x2B,0x3A,0x31,0x5D,0x3D,0x5B,0x23,0x36,0x5D,0x09,0x09,0x09,0x09,0x34,0x2E,
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+ 0x42,0x48,0x2B,0x29,0x0A,0x54,0x52,0x41,0x4E,0x53,0x46,0x4F,0x52,0x4D,0x20,
+ 0x5B,0x6E,0x44,0x32,0x3A,0x31,0x5D,0x28,0x5B,0x23,0x31,0x3A,0x32,0x5D,0x29,
+ 0x31,0x5B,0x6E,0x44,0x32,0x2D,0x30,0x5D,0x5B,0x6E,0x44,0x32,0x2D,0x30,0x5D,
+ 0x5B,0x6E,0x44,0x32,0x2D,0x30,0x5D,0x63,0x31,0x20,0x3E,0x3E,0x20,0x5B,0x6E,
+ 0x2D,0x3A,0x31,0x5D,0x31,0x6E,0x6E,0x6E,0x63,0x31,0x09,0x34,0x2E,0x38,0x39,
+ 0x20,0x23,0x70,0x4B,0x61,0x20,0x66,0x72,0x6F,0x6D,0x20,0x61,0x63,0x69,0x64,
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+ 0x64,0x20,0x28,0x41,0x48,0x29,0x0A,0x54,0x52,0x41,0x4E,0x53,0x46,0x4F,0x52,
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+ 0x32,0x2D,0x30,0x5D,0x5B,0x6E,0x44,0x32,0x2D,0x30,0x5D,0x5B,0x6E,0x44,0x32,
+ 0x2D,0x30,0x5D,0x63,0x31,0x20,0x3E,0x3E,0x20,0x5B,0x6E,0x2D,0x3A,0x31,0x5D,
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+ 0x20,0x3E,0x3E,0x20,0x5B,0x4E,0x2D,0x3A,0x31,0x5D,0x3D,0x5B,0x4E,0x2B,0x3A,
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+ 0x2D,0x31,0x2E,0x30,0x0A,0x53,0x45,0x45,0x44,0x43,0x48,0x41,0x52,0x47,0x45,
+ 0x09,0x43,0x28,0x3D,0x4F,0x29,0x5B,0x4F,0x2D,0x5D,0x09,0x09,0x30,0x2E,0x30,
+ 0x09,0x2D,0x30,0x2E,0x35,0x09,0x2D,0x30,0x2E,0x35,0x0A,0x53,0x45,0x45,0x44,
+ 0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x5B,0x4E,0x2B,0x5D,0x09,0x09,0x31,0x2E,
+ 0x30,0x0A,0x53,0x45,0x45,0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x5B,0x6E,
+ 0x44,0x32,0x5D,0x31,0x5B,0x6E,0x44,0x32,0x5D,0x5B,0x6E,0x44,0x32,0x5D,0x5B,
+ 0x6E,0x44,0x32,0x5D,0x63,0x31,0x09,0x2D,0x30,0x2E,0x32,0x09,0x2D,0x30,0x2E,
+ 0x32,0x09,0x2D,0x30,0x2E,0x32,0x20,0x2D,0x30,0x2E,0x32,0x20,0x2D,0x30,0x2E,
+ 0x32,0x0A,0x53,0x45,0x45,0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x5B,0x53,
+ 0x44,0x33,0x5D,0x28,0x3D,0x4F,0x29,0x5B,0x4F,0x2D,0x5D,0x09,0x09,0x30,0x2E,
+ 0x30,0x09,0x2D,0x30,0x2E,0x35,0x09,0x2D,0x30,0x2E,0x35,0x0A,0x53,0x45,0x45,
+ 0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x5B,0x53,0x44,0x34,0x5D,0x28,0x3D,
+ 0x4F,0x29,0x28,0x3D,0x4F,0x29,0x28,0x5B,0x4F,0x2D,0x5D,0x29,0x5B,0x4F,0x48,
+ 0x31,0x5D,0x09,0x30,0x2E,0x30,0x09,0x2D,0x30,0x2E,0x33,0x33,0x09,0x2D,0x30,
+ 0x2E,0x33,0x33,0x09,0x2D,0x30,0x2E,0x33,0x33,0x09,0x30,0x2E,0x30,0x0A,0x53,
+ 0x45,0x45,0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x5B,0x53,0x44,0x34,0x5D,
+ 0x28,0x5B,0x44,0x32,0x5D,0x29,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x28,
+ 0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x09,0x30,
+ 0x2E,0x30,0x09,0x30,0x2E,0x30,0x09,0x2D,0x30,0x2E,0x33,0x33,0x09,0x2D,0x30,
+ 0x2E,0x33,0x33,0x09,0x2D,0x30,0x2E,0x33,0x33,0x0A,0x53,0x45,0x45,0x44,0x43,
+ 0x48,0x41,0x52,0x47,0x45,0x09,0x5B,0x23,0x37,0x5E,0x32,0x5D,0x7E,0x5B,0x43,
+ 0x5E,0x32,0x5D,0x28,0x7E,0x5B,0x4E,0x5E,0x32,0x5D,0x29,0x7E,0x5B,0x4E,0x5E,
+ 0x32,0x5D,0x09,0x30,0x2E,0x33,0x33,0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,0x33,
+ 0x33,0x09,0x30,0x2E,0x33,0x33,0x0A,0x53,0x45,0x45,0x44,0x43,0x48,0x41,0x52,
+ 0x47,0x45,0x09,0x5B,0x23,0x36,0x5D,0x7E,0x5B,0x43,0x5E,0x32,0x5D,0x28,0x7E,
+ 0x5B,0x4E,0x5E,0x32,0x5D,0x29,0x7E,0x5B,0x4E,0x5E,0x32,0x5D,0x09,0x30,0x2E,
+ 0x30,0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,0x35,0x09,0x30,0x2E,0x35,0x0A,0x53,
+ 0x45,0x45,0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x5B,0x50,0x44,0x34,0x5D,
+ 0x28,0x3D,0x4F,0x29,0x28,0x5B,0x4F,0x44,0x32,0x5D,0x29,0x28,0x5B,0x4F,0x44,
+ 0x32,0x5D,0x29,0x5B,0x4F,0x44,0x31,0x5D,0x09,0x30,0x2E,0x30,0x09,0x2D,0x30,
+ 0x2E,0x35,0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,0x30,0x09,0x2D,0x30,0x2E,0x35,
+ 0x0A,0x53,0x45,0x45,0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x4F,0x3D,0x50,
+ 0x28,0x5B,0x21,0x44,0x31,0x5D,0x29,0x28,0x5B,0x4F,0x2D,0x5D,0x29,0x5B,0x4F,
+ 0x2D,0x5D,0x09,0x2D,0x30,0x2E,0x36,0x36,0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,
+ 0x30,0x09,0x2D,0x30,0x2E,0x36,0x36,0x09,0x2D,0x30,0x2E,0x36,0x36,0x0A,0x53,
+ 0x45,0x45,0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x50,0x28,0x3D,0x4F,0x29,
+ 0x28,0x3D,0x4F,0x29,0x28,0x5B,0x4F,0x2D,0x5D,0x29,0x5B,0x4F,0x2D,0x5D,0x09,
+ 0x30,0x2E,0x30,0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,0x30,0x20,0x2D,0x30,0x2E,
+ 0x35,0x09,0x2D,0x30,0x2E,0x35,0x0A,0x53,0x45,0x45,0x44,0x43,0x48,0x41,0x52,
+ 0x47,0x45,0x09,0x5B,0x23,0x36,0x5D,0x50,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,
+ 0x29,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,
+ 0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,0x30,0x09,0x2D,0x30,0x2E,0x33,0x33,0x20,
+ 0x2D,0x30,0x2E,0x33,0x33,0x20,0x2D,0x30,0x2E,0x33,0x33,0x0A,0x53,0x45,0x45,
+ 0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x4F,0x3D,0x43,0x5B,0x4E,0x3B,0x21,
+ 0x24,0x28,0x4E,0x28,0x43,0x3D,0x4F,0x29,0x43,0x3D,0x4F,0x29,0x5D,0x5B,0x4F,
+ 0x44,0x31,0x5D,0x09,0x2D,0x30,0x2E,0x35,0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,
+ 0x30,0x09,0x2D,0x30,0x2E,0x35,0x0A,0x53,0x45,0x45,0x44,0x43,0x48,0x41,0x52,
+ 0x47,0x45,0x09,0x4F,0x3D,0x43,0x4E,0x28,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x4E,
+ 0x43,0x3D,0x4F,0x09,0x09,0x2D,0x30,0x2E,0x33,0x33,0x09,0x30,0x2E,0x30,0x09,
+ 0x30,0x2E,0x30,0x09,0x2D,0x30,0x2E,0x33,0x33,0x09,0x30,0x2E,0x30,0x20,0x30,
+ 0x2E,0x30,0x09,0x2D,0x30,0x2E,0x33,0x33,0x0A,0x53,0x45,0x45,0x44,0x43,0x48,
+ 0x41,0x52,0x47,0x45,0x09,0x5B,0x6E,0x2B,0x48,0x5D,0x31,0x63,0x5B,0x6E,0x48,
+ 0x5D,0x63,0x63,0x31,0x09,0x09,0x30,0x2E,0x35,0x09,0x30,0x2E,0x30,0x09,0x30,
+ 0x2E,0x35,0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,0x30,0x0A,0x00};
+
+} // namespace OpenBabel
+#endif // OB_PHMODELDATA_H
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/plugindefines.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,67 @@
+# Data file for OBDefinable class.
+# A # in the first column or a # followed by whitespace introduces a comment and
+#   the rest of the characters on a line are ignored.
+# White space is trimmed from the front and back of the line.
+#   
+# There can be any number of lines containing only whitespace and 
+#   comment between objects, but none within an object.
+# Lines which have "\n" at the end have this replaced by a new line
+#   character and the next line is concatenated.
+
+#SmartsDescriptor
+#nHal             # name of descriptor. Use for example --filter "nHal<3" 
+#[F,Cl,Br,I,At]   # SMARTS defining the descriptor
+#Number of halogen atoms\n      #This comment has two lines because of \n at the end.
+#count fluorine, chlorine, etc. #When listing plugins, use verbose option to see lines after the first
+
+#OpTransform      # Description() for the class includes a line "OpTransform is definable"
+#tautomers        # ID. Commandline option to invoke is --tautomers
+#tautomers.txt    # Datafile containing transforms. If filename is * the data follows later in the entry.
+#Replace tautomers with their standard forms. Not reliable at present. # An explanatory description.
+
+#OpTransform
+#nodative        # ID. Commandline option to invoke is --nodative
+#*               # There is no datafile; the transforms are at the end of the entry
+#Replace [N+]([O-])=O by N(=O)=O
+#TRANSFORM [N+:1](=O)[O-:2] >> [N:1](=O)=[O:2]
+
+CompoundFilter
+L5                           # ID
+HBD<5 HBA1<10 MW<500 logP<5  # definition in terms of other descriptors or properties
+Lipinski Rule of Five        # description
+
+PatternFP
+MACCS          # ID of this fingerprint type
+MACCS.txt      # File containing the SMARTS patterns
+
+SmartsDescriptor
+sbonds
+*-*
+Number of single bonds
+
+SmartsDescriptor
+dbonds
+*=*
+Number of double bonds
+
+SmartsDescriptor
+tbonds
+*#*
+Number of triple bonds
+
+SmartsDescriptor
+abonds
+*:*
+Number of aromatic bonds
+
+SmartsDescriptor
+bonds
+*~*
+Number of bonds\n
+Add or remove hydrogens to count total or bonds between heavy atoms
+
+SmartsDescriptor
+atoms
+*
+Number of atoms\n
+Add or remove hydrogens to count total or heavy atoms
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/psa.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,68 @@
+######################################################################
+# Copyright OELIB:          OpenEye Scientific Software, Santa Fe,      
+#                           U.S.A., 1999,2000,2001                      
+# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of  
+#                           Tuebingen, Germany, 2001,2002,2003,2004,2005
+# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany,        
+#                           2003,2004,2005                              
+#                                                                       
+# Authors: Stephen Jelfs                                                                       
+#          Joerg Kurt Wegner, me@cheminformatics.eu         
+#                                                                       
+# This program is free software; you can redistribute it and/or modify  
+# it under the terms of the GNU General Public License as published by  
+# the Free Software Foundation version 2 of the License.                
+#                                                                       
+# This program is distributed in the hope that it will be useful,       
+# but WITHOUT ANY WARRANTY; without even the implied warranty of        
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         
+# GNU General Public License for more details.                          
+######################################################################
+# Atomic Contributions to Polar Surface Area PSA
+# ref. Ertl P., Rohde R., Selzer P., J. Med. Chem. 2000, 43, 3714-3717
+######################################################################
+;heavy
+[*]	0.00
+[N](-*)(-*)-*	3.24
+[N](-*)=*	12.36
+[N]#*	23.79
+[N](-*)(=*)=*	11.68
+[N](=*)#*	13.60
+[N]1(-*)-*-*1	3.01
+[NH](-*)-*	12.03
+[NH]1-*-*1	21.94
+[NH]=*	23.85
+[NH2]-*	26.02
+[N+](-*)(-*)(-*)-*	0.00
+[N+](-*)(-*)=*	3.01
+[N+](-*)#*	4.36
+[NH+](-*)(-*)-*	4.44
+[NH+](-*)=*	13.97
+[NH2+](-*)-*	16.61
+[NH2+]=*	25.59
+[NH3+]-*	27.64
+[n](:*):*	12.89
+[n](:*)(:*):*	4.41
+[n](-*)(:*):*	4.93
+[n](=*)(:*):*	8.39
+[nH](:*):*	15.79
+[n+](:*)(:*):*	4.10
+[n+](-*)(:*):*	3.88
+[nH+](:*):*	14.14
+[O](-*)-*	9.23
+[O]1-*-*1	12.53
+[O]=*	17.07
+[OH]-*	20.23
+[O-]-*	23.06
+[o](:*):*	13.14
+[S](-*)-*	25.30
+[S]=*	32.09
+[S](-*)(-*)=*	19.21
+[S](-*)(-*)(=*)=*	8.38
+[SH]-*	38.80
+[s](:*):*	28.24
+[s](=*)(:*):*	21.70
+[P](-*)(-*)-*	13.59
+[P](-*)=*	34.14
+[P](-*)(-*)(-*)=*	9.81
+[PH](-*)(-*)=*	23.47
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/qeq.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,116 @@
+#
+# Open Babel file: qeq.txt
+#
+# Charge parameters for the QEq and QTPIE methods
+# Used by QEqCharges and QTPIECharges, which are daughters of OBChargeModel
+#
+# Parameters:
+#
+#   Elt: Element symbol
+#   Eneg: Atomic electronegativity (Volts)
+#   Hard: Atomic (chemical) hardness (Volts/e)
+#   Radius: screening radius (Angstrom)
+# Elt   Eneg    Hard    Radius
+H 	4.528 	13.8904  0.8271
+He 	9.66 	29.8400  1.7640
+Li 	3.006 	 4.7720  2.4076
+Be 	4.877 	 8.8860  1.2930
+B 	5.11 	 9.5000  1.2094
+C 	5.343 	10.1260  1.1346
+N 	6.899 	11.7600  0.9770
+O 	8.741 	13.3640  0.8597
+F 	10.874 	14.9480  0.7686
+Ne 	11.04 	21.1000  1.4394
+Na 	2.843 	 4.5920  2.5020
+Mg 	3.951 	 7.3860  1.5555
+Al 	4.06 	 7.1800  1.6002
+Si 	4.168 	 6.9740  1.6474
+P 	5.463 	 8.0000  1.4362
+S 	6.928 	 8.9720  1.2806
+Cl 	8.564 	 9.8920  1.1615
+Ar 	9.465 	12.7100  1.2259
+K 	2.421 	 3.8400  2.9920
+Ca 	3.231 	 5.7600  1.9947
+Sc 	3.395 	 6.1600  1.8651
+Ti 	3.47 	 6.7600  1.6996
+V 	3.65 	 6.8200  1.6846
+Cr 	3.415 	 7.7300  1.4863
+Mn 	3.325 	 8.2100  1.3994
+Fe 	3.76 	 8.2800  1.3876
+Co 	4.105 	 8.3500  1.3760
+Ni 	4.465 	 8.4100  1.3661
+Cu 	4.2 	 8.4400  1.3613
+Zn 	5.106 	 8.5700  1.3406
+Ga 	3.641 	 6.3200  1.8179
+Ge 	4.051 	 6.8760  1.6709
+As 	5.188 	 7.6180  1.5082
+Se 	6.428 	 8.2620  1.3906
+Br 	7.79 	 8.8500  1.2982
+Kr 	8.505 	11.4300  1.0268
+Rb 	2.331 	 3.6920  3.1119
+Sr 	3.024 	 4.8800  2.3544
+Y 	3.83 	 5.6200  2.0444
+Zr 	3.4 	 7.1000  1.6182
+Nb 	3.55 	 6.7600  1.6996
+Mo 	3.465 	 7.5100  1.5299
+Tc 	3.29 	 7.9800  1.4398
+Ru 	3.575 	 8.0300  1.4308
+Rh 	3.975 	 8.0100  1.4344
+Pd 	4.32 	 8.0000  1.4362
+Ag 	4.436 	 6.2680  1.8330
+Cd 	5.034 	 7.9140  1.4518
+In 	3.506 	 5.7920  1.9836
+Sn 	3.987 	 6.2480  1.8389
+Sb 	4.899 	 6.6840  1.7189
+Te 	5.816 	 7.0520  1.6292
+I 	6.822 	 7.5240  1.5270
+Xe 	7.595 	 9.9500  1.1547
+Cs 	2.183 	 3.4220  3.3575
+Ba 	2.814 	 4.7920  2.3976
+La 	2.8355 	 5.4830  2.0954
+Ce 	2.774 	 5.3840  2.1340
+Pr 	2.858 	 5.1280  2.2405
+Nd 	2.8685 	 5.2410  2.1922
+Pm 	2.881 	 5.3460  2.1491
+Sm 	2.9115 	 5.4390  2.1124
+Eu 	2.8785 	 5.5750  2.0609
+Gd 	3.1665 	 5.9490  1.9313
+Tb 	3.018 	 5.6680  2.0270
+Dy 	3.0555 	 5.7430  2.0006
+Ho 	3.127 	 5.7820  1.9871
+Er 	3.1865 	 5.8290  1.9711
+Tm 	3.2514 	 5.8658  1.9587
+Yb 	3.2889 	 5.9300  1.9375
+Lu 	2.9629 	 4.9258  2.3325
+Hf 	3.7 	 6.8000  1.6896
+Ta 	5.1 	 5.7000  2.0157
+W 	4.63 	 6.6200  1.7355
+Re 	3.96 	 7.8400  1.4655
+Os 	5.14 	 7.2600  1.5825
+Ir 	5 	 8.0000  1.4362
+Pt 	4.79 	 8.8600  1.2968
+Au 	4.894 	 5.1720  2.2214
+Hg 	6.27 	 8.3200  1.3809
+Tl 	3.2 	 5.8000  1.9809
+Pb3 	3.9 	 7.0600  1.6274
+Bi 	4.69 	 7.4800  1.5360
+Po 	4.21 	 8.4200  1.3645
+At 	4.75 	 9.5000  1.2094
+Rn 	5.37 	10.7400  1.0698
+Fr 	2 	 4.0000  2.8723
+Ra 	2.843 	 4.8680  2.3602
+Ac 	2.835 	 5.6700  2.0263
+Th 	3.175 	 5.8100  1.9775
+Pa 	2.985 	 5.8100  1.9775
+U 	3.341 	 5.7060  2.0135
+Np 	3.549 	 5.4340  2.1143
+Pu 	3.243 	 5.6380  2.0378
+Am 	2.9895 	 6.0070  1.9126
+Cm 	2.8315 	 6.3790  1.8011
+Bk 	3.1935 	 6.0710  1.8925
+Cf 	3.197 	 6.2020  1.8525
+Es 	3.333 	 6.1780  1.8597
+Fm 	3.4 	 6.2000  1.8531
+Md 	3.47 	 6.2200  1.8471
+No 	3.475 	 6.3500  1.8093
+Lr 	3.5 	 6.4000  1.7952
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/resdata.h	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,920 @@
+/***************************************************************
+This file is part of the Open Babel project.
+This is copyright under the GNU General Public License (GPL)
+For more information, see <http://openbabel.org/>
+
+This file contains a binary representation of data tables
+ used by Open Babel. It is used as a fallback if the textual
+ data table is not found at runtime. It is not a normal header.
+***************************************************************/
+
+
+#ifndef OB_RESDATA_H
+#define OB_RESDATA_H
+
+namespace OpenBabel
+{
+static const char ResidueData[] = {
+ 0x52,0x45,0x53,0x20,0x41,0x4C,0x41,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x41,
+ 0x20,0x43,0x33,0x20,0x33,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x4E,0x20,0x4E,0x61,
+ 0x6D,0x20,0x32,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x42,0x20,0x43,0x33,0x20,
+ 0x33,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x20,0x43,0x61,0x63,0x20,0x32,0x0A,
+ 0x41,0x54,0x4F,0x4D,0x20,0x4F,0x20,0x4F,0x32,0x20,0x32,0x0A,0x42,0x4F,0x4E,
+ 0x44,0x20,0x43,0x41,0x20,0x4E,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,
+ 0x41,0x20,0x43,0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x41,0x20,
+ 0x43,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x20,0x4F,0x20,0x32,0x0A,
+ 0x42,0x4F,0x4E,0x44,0x20,0x4E,0x20,0x48,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,
+ 0x20,0x4E,0x20,0x48,0x4E,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x48,0x41,
+ 0x20,0x43,0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x31,0x48,0x42,0x20,
+ 0x43,0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x32,0x48,0x42,0x20,0x43,
+ 0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x33,0x48,0x42,0x20,0x43,0x42,
+ 0x20,0x31,0x0A,0x45,0x4E,0x44,0x0A,0x52,0x45,0x53,0x20,0x41,0x52,0x47,0x0A,
+ 0x41,0x54,0x4F,0x4D,0x20,0x43,0x41,0x20,0x43,0x33,0x20,0x33,0x0A,0x41,0x54,
+ 0x4F,0x4D,0x20,0x4E,0x20,0x4E,0x61,0x6D,0x20,0x32,0x0A,0x41,0x54,0x4F,0x4D,
+ 0x20,0x43,0x42,0x20,0x43,0x33,0x20,0x33,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,
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+ 0x32,0x20,0x32,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x47,0x20,0x43,0x33,0x20,
+ 0x33,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x44,0x20,0x43,0x33,0x20,0x33,0x0A,
+ 0x41,0x54,0x4F,0x4D,0x20,0x4E,0x45,0x20,0x4E,0x67,0x2B,0x20,0x32,0x0A,0x41,
+ 0x54,0x4F,0x4D,0x20,0x43,0x5A,0x20,0x43,0x2B,0x20,0x32,0x0A,0x41,0x54,0x4F,
+ 0x4D,0x20,0x4E,0x48,0x32,0x20,0x4E,0x67,0x2B,0x20,0x32,0x0A,0x41,0x54,0x4F,
+ 0x4D,0x20,0x4E,0x48,0x31,0x20,0x4E,0x67,0x2B,0x20,0x32,0x0A,0x42,0x4F,0x4E,
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+ 0x43,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x20,0x4F,0x20,0x32,0x0A,
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+ 0x4E,0x44,0x20,0x43,0x47,0x20,0x43,0x44,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,
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+ 0x45,0x20,0x43,0x5A,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x5A,0x20,
+ 0x4E,0x48,0x32,0x20,0x32,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x5A,0x20,0x4E,
+ 0x48,0x31,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,0x20,0x48,0x20,0x31,
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+ 0x4E,0x44,0x20,0x4E,0x48,0x31,0x20,0x31,0x48,0x48,0x31,0x20,0x31,0x0A,0x42,
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+ 0x4E,0x44,0x20,0x4E,0x48,0x32,0x20,0x31,0x48,0x48,0x32,0x20,0x31,0x0A,0x42,
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+ 0x4F,0x4E,0x44,0x20,0x31,0x48,0x42,0x20,0x43,0x42,0x20,0x31,0x0A,0x42,0x4F,
+ 0x4E,0x44,0x20,0x32,0x48,0x42,0x20,0x43,0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,
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+ 0x20,0x32,0x48,0x44,0x20,0x43,0x44,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,
+ 0x31,0x48,0x47,0x20,0x43,0x47,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x32,
+ 0x48,0x47,0x20,0x43,0x47,0x20,0x31,0x0A,0x45,0x4E,0x44,0x0A,0x52,0x45,0x53,
+ 0x20,0x41,0x52,0x5A,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x41,0x20,0x43,0x33,
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+ 0x4F,0x4E,0x44,0x20,0x4E,0x45,0x20,0x43,0x5A,0x20,0x31,0x0A,0x42,0x4F,0x4E,
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+ 0x32,0x20,0x32,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x47,0x20,0x43,0x33,0x20,
+ 0x33,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x4E,0x44,0x32,0x20,0x4E,0x61,0x6D,0x20,
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+ 0x4E,0x44,0x20,0x43,0x41,0x20,0x43,0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,
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+ 0x33,0x41,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x41,0x41,0x0A,0x41,0x54,0x4F,
+ 0x4D,0x20,0x43,0x4D,0x41,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x42,0x41,0x0A,
+ 0x41,0x54,0x4F,0x4D,0x20,0x43,0x47,0x41,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x4F,
+ 0x31,0x41,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x4F,0x32,0x41,0x0A,0x41,0x54,0x4F,
+ 0x4D,0x20,0x43,0x32,0x42,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x33,0x42,0x0A,
+ 0x41,0x54,0x4F,0x4D,0x20,0x43,0x4D,0x42,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,
+ 0x41,0x42,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x42,0x42,0x0A,0x41,0x54,0x4F,
+ 0x4D,0x20,0x43,0x32,0x43,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x33,0x43,0x0A,
+ 0x41,0x54,0x4F,0x4D,0x20,0x43,0x4D,0x43,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,
+ 0x41,0x43,0x20,0x43,0x33,0x20,0x33,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x42,
+ 0x43,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x32,0x44,0x0A,0x41,0x54,0x4F,0x4D,
+ 0x20,0x43,0x33,0x44,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x4D,0x44,0x0A,0x41,
+ 0x54,0x4F,0x4D,0x20,0x43,0x41,0x44,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x42,
+ 0x44,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x47,0x44,0x0A,0x41,0x54,0x4F,0x4D,
+ 0x20,0x4F,0x31,0x44,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x4F,0x32,0x44,0x0A,0x42,
+ 0x4F,0x4E,0x44,0x20,0x46,0x45,0x20,0x4E,0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,
+ 0x44,0x20,0x46,0x45,0x20,0x4E,0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,
+ 0x46,0x45,0x20,0x4E,0x43,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x46,0x45,
+ 0x20,0x4E,0x44,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x41,0x20,
+ 0x43,0x31,0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x41,0x20,
+ 0x43,0x34,0x44,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x42,0x20,
+ 0x43,0x34,0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x42,0x20,
+ 0x43,0x31,0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x43,0x20,
+ 0x43,0x34,0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x43,0x20,
+ 0x43,0x31,0x43,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x44,0x20,
+ 0x43,0x34,0x43,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x44,0x20,
+ 0x43,0x31,0x44,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,0x41,0x20,0x43,
+ 0x31,0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,0x41,0x20,0x43,0x34,
+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x31,0x41,0x20,0x43,0x32,
+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x32,0x41,0x20,0x43,0x33,
+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x32,0x41,0x20,0x43,0x41,
+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x33,0x41,0x20,0x43,0x34,
+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x33,0x41,0x20,0x43,0x4D,
+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x41,0x41,0x20,0x43,0x42,
+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x42,0x41,0x20,0x43,0x47,
+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x47,0x41,0x20,0x4F,0x31,
+ 0x41,0x20,0x32,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x47,0x41,0x20,0x4F,0x32,
+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,0x42,0x20,0x43,0x31,0x42,
+ 0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,0x42,0x20,0x43,0x34,0x42,0x20,
+ 0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x31,0x42,0x20,0x43,0x32,0x42,0x20,
+ 0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x32,0x42,0x20,0x43,0x33,0x42,0x20,
+ 0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x32,0x42,0x20,0x43,0x4D,0x42,0x20,
+ 0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x33,0x42,0x20,0x43,0x34,0x42,0x20,
+ 0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x33,0x42,0x20,0x43,0x41,0x42,0x20,
+ 0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x41,0x42,0x20,0x43,0x42,0x42,0x20,
+ 0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,0x43,0x20,0x43,0x31,0x43,0x20,0x31,
+ 0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,0x43,0x20,0x43,0x34,0x43,0x20,0x31,0x0A,
+ 0x42,0x4F,0x4E,0x44,0x20,0x43,0x31,0x43,0x20,0x43,0x32,0x43,0x20,0x31,0x0A,
+ 0x42,0x4F,0x4E,0x44,0x20,0x43,0x32,0x43,0x20,0x43,0x33,0x43,0x20,0x31,0x0A,
+ 0x42,0x4F,0x4E,0x44,0x20,0x43,0x32,0x43,0x20,0x43,0x4D,0x43,0x20,0x31,0x0A,
+ 0x42,0x4F,0x4E,0x44,0x20,0x43,0x33,0x43,0x20,0x43,0x34,0x43,0x20,0x31,0x0A,
+ 0x42,0x4F,0x4E,0x44,0x20,0x43,0x33,0x43,0x20,0x43,0x41,0x43,0x20,0x31,0x0A,
+ 0x42,0x4F,0x4E,0x44,0x20,0x43,0x41,0x43,0x20,0x43,0x42,0x43,0x20,0x31,0x0A,
+ 0x42,0x4F,0x4E,0x44,0x20,0x4E,0x44,0x20,0x43,0x31,0x44,0x20,0x31,0x0A,0x42,
+ 0x4F,0x4E,0x44,0x20,0x4E,0x44,0x20,0x43,0x34,0x44,0x20,0x31,0x0A,0x42,0x4F,
+ 0x4E,0x44,0x20,0x43,0x31,0x44,0x20,0x43,0x32,0x44,0x20,0x31,0x0A,0x42,0x4F,
+ 0x4E,0x44,0x20,0x43,0x32,0x44,0x20,0x43,0x33,0x44,0x20,0x31,0x0A,0x42,0x4F,
+ 0x4E,0x44,0x20,0x43,0x32,0x44,0x20,0x43,0x4D,0x44,0x20,0x31,0x0A,0x42,0x4F,
+ 0x4E,0x44,0x20,0x43,0x33,0x44,0x20,0x43,0x34,0x44,0x20,0x31,0x0A,0x42,0x4F,
+ 0x4E,0x44,0x20,0x43,0x33,0x44,0x20,0x43,0x41,0x44,0x20,0x31,0x0A,0x42,0x4F,
+ 0x4E,0x44,0x20,0x43,0x41,0x44,0x20,0x43,0x42,0x44,0x20,0x31,0x0A,0x42,0x4F,
+ 0x4E,0x44,0x20,0x43,0x42,0x44,0x20,0x43,0x47,0x44,0x20,0x31,0x0A,0x42,0x4F,
+ 0x4E,0x44,0x20,0x43,0x47,0x44,0x20,0x4F,0x31,0x44,0x20,0x32,0x0A,0x42,0x4F,
+ 0x4E,0x44,0x20,0x43,0x47,0x44,0x20,0x4F,0x32,0x44,0x20,0x31,0x0A,0x45,0x4E,
+ 0x44,0x0A,0x00};
+
+} // namespace OpenBabel
+#endif // OB_RESDATA_H
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/resdata.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,1139 @@
+##############################################################################
+#                                                                            #
+#                   Open Babel file: resdata.txt                             #
+#                                                                            #
+#  Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc.              #
+#  Some portions Copyright (c) 2001-2003 by Geoffrey R. Hutchison            #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+#  Residue records are specified as follows: (used by data.cpp:OBResidueData)#
+#  RES <name>                                                                #
+#  ATOM Name Type Hybridization     (hydrogens are implicit)                 #
+#  BOND Name1 Name2 BondOrder       (where Name1, Name2 are ATOM records)    #
+#  END                                                                       #
+#                                                                            #
+##############################################################################
+
+RES ALA
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND N H 1
+BOND N HN 1
+BOND HA CA 1
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND 3HB CB 1
+END
+
+RES ARG
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C3 3
+ATOM CD C3 3
+ATOM NE Ng+ 2
+ATOM CZ C+ 2
+ATOM NH2 Ng+ 2
+ATOM NH1 Ng+ 2
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG CD 1
+BOND CD NE 1
+BOND NE CZ 1
+BOND CZ NH2 2
+BOND CZ NH1 1
+BOND N H 1
+BOND HN N 1
+BOND NH1 1HH1 1
+BOND NH1 2HH1 1
+BOND NE HE 1
+BOND NH2 1HH2 1
+BOND NH2 2HH2 1
+BOND NH1 HH1 1
+BOND NH2 HH2 1
+BOND HA CA 1	
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND 1HD CD 1
+BOND 2HD CD 1
+BOND 1HG CG 1
+BOND 2HG CG 1
+END
+
+RES ARZ
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C3 3
+ATOM CD C3 3
+ATOM NE Ng+ 2
+ATOM CZ C+ 2
+ATOM NH2 Ng+ 2
+ATOM NH1 Ng+ 2
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG CD 1
+BOND CD NE 1
+BOND NE CZ 1
+BOND CZ NH2 1
+BOND CZ NH1 2
+BOND N H 1
+BOND N HN 1
+BOND NH1 HH1 1
+BOND NE HE 1
+BOND NH2 1HH2 1
+BOND NH2 2HH2 1
+END
+
+RES ASN
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C3 3
+ATOM ND2 Nam 2
+ATOM OD1 O2 2
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG ND2 1
+BOND CG OD1 2
+BOND N H 1
+BOND N HN 1
+BOND HA CA 1
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND ND2 1HD2 1
+BOND ND2 2HD2 1
+BOND ND2 HD2 1
+END
+
+RES ASP
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C2 2
+ATOM OD2 O2 2
+ATOM OD1 O3 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG OD2 2
+BOND CG OD1 1
+BOND N H 1
+BOND N HN 1
+BOND HA CA 1
+BOND 1HB CB 1
+BOND 2HB CB 1
+END
+
+RES ASH
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C2 2
+ATOM OD2 O3 3
+ATOM OD1 O2 2
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG OD2 1
+BOND CG OD1 2
+BOND N H 1
+BOND N HN 1
+BOND OD2 HD2 1
+END
+
+RES CYS
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM SG S3 3
+BOND SG CB 1
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB SG 1
+BOND N H 1
+BOND N HN 1
+BOND CA HA 1
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND SG HG 1
+END
+
+RES CYX
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM SG S3 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB SG 1
+BOND N H 1
+END
+
+RES GLN
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C3 3
+ATOM CD C2 2
+ATOM NE2 Nam 2
+ATOM OE1 O2 2
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG CD 1
+BOND CD NE2 1
+BOND CD OE1 2
+BOND N H 1
+BOND N HN 1
+BOND CA HA 1
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND 1HG CG 1
+BOND 2HG CG 1
+BOND NE2 1HE2 1
+BOND NE2 2HE2 1
+BOND NE2 HE2 1
+END
+
+RES GLU
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C3 3
+ATOM CD C2 2
+ATOM OE2 O3 3
+ATOM OE1 O2 2
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG CD 1
+BOND CD OE2 1
+BOND CD OE1 2
+BOND N H 1
+BOND N 1H 1
+BOND N 2H 1
+BOND N 3H 1
+BOND HA CA 1
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND 1HG CG 1
+BOND 2HG CG 1
+END
+
+RES GLY
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM C Cac 2
+ATOM O O2 2
+BOND CA N 1
+BOND CA C 1
+BOND C O 2
+BOND N H 1
+BOND N HN 1
+BOND 1HA CA 1
+BOND 2HA CA 1
+END
+
+RES GLZ
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C3 3
+ATOM CD C2 2
+ATOM OE2 O3 3
+ATOM OE1 O2 2
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG CD 1
+BOND CD OE2 1
+BOND CD OE1 2
+BOND N H 1
+BOND OE2 HE2 1
+END
+
+RES HID
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C C3 3
+ATOM O O2 2
+ATOM CG C2 2
+ATOM ND1 Npl 2
+ATOM CD2 C2 2
+ATOM NE2 N2 2
+ATOM CE1 C2 2
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG ND1 1
+BOND CG CD2 2
+BOND CD2 NE2 1
+BOND NE2 CE1 2
+BOND CE1 ND1 1
+BOND N H 1
+BOND ND1 HD1 1
+END
+
+RES HIE
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C2 2
+ATOM ND1 Npl 2
+ATOM CD2 C2 2
+ATOM NE2 Npl 2
+ATOM CE1 C3 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG ND1 1
+BOND CG CD2 2
+BOND CD2 NE2 1
+BOND NE2 CE1 1
+BOND CE1 ND1 1
+BOND N H 1
+BOND NE2 HE2 1
+END
+
+RES HIP
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C2 2
+ATOM ND1 Npl 2
+ATOM CD2 C2 2
+ATOM NE2 Npl 2
+ATOM CE1 C3 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG ND1 1
+BOND CG CD2 2
+BOND CD2 NE2 1
+BOND NE2 CE1 1
+BOND CE1 ND1 1
+BOND N H 1
+BOND ND1 HD1 1
+BOND NE2 HE2 1
+END
+
+RES HIS
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C2 2
+ATOM ND1 Npl 2
+ATOM CD2 C2 2
+ATOM NE2 Npl 2
+ATOM CE1 C2 2
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG ND1 1
+BOND CG CD2 2
+BOND CD2 NE2 1
+BOND NE2 CE1 2
+BOND CE1 ND1 1
+BOND N H 1
+BOND N HN 1
+BOND HA CA 1
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND 1HD ND1 1
+BOND 2HD CD2 1
+BOND 1HE CE1 1
+BOND ND1 HD1 1
+BOND NE2 HE2 1
+END
+
+RES ILE
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG2 C3 3
+ATOM CG1 C3 3
+ATOM CD1 C3 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG2 1
+BOND CB CG1 1
+BOND CG1 CD1 1
+BOND N H 1
+BOND N HN 1
+BOND CA HA 1
+BOND HB CB 1
+BOND 1HG1 CG1 1
+BOND 2HG1 CG1 1
+BOND 1HG2 CG2 1
+BOND 2HG2 CG2 1
+BOND 3HG2 CG2 1
+BOND 1HD1 CD1 1
+BOND 2HD1 CD1 1
+BOND 3HD1 CD1 1
+END
+
+RES LEU
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C3 3
+ATOM CD1 C3 3
+ATOM CD2 C3 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG CD1 1
+BOND CG CD2 1
+BOND N H 1
+BOND N HN 1
+BOND HA CA 1
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND 1HD1 CD1 1
+BOND 2HD1 CD1 1
+BOND 3HD1 CD1 1
+BOND 1HD2 CD2 1
+BOND 2HD2 CD2 1
+BOND 3HD2 CD2 1
+BOND HG CG 1
+END
+
+RES LYS
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C3 3
+ATOM CD C3 3
+ATOM CE C3 3
+ATOM NZ N3+ 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG CD 1
+BOND CD CE 1
+BOND CE NZ 1
+BOND N H 1
+BOND N HN 1
+BOND HA CA 1
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND 1HD CD 1
+BOND 2HD CD 1
+BOND 1HG CG 1
+BOND 2HG CG 1
+BOND 1HE CE 1
+BOND 2HE CE 1
+BOND NZ 3HZ 1
+BOND NZ HZ3 1
+BOND NZ 2HZ 1
+BOND NZ HZ2 1
+BOND NZ 1HZ 1
+BOND NZ HZ1 1
+END
+
+RES LYZ
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C3 3
+ATOM CD C3 3
+ATOM CE C3 3
+ATOM NZ N3+ 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG CD 1
+BOND CD CE 1
+BOND CE NZ 1
+BOND N H 1
+BOND NZ HZ2 1
+BOND NZ HZ1 1
+END
+
+RES MET
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG C3 3
+ATOM SD S3 3
+ATOM CE C3 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG SD 1
+BOND SD CE 1
+BOND N H 1
+BOND N HN 1
+BOND HA CA 1
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND 1HG CG 1
+BOND 2HG CG 1
+BOND 1HE CE 1
+BOND 2HE CE 1
+BOND 3HE CE 1
+END
+
+RES PHE
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG Car 2
+ATOM CD1 Car 2
+ATOM CD2 Car 2
+ATOM CE2 Car 2
+ATOM CZ Car 2
+ATOM CE1 Car 2
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG CD1 1
+BOND CG CD2 2
+BOND CD2 CE2 1
+BOND CE2 CZ 2
+BOND CZ CE1 1
+BOND CE1 CD1 2
+BOND N H 1
+BOND N HN 1
+BOND HA CA 1
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND 1HD CD1 1
+BOND 2HD CD2 1
+BOND 1HE CE1 1
+BOND 2HE CE2 1
+BOND HZ CZ 1
+END
+
+RES PRO
+ATOM CA C3 3
+ATOM C Cac 2
+ATOM CB C3 3
+ATOM N Nam 2
+ATOM CD C3 3
+ATOM CG C3 3
+ATOM O O2 2
+BOND CA C 1
+BOND CA CB 1
+BOND CA N 1
+BOND N CD 1
+BOND CD CG 1
+BOND CG CB 1
+BOND C O 2
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND 1HG CG 1
+BOND 2HG CG 1
+BOND 1HD CD 1
+BOND 2HD CD 1
+BOND HA CA 1
+BOND HN N 1
+END
+
+RES PSE
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM OG O3 3
+ATOM PD P3 3
+ATOM OE2 O- 3
+ATOM OE3 O- 3
+ATOM OE1 O- 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB OG 1
+BOND OG PD 1
+BOND PD OE2 1
+BOND PD OE3 1
+BOND PD OE1 1
+BOND N H 1
+END
+
+RES PSM
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM OG O3 3
+ATOM PD P3 3
+ATOM OE2 O- 3
+ATOM OE3 O- 3
+ATOM OE1 O- 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB OG 1
+BOND OG PD 1
+BOND PD OE2 1
+BOND PD OE3 1
+BOND PD OE1 1
+BOND N H 1
+BOND OE3 HE3 1
+END
+
+RES PTM
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG Car 2
+ATOM CD1 Car 2
+ATOM CD2 Car 2
+ATOM CE2 Car 2
+ATOM CZ Car 2
+ATOM OH O3 3
+ATOM CE1 Car 2
+ATOM PQ P3 3
+ATOM OI3 O- 3
+ATOM OI2 O- 3
+ATOM OI1 O- 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG CD1 2
+BOND CG CD2 1
+BOND CD2 CE2 2
+BOND CE2 CZ 1
+BOND CZ OH 1
+BOND CZ CE1 2
+BOND CE1 CD1 1
+BOND OH PQ 1
+BOND PQ OI3 1
+BOND PQ OI2 1
+BOND PQ OI1 1
+BOND N H 1
+BOND OI2 HI2 1
+END
+
+RES PTY
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG Car 2
+ATOM CD1 Car 2
+ATOM CD2 Car 2
+ATOM CE2 Car 2
+ATOM CZ Car 2
+ATOM OH O3 3
+ATOM CE1 Car 2
+ATOM PQ P3 3
+ATOM OI3 O- 3
+ATOM OI2 O- 3
+ATOM OI1 O- 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG CD1 2
+BOND CG CD2 1
+BOND CD2 CE2 2
+BOND CE2 CZ 1
+BOND CZ OH 1
+BOND CZ CE1 2
+BOND CE1 CD1 1
+BOND OH PQ 1
+BOND PQ OI3 1
+BOND PQ OI2 1
+BOND PQ OI1 1
+BOND N H 1
+END
+
+RES SER
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM OG O3 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB OG 1
+BOND N H 1
+BOND N HN 1
+BOND HA CA 1
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND OG HG 1
+END
+
+RES THR
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG2 C3 3
+ATOM OG1 O3 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG2 1
+BOND CB OG1 1
+BOND N H 1
+BOND HN N 1
+BOND N 1H 1
+BOND N 2H 1
+BOND N 3H 1
+BOND OG1 HG1 1
+BOND OG1 1HG 1
+BOND HB CB 1
+BOND HA CA 1
+BOND 1HG2 CG2 1
+BOND 2HG2 CG2 1
+BOND 3HG2 CG2 1
+END
+
+RES TRP
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG Car 2
+ATOM CD1 Car 2
+ATOM CD2 Car 2
+ATOM CE3 Car 2
+ATOM CE2 Car 2
+ATOM CZ2 Car 2
+ATOM NE1 Nar 2
+ATOM CH2 Car 2
+ATOM CZ3 Car 2
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG CD1 2
+BOND CG CD2 1
+BOND CD2 CE3 2
+BOND CD2 CE2 1
+BOND CE2 CZ2 2
+BOND CE2 NE1 1
+BOND NE1 CD1 1
+BOND CZ2 CH2 1
+BOND CH2 CZ3 2
+BOND CZ3 CE3 1
+BOND N H 1
+BOND N HN 1
+BOND HA CA 1
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND 1HD CD1 1
+BOND 1HE CE1 1
+BOND 2HZ CZ2 1
+BOND 3HZ CZ3 1
+BOND 3HE CE3 1
+BOND 2HH CH2 1
+BOND NE1 HE1 1
+BOND NE1 1HE 1
+END
+
+RES TYR
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG Car 2
+ATOM CD1 Car 2
+ATOM CD2 Car 2
+ATOM CE2 Car 2
+ATOM CZ Car 2
+ATOM OH O3 3
+ATOM CE1 Car 2
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG 1
+BOND CG CD1 2
+BOND CG CD2 1
+BOND CD2 CE2 2
+BOND CE2 CZ 1
+BOND CZ OH 1
+BOND CZ CE1 2
+BOND CE1 CD1 1
+BOND N H 1
+BOND OH HH 1
+BOND N HN 1
+BOND HA CA 1
+BOND 1HB CB 1
+BOND 2HB CB 1
+BOND 1HD CD1 1
+BOND 2HD CD2 1
+BOND 1HE CE1 1
+BOND 2HE CE2 1
+BOND HZ CZ 1
+END
+
+RES VAL
+ATOM CA C3 3
+ATOM N Nam 2
+ATOM CB C3 3
+ATOM C Cac 2
+ATOM O O2 2
+ATOM CG2 C3 3
+ATOM CG1 C3 3
+BOND CA N 1
+BOND CA CB 1
+BOND CA C 1
+BOND C O 2
+BOND CB CG2 1
+BOND CB CG1 1
+BOND N H 1
+BOND N HN 1
+BOND HA CA 1
+BOND HB CB 1
+BOND 1HG1 CG1 1
+BOND 2HG1 CG1 1
+BOND 3HG1 CG1 1
+BOND 1HG2 CG2 1
+BOND 2HG2 CG2 1
+BOND 3HG2 CG2 1
+END
+
+RES TIP
+ATOM OH2 O3 3
+BOND OH2 H1 1
+BOND OH2 H2 1
+END
+
+RES HOH
+ATOM O O3 3
+ATOM 1H
+ATOM 2H
+BOND O 1H 1
+BOND O 2H 1
+END
+
+RES WAT
+ATOM O O3 3
+ATOM H1
+ATOM H2
+BOND O H1 1
+BOND O H2 1
+END
+
+RES INH
+ATOM P
+ATOM O1P
+ATOM O2P
+ATOM O3P
+ATOM O5
+ATOM C5
+ATOM C4
+ATOM O4
+ATOM C3
+ATOM C1
+ATOM O3
+ATOM C2
+ATOM O2
+ATOM N9
+ATOM C8
+ATOM N7
+ATOM C6
+ATOM O6
+ATOM N1
+ATOM N3
+BOND P O1P 2
+BOND P O2P 1
+BOND P O3P 1
+BOND P O5 1
+BOND O5 C5 1
+BOND C5 C4 1
+BOND C4 O4 1
+BOND C4 C3 1
+BOND O4 C1 1
+BOND C3 O3 1
+BOND C3 C2 1
+BOND O3 H1 1
+BOND C2 O2 1
+BOND C2 C1 1
+BOND O2 H2 1
+BOND C1 N9 1
+BOND N9 C8 1
+BOND N9 C4 1
+BOND C8 N7 2
+BOND N7 C5 1
+BOND C5 C6 1
+BOND C6 O6 2
+BOND C6 N1 1
+BOND N1 C2 1
+BOND N1 H3 1
+BOND C2 N3 2
+BOND N3 C4 1
+END
+
+RES UMP
+ATOM N1
+ATOM C2
+ATOM C6
+ATOM C1
+ATOM N3
+ATOM O2
+ATOM C4
+ATOM C5
+ATOM O4
+ATOM C3
+ATOM O3
+ATOM O5
+ATOM P
+ATOM O1P
+ATOM O2P
+ATOM O3P
+BOND N1 C2 1
+BOND N1 C6 1
+BOND N1 C1 1
+BOND C2 N3 1
+BOND C2 O2 1
+BOND C2 H5 1
+BOND N3 C4 1
+BOND N3 H1 1
+BOND C4 C5 1
+BOND C4 O4 1
+BOND C4 H6 1
+BOND C5 C6 1
+BOND C5 H7 1
+BOND C5 H8 1
+BOND C6 H9 1
+BOND C6 H10 1
+BOND O2 H2 1
+BOND O4 H3 1
+BOND C1 C2 1
+BOND C1 O4 1
+BOND C1 H11 1
+BOND C2 C3 1
+BOND C2 H12 1
+BOND C2 H13 1
+BOND C3 C4 1
+BOND C3 O3 1
+BOND C3 H14 1
+BOND C4 H15 1
+BOND O3 H4 1
+BOND C5 O5 1
+BOND C5 H16 1
+BOND C5 H17 1
+BOND O5 P 1
+BOND P O1P 2
+BOND P O2P 2
+BOND P O3P 2
+END
+
+RES HED
+ATOM C1
+ATOM O1
+ATOM C2
+ATOM S3
+ATOM S4
+ATOM C5
+ATOM C6
+ATOM O6
+BOND C1 O1 2
+BOND C1 C2 1
+BOND C2 S3 1
+BOND S3 S4 1
+BOND S4 C5 1
+BOND C5 C6 1
+BOND C6 O6 2
+END
+
+RES HEM
+ATOM FE
+ATOM NA
+ATOM NB
+ATOM NC
+ATOM ND
+ATOM CHA
+ATOM C1A
+ATOM C4D
+ATOM CHB
+ATOM C4A
+ATOM C1B
+ATOM CHC
+ATOM C4B
+ATOM C1C
+ATOM CHD
+ATOM C4C
+ATOM C1D
+ATOM C2A
+ATOM C3A
+ATOM CAA
+ATOM CMA
+ATOM CBA
+ATOM CGA
+ATOM O1A
+ATOM O2A
+ATOM C2B
+ATOM C3B
+ATOM CMB
+ATOM CAB
+ATOM CBB
+ATOM C2C
+ATOM C3C
+ATOM CMC
+ATOM CAC C3 3
+ATOM CBC
+ATOM C2D
+ATOM C3D
+ATOM CMD
+ATOM CAD
+ATOM CBD
+ATOM CGD
+ATOM O1D
+ATOM O2D
+BOND FE NA 1
+BOND FE NB 1
+BOND FE NC 1
+BOND FE ND 1
+BOND CHA C1A 1
+BOND CHA C4D 1
+BOND CHB C4A 1
+BOND CHB C1B 1
+BOND CHC C4B 1
+BOND CHC C1C 1
+BOND CHD C4C 1
+BOND CHD C1D 1
+BOND NA C1A 1
+BOND NA C4A 1
+BOND C1A C2A 1
+BOND C2A C3A 1
+BOND C2A CAA 1
+BOND C3A C4A 1
+BOND C3A CMA 1
+BOND CAA CBA 1
+BOND CBA CGA 1
+BOND CGA O1A 2
+BOND CGA O2A 1
+BOND NB C1B 1
+BOND NB C4B 1
+BOND C1B C2B 1
+BOND C2B C3B 1
+BOND C2B CMB 1
+BOND C3B C4B 1
+BOND C3B CAB 1
+BOND CAB CBB 1
+BOND NC C1C 1
+BOND NC C4C 1
+BOND C1C C2C 1
+BOND C2C C3C 1
+BOND C2C CMC 1
+BOND C3C C4C 1
+BOND C3C CAC 1
+BOND CAC CBC 1
+BOND ND C1D 1
+BOND ND C4D 1
+BOND C1D C2D 1
+BOND C2D C3D 1
+BOND C2D CMD 1
+BOND C3D C4D 1
+BOND C3D CAD 1
+BOND CAD CBD 1
+BOND CBD CGD 1
+BOND CGD O1D 2
+BOND CGD O2D 1
+END
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/ringtyp.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,71 @@
+##############################################################################
+#                                                                            #
+#	                Open Babel file: ringtyp.txt                             #
+#                                                                            #
+#  Copyright (c) 2007 Tim Vandermeersch                                      #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+# SMARTS patterns for ring typing (used by typer.cpp:OBRingTyper)            #
+# (involved in MMFF94 atom typing, among other things)                       #
+#                                                                            #
+# RINGTYP: used to assign the ring types                                     #
+#                                                                            #
+##############################################################################
+
+#
+# 5 membered rings
+#
+#	ring name		smarts pattern
+RINGTYP	thiophene		s1cccc1
+RINGTYP	furan			o1cccc1
+RINGTYP	pyrrole			n1cccc1
+
+RINGTYP	thiazole		s1c[nD2]cc1
+RINGTYP	thiazole_cation		s1c[nD3]cc1 # needed by MMFF
+RINGTYP	oxazole			o1c[nD2]cc1
+RINGTYP	oxazole_cation		o1c[nD3]cc1 # needed by MMFF
+RINGTYP	imidazole		[nD3]1c[nD2]cc1
+RINGTYP	imidazole_cation	[nD3]1c[nD3]cc1 # needed by MMFF
+
+RINGTYP	isothiazole		s1[nD2]ccc1
+RINGTYP	isothiazole_cation	s1[nD3]ccc1 # needed by MMFF
+RINGTYP	isoxazole		o1[nD2]ccc1
+RINGTYP	isoxazole_cation	o1[nD3]ccc1 # needed by MMFF
+RINGTYP	pyrazole		[nD3]1[nD2]ccc1
+RINGTYP	pyrazole_anion		[nD2]1[nD2]ccc1 # needed by MMFF
+
+
+RINGTYP	1,2,3-thiadiazole		s1[nD2][nD2]cc1
+RINGTYP	1,2,3-thiadiazole_cation	s1[nD2][nD3]cc1 # needed by MMFF
+RINGTYP	1,2,4-thiadiazole		s1[nD2]c[nD2]c1
+RINGTYP	1,2,4-thiadiazole_cation	s1[nD2]c[nD3]c1 # needed by MMFF
+RINGTYP	1,3,4-thiadiazole		s1c[nD2][nD2]c1
+RINGTYP	1,3,4-thiadiazole_cation	s1c[nD2][nD3]c1 # needed by MMFF
+
+RINGTYP	1,2,3-oxadiazole		o1[nD2][nD2]cc1
+RINGTYP	1,2,3-oxadiazole_cation		o1[nD2][nD3]cc1 # needed by MMFF
+RINGTYP	1,2,4-oxadiazole		o1[nD2]c[nD2]c1
+RINGTYP	1,2,4-oxadiazole_cation		o1[nD2]c[nD3]c1 # needed by MMFF
+
+RINGTYP	1,2,3-triazole		[nD3]1[nD2][nD2]cc1
+RINGTYP	1,2,3-triazole_anion	[nD2]1[nD2][nD2]cc1 # needed by MMFF
+RINGTYP	1,2,4-triazole		[nD3]1[nD2]c[nD2]c1
+RINGTYP	1,2,4-triazole_anion	[nD2]1[nD2]c[nD2]c1 # needed by MMFF
+RINGTYP	1,3,4-triazole		[nD3]1c[nD2][nD2]c1
+RINGTYP	1,3,4-triazole_cation	[nD3]1c[nD3][nD2]c1 # needed by MMFF
+
+RINGTYP	1,2,3,4-tetrazole		[nD3]1[nD2][nD2][nD2]c1
+RINGTYP	1,2,3,4-tetrazole_cation	[nD3]1[nD2][nD2][nD3]c1 # needed by MMFF
+RINGTYP	1,2,3,5-tetrazole		[nD3]1[nD2][nD2]c[nD2]1
+RINGTYP	1,2,3,5-tetrazole_anion 	[nD2]1[nD2][nD2]c[nD2]1 # needed by MMFF
+
+#
+# 6 membered rings
+#
+#	ring name		smarts pattern
+RINGTYP	benzene			c1ccccc1
+RINGTYP	pyridine		n1ccccc1
+RINGTYP	pyridazine		n1ncccc1
+RINGTYP	pyrimidine		n1cnccc1
+RINGTYP	pyrazine		n1ccncc1
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/space-groups.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,9508 @@
+1
+P 1
+P 1
+x,y,z
+
+2
+-P 1
+P -1
+x,y,z
+-x,-y,-z
+
+3
+P 2y
+P 2,P 1 2 1
+x,y,z
+-x,y,-z
+
+3
+P 2x
+P 2 1 1
+x,y,z
+x,-y,-z
+
+3
+P 2
+P 1 1 2
+x,y,z
+-x,-y,z
+
+4
+P 2yb
+P 21,P 1 21 1
+x,y,z
+-x,1/2+y,-z
+
+4
+P 2xa
+P 21 1 1
+x,y,z
+1/2+x,-y,-z
+
+4
+P 2c
+P 1 1 21
+x,y,z
+-x,-y,1/2+z
+
+5
+C 2y
+C 2,C 1 2 1
+x,y,z
+-x,y,-z
+1/2+x,1/2+y,z
+1/2-x,1/2+y,-z
+
+5
+A 2y
+A 1 2 1
+x,y,z
+-x,y,-z
+x,1/2+y,1/2+z
+-x,1/2+y,1/2-z
+
+5
+I 2y
+I 1 2 1
+x,y,z
+-x,y,-z
+1/2+x,1/2+y,1/2+z
+1/2-x,1/2+y,1/2-z
+
+5
+A 2
+A 1 1 2
+x,y,z
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/space-groups.xsl	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,29 @@
+<xsl:stylesheet version = '1.0'
+     xmlns:xsl='http://www.w3.org/1999/XSL/Transform'>
+<xsl:output method="text"/>
+
+<xsl:template match="/">
+     <xsl:apply-templates select="//group"/>
+</xsl:template>
+
+<xsl:template match="group">
+     <xsl:value-of select="@id"/>
+     <xsl:text>&#10;</xsl:text>
+     <xsl:value-of select="@Hall"/>
+     <xsl:text>&#10;</xsl:text>
+     <xsl:if test="@HMs">
+          <xsl:value-of select="@HMs"/>
+          <xsl:text>,</xsl:text>
+     </xsl:if>
+     <xsl:value-of select="@HM"/>
+     <xsl:text>&#10;</xsl:text>
+     <xsl:apply-templates select="transform"/>
+     <xsl:text>&#10;</xsl:text>
+</xsl:template>
+
+<xsl:template match="transform">
+     <xsl:value-of select="."/>
+     <xsl:text>&#10;</xsl:text>
+</xsl:template>
+
+</xsl:stylesheet> 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/superatom.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,113 @@
+# Translations of superatom labels to SMILES.
+# First atom of SMILES string should be the one connected to the rest of
+# the molecule.
+# Empty lines and lines starting with # are ignored.
+# Originally from http://cactus.nci.nih.gov/osra/
+# The left-aligned form is the one recognized in MDL alias lines;
+# the right-aligned form may be used in 2D depiction.
+# The whole list is used to look up alias names;
+# only the part up to a line starting with ## is used to generate aliases.
+# and here the largest fragments should be first; 
+#left    right    SMILES		color
+CO2Et    EtO2C    C(=O)OCC
+COOEt    EtOOC    C(=O)OCC
+OiBu     iBuO     OCC(C)C
+tBu      tBu      C(C)(C)C
+nBu      nBu      CCCC
+iPr      iPr      C(C)C
+nPr      nPr      CCC
+Et       Et       CC
+NCF3     F3CN     NC(F)(F)F
+CF3      F3C      C(F)(F)F
+CCl3	 Cl3C     C(Cl)(Cl)Cl
+CN       NC       C#N
+NC       CN       [N+]#[C-]
+N(OH)CH3 CH3(OH)N N(O)C
+NO2      O2N      N(=O)=O
+NO       ON       N=O
+SO3H     HO3S     S(=O)(=O)O
+COOH     HOOC     C(=O)O		blue
+OEt      EtO      OCC
+OAc      AcO      OC(=O)C
+NHAc     AcNH     NC(=O)C
+Ac       Ac       C(=O)C
+CHO      OHC      C=O
+NMe      MeN      NC
+SMe      MeS      SC
+OMe      MeO      OC
+COO-     -OOC     C(=O)[O-]
+## Only entries above this line are used to *generate* aliases.
+Ph       Ph       c1ccccc1
+OR       RO       O*
+R        R        *
+OBz      BzO      OCc1ccccc1
+THPO     THPO     O[C@@H]1OCCCC1
+NOH      HON      NO 
+CO2Me    MeO2C    C(=O)OC
+COOMe    MeOOC    C(=O)OC
+SO2Me    MeO2S    S(=O)(=O)C
+NMe2     Me2N     N(C)C
+CO2R     RO2C     C(=O)O*
+COOR     ROOC     C(=O)O*
+NHZ      ZNH      NC(=O)OCC1=CC=CC=C1
+CH2OH    HOCH2    CO
+CH2NH2   H2NCH2   CN
+Me       Me       C
+OBn      BnO      OCC1=CC=CC=C1
+NHAm     AmNH     NCCCCC
+OAm      AmO      OCCCCC
+CO2Am    AmO2C    C(=O)OCCCCC
+COOAm    AmOOC    C(=O)OCCCCC
+SAm      AmS      SCCCCC
+NHBn     BnNH     NCC1=CC=CC=C1
+CO2Bn    BnO2C    C(=O)OCC1=CC=CC=C1
+SnBu3    Bu3Sn    [Sn](CCCC)(CCCC)CCCC
+NHBu     BuNH     NCCCC
+OBu      BuO      OCCCC
+CO2Bu    BuO2C    C(=O)OCCCC
+COOBu    BuOOC    C(=O)OCCCC
+SBu      BuS      SCCCC
+CBr3	 Br3C     C(Br)(Br)Br
+NHCbz    CbzNH    NC(=O)OCC1=CC=CC=C1
+SO2Cl    ClSO2    S(Cl)(=O)=O
+COBr     BrCO     C(=O)Br
+COBu     BuCO     C(=O)CCCC
+COCF3    F3CCO    C(=O)C(F)(F)F
+COCl     ClCO     C(=O)Cl
+COCO     COCO     C(=O)C=O
+COEt     EtCO     C(=O)CC
+COF      FCO      C(=O)F
+COMe     MeCO     C(=O)C
+CONEt2   Et2NCO   C(=O)(CC)NCC
+CONH2    H2NCO    C(=O)N
+CONHEt   EtHNCO   C(=O)NCC
+CONHMe   MeHNCO   C(=O)NC
+CONMe2   Me2NCO   C(=O)(C)NC
+COSH     HSOC     C(=O)S
+NEt2     Et2N     N(CC)CC
+NEt3     Et3N     N(CC)(CC)CC
+NHEt     EtNH     NCC
+SO2NH2   H2NSO2   S(=O)(N)=O
+NHOH     HONH     ON
+NMe2     Me2N     N(C)C
+OMs      MsO      CS(O)(=O)=O
+OCN      NCO      N=C=O
+SCN      NCS      N=C=S
+NHAm     AmHN     NCCCCC
+NHBn     BuHN     NCC1=CC=CC=C1
+NHBu     BuHN     NCCCC
+NHEt     EtHB     NCC
+NHOH     HOHN     NO
+NHPr     PrHN     NCCC
+NO       ON       N=O
+POEt2    EtO2P    P(OCC)OCC
+POEt3    EtO3P    P(OCC)(OCC)OCC
+POOEt2   Et2OOP   P(=O)(OCC)OCC
+PrNH     HNPr     CCCN
+SEt      CCS      SCC
+#Aliases from samples provided with InChI
+CH       HC       [CH]
+CH-      HC-      [CH-]
+D        D        [2H]
+ND2      D2N      [N]([2H])[2H]
+DS       SD       [S][2H]  
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/svgformat.script	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,45 @@
+<script type="text/ecmascript">
+  <![CDATA[
+    addEventListener('DOMMouseScroll', wheel, false);
+    onmousewheel = wheel;
+    var svgEl = document.getElementById("topsvg");
+    var startx=0;
+    var starty=0;
+    function wheel(evt){
+      evt = evt ? evt : window.event;
+      var normal = evt.detail ? evt.detail * -1 : evt.wheelDelta / 40;
+      var vb = new Array(4);
+      var vbtext = svgEl.getAttributeNS(null,"viewBox");
+      vb = vbtext.split(" ");
+      var zoom = (normal<0)? 1.41 : 0.71;
+      //var dwidth = parseFloat(Math.max(vb[2],vb[3])) * (1-zoom);
+      vb[0] = parseFloat(vb[0]) + parseFloat(vb[2])*(1-zoom) * evt.clientX/innerWidth;
+      vb[1] = parseFloat(vb[1]) + parseFloat(vb[3])*(1-zoom) * evt.clientY/innerHeight;
+      vb[2] = parseFloat(vb[2]) * zoom;
+      vb[3] = parseFloat(vb[3]) * zoom;
+      svgEl.setAttributeNS(null, "viewBox", vb.join(" "));
+    }
+    onmousedown = function(evt) {
+      startx = evt.clientX;
+      starty = evt.clientY;
+    }
+    onmousemove=function(evt) {
+      if(startx!=0 && starty!=0 
+        && ((evt.clientX - startx)*(evt.clientX - startx)+(evt.clientY - starty)*(evt.clientY - starty)>100))
+      {
+        var vbtext = svgEl.getAttributeNS(null,"viewBox");
+        vb = vbtext.split(" ");
+        var maxwh = Math.max(parseFloat(vb[2]),parseFloat(vb[3]));
+        vb[0] = parseFloat(vb[0]) - (evt.clientX - startx)*maxwh/innerWidth;
+        vb[1] = parseFloat(vb[1]) - (evt.clientY - starty)*maxwh/innerHeight;
+        svgEl.setAttributeNS(null, "viewBox", vb.join(" "));
+        startx = evt.clientX;
+        starty = evt.clientY;
+      }
+    } 
+    onmouseup=function() {
+      startx=0;
+      starty=0;
+   }
+  ]]>
+</script>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/templates.sdf	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,27 @@
+
+  ACD/Labs10200816283D
+
+ 10 12  0  0  0  0  0  0  0  0  1 V2000
+   11.7466   -9.2167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.0827  -10.5962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.4479  -11.8018    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.8589  -12.6696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.3767  -11.8246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.5800  -10.5556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.9565   -9.1175    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.8891   -8.7118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.5532   -9.6158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.4814  -11.1730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  8  1  0  0  0  0
+  1  2  2  0  0  0  0
+  2  3  1  0  0  0  0
+  3  5  1  0  0  0  0
+  3  4  1  0  0  0  0
+  4 10  1  0  0  0  0
+  4  5  1  0  0  0  0
+  5  6  1  0  0  0  0
+  6  7  2  0  0  0  0
+  7  8  1  0  0  0  0
+  8  9  1  0  0  0  0
+  9 10  2  0  0  0  0
+M  END
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/torlib.h	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,479 @@
+/***************************************************************
+This file is part of the Open Babel project.
+This is copyright under the GNU General Public License (GPL)
+For more information, see <http://openbabel.org/>
+
+This file contains a binary representation of data tables
+ used by Open Babel. It is used as a fallback if the textual
+ data table is not found at runtime. It is not a normal header.
+***************************************************************/
+
+
+#ifndef OB_TORLIB_H
+#define OB_TORLIB_H
+
+namespace OpenBabel
+{
+static const char TorsionDefaults[] = {
+ 0x53,0x50,0x33,0x2D,0x53,0x50,0x33,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,
+ 0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x20,0x0A,0x53,0x50,0x32,0x2D,
+ 0x53,0x50,0x32,0x20,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x20,0x2D,
+ 0x33,0x30,0x2E,0x30,0x20,0x33,0x30,0x2E,0x30,0x20,0x31,0x35,0x30,0x2E,0x30,
+ 0x20,0x2D,0x31,0x35,0x30,0x2E,0x30,0x20,0x0A,0x53,0x50,0x33,0x2D,0x53,0x50,
+ 0x32,0x20,0x30,0x2E,0x30,0x20,0x33,0x30,0x2E,0x30,0x20,0x2D,0x33,0x30,0x2E,
+ 0x30,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,0x30,0x2E,0x30,0x20,0x31,0x32,
+ 0x30,0x2E,0x30,0x20,0x2D,0x31,0x32,0x30,0x2E,0x30,0x20,0x2D,0x31,0x35,0x30,
+ 0x2E,0x30,0x20,0x31,0x35,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x20,
+ 0x2D,0x39,0x30,0x2E,0x30,0x20,0x39,0x30,0x2E,0x30,0x0A,0x4F,0x40,0x5B,0x43,
+ 0x44,0x33,0x5D,0x4F,0x5B,0x43,0x44,0x33,0x5D,0x28,0x5B,0x23,0x31,0x5D,0x29,
+ 0x40,0x43,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x35,0x20,0x30,0x2E,0x30,0x20,
+ 0x33,0x30,0x2E,0x30,0x20,0x2D,0x33,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,
+ 0x30,0x0A,0x4F,0x40,0x5B,0x43,0x44,0x33,0x5D,0x28,0x5B,0x23,0x31,0x5D,0x29,
+ 0x4F,0x5B,0x43,0x44,0x33,0x5D,0x28,0x5B,0x23,0x31,0x5D,0x29,0x40,0x43,0x20,
+ 0x33,0x20,0x32,0x20,0x34,0x20,0x35,0x20,0x30,0x2E,0x30,0x20,0x33,0x30,0x2E,
+ 0x30,0x20,0x2D,0x33,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x0A,0x5B,
+ 0x4F,0x44,0x31,0x5D,0x7E,0x43,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5B,
+ 0x43,0x58,0x34,0x5D,0x28,0x2A,0x29,0x2A,0x20,0x31,0x20,0x32,0x20,0x34,0x20,
+ 0x35,0x20,0x33,0x30,0x2E,0x30,0x20,0x2D,0x33,0x30,0x2E,0x30,0x20,0x2D,0x36,
+ 0x30,0x2E,0x30,0x20,0x36,0x30,0x2E,0x30,0x20,0x39,0x30,0x2E,0x30,0x20,0x2D,
+ 0x39,0x30,0x2E,0x30,0x20,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x0A,
+ 0x5B,0x61,0x5D,0x63,0x43,0x28,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x3D,0x4F,0x20,
+ 0x31,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x30,0x2E,0x30,0x20,0x32,0x30,0x2E,
+ 0x30,0x20,0x2D,0x32,0x30,0x2E,0x30,0x0A,0x5B,0x4F,0x44,0x31,0x5D,0x43,0x28,
+ 0x3D,0x4F,0x29,0x5B,0x43,0x44,0x32,0x5D,0x43,0x20,0x31,0x20,0x32,0x20,0x34,
+ 0x20,0x35,0x20,0x30,0x2E,0x30,0x20,0x34,0x35,0x2E,0x30,0x20,0x39,0x30,0x2E,
+ 0x30,0x0A,0x4E,0x53,0x28,0x3D,0x4F,0x29,0x28,0x3D,0x4F,0x29,0x63,0x31,0x5B,
+ 0x63,0x44,0x32,0x5D,0x5B,0x63,0x44,0x32,0x5D,0x61,0x5B,0x63,0x44,0x32,0x5D,
+ 0x5B,0x63,0x44,0x32,0x5D,0x31,0x20,0x31,0x20,0x32,0x20,0x35,0x20,0x36,0x20,
+ 0x39,0x30,0x2E,0x30,0x0A,0x63,0x28,0x5B,0x61,0x44,0x32,0x5D,0x29,0x53,0x28,
+ 0x3D,0x4F,0x29,0x28,0x3D,0x4F,0x29,0x5B,0x4E,0x44,0x32,0x5D,0x5B,0x43,0x44,
+ 0x32,0x5D,0x20,0x31,0x20,0x33,0x20,0x36,0x20,0x37,0x20,0x36,0x30,0x2E,0x30,
+ 0x20,0x2D,0x36,0x30,0x2E,0x30,0x0A,0x4F,0x3D,0x53,0x28,0x3D,0x4F,0x29,0x4E,
+ 0x5B,0x43,0x58,0x34,0x44,0x33,0x5D,0x2A,0x20,0x32,0x20,0x34,0x20,0x35,0x20,
+ 0x36,0x20,0x2D,0x39,0x30,0x2E,0x30,0x20,0x39,0x30,0x2E,0x30,0x20,0x31,0x32,
+ 0x30,0x2E,0x30,0x20,0x2D,0x31,0x32,0x30,0x2E,0x30,0x0A,0x4F,0x3D,0x53,0x28,
+ 0x3D,0x4F,0x29,0x4E,0x5B,0x43,0x58,0x34,0x44,0x32,0x5D,0x2A,0x20,0x32,0x20,
+ 0x34,0x20,0x35,0x20,0x36,0x20,0x2D,0x39,0x30,0x2E,0x30,0x20,0x39,0x30,0x2E,
+ 0x30,0x20,0x31,0x32,0x30,0x2E,0x30,0x20,0x2D,0x31,0x32,0x30,0x2E,0x30,0x0A,
+ 0x5B,0x63,0x5D,0x53,0x28,0x3D,0x4F,0x29,0x28,0x3D,0x4F,0x29,0x4E,0x43,0x20,
+ 0x31,0x20,0x32,0x20,0x35,0x20,0x36,0x20,0x2D,0x37,0x30,0x2E,0x30,0x20,0x37,
+ 0x30,0x2E,0x30,0x20,0x39,0x30,0x2E,0x30,0x20,0x2D,0x39,0x30,0x2E,0x30,0x20,
+ 0x35,0x30,0x2E,0x30,0x20,0x2D,0x35,0x30,0x2E,0x30,0x0A,0x2A,0x3D,0x2A,0x2D,
+ 0x53,0x28,0x3D,0x4F,0x29,0x28,0x3D,0x4F,0x29,0x43,0x20,0x31,0x20,0x32,0x20,
+ 0x33,0x20,0x36,0x20,0x39,0x30,0x2E,0x30,0x20,0x2D,0x39,0x30,0x2E,0x30,0x20,
+ 0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,0x30,0x2E,0x30,0x0A,0x4F,0x3D,0x53,0x28,
+ 0x3D,0x4F,0x29,0x4E,0x5B,0x43,0x48,0x32,0x5D,0x20,0x31,0x20,0x32,0x20,0x34,
+ 0x20,0x35,0x20,0x2D,0x36,0x30,0x2E,0x30,0x20,0x36,0x30,0x2E,0x30,0x20,0x31,
+ 0x38,0x30,0x2E,0x30,0x20,0x30,0x2E,0x30,0x20,0x33,0x30,0x2E,0x30,0x20,0x2D,
+ 0x33,0x30,0x2E,0x30,0x0A,0x5B,0x61,0x44,0x32,0x5D,0x63,0x28,0x5B,0x61,0x44,
+ 0x32,0x5D,0x29,0x53,0x28,0x3D,0x4F,0x29,0x28,0x3D,0x4F,0x29,0x5B,0x4E,0x44,
+ 0x32,0x5E,0x33,0x5D,0x20,0x31,0x20,0x32,0x20,0x34,0x20,0x37,0x20,0x39,0x30,
+ 0x2E,0x30,0x20,0x2D,0x39,0x30,0x2E,0x30,0x20,0x31,0x32,0x30,0x2E,0x30,0x20,
+ 0x2D,0x31,0x32,0x30,0x2E,0x30,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,0x30,
+ 0x2E,0x30,0x0A,0x5B,0x61,0x44,0x32,0x5D,0x63,0x28,0x5B,0x61,0x44,0x33,0x5D,
+ 0x29,0x53,0x28,0x3D,0x4F,0x29,0x28,0x3D,0x4F,0x29,0x5B,0x4E,0x44,0x32,0x5E,
+ 0x33,0x5D,0x20,0x31,0x20,0x32,0x20,0x34,0x20,0x37,0x20,0x38,0x30,0x2E,0x30,
+ 0x20,0x2D,0x38,0x30,0x2E,0x30,0x20,0x31,0x31,0x30,0x2E,0x30,0x20,0x2D,0x31,
+ 0x31,0x30,0x2E,0x30,0x0A,0x5B,0x61,0x44,0x33,0x5D,0x63,0x28,0x5B,0x61,0x44,
+ 0x33,0x5D,0x29,0x53,0x28,0x3D,0x4F,0x29,0x28,0x3D,0x4F,0x29,0x5B,0x4E,0x44,
+ 0x32,0x5E,0x33,0x5D,0x20,0x31,0x20,0x32,0x20,0x34,0x20,0x37,0x20,0x37,0x30,
+ 0x2E,0x30,0x20,0x2D,0x37,0x30,0x2E,0x30,0x20,0x31,0x31,0x30,0x2E,0x30,0x20,
+ 0x2D,0x31,0x31,0x30,0x2E,0x30,0x0A,0x5B,0x61,0x44,0x32,0x5D,0x63,0x28,0x5B,
+ 0x61,0x44,0x32,0x5D,0x29,0x53,0x28,0x3D,0x4F,0x29,0x28,0x3D,0x4F,0x29,0x5B,
+ 0x43,0x44,0x32,0x5E,0x33,0x5D,0x20,0x31,0x20,0x32,0x20,0x34,0x20,0x37,0x20,
+ 0x39,0x30,0x2E,0x30,0x20,0x2D,0x39,0x30,0x2E,0x30,0x20,0x31,0x31,0x30,0x2E,
+ 0x30,0x20,0x2D,0x31,0x31,0x30,0x2E,0x30,0x20,0x37,0x30,0x2E,0x30,0x20,0x2D,
+ 0x37,0x30,0x2E,0x30,0x0A,0x5B,0x61,0x5D,0x63,0x53,0x28,0x3D,0x4F,0x29,0x28,
+ 0x3D,0x4F,0x29,0x5B,0x43,0x2C,0x4E,0x5D,0x20,0x31,0x20,0x32,0x20,0x33,0x20,
+ 0x36,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,0x30,0x2E,0x30,0x20,0x39,0x30,
+ 0x2E,0x30,0x20,0x2D,0x39,0x30,0x2E,0x30,0x20,0x31,0x32,0x30,0x2E,0x30,0x20,
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+ 0x30,0x20,0x38,0x30,0x2E,0x30,0x20,0x2D,0x38,0x30,0x2E,0x30,0x20,0x33,0x30,
+ 0x2E,0x30,0x20,0x2D,0x33,0x30,0x2E,0x30,0x0A,0x5B,0x43,0x44,0x33,0x5D,0x5B,
+ 0x4F,0x44,0x32,0x5D,0x5B,0x43,0x44,0x32,0x5D,0x5B,0x4F,0x44,0x32,0x5D,0x20,
+ 0x31,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,
+ 0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x20,0x31,0x30,0x30,0x2E,0x30,
+ 0x20,0x2D,0x31,0x30,0x30,0x2E,0x30,0x0A,0x5B,0x43,0x44,0x31,0x5D,0x5B,0x43,
+ 0x44,0x32,0x5D,0x5B,0x43,0x44,0x32,0x5D,0x5B,0x2A,0x44,0x32,0x5D,0x5B,0x2A,
+ 0x44,0x32,0x5D,0x5B,0x2A,0x44,0x32,0x5D,0x20,0x32,0x20,0x33,0x20,0x34,0x20,
+ 0x35,0x20,0x31,0x38,0x30,0x2E,0x30,0x0A,0x5B,0x43,0x44,0x31,0x5D,0x5B,0x43,
+ 0x44,0x32,0x5D,0x5B,0x43,0x44,0x32,0x5D,0x5B,0x2A,0x44,0x32,0x5D,0x5B,0x2A,
+ 0x44,0x32,0x5D,0x5B,0x2A,0x44,0x32,0x5D,0x20,0x31,0x20,0x32,0x20,0x33,0x20,
+ 0x34,0x20,0x31,0x38,0x30,0x2E,0x30,0x0A,0x5B,0x2A,0x44,0x32,0x5E,0x33,0x5D,
+ 0x5B,0x2A,0x44,0x32,0x5E,0x33,0x5D,0x5B,0x2A,0x44,0x32,0x5E,0x33,0x5D,0x5B,
+ 0x2A,0x44,0x32,0x5E,0x33,0x5D,0x5B,0x2A,0x44,0x32,0x5E,0x33,0x5D,0x5B,0x2A,
+ 0x44,0x32,0x5E,0x33,0x5D,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x35,0x20,0x31,
+ 0x38,0x30,0x2E,0x30,0x0A,0x5B,0x61,0x44,0x33,0x5D,0x63,0x4E,0x28,0x7E,0x5B,
+ 0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x20,0x31,0x20,0x32,
+ 0x20,0x33,0x20,0x34,0x20,0x30,0x2E,0x30,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,
+ 0x36,0x30,0x2E,0x30,0x0A,0x5B,0x61,0x5D,0x63,0x4E,0x28,0x7E,0x5B,0x4F,0x44,
+ 0x31,0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x20,0x31,0x20,0x32,0x20,0x33,
+ 0x20,0x34,0x20,0x30,0x2E,0x30,0x0A,0x2A,0x2A,0x43,0x28,0x46,0x29,0x28,0x46,
+ 0x29,0x46,0x20,0x31,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x30,0x2E,0x30,0x0A,
+ 0x5B,0x61,0x5D,0x63,0x43,0x28,0x43,0x6C,0x29,0x28,0x43,0x6C,0x29,0x43,0x6C,
+ 0x20,0x31,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x30,0x2E,0x30,0x0A,0x61,0x5B,
+ 0x50,0x44,0x33,0x5D,0x28,0x61,0x29,0x2D,0x5B,0x50,0x44,0x33,0x5D,0x28,0x61,
+ 0x29,0x61,0x20,0x31,0x20,0x32,0x20,0x34,0x20,0x35,0x20,0x31,0x38,0x30,0x2E,
+ 0x30,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,0x30,0x2E,0x30,0x0A,0x50,0x50,
+ 0x63,0x63,0x20,0x31,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x36,0x30,0x2E,0x30,
+ 0x20,0x2D,0x36,0x30,0x2E,0x30,0x0A,0x00};
+
+} // namespace OpenBabel
+#endif // OB_TORLIB_H
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/torlib.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,224 @@
+##############################################################################
+#                                                                            #
+#                       Open Babel file: torlib.txt                          #
+#                                                                            #
+#  Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc.              #
+#  Some portions Copyright (c) 2001-2005 by Geoffrey R. Hutchison            #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+#  First three lines represent: (used by rotor.cpp::OBRotorRules             #
+#  Hybridization pair (atom types around a rotatable bond)                   #
+#   followed by a list of default bond rotation angles (in degrees)          #
+#                                                                            #
+#  Later lines should specify:                                               #
+#   * A SMARTS pattern for the rotor rule                                    #
+#   * A set of 4 "reference atoms" (as integers, numbered from 1             #
+#      in the specified SMARTS pattern                                       #
+#   * At least one torsion value (in degrees)                                #
+#   * Optionally ending with "Delta" and a delta value                       #
+#      (i.e., the resolution of a dihedral step                              #
+#                                                                            #
+#  SMARTS rules will be attempted first, then hybridization                  #
+#                                                                            #
+##############################################################################
+
+SP3-SP3  60.0  -60.0 180.0 
+SP2-SP2   0.0  180.0 -30.0 30.0 150.0 -150.0 
+SP3-SP2   0.0   30.0 -30.0 60.0 -60.0  120.0 -120.0 -150.0 150.0 180.0 -90.0 90.0
+
+# Many of these rules came from the Supporting Information
+# from Irwin, et. al., J. Med. Chem. (2006) 49(23) 6789-6801
+
+#polysaccaride bridges
+O@[CD3]O[CD3]([#1])@C 2 3 4 5 0.0 30.0 -30.0 180.0
+O@[CD3]([#1])O[CD3]([#1])@C 3 2 4 5 0.0 30.0 -30.0 180.0
+
+#acids
+[OD1]~C(~[OD1])[CX4](*)* 1 2 4 5 30.0 -30.0 -60.0 60.0 90.0 -90.0 0.0 180.0
+[a]cC([OD1])=O 1 2 3 4 0.0 20.0 -20.0
+[OD1]C(=O)[CD2]C 1 2 4 5 0.0 45.0 90.0
+
+#sulfonamides
+NS(=O)(=O)c1[cD2][cD2]a[cD2][cD2]1 1 2 5 6 90.0
+c([aD2])S(=O)(=O)[ND2][CD2] 1 3 6 7 60.0 -60.0
+O=S(=O)N[CX4D3]* 2 4 5 6 -90.0 90.0 120.0 -120.0
+O=S(=O)N[CX4D2]* 2 4 5 6 -90.0 90.0 120.0 -120.0
+[c]S(=O)(=O)NC 1 2 5 6 -70.0 70.0 90.0 -90.0 50.0 -50.0
+*=*-S(=O)(=O)C 1 2 3 6 90.0 -90.0 60.0 -60.0
+O=S(=O)N[CH2] 1 2 4 5 -60.0 60.0 180.0 0.0 30.0 -30.0
+[aD2]c([aD2])S(=O)(=O)[ND2^3] 1 2 4 7 90.0 -90.0 120.0 -120.0 60.0 -60.0
+[aD2]c([aD3])S(=O)(=O)[ND2^3] 1 2 4 7 80.0 -80.0 110.0 -110.0
+[aD3]c([aD3])S(=O)(=O)[ND2^3] 1 2 4 7 70.0 -70.0 110.0 -110.0
+[aD2]c([aD2])S(=O)(=O)[CD2^3] 1 2 4 7 90.0 -90.0 110.0 -110.0 70.0 -70.0
+[a]cS(=O)(=O)[C,N] 1 2 3 6 60.0 -60.0 90.0 -90.0 120.0 -120.0 0.0 180.0
+aS(=O)(=O)[ND2]a 1 2 5 6 90.0 -90.0
+aaNS(=O)(=O) 1 2 3 4 90.0 -90.0
+
+#sulfone
+O=S(=O)[CD2][CD3][#1] 2 4 5 6 30.0 -30.0
+
+#hydrazides
+[O,S]=C[ND2][ND2] 1 2 3 4 0.0 180.0
+[O,S]=C[ND2][ND2]-,=* 2 3 4 5 180.0 90.0 -90.0
+
+#cyclopropyl-ketones
+O=CC1([#1])[CD2][CD2]1 1 2 3 4 180.0
+O=CC1([#1])CC1 1 2 3 4 180.0 160.0 -160.0 0.0 20.0 -20.0
+O=CC1([*])CC1 1 2 3 4 180.0 160.0 -160.0 0.0 120.0 -120.0 90.0 -90.0 30.0 -30.0
+
+#epoxy-ketone
+O=C([*D2])C1([#1])O[CD2,CD3]1 1 2 4 5 0.0 180.0
+
+#opposite end of tert amide
+O=C([ND3])[CD2]* 1 2 4 5 0.0 30.0 -30.0 100.0 -100.0 80.0 -80.0
+O=C([CD3^3])[CD2]* 1 2 4 5 0.0 30.0 -30.0
+O=C([ND3])[CD3][#1] 1 2 4 5 180.0 150.0 -150.0 120.0 -120.0
+
+#misc
+[CD2]C(=O)[ND2]-!@[CD3][#1] 2 4 5 6 0.0 30.0 -30.0 60.0 -60.0 180.0
+[cD2]c([cD2])-!@[CD2^3][CD3^3] 1 2 4 5 90.0 -90.0 70.0 -70.0 110.0 -110.0
+c[CD2][ND3](C)c 1 2 3 4 90.0 -90.0 60.0 -60.0 120.0 -120.0
+
+#carbonyls
+O=CC=O 1 2 3 4 180.0 0.0 120.0 -120.0 90.0 -90.0
+C=CC=O 1 2 3 4 0.0 180.0 20.0 -20.0 160.0 -160.0
+O=C[CD2][ND2] 1 2 3 4 0.0 -30.0 30.0 150.0 -150.0 180.0
+O=C[CD2]C=O 1 2 3 4 0.0 -30.0 30.0 60.0 -60.0 130.0 -130.0
+O=C(c)[ND2][CD3][#1] 2 4 5 6 0.0 -30.0 30.0
+O=C[ND2][CD3]* 2 3 4 5 20.0 -20.0 120 -120.0 60.0 -60.0 0.0
+O=CN[CD2]* 2 3 4 5 180.0 150.0 -150.0 -120.0 120.0 0.0 30.0 -30.0
+O=Ccc[OD1] 1 2 3 4 0.0 180.0 90.0 -90.0 30.0 -30.0
+O=C[CD4][CD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0
+O=C[CD3][OD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0
+O=C[CD2][CD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 90.0 -90.0 120.0 -120.0
+O=C[CD3][#1] 1 2 3 4 0.0 30.0 -30.0 180.0
+#O=C[CD3]* 1 2 3 4 0.0 90.0 -90.0 30.0 -30.0 -120.0 120.0 60.0 -60.0
+
+#amidene and guanidine
+[aD3]cC(~[ND1])~[ND1] 1 2 3 4 0.0 30.0
+[a]cC(~[ND1])~[ND1] 1 2 3 4 0.0 30.0
+*[ND2]~C(~[ND1])~[ND1] 1 2 3 4 0.0 30.0
+[CD2][CD2][ND2]~C(~[ND1])~[ND1] 1 2 3 4 -70.0 70.0 90.0 -90.0 110.0 -110.0
+
+#ether
+aCO[CD2] 1 2 3 4 180.0 100.0 -100.0
+
+#isoprene
+C=C[CX4D2]* 1 2 3 4 0.0 180.0 90.0 -90.0 60.0 -60.0 30.0 -30.0
+C=Cc[a] 1 2 3 4 0.0 90.0 -90.0 180.0 30.0 -30.0 150.0 -150.0
+
+#aryl secondary amines
+[aD2]c([aD2])[ND2][CD2] 1 2 4 5 0.0 180.0
+[aD2]c([aD3])[ND2][CD2] 1 2 4 5 0.0
+[aD2]c([aD2])[ND2][CD1] 1 2 4 5 0.0 90.0 -90.0 180.0
+ac[ND2][CD2] 1 2 3 4 90.0 -90.0 160.0 -160.0 20.0 -20.0
+
+#aromatic subtituents
+[aD3]c([aD3])[CD2]C 1 2 4 5 90.0 -90.0 60.0 -60.0 120.0 -120.0
+[aD2]c([aD2])[ND3]([CD1])[CD2] 1 2 4 5 0.0 180.0
+[aD3][c,n]([aD2])[C^3D3][#1] 1 2 4 5 0.0 -30.0 30.0 60.0 -60.0 160.0 -160.0
+a[CD2X4][ND3^3]* 1 2 3 4 60.0 -60.0 180.0 160.0 -160.0 90.0 -90.0 120.0 -120.0
+an[CD2X4][CD1] 1 2 3 4 90.0 -90.0
+[aD3]c([aD2])C(=O)[C^3] 1 2 4 5 0.0 20.0 -20.0 150.0 -150.0 180.0
+[aD3]c([aD2])O[CD2] 1 2 3 4 180.0
+a[ND2][CD2X4][CD2X4] 1 2 3 4 180.0 160.0 -160.0 80.0 -80.0 60.0 -60.0
+[ND1]C(=O)c([aD3]) 1 2 4 5 0.0 180.0 30.0 -30.0 150.0 -150.0
+[aD2]c([aD2])c([aD2])[aD2] 1 2 4 5 -150.0 -30.0 30.0 150.0
+[a]c[CD2][*D2] 1 2 3 4 -90.0 90.0 180.0 0.0 30.0 -30.0 150.0 -150.0
+[a]cC(=O)c[a] 1 2 3 4 -150.0 -30.0 0.0 30.0 150.0 180.0
+[a]cC(=O)[*D2] 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0
+[a]cOC 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0
+
+#borderline low-res
+[CD2]C(=O)[ND2][CD3][#1] 2 4 5 6 90.0 -90.0 60.0 -60.0 120.0 -120.0
+
+#conjugated substituents
+a[CD2]C=* 1 2 3 4 150.0 -150.0 180.0 30.0 -30.0 0.0
+C=CC=C 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0 60.0 -60.0 120.0 -120.0
+cO[CD2]* 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 90.0 -90.0 180.0
+C=N[ND2]*=,:* 2 3 4 5 0.0 30.0 -30.0 150.0 -150.0 180.0
+c[CD2][ND2]c 1 2 3 4 60.0 -60.0 80.0 -80.0 180.0
+C=[CD3][ND3]* 1 2 3 4 30.0 -30.0 60.0 -60.0 90.0 -90.0 0.0 180.0
+
+#ureas
+[ND2]C(=O)Nc[nD2] 2 4 5 6 0.0 180.0
+[ND2]C(=O)[ND2]* 1 2 4 5 0.0 180.0
+
+#carbamates
+C[ND2]C(=O)O 1 2 3 4 0.0 180.0
+[ND2]C(=O)OC 3 2 4 5 0.0
+OC(=O)N* 3 2 4 5 0.0 20.0 -20.0 120.0 -120.0 160.0 -160.0 180.0
+
+#piperidine amide
+O=CN1[CD2][CD2][CD2][CD2][CD2]1 1 2 3 4 0.0
+
+#amides and esters
+[*D2]C(=O)O[CD3][#1] 2 4 5 6 0.0 30.0 -30.0
+[OD2]C(=O)[CD2][CD2^3] 3 2 4 5 0.0 30.0 -30.0 120.0 -120.0 180.0
+[O,SD1]=C(C)[ND2]C=[O,S] 1 2 4 5 0.0 180.0
+[O,SD1]=C(C)[ND2][#7,#8]=* 1 2 4 5 0.0 180.0
+[O,SD1]=C(C)[ND2]N 1 2 4 5 0.0 180.0
+[O,SD1]=C(C)cn 1 2 4 5 0.0 180.0
+[O,SD1]=C([#6])[ND2]* 1 2 4 5 0.0 20.0 -20.0
+[O,SD1]=C[ND2]* 1 2 3 4 0.0 20.0 -20.0 180
+O=C[ND3][CD3X4][#1] 2 3 4 5 0.0 180.0 20.0 -20.0
+O=CNc([aD2,aD3])[aD3] 2 3 4 5 20.0 -20.0 -90.0 90.0 60.0 -60.0 120.0 -120.0 0.0
+O=CNc[a] 2 3 4 5 -20.0 20.0 90.0 -90.0 -160.0 160.0
+O=C([CD2,CD3])O[CD2] 1 2 4 5 0.0
+O=C([CD1])O[CD1] 1 2 4 5 0.0
+[O,S]=CO[CD1] 1 2 3 4 0.0 20.0 -20.0 180.0
+O=CO[CD2][CD1] 2 3 4 5 180.0
+O=CO[CD2]* 2 3 4 5 180.0 60.0 -60.0 90.0 -90.0
+O=CO[CD3]* 2 3 4 5 120.0 -120.0 180.0 0.0 60.0 -60.0
+O=CO[CD4]* 2 3 4 5 -60.0 60.0 120.0 80.0 -80.0
+O=CO[CD3,CD4] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0
+O=CO* 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0
+O=C[ND3]([*D3])[*D3] 1 2 3 4 20.0 -20.0 0.0 180 150.0 -150.0
+O=C[ND3]* 1 2 3 4 0.0 180.0
+CC[ND3](CC)[CD2,CD3]* 2 3 6 7 180.0 60.0 -60.0 120.0 -120.0 0.0 180.0 30.0 -30.0
+[a][CD2][CD2][ND3] 1 2 3 4 90.0 -90.0 180.0 60.0 -60.0
+[ND3]C(=O)[nD3]* 1 2 4 5 90.0 -90.0 60.0 -60.0 120.0 -120.0
+[CD2]OC(=O)[CD2][CD3] 4 3 5 6 0.0 150.0 -150.0
+
+#t-butyl
+C([CD1])([CD1])([CD1])c[a] 2 1 5 6 90.0 30.0
+**C([CD1])([CD1])[CD1] 1 2 3 4 180.0 150.0
+
+#propyl
+[CD1]C([CD1])([#1])[CD2]* 4 2 5 6 60.0 -60.0
+
+#highly substituted alkane
+#[CD2]C(=O)[ND2]-!@[CD3][#1] 2 4 5 6
+*[CD2X4][CD3X4]([#1])[CD3] 1 2 3 4 180.0 60.0 -60.0 40.0 -40.0
+c[CD2^3][CD3^3][#1] 1 2 3 4 180.0 60.0 -60.0
+[CD2^3][CD2^3][CD3^3][#1] 1 2 3 4 60.0 -60.0 180.0 30.0 -30.0 0.0 160.0 -160.0 120.0 -120.0
+[*D2][CD2][CRH]([*R])[*R] 1 2 3 4 30.0 -30.0 120.0 -120.0 150.0 -150.0 60.0 -60.0 180.0 0.0
+[*D2][CD2][CX4D3][*D2] 1 2 3 4 30.0 -30.0 120.0 -120.0 150.0 -150.0 60.0 -60.0 180.0
+*[CHD3][CH2D2]* 1 2 3 4 150.0 -150.0 60.0 -60.0 180.0 -90.0 90.0 0.0 30.0 -30.0
+[CD1]C([CD1])[CD2]* 1 2 4 5 60.0 -60.0 180.0 80.0 -80.0 30.0 -30.0
+
+#long unsubstituted alkanes
+[CD3][OD2][CD2][OD2] 1 2 3 4 60.0 -60.0 180.0 100.0 -100.0
+[CD1][CD2][CD2][*D2][*D2][*D2] 2 3 4 5 180.0
+[CD1][CD2][CD2][*D2][*D2][*D2] 1 2 3 4 180.0
+[*D2^3][*D2^3][*D2^3][*D2^3][*D2^3][*D2^3] 2 3 4 5 180.0
+
+#nitro
+[aD3]cN(~[OD1])~[OD1] 1 2 3 4 0.0 60.0 -60.0
+[a]cN(~[OD1])~[OD1] 1 2 3 4 0.0
+
+#trifluoromethyl
+**C(F)(F)F 1 2 3 4 0.0
+
+#trichloromethyl
+[a]cC(Cl)(Cl)Cl 1 2 3 4 0.0
+
+#CSD SPECIFIC RULES
+a[PD3](a)-[PD3](a)a 1 2 4 5 180.0 60.0 -60.0
+PPcc 1 2 3 4 60.0 -60.0
+
+#phosphorus containing groups
+#[OD1]~PO* 1 2 3 4 0.0 -30.0 30.0 -60.0 60.0 120.0 -120.0
+#[OD1]~P(~[OD1])(~[OD1])[OD2][CD2]* 2 5 6 7 0.0 60.0 120.0 180.0 -120.0 -60.0
+#S=POc 1 2 3 4 0.0 -60.0 60.0 90.0 -90.0
+#[a]cCP(c)(c)c 1 2 3 4 90.0 -90.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/types.h	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,709 @@
+/***************************************************************
+This file is part of the Open Babel project.
+This is copyright under the GNU General Public License (GPL)
+For more information, see <http://openbabel.org/>
+
+This file contains a binary representation of data tables
+ used by Open Babel. It is used as a fallback if the textual
+ data table is not found at runtime. It is not a normal header.
+***************************************************************/
+
+
+#ifndef OB_TYPES_H
+#define OB_TYPES_H
+
+namespace OpenBabel
+{
+static const char TypesData[] = {
+ 0x31,0x39,0x34,0x09,0x32,0x30,0x0A,0x49,0x4E,0x54,0x09,0x41,0x54,0x4E,0x09,
+ 0x48,0x59,0x42,0x09,0x4D,0x4D,0x44,0x09,0x4D,0x4D,0x32,0x09,0x58,0x59,0x5A,
+ 0x09,0x41,0x4C,0x43,0x09,0x48,0x41,0x44,0x09,0x4D,0x43,0x4D,0x4C,0x09,0x43,
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+ 0x31,0x37,0x36,0x09,0x32,0x36,0x20,0x44,0x62,0x0A,0x53,0x67,0x09,0x31,0x30,
+ 0x36,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x53,0x67,0x09,0x30,0x09,0x30,0x09,
+ 0x30,0x09,0x30,0x09,0x53,0x67,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x09,
+ 0x30,0x09,0x30,0x09,0x31,0x37,0x37,0x09,0x32,0x36,0x20,0x53,0x67,0x0A,0x42,
+ 0x68,0x09,0x31,0x30,0x37,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x42,0x68,0x09,
+ 0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x42,0x68,0x09,0x30,0x09,0x30,0x09,
+ 0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x31,0x37,0x38,0x09,0x32,0x36,0x20,
+ 0x42,0x68,0x0A,0x48,0x73,0x09,0x31,0x30,0x38,0x09,0x30,0x09,0x30,0x09,0x30,
+ 0x09,0x48,0x73,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x48,0x73,0x09,
+ 0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x31,0x37,0x39,
+ 0x09,0x32,0x36,0x20,0x48,0x73,0x0A,0x4D,0x74,0x09,0x31,0x30,0x39,0x09,0x30,
+ 0x09,0x30,0x09,0x30,0x09,0x4D,0x74,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x30,
+ 0x09,0x4D,0x74,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x30,
+ 0x09,0x31,0x38,0x30,0x09,0x32,0x36,0x20,0x4D,0x74,0x0A,0x41,0x72,0x09,0x31,
+ 0x38,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x41,0x72,0x09,0x30,0x09,0x30,0x09,
+ 0x30,0x09,0x30,0x09,0x41,0x72,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x09,
+ 0x30,0x09,0x30,0x09,0x31,0x38,0x31,0x09,0x32,0x36,0x20,0x41,0x72,0x0A,0x42,
+ 0x32,0x09,0x35,0x09,0x30,0x09,0x35,0x34,0x09,0x32,0x36,0x09,0x42,0x09,0x42,
+ 0x09,0x30,0x09,0x42,0x09,0x35,0x33,0x09,0x42,0x09,0x32,0x36,0x09,0x42,0x32,
+ 0x09,0x42,0x5F,0x32,0x09,0x32,0x30,0x09,0x32,0x30,0x09,0x42,0x2E,0x30,0x09,
+ 0x31,0x38,0x32,0x09,0x32,0x36,0x20,0x32,0x36,0x0A,0x42,0x33,0x09,0x35,0x09,
+ 0x30,0x09,0x35,0x35,0x09,0x32,0x37,0x09,0x42,0x09,0x42,0x09,0x30,0x09,0x42,
+ 0x09,0x35,0x33,0x09,0x42,0x09,0x32,0x36,0x09,0x42,0x33,0x09,0x42,0x5F,0x33,
+ 0x09,0x32,0x30,0x09,0x32,0x30,0x09,0x42,0x2E,0x30,0x09,0x31,0x38,0x33,0x09,
+ 0x32,0x36,0x20,0x32,0x37,0x0A,0x4E,0x09,0x37,0x09,0x30,0x09,0x36,0x32,0x09,
+ 0x33,0x30,0x09,0x4E,0x09,0x4E,0x09,0x33,0x09,0x4E,0x09,0x32,0x09,0x4E,0x2E,
+ 0x09,0x33,0x33,0x09,0x4E,0x09,0x4E,0x09,0x32,0x09,0x31,0x09,0x4E,0x2E,0x30,
+ 0x09,0x31,0x38,0x34,0x09,0x32,0x36,0x20,0x38,0x0A,0x48,0x53,0x20,0x31,0x20,
+ 0x30,0x20,0x34,0x32,0x20,0x32,0x31,0x20,0x48,0x20,0x48,0x20,0x30,0x20,0x48,
+ 0x20,0x31,0x31,0x20,0x48,0x20,0x31,0x33,0x20,0x48,0x20,0x48,0x5F,0x48,0x42,
+ 0x20,0x31,0x35,0x20,0x32,0x35,0x20,0x48,0x2E,0x31,0x20,0x31,0x38,0x35,0x20,
+ 0x32,0x36,0x20,0x35,0x0A,0x48,0x42,0x20,0x31,0x20,0x30,0x20,0x34,0x32,0x20,
+ 0x32,0x31,0x20,0x48,0x20,0x48,0x20,0x30,0x20,0x48,0x20,0x31,0x31,0x20,0x48,
+ 0x20,0x31,0x33,0x20,0x48,0x20,0x48,0x5F,0x62,0x20,0x31,0x35,0x20,0x32,0x35,
+ 0x20,0x48,0x2E,0x31,0x20,0x31,0x38,0x36,0x20,0x32,0x36,0x20,0x35,0x0A,0x4F,
+ 0x61,0x72,0x20,0x38,0x20,0x32,0x20,0x31,0x35,0x20,0x37,0x20,0x4F,0x20,0x4F,
+ 0x32,0x20,0x30,0x20,0x4F,0x20,0x38,0x31,0x20,0x4F,0x2E,0x32,0x20,0x39,0x20,
+ 0x4F,0x32,0x20,0x4F,0x5F,0x52,0x20,0x31,0x31,0x20,0x31,0x31,0x20,0x4F,0x2E,
+ 0x33,0x20,0x31,0x38,0x37,0x20,0x32,0x36,0x20,0x37,0x0A,0x4F,0x31,0x20,0x38,
+ 0x20,0x30,0x20,0x36,0x32,0x20,0x33,0x30,0x20,0x4F,0x20,0x4F,0x20,0x33,0x20,
+ 0x4F,0x20,0x32,0x20,0x4F,0x2E,0x20,0x33,0x33,0x20,0x4F,0x20,0x4F,0x5F,0x31,
+ 0x20,0x32,0x20,0x31,0x20,0x4F,0x2E,0x30,0x20,0x31,0x38,0x38,0x20,0x32,0x36,
+ 0x20,0x37,0x0A,0x48,0x4F,0x09,0x31,0x09,0x30,0x09,0x34,0x32,0x09,0x32,0x34,
+ 0x09,0x48,0x09,0x48,0x09,0x30,0x09,0x48,0x09,0x31,0x31,0x09,0x48,0x09,0x31,
+ 0x33,0x09,0x48,0x09,0x48,0x5F,0x48,0x42,0x09,0x31,0x35,0x09,0x36,0x09,0x48,
+ 0x2E,0x31,0x09,0x31,0x38,0x39,0x09,0x32,0x36,0x20,0x32,0x34,0x0A,0x48,0x4F,
+ 0x09,0x31,0x09,0x30,0x09,0x34,0x32,0x09,0x32,0x34,0x09,0x48,0x09,0x48,0x09,
+ 0x30,0x09,0x48,0x09,0x31,0x31,0x09,0x48,0x09,0x31,0x33,0x09,0x48,0x09,0x48,
+ 0x5F,0x48,0x42,0x09,0x31,0x35,0x09,0x36,0x09,0x48,0x2E,0x31,0x09,0x31,0x39,
+ 0x30,0x09,0x32,0x36,0x20,0x32,0x38,0x0A,0x4F,0x09,0x38,0x09,0x32,0x09,0x32,
+ 0x30,0x09,0x37,0x09,0x4F,0x09,0x4F,0x33,0x09,0x30,0x09,0x4F,0x09,0x38,0x36,
+ 0x09,0x4F,0x2E,0x09,0x39,0x09,0x4F,0x33,0x09,0x4F,0x5F,0x33,0x09,0x32,0x36,
+ 0x09,0x31,0x32,0x09,0x4F,0x2E,0x33,0x09,0x31,0x39,0x31,0x09,0x32,0x36,0x20,
+ 0x34,0x36,0x0A,0x43,0x33,0x09,0x36,0x09,0x33,0x09,0x33,0x09,0x31,0x09,0x43,
+ 0x09,0x43,0x33,0x09,0x34,0x09,0x43,0x09,0x36,0x34,0x09,0x43,0x2E,0x33,0x09,
+ 0x31,0x09,0x43,0x33,0x09,0x43,0x5F,0x33,0x09,0x31,0x09,0x35,0x09,0x43,0x2E,
+ 0x34,0x09,0x31,0x39,0x32,0x09,0x31,0x20,0x32,0x32,0x0A,0x43,0x72,0x09,0x32,
+ 0x34,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x43,0x72,0x09,0x30,0x09,0x30,0x09,
+ 0x30,0x09,0x30,0x09,0x43,0x72,0x2E,0x74,0x68,0x09,0x30,0x09,0x30,0x09,0x30,
+ 0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x31,0x39,0x33,0x09,0x32,0x36,0x20,0x43,
+ 0x72,0x0A,0x44,0x75,0x09,0x30,0x09,0x30,0x09,0x36,0x31,0x09,0x30,0x09,0x44,
+ 0x75,0x09,0x44,0x75,0x09,0x30,0x09,0x5A,0x09,0x30,0x09,0x4C,0x70,0x09,0x32,
+ 0x36,0x09,0x44,0x75,0x09,0x44,0x75,0x09,0x32,0x30,0x09,0x32,0x35,0x09,0x75,
+ 0x6E,0x2E,0x30,0x09,0x31,0x39,0x34,0x09,0x32,0x36,0x20,0x30,0x0A,0x00};
+
+} // namespace OpenBabel
+#endif // OB_TYPES_H
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/types.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,213 @@
+##############################################################################
+#                                                                            #
+#	                Open Babel file: types.txt                               #
+#                                                                            #
+#  Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc.              #
+#  Some portions Copyright (c) 2001-2005 Geoffrey R. Hutchison               #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+#  Conversion between different external atom types                          #
+#    (used by data.cpp:OBTypeTable)                                          #
+#                                                                            #
+#  First line specifies size of the table: # rows   # columns                #
+#  Second line specifies type names used in the code                         #
+#  Remaining lines specify equivalent atomic type names in each column       #
+#                                                                            #
+##############################################################################
+194	20
+INT	ATN	HYB	MMD	MM2	XYZ	ALC	HAD	MCML	C3D	SYB	MOL	MAP	DRE	XED	DOK	M3D	IDX	SBN PCM
+X	0	0	62	0	X	Du	0	X	0	Du	26	X	X	21	25	un.0	0	26  0
+Mn	25	0	62	0	Mn	Du	0	M	258	Mn	26	Mn	Mn	20	25	Mn.0	1	26  Mn
+Fe	26	0	62	0	Fe	Du	0	M	266	Fe	26	Fe	Fe	20	25	Fe.6	2	26  Fe
+Du	0	0	61	0	Du	Du	0	Z	0	Du	26	Du	Du	20	25	un.0	3	26  0
+C3	6	3	3	1	C	C3	4	C	64	C.3	1	C3	C_3	1	5	C.4	4	1   1
+C2	6	2	2	2	C	C2	3	C	63	C.2	2	C2	C_2	2	1	C.3	5	2   2
+C2	6	2	2	38	C	C2	3	C	63	C.2	2	C2	C_2	2	1	C.3	6	2   2
+C1	6	1	1	4	C	C1	2	C	62	C.1	4	C1	C_1	4	1	C.2	7	4   4
+Cac	6	2	2	3	C	C2	0	C	63	C.2	2	C2	C_2	2	1	C.3	8	2   3
+Cbl	6	2	2	3	C	C2	3	C	63	C.2	2	C2	C_2	2	1	C.3	9	2   2
+C-	6	2	10	27	C	C3	4	C	64	C.3	1	C3	C_3	1	1	C.4	10	1   48
+N3+	7	3	32	39	N	N3+	4	N	79	N.4	31	N3	N_3	5	9	N.4	11	31  41
+N3	7	3	26	8	N	N3	3	N	73	N.3	5	N3	N_3	6	10	N.4	12	5   8
+N2	7	2	25	9	N	NPL3	2	N	72	N.2	19	N2	N_2	8	8	N.3	13	6   9
+Npl	7	2	25	9	N	NPL3	3	N	72	N.pl3	19	N2	N_2	9	8	N.3	14	19  9
+Naz	7	2	25	37	N	N2	0	N	72	N.2	6	N2	N_2	7	8	N.2	15	6   9
+N1	7	1	24	10	N	N1	0	N	71	N.1	7	N1	N_1	23	8	N.2	16	7   10
+Nox	7	2	26	8	N	N2	0	N	72	N.4	6	N2	N_2	6	8	N.3	17	31  9
+Ntr	7	2	25	9	N	N2	0	N	72	N.pl3	6	N2	N_2	8	8	N.3	18	19  9
+Ng+	7	2	35	8	N	NPL3	3	N	79	N.pl3	31	N2	N_2	5	9	N.3	19	19  37
+O3	8	3	16	6	O	O3	2	O	82	O.3	8	O3	O_3	10	12	O.4	20	8   6
+Oes	8	3	16	6	O	O3	2	O	82	O.3	8	O3	O_2	11	12	O.4	21	8   6
+O2	8	2	15	7	O	O2	0	O	81	O.2	9	O2	O_2	11	11	O.3	22	9   7
+O-	8	2	20	7	O	O2	0	O	86	O.co2	9	O2	O_3	26	12	O.R	23	32  42
+S3	16	3	49	15	S	S3	0	S	164	S.3	10	S3	S_3	12	14	S.4	24	10  15
+S	16	3	52	16	S	S3	0	S	164	S.3	10	S3	S_3	12	14	S.2	25	10  15
+S3+	16	3	49	16	S	S3	0	S	164	S.3	10	S3	S_3	12	14	S.4	26	10  16
+S2	16	2	49	17	S	S2	0	S	161	S.2	18	S2	S_3	13	14	S.3	27	18  15
+Sac	16	2	49	17	S	SO	0	S	161	S.3	29	S3	S_3	12	14	S.4	28	10  15
+So2	16	3	49	18	S	SO2	0	S	161	S.O2	30	S3	S_3	12	14	S.4	29	30 17
+Sox	16	2	49	18	S	SO2	0	S	161	S.O	30	S3	S_3	12	14	S.4	30	29 17
+S	16	3	49	15	S	S3	0	S	164	S.3	10	S3	S_3	12	14	S.2	31	10 15
+Bac	5	0	54	27	B	B	0	B	53	B	26	B2	B_2	20	20	B.0	32	26 26
+Box	5	0	54	26	B	B	0	B	53	B	26	B2	B_2	20	20	B.0	33	26 26
+B	5	0	55	27	B	B	0	B	53	B	26	B3	B_3	20	20	B.0	34	26 26
+P3	15	3	53	25	P	P3	0	P	159	P.3	12	P3	P_3	14	13	P.4	35	12 25
+Pac	15	2	53	25	P	P3	0	P	159	P.3	12	P3	P_3	14	13	P.4	36	12 25
+Pox	15	3	53	25	P	P3	0	P	159	P.3	12	P3	P_3	14	13	P.4	37	12 25
+P3+	15	3	53	25	P	P3	0	P	154	P.3	12	P3	P_3	14	13	P.4	38	12 25
+P	15	3	53	25	P	P3	0	P	159	P.3	12	P3	P_3	14	13	P.4	39	12 25
+HC	1	0	41	5	H	H	0	H	11	H	13	H	H_	15	7	H.1	40	13 5
+H-	1	0	45	5	H	H	0	H	11	H	13	H	H_	15	6	H.1	41	13 5
+H	1	0	48	5	H	H	0	H	11	H	13	H	H_	15	6	H.1	42	13 5
+H	1	0	48	5	D	H	0	H	12	H	13	H	H_	15	6	H.1	43	13 5
+DC	1	0	48	36	D	H	0	D	19	H	13	D	H_	15	6	H.1	44	13 36
+D	1	0	48	36	D	H	0	D	19	H	13	D	H_	15	6	H.1	45	13 36
+F	9	0	56	11	F	F	0	F	91	F	16	F	F_	16	15	F.1	46	16 11
+Cl	17	0	57	12	Cl	CL	0	L	171	Cl	15	Cl	Cl	17	16	Cl.1	47	15 12
+Br	35	0	58	13	Br	BR	0	R	351	Br	14	Br	Br	18	17	Br.1	48	14 13
+I	53	0	59	14	I	I	0	I	531	I	17	I	I_	19	18	I.1	49	17 14
+Ge	32	0	62	31	Ge	GE	0	E	324	Ge	26	Ge	Ge3	20	25	Ge.4	50	26 Ge
+Sn	50	0	62	32	Sn	SN	0	X	504	Sn	26	Sn	Xx	20	25	Sn.0	51	26 Sn
+Pb	82	0	62	33	Pb	PB	0	Z	824	Pb	26	Pb	Xx	20	25	Pb.0	52	26 Pb
+Se	34	0	62	34	Se	SE	0	Z	342	Se	26	Se	Se3	20	25	Se.4	53	26 34
+Te	52	0	62	35	Te	TE	0	Z	0	Te	26	Te	Te3	20	25	Te.4	54	26 35
+O	8	0	23	6	O	O	0	Z	82	O.3	8	O	O_3	10	12	O.4	55	8  6
+Lp	0	0	63	20	Lp	Lp	0	Z	10	LP	20	Lp	Xx	30	25	ep.1	56	20 20
+C-	6	0	10	0	C	C2	0	C	61	C.2	2	C-3	Xx	2	5	C.4	57	2  48
+C.	6	0	12	0	C	C2	0	C	0	C.2	2	C.3	Xx	2	5	C.3	58	2  29
+NC	7	0	29	9	N	N2	0	N	72	N.2	6	N2	N_2	8	8	N.3	59	6  8
+N2+	7	0	36	9	N	N2	0	N	78	N.2	6	N2	N_2	7	8	N.3	60	6  9
+Z0	0	0	62	0	Du	Du	0	Z	0	Du	26	Xx	Xx	20	25	un.0	61	26 0
+HO	1	0	42	21	H	H	0	H	11	H	13	H	H_HB	15	25	H.1	62	13 21
+H+	1	0	44	5	H	H	0	H	11	H	13	H	H_	15	6	H.0	63	13 5
+HN	1	0	43	23	H	H	0	H	11	H	13	H	H_HB	15	6	H.1	64	13 23
+C3	6	0	3	22	H	H	0	C	64	H	13	C3	C_3	1	5	C.4	65	13 1
+H	1	0	43	28	H	H	0	H	11	H	13	H	H_	15	6	H.1	66	13 5
+Cx	6	0	62	29	C	C	0	C	64	C	1	Xx	Xx	20	5	un.0	67	26 1
+N2	7	0	25	40	N	N2	0	N	72	N	6	N2	N_2	8	8	N.3	68	26 9
+HO	1	0	42	24	H	H	0	H	11	H	13	H	H_HB	15	6	H.1	69	26 21
+W	74	0	62	0	W	W	0	W	744	W	26	W	Xx	20	25	W.0	70	26 W
+Car	6	2	2	2	C	C2	3	C	2	C.ar	3	C2	C_R	3	1	C.R	71	3  40
+Nar	7	2	25	9	N	NPL3	2	N	37	N.ar	11	N2	N_R	8	8	N.R	72	11 9
+Nam	7	2	25	9	N	NPL3	3	N	9	N.am	28	N2	N_2	8	8	N.3	73	28 9
+Na	11	0	25	9	Na	Na	0	Z	9	Na	21	NA	Na	20	19	Na.6	74	21 Na
+K	19	0	0	0	K	K	0	Z	190	K	22	K	Xx	20	19	K.0	75	22 K
+Ca	20	0	0	0	Ca	Ca	0	Z	200	Ca	23	CA	Ca	20	21	Ca.6	76	23 Ca
+Li	3	0	62	0	Li	LI	0	M	258	Li	26	Li	Li	20	25	Li.0	77	24 Li
+Al	13	0	0	0	Al	Al	0	Z	133	Al	25	AL	Al3	20	20	Al.6	78	25 Al
+Si	14	0	60	0	Si	Si	4	Z	19	Si	27	SI	Si3	20	24	Si.4	79	27 Si
+OCO2	8	0	18	47	O	O	1	O	47	O.co2	32	O2	O_2	11	1	O.3	80	32 7
+C+	6	2	11	30	C	C2	3	C	2	C.cat	33	C2	C_2	2	1	C.3	81	33 30
+O2	8	0	15	41	O	O2	0	O	81	O.2	9	O2	O_2	11	11	O.R	82	9  7
+Pd	46	0	62	464	Pd	Du	0	Z	464	Pd	26	Du	Du	20	25	Pd.0	83	26 Pd
+Pt	78	0	62	464	Pt	Du	0	Z	464	Pt	26	Pt	Du	20	25	Pt.0	84	26 Pt
+Ni	28	0	62	0	Ni	Du	0	M	284	Ni	26	Ni	Ni	20	25	Ni.0	85	26 Ni
+Cu	29	0	62	0	Cu	Du	0	M	000	Cu	26	Cu	Cu	20	25	Cu.0	86	26 Cu
+N4	7	0	32	39	N	N3+	4	N	79	N.4	31	N3	N_3	5	9	N.4	87	31 41
+Npl	7	2	25	9	N	NPL3	3	N	72	N.pl3N	19	N2	N_2	9	8	N.3	88	19 9
+O-	8	2	20	7	O	O2	0	O	86	O.co2O	9	O2	O_3	26	12	O.R	89	32 41
+C+	6	2	11	30	C	C2	3	C	2	C.catC	33	C2	C_2	2	1	C.3	90	33 30
+O	8	2	20	7	O	O3	0	O	86	O.	9	O3	O_3	26	12	O.3	91	26 6
+C	6	3	3	1	C	C3	4	C	64	C.	1	C3	C_3	1	5	C.4	92	26 1
+V	23	0	62	0	V	Du	0	Z	234	V	0	V	Du	20	25	V.0	93	26 V
+Zn	30	0	62	0	Zn	Zn	0	Z	234	Zn	0	V	Zn	20	25	Zn.0	94	26 Zn
+Cany	6	0	62	30	C	C	3	C	2	C.	33	C	C	2	1	C.0	95	26 1
+Nany	7	0	62	30	N	N	3	N	2	N.	33	N	N	2	1	N.0	96	26 8
+Oany	8	0	62	30	O	O	3	O	2	O.	33	O	O	2	1	O.0	97	26 6
+Sany	16	0	62	30	S	S	3	S	2	S.	33	S	S	2	1	S.0	98	26 15
+Rar	6	0	62	30	C	C	3	C	2	R.ar	33	C	C	2	1	C.0	99	26 1
+R	6	0	62	30	C	C	3	C	2	R.	33	C	C	2	1	C.0	100	26 1
+Nr	6	0	62	30	C	C	3	C	2	Nr.	33	C	C	2	1	C.0	101	26 8
+O.co2	8	2	20	7	O	O2	0	O	86	O.co2	9	O2	O_3	26	12	O.R	102	32 7
+So	16	2	49	18	S	SO2	0	S	161	S.O2	30	S3	S_3	12	14	S.4	103	30 17
+He	2	0	0	0	He	0	0	0	0	He	0	0	0	0	0	0	104	26 He
+Be	4	0	0	0	Be	0	0	0	0	Be	0	0	0	0	0	0	105	26 Be
+Ne	10	0	0	0	Ne	0	0	0	0	Ne	0	0	0	0	0	0	106	26 Ne
+Mg	12	0	0	0	Mg	0	0	0	0	Mg	0	0	0	0	0	0	107	26 Mg
+Sc	21	0	0	0	Sc	0	0	0	0	Sc	0	0	0	0	0	0	108	26 Sc
+Ti	22	0	0	0	Ti	0	0	0	0	Ti	0	0	0	0	0	0	109	26 Ti
+Cr	24	0	0	0	Cr	0	0	0	0	Cr.oh	0	0	0	0	0	0	110	26 Cr
+Co	27	0	0	0	Co	0	0	0	0	Co.oh	0	0	0	0	0	0	111	26 Co
+Ga	31	0	0	0	Ga	0	0	0	0	Ga	0	0	0	0	0	0	112	26 Ga
+As	33	0	0	0	As	0	0	0	0	As	0	0	0	0	0	0	113	26 As
+Kr	36	0	0	0	Kr	0	0	0	0	Kr	0	0	0	0	0	0	114	26 Kr
+Rb	37	0	0	0	Rb	0	0	0	0	Rb	0	0	0	0	0	0	115	26 Rb
+Sr	38	0	0	0	Sr	0	0	0	0	Sr	0	0	0	0	0	0	116	26 Sr
+Y	39	0	0	0	Y	0	0	0	0	Y	0	0	0	0	0	0	117	26 Y
+Zr	40	0	0	0	Zr	0	0	0	0	Zr	0	0	0	0	0	0	118	26 Zr
+Nb	41	0	0	0	Nb	0	0	0	0	Nb	0	0	0	0	0	0	119	26 Nb
+Mo	42	0	0	0	Mo	0	0	0	0	Mo	0	0	0	0	0	0	120	26 Mo
+Tc	43	0	0	0	Tc	0	0	0	0	Tc	0	0	0	0	0	0	121	26 Tc
+Ru	44	0	0	0	Ru	0	0	0	0	Ru	0	0	0	0	0	0	122	26 Ru
+Rh	45	0	0	0	Rh	0	0	0	0	Rh	0	0	0	0	0	0	123	26 Rh
+Ag	47	0	0	0	Ag	0	0	0	0	Ag	0	0	0	0	0	0	124	26 Ag
+Cd	48	0	0	0	Cd	0	0	0	0	Cd	0	0	0	0	0	0	125	26 Cd
+In	49	0	0	0	In	0	0	0	0	In	0	0	0	0	0	0	126	26 In
+Sb	51	0	0	0	Sb	0	0	0	0	Sb	0	0	0	0	0	0	127	26 Sb
+Xe	54	0	0	0	Xe	0	0	0	0	Xe	0	0	0	0	0	0	128	26 Xe
+Cs	55	0	0	0	Cs	0	0	0	0	Cs	0	0	0	0	0	0	129	26 Cs
+Ba	56	0	0	0	Ba	0	0	0	0	Ba	0	0	0	0	0	0	130	26 Ba
+La	57	0	0	0	La	0	0	0	0	La	0	0	0	0	0	0	131	26 La
+Ce	58	0	0	0	Ce	0	0	0	0	Ce	0	0	0	0	0	0	132	26 Ce
+Pr	59	0	0	0	Pr	0	0	0	0	Pr	0	0	0	0	0	0	133	26 Pr
+Nd	60	0	0	0	Nd	0	0	0	0	Nd	0	0	0	0	0	0	134	26 Nd
+Pm	61	0	0	0	Pm	0	0	0	0	Pm	0	0	0	0	0	0	135	26 Pm
+Sm	62	0	0	0	Sm	0	0	0	0	Sm	0	0	0	0	0	0	136	26 Sm
+Eu	63	0	0	0	Eu	0	0	0	0	Eu	0	0	0	0	0	0	137	26 Eu
+Gd	64	0	0	0	Gd	0	0	0	0	Gd	0	0	0	0	0	0	138	26 Gd
+Tb	65	0	0	0	Tb	0	0	0	0	Tb	0	0	0	0	0	0	139	26 Tb
+Dy	66	0	0	0	Dy	0	0	0	0	Dy	0	0	0	0	0	0	140	26 Dy
+Ho	67	0	0	0	Ho	0	0	0	0	Ho	0	0	0	0	0	0	141	26 Ho
+Er	68	0	0	0	Er	0	0	0	0	Er	0	0	0	0	0	0	142	26 Er
+Tm	69	0	0	0	Tm	0	0	0	0	Tm	0	0	0	0	0	0	143	26 Tm
+Yb	70	0	0	0	Yb	0	0	0	0	Yb	0	0	0	0	0	0	144	26 Yb
+Lu	71	0	0	0	Lu	0	0	0	0	Lu	0	0	0	0	0	0	145	26 Lu
+Hf	72	0	0	0	Hf	0	0	0	0	Hf	0	0	0	0	0	0	146	26 Hf
+Ta	73	0	0	0	Ta	0	0	0	0	Ta	0	0	0	0	0	0	147	26 Ta
+Re	75	0	0	0	Re	0	0	0	0	Re	0	0	0	0	0	0	148	26 Re
+Os	76	0	0	0	Os	0	0	0	0	Os	0	0	0	0	0	0	149	26 Os
+Ir	77	0	0	0	Ir	0	0	0	0	Ir	0	0	0	0	0	0	150	26 Ir
+Au	79	0	0	0	Au	0	0	0	0	Au	0	0	0	0	0	0	151	26 Au
+Hg	80	0	0	0	Hg	0	0	0	0	Hg	0	0	0	0	0	0	152	26 Hg
+Tl	81	0	0	0	Tl	0	0	0	0	Tl	0	0	0	0	0	0	153	26 Tl
+Bi	83	0	0	0	Bi	0	0	0	0	Bi	0	0	0	0	0	0	154	26 Bi
+Po	84	0	0	0	Po	0	0	0	0	Po	0	0	0	0	0	0	155	26 Po
+At	85	0	0	0	At	0	0	0	0	At	0	0	0	0	0	0	156	26 At
+Rn	86	0	0	0	Rn	0	0	0	0	Rn	0	0	0	0	0	0	157	26 Rn
+Fr	87	0	0	0	Fr	0	0	0	0	Fr	0	0	0	0	0	0	158	26 Fr
+Ra	88	0	0	0	Ra	0	0	0	0	Ra	0	0	0	0	0	0	159	26 Ra
+Ac	89	0	0	0	Ac	0	0	0	0	Ac	0	0	0	0	0	0	160	26 Ac
+Th	90	0	0	0	Th	0	0	0	0	Th	0	0	0	0	0	0	161	26 Th
+Pa	91	0	0	0	Pa	0	0	0	0	Pa	0	0	0	0	0	0	162	26 Pa
+U	92	0	0	0	U	0	0	0	0	U	0	0	0	0	0	0	163	26 U
+Np	93	0	0	0	Np	0	0	0	0	Np	0	0	0	0	0	0	164	26 Np
+Pu	94	0	0	0	Pu	0	0	0	0	Pu	0	0	0	0	0	0	165	26 Pu
+Am	95	0	0	0	Am	0	0	0	0	Am	0	0	0	0	0	0	166	26 Am
+Cm	96	0	0	0	Cm	0	0	0	0	Cm	0	0	0	0	0	0	167	26 Cm
+Bk	97	0	0	0	Bk	0	0	0	0	Bk	0	0	0	0	0	0	168	26 Bk
+Cf	98	0	0	0	Cf	0	0	0	0	Cf	0	0	0	0	0	0	169	26 Cf
+Es	99	0	0	0	Es	0	0	0	0	Es	0	0	0	0	0	0	170	26 Es
+Fm	100	0	0	0	Fm	0	0	0	0	Fm	0	0	0	0	0	0	171	26 Fm
+Md	101	0	0	0	Md	0	0	0	0	Md	0	0	0	0	0	0	172	26 Md
+No	102	0	0	0	No	0	0	0	0	No	0	0	0	0	0	0	173	26 No
+Lr	103	0	0	0	Lr	0	0	0	0	Lr	0	0	0	0	0	0	174	26 Lr
+Rf	104	0	0	0	Rf	0	0	0	0	Rf	0	0	0	0	0	0	175	26 Rf
+Db	105	0	0	0	Db	0	0	0	0	Db	0	0	0	0	0	0	176	26 Db
+Sg	106	0	0	0	Sg	0	0	0	0	Sg	0	0	0	0	0	0	177	26 Sg
+Bh	107	0	0	0	Bh	0	0	0	0	Bh	0	0	0	0	0	0	178	26 Bh
+Hs	108	0	0	0	Hs	0	0	0	0	Hs	0	0	0	0	0	0	179	26 Hs
+Mt	109	0	0	0	Mt	0	0	0	0	Mt	0	0	0	0	0	0	180	26 Mt
+Ar	18	0	0	0	Ar	0	0	0	0	Ar	0	0	0	0	0	0	181	26 Ar
+B2	5	0	54	26	B	B	0	B	53	B	26	B2	B_2	20	20	B.0	182	26 26
+B3	5	0	55	27	B	B	0	B	53	B	26	B3	B_3	20	20	B.0	183	26 27
+N	7	0	62	30	N	N	3	N	2	N.	33	N	N	2	1	N.0	184	26 8
+HS      1       0       42      21      H       H       0       H       11      H       13      H       H_HB    15      25      H.1     185     26 5
+HB      1       0       42      21      H       H       0       H       11      H       13      H       H_b     15      25      H.1     186     26 5
+Oar     8       2       15      7       O       O2      0       O       81      O.2     9       O2      O_R     11      11      O.3     187     26 7
+O1      8       0       62      30      O       O       3       O       2       O.      33      O       O_1     2       1       O.0     188     26 7
+HO	1	0	42	24	H	H	0	H	11	H	13	H	H_HB	15	6	H.1	189	26 24
+HO	1	0	42	24	H	H	0	H	11	H	13	H	H_HB	15	6	H.1	190	26 28
+O	8	2	20	7	O	O3	0	O	86	O.	9	O3	O_3	26	12	O.3	191	26 46
+C3	6	3	3	1	C	C3	4	C	64	C.3	1	C3	C_3	1	5	C.4	192	1   22
+Cr	24	0	0	0	Cr	0	0	0	0	Cr.th	0	0	0	0	0	0	193	26 Cr
+Du	0	0	61	0	Du	Du	0	Z	0	Lp	26	Du	Du	20	25	un.0	194	26  0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/atomic_electron_affinities.data	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,88 @@
+# atomic electron affinities, taken from CRC Handbook of Chemistry and Physics, 79th edition, 1998; non-excistant values like unstable ions have 0.0
+0.754593
+0.0
+0.6180
+0.0
+0.277
+1.2629
+0.0
+1.4611103
+3.401190
+0.0
+0.547926
+0.0
+0.441
+1.385
+0.7465
+2.077104
+3.61269
+0.0
+0.50147
+0.02455
+0.188
+0.079
+0.525
+0.666
+0.0
+0.151
+0.662
+1.156
+1.235
+0.0
+0.3
+1.233
+0.81
+2.020670
+3.363590
+0.0
+0.48592
+0.048
+0.307
+0.426
+0.893
+0.748
+0.55
+1.05
+1.137
+0.562
+1.302
+0.0
+0.3
+1.112
+1.046
+1.9708
+3.059038
+0.0
+0.471626
+0.15
+0.5
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.0
+0.322
+0.815
+0.15
+1.1
+1.5638
+2.128
+2.30863
+0.0
+0.2
+0.364
+0.946
+1.9
+2.8
+0.0
+0.46
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/atomic_ionization_potentials.data	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,73 @@
+# atomic ionization potentials (neutral atom and +1 ion), CRC Handbook of Chemistry and Physics, 79th edition, 1998
+13.59844 20.02
+24.58741 54.41778
+5.39172 75.64018
+9.3227 18.21116
+8.29803 25.15484 
+11.26030 24.38332
+14.53414 29.6013
+13.61806 35.11730
+17.42282 34.97082
+21.5646 40.96328
+5.13908 47.2864
+7.64624 15.03528
+5.98577 18.82856
+8.15169 16.34585
+10.48669 19.7694
+10.36001 23.3379
+12.96764 23.814
+15.75962 27.62967
+4.34066 31.63
+6.11316 11.87172
+6.5615 12.79967
+6.8281 13.5755
+6.7463 14.66
+6.7665 16.4857
+7.43402 15.63999
+7.9024 16.1878
+7.8810 17.083
+7.6398 18.16884
+7.72638 20.29240
+9.3942 17.96440
+5.99930 20.5142
+7.8994 15.93462
+9.7886 18.633
+9.75238 21.19
+11.81381 21.8
+13.99961 24.35985
+4.17713 27.285
+5.6949 11.03013
+6.2171 12.24
+6.63390 13.13
+6.75885 14.32
+7.09243 16.16
+7.28 15.26
+7.36050 16.76
+7.45890 18.08
+8.3369 19.43
+7.5763 21.49
+8.9938 16.90832
+5.78636 18.8698
+7.3439 14.63225
+8.6084 16.53051
+9.0096 18.6
+10.45126 19.1313
+12.1298 21.20979
+3.89390 23.15745
+5.21170 10.00390
+5.770 11.060
+5.5387 10.85
+5.464 10.55
+5.5250 10.73
+5.58 10.9
+5.6436 11.07
+5.6704 11.241
+6.1501 12.09
+5.8638 11.52
+5.9389 11.67
+6.0215 11.80
+6.1077 11.93
+6.18431 12.05
+6.25416 12.1761
+5.4259 13.9
+6.82507 14.9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/atomic_polarizabilities.data	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,101 @@
+# atomic ground state polarizabilities, taken from CRC Handbook of Chemistry and Physics, 79th edition, 1998
+0.666793
+0.204956 
+24.3
+5.6
+3.03 
+1.76 
+1.1 
+0.802 
+0.557 
+0.3956
+24.08 
+10.6 
+6.8
+5.38
+3.63
+2.9 
+2.18
+1.6411
+43.4
+22.8
+17.8
+14.6
+12.4
+11.6
+9.4
+8.4
+7.5
+6.8
+6.1
+7.1
+8.12
+6.07
+4.31
+3.77
+3.05
+2.4844
+47.3
+27.6
+22.7
+17.9
+15.7
+12.8
+11.4
+9.6
+8.6
+4.8
+7.2
+7.2 
+10.2
+7.7
+6.6
+5.5
+5.35
+4.044
+59.6
+39.7
+31.1
+29.6
+28.2
+31.4
+30.1
+28.8
+27.7
+23.5
+25.5
+24.5
+23.6
+22.7
+21.8
+21.0
+21.9
+16.2
+13.1
+11.1
+9.7
+8.5
+7.6
+6.5
+5.8
+5.7
+7.6
+6.8
+7.4
+6.8
+6.0
+5.3
+48.7
+38.3
+32.1
+32.1
+25.4
+24.9
+24.8
+24.5
+23.3
+23.0
+22.7
+20.5
+19.7
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/dragon_descriptors.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,1665 @@
+MW	molecular weight
+AMW	average molecular weight
+Sv	sum of atomic van der Waals volumes (scaled on Carbon atom)
+Se	sum of atomic Sanderson electronegativities (scaled on Carbon atom)
+Sp	sum of atomic polarizabilities (scaled on Carbon atom)
+Ss	sum of Kier-Hall electrotopological states
+Mv	mean atomic van der Waals volume (scaled on Carbon atom)
+Me	mean atomic Sanderson electronegativity (scaled on Carbon atom)
+Mp	mean atomic polarizability (scaled on Carbon atom)
+Ms	mean electrotopological state
+nAT	number of atoms
+nSK	number of non-H atoms
+nBT	number of bonds
+nBO	number of non-H bonds
+nBM	number of multiple bonds
+SCBO	sum of conventional bond orders (H-depleted)
+ARR	aromatic ratio
+nCIC	number of rings
+nCIR	number of circuits
+RBN	number of rotatable bonds
+RBF	rotatable bond fraction
+nDB	number of double bonds
+nTB	number of triple bonds
+nAB	number of aromatic bonds
+nH	number of Hydrogen atoms
+nC	number of Carbon atoms
+nN	number of Nitrogen atoms
+nO	number of Oxygen atoms
+nP	number of Phosphorous atoms
+nS	number of Sulfur atoms
+nF	number of Fluorine atoms
+nCL	number of Chlorine atoms
+nBR	number of Bromine atoms
+nI	number of Iodine atoms
+nB	number of Boron atoms
+nHM	number of heavy atoms
+nX	number of halogen atoms
+nR03	number of 3-membered rings
+nR04	number of 4-membered rings
+nR05	number of 5-membered rings
+nR06	number of 6-membered rings
+nR07	number of 7-membered rings
+nR08	number of 8-membered rings
+nR09	number of 9-membered rings
+nR10	number of 10-membered rings
+nR11	number of 11-membered rings
+nR12	number of 12-membered rings
+nBnz	number of benzene-like rings
+ZM1	first Zagreb index M1
+ZM1V	first Zagreb index by valence vertex degrees
+ZM2	second Zagreb index M2
+ZM2V	second Zagreb index by valence vertex degrees
+Qindex	Quadratic index
+SNar	Narumi simple topological index (log)
+HNar	Narumi harmonic topological index
+GNar	Narumi geometric topological index
+Xt	Total structure connectivity index
+Dz	Pogliani index
+Ram	ramification index
+Pol	polarity number
+LPRS	log of product of row sums (PRS)
+VDA	average vertex distance degree
+MSD	mean square distance index (Balaban)
+SMTI	Schultz Molecular Topological Index (MTI)
+SMTIV	Schultz MTI by valence vertex degrees
+GMTI	Gutman Molecular Topological Index
+GMTIV	Gutman MTI by valence vertex degrees
+Xu	Xu index
+SPI	superpendentic index
+W	Wiener W index
+WA	mean Wiener index
+Har	Harary H index
+Har2	square reciprocal distance sum index
+QW	quasi-Wiener index (Kirchhoff number)
+TI1	first Mohar index TI1
+TI2	second Mohar index TI2
+STN	spanning tree number (log)
+HyDp	hyper-distance-path index
+RHyDp	reciprocal hyper-distance-path index
+w	detour index
+ww	hyper-detour index
+Rww	reciprocal hyper-detour index
+D/D	distance/detour index
+Wap	all-path Wiener index
+WhetZ	Wiener-type index from Z weighted distance matrix (Barysz matrix)
+Whetm	Wiener-type index from mass weighted distance matrix
+Whetv	Wiener-type index from van der Waals weighted distance matrix
+Whete	Wiener-type index from electronegativity weighted distance matrix
+Whetp	Wiener-type index from polarizability weighted distance matrix
+J	Balaban distance connectivity index
+JhetZ	Balaban-type index from Z weighted distance matrix (Barysz matrix)
+Jhetm	Balaban-type index from mass weighted distance matrix
+Jhetv	Balaban-type index from van der Waals weighted distance matrix
+Jhete	Balaban-type index from electronegativity weighted distance matrix
+Jhetp	Balaban-type index from polarizability weighted distance matrix
+MAXDN	maximal electrotopological negative variation
+MAXDP	maximal electrotopological positive variation
+DELS	molecular electrotopological variation
+TIE	E-state topological parameter
+S0K	Kier symmetry index
+S1K	1-path Kier alpha-modified shape index
+S2K	2-path Kier alpha-modified shape index
+S3K	3-path Kier alpha-modified shape index
+PHI	Kier flexibility index
+BLI	Kier benzene-likeliness index
+PW2	path/walk 2 - Randic shape index
+PW3	path/walk 3 - Randic shape index
+PW4	path/walk 4 - Randic shape index
+PW5	path/walk 5 - Randic shape index
+PJI2	2D Petitjean shape index
+CSI	eccentric connectivity index
+ECC	eccentricity
+AECC	average eccentricity
+DECC	eccentric
+MDDD	mean distance degree deviation
+UNIP	unipolarity
+CENT	centralization
+VAR	variation
+BAC	Balaban centric index
+Lop	Lopping centric index
+ICR	radial centric information index
+D/Dr03	distance/detour ring index of order 3
+D/Dr04	distance/detour ring index of order 4
+D/Dr05	distance/detour ring index of order 5
+D/Dr06	distance/detour ring index of order 6
+D/Dr07	distance/detour ring index of order 7
+D/Dr08	distance/detour ring index of order 8
+D/Dr09	distance/detour ring index of order 9
+D/Dr10	distance/detour ring index of order 10
+D/Dr11	distance/detour ring index of order 11
+D/Dr12	distance/detour ring index of order 12
+T(N..N)	sum of topological distances between N..N
+T(N..O)	sum of topological distances between N..O
+T(N..S)	sum of topological distances between N..S
+T(N..P)	sum of topological distances between N..P
+T(N..F)	sum of topological distances between N..F
+T(N..Cl)	sum of topological distances between N..Cl
+T(N..Br)	sum of topological distances between N..Br
+T(N..I)	sum of topological distances between N..I
+T(O..O)	sum of topological distances between O..O
+T(O..S)	sum of topological distances between O..S
+T(O..P)	sum of topological distances between O..P
+T(O..F)	sum of topological distances between O..F
+T(O..Cl)	sum of topological distances between O..Cl
+T(O..Br)	sum of topological distances between O..Br
+T(O..I)	sum of topological distances between O..I
+T(S..S)	sum of topological distances between S..S
+T(S..P)	sum of topological distances between S..P
+T(S..F)	sum of topological distances between S..F
+T(S..Cl)	sum of topological distances between S..Cl
+T(S..Br)	sum of topological distances between S..Br
+T(S..I)	sum of topological distances between S..I
+T(P..P)	sum of topological distances between P..P
+T(P..F)	sum of topological distances between P..F
+T(P..Cl)	sum of topological distances between P..Cl
+T(P..Br)	sum of topological distances between P..Br
+T(P..I)	sum of topological distances between P..I
+T(F..F)	sum of topological distances between F..F
+T(F..Cl)	sum of topological distances between F..Cl
+T(F..Br)	sum of topological distances between F..Br
+T(F..I)	sum of topological distances between F..I
+T(Cl..Cl)	sum of topological distances between Cl..Cl
+T(Cl..Br)	sum of topological distances between Cl..Br
+T(Cl..I)	sum of topological distances between Cl..I
+T(Br..Br)	sum of topological distances between Br..Br
+T(Br..I)	sum of topological distances between Br..I
+T(I..I)	sum of topological distances between I..I
+MWC01	molecular walk count of order 01 (number of non-H bonds, nBO)
+MWC02	molecular walk count of order 02
+MWC03	molecular walk count of order 03
+MWC04	molecular walk count of order 04
+MWC05	molecular walk count of order 05
+MWC06	molecular walk count of order 06
+MWC07	molecular walk count of order 07
+MWC08	molecular walk count of order 08
+MWC09	molecular walk count of order 09
+MWC10	molecular walk count of order 10
+TWC	total walk count
+SRW01	self-returning walk count of order 01 (number of non-H atoms, nSK)
+SRW02	self-returning walk count of order 02 (twice the number of non-H bonds)
+SRW03	self-returning walk count of order 03
+SRW04	self-returning walk count of order 04
+SRW05	self-returning walk count of order 05
+SRW06	self-returning walk count of order 06
+SRW07	self-returning walk count of order 07
+SRW08	self-returning walk count of order 08
+SRW09	self-returning walk count of order 09
+SRW10	self-returning walk count of order 10
+MPC01	molecular path count of order 01 (number of non-H bonds, nBO)
+MPC02	molecular path count of order 02 (Gordon-Scantlebury index)
+MPC03	molecular path count of order 03
+MPC04	molecular path count of order 04
+MPC05	molecular path count of order 05
+MPC06	molecular path count of order 06
+MPC07	molecular path count of order 07
+MPC08	molecular path count of order 08
+MPC09	molecular path count of order 09
+MPC10	molecular path count of order 10
+piPC01	molecular multiple path count of order 01 (sum of conventional bond orders, SCBO)
+piPC02	molecular multiple path count of order 02
+piPC03	molecular multiple path count of order 03
+piPC04	molecular multiple path count of order 04
+piPC05	molecular multiple path count of order 05
+piPC06	molecular multiple path count of order 06
+piPC07	molecular multiple path count of order 07
+piPC08	molecular multiple path count of order 08
+piPC09	molecular multiple path count of order 09
+piPC10	molecular multiple path count of order 10
+TPC	total path count
+piID	conventional bond-order ID number
+PCR	ratio of multiple path count over path count
+PCD	difference between multiple path count and path count
+CID	Randic ID number
+BID	Balaban ID number
+ISIZ	information index on molecular size
+IAC	total information index of atomic composition
+AAC	mean information index on atomic composition
+IDE	mean information content on the distance equality
+IDM	mean information content on the distance magnitude
+IDDE	mean information content on the distance degree equality
+IDDM	mean information content on the distance degree magnitude
+IDET	total information content on the distance equality
+IDMT	total information content on the distance magnitude
+IVDE	mean information content on the vertex degree equality
+IVDM	mean information content on the vertex degree magnitude
+HVcpx	graph vertex complexity index
+HDcpx	graph distance complexity index (log)
+Uindex	Balaban U index
+Vindex	Balaban V index
+Xindex	Balaban X index
+Yindex	Balaban Y index
+IC0	information content index (neighborhood symmetry of 0-order)
+TIC0	total information content index (neighborhood symmetry of 0-order)
+SIC0	structural information content (neighborhood symmetry of 0-order)
+CIC0	complementary information content (neighborhood symmetry of 0-order)
+BIC0	bond information content (neighborhood symmetry of 0-order)
+IC1	information content index (neighborhood symmetry of 1-order)
+TIC1	total information content index (neighborhood symmetry of 1-order)
+SIC1	structural information content (neighborhood symmetry of 1-order)
+CIC1	complementary information content (neighborhood symmetry of 1-order)
+BIC1	bond information content (neighborhood symmetry of 1-order)
+IC2	information content index (neighborhood symmetry of 2-order)
+TIC2	total information content index (neighborhood symmetry of 2-order)
+SIC2	structural information content (neighborhood symmetry of 2-order)
+CIC2	complementary information content (neighborhood symmetry of 2-order)
+BIC2	bond information content (neighborhood symmetry of 2-order)
+IC3	information content index (neighborhood symmetry of 3-order)
+TIC3	total information content index (neighborhood symmetry of 3-order)
+SIC3	structural information content (neighborhood symmetry of 3-order)
+CIC3	complementary information content (neighborhood symmetry of 3-order)
+BIC3	bond information content (neighborhood symmetry of 3-order)
+IC4	information content index (neighborhood symmetry of 4-order)
+TIC4	total information content index (neighborhood symmetry of 4-order)
+SIC4	structural information content (neighborhood symmetry of 4-order)
+CIC4	complementary information content (neighborhood symmetry of 4-order)
+BIC4	bond information content (neighborhood symmetry of 4-order)
+IC5	information content index (neighborhood symmetry of 5-order)
+TIC5	total information content index (neighborhood symmetry of 5-order)
+SIC5	structural information content (neighborhood symmetry of 5-order)
+CIC5	complementary information content (neighborhood symmetry of 5-order)
+BIC5	bond information content (neighborhood symmetry of 5-order)
+ATS1m	Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic masses
+ATS2m	Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic masses
+ATS3m	Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic masses
+ATS4m	Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic masses
+ATS5m	Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic masses
+ATS6m	Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic masses
+ATS7m	Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic masses
+ATS8m	Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic masses
+ATS1v	Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic van der Waals volumes
+ATS2v	Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic van der Waals volumes
+ATS3v	Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic van der Waals volumes
+ATS4v	Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic van der Waals volumes
+ATS5v	Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic van der Waals volumes
+ATS6v	Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic van der Waals volumes
+ATS7v	Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic van der Waals volumes
+ATS8v	Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic van der Waals volumes
+ATS1e	Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic Sanderson electronegativities
+ATS2e	Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic Sanderson electronegativities
+ATS3e	Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic Sanderson electronegativities
+ATS4e	Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic Sanderson electronegativities
+ATS5e	Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic Sanderson electronegativities
+ATS6e	Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic Sanderson electronegativities
+ATS7e	Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic Sanderson electronegativities
+ATS8e	Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic Sanderson electronegativities
+ATS1p	Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic polarizabilities
+ATS2p	Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic polarizabilities
+ATS3p	Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic polarizabilities
+ATS4p	Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic polarizabilities
+ATS5p	Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic polarizabilities
+ATS6p	Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic polarizabilities
+ATS7p	Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic polarizabilities
+ATS8p	Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic polarizabilities
+MATS1m	Moran autocorrelation - lag 1 / weighted by atomic masses
+MATS2m	Moran autocorrelation - lag 2 / weighted by atomic masses
+MATS3m	Moran autocorrelation - lag 3 / weighted by atomic masses
+MATS4m	Moran autocorrelation - lag 4 / weighted by atomic masses
+MATS5m	Moran autocorrelation - lag 5 / weighted by atomic masses
+MATS6m	Moran autocorrelation - lag 6 / weighted by atomic masses
+MATS7m	Moran autocorrelation - lag 7 / weighted by atomic masses
+MATS8m	Moran autocorrelation - lag 8 / weighted by atomic masses
+MATS1v	Moran autocorrelation - lag 1 / weighted by atomic van der Waals volumes
+MATS2v	Moran autocorrelation - lag 2 / weighted by atomic van der Waals volumes
+MATS3v	Moran autocorrelation - lag 3 / weighted by atomic van der Waals volumes
+MATS4v	Moran autocorrelation - lag 4 / weighted by atomic van der Waals volumes
+MATS5v	Moran autocorrelation - lag 5 / weighted by atomic van der Waals volumes
+MATS6v	Moran autocorrelation - lag 6 / weighted by atomic van der Waals volumes
+MATS7v	Moran autocorrelation - lag 7 / weighted by atomic van der Waals volumes
+MATS8v	Moran autocorrelation - lag 8 / weighted by atomic van der Waals volumes
+MATS1e	Moran autocorrelation - lag 1 / weighted by atomic Sanderson electronegativities
+MATS2e	Moran autocorrelation - lag 2 / weighted by atomic Sanderson electronegativities
+MATS3e	Moran autocorrelation - lag 3 / weighted by atomic Sanderson electronegativities
+MATS4e	Moran autocorrelation - lag 4 / weighted by atomic Sanderson electronegativities
+MATS5e	Moran autocorrelation - lag 5 / weighted by atomic Sanderson electronegativities
+MATS6e	Moran autocorrelation - lag 6 / weighted by atomic Sanderson electronegativities
+MATS7e	Moran autocorrelation - lag 7 / weighted by atomic Sanderson electronegativities
+MATS8e	Moran autocorrelation - lag 8 / weighted by atomic Sanderson electronegativities
+MATS1p	Moran autocorrelation - lag 1 / weighted by atomic polarizabilities
+MATS2p	Moran autocorrelation - lag 2 / weighted by atomic polarizabilities
+MATS3p	Moran autocorrelation - lag 3 / weighted by atomic polarizabilities
+MATS4p	Moran autocorrelation - lag 4 / weighted by atomic polarizabilities
+MATS5p	Moran autocorrelation - lag 5 / weighted by atomic polarizabilities
+MATS6p	Moran autocorrelation - lag 6 / weighted by atomic polarizabilities
+MATS7p	Moran autocorrelation - lag 7 / weighted by atomic polarizabilities
+MATS8p	Moran autocorrelation - lag 8 / weighted by atomic polarizabilities
+GATS1m	Geary autocorrelation - lag 1 / weighted by atomic masses
+GATS2m	Geary autocorrelation - lag 2 / weighted by atomic masses
+GATS3m	Geary autocorrelation - lag 3 / weighted by atomic masses
+GATS4m	Geary autocorrelation - lag 4 / weighted by atomic masses
+GATS5m	Geary autocorrelation - lag 5 / weighted by atomic masses
+GATS6m	Geary autocorrelation - lag 6 / weighted by atomic masses
+GATS7m	Geary autocorrelation - lag 7 / weighted by atomic masses
+GATS8m	Geary autocorrelation - lag 8 / weighted by atomic masses
+GATS1v	Geary autocorrelation - lag 1 / weighted by atomic van der Waals volumes
+GATS2v	Geary autocorrelation - lag 2 / weighted by atomic van der Waals volumes
+GATS3v	Geary autocorrelation - lag 3 / weighted by atomic van der Waals volumes
+GATS4v	Geary autocorrelation - lag 4 / weighted by atomic van der Waals volumes
+GATS5v	Geary autocorrelation - lag 5 / weighted by atomic van der Waals volumes
+GATS6v	Geary autocorrelation - lag 6 / weighted by atomic van der Waals volumes
+GATS7v	Geary autocorrelation - lag 7 / weighted by atomic van der Waals volumes
+GATS8v	Geary autocorrelation - lag 8 / weighted by atomic van der Waals volumes
+GATS1e	Geary autocorrelation - lag 1 / weighted by atomic Sanderson electronegativities
+GATS2e	Geary autocorrelation - lag 2 / weighted by atomic Sanderson electronegativities
+GATS3e	Geary autocorrelation - lag 3 / weighted by atomic Sanderson electronegativities
+GATS4e	Geary autocorrelation - lag 4 / weighted by atomic Sanderson electronegativities
+GATS5e	Geary autocorrelation - lag 5 / weighted by atomic Sanderson electronegativities
+GATS6e	Geary autocorrelation - lag 6 / weighted by atomic Sanderson electronegativities
+GATS7e	Geary autocorrelation - lag 7 / weighted by atomic Sanderson electronegativities
+GATS8e	Geary autocorrelation - lag 8 / weighted by atomic Sanderson electronegativities
+GATS1p	Geary autocorrelation - lag 1 / weighted by atomic polarizabilities
+GATS2p	Geary autocorrelation - lag 2 / weighted by atomic polarizabilities
+GATS3p	Geary autocorrelation - lag 3 / weighted by atomic polarizabilities
+GATS4p	Geary autocorrelation - lag 4 / weighted by atomic polarizabilities
+GATS5p	Geary autocorrelation - lag 5 / weighted by atomic polarizabilities
+GATS6p	Geary autocorrelation - lag 6 / weighted by atomic polarizabilities
+GATS7p	Geary autocorrelation - lag 7 / weighted by atomic polarizabilities
+GATS8p	Geary autocorrelation - lag 8 / weighted by atomic polarizabilities
+EPS0	edge connectivity index of order 0
+EPS1	edge connectivity index of order 1
+EEig01x	Eigenvalue 01from edge adj. matrix weighted by edge degrees
+EEig02x	Eigenvalue 02from edge adj. matrix weighted by edge degrees
+EEig03x	Eigenvalue 03from edge adj. matrix weighted by edge degrees
+EEig04x	Eigenvalue 04from edge adj. matrix weighted by edge degrees
+EEig05x	Eigenvalue 05from edge adj. matrix weighted by edge degrees
+EEig06x	Eigenvalue 06from edge adj. matrix weighted by edge degrees
+EEig07x	Eigenvalue 07from edge adj. matrix weighted by edge degrees
+EEig08x	Eigenvalue 08from edge adj. matrix weighted by edge degrees
+EEig09x	Eigenvalue 09from edge adj. matrix weighted by edge degrees
+EEig10x	Eigenvalue 10from edge adj. matrix weighted by edge degrees
+EEig11x	Eigenvalue 11from edge adj. matrix weighted by edge degrees
+EEig12x	Eigenvalue 12from edge adj. matrix weighted by edge degrees
+EEig13x	Eigenvalue 13from edge adj. matrix weighted by edge degrees
+EEig14x	Eigenvalue 14from edge adj. matrix weighted by edge degrees
+EEig15x	Eigenvalue 15from edge adj. matrix weighted by edge degrees
+EEig01d	Eigenvalue 01 from edge adj. matrix weighted by dipole moments
+EEig02d	Eigenvalue 02 from edge adj. matrix weighted by dipole moments
+EEig03d	Eigenvalue 03 from edge adj. matrix weighted by dipole moments
+EEig04d	Eigenvalue 04 from edge adj. matrix weighted by dipole moments
+EEig05d	Eigenvalue 05 from edge adj. matrix weighted by dipole moments
+EEig06d	Eigenvalue 06 from edge adj. matrix weighted by dipole moments
+EEig07d	Eigenvalue 07 from edge adj. matrix weighted by dipole moments
+EEig08d	Eigenvalue 08 from edge adj. matrix weighted by dipole moments
+EEig09d	Eigenvalue 09 from edge adj. matrix weighted by dipole moments
+EEig10d	Eigenvalue 10 from edge adj. matrix weighted by dipole moments
+EEig11d	Eigenvalue 11 from edge adj. matrix weighted by dipole moments
+EEig12d	Eigenvalue 12 from edge adj. matrix weighted by dipole moments
+EEig13d	Eigenvalue 13 from edge adj. matrix weighted by dipole moments
+EEig14d	Eigenvalue 14 from edge adj. matrix weighted by dipole moments
+EEig15d	Eigenvalue 15 from edge adj. matrix weighted by dipole moments
+EEig01r	Eigenvalue 01 from edge adj. matrix weighted by resonance integrals
+EEig02r	Eigenvalue 02 from edge adj. matrix weighted by resonance integrals
+EEig03r	Eigenvalue 03 from edge adj. matrix weighted by resonance integrals
+EEig04r	Eigenvalue 04 from edge adj. matrix weighted by resonance integrals
+EEig05r	Eigenvalue 05 from edge adj. matrix weighted by resonance integrals
+EEig06r	Eigenvalue 06 from edge adj. matrix weighted by resonance integrals
+EEig07r	Eigenvalue 07 from edge adj. matrix weighted by resonance integrals
+EEig08r	Eigenvalue 08 from edge adj. matrix weighted by resonance integrals
+EEig09r	Eigenvalue 09 from edge adj. matrix weighted by resonance integrals
+EEig10r	Eigenvalue 10 from edge adj. matrix weighted by resonance integrals
+EEig11r	Eigenvalue 11 from edge adj. matrix weighted by resonance integrals
+EEig12r	Eigenvalue 12 from edge adj. matrix weighted by resonance integrals
+EEig13r	Eigenvalue 13 from edge adj. matrix weighted by resonance integrals
+EEig14r	Eigenvalue 14 from edge adj. matrix weighted by resonance integrals
+EEig15r	Eigenvalue 15 from edge adj. matrix weighted by resonance integrals
+ESpm01u	Spectral moment 01 from edge adj. matrix
+ESpm02u	Spectral moment 02 from edge adj. matrix
+ESpm03u	Spectral moment 03 from edge adj. matrix
+ESpm04u	Spectral moment 04 from edge adj. matrix
+ESpm05u	Spectral moment 05 from edge adj. matrix
+ESpm06u	Spectral moment 06 from edge adj. matrix
+ESpm07u	Spectral moment 07 from edge adj. matrix
+ESpm08u	Spectral moment 08 from edge adj. matrix
+ESpm09u	Spectral moment 09 from edge adj. matrix
+ESpm10u	Spectral moment 10 from edge adj. matrix
+ESpm11u	Spectral moment 11 from edge adj. matrix
+ESpm12u	Spectral moment 12 from edge adj. matrix
+ESpm13u	Spectral moment 13 from edge adj. matrix
+ESpm14u	Spectral moment 14 from edge adj. matrix
+ESpm15u	Spectral moment 15 from edge adj. matrix
+ESpm01x	Spectral moment 01 from edge adj. matrix weighted by edge degrees
+ESpm02x	Spectral moment 02 from edge adj. matrix weighted by edge degrees
+ESpm03x	Spectral moment 03 from edge adj. matrix weighted by edge degrees
+ESpm04x	Spectral moment 04 from edge adj. matrix weighted by edge degrees
+ESpm05x	Spectral moment 05 from edge adj. matrix weighted by edge degrees
+ESpm06x	Spectral moment 06 from edge adj. matrix weighted by edge degrees
+ESpm07x	Spectral moment 07 from edge adj. matrix weighted by edge degrees
+ESpm08x	Spectral moment 08 from edge adj. matrix weighted by edge degrees
+ESpm09x	Spectral moment 09 from edge adj. matrix weighted by edge degrees
+ESpm10x	Spectral moment 10 from edge adj. matrix weighted by edge degrees
+ESpm11x	Spectral moment 11 from edge adj. matrix weighted by edge degrees
+ESpm12x	Spectral moment 12 from edge adj. matrix weighted by edge degrees
+ESpm13x	Spectral moment 13 from edge adj. matrix weighted by edge degrees
+ESpm14x	Spectral moment 14 from edge adj. matrix weighted by edge degrees
+ESpm15x	Spectral moment 15 from edge adj. matrix weighted by edge degrees
+ESpm01d	Spectral moment 01 from edge adj. matrix weighted by dipole moments
+ESpm02d	Spectral moment 02 from edge adj. matrix weighted by dipole moments
+ESpm03d	Spectral moment 03 from edge adj. matrix weighted by dipole moments
+ESpm04d	Spectral moment 04 from edge adj. matrix weighted by dipole moments
+ESpm05d	Spectral moment 05 from edge adj. matrix weighted by dipole moments
+ESpm06d	Spectral moment 06 from edge adj. matrix weighted by dipole moments
+ESpm07d	Spectral moment 07 from edge adj. matrix weighted by dipole moments
+ESpm08d	Spectral moment 08 from edge adj. matrix weighted by dipole moments
+ESpm09d	Spectral moment 09 from edge adj. matrix weighted by dipole moments
+ESpm10d	Spectral moment 10 from edge adj. matrix weighted by dipole moments
+ESpm11d	Spectral moment 11 from edge adj. matrix weighted by dipole moments
+ESpm12d	Spectral moment 12 from edge adj. matrix weighted by dipole moments
+ESpm13d	Spectral moment 13 from edge adj. matrix weighted by dipole moments
+ESpm14d	Spectral moment 14 from edge adj. matrix weighted by dipole moments
+ESpm15d	Spectral moment 15 from edge adj. matrix weighted by dipole moments
+ESpm01r	Spectral moment 01 from edge adj. matrix weighted by resonance integrals
+ESpm02r	Spectral moment 02 from edge adj. matrix weighted by resonance integrals
+ESpm03r	Spectral moment 03 from edge adj. matrix weighted by resonance integrals
+ESpm04r	Spectral moment 04 from edge adj. matrix weighted by resonance integrals
+ESpm05r	Spectral moment 05 from edge adj. matrix weighted by resonance integrals
+ESpm06r	Spectral moment 06 from edge adj. matrix weighted by resonance integrals
+ESpm07r	Spectral moment 07 from edge adj. matrix weighted by resonance integrals
+ESpm08r	Spectral moment 08 from edge adj. matrix weighted by resonance integrals
+ESpm09r	Spectral moment 09 from edge adj. matrix weighted by resonance integrals
+ESpm10r	Spectral moment 10 from edge adj. matrix weighted by resonance integrals
+ESpm11r	Spectral moment 11 from edge adj. matrix weighted by resonance integrals
+ESpm12r	Spectral moment 12 from edge adj. matrix weighted by resonance integrals
+ESpm13r	Spectral moment 13 from edge adj. matrix weighted by resonance integrals
+ESpm14r	Spectral moment 14 from edge adj. matrix weighted by resonance integrals
+ESpm15r	Spectral moment 15 from edge adj. matrix weighted by resonance integrals
+BEHm1	highest eigenvalue n. 1 of Burden matrix / weighted by atomic masses
+BEHm2	highest eigenvalue n. 2 of Burden matrix / weighted by atomic masses
+BEHm3	highest eigenvalue n. 3 of Burden matrix / weighted by atomic masses
+BEHm4	highest eigenvalue n. 4 of Burden matrix / weighted by atomic masses
+BEHm5	highest eigenvalue n. 5 of Burden matrix / weighted by atomic masses
+BEHm6	highest eigenvalue n. 6 of Burden matrix / weighted by atomic masses
+BEHm7	highest eigenvalue n. 7 of Burden matrix / weighted by atomic masses
+BEHm8	highest eigenvalue n. 8 of Burden matrix / weighted by atomic masses
+BELm1	lowest eigenvalue n. 1 of Burden matrix / weighted by atomic masses
+BELm2	lowest eigenvalue n. 2 of Burden matrix / weighted by atomic masses
+BELm3	lowest eigenvalue n. 3 of Burden matrix / weighted by atomic masses
+BELm4	lowest eigenvalue n. 4 of Burden matrix / weighted by atomic masses
+BELm5	lowest eigenvalue n. 5 of Burden matrix / weighted by atomic masses
+BELm6	lowest eigenvalue n. 6 of Burden matrix / weighted by atomic masses
+BELm7	lowest eigenvalue n. 7 of Burden matrix / weighted by atomic masses
+BELm8	lowest eigenvalue n. 8 of Burden matrix / weighted by atomic masses
+BEHv1	highest eigenvalue n. 1 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv2	highest eigenvalue n. 2 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv3	highest eigenvalue n. 3 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv4	highest eigenvalue n. 4 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv5	highest eigenvalue n. 5 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv6	highest eigenvalue n. 6 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv7	highest eigenvalue n. 7 of Burden matrix / weighted by atomic van der Waals volumes
+BEHv8	highest eigenvalue n. 8 of Burden matrix / weighted by atomic van der Waals volumes
+BELv1	lowest eigenvalue n. 1 of Burden matrix / weighted by atomic van der Waals volumes
+BELv2	lowest eigenvalue n. 2 of Burden matrix / weighted by atomic van der Waals volumes
+BELv3	lowest eigenvalue n. 3 of Burden matrix / weighted by atomic van der Waals volumes
+BELv4	lowest eigenvalue n. 4 of Burden matrix / weighted by atomic van der Waals volumes
+BELv5	lowest eigenvalue n. 5 of Burden matrix / weighted by atomic van der Waals volumes
+BELv6	lowest eigenvalue n. 6 of Burden matrix / weighted by atomic van der Waals volumes
+BELv7	lowest eigenvalue n. 7 of Burden matrix / weighted by atomic van der Waals volumes
+BELv8	lowest eigenvalue n. 8 of Burden matrix / weighted by atomic van der Waals volumes
+BEHe1	highest eigenvalue n. 1 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe2	highest eigenvalue n. 2 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe3	highest eigenvalue n. 3 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe4	highest eigenvalue n. 4 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe5	highest eigenvalue n. 5 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe6	highest eigenvalue n. 6 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe7	highest eigenvalue n. 7 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHe8	highest eigenvalue n. 8 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe1	lowest eigenvalue n. 1 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe2	lowest eigenvalue n. 2 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe3	lowest eigenvalue n. 3 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe4	lowest eigenvalue n. 4 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe5	lowest eigenvalue n. 5 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe6	lowest eigenvalue n. 6 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe7	lowest eigenvalue n. 7 of Burden matrix / weighted by atomic Sanderson electronegativities
+BELe8	lowest eigenvalue n. 8 of Burden matrix / weighted by atomic Sanderson electronegativities
+BEHp1	highest eigenvalue n. 1 of Burden matrix / weighted by atomic polarizabilities
+BEHp2	highest eigenvalue n. 2 of Burden matrix / weighted by atomic polarizabilities
+BEHp3	highest eigenvalue n. 3 of Burden matrix / weighted by atomic polarizabilities
+BEHp4	highest eigenvalue n. 4 of Burden matrix / weighted by atomic polarizabilities
+BEHp5	highest eigenvalue n. 5 of Burden matrix / weighted by atomic polarizabilities
+BEHp6	highest eigenvalue n. 6 of Burden matrix / weighted by atomic polarizabilities
+BEHp7	highest eigenvalue n. 7 of Burden matrix / weighted by atomic polarizabilities
+BEHp8	highest eigenvalue n. 8 of Burden matrix / weighted by atomic polarizabilities
+BELp1	lowest eigenvalue n. 1 of Burden matrix / weighted by atomic polarizabilities
+BELp2	lowest eigenvalue n. 2 of Burden matrix / weighted by atomic polarizabilities
+BELp3	lowest eigenvalue n. 3 of Burden matrix / weighted by atomic polarizabilities
+BELp4	lowest eigenvalue n. 4 of Burden matrix / weighted by atomic polarizabilities
+BELp5	lowest eigenvalue n. 5 of Burden matrix / weighted by atomic polarizabilities
+BELp6	lowest eigenvalue n. 6 of Burden matrix / weighted by atomic polarizabilities
+BELp7	lowest eigenvalue n. 7 of Burden matrix / weighted by atomic polarizabilities
+BELp8	lowest eigenvalue n. 8 of Burden matrix / weighted by atomic polarizabilities
+GGI1	topological charge index of order 1
+GGI2	topological charge index of order 2
+GGI3	topological charge index of order 3
+GGI4	topological charge index of order 4
+GGI5	topological charge index of order 5
+GGI6	topological charge index of order 6
+GGI7	topological charge index of order 7
+GGI8	topological charge index of order 8
+GGI9	topological charge index of order 9
+GGI10	topological charge index of order 10
+JGI1	mean topological charge index of order1
+JGI2	mean topological charge index of order2
+JGI3	mean topological charge index of order3
+JGI4	mean topological charge index of order4
+JGI5	mean topological charge index of order5
+JGI6	mean topological charge index of order6
+JGI7	mean topological charge index of order7
+JGI8	mean topological charge index of order8
+JGI9	mean topological charge index of order9
+JGI10	mean topological charge index of order10
+JGT	global topological charge index
+LP1	Lovasz-Pelikan index (leading eigenvalue)
+Eig1Z	Leading eigenvalue from Z weighted distance matrix (Barysz matrix)
+Eig1m	Leading eigenvalue from mass weighted distance matrix
+Eig1v	Leading eigenvalue from van der Waals weighted distance matrix
+Eig1e	Leading eigenvalue from electronegativity weighted distance matrix
+Eig1p	Leading eigenvalue from polarizability weighted distance matrix
+SEigZ	Eigenvalue sum from Z weighted distance matrix (Barysz matrix)
+SEigm	Eigenvalue sum from mass weighted distance matrix
+SEigv	Eigenvalue sum from van der Waals weighted distance matrix
+SEige	Eigenvalue sum from electronegativity weighted distance matrix
+SEigp	Eigenvalue sum from polarizability weighted distance matrix
+AEigZ	Absolute eigenvalue sum from Z weighted distance matrix (Barysz matrix)
+AEigm	Absolute eigenvalue sum from mass weighted distance matrix
+AEigv	Absolute eigenvalue sum from van der Waals weighted distance matrix
+AEige	Absolute eigenvalue sum from electronegativity weighted distance matrix
+AEigp	Absolute eigenvalue sum from polarizability weighted distance matrix
+VEA1	eigenvector coefficient sum from adjacency matrix
+VEA2	average eigenvector coefficient sum from adjacency matrix
+VRA1	Randic-type eigenvector-based index from adjacency matrix
+VRA2	average Randic-type eigenvector-based index from adjacency matrix
+VED1	eigenvector coefficient sum from distance matrix
+VED2	average eigenvector coefficient sum from distance matrix
+VRD1	Randic-type eigenvector-based index from distance matrix
+VRD2	average Randic-type eigenvector-based index from distance matrix
+VEZ1	eigenvector coefficient sum from Z weighted distance matrix (Barysz matrix)
+VEZ2	average eigenvector coefficient sum from Z weighted distance matrix (Barysz matrix)
+VRZ1	Randic-type eigenvector-based index from Z weighted distance matrix (Barysz matrix)
+VRZ2	average Randic-type eigenvector-based index from Z weighted distance matrix (Barysz matrix)
+VEm1	eigenvector coefficient sum from mass weighted distance matrix
+VEm2	average eigenvector coefficient sum from mass weighted distance matrix
+VRm1	Randic-type eigenvector-based index from mass weighted distance matrix
+VRm2	average Randic-type eigenvector-based index from mass weighted distance matrix
+VEv1	eigenvector coefficient sum from van der Waals weighted distance matrix
+VEv2	average eigenvector coefficient sum from van der Waals weighted distance matrix
+VRv1	Randic-type eigenvector-based index from van der Waals weighted distance matrix
+VRv2	average Randic-type eigenvector-based index from van der Waals weighted distance matrix
+VEe1	eigenvector coefficient sum from electronegativity weighted distance matrix
+VEe2	average eigenvector coefficient sum from electronegativity weighted distance matrix
+VRe1	Randic-type eigenvector-based index from electronegativity weighted distance matrix
+VRe2	average Randic-type eigenvector-based index from electronegativity weighted distance matrix
+VEp1	eigenvector coefficient sum from polarizability weighted distance matrix
+VEp2	average eigenvector coefficient sum from polarizability weighted distance matrix
+VRp1	Randic-type eigenvector-based index from polarizability weighted distance matrix
+VRp2	average Randic-type eigenvector-based index from polarizability weighted distance matrix
+DP01	molecular profile no. 01
+DP02	molecular profile no. 02
+DP03	molecular profile no. 03
+DP04	molecular profile no. 04
+DP05	molecular profile no. 05
+DP06	molecular profile no. 06
+DP07	molecular profile no. 07
+DP08	molecular profile no. 08
+DP09	molecular profile no. 09
+DP10	molecular profile no. 10
+DP11	molecular profile no. 11
+DP12	molecular profile no. 12
+DP13	molecular profile no. 13
+DP14	molecular profile no. 14
+DP15	molecular profile no. 15
+DP16	molecular profile no. 16
+DP17	molecular profile no. 17
+DP18	molecular profile no. 18
+DP19	molecular profile no. 19
+DP20	molecular profile no. 20
+SP01	shape profile no. 01
+SP02	shape profile no. 02
+SP03	shape profile no. 03
+SP04	shape profile no. 04
+SP05	shape profile no. 05
+SP06	shape profile no. 06
+SP07	shape profile no. 07
+SP08	shape profile no. 08
+SP09	shape profile no. 09
+SP10	shape profile no. 10
+SP11	shape profile no. 11
+SP12	shape profile no. 12
+SP13	shape profile no. 13
+SP14	shape profile no. 14
+SP15	shape profile no. 15
+SP16	shape profile no. 16
+SP17	shape profile no. 17
+SP18	shape profile no. 18
+SP19	shape profile no. 19
+SP20	shape profile no. 20
+SHP2	average shape profile index of order 2
+W3D	3D-Wiener index
+J3D	3D-Balaban index
+H3D	3D-Harary index
+AGDD	average geometric distance degree
+DDI	D/D index
+ADDD	average distance/distance degree
+G1	gravitational index G1
+G2	gravitational index G2 (bond-restricted)
+RGyr	radius of gyration (mass weighted)
+SPAN	span R
+SPAM	average span R
+MEcc	molecular eccentricity
+SPH	spherosity
+ASP	asphericity
+FDI	folding degree index
+PJI3	3D Petijean shape index
+L/Bw	length-to-breadth ratio by WHIM
+SEig	absolute eigenvalue sum on geometry matrix
+HOMA	Harmonic Oscillator Model of Aromaticity index
+RCI	Jug RC index
+AROM	aromaticity (trial)
+HOMT	HOMA total (trial)
+DISPm	d COMMA2 value / weighted by atomic masses
+QXXm	Qxx COMMA2 value / weighted by atomic masses
+QYYm	Qyy COMMA2 value / weighted by atomic masses
+QZZm	Qzz COMMA2 value / weighted by atomic masses
+DISPv	d COMMA2 value / weighted by atomic van der Waals volumes
+QXXv	Qxx COMMA2 value / weighted by atomic van der Waals volumes
+QYYv	Qyy COMMA2 value / weighted by atomic van der Waals volumes
+QZZv	Qzz COMMA2 value / weighted by atomic van der Waals volumes
+DISPe	d COMMA2 value / weighted by atomic Sanderson electronegativities
+QXXe	Qxx COMMA2 value / weighted by atomic Sanderson electronegativities
+QYYe	Qyy COMMA2 value / weighted by atomic Sanderson electronegativities
+QZZe	Qzz COMMA2 value / weighted by atomic Sanderson electronegativities
+DISPp	d COMMA2 value / weighted by atomic polarizabilities
+QXXp	Qxx COMMA2 value / weighted by atomic polarizabilities
+QYYp	Qyy COMMA2 value / weighted by atomic polarizabilities
+QZZp	Qzz COMMA2 value / weighted by atomic polarizabilities
+G(N..N)	sum of geometrical distances between N..N
+G(N..O)	sum of geometrical distances between N..O
+G(N..S)	sum of geometrical distances between N..S
+G(N..P)	sum of geometrical distances between N..P
+G(N..F)	sum of geometrical distances between N..F
+G(N..Cl)	sum of geometrical distances between N..Cl
+G(N..Br)	sum of geometrical distances between N..Br
+G(N..I)	sum of geometrical distances between N..I
+G(O..O)	sum of geometrical distances between O..O
+G(O..S)	sum of geometrical distances between O..S
+G(O..P)	sum of geometrical distances between O..P
+G(O..F)	sum of geometrical distances between O..F
+G(O..Cl)	sum of geometrical distances between O..Cl
+G(O..Br)	sum of geometrical distances between O..Br
+G(O..I)	sum of geometrical distances between O..I
+G(S..S)	sum of geometrical distances between S..S
+G(S..P)	sum of geometrical distances between S..P
+G(S..F)	sum of geometrical distances between S..F
+G(S..Cl)	sum of geometrical distances between S..Cl
+G(S..Br)	sum of geometrical distances between S..Br
+G(S..I)	sum of geometrical distances between S..I
+G(P..P)	sum of geometrical distances between P..P
+G(P..F)	sum of geometrical distances between P..F
+G(P..Cl)	sum of geometrical distances between P..Cl
+G(P..Br)	sum of geometrical distances between P..Br
+G(P..I)	sum of geometrical distances between P..I
+G(F..F)	sum of geometrical distances between F..F
+G(F..Cl)	sum of geometrical distances between F..Cl
+G(F..Br)	sum of geometrical distances between F..Br
+G(F..I)	sum of geometrical distances between F..I
+G(Cl..Cl)	sum of geometrical distances between Cl..Cl
+G(Cl..Br)	sum of geometrical distances between Cl..Br
+G(Cl..I)	sum of geometrical distances between Cl..I
+G(Br..Br)	sum of geometrical distances between Br..Br
+G(Br..I)	sum of geometrical distances between Br..I
+G(I..I)	sum of geometrical distances between I..I
+RDF010u	Radial Distribution Function - 1.0 / unweighted
+RDF015u	Radial Distribution Function - 1.5 / unweighted
+RDF020u	Radial Distribution Function - 2.0 / unweighted
+RDF025u	Radial Distribution Function - 2.5 / unweighted
+RDF030u	Radial Distribution Function - 3.0 / unweighted
+RDF035u	Radial Distribution Function - 3.5 / unweighted
+RDF040u	Radial Distribution Function - 4.0 / unweighted
+RDF045u	Radial Distribution Function - 4.5 / unweighted
+RDF050u	Radial Distribution Function - 5.0 / unweighted
+RDF055u	Radial Distribution Function - 5.5 / unweighted
+RDF060u	Radial Distribution Function - 6.0 / unweighted
+RDF065u	Radial Distribution Function - 6.5 / unweighted
+RDF070u	Radial Distribution Function - 7.0 / unweighted
+RDF075u	Radial Distribution Function - 7.5 / unweighted
+RDF080u	Radial Distribution Function - 8.0 / unweighted
+RDF085u	Radial Distribution Function - 8.5 / unweighted
+RDF090u	Radial Distribution Function - 9.0 / unweighted
+RDF095u	Radial Distribution Function - 9.5 / unweighted
+RDF100u	Radial Distribution Function - 10.0 / unweighted
+RDF105u	Radial Distribution Function - 10.5 / unweighted
+RDF110u	Radial Distribution Function - 11.0 / unweighted
+RDF115u	Radial Distribution Function - 11.5 / unweighted
+RDF120u	Radial Distribution Function - 12.0 / unweighted
+RDF125u	Radial Distribution Function - 12.5 / unweighted
+RDF130u	Radial Distribution Function - 13.0 / unweighted
+RDF135u	Radial Distribution Function - 13.5 / unweighted
+RDF140u	Radial Distribution Function - 14.0 / unweighted
+RDF145u	Radial Distribution Function - 14.5 / unweighted
+RDF150u	Radial Distribution Function - 15.0 / unweighted
+RDF155u	Radial Distribution Function - 15.5 / unweighted
+RDF010m	Radial Distribution Function - 1.0 / weighted by atomic masses
+RDF015m	Radial Distribution Function - 1.5 / weighted by atomic masses
+RDF020m	Radial Distribution Function - 2.0 / weighted by atomic masses
+RDF025m	Radial Distribution Function - 2.5 / weighted by atomic masses
+RDF030m	Radial Distribution Function - 3.0 / weighted by atomic masses
+RDF035m	Radial Distribution Function - 3.5 / weighted by atomic masses
+RDF040m	Radial Distribution Function - 4.0 / weighted by atomic masses
+RDF045m	Radial Distribution Function - 4.5 / weighted by atomic masses
+RDF050m	Radial Distribution Function - 5.0 / weighted by atomic masses
+RDF055m	Radial Distribution Function - 5.5 / weighted by atomic masses
+RDF060m	Radial Distribution Function - 6.0 / weighted by atomic masses
+RDF065m	Radial Distribution Function - 6.5 / weighted by atomic masses
+RDF070m	Radial Distribution Function - 7.0 / weighted by atomic masses
+RDF075m	Radial Distribution Function - 7.5 / weighted by atomic masses
+RDF080m	Radial Distribution Function - 8.0 / weighted by atomic masses
+RDF085m	Radial Distribution Function - 8.5 / weighted by atomic masses
+RDF090m	Radial Distribution Function - 9.0 / weighted by atomic masses
+RDF095m	Radial Distribution Function - 9.5 / weighted by atomic masses
+RDF100m	Radial Distribution Function - 10.0 / weighted by atomic masses
+RDF105m	Radial Distribution Function - 10.5 / weighted by atomic masses
+RDF110m	Radial Distribution Function - 11.0 / weighted by atomic masses
+RDF115m	Radial Distribution Function - 11.5 / weighted by atomic masses
+RDF120m	Radial Distribution Function - 12.0 / weighted by atomic masses
+RDF125m	Radial Distribution Function - 12.5 / weighted by atomic masses
+RDF130m	Radial Distribution Function - 13.0 / weighted by atomic masses
+RDF135m	Radial Distribution Function - 13.5 / weighted by atomic masses
+RDF140m	Radial Distribution Function - 14.0 / weighted by atomic masses
+RDF145m	Radial Distribution Function - 14.5 / weighted by atomic masses
+RDF150m	Radial Distribution Function - 15.0 / weighted by atomic masses
+RDF155m	Radial Distribution Function - 15.5 / weighted by atomic masses
+RDF010v	Radial Distribution Function - 1.0 / weighted by atomic van der Waals volumes
+RDF015v	Radial Distribution Function - 1.5 / weighted by atomic van der Waals volumes
+RDF020v	Radial Distribution Function - 2.0 / weighted by atomic van der Waals volumes
+RDF025v	Radial Distribution Function - 2.5 / weighted by atomic van der Waals volumes
+RDF030v	Radial Distribution Function - 3.0 / weighted by atomic van der Waals volumes
+RDF035v	Radial Distribution Function - 3.5 / weighted by atomic van der Waals volumes
+RDF040v	Radial Distribution Function - 4.0 / weighted by atomic van der Waals volumes
+RDF045v	Radial Distribution Function - 4.5 / weighted by atomic van der Waals volumes
+RDF050v	Radial Distribution Function - 5.0 / weighted by atomic van der Waals volumes
+RDF055v	Radial Distribution Function - 5.5 / weighted by atomic van der Waals volumes
+RDF060v	Radial Distribution Function - 6.0 / weighted by atomic van der Waals volumes
+RDF065v	Radial Distribution Function - 6.5 / weighted by atomic van der Waals volumes
+RDF070v	Radial Distribution Function - 7.0 / weighted by atomic van der Waals volumes
+RDF075v	Radial Distribution Function - 7.5 / weighted by atomic van der Waals volumes
+RDF080v	Radial Distribution Function - 8.0 / weighted by atomic van der Waals volumes
+RDF085v	Radial Distribution Function - 8.5 / weighted by atomic van der Waals volumes
+RDF090v	Radial Distribution Function - 9.0 / weighted by atomic van der Waals volumes
+RDF095v	Radial Distribution Function - 9.5 / weighted by atomic van der Waals volumes
+RDF100v	Radial Distribution Function - 10.0 / weighted by atomic van der Waals volumes
+RDF105v	Radial Distribution Function - 10.5 / weighted by atomic van der Waals volumes
+RDF110v	Radial Distribution Function - 11.0 / weighted by atomic van der Waals volumes
+RDF115v	Radial Distribution Function - 11.5 / weighted by atomic van der Waals volumes
+RDF120v	Radial Distribution Function - 12.0 / weighted by atomic van der Waals volumes
+RDF125v	Radial Distribution Function - 12.5 / weighted by atomic van der Waals volumes
+RDF130v	Radial Distribution Function - 13.0 / weighted by atomic van der Waals volumes
+RDF135v	Radial Distribution Function - 13.5 / weighted by atomic van der Waals volumes
+RDF140v	Radial Distribution Function - 14.0 / weighted by atomic van der Waals volumes
+RDF145v	Radial Distribution Function - 14.5 / weighted by atomic van der Waals volumes
+RDF150v	Radial Distribution Function - 15.0 / weighted by atomic van der Waals volumes
+RDF155v	Radial Distribution Function - 15.5 / weighted by atomic van der Waals volumes
+RDF010e	Radial Distribution Function - 1.0 / weighted by atomic Sanderson electronegativities
+RDF015e	Radial Distribution Function - 1.5 / weighted by atomic Sanderson electronegativities
+RDF020e	Radial Distribution Function - 2.0 / weighted by atomic Sanderson electronegativities
+RDF025e	Radial Distribution Function - 2.5 / weighted by atomic Sanderson electronegativities
+RDF030e	Radial Distribution Function - 3.0 / weighted by atomic Sanderson electronegativities
+RDF035e	Radial Distribution Function - 3.5 / weighted by atomic Sanderson electronegativities
+RDF040e	Radial Distribution Function - 4.0 / weighted by atomic Sanderson electronegativities
+RDF045e	Radial Distribution Function - 4.5 / weighted by atomic Sanderson electronegativities
+RDF050e	Radial Distribution Function - 5.0 / weighted by atomic Sanderson electronegativities
+RDF055e	Radial Distribution Function - 5.5 / weighted by atomic Sanderson electronegativities
+RDF060e	Radial Distribution Function - 6.0 / weighted by atomic Sanderson electronegativities
+RDF065e	Radial Distribution Function - 6.5 / weighted by atomic Sanderson electronegativities
+RDF070e	Radial Distribution Function - 7.0 / weighted by atomic Sanderson electronegativities
+RDF075e	Radial Distribution Function - 7.5 / weighted by atomic Sanderson electronegativities
+RDF080e	Radial Distribution Function - 8.0 / weighted by atomic Sanderson electronegativities
+RDF085e	Radial Distribution Function - 8.5 / weighted by atomic Sanderson electronegativities
+RDF090e	Radial Distribution Function - 9.0 / weighted by atomic Sanderson electronegativities
+RDF095e	Radial Distribution Function - 9.5 / weighted by atomic Sanderson electronegativities
+RDF100e	Radial Distribution Function - 10.0 / weighted by atomic Sanderson electronegativities
+RDF105e	Radial Distribution Function - 10.5 / weighted by atomic Sanderson electronegativities
+RDF110e	Radial Distribution Function - 11.0 / weighted by atomic Sanderson electronegativities
+RDF115e	Radial Distribution Function - 11.5 / weighted by atomic Sanderson electronegativities
+RDF120e	Radial Distribution Function - 12.0 / weighted by atomic Sanderson electronegativities
+RDF125e	Radial Distribution Function - 12.5 / weighted by atomic Sanderson electronegativities
+RDF130e	Radial Distribution Function - 13.0 / weighted by atomic Sanderson electronegativities
+RDF135e	Radial Distribution Function - 13.5 / weighted by atomic Sanderson electronegativities
+RDF140e	Radial Distribution Function - 14.0 / weighted by atomic Sanderson electronegativities
+RDF145e	Radial Distribution Function - 14.5 / weighted by atomic Sanderson electronegativities
+RDF150e	Radial Distribution Function - 15.0 / weighted by atomic Sanderson electronegativities
+RDF155e	Radial Distribution Function - 15.5 / weighted by atomic Sanderson electronegativities
+RDF010p	Radial Distribution Function - 1.0 / weighted by atomic polarizabilities
+RDF015p	Radial Distribution Function - 1.5 / weighted by atomic polarizabilities
+RDF020p	Radial Distribution Function - 2.0 / weighted by atomic polarizabilities
+RDF025p	Radial Distribution Function - 2.5 / weighted by atomic polarizabilities
+RDF030p	Radial Distribution Function - 3.0 / weighted by atomic polarizabilities
+RDF035p	Radial Distribution Function - 3.5 / weighted by atomic polarizabilities
+RDF040p	Radial Distribution Function - 4.0 / weighted by atomic polarizabilities
+RDF045p	Radial Distribution Function - 4.5 / weighted by atomic polarizabilities
+RDF050p	Radial Distribution Function - 5.0 / weighted by atomic polarizabilities
+RDF055p	Radial Distribution Function - 5.5 / weighted by atomic polarizabilities
+RDF060p	Radial Distribution Function - 6.0 / weighted by atomic polarizabilities
+RDF065p	Radial Distribution Function - 6.5 / weighted by atomic polarizabilities
+RDF070p	Radial Distribution Function - 7.0 / weighted by atomic polarizabilities
+RDF075p	Radial Distribution Function - 7.5 / weighted by atomic polarizabilities
+RDF080p	Radial Distribution Function - 8.0 / weighted by atomic polarizabilities
+RDF085p	Radial Distribution Function - 8.5 / weighted by atomic polarizabilities
+RDF090p	Radial Distribution Function - 9.0 / weighted by atomic polarizabilities
+RDF095p	Radial Distribution Function - 9.5 / weighted by atomic polarizabilities
+RDF100p	Radial Distribution Function - 10.0 / weighted by atomic polarizabilities
+RDF105p	Radial Distribution Function - 10.5 / weighted by atomic polarizabilities
+RDF110p	Radial Distribution Function - 11.0 / weighted by atomic polarizabilities
+RDF115p	Radial Distribution Function - 11.5 / weighted by atomic polarizabilities
+RDF120p	Radial Distribution Function - 12.0 / weighted by atomic polarizabilities
+RDF125p	Radial Distribution Function - 12.5 / weighted by atomic polarizabilities
+RDF130p	Radial Distribution Function - 13.0 / weighted by atomic polarizabilities
+RDF135p	Radial Distribution Function - 13.5 / weighted by atomic polarizabilities
+RDF140p	Radial Distribution Function - 14.0 / weighted by atomic polarizabilities
+RDF145p	Radial Distribution Function - 14.5 / weighted by atomic polarizabilities
+RDF150p	Radial Distribution Function - 15.0 / weighted by atomic polarizabilities
+RDF155p	Radial Distribution Function - 15.5 / weighted by atomic polarizabilities
+Mor01u	3D-MoRSE - signal 01 / unweighted
+Mor02u	3D-MoRSE - signal 02 / unweighted
+Mor03u	3D-MoRSE - signal 03 / unweighted
+Mor04u	3D-MoRSE - signal 04 / unweighted
+Mor05u	3D-MoRSE - signal 05 / unweighted
+Mor06u	3D-MoRSE - signal 06 / unweighted
+Mor07u	3D-MoRSE - signal 07 / unweighted
+Mor08u	3D-MoRSE - signal 08 / unweighted
+Mor09u	3D-MoRSE - signal 09 / unweighted
+Mor10u	3D-MoRSE - signal 10 / unweighted
+Mor11u	3D-MoRSE - signal 11 / unweighted
+Mor12u	3D-MoRSE - signal 12 / unweighted
+Mor13u	3D-MoRSE - signal 13 / unweighted
+Mor14u	3D-MoRSE - signal 14 / unweighted
+Mor15u	3D-MoRSE - signal 15 / unweighted
+Mor16u	3D-MoRSE - signal 16 / unweighted
+Mor17u	3D-MoRSE - signal 17 / unweighted
+Mor18u	3D-MoRSE - signal 18 / unweighted
+Mor19u	3D-MoRSE - signal 19 / unweighted
+Mor20u	3D-MoRSE - signal 20 / unweighted
+Mor21u	3D-MoRSE - signal 21 / unweighted
+Mor22u	3D-MoRSE - signal 22 / unweighted
+Mor23u	3D-MoRSE - signal 23 / unweighted
+Mor24u	3D-MoRSE - signal 24 / unweighted
+Mor25u	3D-MoRSE - signal 25 / unweighted
+Mor26u	3D-MoRSE - signal 26 / unweighted
+Mor27u	3D-MoRSE - signal 27 / unweighted
+Mor28u	3D-MoRSE - signal 28 / unweighted
+Mor29u	3D-MoRSE - signal 29 / unweighted
+Mor30u	3D-MoRSE - signal 30 / unweighted
+Mor31u	3D-MoRSE - signal 31 / unweighted
+Mor32u	3D-MoRSE - signal 32 / unweighted
+Mor01m	3D-MoRSE - signal 01 / weighted by atomic masses
+Mor02m	3D-MoRSE - signal 02 / weighted by atomic masses
+Mor03m	3D-MoRSE - signal 03 / weighted by atomic masses
+Mor04m	3D-MoRSE - signal 04 / weighted by atomic masses
+Mor05m	3D-MoRSE - signal 05 / weighted by atomic masses
+Mor06m	3D-MoRSE - signal 06 / weighted by atomic masses
+Mor07m	3D-MoRSE - signal 07 / weighted by atomic masses
+Mor08m	3D-MoRSE - signal 08 / weighted by atomic masses
+Mor09m	3D-MoRSE - signal 09 / weighted by atomic masses
+Mor10m	3D-MoRSE - signal 10 / weighted by atomic masses
+Mor11m	3D-MoRSE - signal 11 / weighted by atomic masses
+Mor12m	3D-MoRSE - signal 12 / weighted by atomic masses
+Mor13m	3D-MoRSE - signal 13 / weighted by atomic masses
+Mor14m	3D-MoRSE - signal 14 / weighted by atomic masses
+Mor15m	3D-MoRSE - signal 15 / weighted by atomic masses
+Mor16m	3D-MoRSE - signal 16 / weighted by atomic masses
+Mor17m	3D-MoRSE - signal 17 / weighted by atomic masses
+Mor18m	3D-MoRSE - signal 18 / weighted by atomic masses
+Mor19m	3D-MoRSE - signal 19 / weighted by atomic masses
+Mor20m	3D-MoRSE - signal 20 / weighted by atomic masses
+Mor21m	3D-MoRSE - signal 21 / weighted by atomic masses
+Mor22m	3D-MoRSE - signal 22 / weighted by atomic masses
+Mor23m	3D-MoRSE - signal 23 / weighted by atomic masses
+Mor24m	3D-MoRSE - signal 24 / weighted by atomic masses
+Mor25m	3D-MoRSE - signal 25 / weighted by atomic masses
+Mor26m	3D-MoRSE - signal 26 / weighted by atomic masses
+Mor27m	3D-MoRSE - signal 27 / weighted by atomic masses
+Mor28m	3D-MoRSE - signal 28 / weighted by atomic masses
+Mor29m	3D-MoRSE - signal 29 / weighted by atomic masses
+Mor30m	3D-MoRSE - signal 30 / weighted by atomic masses
+Mor31m	3D-MoRSE - signal 31 / weighted by atomic masses
+Mor32m	3D-MoRSE - signal 32 / weighted by atomic masses
+Mor01v	3D-MoRSE - signal 01 / weighted by atomic van der Waals volumes
+Mor02v	3D-MoRSE - signal 02 / weighted by atomic van der Waals volumes
+Mor03v	3D-MoRSE - signal 03 / weighted by atomic van der Waals volumes
+Mor04v	3D-MoRSE - signal 04 / weighted by atomic van der Waals volumes
+Mor05v	3D-MoRSE - signal 05 / weighted by atomic van der Waals volumes
+Mor06v	3D-MoRSE - signal 06 / weighted by atomic van der Waals volumes
+Mor07v	3D-MoRSE - signal 07 / weighted by atomic van der Waals volumes
+Mor08v	3D-MoRSE - signal 08 / weighted by atomic van der Waals volumes
+Mor09v	3D-MoRSE - signal 09 / weighted by atomic van der Waals volumes
+Mor10v	3D-MoRSE - signal 10 / weighted by atomic van der Waals volumes
+Mor11v	3D-MoRSE - signal 11 / weighted by atomic van der Waals volumes
+Mor12v	3D-MoRSE - signal 12 / weighted by atomic van der Waals volumes
+Mor13v	3D-MoRSE - signal 13 / weighted by atomic van der Waals volumes
+Mor14v	3D-MoRSE - signal 14 / weighted by atomic van der Waals volumes
+Mor15v	3D-MoRSE - signal 15 / weighted by atomic van der Waals volumes
+Mor16v	3D-MoRSE - signal 16 / weighted by atomic van der Waals volumes
+Mor17v	3D-MoRSE - signal 17 / weighted by atomic van der Waals volumes
+Mor18v	3D-MoRSE - signal 18 / weighted by atomic van der Waals volumes
+Mor19v	3D-MoRSE - signal 19 / weighted by atomic van der Waals volumes
+Mor20v	3D-MoRSE - signal 20 / weighted by atomic van der Waals volumes
+Mor21v	3D-MoRSE - signal 21 / weighted by atomic van der Waals volumes
+Mor22v	3D-MoRSE - signal 22 / weighted by atomic van der Waals volumes
+Mor23v	3D-MoRSE - signal 23 / weighted by atomic van der Waals volumes
+Mor24v	3D-MoRSE - signal 24 / weighted by atomic van der Waals volumes
+Mor25v	3D-MoRSE - signal 25 / weighted by atomic van der Waals volumes
+Mor26v	3D-MoRSE - signal 26 / weighted by atomic van der Waals volumes
+Mor27v	3D-MoRSE - signal 27 / weighted by atomic van der Waals volumes
+Mor28v	3D-MoRSE - signal 28 / weighted by atomic van der Waals volumes
+Mor29v	3D-MoRSE - signal 29 / weighted by atomic van der Waals volumes
+Mor30v	3D-MoRSE - signal 30 / weighted by atomic van der Waals volumes
+Mor31v	3D-MoRSE - signal 31 / weighted by atomic van der Waals volumes
+Mor32v	3D-MoRSE - signal 32 / weighted by atomic van der Waals volumes
+Mor01e	3D-MoRSE - signal 01 / weighted by atomic Sanderson electronegativities
+Mor02e	3D-MoRSE - signal 02 / weighted by atomic Sanderson electronegativities
+Mor03e	3D-MoRSE - signal 03 / weighted by atomic Sanderson electronegativities
+Mor04e	3D-MoRSE - signal 04 / weighted by atomic Sanderson electronegativities
+Mor05e	3D-MoRSE - signal 05 / weighted by atomic Sanderson electronegativities
+Mor06e	3D-MoRSE - signal 06 / weighted by atomic Sanderson electronegativities
+Mor07e	3D-MoRSE - signal 07 / weighted by atomic Sanderson electronegativities
+Mor08e	3D-MoRSE - signal 08 / weighted by atomic Sanderson electronegativities
+Mor09e	3D-MoRSE - signal 09 / weighted by atomic Sanderson electronegativities
+Mor10e	3D-MoRSE - signal 10 / weighted by atomic Sanderson electronegativities
+Mor11e	3D-MoRSE - signal 11 / weighted by atomic Sanderson electronegativities
+Mor12e	3D-MoRSE - signal 12 / weighted by atomic Sanderson electronegativities
+Mor13e	3D-MoRSE - signal 13 / weighted by atomic Sanderson electronegativities
+Mor14e	3D-MoRSE - signal 14 / weighted by atomic Sanderson electronegativities
+Mor15e	3D-MoRSE - signal 15 / weighted by atomic Sanderson electronegativities
+Mor16e	3D-MoRSE - signal 16 / weighted by atomic Sanderson electronegativities
+Mor17e	3D-MoRSE - signal 17 / weighted by atomic Sanderson electronegativities
+Mor18e	3D-MoRSE - signal 18 / weighted by atomic Sanderson electronegativities
+Mor19e	3D-MoRSE - signal 19 / weighted by atomic Sanderson electronegativities
+Mor20e	3D-MoRSE - signal 20 / weighted by atomic Sanderson electronegativities
+Mor21e	3D-MoRSE - signal 21 / weighted by atomic Sanderson electronegativities
+Mor22e	3D-MoRSE - signal 22 / weighted by atomic Sanderson electronegativities
+Mor23e	3D-MoRSE - signal 23 / weighted by atomic Sanderson electronegativities
+Mor24e	3D-MoRSE - signal 24 / weighted by atomic Sanderson electronegativities
+Mor25e	3D-MoRSE - signal 25 / weighted by atomic Sanderson electronegativities
+Mor26e	3D-MoRSE - signal 26 / weighted by atomic Sanderson electronegativities
+Mor27e	3D-MoRSE - signal 27 / weighted by atomic Sanderson electronegativities
+Mor28e	3D-MoRSE - signal 28 / weighted by atomic Sanderson electronegativities
+Mor29e	3D-MoRSE - signal 29 / weighted by atomic Sanderson electronegativities
+Mor30e	3D-MoRSE - signal 30 / weighted by atomic Sanderson electronegativities
+Mor31e	3D-MoRSE - signal 31 / weighted by atomic Sanderson electronegativities
+Mor32e	3D-MoRSE - signal 32 / weighted by atomic Sanderson electronegativities
+Mor01p	3D-MoRSE - signal 01 / weighted by atomic polarizabilities
+Mor02p	3D-MoRSE - signal 02 / weighted by atomic polarizabilities
+Mor03p	3D-MoRSE - signal 03 / weighted by atomic polarizabilities
+Mor04p	3D-MoRSE - signal 04 / weighted by atomic polarizabilities
+Mor05p	3D-MoRSE - signal 05 / weighted by atomic polarizabilities
+Mor06p	3D-MoRSE - signal 06 / weighted by atomic polarizabilities
+Mor07p	3D-MoRSE - signal 07 / weighted by atomic polarizabilities
+Mor08p	3D-MoRSE - signal 08 / weighted by atomic polarizabilities
+Mor09p	3D-MoRSE - signal 09 / weighted by atomic polarizabilities
+Mor10p	3D-MoRSE - signal 10 / weighted by atomic polarizabilities
+Mor11p	3D-MoRSE - signal 11 / weighted by atomic polarizabilities
+Mor12p	3D-MoRSE - signal 12 / weighted by atomic polarizabilities
+Mor13p	3D-MoRSE - signal 13 / weighted by atomic polarizabilities
+Mor14p	3D-MoRSE - signal 14 / weighted by atomic polarizabilities
+Mor15p	3D-MoRSE - signal 15 / weighted by atomic polarizabilities
+Mor16p	3D-MoRSE - signal 16 / weighted by atomic polarizabilities
+Mor17p	3D-MoRSE - signal 17 / weighted by atomic polarizabilities
+Mor18p	3D-MoRSE - signal 18 / weighted by atomic polarizabilities
+Mor19p	3D-MoRSE - signal 19 / weighted by atomic polarizabilities
+Mor20p	3D-MoRSE - signal 20 / weighted by atomic polarizabilities
+Mor21p	3D-MoRSE - signal 21 / weighted by atomic polarizabilities
+Mor22p	3D-MoRSE - signal 22 / weighted by atomic polarizabilities
+Mor23p	3D-MoRSE - signal 23 / weighted by atomic polarizabilities
+Mor24p	3D-MoRSE - signal 24 / weighted by atomic polarizabilities
+Mor25p	3D-MoRSE - signal 25 / weighted by atomic polarizabilities
+Mor26p	3D-MoRSE - signal 26 / weighted by atomic polarizabilities
+Mor27p	3D-MoRSE - signal 27 / weighted by atomic polarizabilities
+Mor28p	3D-MoRSE - signal 28 / weighted by atomic polarizabilities
+Mor29p	3D-MoRSE - signal 29 / weighted by atomic polarizabilities
+Mor30p	3D-MoRSE - signal 30 / weighted by atomic polarizabilities
+Mor31p	3D-MoRSE - signal 31 / weighted by atomic polarizabilities
+Mor32p	3D-MoRSE - signal 32 / weighted by atomic polarizabilities
+L1u	1st component size directional WHIM index / unweighted
+L2u	2nd component size directional WHIM index / unweighted
+L3u	3rd component size directional WHIM index / unweighted
+P1u	1st component shape directional WHIM index / unweighted
+P2u	2nd component shape directional WHIM index / unweighted
+G1u	1st component symmetry directional WHIM index / unweighted
+G2u	2st component symmetry directional WHIM index / unweighted
+G3u	3st component symmetry directional WHIM index / unweighted
+E1u	1st component accessibility directional WHIM index / unweighted
+E2u	2nd component accessibility directional WHIM index / unweighted
+E3u	3rd component accessibility directional WHIM index / unweighted
+L1m	1st component size directional WHIM index / weighted by atomic masses
+L2m	2nd component size directional WHIM index / weighted by atomic masses
+L3m	3rd component size directional WHIM index / weighted by atomic masses
+P1m	1st component shape directional WHIM index / weighted by atomic masses
+P2m	2nd component shape directional WHIM index / weighted by atomic masses
+G1m	1st component symmetry directional WHIM index / weighted by atomic masses
+G2m	2st component symmetry directional WHIM index / weighted by atomic masses
+G3m	3st component symmetry directional WHIM index / weighted by atomic masses
+E1m	1st component accessibility directional WHIM index / weighted by atomic masses
+E2m	2nd component accessibility directional WHIM index / weighted by atomic masses
+E3m	3rd component accessibility directional WHIM index / weighted by atomic masses
+L1v	1st component size directional WHIM index / weighted by atomic van der Waals volumes
+L2v	2nd component size directional WHIM index / weighted by atomic van der Waals volumes
+L3v	3rd component size directional WHIM index / weighted by atomic van der Waals volumes
+P1v	1st component shape directional WHIM index / weighted by atomic van der Waals volumes
+P2v	2nd component shape directional WHIM index / weighted by atomic van der Waals volumes
+G1v	1st component symmetry directional WHIM index / weighted by atomic van der Waals volumes
+G2v	2st component symmetry directional WHIM index / weighted by atomic van der Waals volumes
+G3v	3st component symmetry directional WHIM index / weighted by atomic van der Waals volumes
+E1v	1st component accessibility directional WHIM index / weighted by atomic van der Waals volumes
+E2v	2nd component accessibility directional WHIM index / weighted by atomic van der Waals volumes
+E3v	3rd component accessibility directional WHIM index / weighted by atomic van der Waals volumes
+L1e	1st component size directional WHIM index / weighted by atomic Sanderson electronegativities
+L2e	2nd component size directional WHIM index / weighted by atomic Sanderson electronegativities
+L3e	3rd component size directional WHIM index / weighted by atomic Sanderson electronegativities
+P1e	1st component shape directional WHIM index / weighted by atomic Sanderson electronegativities
+P2e	2nd component shape directional WHIM index / weighted by atomic Sanderson electronegativities
+G1e	1st component symmetry directional WHIM index / weighted by atomic Sanderson electronegativities
+G2e	2st component symmetry directional WHIM index / weighted by atomic Sanderson electronegativities
+G3e	3st component symmetry directional WHIM index / weighted by atomic Sanderson electronegativities
+E1e	1st component accessibility directional WHIM index / weighted by atomic Sanderson electronegativities
+E2e	2nd component accessibility directional WHIM index / weighted by atomic Sanderson electronegativities
+E3e	3rd component accessibility directional WHIM index / weighted by atomic Sanderson electronegativities
+L1p	1st component size directional WHIM index / weighted by atomic polarizabilities
+L2p	2nd component size directional WHIM index / weighted by atomic polarizabilities
+L3p	3rd component size directional WHIM index / weighted by atomic polarizabilities
+P1p	1st component shape directional WHIM index / weighted by atomic polarizabilities
+P2p	2nd component shape directional WHIM index / weighted by atomic polarizabilities
+G1p	1st component symmetry directional WHIM index / weighted by atomic polarizabilities
+G2p	2st component symmetry directional WHIM index / weighted by atomic polarizabilities
+G3p	3st component symmetry directional WHIM index / weighted by atomic polarizabilities
+E1p	1st component accessibility directional WHIM index / weighted by atomic polarizabilities
+E2p	2nd component accessibility directional WHIM index / weighted by atomic polarizabilities
+E3p	3rd component accessibility directional WHIM index / weighted by atomic polarizabilities
+L1s	1st component size directional WHIM index / weighted by atomic electrotopological states
+L2s	2nd component size directional WHIM index / weighted by atomic electrotopological states
+L3s	3rd component size directional WHIM index / weighted by atomic electrotopological states
+P1s	1st component shape directional WHIM index / weighted by atomic electrotopological states
+P2s	2nd component shape directional WHIM index / weighted by atomic electrotopological states
+G1s	1st component symmetry directional WHIM index / weighted by atomic electrotopological states
+G2s	2st component symmetry directional WHIM index / weighted by atomic electrotopological states
+G3s	3st component symmetry directional WHIM index / weighted by atomic electrotopological states
+E1s	1st component accessibility directional WHIM index / weighted by atomic electrotopological states
+E2s	2nd component accessibility directional WHIM index / weighted by atomic electrotopological states
+E3s	3rd component accessibility directional WHIM index / weighted by atomic electrotopological states
+Tu	T total size index / unweighted
+Tm	T total size index / weighted by atomic masses
+Tv	T total size index / weighted by atomic van der Waals volumes
+Te	T total size index / weighted by atomic Sanderson electronegativities
+Tp	T total size index / weighted by atomic polarizabilities
+Ts	T total size index / weighted by atomic electrotopological states
+Au	A total size index / unweighted
+Am	A total size index / weighted by atomic masses
+Av	A total size index / weighted by atomic van der Waals volumes
+Ae	A total size index / weighted by atomic Sanderson electronegativities
+Ap	A total size index / weighted by atomic polarizabilities
+As	A total size index / weighted by atomic electrotopological states
+Gu	G total symmetry index / unweighted
+Gm	G total symmetry index / weighted by atomic masses
+Gs	G total symmetry index / weighted by atomic electrotopological states
+Ku	K global shape index / unweighted
+Km	K global shape index / weighted by atomic masses
+Kv	K global shape index / weighted by atomic van der Waals volumes
+Ke	K global shape index / weighted by atomic Sanderson electronegativities
+Kp	K global shape index / weighted by atomic polarizabilities
+Ks	K global shape index / weighted by atomic electrotopological states
+Du	D total accessibility index / unweighted
+Dm	D total accessibility index / weighted by atomic masses
+Dv	D total accessibility index / weighted by atomic van der Waals volumes
+De	D total accessibility index / weighted by atomic Sanderson electronegativities
+Dp	D total accessibility index / weighted by atomic polarizabilities
+Ds	D total accessibility index / weighted by atomic electrotopological states
+Vu	V total size index / unweighted
+Vm	V total size index / weighted by atomic masses
+Vv	V total size index / weighted by atomic van der Waals volumes
+Ve	V total size index / weighted by atomic Sanderson electronegativities
+Vp	V total size index / weighted by atomic polarizabilities
+Vs	V total size index / weighted by atomic electrotopological states
+ITH	total information content on the leverage equality
+ISH	standardized information content on the leverage equality
+HIC	mean information content on the leverage magnitude
+HGM	geometric mean on the leverage magnitude
+H0u	H autocorrelation of lag 0 / unweighted
+H1u	H autocorrelation of lag 1 / unweighted
+H2u	H autocorrelation of lag 2 / unweighted
+H3u	H autocorrelation of lag 3 / unweighted
+H4u	H autocorrelation of lag 4 / unweighted
+H5u	H autocorrelation of lag 5 / unweighted
+H6u	H autocorrelation of lag 6 / unweighted
+H7u	H autocorrelation of lag 7 / unweighted
+H8u	H autocorrelation of lag 8 / unweighted
+HTu	H total index / unweighted
+HATS0u	leverage-weighted autocorrelation of lag 0 / unweighted
+HATS1u	leverage-weighted autocorrelation of lag 1 / unweighted
+HATS2u	leverage-weighted autocorrelation of lag 2 / unweighted
+HATS3u	leverage-weighted autocorrelation of lag 3 / unweighted
+HATS4u	leverage-weighted autocorrelation of lag 4 / unweighted
+HATS5u	leverage-weighted autocorrelation of lag 5 / unweighted
+HATS6u	leverage-weighted autocorrelation of lag 6 / unweighted
+HATS7u	leverage-weighted autocorrelation of lag 7 / unweighted
+HATS8u	leverage-weighted autocorrelation of lag 8 / unweighted
+HATSu	leverage-weighted total index / unweighted
+H0m	H autocorrelation of lag 0 / weighted by atomic masses
+H1m	H autocorrelation of lag 1 / weighted by atomic masses
+H2m	H autocorrelation of lag 2 / weighted by atomic masses
+H3m	H autocorrelation of lag 3 / weighted by atomic masses
+H4m	H autocorrelation of lag 4 / weighted by atomic masses
+H5m	H autocorrelation of lag 5 / weighted by atomic masses
+H6m	H autocorrelation of lag 6 / weighted by atomic masses
+H7m	H autocorrelation of lag 7 / weighted by atomic masses
+H8m	H autocorrelation of lag 8 / weighted by atomic masses
+HTm	H total index / weighted by atomic masses
+HATS0m	leverage-weighted autocorrelation of lag 0 / weighted by atomic masses
+HATS1m	leverage-weighted autocorrelation of lag 1 / weighted by atomic masses
+HATS2m	leverage-weighted autocorrelation of lag 2 / weighted by atomic masses
+HATS3m	leverage-weighted autocorrelation of lag 3 / weighted by atomic masses
+HATS4m	leverage-weighted autocorrelation of lag 4 / weighted by atomic masses
+HATS5m	leverage-weighted autocorrelation of lag 5 / weighted by atomic masses
+HATS6m	leverage-weighted autocorrelation of lag 6 / weighted by atomic masses
+HATS7m	leverage-weighted autocorrelation of lag 7 / weighted by atomic masses
+HATS8m	leverage-weighted autocorrelation of lag 8 / weighted by atomic masses
+HATSm	leverage-weighted total index / weighted by atomic masses
+H0v	H autocorrelation of lag 0 / weighted by atomic van der Waals volumes
+H1v	H autocorrelation of lag 1 / weighted by atomic van der Waals volumes
+H2v	H autocorrelation of lag 2 / weighted by atomic van der Waals volumes
+H3v	H autocorrelation of lag 3 / weighted by atomic van der Waals volumes
+H4v	H autocorrelation of lag 4 / weighted by atomic van der Waals volumes
+H5v	H autocorrelation of lag 5 / weighted by atomic van der Waals volumes
+H6v	H autocorrelation of lag 6 / weighted by atomic van der Waals volumes
+H7v	H autocorrelation of lag 7 / weighted by atomic van der Waals volumes
+H8v	H autocorrelation of lag 8 / weighted by atomic van der Waals volumes
+HTv	H total index / weighted by atomic van der Waals volumes
+HATS0v	leverage-weighted autocorrelation of lag 0 / weighted by atomic van der Waals volumes
+HATS1v	leverage-weighted autocorrelation of lag 1 / weighted by atomic van der Waals volumes
+HATS2v	leverage-weighted autocorrelation of lag 2 / weighted by atomic van der Waals volumes
+HATS3v	leverage-weighted autocorrelation of lag 3 / weighted by atomic van der Waals volumes
+HATS4v	leverage-weighted autocorrelation of lag 4 / weighted by atomic van der Waals volumes
+HATS5v	leverage-weighted autocorrelation of lag 5 / weighted by atomic van der Waals volumes
+HATS6v	leverage-weighted autocorrelation of lag 6 / weighted by atomic van der Waals volumes
+HATS7v	leverage-weighted autocorrelation of lag 7 / weighted by atomic van der Waals volumes
+HATS8v	leverage-weighted autocorrelation of lag 8 / weighted by atomic van der Waals volumes
+HATSv	leverage-weighted total index / weighted by atomic van der Waals volumes
+H0e	H autocorrelation of lag 0 / weighted by atomic Sanderson electronegativities
+H1e	H autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities
+H2e	H autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities
+H3e	H autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities
+H4e	H autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities
+H5e	H autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities
+H6e	H autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities
+H7e	H autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities
+H8e	H autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities
+HTe	H total index / weighted by atomic Sanderson electronegativities
+HATS0e	leverage-weighted autocorrelation of lag 0 / weighted by atomic Sanderson electronegativities
+HATS1e	leverage-weighted autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities
+HATS2e	leverage-weighted autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities
+HATS3e	leverage-weighted autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities
+HATS4e	leverage-weighted autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities
+HATS5e	leverage-weighted autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities
+HATS6e	leverage-weighted autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities
+HATS7e	leverage-weighted autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities
+HATS8e	leverage-weighted autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities
+HATSe	leverage-weighted total index / weighted by atomic Sanderson electronegativities
+H0p	H autocorrelation of lag 0 / weighted by atomic polarizabilities
+H1p	H autocorrelation of lag 1 / weighted by atomic polarizabilities
+H2p	H autocorrelation of lag 2 / weighted by atomic polarizabilities
+H3p	H autocorrelation of lag 3 / weighted by atomic polarizabilities
+H4p	H autocorrelation of lag 4 / weighted by atomic polarizabilities
+H5p	H autocorrelation of lag 5 / weighted by atomic polarizabilities
+H6p	H autocorrelation of lag 6 / weighted by atomic polarizabilities
+H7p	H autocorrelation of lag 7 / weighted by atomic polarizabilities
+H8p	H autocorrelation of lag 8 / weighted by atomic polarizabilities
+HTp	H total index / weighted by atomic polarizabilities
+HATS0p	leverage-weighted autocorrelation of lag 0 / weighted by atomic polarizabilities
+HATS1p	leverage-weighted autocorrelation of lag 1 / weighted by atomic polarizabilities
+HATS2p	leverage-weighted autocorrelation of lag 2 / weighted by atomic polarizabilities
+HATS3p	leverage-weighted autocorrelation of lag 3 / weighted by atomic polarizabilities
+HATS4p	leverage-weighted autocorrelation of lag 4 / weighted by atomic polarizabilities
+HATS5p	leverage-weighted autocorrelation of lag 5 / weighted by atomic polarizabilities
+HATS6p	leverage-weighted autocorrelation of lag 6 / weighted by atomic polarizabilities
+HATS7p	leverage-weighted autocorrelation of lag 7 / weighted by atomic polarizabilities
+HATS8p	leverage-weighted autocorrelation of lag 8 / weighted by atomic polarizabilities
+HATSp	leverage-weighted total index / weighted by atomic polarizabilities
+RCON	Randic-type R matrix connectivity
+RARS	R matrix average row sum
+REIG	first eigenvalue of the R matrix
+R1u	R autocorrelation of lag 1 / unweighted
+R2u	R autocorrelation of lag 2 / unweighted
+R3u	R autocorrelation of lag 3 / unweighted
+R4u	R autocorrelation of lag 4 / unweighted
+R5u	R autocorrelation of lag 5 / unweighted
+R6u	R autocorrelation of lag 6 / unweighted
+R7u	R autocorrelation of lag 7 / unweighted
+R8u	R autocorrelation of lag 8 / unweighted
+RTu	R total index / unweighted
+R1u+	R maximal autocorrelation of lag 1 / unweighted
+R2u+	R maximal autocorrelation of lag 2 / unweighted
+R3u+	R maximal autocorrelation of lag 3 / unweighted
+R4u+	R maximal autocorrelation of lag 4 / unweighted
+R5u+	R maximal autocorrelation of lag 5 / unweighted
+R6u+	R maximal autocorrelation of lag 6 / unweighted
+R7u+	R maximal autocorrelation of lag 7 / unweighted
+R8u+	R maximal autocorrelation of lag 8 / unweighted
+RTu+	R maximal index / unweighted
+R1m	R autocorrelation of lag 1 / weighted by atomic masses
+R2m	R autocorrelation of lag 2 / weighted by atomic masses
+R3m	R autocorrelation of lag 3 / weighted by atomic masses
+R4m	R autocorrelation of lag 4 / weighted by atomic masses
+R5m	R autocorrelation of lag 5 / weighted by atomic masses
+R6m	R autocorrelation of lag 6 / weighted by atomic masses
+R7m	R autocorrelation of lag 7 / weighted by atomic masses
+R8m	R autocorrelation of lag 8 / weighted by atomic masses
+RTm	R total index / weighted by atomic masses
+R1m+	R maximal autocorrelation of lag 1 / weighted by atomic masses
+R2m+	R maximal autocorrelation of lag 2 / weighted by atomic masses
+R3m+	R maximal autocorrelation of lag 3 / weighted by atomic masses
+R4m+	R maximal autocorrelation of lag 4 / weighted by atomic masses
+R5m+	R maximal autocorrelation of lag 5 / weighted by atomic masses
+R6m+	R maximal autocorrelation of lag 6 / weighted by atomic masses
+R7m+	R maximal autocorrelation of lag 7 / weighted by atomic masses
+R8m+	R maximal autocorrelation of lag 8 / weighted by atomic masses
+RTm+	R maximal index / weighted by atomic masses
+R1v	R autocorrelation of lag 1 / weighted by atomic van der Waals volumes
+R2v	R autocorrelation of lag 2 / weighted by atomic van der Waals volumes
+R3v	R autocorrelation of lag 3 / weighted by atomic van der Waals volumes
+R4v	R autocorrelation of lag 4 / weighted by atomic van der Waals volumes
+R5v	R autocorrelation of lag 5 / weighted by atomic van der Waals volumes
+R6v	R autocorrelation of lag 6 / weighted by atomic van der Waals volumes
+R7v	R autocorrelation of lag 7 / weighted by atomic van der Waals volumes
+R8v	R autocorrelation of lag 8 / weighted by atomic van der Waals volumes
+RTv	R total index / weighted by atomic van der Waals volumes
+R1v+	R maximal autocorrelation of lag 1 / weighted by atomic van der Waals volumes
+R2v+	R maximal autocorrelation of lag 2 / weighted by atomic van der Waals volumes
+R3v+	R maximal autocorrelation of lag 3 / weighted by atomic van der Waals volumes
+R4v+	R maximal autocorrelation of lag 4 / weighted by atomic van der Waals volumes
+R5v+	R maximal autocorrelation of lag 5 / weighted by atomic van der Waals volumes
+R6v+	R maximal autocorrelation of lag 6 / weighted by atomic van der Waals volumes
+R7v+	R maximal autocorrelation of lag 7 / weighted by atomic van der Waals volumes
+R8v+	R maximal autocorrelation of lag 8 / weighted by atomic van der Waals volumes
+RTv+	R maximal index / weighted by atomic van der Waals volumes
+R1e	R autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities
+R2e	R autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities
+R3e	R autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities
+R4e	R autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities
+R5e	R autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities
+R6e	R autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities
+R7e	R autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities
+R8e	R autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities
+RTe	R total index / weighted by atomic Sanderson electronegativities
+R1e+	R maximal autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities
+R2e+	R maximal autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities
+R3e+	R maximal autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities
+R4e+	R maximal autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities
+R5e+	R maximal autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities
+R6e+	R maximal autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities
+R7e+	R maximal autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities
+R8e+	R maximal autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities
+RTe+	R maximal index / weighted by atomic Sanderson electronegativities
+R1p	R autocorrelation of lag 1 / weighted by atomic polarizabilities
+R2p	R autocorrelation of lag 2 / weighted by atomic polarizabilities
+R3p	R autocorrelation of lag 3 / weighted by atomic polarizabilities
+R4p	R autocorrelation of lag 4 / weighted by atomic polarizabilities
+R5p	R autocorrelation of lag 5 / weighted by atomic polarizabilities
+R6p	R autocorrelation of lag 6 / weighted by atomic polarizabilities
+R7p	R autocorrelation of lag 7 / weighted by atomic polarizabilities
+R8p	R autocorrelation of lag 8 / weighted by atomic polarizabilities
+RTp	R total index / weighted by atomic polarizabilities
+R1p+	R maximal autocorrelation of lag 1 / weighted by atomic polarizabilities
+R2p+	R maximal autocorrelation of lag 2 / weighted by atomic polarizabilities
+R3p+	R maximal autocorrelation of lag 3 / weighted by atomic polarizabilities
+R4p+	R maximal autocorrelation of lag 4 / weighted by atomic polarizabilities
+R5p+	R maximal autocorrelation of lag 5 / weighted by atomic polarizabilities
+R6p+	R maximal autocorrelation of lag 6 / weighted by atomic polarizabilities
+R7p+	R maximal autocorrelation of lag 7 / weighted by atomic polarizabilities
+R8p+	R maximal autocorrelation of lag 8 / weighted by atomic polarizabilities
+RTp+	R maximal index / weighted by atomic polarizabilities
+nCp	number of terminal primary C(sp3) Y = any terminal atom or heteroaromatic group (i.e. H, X, OH, NH2, etc.)
+nCs	number of total secondary C(sp3) Y = H or any heteroatom
+nCt	number of total tertiary C(sp3) Y = H or any heteroatom
+nCq	number of total quaternary C(sp3)
+nCrs	number of ring secondary C(sp3) Y = H or any heteroatom
+nCrt	number of ring tertiary C(sp3) Y = H or any heteroatom
+nCrq	number of ring quaternary C(sp3)
+nCar	number of aromatic C(sp2)
+nCbH	number of unsubstituted benzene C(sp2)
+nCb–	number of substituted benzene C(sp2) Y = carbon or any heteroatom
+nCconj	number of non-aromatic conjugated C(sp2)
+nR=Cp	number of terminal primary C(sp2) Y = any terminal atom or heteroaromatic group (i.e. H, X, OH, NH2, etc.)
+nR=Cs	number of aliphatic secondary C(sp2) Y = H or any heteroatom
+nR=Ct	number of aliphatic tertiary C(sp2)
+n=C=	number of allenes groups
+nR#CH/X	number of terminal C(sp) Y = any terminal atom or heteroaromatic group (i.e. H, X, OH, NH2, etc.)
+nR#C–	number of non-terminal C(sp) Y = C or any non-terminal heteroatom
+nROCN	number of cyanates (aliphatic)
+nArOCN	number of cyanates (aromatic)
+nRNCO	number of isocyanates (aliphatic)
+nArNCO	number of isocyanates (aromatic)
+nRSCN	number of thiocyanates (aliphatic)
+nArSCN	number of thiocyanates (aromatic)
+nRNCS	number of isothiocyanates (aliphatic)
+nArNCS	number of isothiocyanates (aromatic)
+nRCOOH	number of carboxylic acids (aliphatic)
+nArCOOH	number of carboxylic acids (aromatic)
+nRCOOR	number of esters (aliphatic) Y = Ar or Al (not H)                                  Al = H or aliphatic group linked through C
+nArCOOR	number of esters (aromatic) Y = Al or Ar
+nRCONH2	number of primary amides (aliphatic) Al = H or aliphatic group linked through C
+nArCONH2	number of primary amides (aromatic)
+nRCONHR	number of secondary amides (aliphatic)   Y = Ar or Al (not H, not C = O) Al = H or aliphatic group linked through C
+nArCONHR	number of secondary amides (aromatic) Y = Ar or Al (not H, not C = O)
+nRCONR2	number of tertiary amides (aliphatic)  Y = Ar or Al (not H, not C = O) Al = H or aliphatic group linked through C
+nArCONR2	number of tertiary amides (aromatic) Y = Ar or Al (not H, not C = O)
+nROCON	number of (thio-) carbamates (aliphatic) Y = O or S Al = H or aliphatic group linked through any atom
+nArOCON	number of (thio-) carbamates (aromatic) Y1 = O or S Y2 = H or aliphatic or aromatic group linked through any atom Ar = aromatic group linked through any atom
+nRCOX	number of acyl halogenides (aliphatic)
+nArCOX	number of acyl halogenides (aromatic)
+nRCSOH	number of thioacids (aliphatic)
+nArCSOH	number of thioacids (aromatic)
+nRCSSH	number of dithioacids (aliphatic)
+nArCSSH	number of dithioacids (aromatic)
+nRCOSR	number of thioesters (aliphatic) Y = Ar or Al (not H) Al = H or aliphatic group linked through C
+nArCOSR	number of thioesters (aromatic)
+nRCSSR	number of dithioesters (aliphatic) Y = Ar or Al (not H) Al = H or aliphatic group linked through C
+nArCSSR	number of dithioesters (aromatic) Y = Ar or Al (not H)
+nRCHO	number of aldehydes (aliphatic)
+nArCHO	number of aldehydes (aromatic)
+nRCO	number of ketones (aliphatic)
+nArCO	number of ketones (aromatic) Y = Al or Ar
+nCONN	number of urea (-thio) derivatives Y = O or S
+nC=O(OR)2	number of carbonate (-thio) derivatives Y = O or S
+nN=C-N<	number of amidine derivatives Y = C or H
+nC(=N)N2	number of guanidine derivatives
+nRC=N	number of imines (aliphatic)  Y = H,C or N (two-connected) Al = H or aliphatic group linked through C
+nArC=N	number of imines (aromatic) Y = H,C or N (two-connected)
+nRCNO	number of oximes (aliphatic) Y = H, Ar or Al
+nArCNO	number of oximes (aromatic) Y = H, Ar or Al
+nRNH2	number of primary amines (aliphatic) Al = aliphatic group linked through C  (not C = O)
+nArNH2	number of primary amines (aromatic)
+nRNHR	number of secondary amines (aliphatic) Al = aliphatic group linked through C  (not C = O)
+nArNHR	number of secondary amines (aromatic) Y = Ar or Al (not C = O)
+nRNR2	number of tertiary amines (aliphatic) Al = aliphatic group linked through C  (not C = O)
+nArNR2	number of tertiary amines (aromatic) Y = Ar or Al (not C = O)
+nN-N	number of N hydrazines Y = C or H
+nN=N	number of N azo-derivatives Y = C or H
+nRCN	number of nitriles (aliphatic)
+nArCN	number of nitriles (aromatic)
+nN+	number of positive charged N
+nNq	number of quaternary N
+nRNHO	number of hydroxylamines (aliphatic) Y = H, Al or Ar
+nArNHO	number of hydroxylamines (aromatic) Y = H, Al or Ar
+nRNNOx	number of N-nitroso groups (aliphatic) Al = H or aliphatic group linked through C
+nArNNOx	number of N-nitroso groups (aromatic) Y = H, Al or Ar
+nRNO	number of nitroso groups (aliphatic)
+nArNO	number of nitroso groups (aromatic)
+nRNO2	number of nitro groups (aliphatic) Al = H or aliphatic group linked through carbon
+nArNO2	number of nitro groups (aromatic) Al = aromatic group linked through carbon
+nN(CO)2	number of imides (thio-) Y = H or C                 Y1 = O or S
+nC=N-N<	number of hydrazones Y = C or H
+nROH	number of hydroxyl groups Al = aliphatic group linked through any atom
+nArOH	number of aromatic hydroxyls Ar = aromatic group linked through any atom
+nOHp	number of primary alcohols
+nOHs	number of secondary alcohols
+nOHt	number of tertiary alcohols
+nROR	number of ethers (aliphatic) Al = aliphatic group linked through C (not C = O, not C # N)
+nArOR	number of ethers (aromatic) Y = Ar or Al (not C = O, not C # N)
+nROX	number of hypohalogenides (aliphatic)
+nArOX	number of hypohalogenides (aromatic)
+nO(C=O)2	number of anhydrides (thio-) Y = O or S
+nH2O	number of water molecules
+nSH	number of thiols
+nC=S	number of thioketones
+nRSR	number of sulfides
+nRSSR	number of disulfides
+nSO	number of sulfoxides
+nS(=O)2	number of sulfones
+nSOH	number of sulfenic (thio-) acids Y = O or S
+nSOOH	number of sulfinic (thio-/dithio-)acids Y = O or S
+nSO2OH	number of sulfonic (thio-/dithio-) acids Y = O or S
+nSO3OH	number of sulfuric (thio-/dithio-) acids Y = O or S
+nSO2	number of sulfites (thio-/ dithio-) Y = O or S
+nSO3	number of sulfonates (thio- / dithio-) Y = O or S
+nSO4	number of sulfates (thio- / dithio-) Y = O or S
+nSO2N	number of sulfonamides / sulfinamides / sulfenamides (thio- / dithio-)
+nPO3	number of phosphites / thiophosphites Y = O or S
+nPO4	number of phosphates / thiophosphates Y = O or S
+nPR3	number of phosphanes Y = H, C, halogens
+nP(=O)O2R	number of phosphonates / thiophosphonates Y = O or S Y1 = H, C, halogens
+nP(=O)R3/nPR5	number of phosphoranes / thiophosphoranes Y = O or S
+nCH2RX	number of CH2RX
+nCHR2X	number of CHR2X
+nCR3X	number of CR3X
+nR=CHX	number of R=CHX
+nR=CRX	number of R=CRX
+nR#CX	number of R#CX
+nCHRX2	number of CHRX2
+nCR2X2	number of CR2X2
+nR=CX2	number of R=CX2
+nCRX3	number of CRX3
+nArX	number of X on aromatic ring
+nCXr	number of X on ring C(sp3)
+nCXr=	number of X on ring C(sp2)
+nCconjX	number of X on exo-conjugated C
+nAziridines	number of Aziridines
+nOxiranes	number of Oxiranes
+nThiranes	number of Thiranes
+nAzetidines	number of Azetidines
+nOxetanes	number of Oxetanes
+nThioethanes	number of Thioethanes
+nBeta-Lactams	number of Beta-Lactams
+nPyrrolidines	number of Pyrrolidines
+nOxolanes	number of Oxolanes
+nth-Thiophenes	number of tetrahydro-Thiophenes
+nPyrroles	number of Pyrroles
+nPyrazoles	number of Pyrazoles
+nImidazoles	number of Imidazoles
+nFuranes	number of Furanes
+nThiophenes	number of Thiophenes
+nOxazoles	number of Oxazoles
+nIsoxazoles	number of Isoxazoles
+nThiazoles	number of Thiazoles
+nIsothiazoles	number of Isothiazoles
+nTriazoles	number of Triazoles
+nPyridines	number of Pyridines
+nPyridazines	number of Pyridazines
+nPyrimidines	number of Pyrimidines
+nPyrazines	number of Pyrazines
+n135-Triazines	number of 135-Triazines
+n124-Triazines	number of 124-Triazines
+nHDon	number of donor atoms for H-bonds (N and O)
+nHAcc	number of acceptor atoms for H-bonds (N, O, F)
+nHBonds	number of intramolecular H-bonds Y1 = B, N, O, Al, P, S Y2 = N, O, F The geometric distance between H and Y2 must be in the range 1 - 2,7 A.
+C-001	CH3R / CH4
+C-002	CH2R2
+C-003	CHR3
+C-004	CR4
+C-005	CH3X
+C-006	CH2RX
+C-007	CH2X2
+C-008	CHR2X
+C-009	CHRX2
+C-010	CHX3
+C-011	CR3X
+C-012	CR2X2
+C-013	CRX3
+C-014	CX4
+C-015	=CH2
+C-016	=CHR
+C-017	=CR2
+C-018	=CHX
+C-019	=CRX
+C-020	=CX2
+C-021	#CH
+C-022	#CR / R=C=R
+C-023	#CX
+C-024	R--CH--R
+C-025	R--CR--R
+C-026	R--CX--R
+C-027	R--CH--X
+C-028	R--CR--X
+C-029	R--CX--X
+C-030	X--CH--X
+C-031	X--CR--X
+C-032	X--CX--X
+C-033	R--CH..X
+C-034	R--CR..X
+C-035	R--CX..X
+C-036	Al-CH=X
+C-037	Ar-CH=X
+C-038	Al-C(=X)-Al
+C-039	Ar-C(=X)-R
+C-040	R-C(=X)-X / R-C#X / X=C=X
+C-041	X-C(=X)-X
+C-042	X--CH..X
+C-043	X--CR..X
+C-044	X--CX..X
+U-045	undefined
+H-046	Ha attached to C0(sp3) no X attached to next C
+H-047	Ha attached to C1(sp3) / C0(sp2)
+H-048	Ha attached to C2(sp3) / C1(sp2) / C0(sp)
+H-049	Ha attached to C3(sp3) / C2(sp2) / C3(sp2) / C3(sp)
+H-050	H attached to heteroatom
+H-051	H attached to alpha-Cb
+H-052	Ha attached to C0(sp3) with 1X attached to next C
+H-053	Ha attached to C0(sp3) with 2X attached to next C
+H-054	Ha attached to C0(sp3) with 3X attached to next C
+H-055	Ha attached to C0(sp3) with 4X attached to next C
+O-056	alcohol
+O-057	phenol / enol / carboxyl OH
+O-058	=O
+O-059	Al-O-Al
+O-060	Al-O-Ar / Ar-O-Ar / R..O..R / R-O-C=X
+O-061	O-- c
+O-062	O- (negatively charged)
+O-063	R-O-O-R
+Se-064	Any-Se-Any
+Se-065	=Se
+N-066	Al-NH2
+N-067	Al2-NH
+N-068	Al3-N
+N-069	Ar-NH2 / X-NH2
+N-070	Ar-NH-Al
+N-071	Ar-NAl2
+N-072	RCO-N< / >N-X=X
+N-073	Ar2NH / Ar3N / Ar2N-Al / R..N..Rd
+N-074	R#N / R=N-
+N-075	R--N--Re / R--N--X
+N-076	Ar-NO2 / R--N(--R)--Of / RO-NO
+N-077	Al-NO2
+N-078	Ar-N=X / X-N=X
+N-079	N+ (positively charged)
+U-080	undefined
+F-081	Fa attached to C1(sp3)
+F-082	Fa attached to C2(sp3)
+F-083	Fa attached to C3(sp3)
+F-084	Fa attached to C1(sp2)
+F-085	Fa attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X
+Cl-086	Cla attached to C1(sp3)
+Cl-087	Cla attached to C2(sp3)
+Cl-088	Cla attached to C3(sp3)
+Cl-089	Cla attached to C1(sp2)
+Cl-090	Cla attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X
+Br-091	Bra attached to C1(sp3)
+Br-092	Bra attached to C2(sp3)
+Br-093	Bra attached to C3(sp3)
+Br-094	Bra attached to C1(sp2)
+Br-095	Bra attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X
+I-096	Ia attached to C1(sp3)
+I-097	Ia attached to C2(sp3)
+I-098	Ia attached to C3(sp3)
+I-099	Ia attached to C1(sp2)
+I-100	Ia attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X
+F-101	fluoride ion
+Cl-102	chloride ion
+Br-103	bromide ion
+I-104	iodide ion
+U-105	undefined
+S-106	R-SH
+S-107	R2S / RS-SR
+S-108	R=S
+S-109	R-SO-R
+S-110	R-SO2-R
+Si-111	>Si<
+B-112	>B- as in boranes
+U-113	undefined
+U-114	undefined
+P-115	P ylids
+P-116	R3-P=X
+P-117	X3-P=X (phosphate)
+P-118	PX3 (phosphite)
+P-119	PR3 (phosphine)
+P-120	C-P(X)2=X (phosphonate)
+qpmax	maximum positive charge
+qnmax	maximum negative charge
+Qpos	total positive charge
+Qneg	total negative charge
+Qtot	total absolute charge (electronic charge index - ECI)
+Qmean	mean absolute charge (charge polarization)
+Q2	total squared charge
+RPCG	relative positive charge
+RNCG	relative negative charge
+SPP	submolecular polarity parameter
+TE1	topological electronic descriptor
+TE2	topological electronic descriptor (bond resctricted)
+PCWTe	partial charge weighted topological electronic descriptor
+LDI	local dipole index
+Ui	unsaturation index
+Hy	hydrophilic factor
+AMR	molar refractivity
+TPSA(NO)	topological polar surface area using N, O polar contributions
+TPSA(tot)	topological polar surface area using N, O, S, P polar contributions
+MLogP	Moriguchi octanol-water partition coefficient
+MLOGP2	Squared Moriguchi octanol-water partition coeff. (logP^2)
+ALOGP	Ghose-Crippen octanol-water partition coeff. (logP)
+ALOGP2	Squared Ghose-Crippen octanol-water partition coeff. (logP^2)
+LAI	Lipinski alert index
+GVWAI-80	Ghose-Viswanadhan-Wendoloski drug-like index at 80%
+GVWAI-50	Ghose-Viswanadhan-Wendoloski drug-like index at 50%
+Inflammat-80	Ghose-Viswanadhan-Wendoloski antiinflammatory-like index at 80%
+Inflammat-50	Ghose-Viswanadhan-Wendoloski antiinflammatory-like index at 50%
+Depressant-80	Ghose-Viswanadhan-Wendoloski antidepressant-like index at 80%
+Depressant-50	Ghose-Viswanadhan-Wendoloski antidepressant-like index at 50%
+Psychotic-80	Ghose-Viswanadhan-Wendoloski antipsychotic-like index at 80%
+Psychotic-50	Ghose-Viswanadhan-Wendoloski antipsychotic-like index at 50%
+Hypertens-80	Ghose-Viswanadhan-Wendoloski antihypertensive-like index at 80%
+Hypertens-50	Ghose-Viswanadhan-Wendoloski antihypertensive-like index at 50%
+Hypnotic-80	Ghose-Viswanadhan-Wendoloski hypnotic-like index at 80%
+Hypnotic-50	Ghose-Viswanadhan-Wendoloski hypnotic-like index at 50%
+Neoplastic-80	Ghose-Viswanadhan-Wendoloski antineoplastic-like index at 80%
+Neoplastic-50	Ghose-Viswanadhan-Wendoloski antineoplastic-like index at 50%
+Infective-80	Ghose-Viswanadhan-Wendoloski antiinfective-like index at 80%
+Infective-50	Ghose-Viswanadhan-Wendoloski antiinfective-like index at 50% 
+BLTF96	Verhaar model of Fish base-line toxicity for Fish (96h) from MLOGP (mmol/l)
+BLTD48	Verhaar model of Daphnia base-line toxicity  for Daphnia (48h) from MLOGP (mmol/l)
+BLTA96	Verhaar model of Algae base-line toxicity for Algae (96h) from MLOGP (mmol/l)
+B01[C-C]	presence/absence of C-C at topological distance 1
+B01[C-N]	presence/absence of C-N at topological distance 1
+B01[C-O]	presence/absence of C-O at topological distance 1
+B01[C-S]	presence/absence of C-S at topological distance 1
+B01[C-P]	presence/absence of C-P at topological distance 1
+B01[C-F]	presence/absence of C-F at topological distance 1
+B01[C-Cl]	presence/absence of C-Cl at topological distance 1
+B01[C-Br]	presence/absence of C-Br at topological distance 1
+B01[C-I]	presence/absence of C-I at topological distance 1
+B01[C-B]	presence/absence of C-B at topological distance 1
+B01[C-Si]	presence/absence of C-Si at topological distance 1
+B01[C-X]	presence/absence of C-X at topological distance 1
+B01[N-N]	presence/absence of N-N at topological distance 1
+B01[N-O]	presence/absence of N-O at topological distance 1
+.........	..........................................................
+B10[Si-X]	presence/absence of Si-X at topological distance 10
+B10[X-X]	presence/absence of X-X at topological distance 10
+F01[C-C]	frequency of C-C at topological distance 1
+F01[C-N]	frequency of C-N at topological distance 1
+F01[C-O]	frequency of C-O at topological distance 1
+F01[C-S]	frequency of C-S at topological distance 1
+F01[C-P]	frequency of C-P at topological distance 1
+F01[C-F]	frequency of C-F at topological distance 1
+F01[C-Cl]	frequency of C-Cl at topological distance 1
+F01[C-Br]	frequency of C-Br at topological distance 1
+F01[C-I]	frequency of C-I at topological distance 1
+F01[C-B]	frequency of C-B at topological distance 1
+F01[C-Si]	frequency of C-Si at topological distance 1
+F01[C-X]	frequency of C-X at topological distance 1
+F01[N-N]	frequency of N-N at topological distance 1
+F01[N-O]	frequency of N-O at topological distance 1
+.........	..........................................................
+F10[Si-X]	frequency of Si-X at topological distance 10
+F10[X-X]	frequency of X-X at topological distance 10
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/XRAY/spacegroups.dat	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4926 @@
+P 1	1
+(X,Y,Z)
+
+P 1-	2
+(X,Y,Z)
+(-X,-Y,-Z)
+
+P -1	2
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+(-Y,X,1/2-Z)
+(1/2+Y,-X,-Z)
+(1/2-X,1/2-Z,1/2+Y)
+(1/2+X,-Z,-Y)
+(X,1/2+Z,Y)
+(-X,Z,1/2-Y)
+(1/2-Z,1/2-Y,1/2+X)
+(-Z,Y,1/2-X)
+(1/2+Z,-Y,-X)
+(Z,1/2+Y,X)
+(1/2+X,1/2+Y,Z)
+(1/2-X,-Y,1/2+Z)
+(-X,Y,-Z)
+(X,1/2-Y,1/2-Z)
+(1/2+Z,1/2+X,Y)
+(Z,1/2-X,1/2-Y)
+(1/2-Z,-X,1/2+Y)
+(-Z,X,-Y)
+(1/2+Y,1/2+Z,X)
+(-Y,Z,-X)
+(Y,1/2-Z,1/2-X)
+(1/2-Y,-Z,1/2+X)
+(1/4+Y,3/4+X,3/4-Z)
+(3/4-Y,3/4-X,1/4-Z)
+(3/4+Y,1/4-X,3/4+Z)
+(1/4-Y,1/4+X,1/4+Z)
+(1/4+X,3/4+Z,3/4-Y)
+(1/4-X,1/4+Z,1/4+Y)
+(3/4-X,3/4-Z,1/4-Y)
+(3/4+X,1/4-Z,3/4+Y)
+(1/4+Z,3/4+Y,3/4-X)
+(3/4+Z,1/4-Y,3/4+X)
+(1/4-Z,1/4+Y,1/4+X)
+(3/4-Z,3/4-Y,1/4-X)
+(1/4-X,1/4-Y,3/4-Z)
+(1/4+X,3/4+Y,1/4-Z)
+(3/4+X,3/4-Y,3/4+Z)
+(3/4-X,1/4+Y,1/4+Z)
+(1/4-Z,1/4-X,3/4-Y)
+(3/4-Z,1/4+X,1/4+Y)
+(1/4+Z,3/4+X,1/4-Y)
+(3/4+Z,3/4-X,3/4+Y)
+(1/4-Y,1/4-Z,3/4-X)
+(3/4+Y,3/4-Z,3/4+X)
+(3/4-Y,1/4+Z,1/4+X)
+(1/4+Y,3/4+Z,1/4-X)
+(1/2-Y,-X,Z)
+(Y,X,1/2+Z)
+(-Y,1/2+X,-Z)
+(1/2+Y,1/2-X,1/2-Z)
+(1/2-X,-Z,Y)
+(1/2+X,1/2-Z,1/2-Y)
+(X,Z,1/2+Y)
+(-X,1/2+Z,-Y)
+(1/2-Z,-Y,X)
+(-Z,1/2+Y,-X)
+(1/2+Z,1/2-Y,1/2-X)
+(Z,Y,1/2+X)
+
+I M -3 M	96
+(X,Y,Z)
+(-X,-Y,Z)
+(-X,Y,-Z)
+(X,-Y,-Z)
+(Z,X,Y)
+(Z,-X,-Y)
+(-Z,-X,Y)
+(-Z,X,-Y)
+(Y,Z,X)
+(-Y,Z,-X)
+(Y,-Z,-X)
+(-Y,-Z,X)
+(Y,X,-Z)
+(-Y,-X,-Z)
+(Y,-X,Z)
+(-Y,X,Z)
+(X,Z,-Y)
+(-X,Z,Y)
+(-X,-Z,-Y)
+(X,-Z,Y)
+(Z,Y,-X)
+(Z,-Y,X)
+(-Z,Y,X)
+(-Z,-Y,-X)
+(-X,-Y,-Z)
+(X,Y,-Z)
+(X,-Y,Z)
+(-X,Y,Z)
+(-Z,-X,-Y)
+(-Z,X,Y)
+(Z,X,-Y)
+(Z,-X,Y)
+(-Y,-Z,-X)
+(Y,-Z,X)
+(-Y,Z,X)
+(Y,Z,-X)
+(-Y,-X,Z)
+(Y,X,Z)
+(-Y,X,-Z)
+(Y,-X,-Z)
+(-X,-Z,Y)
+(X,-Z,-Y)
+(X,Z,Y)
+(-X,Z,-Y)
+(-Z,-Y,X)
+(-Z,Y,-X)
+(Z,-Y,-X)
+(Z,Y,X)
+(1/2+X,1/2+Y,1/2+Z)
+(1/2-X,1/2-Y,1/2+Z)
+(1/2-X,1/2+Y,1/2-Z)
+(1/2+X,1/2-Y,1/2-Z)
+(1/2+Z,1/2+X,1/2+Y)
+(1/2+Z,1/2-X,1/2-Y)
+(1/2-Z,1/2-X,1/2+Y)
+(1/2-Z,1/2+X,1/2-Y)
+(1/2+Y,1/2+Z,1/2+X)
+(1/2-Y,1/2+Z,1/2-X)
+(1/2+Y,1/2-Z,1/2-X)
+(1/2-Y,1/2-Z,1/2+X)
+(1/2+Y,1/2+X,1/2-Z)
+(1/2-Y,1/2-X,1/2-Z)
+(1/2+Y,1/2-X,1/2+Z)
+(1/2-Y,1/2+X,1/2+Z)
+(1/2+X,1/2+Z,1/2-Y)
+(1/2-X,1/2+Z,1/2+Y)
+(1/2-X,1/2-Z,1/2-Y)
+(1/2+X,1/2-Z,1/2+Y)
+(1/2+Z,1/2+Y,1/2-X)
+(1/2+Z,1/2-Y,1/2+X)
+(1/2-Z,1/2+Y,1/2+X)
+(1/2-Z,1/2-Y,1/2-X)
+(1/2-X,1/2-Y,1/2-Z)
+(1/2+X,1/2+Y,1/2-Z)
+(1/2+X,1/2-Y,1/2+Z)
+(1/2-X,1/2+Y,1/2+Z)
+(1/2-Z,1/2-X,1/2-Y)
+(1/2-Z,1/2+X,1/2+Y)
+(1/2+Z,1/2+X,1/2-Y)
+(1/2+Z,1/2-X,1/2+Y)
+(1/2-Y,1/2-Z,1/2-X)
+(1/2+Y,1/2-Z,1/2+X)
+(1/2-Y,1/2+Z,1/2+X)
+(1/2+Y,1/2+Z,1/2-X)
+(1/2-Y,1/2-X,1/2+Z)
+(1/2+Y,1/2+X,1/2+Z)
+(1/2-Y,1/2+X,1/2-Z)
+(1/2+Y,1/2-X,1/2-Z)
+(1/2-X,1/2-Z,1/2+Y)
+(1/2+X,1/2-Z,1/2-Y)
+(1/2+X,1/2+Z,1/2+Y)
+(1/2-X,1/2+Z,1/2-Y)
+(1/2-Z,1/2-Y,1/2+X)
+(1/2-Z,1/2+Y,1/2-X)
+(1/2+Z,1/2-Y,1/2-X)
+(1/2+Z,1/2+Y,1/2+X)
+
+I A -3 D	96
+(X,Y,Z)
+(1/2-X,-Y,1/2+Z)
+(-X,1/2+Y,1/2-Z)
+(1/2+X,1/2-Y,-Z)
+(Z,X,Y)
+(1/2+Z,1/2-X,-Y)
+(1/2-Z,-X,1/2+Y)
+(-Z,1/2+X,1/2-Y)
+(Y,Z,X)
+(-Y,1/2+Z,1/2-X)
+(1/2+Y,1/2-Z,-X)
+(1/2-Y,-Z,1/2+X)
+(3/4+Y,1/4+X,1/4-Z)
+(3/4-Y,3/4-X,3/4-Z)
+(1/4+Y,1/4-X,3/4+Z)
+(1/4-Y,3/4+X,1/4+Z)
+(3/4+X,1/4+Z,1/4-Y)
+(1/4-X,3/4+Z,1/4+Y)
+(3/4-X,3/4-Z,3/4-Y)
+(1/4+X,1/4-Z,3/4+Y)
+(3/4+Z,1/4+Y,1/4-X)
+(1/4+Z,1/4-Y,3/4+X)
+(1/4-Z,3/4+Y,1/4+X)
+(3/4-Z,3/4-Y,3/4-X)
+(-X,-Y,-Z)
+(1/2+X,Y,1/2-Z)
+(X,1/2-Y,1/2+Z)
+(1/2-X,1/2+Y,Z)
+(-Z,-X,-Y)
+(1/2-Z,1/2+X,Y)
+(1/2+Z,X,1/2-Y)
+(Z,1/2-X,1/2+Y)
+(-Y,-Z,-X)
+(Y,1/2-Z,1/2+X)
+(1/2-Y,1/2+Z,X)
+(1/2+Y,Z,1/2-X)
+(1/4-Y,3/4-X,3/4+Z)
+(1/4+Y,1/4+X,1/4+Z)
+(3/4-Y,3/4+X,1/4-Z)
+(3/4+Y,1/4-X,3/4-Z)
+(1/4-X,3/4-Z,3/4+Y)
+(3/4+X,1/4-Z,3/4-Y)
+(1/4+X,1/4+Z,1/4+Y)
+(3/4-X,3/4+Z,1/4-Y)
+(1/4-Z,3/4-Y,3/4+X)
+(3/4-Z,3/4+Y,1/4-X)
+(3/4+Z,1/4-Y,3/4-X)
+(1/4+Z,1/4+Y,1/4+X)
+(1/2+X,1/2+Y,1/2+Z)
+(-X,1/2-Y,Z)
+(1/2-X,Y,-Z)
+(X,-Y,1/2-Z)
+(1/2+Z,1/2+X,1/2+Y)
+(Z,-X,1/2-Y)
+(-Z,1/2-X,Y)
+(1/2-Z,X,-Y)
+(1/2+Y,1/2+Z,1/2+X)
+(1/2-Y,Z,-X)
+(Y,-Z,1/2-X)
+(-Y,1/2-Z,X)
+(1/4+Y,3/4+X,3/4-Z)
+(1/4-Y,1/4-X,1/4-Z)
+(3/4+Y,3/4-X,1/4+Z)
+(3/4-Y,1/4+X,3/4+Z)
+(1/4+X,3/4+Z,3/4-Y)
+(3/4-X,1/4+Z,3/4+Y)
+(1/4-X,1/4-Z,1/4-Y)
+(3/4+X,3/4-Z,1/4+Y)
+(1/4+Z,3/4+Y,3/4-X)
+(3/4+Z,3/4-Y,1/4+X)
+(3/4-Z,1/4+Y,3/4+X)
+(1/4-Z,1/4-Y,1/4-X)
+(1/2-X,1/2-Y,1/2-Z)
+(X,1/2+Y,-Z)
+(1/2+X,-Y,Z)
+(-X,Y,1/2+Z)
+(1/2-Z,1/2-X,1/2-Y)
+(-Z,X,1/2+Y)
+(Z,1/2+X,-Y)
+(1/2+Z,-X,Y)
+(1/2-Y,1/2-Z,1/2-X)
+(1/2+Y,-Z,X)
+(-Y,Z,1/2+X)
+(Y,1/2+Z,-X)
+(3/4-Y,1/4-X,1/4+Z)
+(3/4+Y,3/4+X,3/4+Z)
+(1/4-Y,1/4+X,3/4-Z)
+(1/4+Y,3/4-X,1/4-Z)
+(3/4-X,1/4-Z,1/4+Y)
+(1/4+X,3/4-Z,1/4-Y)
+(3/4+X,3/4+Z,3/4+Y)
+(1/4-X,1/4+Z,3/4-Y)
+(3/4-Z,1/4-Y,1/4+X)
+(1/4-Z,1/4+Y,3/4-X)
+(1/4+Z,3/4-Y,1/4-X)
+(3/4+Z,3/4+Y,3/4+X)
+
+B 2	4
+(X,Y,Z)
+(-X,-Y,Z)
+(1/2+X,+Y,1/2+Z)
+(1/2-X,-Y,1/2+Z)
+
+P 1 1 21	2
+(X,Y,Z)
+(-X,-Y,1/2+Z)
+
+P 2 21 21	4
+(X,Y,Z)
+(X,-Y,-Z)
+(-X,1/2+Y,1/2-Z)
+(-X,1/2-Y,1/2+Z)
+
+P 21 2 21	4
+(X,Y,Z)
+(-X,Y,-Z)
+(1/2+X,-Y,1/2-Z)
+(1/2-X,-Y,1/2+Z)
+
+I 1 2 1	4
+(X,Y,Z)
+(-X,Y,-Z)
+(1/2+X,1/2+Y,1/2+Z)
+(1/2-X,1/2+Y,1/2-Z)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/atomtyping/AMBERTypes.dat	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,61 @@
+CT	6	4	*	*	*						*
+C	6	3	*	*	*						(XA1)
+CN	6	3	*	*	[RG5,RG6,AR1.AR2.AR3]	(C3,C3,N3(H))
+CB	6	3	*	*	[RG5,RG6,AR1.AR2.AR3]	*
+CR	6	3	*	*	[RG5,AR1.AR2.AR3]		(N3,N3)
+CR	6	3	*	*	[RG5,AR1.AR2.AR3]		(N2,N3(H))
+CK	6	3	*	*	[RG5,AR1.AR2.AR3]		(N2,N3)
+CC	6	3	0	*	[RG5,AR1.AR2.AR3]		(C3,N3(C3,H))
+CC	6	3	0	*	[RG5,AR1.AR2.AR3]		(C3,N2(C3))
+CW	6	3	*	*	[RG5,AR1.AR2.AR3]		(C3,N3(H))
+CV	6	3	*	*	[RG5,AR1.AR2.AR3]		(C3,N2)
+C*	6	3	*	*	[RG5,AR1.AR2.AR3]		(C3,C3)
+CQ	6	3	*	*	[RG6,AR1.AR2.AR3]		(N2,N2)
+CM	6	3	*	*	[RG6,AR1.AR2.AR3]		(C3,C3(N2(C3(N3(C3)))))
+CM	6	3	*	*	[RG6,AR1.AR2.AR3]		(C3,C3(N3(C3(N3(C3)))))
+CM	6	3	*	*	[RG6,AR1.AR2.AR3]		(C3,N3(C3(N2(C3(C3)))))
+CM	6	3	*	*	[RG6,AR1.AR2.AR3]		(N3,C3(C3(N3(C3(N3)))))
+CA	6	3	*	*	[AR1.AR2.AR3]			*
+CD	6	3	*	*	*						(C3,C3)
+CM	6	3	*	*	*						*
+CZ	6	2	*	*	*						*
+H	1	1	*	*	*						(N)
+HS	1	1	*	*	*						(S)
+HP	1	1	*	*	*						(C(N4))
+HW	1	1	*	*	*						(O(H1))
+HO	1	1	*	*	*						(O)
+H1	1	1	*	1	*						(C4)
+H2	1	1	*	2	*						(C4)
+H3	1	1	*	3	*						(C4)
+HC	1	1	*	*	*						(C4)
+H4	1	1	*	1	*						(XX[AR1.AR2.AR3])
+H5	1	1	*	2	*						(XX[AR1.AR2.AR3])
+HA	1	1	*	*	*						(XX[AR1.AR2.AR3])
+F	9	1	*	*	*						*
+Cl	17	1	*	*	*						*
+Br	35	1	*	*	*						*
+I	53	1	*	*	*						*
+N1	7	1	*	*	*						*
+NB	7	2	*	*	[RG5,AR1.AR2.AR3]		*
+NC	7	2	*	*	[RG6,AR1.AR2.AR3]		*
+N2	7	-1	*	*	*						(C3(N3,N3))
+NO	7	-1	*	*	*						(O1,O1)
+NA	7	3	1	*	[RG5.RG6,AR1.AR2.AR3]	*
+N2	7	3	*	*	[NR]					(XX[AR1.AR2.AR3])
+N*	7	3	*	*	[AR1.AR2.AR3]			*
+N	7	3	*	*	*						(C3(XA1))
+NT	7	3	*	*	*						*
+N3	7	4	*	*	*						*
+O2	8	1	*	*	*						(C(O1))
+O2	8	1	*	*	*						(P)
+O	8	1	*	*	*						(C)
+O	8	1	*	*	*						(S)
+OH	8	2	1	*	*						*
+OW	8	2	2	*	*						*
+OS	8	2	*	*	*						*
+SH	16	2	1	*	*						*	
+SH	16	2	2	*	*						*
+S	16	2	*	*	*						*
+SO	16	4	*	*	*						*
+LP	0	-1	*	*	*						*
+DU	-1	-1	*	*	*						*
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/atomtyping/GAFFTypes.dat	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,208 @@
+cx    6   4   *   *   [RG3]       *
+cy    6		4   *   *   [RG4]       *    
+c3    6   4   *		*		*						*
+c     6   3   *   *   [2DL]   		(XA1)	
+c     6   3   *   *   [1DB,0DL]  	(XA1)	
+c     6   3   *   *   [3sb]   		(XA1)
+cz    6   3   *   *   *           (N3,N3,N3) 
+cp    6   3   *   *   [AR1,1RG6]  (XX[AR1],XX[AR1],XX[AR1]) 
+ca    6   3   *   *   [AR1]    		*
+cc    6   3   *   *   [sb,db,AR2]       (C3(C3))	
+cc    6   3   *   *   [sb,db,AR2]       (C3(C2))	
+cc    6   3   *   *   [sb,db,AR2]       (C3(XB2))	
+cc    6   3   *   *   [sb,db,AR2]       (XB2(XB2))	 
+cc    6   3   *   *   [sb,db,AR2]       (XB2(C2))	
+cc    6   3   *   *   [sb,db,AR2]       (XB2(C3))	
+cc    6   3   *   *   [sb,db,AR2]       (C3[sb'])	
+cc    6   3   *   *   [sb,db,AR2]       (XB2[sb'])	
+cc    6   3   *   *   [sb,db,AR2]       (XD3[sb',db])	
+cc    6   3   *   *   [sb,db,AR2]       (XD4[sb',db])	
+cc    6   3   *   *   [sb,db,AR3]       (C3(C3))	
+cc    6   3   *   *   [sb,db,AR3]       (C3(C2))	
+cc    6   3   *   *   [sb,db,AR3]       (C3(XB2))	
+cc   	6   3   *   *   [sb,db,AR3]       (XB2(XB2)) 	
+cc    6   3   *   *   [sb,db,AR3]       (XB2(C2))	
+cc    6   3   *   *   [sb,db,AR3]       (XB2(C3))	
+cc    6   3   *   *   [sb,db,AR3]       (C3[sb'])	
+cc    6   3   *   *   [sb,db,AR3]       (XB2[sb'])	
+cc    6   3   *   *   [sb,db,AR3]       (XD3[sb',db])	
+cc    6   3   *   *   [sb,db,AR3]       (XD4[sb',db])	
+ce    6   3   *   *   [sb,db]          (C3[SB'])	
+ce    6   3   *   *   [sb,db]          (C2[SB'])	
+ce    6   3   *   *   [sb,db]          (XB2[SB'])	
+ce    6   3   *   *   [sb,db]          (XD3[SB',db])	
+ce    6   3   *   *   [sb,db]          (XD4[SB',db])	
+cu    6   3   *   *   [RG3]       *
+cv    6   3   *   *   [RG4]       *
+c2    6   3   *		*		*						*
+cg    6   2   *   *   [sb,tb]          (C2[SB'])	
+cg    6   2   *   *   [sb,tb]          (C3[SB'])	
+cg    6   2   *   *   [sb,tb]          (N1[SB'])	
+cg    6   2   *   *   [sb,tb]          (XB2[SB'])	
+c1    6   2   *		*		*						*
+c1    6   1   *		*		*						*
+hn    1   1   *   *   *       		(N)
+ho    1   1   *   *   *       		(O)
+hs    1   1   *   *   *       		(S)
+hp    1   1   *   *   *       		(P)
+hx    1   1   *   *   *       		(C(N4))
+hw    1   1   *   *   *       		(O(H1))
+h3    1   1   *		3   *       		(C4)
+h2    1   1   *   2   *       		(C4)
+h1    1   1   *   1   *       		(C4)
+hc    1   1   *   *   *       		(C4)
+h5    1   1   *   2   *       		(C3)
+h4    1   1   *   1   *       		(C3)
+ha    1   1   *		*		*						*
+f     9  -1		*		*		*						*
+cl    17 -1		*		*		*						*
+br    35 -1		*		*		*						*
+i     53 -1		*		*		*						*
+pc    15  2   *   *   [sb,db,AR2]       (C3(C3))	
+pc    15  2   *   *   [sb,db,AR2]       (C3(C2))	
+pc    15  2   *   *   [sb,db,AR2]       (C3(XB2))	
+pc    15  2   *   *   [sb,db,AR2]       (XB2(C3))	
+pc    15  2   *   *   [sb,db,AR2]       (XB2(C2))	
+pc    15  2   *   *   [sb,db,AR2]       (XB2(XB2))	
+pc    15  2   *   *   [sb,db,AR2]       (C3[sb'])	
+pc    15  2   *   *   [sb,db,AR2]       (C2[sb'])	
+pc    15  2   *   *   [sb,db,AR2]       (XB2[sb'])	
+pc    15  2   *   *   [sb,db,AR2]       (XD3[sb',db])	
+pc    15  2   *   *   [sb,db,AR2]       (XD4[sb',db])	
+pc    15  2   *   *   [sb,db,AR3]       (C3(C3))	
+pc    15  2   *   *   [sb,db,AR3]       (C3(C2))	
+pc    15  2   *   *   [sb,db,AR3]       (C3(XB2))	
+pc    15  2   *   *   [sb,db,AR3]       (XB2(C3))	
+pc    15  2   *   *   [sb,db,AR3]       (XB2(C2))	
+pc    15  2   *   *   [sb,db,AR3]       (XB2(XB2))
+pc   	15  2   *   *   [sb,db,AR3]       (C3[sb'])	
+pc    15  2   *   *   [sb,db,AR3]       (C2[sb'])	
+pc    15  2   *   *   [sb,db,AR3]       (XB2[sb'])	
+pc    15  2   *   *   [sb,db,AR3]       (XD3[sb',db])	
+pc    15  2   *   *   [sb,db,AR3]       (XD4[sb',db])	
+pb    15  2   *   *   [AR1]        *
+pe    15  2   *   *   [sb,db]          (C3[sb'])	
+pe    15  2   *   *   [sb,db]          (C2[SB'])	
+pe    15  2   *   *   [sb,db]          (XA1[SB'])	
+pe    15  2   *   *   [sb,db]          (XB2[SB'])	
+pe    15  2   *   *   [sb,db]          (XD3[SB',DB])	
+pe    15  2   *   *   [sb,db]          (XD4[SB',DB])	
+p2    15  2   *		*		*						*
+p2    15  1   *		*		*						*
+px    15  3   *   *   [db]    		(XB2[sb'])      
+px    15  3   *   *   [db]    		(C3[sb'])      
+px    15  3   *   *   [db]    		(XD3[sb',db])      
+px    15  3   *   *   [db]    		(XD4[sb',db])      
+p4    15  3   *   *   [db]    		(XA1)    
+p3    15  3   *		*		*						*
+py    15  4   *   *   [db]    		(XB2[sb'])      
+py    15  4   *   *   [db]    		(C3[sb'])     
+py    15  4   *   *   [db]    		(XD3[sb',db])     
+py    15  4   *   *   [db]    		(XD4[sb',db])     
+p5    15  4   *		*		*						*
+p5    15  5   *		*		*						*
+p5    15  6   *		*		*						*
+n     7   3   *   *   *       		(C3(XA1)) 
+n4    7   4   *		*		*						*
+no    7   3   *   *   *       		(O1,O1)
+na    7   3   *   *   [AR1.AR2.AR3]    *
+nh    7   3   *   *   *       		(XX[AR1.AR2.AR3]) 
+nh    7   3   *   *   *       		(C3[DB]) 	
+nh    7   3   *   *   *       		(N2[DB]) 
+nh    7   3   *   *   *       		(P2[DB]) 
+n3    7   3   *		*		*						*
+nb    7   2   *   *   [AR1]       *
+nc    7   2   *   *   [sb,db,AR2]       (C3(C3))	
+nc    7   2   *   *   [sb,db,AR2]       (C3(C2))	
+nc    7   2   *   *   [sb,db,AR2]       (C3(XB2))	
+nc    7   2   *   *   [sb,db,AR2]       (XB2(C3))	
+nc    7   2   *   *   [sb,db,AR2]       (XB2(C2))	
+nc    7   2   *   *   [sb,db,AR2]       (XB2(XB2))	
+nc    7   2   *   *   [sb,db,AR2]       (C3[sb'])	
+nc    7   2   *   *   [sb,db,AR2]       (XB2[sb'])	
+nc    7   2   *   *   [sb,db,AR2]       (XD3[sb',db])	
+nc    7   2   *   *   [sb,db,AR2]       (XD4[sb',db])	
+nc    7   2   *   *   [sb,db,AR3]       (C3(C3))	
+nc    7   2   *   *   [sb,db,AR3]       (C3(C2))	
+nc    7   2   *   *   [sb,db,AR3]       (C3(XB2))	
+nc    7   2   *   *   [sb,db,AR3]       (XB2(C3))	
+nc    7   2   *   *   [sb,db,AR3]       (XB2(C2))	
+nc    7   2   *   *   [sb,db,AR3]       (XB2(XB2))	
+nc    7   2   *   *   [sb,db,AR3]       (C3[sb'])	
+nc    7   2   *   *   [sb,db,AR3]       (XB2[sb'])	
+nc    7   2   *   *   [sb,db,AR3]       (XD3[sb',db])
+nc    7   2   *   *   [sb,db,AR3]       (XD4[sb',db])	
+ne    7   2   *   *   [sb,db]          (C2[SB'])
+ne    7   2   *   *   [sb,db]          (C3[SB'])
+ne    7   2   *   *   [sb,db]          (XA1[SB'])
+ne    7   2   *   *   [sb,db]          (XB2[SB'])
+ne    7   2   *   *   [sb,db]          (XD3[SB',db])
+ne    7   2   *   *   [sb,db]          (XD4[SB',db])
+n1    7   2   *   *   [2db]             *
+n1    7   2   *   *   [tb,sb]           *
+n2    7   2   *		*		*									*
+n1    7   1   *		*		*									*
+o     8   1   *		*		*									*
+oh    8   2   1   *		*									*
+oh    8   2   2   *		*									*
+oh    8   3   1   *		*									*
+oh    8   3   2   *		*									*
+oh    8   3   3   *		*									*
+os    8   2   *		*		*									*
+os    8   3   *		*		*									*
+os    8  -1		*		*		*									*
+s     16  1   *		*		*									*
+s2    16  2   *   *   [DB]              * 
+s2    16  2   *   *   [TB]              * 
+sh    16  2   1   *		*									*
+sh    16  2   2   *		*									*
+ss   	16  2   *		*		*									*
+sx    16  3   *   *   [db]    		(XB2[sb'])  	
+sx    16  3   *   *   [db]    		(C3[sb'])      
+sx    16  3   *   *   [db]    		(XD3[sb',db])     
+sx    16  3   *   *   [db]    		(XD4[sb',db])      
+s4    16  3   *		*		*						*
+sy    16  4   *   *   [db]    		(XB2[sb'])      
+sy    16  4   *   *   [db]    		(C3[sb'])       
+sy    16  4   *   *   [db]    		(XD3[sb',db])       
+sy    16  4   *   *   [db]    		(XD4[sb',db])       
+s6    16  4   *		*		*						*
+s6    16  5   *		*		*						*
+s6    16  6   *		*		*						*
+Li    3  -1		*		*		*						*
+Be    4  -1		*		*		*						* 
+B     5  -1		*		*		*						* 
+Na    11 -1		*		*		*						*
+Mg    12 -1		*		*		*						*	 
+Al    13 -1 	*		*		*						*
+Si    14 -1 	*		*		*						*
+K     19 -1		*		*		*						* 
+Ca    20 -1		*		*		*						* 
+Sr    38 -1		*		*		*						*
+Ba   	56 -1		*		*		*						* 
+Sc    21 -1		*		*		*						* 
+Ti    22 -1		*		* 	*						*
+V     23 -1		*		*		*						*
+Cr    24 -1		*		*		*						* 
+Mn    25 -1		*		*		*						* 
+Fe    26 -1		*		*		*						* 
+Co    27 -1		*		*		*						*
+Ni    28 -1		*		*		*						* 
+Cu    29 -1		*		*		*						* 
+Zn    30 -1		*		*		*						* 
+Ga    31 -1		*		*		*						* 
+Ge    32 -1		*		*		*						* 
+As    33 -1		*		*		*						*  
+Se    34 -1		*		*		*						*  
+Ru    44 -1		*		*		*						*  
+Rh    45 -1		*		*		*						*  
+Pd    46 -1		*		*		*						*  
+Ag    47 -1		*		*		*						*  
+Cd    48 -1		*		*		*						*  
+Pt    78 -1		*		*		*						*  
+Au    79 -1		*		*		*						*  
+Hg    80 -1	  *		*		*						*  
+Tl    81 -1	  *		*		*						*  
+Pb    82 -1	  *		*		*						* 
+lp    0   1   *   *		*						* 
+DU    -1 -1		*   *		*						* 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/atomtyping/SYBYLTypes.dat	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,66 @@
+C.3	6	4	*	*	*	*
+C.cat	6	3	*	*	*	(N3,N3,N3)
+C.ar	6	3	*	*	[AR1]	*
+C.2	6	3	*	*	*	*
+C.1	6	2	*	*	*	*
+C.1	6	1	*	*	*	*
+H	1	-1	*	*	*	*
+F	9	-1	*	*	*	*
+Cl	17	-1	*	*	*	*
+Br	35	-1	*	*	*	*
+I	53	-1	*	*	*	*
+P.3	15	-1	*	*	*	*
+N.4	7	4	*	*	*	*
+N.am	7	3	*	*	*	(C3(XA1))
+N.pl3	7	3	*	*	*	(O1,O1)
+N.pl3	7	3	*	*	[AR1.AR2.AR3]	*
+N.3	7	3	*	*	*	*
+N.ar	7	2	*	*	[AR1]	*
+N.2	7	2	*	*	*	*
+N.1	7	1	*	*	*	*
+O.co2	8	1	*	*	*	(C3(O1))
+O.co2	8	1	*	*	*	(P(O1))
+O.2	8	1	*	*	*	*
+O.3	8	2	*	*	*	*
+S.2	16	1	*	*	*	*
+S.3	16	2	*	*	*	*
+S.o	16	3	*	*	*	(O1[DB'])
+S.o2	16	4	*	*	*	(O1[DB'],O1[DB'])
+s.3	16	-1	*	*	*	*
+Li	3	-1	*	*	*	*
+Be	4	-1	*	*	*	*
+B	5	-1	*	*	*	*
+Na	11	-1	*	*	*	*
+Mg	12	-1	*	*	*	*
+Al	13	-1	*	*	*	*
+Si	14	-1	*	*	*	*
+K	19	-1	*	*	*	*
+Ca	20	-1	*	*	*	*
+Sr	38	-1	*	*	*	*
+Ba	56	-1	*	*	*	*
+Sc	21	-1	*	*	*	*
+Ti	22	-1	*	*	*	*
+V	23	-1	*	*	*	*
+Cr	24	-1	*	*	*	*
+Mn	25	-1	*	*	*	*
+Fe	26	-1	*	*	*	*
+Co	27	-1	*	*	*	*
+Ni	28	-1	*	*	*	*
+Cu	29	-1	*	*	*	*
+Zn	30	-1	*	*	*	*
+Ga	31	-1	*	*	*	*
+Ge	32	-1	*	*	*	*
+As	33	-1	*	*	*	*
+Se	34	-1	*	*	*	*
+Ru	44	-1	*	*	*	*
+Rh	45	-1	*	*	*	*
+Pd	46	-1	*	*	*	*
+Ag	47	-1	*	*	*	*
+Cd	48	-1	*	*	*	*
+Pt	78	-1	*	*	*	*
+Au	79	-1	*	*	*	*
+Hg	80	-1	*	*	*	*
+Tl	81	-1	*	*	*	*
+Pb	82	-1	*	*	*	*
+lp	0	1	*	*	*	*
+ANY	-1	-1	*	*	*	*	*
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/BondOrder.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,366 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<table>
+	<!-- 	This file supplies improved penalty scores for different 
+	  		atom types in bond type perception based on the work of 
+	 								 	
+	 				Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and 
+	 				bond type perception in molecular mechanical calculations". Journal of 
+	 				Molecular Graphics and Modelling , 25, 2006, 247260	
+
+				A penalty score of 0 means that the corresponding valence is optimal.
+				Note that the first matching entry is taken as the final atom type.
+
+				Note that in the SMARTS strings we use atomic numbers rather than symbols (e.g. #8 instead of O).
+				The reason is that wrongly assigned aromatic bonds in the input would lead to failure to identify the
+				right rule!
+	-->	
+	<!-- for charged H -->
+	<entry id="0">
+		<elementstring>H</elementstring>
+		<smartstring>SMARTS([#1+])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="1">
+		<elementstring>H</elementstring>
+		<smartstring>SMARTS([#1])</smartstring>
+		<penalty valence="1">0</penalty>
+	</entry>
+	<entry id="2">
+		<elementstring>F</elementstring>
+		<smartstring>SMARTS(F)</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>	
+	<entry id="4">
+		<elementstring>Br</elementstring>
+		<smartstring>SMARTS(Br)</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="5">
+		<elementstring>I</elementstring>
+		<smartstring>SMARTS(I)</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="6"> <!-- 	SMARTS([CD1]~[ND2]) AND element(C)</smartstring> -->
+		<elementstring>C</elementstring>
+		<smartstring>SMARTS([$([#6D1](~[#7D2]))])</smartstring>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">32</penalty>
+	</entry>
+	<entry id="7">
+		<elementstring>C</elementstring>
+		<smartstring>SMARTS([#6D1])</smartstring>
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+		<penalty valence="5">32</penalty>
+	</entry>
+	<entry id="9">
+		<elementstring>C</elementstring>
+		<smartstring>SMARTS([#6])</smartstring>
+		<penalty valence="2">64</penalty>
+		<penalty valence="3">32</penalty>
+		<penalty valence="4">0</penalty>
+		<penalty valence="5">32</penalty>
+		<penalty valence="6">64</penalty>
+	</entry>
+	<entry id="10">
+		<elementstring>Si</elementstring>
+		<smartstring>SMARTS(Si)</smartstring>
+		<penalty valence="4">0</penalty>
+	</entry>
+	<entry id="11">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([$([#7D1](~[#7D2]))])</smartstring> <!--SMARTS([ND1]~[ND2]) AND SMARTS([ND1])</smartstring> -->
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">0</penalty>
+	</entry>
+	<entry id="12">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D1])</smartstring>
+		<penalty valence="2">3</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">32</penalty>
+	</entry>
+	<entry id="13">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([$([#7D2](~[#7D1]))])</smartstring> <!--SMARTS([ND1]~[ND2]) AND SMARTS([ND2])</smartstring> -->
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+	</entry>
+	<entry id="14">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D2])</smartstring>
+		<penalty valence="2">4</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">2</penalty>
+	</entry>
+	<entry id="151"><!-- for charged N in  O == N+ __ O- -->	
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([$([#7D3](~[#8D1-,#16D1-])~[#8D1,#16D1])])</smartstring>
+		<penalty valence="3">32</penalty>
+		<penalty valence="4">0</penalty>
+		<penalty valence="5">32</penalty>
+		<penalty valence="6">64</penalty>
+	</entry>
+	<entry id="15">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])~[#8D1,#16D1])])</smartstring>
+		<penalty valence="3">64</penalty>
+		<penalty valence="4">32</penalty>
+		<penalty valence="5">0</penalty>
+		<penalty valence="6">32</penalty>
+	</entry>
+	<entry id="16">
+		<elementstring>N</elementstring>
+		<!-- <smartstring>SMARTS([$(*OD1)&amp;$(*aR)&amp;n]) OR SMARTS([$(*OD1);$(*R);N])</smartstring> -->	
+		<smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+	</entry>
+	<entry id="17">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D3])</smartstring>
+		<penalty valence="2">32</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">2</penalty>
+	</entry>
+	<entry id="181"><!-- for charged N in   N+ H_4 -->
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D4+])</smartstring>
+		<penalty valence="3">32</penalty>
+		<penalty valence="4">0</penalty>
+	</entry>
+	<entry id="18">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D4])</smartstring>
+		<penalty valence="2">64</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">64</penalty>
+	</entry>
+	<entry id="182">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D5])</smartstring>
+		<penalty valence="5">0</penalty>
+	</entry>
+	<entry id="191"><!-- for charged O- -->	
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([#8D1-])</smartstring>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">32</penalty>
+	</entry>
+	<entry id="192">
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([$([#8D1](~[#6D3]~[#8D1,#16D1]))])</smartstring>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">0</penalty>
+	</entry>
+	<entry id="19">
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([#7D3](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])) AND element(O)</smartstring>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">1</penalty>
+	</entry>
+	<entry id="20">
+		<elementstring>O</elementstring>
+		<smartstring> SMARTS([#8D1])</smartstring> 
+		<penalty valence="1">1</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="21">
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([#8D2])</smartstring> 
+		<penalty valence="1">32</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="211">
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([#8D3])</smartstring>
+		<penalty valence="3">0</penalty>
+	</entry>
+	<entry id="22">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS(#15D1)</smartstring>
+		<penalty valence="2">2</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">32</penalty>
+	</entry>
+	<entry id="23">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS(#15D2)</smartstring>
+		<penalty valence="2">4</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">2</penalty>
+	</entry>
+	<entry id="24">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS(#15D3)</smartstring>
+		<penalty valence="2">32</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">2</penalty>
+	</entry>	
+	<entry id="251">
+		<elementstring>P</elementstring>
+		<!-- Note: this is _SLOW_ -->
+		<smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1,#8D1-,#16D1-])(~[#8D1-,#16D1-]))])</smartstring>
+		<penalty valence="5">0</penalty>
+		<penalty valence="6">32</penalty>
+	</entry>
+	<entry id="25">
+		<elementstring>P</elementstring>
+		<!-- Note: this is _SLOW_ -->
+		<smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])(~[#8D1,#16D1]))])</smartstring>
+		<penalty valence="5">32</penalty>
+		<penalty valence="6">0</penalty>
+		<penalty valence="7">32</penalty>
+	</entry>
+	<entry id="26">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="6">32</penalty>
+		<penalty valence="7">0</penalty>
+	</entry>
+	<entry id="27">
+		<elementstring>P</elementstring>
+		<!-- This rule should be the last PD4 rule because it should only match when the other rules fail! -->
+		<smartstring>SMARTS(#15D4)</smartstring>
+		<penalty valence="3">64</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">0</penalty>
+		<penalty valence="6">32</penalty>
+	</entry>
+	<entry id="28">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#7D3](~[#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])) AND element(S)</smartstring>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">1</penalty>
+		</entry>
+	<entry id="291">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([$([#16D1](~[#6D3]~[#8D1,#16D1]))])</smartstring>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">0</penalty>
+	</entry>
+	<entry id="29">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D1])</smartstring>
+		<penalty valence="1">2</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="30">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D2])</smartstring>
+		<penalty valence="1">2</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="31">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D3])</smartstring>
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+		<penalty valence="5">2</penalty>
+		<penalty valence="6">2</penalty>
+	</entry>
+	<entry id="32">
+		<elementstring>S</elementstring>
+		<smartstring>	SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="6">0</penalty>
+		<penalty valence="7">32</penalty>
+		</entry>	
+	<entry id="331"><!--for a charged O in SO_4 -->
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([$([#16D4](~[#8D1-,#16D1-])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>		
+		<penalty valence="6">0</penalty>
+	</entry>
+	<entry id="33">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>		
+		<penalty valence="6">32</penalty>
+		<penalty valence="7">0</penalty>
+	</entry>
+	<entry id="34">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>
+		<penalty valence="6">32</penalty>
+		<penalty valence="7">0</penalty>
+	</entry>
+	<entry id="35">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D4])</smartstring>
+		<penalty valence="4">4</penalty>
+		<penalty valence="5">2</penalty>
+		<penalty valence="6">0</penalty>
+		</entry>	
+	<entry id="36">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D5])</smartstring>
+		<penalty valence="5">2</penalty>
+		<penalty valence="6">0</penalty>
+	</entry>
+<!-- The following rules are added to cope with ions -->
+	<entry id="40">
+		<elementstring>Li</elementstring>
+		<smartstring>SMARTS([#3])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="41">
+		<elementstring>Na</elementstring>
+		<smartstring>SMARTS([#11])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="42">
+		<elementstring>Mg</elementstring>
+		<smartstring>SMARTS([#12])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="43">
+		<elementstring>K</elementstring>
+		<smartstring>SMARTS([#19])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="44">
+		<elementstring>Ca</elementstring>
+		<smartstring>SMARTS([#20])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="45">
+		<elementstring>Cu</elementstring>
+		<smartstring>SMARTS([#29])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="46">
+		<elementstring>Zn</elementstring>
+		<smartstring>SMARTS([#30])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="47">
+		<elementstring>Fe</elementstring>
+		<smartstring>SMARTS([#26])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="48">
+		<elementstring>Cl</elementstring>
+		<smartstring>SMARTS([#17-])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="49">
+		<elementstring>Cl</elementstring>
+		<smartstring>SMARTS([#17])</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>	
+		<penalty valence="3">128</penalty>
+		<penalty valence="4">128</penalty>
+	</entry>
+</table>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/BondOrderGAFF.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,306 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<table>
+	<!-- 	This file supplies penalty scores for different 
+	  		atom types in bond type perception accoring to 
+	 								 	
+	 				Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and 
+	 				bond type perception in molecular mechanical calculations". Journal of 
+	 				Molecular Graphics and Modelling , 25, 2006, 247260	
+
+				A penalty score of 0 means that the corresponding valence is optimal.
+				Note that the first matching entry is taken as the final atom type.
+
+				Note that in the SMARTS strings we use atomic numbers rather than symbols (e.g. #8 instead of O).
+				The reason is that wrongly assigned aromatic bonds in the input would lead to failure to identify the
+				right rule!
+
+	 			Rev 14.12.2007  Conversion was done by Anna Dehof
+ -->	
+	<entry id="1">
+		<elementstring>H</elementstring>
+		<smartstring>SMARTS([#1])</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="2">
+		<elementstring>F</elementstring>
+		<smartstring>SMARTS(F)</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="3">
+		<elementstring>Cl</elementstring>
+		<smartstring>SMARTS(Cl)</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="4">
+		<elementstring>Br</elementstring>
+		<smartstring>SMARTS(Br)</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="5">
+		<elementstring>I</elementstring>
+		<smartstring>SMARTS(I)</smartstring>
+		<penalty valence="0">64</penalty>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">64</penalty>
+	</entry>
+	<entry id="6">
+		<elementstring>C</elementstring>
+		<smartstring>SMARTS([$([#6D1](~[#7D2]))])</smartstring>
+		<!--SMARTS([CD1]~[ND2]) AND element(C)</smartstring> -->
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">32</penalty>
+	</entry>
+	<entry id="7">
+		<elementstring>C</elementstring>
+		<smartstring>SMARTS([#6D1])</smartstring>
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+		<penalty valence="5">32</penalty>
+	</entry>
+	<entry id="8">
+		<elementstring>C</elementstring>
+		<smartstring>SMARTS([$([#6D3](~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>
+		<penalty valence="4">32</penalty>
+		<penalty valence="5">0</penalty>
+		<penalty valence="6">32</penalty>
+	</entry>
+	<entry id="9">
+		<elementstring>C</elementstring>
+		<smartstring>SMARTS([#6])</smartstring>
+		<penalty valence="2">64</penalty>
+		<penalty valence="3">32</penalty>
+		<penalty valence="4">0</penalty>
+		<penalty valence="5">32</penalty>
+		<penalty valence="6">64</penalty>
+	</entry>
+	<entry id="10">
+		<elementstring>Si</elementstring>
+		<smartstring>SMARTS([#14])</smartstring>
+		<penalty valence="4">0</penalty>
+	</entry>
+	<entry id="11">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([$([#7D1](~[#7D2]))])</smartstring>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">0</penalty>
+	</entry>
+	<entry id="12">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D1])</smartstring>
+		<penalty valence="2">3</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">32</penalty>
+	</entry>
+	<entry id="13">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([$([#7D2](~[#7D1]))])</smartstring>
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+	</entry>
+	<entry id="14">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D2])</smartstring>
+		<penalty valence="2">4</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">2</penalty>
+	</entry>
+	<entry id="15">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])~[#8D1,#16D1])])</smartstring>
+		<penalty valence="3">64</penalty>
+		<penalty valence="4">32</penalty>
+		<penalty valence="5">0</penalty>
+		<penalty valence="6">32</penalty>
+	</entry>
+	<entry id="16">
+		<elementstring>N</elementstring>
+		<!-- <smartstring>SMARTS([$(*OD1)&amp;$(*aR)&amp;n]) OR SMARTS([$(*OD1);$(*R);N])</smartstring> -->	
+		<smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+	</entry>
+	<entry id="17">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D3])</smartstring>
+		<penalty valence="2">32</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">2</penalty>
+	</entry>
+	<entry id="18">
+		<elementstring>N</elementstring>
+		<smartstring>SMARTS([#7D4])</smartstring>
+		<penalty valence="2">64</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">64</penalty>
+	</entry>
+	<entry id="19">
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([#7D3](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])) AND element(O)</smartstring>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">1</penalty>
+	</entry>
+	<entry id="20">
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([#8D1])</smartstring>
+		<penalty valence="1">1</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="21">
+		<elementstring>O</elementstring>
+		<smartstring>SMARTS([#8D2])</smartstring>
+		<penalty valence="1">32</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="22">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS(#15D1)</smartstring>
+		<penalty valence="2">2</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">32</penalty>
+	</entry>
+	<entry id="23">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS(#15D2)</smartstring>
+		<penalty valence="2">4</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">2</penalty>
+	</entry>
+	<entry id="24">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS(#15D3)</smartstring>
+		<penalty valence="2">32</penalty>
+		<penalty valence="3">0</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">2</penalty>
+	</entry>
+	<entry id="25">
+		<elementstring>P</elementstring>
+		<!-- Note: this is _SLOW_ -->
+		<smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])(~[#8D1,#16D1]))])</smartstring>
+		<penalty valence="5">32</penalty>
+		<penalty valence="6">0</penalty>
+		<penalty valence="7">32</penalty>
+	</entry>
+	<entry id="26">
+		<elementstring>P</elementstring>
+		<smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="6">32</penalty>
+		<penalty valence="7">0</penalty>
+	</entry>
+	<entry id="27">
+		<elementstring>P</elementstring>
+		<!-- This rule should be the last PD4 rule because it should only match when the other rules fail! -->
+		<smartstring>SMARTS(#15D4)</smartstring>
+		<penalty valence="3">64</penalty>
+		<penalty valence="4">1</penalty>
+		<penalty valence="5">0</penalty>
+		<penalty valence="6">32</penalty>
+	</entry>
+	<entry id="28">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#7D3](~[#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1])) AND element(S)</smartstring>
+		<penalty valence="1">0</penalty>
+		<penalty valence="2">1</penalty>
+	</entry>
+	<entry id="29">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D1])</smartstring>
+		<penalty valence="1">2</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="30">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D2])</smartstring>
+		<!-- These are the penalties given in the GAFF - paper; unfortunately, the values implemented in antechamber are different!		
+		<penalty valence="1">32</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">32</penalty>
+		<penalty valence="4">1</penalty> -->
+		<penalty valence="1">2</penalty>
+		<penalty valence="2">0</penalty>
+		<penalty valence="3">64</penalty>
+	</entry>
+	<entry id="31">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D3])</smartstring>
+		<penalty valence="3">1</penalty>
+		<penalty valence="4">0</penalty>
+		<penalty valence="5">2</penalty>
+		<penalty valence="6">2</penalty>
+	</entry>
+	<entry id="32">
+		<elementstring>S</elementstring>
+		<smartstring>	SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1])(~[!#8&amp;!#16,!D1]))])</smartstring>
+		<penalty valence="6">0</penalty>
+		<penalty valence="7">32</penalty>
+	</entry>
+	<entry id="33">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&amp;!#16,!D1]))])</smartstring>		
+		<penalty valence="6">32</penalty>
+		<penalty valence="7">0</penalty>
+	</entry>
+	<entry id="34">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>
+		<penalty valence="6">32</penalty>
+		<penalty valence="7">0</penalty>
+	</entry>
+	<entry id="35">
+		<elementstring>S</elementstring>
+		<smartstring>SMARTS([#16D4])</smartstring>
+		<penalty valence="4">4</penalty>
+		<penalty valence="5">2</penalty>
+		<penalty valence="6">0</penalty>
+	</entry>
+	<!-- The following rules are added to cope with ions -->
+	<entry id="40">
+		<elementstring>Li</elementstring>
+		<smartstring>SMARTS([#3])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="41">
+		<elementstring>Na</elementstring>
+		<smartstring>SMARTS([#11])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="42">
+		<elementstring>Mg</elementstring>
+		<smartstring>SMARTS([#12])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="43">
+		<elementstring>K</elementstring>
+		<smartstring>SMARTS([#19])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="44">
+		<elementstring>Ca</elementstring>
+		<smartstring>SMARTS([#20])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="45">
+		<elementstring>Cu</elementstring>
+		<smartstring>SMARTS([#29])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+	<entry id="46">
+		<elementstring>Zn</elementstring>
+		<smartstring>SMARTS([#30])</smartstring>
+		<penalty valence="0">0</penalty>
+	</entry>
+
+</table>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/bond_lengths.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,257 @@
+<node>BondLengthsDB
+	<node>1
+		<node>Names
+			<node>Hydrogen</node>
+			<node>H</node>
+		</node>
+		<node>Partners
+			<node>6
+				<node>BondLengths
+					<node>max<value>1.15</value></node>
+					<node>single<value>1.09</value></node>
+					<node>min<value>0.95</value></node>
+				</node>
+			</node>
+			<node>7
+				<node>BondLengths
+					<node>max<value>1.10</value></node>
+					<node>single<value>1.03</value></node>
+					<node>min<value>0.9</value></node>
+				</node>
+			</node>
+			<node>8
+				<node>BondLengths
+					<node>max<value>1.1</value></node>
+					<node>single<value>0.96</value></node>
+					<node>min<value>0.9</value></node>
+				</node>
+			</node>
+			<node>15
+				<node>BondLengths
+					<node>max<value>1.5</value></node>
+					<node>single<value>1.0</value></node>
+					<node>min<value>0.9</value></node>
+				</node>
+			</node>
+			<node>16
+				<node>BondLengths
+					<node>max<value>1.5</value></node>
+					<node>single<value>1.34</value></node>
+					<node>min<value>1.1</value></node>
+				</node>
+			</node>
+		</node>
+	</node>
+	<node>6
+		<node>Names
+			<node>Carbon</node>
+			<node>C</node>
+		</node>
+		<node>Partners
+			<node>6
+				<node>BondLengths
+					<node>max<value>1.75</value></node>
+					<node>single<value>1.47</value></node>
+					<node>aromatic<value>1.39</value></node>
+					<node>double<value>1.34</value></node>
+					<node>triple<value>1.18</value></node>
+					<node>min<value>1.15</value></node>
+				</node>
+			</node>
+			<node>7
+				<node>BondLengths
+					<node>max<value>1.65</value></node>
+					<node>single<value>1.38</value></node>
+					<node>aromatic<value>1.33</value></node>
+					<node>double<value>1.29</value></node>
+					<node>triple<value>1.15</value></node>
+					<node>min<value>1.1</value></node>
+				</node>
+			</node>
+			<node>8
+				<node>BondLengths
+					<node>max<value>1.55</value></node>
+					<node>single<value>1.42</value></node>
+					<node>double<value>1.20</value></node>
+					<node>min<value>1.10</value></node>
+				</node>
+			</node>
+			<node>9
+				<node>BondLengths
+					<node>max<value>1.45</value></node>
+					<node>single<value>1.38</value></node>
+					<node>min<value>1.0</value></node>
+				</node>
+			</node>
+			<node>15
+				<node>BondLengths
+					<node>max<value>1.95</value></node>
+					<node>single<value>1.8</value></node>
+					<node>min<value>1.7</value></node>
+				</node>
+			</node>
+			<node>16
+				<node>BondLengths
+					<node>max<value>1.95</value></node>
+					<node>single<value>1.70</value></node>
+					<node>double<value>1.63</value></node>
+					<node>min<value>1.5</value></node>
+				</node>
+			</node>
+			<node>17
+				<node>BondLengths
+					<node>max<value>1.9</value></node>
+					<node>single<value>1.8</value></node>
+					<node>min<value>1.0</value></node>
+				</node>
+			</node>
+			<node>35
+				<node>BondLengths
+					<node>max<value>2.05</value></node>
+					<node>single<value>1.96</value></node>
+					<node>min<value>1.0</value></node>
+				</node>
+			</node>
+			<node>53
+				<node>BondLengths
+					<node>max<value>2.3</value></node>
+					<node>single<value>2.1</value></node>
+					<node>min<value>1.0</value></node>
+				</node>
+			</node>
+		</node>
+	</node>
+	<node>7
+		<node>Names
+			<node>Nitrogen</node>
+			<node>N</node>
+		</node>
+		<node>Partners
+			<node>7
+				<node>BondLengths
+					<node>max<value>1.55</value></node>
+					<node>single<value>1.40</value></node>
+					<node>aromatic<value>1.32</value></node>
+					<node>double<value>1.22</value></node>
+					<node>min<value>1.0</value></node>
+				</node>
+			</node>
+			<node>8
+				<node>BondLengths
+					<node>max<value>1.5</value></node>
+					<node>single<value>1.4</value></node>
+					<node>double<value>1.21</value></node>
+					<node>min<value>1.15</value></node>
+				</node>
+			</node>
+			<node>9
+				<node>BondLengths
+					<node>max<value>1.5</value></node>
+					<node>single<value>1.35</value></node>
+					<node>min<value>1.25</value></node>
+				</node>
+			</node>
+			<node>15
+				<node>BondLengths
+					<node>max<value>1.8</value></node>
+					<node>single<value>1.68</value></node>
+					<node>aromatic<value>1.60</value></node>
+					<node>double<value>1.58</value></node>
+					<node>min<value>1.5</value></node>
+				</node>
+			</node>
+			<node>16
+				<node>BondLengths
+					<node>max<value>1.80</value></node>
+					<node>single<value>1.65</value></node>
+					<node>aromatic<value>1.56</value></node>
+					<node>double<value>1.54</value></node>
+					<node>min<value>1.50</value></node>
+				</node>
+			</node>
+			<node>17
+				<node>BondLengths
+					<node>max<value>1.85</value></node>
+					<node>single<value>1.74</value></node>
+					<node>min<value>1.65</value></node>
+				</node>
+			</node>
+			<node>35
+				<node>BondLengths
+					<node>max<value>2.0</value></node>
+					<node>single<value>1.84</value></node>
+					<node>min<value>1.7</value></node>
+				</node>
+			</node>
+		</node>
+	</node>
+	<node>8
+		<node>Names
+			<node>Oxygen</node>
+			<node>O</node>
+		</node>
+		<node>Partners
+			<node>8
+				<node>BondLengths
+					<node>max<value>1.55</value></node>
+					<node>single<value>1.47</value></node>
+					<node>min<value>1.40</value></node>
+				</node>
+			</node>
+			<node>15
+				<node>BondLengths
+					<node>max<value>1.75</value></node>
+					<node>single<value>1.59</value></node>
+					<node>double<value>1.49</value></node>
+					<node>min<value>1.40</value></node>
+				</node>
+			</node>
+			<node>16
+				<node>BondLengths
+					<node>max<value>1.75</value></node>
+					<node>single<value>1.56</value></node>
+					<node>double<value>1.43</value></node>
+					<node>min<value>1.38</value></node>
+				</node>
+			</node>
+		</node>
+	</node>
+	<node>15
+		<node>Names
+			<node>Phosphorus</node>
+			<node>P</node>
+		</node>
+		<node>Partners
+			<node>15
+				<node>BondLengths
+					<node>max<value>2.3</value></node>
+					<node>single<value>2.2</value></node>
+					<node>double<value>2.0</value></node>
+					<node>min<value>1.9</value></node>
+				</node>
+			</node>
+			<node>16
+				<node>BondLengths
+					<node>max<value>2.2</value></node>
+					<node>double<value>1.95</value></node>
+					<node>min<value>1.85</value></node>
+				</node>
+			</node>
+		</node>
+	</node>
+	<node>16
+		<node>Names
+			<node>Sulfur</node>
+			<node>S</node>
+		</node>
+		<node>Partners
+			<node>16
+				<node>BondLengths
+					<node>max<value>2.2</value></node>
+					<node>single<value>2.07</value></node>
+					<node>min<value>1.9</value></node>
+				</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/bond_lengths_mmff94.ini	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,1505 @@
+[BondLengths]
+key:I key:deg_I key:J key:deg_J key:order value:r0
+@unit_r0=Angstrom
+;
+;
+;	 I   deg_I   J   deg_J   order      r0    
+	--- ------- --- ------- ------- --------- 
+	 C     1     C     1       1     1.508
+	 C     1     C     2       1     1.508
+	 C     1     C     3       1     1.508
+	 C     1     C     4       1     1.5086
+	 C     2     C     1       1     1.508
+	 C     2     C     2       1     1.5086
+	 C     2     C     3       1     1.5072
+	 C     2     C     4       1     1.5093
+	 C     3     C     1       1     1.508
+	 C     3     C     2       1     1.5072
+	 C     3     C     3       1     1.5066
+	 C     3     C     4       1     1.51
+	 C     4     C     1       1     1.5086
+	 C     4     C     2       1     1.5093
+	 C     4     C     3       1     1.51
+	 C     4     C     4       1     1.5121
+	 C     1     C     1       2     1.333
+	 C     1     C     2       2     1.333
+	 C     1     C     3       2     1.3333
+	 C     1     C     4       2     1.344
+	 C     2     C     1       2     1.333
+	 C     2     C     2       2     1.3333
+	 C     2     C     3       2     1.3341
+	 C     2     C     4       2     1.3453
+	 C     3     C     1       2     1.3333
+	 C     3     C     2       2     1.3341
+	 C     3     C     3       2     1.3358
+	 C     3     C     4       2     1.3477
+	 C     4     C     1       2     1.344
+	 C     4     C     2       2     1.3453
+	 C     4     C     3       2     1.3477
+	 C     4     C     4       2     1.3624
+	 C     1     C     1       3     1.192
+	 C     1     C     2       3     1.4529
+	 C     1     C     3       3     1.192
+	 C     1     C     4       3     1.1917
+	 C     2     C     1       3     1.452
+	 C     2     C     2       3     1.211
+	 C     2     C     3       3     1.3034
+	 C     2     C     4       3     1.4768
+	 C     3     C     1       3     1.192
+	 C     3     C     2       3     1.299
+	 C     3     C     3       3     1.3358
+	 C     3     C     4       3     1.4835
+	 C     4     C     1       3     1.1917
+	 C     4     C     2       3     1.468
+	 C     4     C     3       3     1.4833
+	 C     4     C     4       3     1.5121
+	 C     1     N     1       1     1.4556
+	 C     1     N     2       1     1.4556
+	 C     1     N     3       1     1.451
+	 C     1     N     4       1     1.4801
+	 C     1     N     5       1     1.5343
+	 C     2     N     1       1     1.4556
+	 C     2     N     3       1     1.4508
+	 C     2     N     4       1     1.4808
+	 C     3     N     1       1     1.4556
+	 C     3     N     3       1     1.4507
+	 C     3     N     4       1     1.4814
+	 C     4     N     1       1     1.4545
+	 C     4     N     3       1     1.452
+	 C     4     N     4       1     1.4757
+	 C     1     N     1       2     1.29
+	 C     1     N     2       2     1.29
+	 C     1     N     3       2     1.28
+	 C     1     N     4       2     1.2913
+	 C     1     N     5       2     1.2904
+	 C     2     N     1       2     1.29
+	 C     2     N     2       2     1.289
+	 C     2     N     3       2     1.2811
+	 C     2     N     4       2     1.2904
+	 C     2     N     5       2     1.2901
+	 C     3     N     1       2     1.2866
+	 C     3     N     2       2     1.2868
+	 C     3     N     3       2     1.2798
+	 C     3     N     4       2     1.2881
+	 C     3     N     5       2     1.2904
+	 C     4     N     1       2     1.3265
+	 C     4     N     2       2     1.3277
+	 C     4     N     3       2     1.29
+	 C     4     N     4       2     1.3347
+	 C     4     N     5       2     1.3364
+	 C     1     N     1       3     1.3756
+	 C     1     N     2       3     1.2075
+	 C     1     N     3       3     1.3756
+	 C     1     N     4       3     1.4018
+	 C     1     N     5       3     1.4163
+	 C     2     N     1       3     1.1897
+	 C     3     N     1       3     1.1154
+	 C     4     N     1       3     1.3758
+	 C     1     O     1       1     1.402
+	 C     1     O     2       1     1.418
+	 C     1     O     3       1     1.402
+	 C     2     O     1       1     1.402
+	 C     2     O     2       1     1.4184
+	 C     2     O     3       1     1.4023
+	 C     3     O     1       1     1.402
+	 C     3     O     2       1     1.4176
+	 C     3     O     3       1     1.4025
+	 C     4     O     1       1     1.3246
+	 C     4     O     2       1     1.4157
+	 C     4     O     3       1     1.4014
+	 C     1     O     1       2     1.222
+	 C     1     O     2       2     1.29
+	 C     1     O     3       2     1.222
+	 C     2     O     1       2     1.222
+	 C     2     O     2       2     1.2905
+	 C     3     O     1       2     1.2246
+	 C     3     O     2       2     1.2928
+	 C     4     O     1       2     1.2649
+	 C     4     O     2       2     1.3136
+	 C     1     O     1       3     1.062
+	 C     1     O     2       3     1.062
+	 C     1     O     3       3     1.062
+	 C     2     O     1       3     1.3947
+	 C     2     O     3       3     1.4092
+	 C     3     O     1       3     1.0599
+	 C     3     O     3       3     1.3525
+	 C     4     O     1       3     1.0617
+	 C     4     O     3       3     1.4161
+	 C     1     P     1       1     1.8346
+	 C     1     P     2       1     1.8347
+	 C     1     P     3       1     1.83
+	 C     1     P     4       1     1.7992
+	 C     1     P     5       1     2.0222
+	 C     1     P     6       1     2.2431
+	 C     2     P     1       1     1.8347
+	 C     2     P     3       1     1.8304
+	 C     2     P     4       1     1.7982
+	 C     3     P     1       1     1.8347
+	 C     3     P     3       1     1.8299
+	 C     3     P     4       1     1.7971
+	 C     4     P     1       1     1.8321
+	 C     4     P     3       1     1.8344
+	 C     4     P     4       1     1.7955
+	 C     1     P     1       2     1.6347
+	 C     1     P     2       2     1.71
+	 C     1     P     3       2     1.6346
+	 C     1     P     4       2     1.6475
+	 C     1     P     5       2     1.6547
+	 C     1     P     6       2     1.6704
+	 C     2     P     1       2     1.6347
+	 C     2     P     2       2     1.7099
+	 C     3     P     1       2     1.6347
+	 C     3     P     2       2     1.7011
+	 C     4     P     1       2     1.6743
+	 C     4     P     2       2     1.7554
+	 C     1     P     1       3     1.4947
+	 C     1     P     2       3     1.4947
+	 C     1     P     3       3     1.4947
+	 C     1     P     4       3     1.5018
+	 C     1     P     5       3     1.5058
+	 C     1     P     6       3     1.5137
+	 C     2     P     1       3     1.7624
+	 C     3     P     1       3     1.4947
+	 C     4     P     1       3     1.494
+	 C     1     S     1       1     1.801
+	 C     1     S     2       1     1.805
+	 C     1     S     3       1     1.805
+	 C     1     S     4       1     1.7882
+	 C     1     S     5       1     1.779
+	 C     1     S     6       1     1.7789
+	 C     2     S     1       1     1.801
+	 C     2     S     2       1     1.8055
+	 C     2     S     3       1     1.805
+	 C     2     S     4       1     1.7875
+	 C     2     S     5       1     1.778
+	 C     2     S     6       1     1.7802
+	 C     3     S     1       1     1.801
+	 C     3     S     2       1     1.8052
+	 C     3     S     3       1     1.8051
+	 C     3     S     4       1     1.7868
+	 C     3     S     5       1     1.777
+	 C     3     S     6       1     1.777
+	 C     4     S     1       1     1.8265
+	 C     4     S     2       1     1.804
+	 C     4     S     3       1     1.8042
+	 C     4     S     4       1     1.786
+	 C     4     S     5       1     1.7765
+	 C     4     S     6       1     1.7805
+	 C     1     S     1       2     1.665
+	 C     1     S     2       2     1.665
+	 C     1     S     3       2     1.665
+	 C     1     S     4       2     1.6803
+	 C     1     S     5       2     1.6889
+	 C     1     S     6       2     1.7087
+	 C     2     S     1       2     1.665
+	 C     3     S     1       2     1.6701
+	 C     4     S     1       2     1.7243
+	 C     1     S     1       3     1.4584
+	 C     1     S     2       3     1.4584
+	 C     1     S     3       3     1.4584
+	 C     1     S     4       3     1.4502
+	 C     1     S     5       3     1.4442
+	 C     1     S     6       3     1.4468
+	 C     2     S     1       3     1.7357
+	 C     2     S     2       3     1.7594
+	 C     2     S     3       3     1.7704
+	 C     2     S     4       3     1.741
+	 C     2     S     5       3     1.7226
+	 C     2     S     6       3     1.7233
+	 C     3     S     1       3     1.7187
+	 C     3     S     2       3     1.7203
+	 C     3     S     3       3     1.7213
+	 C     3     S     4       3     1.6958
+	 C     3     S     5       3     1.6865
+	 C     3     S     6       3     1.6844
+	 C     4     S     1       3     1.8039
+	 C     4     S     2       3     1.804
+	 C     4     S     3       3     1.8042
+	 C     4     S     4       3     1.786
+	 C     4     S     5       3     1.7765
+	 C     4     S     6       3     1.7805
+	 C     1     H     1       1     1.093
+	 C     2     H     1       1     1.093
+	 C     3     H     1       1     1.093
+	 C     4     H     1       1     1.0922
+	 C     1     H     1       2     1.083
+	 C     2     H     1       2     1.083
+	 C     3     H     1       2     1.0826
+	 C     4     H     1       2     1.0922
+	 C     1     H     1       3     1.0907
+	 C     2     H     1       3     1.0701
+	 C     3     H     1       3     1.0826
+	 C     4     H     1       3     1.0922
+	 C     1     Cl     1       1     1.773
+	 C     1     Cl     2       1     1.773
+	 C     1     Cl     3       1     1.773
+	 C     1     Cl     4       1     1.7993
+	 C     2     Cl     1       1     1.773
+	 C     3     Cl     1       1     1.773
+	 C     4     Cl     1       1     1.767
+	 C     1     Cl     1       2     1.72
+	 C     1     Cl     2       2     1.72
+	 C     1     Cl     3       2     1.72
+	 C     1     Cl     4       2     1.7425
+	 C     2     Cl     1       2     1.72
+	 C     3     Cl     1       2     1.7018
+	 C     4     Cl     1       2     1.767
+	 C     1     Cl     1       3     1.4231
+	 C     1     Cl     2       3     1.4231
+	 C     1     Cl     3       3     1.4231
+	 C     1     Cl     4       3     1.4294
+	 C     2     Cl     1       3     1.774
+	 C     3     Cl     1       3     1.7018
+	 C     4     Cl     1       3     1.767
+	 N     1     C     1       1     1.4556
+	 N     1     C     2       1     1.4556
+	 N     1     C     3       1     1.4556
+	 N     1     C     4       1     1.4545
+	 N     2     C     1       1     1.4556
+	 N     3     C     1       1     1.451
+	 N     3     C     2       1     1.4508
+	 N     3     C     3       1     1.4507
+	 N     3     C     4       1     1.452
+	 N     4     C     1       1     1.4801
+	 N     4     C     2       1     1.4808
+	 N     4     C     3       1     1.4814
+	 N     4     C     4       1     1.4757
+	 N     5     C     1       1     1.5343
+	 N     1     C     1       2     1.29
+	 N     1     C     2       2     1.29
+	 N     1     C     3       2     1.2866
+	 N     1     C     4       2     1.3265
+	 N     2     C     1       2     1.29
+	 N     2     C     2       2     1.289
+	 N     2     C     3       2     1.2868
+	 N     2     C     4       2     1.3278
+	 N     3     C     1       2     1.28
+	 N     3     C     2       2     1.2811
+	 N     3     C     3       2     1.2798
+	 N     3     C     4       2     1.29
+	 N     4     C     1       2     1.2913
+	 N     4     C     2       2     1.2904
+	 N     4     C     3       2     1.2881
+	 N     4     C     4       2     1.3347
+	 N     5     C     1       2     1.2904
+	 N     5     C     2       2     1.29
+	 N     5     C     3       2     1.2894
+	 N     5     C     4       2     1.3364
+	 N     1     C     1       3     1.3756
+	 N     1     C     2       3     1.1897
+	 N     1     C     3       3     1.1154
+	 N     1     C     4       3     1.3758
+	 N     2     C     1       3     1.2047
+	 N     3     C     1       3     1.3756
+	 N     4     C     1       3     1.4018
+	 N     5     C     1       3     1.4163
+	 N     1     N     1       1     1.452
+	 N     1     N     2       1     1.452
+	 N     1     N     3       1     1.452
+	 N     1     N     4       1     1.4477
+	 N     1     N     5       1     1.559
+	 N     2     N     1       1     1.452
+	 N     3     N     1       1     1.452
+	 N     3     N     3       1     1.4347
+	 N     3     N     4       1     1.4209
+	 N     4     N     1       1     1.4477
+	 N     4     N     3       1     1.4209
+	 N     4     N     4       1     1.5959
+	 N     5     N     1       1     1.559
+	 N     1     N     1       2     1.243
+	 N     1     N     2       2     1.243
+	 N     1     N     3       2     1.3196
+	 N     1     N     4       2     1.2464
+	 N     1     N     5       2     1.2479
+	 N     2     N     1       2     1.243
+	 N     2     N     2       2     1.2458
+	 N     2     N     3       2     1.3274
+	 N     2     N     4       2     1.2558
+	 N     2     N     5       2     1.262
+	 N     3     N     1       2     1.3196
+	 N     3     N     2       2     1.3274
+	 N     3     N     3       2     1.2614
+	 N     3     N     4       2     1.3566
+	 N     3     N     5       2     1.3758
+	 N     4     N     1       2     1.2464
+	 N     4     N     2       2     1.2558
+	 N     4     N     3       2     1.3565
+	 N     4     N     4       2     1.2902
+	 N     4     N     5       2     1.3128
+	 N     5     N     1       2     1.2479
+	 N     5     N     2       2     1.262
+	 N     5     N     3       2     1.3758
+	 N     5     N     4       2     1.3128
+	 N     5     N     5       2     1.3457
+	 N     1     N     1       3     1.112
+	 N     1     N     2       3     1.1265
+	 N     1     N     3       3     1.112
+	 N     1     N     4       3     1.1212
+	 N     1     N     5       3     1.1263
+	 N     2     N     1       3     1.1265
+	 N     3     N     1       3     1.1121
+	 N     4     N     1       3     1.1212
+	 N     5     N     1       3     1.1263
+	 N     1     O     1       1     1.4175
+	 N     1     O     2       1     1.4175
+	 N     1     O     3       1     1.4175
+	 N     2     O     1       1     1.4175
+	 N     3     O     1       1     1.3875
+	 N     3     O     2       1     1.4537
+	 N     3     O     3       1     1.4468
+	 N     4     O     1       1     1.385
+	 N     4     O     2       1     1.4329
+	 N     4     O     3       1     1.4762
+	 N     5     O     1       1     1.4778
+	 N     1     O     1       2     1.235
+	 N     1     O     2       2     1.2175
+	 N     1     O     3       2     1.235
+	 N     2     O     1       2     1.235
+	 N     3     O     1       2     1.235
+	 N     4     O     1       2     1.2441
+	 N     5     O     1       2     1.2506
+	 N     1     O     1       3     1.3375
+	 N     1     O     2       3     1.3375
+	 N     1     O     3       3     1.3375
+	 N     2     O     1       3     1.4103
+	 N     3     O     1       3     1.3375
+	 N     4     O     1       3     1.3616
+	 N     5     O     1       3     1.376
+	 N     1     P     1       1     1.7389
+	 N     1     P     2       1     1.7389
+	 N     1     P     3       1     1.7389
+	 N     1     P     4       1     1.7303
+	 N     1     P     5       1     1.7713
+	 N     1     P     6       1     1.7981
+	 N     2     P     1       1     1.7389
+	 N     3     P     1       1     1.7389
+	 N     3     P     3       1     1.6998
+	 N     3     P     4       1     1.6531
+	 N     4     P     1       1     1.7339
+	 N     4     P     3       1     1.7493
+	 N     4     P     4       1     1.7184
+	 N     5     P     1       1     1.9769
+	 N     1     P     1       2     1.5389
+	 N     1     P     2       2     1.5389
+	 N     1     P     3       2     1.5389
+	 N     1     P     4       2     1.5479
+	 N     1     P     5       2     1.5531
+	 N     1     P     6       2     1.5625
+	 N     2     P     1       2     1.5389
+	 N     3     P     1       2     1.5389
+	 N     4     P     1       2     1.566
+	 N     5     P     1       2     1.58
+	 N     1     P     1       3     1.6589
+	 N     1     P     2       3     1.6589
+	 N     1     P     3       3     1.6589
+	 N     1     P     4       3     1.6736
+	 N     1     P     5       3     1.6823
+	 N     1     P     6       3     1.7
+	 N     2     P     1       3     1.6808
+	 N     3     P     1       3     1.6589
+	 N     4     P     1       3     1.7072
+	 N     5     P     1       3     1.7778
+	 N     1     S     1       1     1.7181
+	 N     1     S     2       1     1.7181
+	 N     1     S     3       1     1.7181
+	 N     1     S     4       1     1.6908
+	 N     1     S     5       1     1.6742
+	 N     1     S     6       1     1.6812
+	 N     2     S     1       1     1.7181
+	 N     3     S     1       1     1.652
+	 N     3     S     2       1     1.6536
+	 N     3     S     3       1     1.6568
+	 N     3     S     4       1     1.6347
+	 N     3     S     5       1     1.6265
+	 N     3     S     6       1     1.6263
+	 N     4     S     1       1     1.7132
+	 N     4     S     2       1     1.7215
+	 N     4     S     3       1     1.7302
+	 N     4     S     4       1     1.7048
+	 N     4     S     5       1     1.7001
+	 N     4     S     6       1     1.7058
+	 N     5     S     1       1     1.8398
+	 N     1     S     1       2     1.5181
+	 N     1     S     2       2     1.5181
+	 N     1     S     3       2     1.5181
+	 N     1     S     4       2     1.5063
+	 N     1     S     5       2     1.4972
+	 N     1     S     6       2     1.5004
+	 N     2     S     1       2     1.5181
+	 N     3     S     1       2     1.5181
+	 N     3     S     2       2     1.5188
+	 N     3     S     3       2     1.5191
+	 N     3     S     4       2     1.5103
+	 N     3     S     5       2     1.5064
+	 N     3     S     6       2     1.5047
+	 N     4     S     1       2     1.5442
+	 N     5     S     1       2     1.5591
+	 N     1     S     1       3     1.6381
+	 N     1     S     2       3     1.6381
+	 N     1     S     3       3     1.6381
+	 N     1     S     4       3     1.6171
+	 N     1     S     5       3     1.607
+	 N     1     S     6       3     1.6054
+	 N     2     S     1       3     1.7147
+	 N     3     S     1       3     1.6381
+	 N     4     S     1       3     1.6849
+	 N     5     S     1       3     1.7141
+	 N     1     H     1       1     1.0189
+	 N     2     H     1       1     1.0189
+	 N     3     H     1       1     1.019
+	 N     4     H     1       1     1.0268
+	 N     5     H     1       1     1.0449
+	 N     1     H     1       2     1.0189
+	 N     2     H     1       2     1.0189
+	 N     3     H     1       2     1.028
+	 N     4     H     1       2     1.0319
+	 N     5     H     1       2     1.0449
+	 N     1     H     1       3     1.0189
+	 N     2     H     1       3     1.0268
+	 N     3     H     1       3     1.0189
+	 N     4     H     1       3     1.0319
+	 N     5     H     1       3     1.0449
+	 N     1     Cl     1       1     1.7292
+	 N     1     Cl     2       1     1.7291
+	 N     1     Cl     3       1     1.7292
+	 N     1     Cl     4       1     1.7485
+	 N     2     Cl     1       1     1.7292
+	 N     3     Cl     1       1     1.761
+	 N     4     Cl     1       1     1.725
+	 N     5     Cl     1       1     1.8244
+	 N     1     Cl     1       2     1.5292
+	 N     1     Cl     2       2     1.5292
+	 N     1     Cl     3       2     1.5292
+	 N     1     Cl     4       2     1.5376
+	 N     2     Cl     1       2     1.5292
+	 N     3     Cl     1       2     1.5292
+	 N     4     Cl     1       2     1.5515
+	 N     5     Cl     1       2     1.5638
+	 N     1     Cl     1       3     1.6492
+	 N     1     Cl     2       3     1.6492
+	 N     1     Cl     3       3     1.6492
+	 N     1     Cl     4       3     1.6631
+	 N     2     Cl     1       3     1.6958
+	 N     3     Cl     1       3     1.6492
+	 N     4     Cl     1       3     1.6884
+	 N     5     Cl     1       3     1.7114
+	 O     1     C     1       1     1.402
+	 O     1     C     2       1     1.402
+	 O     1     C     3       1     1.402
+	 O     1     C     4       1     1.3246
+	 O     2     C     1       1     1.418
+	 O     2     C     2       1     1.4184
+	 O     2     C     3       1     1.4184
+	 O     2     C     4       1     1.4157
+	 O     3     C     1       1     1.402
+	 O     3     C     2       1     1.4023
+	 O     3     C     3       1     1.4025
+	 O     3     C     4       1     1.4019
+	 O     1     C     1       2     1.222
+	 O     1     C     2       2     1.222
+	 O     1     C     3       2     1.2246
+	 O     1     C     4       2     1.2649
+	 O     2     C     1       2     1.29
+	 O     2     C     2       2     1.2905
+	 O     2     C     3       2     1.2928
+	 O     2     C     4       2     1.3136
+	 O     3     C     1       2     1.222
+	 O     1     C     1       3     1.062
+	 O     1     C     2       3     1.3947
+	 O     1     C     3       3     1.06
+	 O     1     C     4       3     1.0617
+	 O     2     C     1       3     1.062
+	 O     3     C     1       3     1.062
+	 O     3     C     2       3     1.4126
+	 O     3     C     3       3     1.3525
+	 O     3     C     4       3     1.4181
+	 O     1     N     1       1     1.4175
+	 O     1     N     2       1     1.4175
+	 O     1     N     3       1     1.3875
+	 O     1     N     4       1     1.385
+	 O     1     N     5       1     1.4778
+	 O     2     N     1       1     1.4175
+	 O     2     N     3       1     1.4538
+	 O     2     N     4       1     1.4329
+	 O     3     N     1       1     1.4175
+	 O     3     N     3       1     1.4468
+	 O     3     N     4       1     1.4762
+	 O     1     N     1       2     1.235
+	 O     1     N     2       2     1.235
+	 O     1     N     3       2     1.235
+	 O     1     N     4       2     1.2441
+	 O     1     N     5       2     1.2506
+	 O     2     N     1       2     1.2175
+	 O     3     N     1       2     1.235
+	 O     1     N     1       3     1.3375
+	 O     1     N     2       3     1.4103
+	 O     1     N     3       3     1.3374
+	 O     1     N     4       3     1.3616
+	 O     1     N     5       3     1.376
+	 O     2     N     1       3     1.3375
+	 O     3     N     1       3     1.3375
+	 O     1     O     1       1     1.432
+	 O     1     O     2       1     1.432
+	 O     1     O     3       1     1.432
+	 O     2     O     1       1     1.432
+	 O     2     O     2       1     1.4659
+	 O     2     O     3       1     1.4468
+	 O     3     O     1       1     1.432
+	 O     3     O     2       1     1.4468
+	 O     3     O     3       1     1.4631
+	 O     1     O     1       2     1.232
+	 O     1     O     2       2     1.232
+	 O     1     O     3       2     1.232
+	 O     2     O     1       2     1.232
+	 O     2     O     2       2     1.2369
+	 O     2     O     3       2     1.2375
+	 O     3     O     1       2     1.232
+	 O     3     O     2       2     1.2375
+	 O     3     O     3       2     1.4667
+	 O     1     O     1       3     1.092
+	 O     1     O     2       3     1.092
+	 O     1     O     3       3     1.092
+	 O     2     O     1       3     1.092
+	 O     3     O     1       3     1.092
+	 O     3     O     3       3     1.4667
+	 O     1     P     1       1     1.51
+	 O     1     P     2       1     1.51
+	 O     1     P     3       1     1.6467
+	 O     1     P     4       1     1.5102
+	 O     1     P     5       1     1.5119
+	 O     1     P     6       1     1.5149
+	 O     2     P     1       1     1.63
+	 O     2     P     2       1     1.6298
+	 O     2     P     3       1     1.6192
+	 O     2     P     4       1     1.6219
+	 O     2     P     5       1     1.6147
+	 O     2     P     6       1     1.6169
+	 O     3     P     1       1     1.6767
+	 O     3     P     2       1     1.6765
+	 O     3     P     3       1     1.6799
+	 O     3     P     4       1     1.6668
+	 O     3     P     5       1     1.6617
+	 O     3     P     6       1     1.6635
+	 O     1     P     1       2     1.4767
+	 O     1     P     2       2     1.4767
+	 O     1     P     3       2     1.4767
+	 O     1     P     4       2     1.474
+	 O     1     P     5       2     1.4732
+	 O     1     P     6       2     1.4742
+	 O     2     P     1       2     1.4767
+	 O     2     P     2       2     1.4766
+	 O     2     P     3       2     1.476
+	 O     2     P     4       2     1.4729
+	 O     2     P     5       2     1.4709
+	 O     2     P     6       2     1.4712
+	 O     3     P     1       2     1.63
+	 O     3     P     2       2     1.6298
+	 O     3     P     3       2     1.6293
+	 O     3     P     4       2     1.6213
+	 O     3     P     5       2     1.6135
+	 O     3     P     6       2     1.6154
+	 O     1     P     1       3     1.3367
+	 O     1     P     2       3     1.3367
+	 O     1     P     3       3     1.3367
+	 O     1     P     4       3     1.3349
+	 O     1     P     5       3     1.334
+	 O     1     P     6       3     1.3342
+	 O     2     P     1       3     1.3367
+	 O     3     P     1       3     1.63
+	 O     3     P     2       3     1.6298
+	 O     3     P     3       3     1.6293
+	 O     3     P     4       3     1.6213
+	 O     3     P     5       3     1.6135
+	 O     3     P     6       3     1.6154
+	 O     1     S     1       1     1.6632
+	 O     1     S     2       1     1.6632
+	 O     1     S     3       1     1.661
+	 O     1     S     4       1     1.6179
+	 O     1     S     5       1     1.6344
+	 O     1     S     6       1     1.633
+	 O     2     S     1       1     1.661
+	 O     2     S     2       1     1.6636
+	 O     2     S     3       1     1.6638
+	 O     2     S     4       1     1.6478
+	 O     2     S     5       1     1.6402
+	 O     2     S     6       1     1.6398
+	 O     3     S     1       1     1.6632
+	 O     3     S     2       1     1.6606
+	 O     3     S     3       1     1.6738
+	 O     3     S     4       1     1.6549
+	 O     3     S     5       1     1.6498
+	 O     3     S     6       1     1.6489
+	 O     1     S     1       2     1.5
+	 O     1     S     2       2     1.5
+	 O     1     S     3       2     1.5
+	 O     1     S     4       2     1.5008
+	 O     1     S     5       2     1.503
+	 O     1     S     6       2     1.5062
+	 O     2     S     1       2     1.4632
+	 O     3     S     1       2     1.5
+	 O     1     S     1       3     1.3232
+	 O     1     S     2       3     1.3232
+	 O     1     S     3       3     1.3232
+	 O     1     S     4       3     1.3194
+	 O     1     S     5       3     1.3167
+	 O     1     S     6       3     1.3164
+	 O     2     S     1       3     1.3232
+	 O     2     S     3       3     1.6638
+	 O     2     S     4       3     1.6478
+	 O     2     S     5       3     1.6402
+	 O     2     S     6       3     1.6398
+	 O     3     S     1       3     1.661
+	 O     3     S     2       3     1.6593
+	 O     3     S     3       3     1.6685
+	 O     3     S     4       3     1.6505
+	 O     3     S     5       3     1.6437
+	 O     3     S     6       3     1.6421
+	 O     1     H     1       1     0.97781
+	 O     2     H     1       1     0.969
+	 O     3     H     1       1     0.991
+	 O     1     H     1       2     0.97781
+	 O     2     H     1       2     0.987
+	 O     3     H     1       2     0.97781
+	 O     1     H     1       3     0.991
+	 O     2     H     1       3     0.97781
+	 O     3     H     1       3     0.97781
+	 O     1     Cl     1       1     1.6843
+	 O     1     Cl     2       1     1.6843
+	 O     1     Cl     3       1     1.6843
+	 O     1     Cl     4       1     1.6998
+	 O     2     Cl     1       1     1.6843
+	 O     3     Cl     1       1     1.6843
+	 O     1     Cl     1       2     1.4843
+	 O     1     Cl     2       2     1.4843
+	 O     1     Cl     3       2     1.4843
+	 O     1     Cl     4       2     1.491
+	 O     2     Cl     1       2     1.4843
+	 O     3     Cl     1       2     1.4843
+	 O     1     Cl     1       3     1.3443
+	 O     1     Cl     2       3     1.3443
+	 O     1     Cl     3       3     1.3443
+	 O     1     Cl     4       3     1.3479
+	 O     2     Cl     1       3     1.3443
+	 O     3     Cl     1       3     1.3443
+	 P     1     C     1       1     1.8346
+	 P     1     C     2       1     1.8347
+	 P     1     C     3       1     1.8347
+	 P     1     C     4       1     1.8321
+	 P     2     C     1       1     1.8347
+	 P     3     C     1       1     1.83
+	 P     3     C     2       1     1.8299
+	 P     3     C     3       1     1.8299
+	 P     3     C     4       1     1.8344
+	 P     4     C     1       1     1.7992
+	 P     4     C     2       1     1.7982
+	 P     4     C     3       1     1.7971
+	 P     4     C     4       1     1.7955
+	 P     5     C     1       1     2.0222
+	 P     6     C     1       1     2.2431
+	 P     1     C     1       2     1.6347
+	 P     1     C     2       2     1.6347
+	 P     1     C     3       2     1.6346
+	 P     1     C     4       2     1.6743
+	 P     2     C     1       2     1.71
+	 P     2     C     2       2     1.7099
+	 P     2     C     3       2     1.7011
+	 P     2     C     4       2     1.7571
+	 P     3     C     1       2     1.6347
+	 P     4     C     1       2     1.6475
+	 P     5     C     1       2     1.6547
+	 P     6     C     1       2     1.6704
+	 P     1     C     1       3     1.4947
+	 P     1     C     2       3     1.7548
+	 P     1     C     3       3     1.4947
+	 P     1     C     4       3     1.494
+	 P     2     C     1       3     1.4947
+	 P     3     C     1       3     1.4947
+	 P     4     C     1       3     1.5018
+	 P     5     C     1       3     1.5058
+	 P     6     C     1       3     1.5137
+	 P     1     N     1       1     1.7389
+	 P     1     N     2       1     1.7389
+	 P     1     N     3       1     1.7389
+	 P     1     N     4       1     1.7339
+	 P     1     N     5       1     1.9769
+	 P     2     N     1       1     1.7389
+	 P     3     N     1       1     1.7389
+	 P     3     N     3       1     1.6998
+	 P     3     N     4       1     1.7493
+	 P     4     N     1       1     1.7303
+	 P     4     N     3       1     1.6508
+	 P     4     N     4       1     1.7184
+	 P     5     N     1       1     1.7713
+	 P     6     N     1       1     1.7981
+	 P     1     N     1       2     1.5389
+	 P     1     N     2       2     1.5389
+	 P     1     N     3       2     1.5389
+	 P     1     N     4       2     1.566
+	 P     1     N     5       2     1.58
+	 P     2     N     1       2     1.5389
+	 P     3     N     1       2     1.5389
+	 P     4     N     1       2     1.5479
+	 P     5     N     1       2     1.5531
+	 P     6     N     1       2     1.5625
+	 P     1     N     1       3     1.6589
+	 P     1     N     2       3     1.6808
+	 P     1     N     3       3     1.6589
+	 P     1     N     4       3     1.7072
+	 P     1     N     5       3     1.7778
+	 P     2     N     1       3     1.6589
+	 P     3     N     1       3     1.6589
+	 P     4     N     1       3     1.6736
+	 P     5     N     1       3     1.6823
+	 P     6     N     1       3     1.7
+	 P     1     O     1       1     1.51
+	 P     1     O     2       1     1.63
+	 P     1     O     3       1     1.6767
+	 P     2     O     1       1     1.51
+	 P     2     O     2       1     1.6298
+	 P     2     O     3       1     1.6765
+	 P     3     O     1       1     1.6467
+	 P     3     O     2       1     1.6194
+	 P     3     O     3       1     1.6799
+	 P     4     O     1       1     1.5102
+	 P     4     O     2       1     1.6219
+	 P     4     O     3       1     1.6664
+	 P     5     O     1       1     1.5119
+	 P     5     O     2       1     1.6147
+	 P     5     O     3       1     1.6617
+	 P     6     O     1       1     1.5148
+	 P     6     O     2       1     1.617
+	 P     6     O     3       1     1.6635
+	 P     1     O     1       2     1.4767
+	 P     1     O     2       2     1.4767
+	 P     1     O     3       2     1.63
+	 P     2     O     1       2     1.4767
+	 P     2     O     2       2     1.4766
+	 P     2     O     3       2     1.6298
+	 P     3     O     1       2     1.4767
+	 P     3     O     2       2     1.476
+	 P     3     O     3       2     1.6293
+	 P     4     O     1       2     1.474
+	 P     4     O     2       2     1.4728
+	 P     4     O     3       2     1.6213
+	 P     5     O     1       2     1.4732
+	 P     5     O     2       2     1.4706
+	 P     5     O     3       2     1.6134
+	 P     6     O     1       2     1.4741
+	 P     6     O     2       2     1.4719
+	 P     6     O     3       2     1.6153
+	 P     1     O     1       3     1.3367
+	 P     1     O     2       3     1.3367
+	 P     1     O     3       3     1.63
+	 P     2     O     1       3     1.3367
+	 P     2     O     3       3     1.6298
+	 P     3     O     1       3     1.3367
+	 P     3     O     3       3     1.6293
+	 P     4     O     1       3     1.3349
+	 P     4     O     3       3     1.6213
+	 P     5     O     1       3     1.334
+	 P     5     O     3       3     1.6134
+	 P     6     O     1       3     1.3342
+	 P     6     O     3       3     1.6153
+	 P     1     P     1       1     2.18
+	 P     1     P     2       1     2.18
+	 P     1     P     3       1     2.18
+	 P     1     P     4       1     2.1607
+	 P     1     P     5       1     2.2615
+	 P     1     P     6       1     2.3913
+	 P     2     P     1       1     2.18
+	 P     3     P     1       1     2.18
+	 P     3     P     3       1     2.2788
+	 P     3     P     4       1     2.1532
+	 P     4     P     1       1     2.1607
+	 P     4     P     3       1     2.1532
+	 P     4     P     4       1     2.1946
+	 P     5     P     1       1     2.2616
+	 P     6     P     1       1     2.3913
+	 P     1     P     1       2     1.98
+	 P     1     P     2       2     1.98
+	 P     1     P     3       2     1.98
+	 P     1     P     4       2     2.0047
+	 P     1     P     5       2     2.0183
+	 P     1     P     6       2     2.0574
+	 P     2     P     1       2     1.98
+	 P     3     P     1       2     1.9801
+	 P     4     P     1       2     2.0047
+	 P     5     P     1       2     2.0183
+	 P     6     P     1       2     2.0574
+	 P     1     P     1       3     1.84
+	 P     1     P     2       3     1.84
+	 P     1     P     3       3     1.84
+	 P     1     P     4       3     1.8549
+	 P     1     P     5       3     1.8629
+	 P     1     P     6       3     1.8829
+	 P     2     P     1       3     1.84
+	 P     3     P     1       3     1.84
+	 P     4     P     1       3     1.8549
+	 P     5     P     1       3     1.8629
+	 P     6     P     1       3     1.8829
+	 P     1     S     1       1     2.0694
+	 P     1     S     2       1     2.0994
+	 P     1     S     3       1     2.0994
+	 P     1     S     4       1     2.0512
+	 P     1     S     5       1     2.0582
+	 P     1     S     6       1     2.0526
+	 P     2     S     1       1     2.0694
+	 P     3     S     1       1     2.0694
+	 P     3     S     2       1     2.107
+	 P     3     S     3       1     2.1076
+	 P     3     S     4       1     2.0602
+	 P     3     S     5       1     2.0668
+	 P     3     S     6       1     2.0404
+	 P     4     S     1       1     1.9399
+	 P     4     S     2       1     2.0942
+	 P     4     S     3       1     2.0932
+	 P     4     S     4       1     2.0484
+	 P     4     S     5       1     2.0344
+	 P     4     S     6       1     2.0272
+	 P     5     S     1       1     2.1158
+	 P     6     S     1       1     2.1603
+	 P     1     S     1       2     1.8994
+	 P     1     S     2       2     1.8994
+	 P     1     S     3       2     1.8994
+	 P     1     S     4       2     1.8737
+	 P     1     S     5       2     1.8769
+	 P     1     S     6       2     1.8723
+	 P     2     S     1       2     1.8994
+	 P     3     S     1       2     1.8994
+	 P     4     S     1       2     1.9151
+	 P     5     S     1       2     1.9244
+	 P     6     S     1       2     1.9437
+	 P     1     S     1       3     1.7594
+	 P     1     S     2       3     1.7594
+	 P     1     S     3       3     1.7594
+	 P     1     S     4       3     1.7438
+	 P     1     S     5       3     1.7452
+	 P     1     S     6       3     1.7418
+	 P     2     S     1       3     1.7594
+	 P     3     S     1       3     1.7594
+	 P     4     S     1       3     1.7688
+	 P     5     S     1       3     1.7743
+	 P     6     S     1       3     1.7843
+	 P     1     H     1       1     1.4168
+	 P     2     H     1       1     1.4168
+	 P     3     H     1       1     1.415
+	 P     4     H     1       1     1.411
+	 P     5     H     1       1     1.4168
+	 P     6     H     1       1     1.4168
+	 P     1     H     1       2     1.4168
+	 P     2     H     1       2     1.4168
+	 P     3     H     1       2     1.4168
+	 P     4     H     1       2     1.4168
+	 P     5     H     1       2     1.4168
+	 P     6     H     1       2     1.4168
+	 P     1     H     1       3     1.4168
+	 P     2     H     1       3     1.4168
+	 P     3     H     1       3     1.4168
+	 P     4     H     1       3     1.4168
+	 P     5     H     1       3     1.4168
+	 P     6     H     1       3     1.4168
+	 P     1     Cl     1       1     2.0445
+	 P     1     Cl     2       1     2.0445
+	 P     1     Cl     3       1     2.0445
+	 P     1     Cl     4       1     2.0745
+	 P     2     Cl     1       1     2.0445
+	 P     3     Cl     1       1     2.1
+	 P     4     Cl     1       1     2.0103
+	 P     5     Cl     1       1     2.0863
+	 P     6     Cl     1       1     2.1254
+	 P     1     Cl     1       2     1.8445
+	 P     1     Cl     2       2     1.8445
+	 P     1     Cl     3       2     1.8445
+	 P     1     Cl     4       2     1.8591
+	 P     2     Cl     1       2     1.8445
+	 P     3     Cl     1       2     1.8445
+	 P     4     Cl     1       2     1.8573
+	 P     5     Cl     1       2     1.8648
+	 P     6     Cl     1       2     1.8799
+	 P     1     Cl     1       3     1.7045
+	 P     1     Cl     2       3     1.7045
+	 P     1     Cl     3       3     1.7044
+	 P     1     Cl     4       3     1.7132
+	 P     2     Cl     1       3     1.7045
+	 P     3     Cl     1       3     1.7046
+	 P     4     Cl     1       3     1.7121
+	 P     5     Cl     1       3     1.7165
+	 P     6     Cl     1       3     1.7244
+	 S     1     C     1       1     1.801
+	 S     1     C     2       1     1.801
+	 S     1     C     3       1     1.801
+	 S     1     C     4       1     1.8265
+	 S     2     C     1       1     1.805
+	 S     2     C     2       1     1.8055
+	 S     2     C     3       1     1.8052
+	 S     2     C     4       1     1.804
+	 S     3     C     1       1     1.805
+	 S     3     C     2       1     1.8053
+	 S     3     C     3       1     1.8052
+	 S     3     C     4       1     1.8042
+	 S     4     C     1       1     1.7882
+	 S     4     C     2       1     1.7875
+	 S     4     C     3       1     1.7868
+	 S     4     C     4       1     1.786
+	 S     5     C     1       1     1.779
+	 S     5     C     2       1     1.7781
+	 S     5     C     3       1     1.777
+	 S     5     C     4       1     1.7765
+	 S     6     C     1       1     1.7815
+	 S     6     C     2       1     1.78
+	 S     6     C     3       1     1.7812
+	 S     6     C     4       1     1.7808
+	 S     1     C     1       2     1.665
+	 S     1     C     2       2     1.665
+	 S     1     C     3       2     1.6701
+	 S     1     C     4       2     1.7243
+	 S     2     C     1       2     1.665
+	 S     3     C     1       2     1.665
+	 S     4     C     1       2     1.6803
+	 S     5     C     1       2     1.6889
+	 S     6     C     1       2     1.7086
+	 S     1     C     1       3     1.4584
+	 S     1     C     2       3     1.7389
+	 S     1     C     3       3     1.7187
+	 S     1     C     4       3     1.8039
+	 S     2     C     1       3     1.4584
+	 S     2     C     2       3     1.7594
+	 S     2     C     3       3     1.7203
+	 S     2     C     4       3     1.804
+	 S     3     C     1       3     1.4584
+	 S     3     C     2       3     1.7586
+	 S     3     C     3       3     1.7213
+	 S     3     C     4       3     1.8042
+	 S     4     C     1       3     1.4502
+	 S     4     C     2       3     1.737
+	 S     4     C     3       3     1.6958
+	 S     4     C     4       3     1.786
+	 S     5     C     1       3     1.4442
+	 S     5     C     2       3     1.7251
+	 S     5     C     3       3     1.6865
+	 S     5     C     4       3     1.7765
+	 S     6     C     1       3     1.4468
+	 S     6     C     2       3     1.7195
+	 S     6     C     3       3     1.6847
+	 S     6     C     4       3     1.7808
+	 S     1     N     1       1     1.7181
+	 S     1     N     2       1     1.7181
+	 S     1     N     3       1     1.652
+	 S     1     N     4       1     1.7132
+	 S     1     N     5       1     1.8397
+	 S     2     N     1       1     1.7181
+	 S     2     N     3       1     1.6536
+	 S     2     N     4       1     1.7215
+	 S     3     N     1       1     1.7181
+	 S     3     N     3       1     1.6568
+	 S     3     N     4       1     1.7302
+	 S     4     N     1       1     1.6908
+	 S     4     N     3       1     1.6347
+	 S     4     N     4       1     1.7048
+	 S     5     N     1       1     1.6742
+	 S     5     N     3       1     1.626
+	 S     5     N     4       1     1.7001
+	 S     6     N     1       1     1.6812
+	 S     6     N     3       1     1.6271
+	 S     6     N     4       1     1.7058
+	 S     1     N     1       2     1.5181
+	 S     1     N     2       2     1.5181
+	 S     1     N     3       2     1.5181
+	 S     1     N     4       2     1.5442
+	 S     1     N     5       2     1.5591
+	 S     2     N     1       2     1.5181
+	 S     2     N     3       2     1.5188
+	 S     3     N     1       2     1.5181
+	 S     3     N     3       2     1.5191
+	 S     4     N     1       2     1.5063
+	 S     4     N     3       2     1.5102
+	 S     5     N     1       2     1.4972
+	 S     5     N     3       2     1.5058
+	 S     6     N     1       2     1.5003
+	 S     6     N     3       2     1.5046
+	 S     1     N     1       3     1.6381
+	 S     1     N     2       3     1.7093
+	 S     1     N     3       3     1.6381
+	 S     1     N     4       3     1.6849
+	 S     1     N     5       3     1.7141
+	 S     2     N     1       3     1.6381
+	 S     3     N     1       3     1.6381
+	 S     4     N     1       3     1.6171
+	 S     5     N     1       3     1.607
+	 S     6     N     1       3     1.6054
+	 S     1     O     1       1     1.6632
+	 S     1     O     2       1     1.661
+	 S     1     O     3       1     1.6632
+	 S     2     O     1       1     1.6632
+	 S     2     O     2       1     1.6636
+	 S     2     O     3       1     1.6606
+	 S     3     O     1       1     1.661
+	 S     3     O     2       1     1.6638
+	 S     3     O     3       1     1.6738
+	 S     4     O     1       1     1.6179
+	 S     4     O     2       1     1.6478
+	 S     4     O     3       1     1.6549
+	 S     5     O     1       1     1.6344
+	 S     5     O     2       1     1.6399
+	 S     5     O     3       1     1.6498
+	 S     6     O     1       1     1.6331
+	 S     6     O     2       1     1.6397
+	 S     6     O     3       1     1.6488
+	 S     1     O     1       2     1.5
+	 S     1     O     2       2     1.4632
+	 S     1     O     3       2     1.5
+	 S     2     O     1       2     1.5
+	 S     3     O     1       2     1.5
+	 S     4     O     1       2     1.5008
+	 S     5     O     1       2     1.503
+	 S     6     O     1       2     1.5062
+	 S     1     O     1       3     1.3232
+	 S     1     O     2       3     1.3232
+	 S     1     O     3       3     1.661
+	 S     2     O     1       3     1.3232
+	 S     2     O     3       3     1.6592
+	 S     3     O     1       3     1.3232
+	 S     3     O     2       3     1.6638
+	 S     3     O     3       3     1.6685
+	 S     4     O     1       3     1.3194
+	 S     4     O     2       3     1.6478
+	 S     4     O     3       3     1.65
+	 S     5     O     1       3     1.3167
+	 S     5     O     2       3     1.6399
+	 S     5     O     3       3     1.6437
+	 S     6     O     1       3     1.3163
+	 S     6     O     2       3     1.6397
+	 S     6     O     3       3     1.6422
+	 S     1     P     1       1     2.0694
+	 S     1     P     2       1     2.0694
+	 S     1     P     3       1     2.0694
+	 S     1     P     4       1     1.94
+	 S     1     P     5       1     2.1158
+	 S     1     P     6       1     2.1603
+	 S     2     P     1       1     2.0994
+	 S     2     P     3       1     2.107
+	 S     2     P     4       1     2.0942
+	 S     3     P     1       1     2.0994
+	 S     3     P     3       1     2.1076
+	 S     3     P     4       1     2.0932
+	 S     4     P     1       1     2.0924
+	 S     4     P     3       1     2.0602
+	 S     4     P     4       1     2.0484
+	 S     5     P     1       1     2.0582
+	 S     5     P     3       1     2.0471
+	 S     5     P     4       1     2.0344
+	 S     6     P     1       1     2.0526
+	 S     6     P     3       1     2.0396
+	 S     6     P     4       1     2.0263
+	 S     1     P     1       2     1.8994
+	 S     1     P     2       2     1.8994
+	 S     1     P     3       2     1.8994
+	 S     1     P     4       2     1.9151
+	 S     1     P     5       2     1.9244
+	 S     1     P     6       2     1.9437
+	 S     2     P     1       2     1.8994
+	 S     3     P     1       2     1.8994
+	 S     4     P     1       2     1.8737
+	 S     5     P     1       2     1.8624
+	 S     6     P     1       2     1.8723
+	 S     1     P     1       3     1.7594
+	 S     1     P     2       3     1.7594
+	 S     1     P     3       3     1.7595
+	 S     1     P     4       3     1.7688
+	 S     1     P     5       3     1.7743
+	 S     1     P     6       3     1.7843
+	 S     2     P     1       3     1.7594
+	 S     3     P     1       3     1.7594
+	 S     4     P     1       3     1.7438
+	 S     5     P     1       3     1.7359
+	 S     6     P     1       3     1.7418
+	 S     1     S     1       1     2.05
+	 S     1     S     2       1     2.05
+	 S     1     S     3       1     2.05
+	 S     1     S     4       1     2.007
+	 S     1     S     5       1     1.9923
+	 S     1     S     6       1     1.9875
+	 S     2     S     1       1     2.05
+	 S     2     S     2       1     2.0515
+	 S     2     S     3       1     2.0496
+	 S     2     S     4       1     2.0082
+	 S     2     S     5       1     1.9947
+	 S     2     S     6       1     1.9865
+	 S     3     S     1       1     2.05
+	 S     3     S     2       1     2.0496
+	 S     3     S     3       1     2.0528
+	 S     3     S     4       1     2.0097
+	 S     3     S     5       1     1.9973
+	 S     3     S     6       1     1.9924
+	 S     4     S     1       1     2.007
+	 S     4     S     2       1     2.0082
+	 S     4     S     3       1     2.0097
+	 S     4     S     4       1     1.9769
+	 S     4     S     5       1     1.9671
+	 S     4     S     6       1     1.9605
+	 S     5     S     1       1     1.9923
+	 S     5     S     2       1     1.9947
+	 S     5     S     3       1     1.9972
+	 S     5     S     4       1     1.9671
+	 S     5     S     5       1     1.9587
+	 S     5     S     6       1     1.9559
+	 S     6     S     1       1     1.9875
+	 S     6     S     2       1     1.9866
+	 S     6     S     3       1     1.9924
+	 S     6     S     4       1     1.9606
+	 S     6     S     5       1     1.9566
+	 S     6     S     6       1     1.9493
+	 S     1     S     1       2     2.05
+	 S     1     S     2       2     2.05
+	 S     1     S     3       2     2.05
+	 S     1     S     4       2     2.007
+	 S     1     S     5       2     1.9923
+	 S     1     S     6       2     1.9875
+	 S     2     S     1       2     2.05
+	 S     2     S     2       2     2.0515
+	 S     2     S     3       2     2.0496
+	 S     2     S     4       2     2.0082
+	 S     2     S     5       2     1.9947
+	 S     2     S     6       2     1.9865
+	 S     3     S     1       2     2.05
+	 S     3     S     2       2     2.0496
+	 S     3     S     3       2     2.0528
+	 S     3     S     4       2     2.0097
+	 S     3     S     5       2     1.9973
+	 S     3     S     6       2     1.9924
+	 S     4     S     1       2     2.007
+	 S     4     S     2       2     2.0082
+	 S     4     S     3       2     2.0097
+	 S     4     S     4       2     1.9769
+	 S     4     S     5       2     1.9671
+	 S     4     S     6       2     1.9605
+	 S     5     S     1       2     1.9923
+	 S     5     S     2       2     1.9947
+	 S     5     S     3       2     1.9972
+	 S     5     S     4       2     1.9671
+	 S     5     S     5       2     1.9587
+	 S     5     S     6       2     1.9559
+	 S     6     S     1       2     1.9875
+	 S     6     S     2       2     1.9866
+	 S     6     S     3       2     1.9924
+	 S     6     S     4       2     1.9606
+	 S     6     S     5       2     1.9566
+	 S     6     S     6       2     1.9493
+	 S     1     S     1       3     2.05
+	 S     1     S     2       3     2.05
+	 S     1     S     3       3     2.05
+	 S     1     S     4       3     2.007
+	 S     1     S     5       3     1.9923
+	 S     1     S     6       3     1.9875
+	 S     2     S     1       3     2.05
+	 S     2     S     2       3     2.0515
+	 S     2     S     3       3     2.0496
+	 S     2     S     4       3     2.0082
+	 S     2     S     5       3     1.9947
+	 S     2     S     6       3     1.9865
+	 S     3     S     1       3     2.05
+	 S     3     S     2       3     2.0496
+	 S     3     S     3       3     2.0528
+	 S     3     S     4       3     2.0097
+	 S     3     S     5       3     1.9973
+	 S     3     S     6       3     1.9924
+	 S     4     S     1       3     2.007
+	 S     4     S     2       3     2.0082
+	 S     4     S     3       3     2.0097
+	 S     4     S     4       3     1.9769
+	 S     4     S     5       3     1.9671
+	 S     4     S     6       3     1.9605
+	 S     5     S     1       3     1.9923
+	 S     5     S     2       3     1.9947
+	 S     5     S     3       3     1.9972
+	 S     5     S     4       3     1.9671
+	 S     5     S     5       3     1.9587
+	 S     5     S     6       3     1.9559
+	 S     6     S     1       3     1.9875
+	 S     6     S     2       3     1.9866
+	 S     6     S     3       3     1.9924
+	 S     6     S     4       3     1.9606
+	 S     6     S     5       3     1.9566
+	 S     6     S     6       3     1.9493
+	 S     1     H     1       1     1.341
+	 S     2     H     1       1     1.341
+	 S     3     H     1       1     1.341
+	 S     4     H     1       1     1.3318
+	 S     5     H     1       1     1.3272
+	 S     6     H     1       1     1.3317
+	 S     1     H     1       2     1.341
+	 S     2     H     1       2     1.341
+	 S     3     H     1       2     1.341
+	 S     4     H     1       2     1.3318
+	 S     5     H     1       2     1.3272
+	 S     6     H     1       2     1.3317
+	 S     1     H     1       3     1.341
+	 S     2     H     1       3     1.341
+	 S     3     H     1       3     1.341
+	 S     4     H     1       3     1.3318
+	 S     5     H     1       3     1.3272
+	 S     6     H     1       3     1.3317
+	 S     1     Cl     1       1     2.031
+	 S     1     Cl     2       1     2.031
+	 S     1     Cl     3       1     2.031
+	 S     1     Cl     4       1     2.0566
+	 S     2     Cl     1       1     2.031
+	 S     3     Cl     1       1     2.031
+	 S     4     Cl     1       1     1.9985
+	 S     5     Cl     1       1     1.9855
+	 S     6     Cl     1       1     1.9827
+	 S     1     Cl     1       2     2.031
+	 S     1     Cl     2       2     2.031
+	 S     1     Cl     3       2     2.031
+	 S     1     Cl     4       2     2.0566
+	 S     2     Cl     1       2     2.031
+	 S     3     Cl     1       2     2.031
+	 S     4     Cl     1       2     1.9985
+	 S     5     Cl     1       2     1.9855
+	 S     6     Cl     1       2     1.9827
+	 S     1     Cl     1       3     2.031
+	 S     1     Cl     2       3     2.031
+	 S     1     Cl     3       3     2.031
+	 S     1     Cl     4       3     2.0566
+	 S     2     Cl     1       3     2.031
+	 S     3     Cl     1       3     2.031
+	 S     4     Cl     1       3     1.9985
+	 S     5     Cl     1       3     1.9855
+	 S     6     Cl     1       3     1.9827
+	 H     1     C     1       1     1.093
+	 H     1     C     2       1     1.093
+	 H     1     C     3       1     1.093
+	 H     1     C     4       1     1.0922
+	 H     1     C     1       2     1.083
+	 H     1     C     2       2     1.083
+	 H     1     C     3       2     1.0826
+	 H     1     C     4       2     1.0922
+	 H     1     C     1       3     1.0907
+	 H     1     C     2       3     1.0701
+	 H     1     C     3       3     1.0826
+	 H     1     C     4       3     1.0922
+	 H     1     N     1       1     1.0189
+	 H     1     N     2       1     1.0189
+	 H     1     N     3       1     1.019
+	 H     1     N     4       1     1.0268
+	 H     1     N     5       1     1.0449
+	 H     1     N     1       2     1.0189
+	 H     1     N     2       2     1.0189
+	 H     1     N     3       2     1.028
+	 H     1     N     4       2     1.0319
+	 H     1     N     5       2     1.0449
+	 H     1     N     1       3     1.0189
+	 H     1     N     2       3     1.0268
+	 H     1     N     3       3     1.0189
+	 H     1     N     4       3     1.0319
+	 H     1     N     5       3     1.0449
+	 H     1     O     1       1     0.97781
+	 H     1     O     2       1     0.969
+	 H     1     O     3       1     0.991
+	 H     1     O     1       2     0.97781
+	 H     1     O     2       2     0.987
+	 H     1     O     3       2     0.97784
+	 H     1     O     1       3     0.991
+	 H     1     O     2       3     0.97781
+	 H     1     O     3       3     0.97784
+	 H     1     P     1       1     1.4168
+	 H     1     P     2       1     1.4168
+	 H     1     P     3       1     1.415
+	 H     1     P     4       1     1.411
+	 H     1     P     5       1     1.4168
+	 H     1     P     6       1     1.4168
+	 H     1     P     1       2     1.4168
+	 H     1     P     2       2     1.4168
+	 H     1     P     3       2     1.4168
+	 H     1     P     4       2     1.4168
+	 H     1     P     5       2     1.4168
+	 H     1     P     6       2     1.4168
+	 H     1     P     1       3     1.4168
+	 H     1     P     2       3     1.4168
+	 H     1     P     3       3     1.4168
+	 H     1     P     4       3     1.4168
+	 H     1     P     5       3     1.4168
+	 H     1     P     6       3     1.4168
+	 H     1     S     1       1     1.341
+	 H     1     S     2       1     1.341
+	 H     1     S     3       1     1.341
+	 H     1     S     4       1     1.3318
+	 H     1     S     5       1     1.3335
+	 H     1     S     6       1     1.3317
+	 H     1     S     1       2     1.341
+	 H     1     S     2       2     1.341
+	 H     1     S     3       2     1.341
+	 H     1     S     4       2     1.3318
+	 H     1     S     5       2     1.3335
+	 H     1     S     6       2     1.3317
+	 H     1     S     1       3     1.341
+	 H     1     S     2       3     1.341
+	 H     1     S     3       3     1.341
+	 H     1     S     4       3     1.3318
+	 H     1     S     5       3     1.3335
+	 H     1     S     6       3     1.3317
+	 H     1     H     1       1     0.66
+	 H     1     H     1       2     0.66
+	 H     1     H     1       3     0.66
+	 H     1     Cl     1       1     1.3138
+	 H     1     Cl     2       1     1.3138
+	 H     1     Cl     3       1     1.3138
+	 H     1     Cl     4       1     1.3138
+	 H     1     Cl     1       2     1.3138
+	 H     1     Cl     2       2     1.3138
+	 H     1     Cl     3       2     1.3138
+	 H     1     Cl     4       2     1.3138
+	 H     1     Cl     1       3     1.3138
+	 H     1     Cl     2       3     1.3138
+	 H     1     Cl     3       3     1.3138
+	 H     1     Cl     4       3     1.3138
+	 Cl     1     C     1       1     1.773
+	 Cl     1     C     2       1     1.773
+	 Cl     1     C     3       1     1.773
+	 Cl     1     C     4       1     1.767
+	 Cl     2     C     1       1     1.773
+	 Cl     3     C     1       1     1.773
+	 Cl     4     C     1       1     1.7993
+	 Cl     1     C     1       2     1.72
+	 Cl     1     C     2       2     1.72
+	 Cl     1     C     3       2     1.7018
+	 Cl     1     C     4       2     1.767
+	 Cl     2     C     1       2     1.72
+	 Cl     3     C     1       2     1.72
+	 Cl     4     C     1       2     1.7425
+	 Cl     1     C     1       3     1.4231
+	 Cl     1     C     2       3     1.7739
+	 Cl     1     C     3       3     1.7018
+	 Cl     1     C     4       3     1.767
+	 Cl     2     C     1       3     1.4231
+	 Cl     3     C     1       3     1.423
+	 Cl     4     C     1       3     1.4294
+	 Cl     1     N     1       1     1.7292
+	 Cl     1     N     2       1     1.7292
+	 Cl     1     N     3       1     1.761
+	 Cl     1     N     4       1     1.725
+	 Cl     1     N     5       1     1.8244
+	 Cl     2     N     1       1     1.7291
+	 Cl     3     N     1       1     1.7292
+	 Cl     4     N     1       1     1.7485
+	 Cl     1     N     1       2     1.5292
+	 Cl     1     N     2       2     1.5292
+	 Cl     1     N     3       2     1.5292
+	 Cl     1     N     4       2     1.5515
+	 Cl     1     N     5       2     1.5638
+	 Cl     2     N     1       2     1.5292
+	 Cl     3     N     1       2     1.5292
+	 Cl     4     N     1       2     1.5376
+	 Cl     1     N     1       3     1.6492
+	 Cl     1     N     2       3     1.6956
+	 Cl     1     N     3       3     1.6492
+	 Cl     1     N     4       3     1.6884
+	 Cl     1     N     5       3     1.7114
+	 Cl     2     N     1       3     1.6492
+	 Cl     3     N     1       3     1.6492
+	 Cl     4     N     1       3     1.6631
+	 Cl     1     O     1       1     1.6843
+	 Cl     1     O     2       1     1.6843
+	 Cl     1     O     3       1     1.6843
+	 Cl     2     O     1       1     1.6843
+	 Cl     3     O     1       1     1.6843
+	 Cl     4     O     1       1     1.6998
+	 Cl     1     O     1       2     1.4843
+	 Cl     1     O     2       2     1.4843
+	 Cl     1     O     3       2     1.4843
+	 Cl     2     O     1       2     1.4843
+	 Cl     3     O     1       2     1.4844
+	 Cl     4     O     1       2     1.491
+	 Cl     1     O     1       3     1.3443
+	 Cl     1     O     2       3     1.3443
+	 Cl     1     O     3       3     1.3443
+	 Cl     2     O     1       3     1.3443
+	 Cl     3     O     1       3     1.3444
+	 Cl     4     O     1       3     1.3479
+	 Cl     1     P     1       1     2.0445
+	 Cl     1     P     2       1     2.0445
+	 Cl     1     P     3       1     2.1
+	 Cl     1     P     4       1     2.0103
+	 Cl     1     P     5       1     2.0863
+	 Cl     1     P     6       1     2.1254
+	 Cl     2     P     1       1     2.0445
+	 Cl     3     P     1       1     2.0447
+	 Cl     4     P     1       1     2.0745
+	 Cl     1     P     1       2     1.8445
+	 Cl     1     P     2       2     1.8445
+	 Cl     1     P     3       2     1.8446
+	 Cl     1     P     4       2     1.8573
+	 Cl     1     P     5       2     1.8648
+	 Cl     1     P     6       2     1.8799
+	 Cl     2     P     1       2     1.8445
+	 Cl     3     P     1       2     1.8445
+	 Cl     4     P     1       2     1.8591
+	 Cl     1     P     1       3     1.7045
+	 Cl     1     P     2       3     1.7045
+	 Cl     1     P     3       3     1.7045
+	 Cl     1     P     4       3     1.7121
+	 Cl     1     P     5       3     1.7165
+	 Cl     1     P     6       3     1.7244
+	 Cl     2     P     1       3     1.7045
+	 Cl     3     P     1       3     1.7045
+	 Cl     4     P     1       3     1.7132
+	 Cl     1     S     1       1     2.031
+	 Cl     1     S     2       1     2.031
+	 Cl     1     S     3       1     2.031
+	 Cl     1     S     4       1     1.9985
+	 Cl     1     S     5       1     1.9855
+	 Cl     1     S     6       1     1.9827
+	 Cl     2     S     1       1     2.031
+	 Cl     3     S     1       1     2.031
+	 Cl     4     S     1       1     2.0566
+	 Cl     1     S     1       2     2.031
+	 Cl     1     S     2       2     2.031
+	 Cl     1     S     3       2     2.031
+	 Cl     1     S     4       2     1.9985
+	 Cl     1     S     5       2     1.9855
+	 Cl     1     S     6       2     1.9827
+	 Cl     2     S     1       2     2.031
+	 Cl     3     S     1       2     2.031
+	 Cl     4     S     1       2     2.0566
+	 Cl     1     S     1       3     2.031
+	 Cl     1     S     2       3     2.031
+	 Cl     1     S     3       3     2.031
+	 Cl     1     S     4       3     1.9985
+	 Cl     1     S     5       3     1.9855
+	 Cl     1     S     6       3     1.9827
+	 Cl     2     S     1       3     2.031
+	 Cl     3     S     1       3     2.031
+	 Cl     4     S     1       3     2.0566
+	 Cl     1     H     1       1     1.3138
+	 Cl     2     H     1       1     1.3138
+	 Cl     3     H     1       1     1.3138
+	 Cl     4     H     1       1     1.3138
+	 Cl     1     H     1       2     1.3138
+	 Cl     2     H     1       2     1.3138
+	 Cl     3     H     1       2     1.3138
+	 Cl     4     H     1       2     1.3138
+	 Cl     1     H     1       3     1.3138
+	 Cl     2     H     1       3     1.3138
+	 Cl     3     H     1       3     1.3138
+	 Cl     4     H     1       3     1.3138
+	 Cl     1     Cl     1       1     2.02
+	 Cl     1     Cl     2       1     2.02
+	 Cl     1     Cl     3       1     2.02
+	 Cl     1     Cl     4       1     2.0439
+	 Cl     2     Cl     1       1     2.02
+	 Cl     3     Cl     1       1     2.02
+	 Cl     4     Cl     1       1     2.0439
+	 Cl     1     Cl     1       2     1.82
+	 Cl     1     Cl     2       2     1.82
+	 Cl     1     Cl     3       2     1.82
+	 Cl     1     Cl     4       2     1.8317
+	 Cl     2     Cl     1       2     1.82
+	 Cl     3     Cl     1       2     1.8201
+	 Cl     4     Cl     1       2     1.8317
+	 Cl     1     Cl     1       3     1.68
+	 Cl     1     Cl     2       3     1.68
+	 Cl     1     Cl     3       3     1.68
+	 Cl     1     Cl     4       3     1.6869
+	 Cl     2     Cl     1       3     1.68
+	 Cl     3     Cl     1       3     1.68
+	 Cl     4     Cl     1       3     1.6869
Binary file CADDSuite/data/fonts/FreeSans.ttf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/A.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,107 @@
+<node>A
+	<node>Names
+		<node>Adenine</node>
+		<node>Adenin</node>	 
+		<node>A</node>	 
+	</node>
+	<node>Atoms
+		<node>P<value>P 23.872 39.165 31.119</value></node>
+		<node>O1P<value>O 25.231 39.217 30.523</value></node> 
+		<node>O2P<value>O 22.847 40.110 30.636</value></node> 
+		<node>O5*<value>O 24.015 39.407 32.681</value></node> 
+		<node>C5*<value>C 23.898 38.444 33.717</value></node>
+		<node>1H5*<value>H 23.427 37.536 33.341</value></node> 
+		<node>2H5*<value>H 23.266 38.889 34.485</value></node>
+		<node>C4*<value>C 25.259 38.091 34.326</value></node>
+		<node>H4*<value>H 25.156 37.622 35.304</value></node> 
+		<node>O4*<value>O 25.979 37.144 33.552</value></node> 
+		<node>C3*<value>C 26.180 39.302 34.326</value></node>
+		<node>H3*<value>H 26.158 39.977 33.470</value></node>
+		<node>O3*<value>O 25.805 40.074 35.470</value></node>
+		<node>C2*<value>C 27.544 38.641 34.414</value></node>
+		<node>1H2*<value>H 28.301 39.314 34.011</value></node>
+		<node>2H2*<value>H 27.774 38.419 35.456</value></node>
+		<node>C1*<value>C 27.277 37.165 34.164</value></node> 
+		<node>H1*<value>H 27.382 36.562 35.066</value></node>
+		<node>N9<value>N 28.236 36.536 33.230</value></node>
+		<node>C8<value>C 28.440 36.783 31.901</value></node>
+		<node>H8<value>H 27.912 37.594 31.421</value></node>
+		<node>N7<value>N 29.329 36.020 31.347</value></node>
+		<node>C5<value>C 29.751 35.206 32.384</value></node>
+		<node>C6<value>C 30.698 34.181 32.452</value></node>
+		<node>N6<value>N 31.417 33.777 31.410</value></node>
+		<node>1H6<value>H 32.088 33.030 31.518</value></node>
+		<node>2H6<value>H 31.292 34.217 30.509</value></node>
+		<node>N1<value>N 30.867 33.595 33.636</value></node>
+		<node>C2<value>C 30.158 33.991 34.674</value></node>
+		<node>2H<value>H 30.296 33.518 35.635</value></node>
+		<node>N3<value>N 29.245 34.933 34.744</value></node>
+		<node>C4<value>C 29.090 35.512 33.538</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>P O1P s</value></node>
+		<node>2<value>P O2P d</value></node>
+		<node>3<value>P O5* s</value></node>		
+		<node>4<value>O5* C5* s</value></node>
+		<node>5<value>C5* C4* s</value></node>
+		<node>6<value>C4* O4* s</value></node>	
+		<node>7<value>C4* C3* s</value></node>
+		<node>8<value>C3* O3* s</value></node>
+		<node>9<value>C3* C2* s</value></node>
+		<node>10<value>C2* C1* s</value></node>
+		<node>11<value>C1* O4* s</value></node>
+		<node>12<value>C1* N9 s</value></node>
+		<node>13<value>N9 C8 s</value></node>
+		<node>14<value>C8 N7 d</value></node>
+		<node>15<value>N7 C5 s</value></node>
+		<node>16<value>C5 C6 s</value></node>
+		<node>17<value>C5 C4 d</value></node>
+		<node>18<value>C4 N9 s</value></node>
+		<node>19<value>C6 N6 s</value></node>
+		<node>20<value>C6 N1 d</value></node>
+		<node>21<value>N1 C2 s</value></node>
+		<node>22<value>C2 N3 d</value></node>
+		<node>23<value>N3 C4 s</value></node>
+		<node>24<value>C5* 1H5* s</value></node>
+		<node>25<value>C5* 2H5* s</value></node>
+		<node>26<value>C4* H4* s</value></node>
+		<node>27<value>C1* H1* s</value></node>
+		<node>28<value>C3* H3* s</value></node>
+		<node>29<value>C2* 1H2* s</value></node>
+    <node>30<value>C2* 2H2* s</value></node>
+		<node>31<value>C8 H8 s</value></node>
+		<node>32<value>N6 1H6 s</value></node>
+		<node>33<value>N6 2H6 s</value></node>
+		<node>34<value>C2 2H s</value></node>
+ 	</node>
+	<node>Connections
+		<node>5-term<value>P 3-term s 1.62 0.5</value></node>
+		<node>3-term<value>O3* 5-term s 1.62 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>NUCLEOTIDE</node>
+	</node>
+	<node>Variants
+    		<node>A-M
+      			<node>Properties
+        			<node>5_PRIME</node>
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>Default
+      			<node>Properties
+      			</node>
+    		</node>
+    		<node>A-3
+      			<node>Properties
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>A-5
+      			<node>Properties
+        			<node>5_PRIME</node>
+      			</node>
+    		</node>
+ 	</node>
+</node>
+	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ACE.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,47 @@
+<node>ACE
+	<node>Names
+		<node>ACE</node>
+		<node>acetic acid</node>
+	</node>
+	<node>Atoms
+		<node>C<value>C -0.710977 -1.12008 0.000774821</value></node>
+		<node>CH3<value>C 0.0997794 -2.40762 0.00202052</value></node>
+		<node>O<value>O -1.92224 -1.17518 0.00112378</value></node>
+		<node>1HH3<value>H -0.167239 -2.98461 0.880642</value></node>
+		<node>2HH3<value>H 1.1711 -2.24422 -0.00400307</value></node>
+		<node>3HH3<value>H -0.176322 -2.99236 -0.868617</value></node>
+		<node>OXT<value>O -0.0809243 0.0851695 -0.000720861</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>C CH3 s</value></node>
+		<node>2<value>C O d</value></node>
+		<node>3<value>C OXT s</value></node>
+		<node>4<value>CH3 1HH3 s</value></node>
+		<node>5<value>CH3 2HH3 s</value></node>
+		<node>6<value>CH3 3HH3 s</value></node>
+	</node>
+	<node>Connections
+		<node>C-term
+			<value>C N-term s 1.33 0.5
+			</value>
+		</node>
+	</node>
+	<node>Properties
+	</node>
+	<node>Variants
+		<node>ACE-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+    <node>ACE-M
+      <node>Properties
+        <node>C_TERMINAL</node>
+        <node>N_TERMINAL</node>
+      </node>
+    </node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ALA.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,82 @@
+<node>ALA
+	<node>Names
+		<node>Alanine</node>
+		<node>Alanin</node>
+		<node>Ala</node>
+		<node>A</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.09952427 1.425946 -0.01392276</value></node>
+		<node>3H<value>H 0.9122966 2.021833 0.09543685</value></node>
+		<node>CA<value>C -0.6343572 1.904422 -1.199327</value></node>
+		<node>HA<value>H -0.06613517 1.608824 -2.082189</value></node>
+		<node>C<value>C -0.7061328 3.434369 -1.195026</value></node>
+		<node>O<value>O 0.2770563 4.020259 -0.6877273</value></node>
+		<node>CB<value>C -2.018631 1.250585 -1.273356</value></node>
+		<node>1HB<value>H -2.525042 1.535779 -2.196084</value></node>
+		<node>2HB<value>H -1.909473 0.1656088 -1.256012</value></node>
+		<node>3HB<value>H -2.621985 1.560564 -0.4192078</value></node>
+		<node>OXT<value>O -1.554726 3.968913 -1.942107</value></node>
+		<node>1H<value>H -0.4859746 1.514033 0.8043322</value></node>
+		<node>2H<value>H 0.3756785 0.4622824 -0.137128</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>3HB CB s</value></node>
+		<node>22<value>OXT C s</value></node>
+		<node>23<value>1H N s</value></node>
+		<node>24<value>2H N s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT<value></value></node>
+				<node>1H<value></value></node>
+				<node>2H<value></value></node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>ALA-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>ALA-C
+			<node>Delete
+				<node>1H<value></value></node>
+				<node>2H<value></value></node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>ALA-N
+			<node>Delete
+				<node>OXT<value></value></node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node> 
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ARG.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,110 @@
+<node>ARG
+	<node>Names
+		<node>Arginine</node>
+		<node>Arginin</node>
+		<node>Arg</node>
+		<node>R</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.04658213 1.228698 -0.008203848</value></node>
+		<node>3H<value>H 1.029144 1.468065 -0.01885969</value></node>
+		<node>CA<value>C -0.651675 1.900984 -1.120636</value></node>
+		<node>HA<value>H -0.1560273 1.589999 -2.041618</value></node>
+		<node>C<value>C -0.5384113 3.425156 -1.007164</value></node>
+		<node>O<value>O -0.4560871 4.056512 -2.083366</value></node>
+		<node>CB<value>C -2.115081 1.438444 -1.186192</value></node>
+		<node>1HB<value>H -2.126043 0.3475202 -1.20068</value></node>
+		<node>2HB<value>H -2.643967 1.778842 -0.2945162</value></node>
+		<node>CG<value>C -2.829752 1.953359 -2.443151</value></node>
+		<node>1HG<value>H -2.889884 3.042607 -2.412891</value></node>
+		<node>2HG<value>H -2.25911 1.654155 -3.324525</value></node>
+		<node>CD<value>C -4.246704 1.376451 -2.533151</value></node>
+		<node>1HD<value>H -4.174877 0.2870844 -2.574071</value></node>
+		<node>2HD<value>H -4.797596 1.672022 -1.637285</value></node>
+		<node>NE<value>N -4.940577 1.875193 -3.731703</value></node>
+		<node>HE<value>H -4.414851 2.512341 -4.314554</value></node>
+		<node>CZ<value>C -6.193176 1.546153 -4.088384</value></node>
+		<node>NH1<value>N -6.900425 0.7030471 -3.327994</value></node>
+		<node>1HH1<value>H -6.480561 0.3232263 -2.492691</value></node>
+		<node>2HH1<value>H -7.843661 0.4323652 -3.563007</value></node>
+		<node>NH2<value>N -6.730267 2.060851 -5.200565</value></node>
+		<node>1HH2<value>H -6.201764 2.698435 -5.778988</value></node>
+		<node>2HH2<value>H -7.669785 1.826959 -5.486362</value></node>
+		<node>OXT<value>O -0.796168 3.930999 0.1074273</value></node>
+		<node>1H<value>H -0.3621705 1.521632 0.867786</value></node>
+		<node>2H<value>H -0.05222332 0.2284002 -0.1067282</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>CG CB s</value></node>
+		<node>25<value>1HG CG s</value></node>
+		<node>26<value>2HG CG s</value></node>
+		<node>27<value>CD CG s</value></node>
+		<node>31<value>1HD CD s</value></node>
+		<node>32<value>2HD CD s</value></node>
+		<node>33<value>NE CD s</value></node>
+		<node>36<value>HE NE s</value></node>
+		<node>37<value>CZ NE s</value></node>
+		<node>40<value>NH1 CZ a</value></node>
+		<node>43<value>1HH1 NH1 s</value></node>
+		<node>44<value>2HH1 NH1 s</value></node>
+		<node>45<value>NH2 CZ a</value></node>
+		<node>48<value>1HH2 NH2 s</value></node>
+		<node>49<value>2HH2 NH2 s</value></node>
+		<node>50<value>OXT C s</value></node>
+		<node>51<value>1H N s</value></node>
+		<node>52<value>2H N s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties 
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>ARG-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>ARG-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>ARG-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ASN.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,90 @@
+<node>ASN
+	<node>Names
+		<node>Asparagine</node>
+		<node>Asparagin</node>
+		<node>Asn</node>
+		<node>N</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N -0.01239826 1.297873 -0.0455736</value></node>
+		<node>3H<value>H 0.8807231 1.768826 0.03701005</value></node>
+		<node>CA<value>C -0.7474616 1.91653 -1.164926</value></node>
+		<node>HA<value>H -0.1937652 1.691628 -2.077897</value></node>
+		<node>C<value>C -0.757567 3.441771 -1.010304</value></node>
+		<node>O<value>O 0.3769885 3.962902 -0.9276295</value></node>
+		<node>CB<value>C -2.149851 1.302218 -1.30196</value></node>
+		<node>1HB<value>H -2.042859 0.2235991 -1.423685</value></node>
+		<node>2HB<value>H -2.723301 1.490943 -0.3934487</value></node>
+		<node>CG<value>C -2.91901 1.84635 -2.50453</value></node>
+		<node>OD1<value>O -2.442698 2.721974 -3.218464</value></node>
+		<node>ND2<value>N -4.125435 1.339006 -2.736042</value></node>
+		<node>1HD2<value>H -4.50376 0.6180301 -2.140929</value></node>
+		<node>2HD2<value>H -4.647904 1.686222 -3.525954</value></node>
+		<node>1H<value>H -0.5352049 1.417775 0.8102037</value></node>
+		<node>2H<value>H 0.1272759 0.3139404 -0.2256562</value></node>
+		<node>OXT<value>O -1.806735 3.963976 -0.572751</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>CG CB s</value></node>
+		<node>24<value>OD1 CG d</value></node>
+		<node>25<value>ND2 CG s</value></node>
+		<node>28<value>1HD2 ND2 s</value></node>
+		<node>29<value>2HD2 ND2 s</value></node>
+		<node>30<value>1H N s</value></node>
+		<node>31<value>2H N s</value></node>
+		<node>32<value>OXT C s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>ASN-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>ASN-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>ASN-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ASP.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,86 @@
+<node>ASP
+	<node>Names
+		<node>Aspartate</node>
+		<node>Aspartat</node>
+		<node>Asp</node>
+		<node>D</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.1006113 1.231053 -0.1065504</value></node>
+		<node>3H<value>H 0.7826706 1.919109 0.1901606</value></node>
+		<node>CA<value>C -0.6776782 1.854581 -1.196471</value></node>
+		<node>HA<value>H -0.140641 1.67647 -2.129506</value></node>
+		<node>C<value>C -0.7684437 3.377808 -1.00658</value></node>
+		<node>O<value>O -0.1755398 3.814352 0.008837678</value></node>
+		<node>CB<value>C -2.059715 1.201639 -1.304611</value></node>
+		<node>1HB<value>H -1.947421 0.1437317 -1.541582</value></node>
+		<node>2HB<value>H -2.583309 1.296861 -0.3531539</value></node>
+		<node>CG<value>C -2.895658 1.868856 -2.384729</value></node>
+		<node>OD1<value>O -2.861295 1.365629 -3.526181</value></node>
+		<node>OD2<value>O -3.508188 2.905267 -2.052321</value></node>
+		<node>OXT<value>O -0.9198192 4.048685 -2.051676</value></node>
+		<node>1H<value>H -0.5109496 1.02733 0.6709606</value></node>
+		<node>2H<value>H 0.5472904 0.3836241 -0.4264945</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>CG CB s</value></node>
+		<node>24<value>OD1 CG a</value></node>
+		<node>25<value>OD2 CG a</value></node>
+		<node>26<value>OXT C s</value></node>
+		<node>27<value>1H N s</value></node>
+		<node>28<value>2H N s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node> 
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>ASP-M
+			<node>Properties
+				<node>N_TERMINAL</node>
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>ASP-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>ASP-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Benzene-Skeleton.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,23 @@
+<node>Benzene-Skeleton
+	<node>Names
+		<node>Benzene-Skeleton</node>
+	</node>
+	<node>Atoms
+		<node>C1<value>C 0.066248 -1.287634 0.144514</value></node>
+		<node>C2<value>C 0.057081 -0.613884 1.337852</value></node>
+		<node>C3<value>C 0.045766 0.796088 1.307799</value></node>
+		<node>C4<value>C 0.054862 1.462219 0.071058</value></node>
+		<node>C5<value>C 0.073086 0.728404 -1.129738</value></node>
+		<node>C6<value>C 0.091744 -0.671622 -1.107443</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>C1 C2 s</value></node>
+		<node>2<value>C2 C3 d</value></node>
+		<node>3<value>C3 C4 s</value></node>
+		<node>4<value>C4 C5 d</value></node>
+		<node>5<value>C5 C6 s</value></node>
+		<node>6<value>C6 C1 d</value></node>
+	</node>
+	<node>Properties
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/C.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,102 @@
+<node>C
+	<node>Names
+		<node>Cytosine</node>
+		<node>Cytosin</node>
+		<node>C</node>	 
+	</node>
+	<node>Atoms
+		<node>P<value>P 15.644 29.327 35.222</value></node>
+		<node>O1P<value>O 15.393 28.440 36.382</value></node>
+		<node>O2P<value>O 14.638 30.335 34.831</value></node>
+		<node>O5*<value>O 15.947 28.383 33.968</value></node>
+		<node>C5*<value>C 16.069 28.915 32.657</value></node>
+		<node>1H5*<value>H 16.821 29.704 32.690</value></node>
+		<node>2H5*<value>H 15.119 29.333 32.322</value></node>
+		<node>C4*<value>C 16.513 27.844 31.682</value></node>
+		<node>H4*<value>H 16.609 28.228 30.666</value></node>
+		<node>O4*<value>O 17.830 27.370 32.014</value></node>
+		<node>C3*<value>C 15.542 26.637 31.746</value></node>
+		<node>H3*<value>H 14.654 26.736 32.370</value></node>
+		<node>O3*<value>O 15.186 26.233 30.429</value></node>
+		<node>C2*<value>C 16.448 25.569 32.322</value></node>
+		<node>1H2*<value>H 16.102 25.297 33.319</value></node>
+		<node>2H2*<value>H 16.428 24.689 31.678</value></node>
+		<node>C1*<value>C 17.781 25.967 31.722</value></node>
+		<node>H1*<value>H 17.935 25.853 30.649</value></node>
+		<node>N1<value>N 18.940 25.252 32.322</value></node>
+		<node>C6<value>C 18.970 24.882 33.637</value></node>
+		<node>H6<value>H 18.141 25.127 34.285</value></node>
+		<node>C5<value>C 20.022 24.211 34.147</value></node>
+		<node>H5<value>H 20.029 23.926 35.199</value></node>
+		<node>C4<value>C 21.100 23.907 33.243</value></node>
+		<node>N4<value>N 22.167 23.241 33.694</value></node>
+		<node>1H4<value>H 22.908 23.042 33.037</value></node>
+		<node>2H4<value>H 22.216 22.954 34.661</value></node>
+		<node>N3<value>N 21.059 24.280 31.953</value></node>
+		<node>C2<value>C 19.992 24.955 31.461</value></node>
+		<node>O2<value>O 19.963 25.291 30.279</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>P O1P s</value></node>
+		<node>2<value>P O2P d</value></node>
+		<node>3<value>P O5* s</value></node>		
+		<node>4<value>O5* C5* s</value></node>
+		<node>5<value>C5* C4* s</value></node>
+		<node>6<value>C4* O4* s</value></node>	
+		<node>7<value>C4* C3* s</value></node>
+		<node>8<value>C3* O3* s</value></node>
+		<node>9<value>C3* C2* s</value></node>
+		<node>10<value>C2* C1* s</value></node>
+		<node>11<value>C1* O4* s</value></node>
+		<node>12<value>C1* N1 s</value></node>
+		<node>13<value>N1 C6 s</value></node>
+		<node>14<value>C6 C5 d</value></node>
+		<node>15<value>C5 C4 s</value></node>
+		<node>16<value>C4 N4 s</value></node>
+		<node>17<value>C4 N3 d</value></node>
+		<node>18<value>N3 C2 s</value></node>
+		<node>19<value>C2 O2 d</value></node>
+		<node>20<value>C2 N1 s</value></node>
+		<node>21<value>C5* 1H5* s</value></node>
+		<node>22<value>C5* 2H5* s</value></node>
+		<node>23<value>C4* H4* s</value></node>
+		<node>24<value>C1* H1* s</value></node>
+		<node>25<value>C3* H3* s</value></node>
+		<node>26<value>C2* 1H2* s</value></node>
+    <node>27<value>C2* 2H2* s</value></node>
+		<node>28<value>C6 H6 s</value></node>
+		<node>29<value>C5 H5 s</value></node>
+		<node>30<value>N4 1H4 s</value></node>
+		<node>31<value>N4 2H4 s</value></node>
+ 	</node>
+	<node>Connections
+		<node>5-term<value>P 3-term s 1.62 0.5</value></node>
+		<node>3-term<value>O3* 5-term s 1.62 0.5</value></node>
+	</node>
+	<node>Properties
+    		<node>NUCLEOTIDE</node>
+  	</node>
+  	<node>Variants
+    		<node>C-M
+      			<node>Properties
+        			<node>5_PRIME</node>
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>Default
+      			<node>Properties
+      			</node>
+    		</node>
+    		<node>C-3
+      			<node>Properties
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>C-5
+      			<node>Properties
+        			<node>5_PRIME</node>
+      			</node>
+    		</node>
+  	</node>
+</node>
+	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/CA.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,18 @@
+<node>CA
+	<node>Names
+ 		<node>Calcium ion</node>
+ 		<node>Ca2+</node>
+	</node>
+	<node>Atoms
+		<node>CA<value>Ca 0.0 0.0 0.0</value></node>
+	</node>
+	<node>Bonds
+	</node>
+	<node>Connections
+	</node>
+	<node>Properties
+	</node>
+	<node>Variants
+		<node>Default</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/CYS.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,123 @@
+<node>CYS
+	<node>Names
+		<node>Cysteine</node>
+		<node>Cystein</node>
+		<node>Cys</node>
+		<node>C</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.02405081 1.288152 -0.04523527</value></node>
+		<node>3H<value>H 0.9139157 1.764642 0.02587458</value></node>
+		<node>CA<value>C -0.7231978 1.84877 -1.18869</value></node>
+		<node>HA<value>H -0.1383485 1.663318 -2.090963</value></node>
+		<node>C<value>C -0.8891953 3.364114 -1.049031</value></node>
+		<node>O<value>O 0.1143772 4.039036 -1.368143</value></node>
+		<node>CB<value>C -2.074845 1.154028 -1.367605</value></node>
+		<node>1HB<value>H -1.930864 0.09969049 -1.603445</value></node>
+		<node>2HB<value>H -2.672614 1.244251 -0.4604313</value></node>
+		<node>SG<value>S -2.936402 1.968095 -2.733035</value></node>
+		<node>HG<value>H -4.084388 1.292503 -2.621688</value></node>
+		<node>1H<value>H -0.5030248 1.428972 0.8047693</value></node>
+		<node>2H<value>H 0.1769028 0.3003187 -0.1898637</value></node>
+		<node>OXT<value>O -1.790595 3.760744 -0.2774832</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>SG CB s</value></node>
+		<node>25<value>HG SG s</value></node>
+		<node>28<value>1H N s</value></node>
+		<node>29<value>2H N s</value></node>
+		<node>30<value>OXT C s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+		<node>S-term<value>SG S-term s 2.05 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>CYS-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>CYS-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>CYS-S
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+				<node>HG</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>HAS_SSBOND</node>
+			</node>
+		</node>
+		<node>CYS-CS
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+				<node>HG</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>HAS_SSBOND</node>
+			</node>
+		</node>
+		<node>CYS-NS
+			<node>Delete
+				<node>OXT</node>
+				<node>HG</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+				<node>HAS_SSBOND</node>
+			</node>
+		</node>
+		<node>CYS-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Editing-Fragments.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,47 @@
+<node>Fragments
+	<node>#include:ALA<value>fragments/ALA.db:/ALA</value></node>
+	<node>#include:ARG<value>fragments/ARG.db:/ARG</value></node>
+	<node>#include:ASP<value>fragments/ASP.db:/ASP</value></node>
+	<node>#include:ASN<value>fragments/ASN.db:/ASN</value></node>
+	<node>#include:CYS<value>fragments/CYS.db:/CYS</value></node>
+	<node>#include:GLN<value>fragments/GLN.db:/GLN</value></node>
+	<node>#include:GLU<value>fragments/GLU.db:/GLU</value></node>
+	<node>#include:GLY<value>fragments/GLY.db:/GLY</value></node>
+	<node>#include:HIS<value>fragments/HIS.db:/HIS</value></node>
+	<node>#include:ILE<value>fragments/ILE.db:/ILE</value></node>
+	<node>#include:LEU<value>fragments/LEU.db:/LEU</value></node>
+	<node>#include:LYS<value>fragments/LYS.db:/LYS</value></node>
+	<node>#include:MET<value>fragments/MET.db:/MET</value></node>
+	<node>#include:PHE<value>fragments/PHE.db:/PHE</value></node>
+	<node>#include:PRO<value>fragments/PRO.db:/PRO</value></node>
+	<node>#include:SER<value>fragments/SER.db:/SER</value></node>
+	<node>#include:THR<value>fragments/THR.db:/THR</value></node>
+	<node>#include:TRP<value>fragments/TRP.db:/TRP</value></node>
+	<node>#include:TYR<value>fragments/TYR.db:/TYR</value></node>
+	<node>#include:VAL<value>fragments/VAL.db:/VAL</value></node>
+	<node>#include:PCA<value>fragments/PCA.db:/PCA</value></node>
+	<node>#include:ACE<value>fragments/ACE.db:/ACE</value></node>
+	<node>#include:NME<value>fragments/NME.db:/NME</value></node>
+	<node>#include:CA<value>fragments/CA.db:/CA</value></node>
+	<node>#include:MG<value>fragments/MG.db:/MG</value></node>
+	<node>#include:ZN<value>fragments/ZN.db:/ZN</value></node>
+	<node>#include:HOH<value>fragments/HOH.db:/HOH</value></node>
+	<node>#include:A<value>fragments/A.db:/A</value></node>
+	<node>#include:C<value>fragments/C.db:/C</value></node>
+	<node>#include:G<value>fragments/G.db:/G</value></node>
+	<node>#include:T<value>fragments/T.db:/T</value></node>
+	<node>#include:U<value>fragments/U.db:/U</value></node>
+	<node>#include:Pyrrole-Skeleton<value>fragments/Pyrrole-Skeleton.db:/Pyrrole-Skeleton</value></node>
+	<node>#include:Benzene-Skeleton<value>fragments/Benzene-Skeleton.db:/Benzene-Skeleton</value></node>
+	<node>#include:Indole-Skeleton<value>fragments/Indole-Skeleton.db:/Indole-Skeleton</value></node>
+</node>
+<node>Names
+	<node>#include:Discover<value>fragments/Names.Discover.db:/Discover</value></node>
+	<node>#include:Amber<value>fragments/Names.Amber.db:/Amber</value></node>
+	<node>#include:CHARMM<value>fragments/Names.CHARMM.db:/CHARMM</value></node>
+	<node>#include:XPLOR<value>fragments/Names.XPLOR.db:/XPLOR</value></node>
+	<node>#include:Star<value>fragments/Names.Star.db:/Star</value></node>
+</node>
+<node>Defaults
+	<node>Naming<value>PDB</value></node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Fragments.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,46 @@
+<node>Fragments
+	<node>#include:ALA<value>fragments/ALA.db:/ALA</value></node>
+	<node>#include:ARG<value>fragments/ARG.db:/ARG</value></node>
+	<node>#include:ASP<value>fragments/ASP.db:/ASP</value></node>
+	<node>#include:ASN<value>fragments/ASN.db:/ASN</value></node>
+	<node>#include:CYS<value>fragments/CYS.db:/CYS</value></node>
+	<node>#include:GLN<value>fragments/GLN.db:/GLN</value></node>
+	<node>#include:GLU<value>fragments/GLU.db:/GLU</value></node>
+	<node>#include:GLY<value>fragments/GLY.db:/GLY</value></node>
+	<node>#include:HIS<value>fragments/HIS.db:/HIS</value></node>
+	<node>#include:ILE<value>fragments/ILE.db:/ILE</value></node>
+	<node>#include:LEU<value>fragments/LEU.db:/LEU</value></node>
+	<node>#include:LYS<value>fragments/LYS.db:/LYS</value></node>
+	<node>#include:MET<value>fragments/MET.db:/MET</value></node>
+	<node>#include:MSE<value>fragments/MSE.db:/MSE</value></node>
+	<node>#include:PHE<value>fragments/PHE.db:/PHE</value></node>
+	<node>#include:PRO<value>fragments/PRO.db:/PRO</value></node>
+	<node>#include:SER<value>fragments/SER.db:/SER</value></node>
+	<node>#include:THR<value>fragments/THR.db:/THR</value></node>
+	<node>#include:TRP<value>fragments/TRP.db:/TRP</value></node>
+	<node>#include:TYR<value>fragments/TYR.db:/TYR</value></node>
+	<node>#include:VAL<value>fragments/VAL.db:/VAL</value></node>
+	<node>#include:PCA<value>fragments/PCA.db:/PCA</value></node>
+	<node>#include:ACE<value>fragments/ACE.db:/ACE</value></node>
+	<node>#include:NME<value>fragments/NME.db:/NME</value></node>
+	<node>#include:CA<value>fragments/CA.db:/CA</value></node>
+	<node>#include:MG<value>fragments/MG.db:/MG</value></node>
+	<node>#include:ZN<value>fragments/ZN.db:/ZN</value></node>
+	<node>#include:HOH<value>fragments/HOH.db:/HOH</value></node>
+	<node>#include:A<value>fragments/A.db:/A</value></node>
+	<node>#include:C<value>fragments/C.db:/C</value></node>
+	<node>#include:G<value>fragments/G.db:/G</value></node>
+	<node>#include:T<value>fragments/T.db:/T</value></node>
+	<node>#include:U<value>fragments/U.db:/U</value></node>
+</node>
+<node>Names
+	<node>#include:Discover<value>fragments/Names.Discover.db:/Discover</value></node>
+	<node>#include:Amber<value>fragments/Names.Amber.db:/Amber</value></node>
+	<node>#include:CHARMM<value>fragments/Names.CHARMM.db:/CHARMM</value></node>
+	<node>#include:XPLOR<value>fragments/Names.XPLOR.db:/XPLOR</value></node>
+	<node>#include:Star<value>fragments/Names.Star.db:/Star</value></node>
+	<node>#include:DNA<value>fragments/Names.DNA.db:/DNA</value></node>
+</node>
+<node>Defaults
+	<node>Naming<value>PDB</value></node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/G.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,107 @@
+<node>G
+	<node>Names
+		<node>Guanine</node>
+		<node>Guanin</node>
+		<node>G</node>	 
+	</node>
+	<node>Atoms
+		<node>P<value>P 32.612 26.662 40.051</value></node>
+		<node>O1P<value>O 33.579 26.377 41.135</value></node>
+		<node>O2P<value>O 32.257 25.612 39.055</value></node>
+		<node>O5*<value>O 31.233 27.248 40.656</value></node>
+		<node>C5*<value>C 31.159 28.416 41.468</value></node>
+		<node>1H5*<value>H 32.062 29.003 41.301</value></node>
+		<node>2H5*<value>H 31.095 28.140 42.520</value></node>
+		<node>C4*<value>C 29.940 29.254 41.095</value></node>
+		<node>H4*<value>H 29.785 30.090 41.777</value></node>
+		<node>O4*<value>O 30.102 29.870 39.801</value></node>
+		<node>C3*<value>C 28.712 28.348 41.021</value></node>
+		<node>O3*<value>O 27.645 28.918 41.772</value></node>
+		<node>H3*<value>H 28.886 27.326 41.358</value></node>
+		<node>C2*<value>C 28.364 28.341 39.559</value></node>
+		<node>1H2*<value>H 28.348 27.314 39.193</value></node>
+		<node>2H2*<value>H 27.382 28.792 39.416</value></node>
+		<node>C1*<value>C 28.928 29.637 39.018</value></node>
+		<node>H1*<value>H 28.284 30.517 39.013</value></node>
+		<node>N9<value>N 29.311 29.477 37.601</value></node>
+		<node>C8<value>C 30.238 28.616 37.067</value></node>
+		<node>H8<value>H 30.771 27.925 37.703</value></node>
+		<node>N7<value>N 30.381 28.736 35.780</value></node>
+		<node>C5<value>C 29.485 29.746 35.436</value></node>
+		<node>C6<value>C 29.204 30.305 34.166</value></node>
+		<node>O6<value>O 29.745 30.037 33.101</value></node>
+		<node>N1<value>N 28.225 31.296 34.247</value></node>
+		<node>1H<value>H 27.948 31.750 33.400</value></node>
+		<node>C2<value>C 27.605 31.699 35.418</value></node>
+		<node>N2<value>N 26.693 32.662 35.319</value></node>
+		<node>1H2<value>H 26.407 33.145 34.479</value></node>
+		<node>2H2<value>H 26.252 32.956 36.179</value></node>
+		<node>N3<value>N 27.881 31.170 36.610</value></node>
+		<node>C4<value>C 28.823 30.204 36.543</value></node>
+	</node>  
+	<node>Bonds
+		<node>1<value>P O1P s</value></node>
+		<node>2<value>P O2P d</value></node>
+		<node>3<value>P O5* s</value></node>		
+		<node>4<value>O5* C5* s</value></node>
+		<node>5<value>C5* C4* s</value></node>
+		<node>6<value>C4* O4* s</value></node>	
+		<node>7<value>C4* C3* s</value></node>
+		<node>8<value>C3* O3* s</value></node>
+		<node>9<value>C3* C2* s</value></node>
+		<node>10<value>C2* C1* s</value></node>
+		<node>11<value>C1* O4* s</value></node>
+		<node>12<value>C1* N9 s</value></node>
+		<node>13<value>N9 C8 s</value></node>
+		<node>14<value>C8 N7 d</value></node>
+		<node>15<value>N7 C5 s</value></node>
+		<node>16<value>C5 C4 d</value></node>
+		<node>17<value>C4 N9 s</value></node>
+		<node>18<value>C5 C6 s</value></node>
+		<node>19<value>C6 O6 d</value></node>
+		<node>20<value>C6 N1 s</value></node>
+		<node>21<value>N1 C2 s</value></node>
+		<node>22<value>C2 N2 s</value></node>
+		<node>23<value>C2 N3 d</value></node>
+		<node>24<value>N3 C4 s</value></node>
+		<node>25<value>C5* 1H5* s</value></node>
+		<node>26<value>C5* 2H5* s</value></node>
+		<node>27<value>C4* H4* s</value></node>
+		<node>28<value>C1* H1* s</value></node>
+		<node>29<value>C3* H3* s</value></node>
+		<node>30<value>C2* 1H2* s</value></node>
+	        <node>31<value>C2* 2H2* s</value></node>
+		<node>32<value>C8 H8 s</value></node>
+		<node>33<value>N1 1H s</value></node>
+		<node>34<value>N2 1H2 s</value></node>
+		<node>35<value>N2 2H2 s</value></node>
+ 	</node>
+	<node>Connections
+    		<node>5-term<value>P 3-term s 1.62 0.5</value></node>
+    		<node>3-term<value>O3* 5-term s 1.62 0.5</value></node>
+	</node>
+  	<node>Properties
+    		<node>NUCLEOTIDE</node>
+  		</node>
+  	<node>Variants
+    		<node>G-M
+      			<node>Properties
+        			<node>5_PRIME</node>
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>Default
+      			<node>Properties
+      			</node>
+    		</node>
+    		<node>G-5
+      		<node>Properties
+        		<node>5_PRIME</node>
+      		</node>
+    		<node>G-3
+      			<node>Properties
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+  	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/GLN.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,96 @@
+<node>GLN
+	<node>Names
+		<node>Glutamine</node> 
+		<node>Glutamin</node>
+		<node>Gln</node>
+		<node>Q</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N -1.694353 -0.2940789 3.487573</value></node>
+		<node>3H<value>H -1.993324 -0.7771879 2.60663</value></node>
+		<node>CA<value>C -1.339968 1.106833 3.061471</value></node>
+		<node>HA<value>H -2.035373 1.840381 3.535663</value></node>
+		<node>C<value>C -1.613526 1.110178 1.459362</value></node>
+		<node>O<value>O -1.452083 2.138383 0.8146671</value></node>
+		<node>CB<value>C 0.1053884 1.466314 3.38408</value></node>
+		<node>2HB<value>H 0.4078564 1.068117 4.376333</value></node>
+		<node>1HB<value>H 0.7844938 0.9955081 2.644168</value></node>
+		<node>CG<value>C 0.2953307 2.976142 3.377398</value></node>
+		<node>2HG<value>H -0.08479181 3.405704 2.425381</value></node>
+		<node>1HG<value>H -0.3113416 3.443596 4.179154</value></node>
+		<node>CD<value>C 1.757013 3.318817 3.588054</value></node>
+		<node>OE1<value>O 2.263759 3.493683 4.689262</value></node>
+		<node>NE2<value>N 2.607646 3.349533 2.459146</value></node>
+		<node>2HE2<value>H 3.553186 3.659591 2.602335</value></node>
+		<node>1HE2<value>H 2.182977 3.3032491 1.543895</value></node>
+		<node>OXT<value>O -2.00241 -0.02523248 1.056456</value></node>
+		<node>2H<value>H -2.440811 -0.2844597 4.149324</value></node>
+		<node>1H<value>H -0.9086809 -0.7656706 3.887856</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>3H N s</value></node>
+		<node>2<value>CA N s</value></node>
+		<node>3<value>HA CA s</value></node>
+		<node>4<value>C CA s</value></node>
+		<node>5<value>O C d</value></node>
+		<node>6<value>CB CA s</value></node>
+		<node>7<value>2HB CB s</value></node>
+		<node>8<value>1HB CB s</value></node>
+		<node>9<value>CG CB s</value></node>
+		<node>10<value>2HG CG s</value></node>
+		<node>11<value>1HG CG s</value></node>
+		<node>12<value>CD CG s</value></node>
+		<node>13<value>OE1 CD d</value></node>
+		<node>14<value>NE2 CD s</value></node>
+		<node>15<value>2HE2 NE2 s</value></node>
+		<node>16<value>1HE2 NE2 s</value></node>
+		<node>17<value>OXT C s</value></node>
+		<node>18<value>2H N s</value></node>
+		<node>19<value>1H N s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>GLN-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>GLN-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>GLN-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/GLU.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,92 @@
+<node>GLU
+	<node>Names
+		<node>Glutamate</node>
+		<node>Glutamat</node>
+		<node>Glu</node>
+		<node>Q</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.09036078 1.20944 -0.09877955</value></node>
+		<node>3H<value>H 0.992178 1.663159 -0.02552702</value></node>
+		<node>CA<value>C -0.6644503 1.887128 -1.167784</value></node>
+		<node>HA<value>H -0.1401839 1.690991 -2.10393</value></node>
+		<node>C<value>C -0.6415405 3.403009 -0.9416856</value></node>
+		<node>O<value>O 0.5018099 3.910433 -0.8834405</value></node>
+		<node>CB<value>C -2.078524 1.299661 -1.288965</value></node>
+		<node>1HB<value>H -2.006071 0.2127525 -1.352877</value></node>
+		<node>2HB<value>H -2.670931 1.54428 -0.4052964</value></node>
+		<node>CG<value>C -2.807634 1.790975 -2.546677</value></node>
+		<node>1HG<value>H -2.881274 2.877187 -2.559357</value></node>
+		<node>2HG<value>H -2.268831 1.463546 -3.436255</value></node>
+		<node>CD<value>C -4.223983 1.236637 -2.597517</value></node>
+		<node>OE1<value>O -5.044554 1.733033 -1.797006</value></node>
+		<node>OE2<value>O -4.450723 0.3260741 -3.421581</value></node>
+		<node>1H<value>H -0.4043283 1.301303 0.7769806</value></node>
+		<node>2H<value>H 0.2085563 0.2320959 -0.3244812</value></node>
+		<node>OXT<value>O -1.674247 3.928742 -0.470977</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>CG CB s</value></node>
+		<node>25<value>1HG CG s</value></node>
+		<node>26<value>2HG CG s</value></node>
+		<node>27<value>CD CG s</value></node>
+		<node>30<value>OE1 CD a</value></node>
+		<node>31<value>OE2 CD a</value></node>
+		<node>32<value>1H N s</value></node>
+		<node>33<value>2H N s</value></node>
+		<node>34<value>OXT C s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>GLU-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>GLU-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>GLU-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/GLY.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,76 @@
+<node>GLY
+	<node>Names
+		<node>Glycine</node>
+		<node>Glycin</node>
+		<node>Gly</node>
+		<node>G</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.09000722 1.216287 -0.1108443</value></node>
+		<node>3H<value>H 0.8807056 1.803007 0.1270226</value></node>
+		<node>CA<value>C -0.6332095 1.869306 -1.215941</value></node>
+		<node>1HA<value>H -0.02850649 1.801736 -2.120623</value></node>
+		<node>2HA<value>H -1.579168 1.352425 -1.380715</value></node>
+		<node>C<value>C -0.8818576 3.344497 -0.910938</value></node>
+		<node>O<value>O 0.06351577 3.962237 -0.3713815</value></node>
+		<node>1H<value>H -0.5183882 1.138782 0.691625</value></node>
+		<node>2H<value>H 0.4027565 0.2984461 -0.3934918</value></node>
+		<node>OXT<value>O -1.901015 3.866009 -1.413833</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>1HA CA s</value></node>
+		<node>11<value>2HA CA s</value></node>
+		<node>12<value>C CA s</value></node>
+		<node>15<value>O C d</value></node>
+		<node>16<value>1H N s</value></node>
+		<node>17<value>2H N s</value></node>
+		<node>18<value>OXT C s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>GLY-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node> 
+		<node>GLY-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>GLY-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/HIS.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,99 @@
+<node>HIS
+	<node>Names
+		<node>Histidine</node>
+		<node>Histidin</node>
+		<node>His</node>
+		<node>H</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.2528806 1.616447 -0.2212145</value></node>
+		<node>3H<value>H 0.7991534 2.328624 0.245802</value></node>
+		<node>CA<value>C -0.9251888 2.215651 -0.8776516</value></node>
+		<node>HA<value>H -0.5465931 2.966134 -1.573552</value></node>
+		<node>C<value>C -1.833067 2.919479 0.1419996</value></node>
+		<node>O<value>O -2.654072 3.735267 -0.3389743</value></node>
+		<node>CB<value>C -1.677425 1.144471 -1.688265</value></node>
+		<node>1HB<value>H -0.9314069 0.53022 -2.195623</value></node>
+		<node>2HB<value>H -2.228334 0.4977131 -1.00345</value></node>
+		<node>CG<value>C -2.625881 1.668474 -2.74672</value></node>
+		<node>ND1<value>N -3.385668 2.821612 -2.671887</value></node>
+		<node>HD1<value>H -3.38348 3.467654 -1.88095</value></node>
+		<node>CD2<value>C -2.893428 1.068907 -3.947961</value></node>
+		<node>HD2<value>H -2.46763 0.1453506 -4.317409</value></node>
+		<node>CE1<value>C -4.09971 2.924621 -3.807559</value></node>
+		<node>HE1<value>H -4.788648 3.724259 -4.045286</value></node>
+		<node>NE2<value>N -3.815619 1.869323 -4.597533</value></node>
+		<node>HE2<value>H -4.210977 1.69118 -5.511979</value></node>
+		<node>1H<value>H -0.05550323 0.9331897 0.4557269</value></node>
+		<node>2H<value>H 0.827899 1.162407 -0.9164186</value></node>
+		<node>OXT<value>O -1.921441 2.400639 1.276749</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>CG CB s</value></node>
+		<node>24<value>ND1 CG a</value></node>
+		<node>27<value>HD1 ND1 s</value></node>
+		<node>28<value>CD2 CG a</value></node>
+		<node>31<value>HD2 CD2 s</value></node>
+		<node>32<value>CE1 ND1 a</value></node>
+		<node>35<value>HE1 CE1 s</value></node>
+		<node>36<value>NE2 CE1 a</value></node>
+		<node>37<value>NE2 CD2 a</value></node>
+		<node>39<value>HE2 NE2 s</value></node>
+		<node>40<value>1H N s</value></node>
+		<node>41<value>2H N s</value></node>
+		<node>42<value>OXT C s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>HIS-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>HIS-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>HIS-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/HOH.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,21 @@
+<node>HOH
+	<node>Names
+ 		<node>Water</node>
+	</node>
+	<node>Atoms
+		<node>O <value>O  15.118 9.944 8.582</value></node>
+		<node>1H<value>H  15.211 9.386 7.809</value></node>
+		<node>2H<value>H  14.173 9.992 8.730</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>1H O s</value></node>
+		<node>2<value>2H O s</value></node>
+	</node>
+	<node>Connections
+	</node>
+	<node>Properties
+	</node>
+	<node>Variants
+		<node>Default</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ILE.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,100 @@
+<node>ILE
+	<node>Names
+		<node>Isoleucine</node>
+		<node>Isoleucin</node>
+		<node>Ile</node>
+		<node>I</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.1219419 1.159209 -0.1919851</value></node>
+		<node>3H<value>H 0.9740559 1.689959 -0.04711162</value></node>
+		<node>CA<value>C -0.7030041 1.935257 -1.138673</value></node>
+		<node>HA<value>H -0.2842833 1.745549 -2.127681</value></node>
+		<node>C<value>C -0.5392811 3.43721 -0.8683466</value></node>
+		<node>O<value>O 0.4636989 3.750649 -0.1867381</value></node>
+		<node>CB<value>C -2.165631 1.439687 -1.121375</value></node>
+		<node>HB<value>H -2.124804 0.349284 -1.14618</value></node>
+		<node>CG1<value>C -2.945574 1.890833 -2.370761</value></node>
+		<node>1HG1<value>H -3.189406 2.951118 -2.312008</value></node>
+		<node>2HG1<value>H -2.330654 1.72068 -3.255403</value></node>
+		<node>CG2<value>C -2.890608 1.852801 0.1693949</value></node>
+		<node>1HG2<value>H -3.851115 1.343782 0.2388784</value></node>
+		<node>2HG2<value>H -2.299751 1.573039 1.041283</value></node>
+		<node>3HG2<value>H -3.060911 2.929328 0.1868919</value></node>
+		<node>CD1<value>C -4.249351 1.108805 -2.558935</value></node>
+		<node>1HD1<value>H -4.709754 1.403511 -3.502415</value></node>
+		<node>2HD1<value>H -4.043807 0.03831363 -2.586494</value></node>
+		<node>3HD1<value>H -4.947758 1.324118 -1.751006</value></node>
+		<node>1H<value>H -0.3580201 1.071109 0.6916124</value></node>
+		<node>2H<value>H 0.3236403 0.2433889 -0.5670705</value></node>
+		<node>OXT<value>O -1.135264 4.21782 -1.641576</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>HB CB s</value></node>
+		<node>20<value>CG1 CB s</value></node>
+		<node>24<value>1HG1 CG1 s</value></node>
+		<node>25<value>2HG1 CG1 s</value></node>
+		<node>26<value>CG2 CB s</value></node>
+		<node>30<value>1HG2 CG2 s</value></node>
+		<node>31<value>2HG2 CG2 s</value></node>
+		<node>32<value>3HG2 CG2 s</value></node>
+		<node>33<value>CD1 CG1 s</value></node>
+		<node>37<value>1HD1 CD1 s</value></node>
+		<node>38<value>2HD1 CD1 s</value></node>
+		<node>39<value>3HD1 CD1 s</value></node>
+		<node>40<value>1H N s</value></node>
+		<node>41<value>2H N s</value></node>
+		<node>42<value>OXT C s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>ILE-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>ILE-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>ILE-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Indole-Skeleton.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,30 @@
+<node>Indole-Skeleton
+	<node>Names
+		<node>Indole-Skeleton</node>
+	</node>
+	<node>Atoms
+		<node>C1<value>C 0.098272 0.968184 -2.108448</value></node>
+		<node>N2<value>N 0.106846 2.054217 -1.259124</value></node>
+		<node>C3<value>C 0.08464 1.665738 0.063892</value></node>
+		<node>C4<value>C 0.060104 0.240281 0.014949</value></node>
+		<node>C5<value>C 0.062069 -0.174574 -1.386187</value></node>
+		<node>C6<value>C 0.084854 2.377612 1.27264</value></node>
+		<node>C7<value>C 0.060305 1.667968 2.483589</value></node>
+		<node>C8<value>C 0.039354 0.262233 2.470668</value></node>
+		<node>C9<value>C 0.039595 -0.441663 1.251419</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>C1 N2 s</value></node>
+		<node>2<value>N2 C3 s</value></node>
+		<node>3<value>C3 C4 d</value></node>
+		<node>4<value>C4 C5 s</value></node>
+		<node>5<value>C5 C1 d</value></node>
+		<node>6<value>C3 C6 s</value></node>
+		<node>7<value>C6 C7 d</value></node>
+		<node>8<value>C7 C8 s</value></node>
+		<node>9<value>C8 C9 d</value></node>
+		<node>10<value>C9 C4 s</value></node>
+	</node>
+	<node>Properties
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/LEU.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,100 @@
+<node>LEU
+	<node>Names
+		<node>Leucine</node>
+		<node>Leucin</node>
+		<node>Leu</node>
+		<node>L</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N -0.003476313 1.235853 0.02699674</value></node>
+		<node>3H<value>H 0.7720473 1.82942 0.3005252</value></node>
+		<node>CA<value>C -0.6514053 1.883178 -1.129898</value></node>
+		<node>HA<value>H -0.07017973 1.598957 -2.006831</value></node>
+		<node>C<value>C -0.5708863 3.410168 -0.9936234</value></node>
+		<node>O<value>O 0.1419036 3.827524 -0.05211589</value></node>
+		<node>CB<value>C -2.091007 1.359104 -1.274005</value></node>
+		<node>1HB<value>H -2.046227 0.2694775 -1.310338</value></node>
+		<node>2HB<value>H -2.646399 1.642544 -0.3785246</value></node>
+		<node>CG<value>C -2.872831 1.847369 -2.507179</value></node>
+		<node>HG<value>H -3.019899 2.926006 -2.455012</value></node>
+		<node>CD1<value>C -2.162796 1.498542 -3.821336</value></node>
+		<node>1HD1<value>H -2.800384 1.766798 -4.664294</value></node>
+		<node>2HD1<value>H -1.228827 2.051352 -3.913459</value></node>
+		<node>3HD1<value>H -1.954294 0.4288859 -3.861405</value></node>
+		<node>CD2<value>C -4.261661 1.198464 -2.502073</value></node>
+		<node>1HD2<value>H -4.845348 1.564912 -3.347144</value></node>
+		<node>2HD2<value>H -4.171115 0.1141629 -2.575422</value></node>
+		<node>3HD2<value>H -4.785489 1.451318 -1.579679</value></node>
+		<node>OXT<value>O -0.8228753 4.072413 -2.02374</value></node>
+		<node>1H<value>H -0.6580312 1.186075 0.7945588</value></node>
+		<node>2H<value>H 0.3136166 0.3082535 -0.2161924</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>1HB CB s</value></node>
+    <node>20<value>2HB CB s</value></node>
+    <node>21<value>CG CB s</value></node>
+    <node>25<value>HG CG s</value></node>
+    <node>26<value>CD1 CG s</value></node>
+    <node>30<value>1HD1 CD1 s</value></node>
+    <node>31<value>2HD1 CD1 s</value></node>
+    <node>32<value>3HD1 CD1 s</value></node>
+    <node>33<value>CD2 CG s</value></node>
+    <node>37<value>1HD2 CD2 s</value></node>
+    <node>38<value>2HD2 CD2 s</value></node>
+    <node>39<value>3HD2 CD2 s</value></node>
+    <node>40<value>OXT C s</value></node>
+    <node>41<value>1H N s</value></node>
+    <node>42<value>2H N s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>LEU-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>LEU-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>LEU-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/LYS.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,106 @@
+<node>LYS
+	<node>Names
+		<node>Lysine</node>
+		<node>Lysin</node>
+		<node>Lys</node>
+		<node>K</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.03796386 1.172592 -0.009692425</value></node>
+		<node>3H<value>H 1.016744 1.426445 0.004398665</value></node>
+		<node>CA<value>C -0.6562778 1.887361 -1.097957</value></node>
+		<node>HA<value>H -0.1455905 1.623495 -2.025311</value></node>
+		<node>C<value>C -0.5601511 3.406333 -0.9147748</value></node>
+		<node>O<value>O -0.5440148 4.087965 -1.963232</value></node>
+		<node>CB<value>C -2.114089 1.411355 -1.200695</value></node>
+		<node>1HB<value>H -2.113627 0.3206328 -1.233166</value></node>
+		<node>2HB<value>H -2.662723 1.730462 -0.3130743</value></node>
+		<node>CG<value>C -2.816849 1.934443 -2.461919</value></node>
+		<node>1HG<value>H -2.878444 3.023734 -2.425601</value></node>
+		<node>2HG<value>H -2.232982 1.645706 -3.338356</value></node>
+		<node>CD<value>C -4.230651 1.346997 -2.563318</value></node>
+		<node>1HD<value>H -4.153291 0.2577495 -2.598617</value></node>
+		<node>2HD<value>H -4.790445 1.632903 -1.669734</value></node>
+		<node>CE<value>C -4.93697 1.869824 -3.82334</value></node>
+		<node>1HE<value>H -4.991973 2.959915 -3.77821</value></node>
+		<node>2HE<value>H -4.353527 1.590667 -4.70365</value></node>
+		<node>NZ<value>N -6.304516 1.325968 -3.962642</value></node>
+		<node>1HZ<value>H -6.733165 1.692468 -4.802127</value></node>
+		<node>2HZ<value>H -6.276195 0.31765 -4.027733</value></node>
+		<node>3HZ<value>H -6.870414 1.591293 -3.16824</value></node>
+		<node>1H<value>H -0.3857403 1.416816 0.8740513</value></node>
+		<node>2H<value>H -0.04427324 0.17682 -0.1571643</value></node>
+		<node>OXT<value>O -0.7869474 3.85405 0.2308864</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>1HB CB s</value></node>
+    <node>20<value>2HB CB s</value></node>
+    <node>21<value>CG CB s</value></node>
+    <node>25<value>1HG CG s</value></node>
+    <node>26<value>2HG CG s</value></node>
+    <node>27<value>CD CG s</value></node>
+    <node>31<value>1HD CD s</value></node>
+    <node>32<value>2HD CD s</value></node>
+    <node>33<value>CE CD s</value></node>
+    <node>37<value>1HE CE s</value></node>
+    <node>38<value>2HE CE s</value></node>
+    <node>39<value>NZ CE s</value></node>
+    <node>43<value>1HZ NZ s</value></node>
+    <node>44<value>2HZ NZ s</value></node>
+    <node>45<value>3HZ NZ s</value></node>
+    <node>46<value>1H N s</value></node>
+    <node>47<value>2H N s</value></node>
+    <node>48<value>OXT C s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node> 
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>LYS-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>LYS-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>LYS-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/MET.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,96 @@
+<node>MET
+	<node>Names
+		<node>Methionine</node>
+		<node>Methionin</node>
+		<node>Met</node>
+		<node>M</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.0654056 1.215812 -0.06949145</value></node>
+		<node>3H<value>H 0.9974914 1.608735 -0.04203663</value></node>
+		<node>CA<value>C -0.6988745 1.893029 -1.131979</value></node>
+		<node>HA<value>H -0.1911148 1.68141 -2.074138</value></node>
+		<node>C<value>C -0.6694928 3.410054 -0.9194202</value></node>
+		<node>O<value>O 0.4107355 3.973423 -1.201833</value></node>
+		<node>CB<value>C -2.121216 1.317703 -1.225039</value></node>
+		<node>1HB<value>H -2.050125 0.2325057 -1.312704</value></node>
+		<node>2HB<value>H -2.682049 1.549083 -0.318349</value></node>
+		<node>CG<value>C -2.887041 1.8377 -2.448318</value></node>
+		<node>1HG<value>H -2.99595 2.919347 -2.383954</value></node>
+		<node>2HG<value>H -2.322049 1.593525 -3.347709</value></node>
+		<node>SD<value>S -4.546617 1.137771 -2.634913</value></node>
+		<node>CE<value>C -5.081393 1.965263 -4.148402</value></node>
+		<node>1HE<value>H -6.08969 1.634787 -4.393987</value></node>
+		<node>2HE<value>H -5.078839 3.043304 -3.993342</value></node>
+		<node>3HE<value>H -4.404794 1.706412 -4.961773</value></node>
+		<node>OXT<value>O -1.565656 3.902471 -0.1992161</value></node>
+		<node>1H<value>H -0.3889995 1.363342 0.8203897</value></node>
+		<node>2H<value>H 0.1172404 0.226119 -0.264187</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>1HB CB s</value></node>
+    <node>20<value>2HB CB s</value></node>
+    <node>21<value>CG CB s</value></node>
+    <node>25<value>1HG CG s</value></node>
+    <node>26<value>2HG CG s</value></node>
+    <node>27<value>SD CG s</value></node>
+    <node>33<value>CE SD s</value></node>
+    <node>37<value>1HE CE s</value></node>
+    <node>38<value>2HE CE s</value></node>
+    <node>39<value>3HE CE s</value></node>
+    <node>40<value>OXT C s</value></node>
+    <node>41<value>1H N s</value></node>
+    <node>42<value>2H N s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>MET-M
+			<node>Properties
+				<node>N_TERMINAL</node>
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>MET-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>MET-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/MG.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,18 @@
+<node>MG
+	<node>Names
+ 		<node>Magnesium ion</node>
+ 		<node>Mg2+</node>
+	</node>
+	<node>Atoms
+		<node>MG<value>Mg 0.0 0.0 0.0</value></node>
+	</node>
+	<node>Bonds
+	</node>
+	<node>Connections
+	</node>
+	<node>Properties
+	</node>
+	<node>Variants
+		<node>Default</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/MSE.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,95 @@
+<node>MSE
+	<node>Names
+		<node>Selenomethionine</node>
+		<node>Selenomethionin</node>
+		<node>Mse</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.0654056 1.215812 -0.06949145</value></node>
+		<node>3H<value>H 0.9974914 1.608735 -0.04203663</value></node>
+		<node>CA<value>C -0.6988745 1.893029 -1.131979</value></node>
+		<node>HA<value>H -0.1911148 1.68141 -2.074138</value></node>
+		<node>C<value>C -0.6694928 3.410054 -0.9194202</value></node>
+		<node>O<value>O 0.4107355 3.973423 -1.201833</value></node>
+		<node>CB<value>C -2.121216 1.317703 -1.225039</value></node>
+		<node>1HB<value>H -2.050125 0.2325057 -1.312704</value></node>
+		<node>2HB<value>H -2.682049 1.549083 -0.318349</value></node>
+		<node>CG<value>C -2.887041 1.8377 -2.448318</value></node>
+		<node>1HG<value>H -2.99595 2.919347 -2.383954</value></node>
+		<node>2HG<value>H -2.322049 1.593525 -3.347709</value></node>
+		<node>SE<value>Se -4.546617 1.137771 -2.634913</value></node>
+		<node>CE<value>C -5.081393 1.965263 -4.148402</value></node>
+		<node>1HE<value>H -6.08969 1.634787 -4.393987</value></node>
+		<node>2HE<value>H -5.078839 3.043304 -3.993342</value></node>
+		<node>3HE<value>H -4.404794 1.706412 -4.961773</value></node>
+		<node>OXT<value>O -1.565656 3.902471 -0.1992161</value></node>
+		<node>1H<value>H -0.3889995 1.363342 0.8203897</value></node>
+		<node>2H<value>H 0.1172404 0.226119 -0.264187</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>1HB CB s</value></node>
+    <node>20<value>2HB CB s</value></node>
+    <node>21<value>CG CB s</value></node>
+    <node>25<value>1HG CG s</value></node>
+    <node>26<value>2HG CG s</value></node>
+    <node>27<value>SE CG s</value></node>
+    <node>33<value>CE SE s</value></node>
+    <node>37<value>1HE CE s</value></node>
+    <node>38<value>2HE CE s</value></node>
+    <node>39<value>3HE CE s</value></node>
+    <node>40<value>OXT C s</value></node>
+    <node>41<value>1H N s</value></node>
+    <node>42<value>2H N s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>MET-M
+			<node>Properties
+				<node>N_TERMINAL</node>
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>MET-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>MET-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/NME.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,46 @@
+<node>NME
+	<node>Names
+		<node>Methylamine</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N  0.724  0.000 -0.079</value></node>
+		<node>CH3<value>C -0.742  0.000  0.011</value></node>
+		<node>1H<value>H 1.046  0.810  0.431</value></node>
+		<node>2H<value>H 1.046 -0.810  0.431</value></node>
+		<node>1HH3<value>H -1.139 -0.861 -0.527</value></node>
+		<node>2HH3<value>H -1.042 -0.056  1.057</value></node>
+		<node>3HH3<value>H -1.133  0.917 -0.431</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>N CH3 s</value></node>
+		<node>2<value>N 1H s</value></node>
+		<node>3<value>N 2H s</value></node>
+		<node>4<value>CH3 1HH3 s</value></node>
+		<node>5<value>CH3 2HH3 s</value></node>
+		<node>6<value>CH3 3HH3 s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+	</node>
+	<node>Variants
+		<node>NME-C
+			<node>Delete
+				<node>2H</node>
+			</node>
+			<node>Rename	
+				<node>1H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>NME-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.Amber.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,486 @@
+<node>Amber<value>PDB</value>
+ <node>*:H1<value>*:1H</value></node>
+ <node>*:H2<value>*:2H</value></node>
+ <node>*:H3<value>*:3H</value></node>
+ <node>*:N<value>*:N</value></node>
+ <node>*:C<value>*:C</value></node>
+ <node>*:O<value>*:O</value></node>
+ <node>*:H<value>*:H</value></node>
+ <node>ALA:CA<value>ALA:CA</value></node>
+ <node>ALA:HA<value>ALA:HA</value></node>
+ <node>ALA:CB<value>ALA:CB</value></node>
+ <node>ALA:HB1<value>ALA:1HB</value></node>
+ <node>ALA:HB2<value>ALA:2HB</value></node>
+ <node>ALA:HB3<value>ALA:3HB</value></node>
+ <node>ARG:CA<value>ARG:CA</value></node>
+ <node>ARG:HA<value>ARG:HA</value></node>
+ <node>ARG:CB<value>ARG:CB</value></node>
+ <node>ARG:HB2<value>ARG:1HB</value></node>
+ <node>ARG:HB3<value>ARG:2HB</value></node>
+ <node>ARG:CG<value>ARG:CG</value></node>
+ <node>ARG:HG2<value>ARG:1HG</value></node>
+ <node>ARG:HG3<value>ARG:2HG</value></node>
+ <node>ARG:CD<value>ARG:CD</value></node>
+ <node>ARG:HD2<value>ARG:1HD</value></node>
+ <node>ARG:HD3<value>ARG:2HD</value></node>
+ <node>ARG:NE<value>ARG:NE</value></node>
+ <node>ARG:HE<value>ARG:HE</value></node>
+ <node>ARG:CZ<value>ARG:CZ</value></node>
+ <node>ARG:NH1<value>ARG:NH1</value></node>
+ <node>ARG:HH11<value>ARG:1HH1</value></node>
+ <node>ARG:HH12<value>ARG:2HH1</value></node>
+ <node>ARG:NH2<value>ARG:NH2</value></node>
+ <node>ARG:HH21<value>ARG:1HH2</value></node>
+ <node>ARG:HH22<value>ARG:2HH2</value></node>
+ <node>ASN:CA<value>ASN:CA</value></node>
+ <node>ASN:HA<value>ASN:HA</value></node>
+ <node>ASN:CB<value>ASN:CB</value></node>
+ <node>ASN:HB2<value>ASN:1HB</value></node>
+ <node>ASN:HB3<value>ASN:2HB</value></node>
+ <node>ASN:CG<value>ASN:CG</value></node>
+ <node>ASN:OD1<value>ASN:OD1</value></node>
+ <node>ASN:ND2<value>ASN:ND2</value></node>
+ <node>ASN:HD21<value>ASN:1HD2</value></node>
+ <node>ASN:HD22<value>ASN:2HD2</value></node>
+ <node>ASP:CA<value>ASP:CA</value></node>
+ <node>ASP:HA<value>ASP:HA</value></node>
+ <node>ASP:CB<value>ASP:CB</value></node>
+ <node>ASP:HB2<value>ASP:1HB</value></node>
+ <node>ASP:HB3<value>ASP:2HB</value></node>
+ <node>ASP:CG<value>ASP:CG</value></node>
+ <node>ASP:OD1<value>ASP:OD1</value></node>
+ <node>ASP:OD2<value>ASP:OD2</value></node>
+ <node>CYS:CA<value>CYS:CA</value></node>
+ <node>CYS:HA<value>CYS:HA</value></node>
+ <node>CYS:CB<value>CYS:CB</value></node>
+ <node>CYS:HB2<value>CYS:1HB</value></node>
+ <node>CYS:HB3<value>CYS:2HB</value></node>
+ <node>CYS:SG<value>CYS:SG</value></node>
+ <node>CYS:HG<value>CYS:HG</value></node>
+ <node>CYS:HSG<value>CYS:HG</value></node>
+ <node>GLU:CA<value>GLU:CA</value></node>
+ <node>GLU:HA<value>GLU:HA</value></node>
+ <node>GLU:CB<value>GLU:CB</value></node>
+ <node>GLU:HB2<value>GLU:1HB</value></node>
+ <node>GLU:HB3<value>GLU:2HB</value></node>
+ <node>GLU:CG<value>GLU:CG</value></node>
+ <node>GLU:HG2<value>GLU:1HG</value></node>
+ <node>GLU:HG3<value>GLU:2HG</value></node>
+ <node>GLU:CD<value>GLU:CD</value></node>
+ <node>GLU:OE1<value>GLU:OE1</value></node>
+ <node>GLU:OE2<value>GLU:OE2</value></node>
+ <node>GLN:CA<value>GLN:CA</value></node>
+ <node>GLN:HA<value>GLN:HA</value></node>
+ <node>GLN:CB<value>GLN:CB</value></node>
+ <node>GLN:HB2<value>GLN:1HB</value></node>
+ <node>GLN:HB3<value>GLN:2HB</value></node>
+ <node>GLN:CG<value>GLN:CG</value></node>
+ <node>GLN:HG2<value>GLN:1HG</value></node>
+ <node>GLN:HG3<value>GLN:2HG</value></node>
+ <node>GLN:CD<value>GLN:CD</value></node>
+ <node>GLN:OE1<value>GLN:OE1</value></node>
+ <node>GLN:NE2<value>GLN:NE2</value></node>
+ <node>GLN:HE21<value>GLN:1HE2</value></node>
+ <node>GLN:HE22<value>GLN:2HE2</value></node>
+ <node>GLY:CA<value>GLY:CA</value></node>
+ <node>GLY:HA2<value>GLY:1HA</value></node>
+ <node>GLY:HA3<value>GLY:2HA</value></node>
+ <node>HIS:CA<value>HIS:CA</value></node>
+ <node>HIS:HA<value>HIS:HA</value></node>
+ <node>HIS:CB<value>HIS:CB</value></node>
+ <node>HIS:HB2<value>HIS:1HB</value></node>
+ <node>HIS:HB3<value>HIS:2HB</value></node>
+ <node>HIS:CG<value>HIS:CG</value></node>
+ <node>HIS:ND1<value>HIS:ND1</value></node>
+ <node>HIS:HD1<value>HIS:HD1</value></node>
+ <node>HIS:CE1<value>HIS:CE1</value></node>
+ <node>HIS:HE1<value>HIS:HE1</value></node>
+ <node>HIS:NE2<value>HIS:NE2</value></node>
+ <node>HIS:HE2<value>HIS:HE2</value></node>
+ <node>HIS:CD2<value>HIS:CD2</value></node>
+ <node>HIS:HD2<value>HIS:HD2</value></node>
+ <node>ILE:CA<value>ILE:CA</value></node>
+ <node>ILE:HA<value>ILE:HA</value></node>
+ <node>ILE:CB<value>ILE:CB</value></node>
+ <node>ILE:HB<value>ILE:HB</value></node>
+ <node>ILE:CG2<value>ILE:CG2</value></node>
+ <node>ILE:HG21<value>ILE:1HG2</value></node>
+ <node>ILE:HG22<value>ILE:2HG2</value></node>
+ <node>ILE:HG23<value>ILE:3HG2</value></node>
+ <node>ILE:CG1<value>ILE:CG1</value></node>
+ <node>ILE:HG12<value>ILE:1HG1</value></node>
+ <node>ILE:HG13<value>ILE:2HG1</value></node>
+ <node>ILE:CD1<value>ILE:CD1</value></node>
+ <node>ILE:HD11<value>ILE:1HD1</value></node>
+ <node>ILE:HD12<value>ILE:2HD1</value></node>
+ <node>ILE:HD13<value>ILE:3HD1</value></node>
+ <node>LEU:CA<value>LEU:CA</value></node>
+ <node>LEU:HA<value>LEU:HA</value></node>
+ <node>LEU:CB<value>LEU:CB</value></node>
+ <node>LEU:HB2<value>LEU:1HB</value></node>
+ <node>LEU:HB3<value>LEU:2HB</value></node>
+ <node>LEU:CG<value>LEU:CG</value></node>
+ <node>LEU:HG<value>LEU:HG</value></node>
+ <node>LEU:CD1<value>LEU:CD1</value></node>
+ <node>LEU:HD11<value>LEU:1HD1</value></node>
+ <node>LEU:HD12<value>LEU:2HD1</value></node>
+ <node>LEU:HD13<value>LEU:3HD1</value></node>
+ <node>LEU:CD2<value>LEU:CD2</value></node>
+ <node>LEU:HD21<value>LEU:1HD2</value></node>
+ <node>LEU:HD22<value>LEU:2HD2</value></node>
+ <node>LEU:HD23<value>LEU:3HD2</value></node>
+ <node>LYS:CA<value>LYS:CA</value></node>
+ <node>LYS:HA<value>LYS:HA</value></node>
+ <node>LYS:CB<value>LYS:CB</value></node>
+ <node>LYS:HB2<value>LYS:1HB</value></node>
+ <node>LYS:HB3<value>LYS:2HB</value></node>
+ <node>LYS:CG<value>LYS:CG</value></node>
+ <node>LYS:HG2<value>LYS:1HG</value></node>
+ <node>LYS:HG3<value>LYS:2HG</value></node>
+ <node>LYS:CD<value>LYS:CD</value></node>
+ <node>LYS:HD2<value>LYS:1HD</value></node>
+ <node>LYS:HD3<value>LYS:2HD</value></node>
+ <node>LYS:CE<value>LYS:CE</value></node>
+ <node>LYS:HE2<value>LYS:1HE</value></node>
+ <node>LYS:HE3<value>LYS:2HE</value></node>
+ <node>LYS:NZ<value>LYS:NZ</value></node>
+ <node>LYS:HZ1<value>LYS:1HZ</value></node>
+ <node>LYS:HZ2<value>LYS:2HZ</value></node>
+ <node>LYS:HZ3<value>LYS:3HZ</value></node>
+ <node>MET:CA<value>MET:CA</value></node>
+ <node>MET:HA<value>MET:HA</value></node>
+ <node>MET:CB<value>MET:CB</value></node>
+ <node>MET:HB2<value>MET:1HB</value></node>
+ <node>MET:HB3<value>MET:2HB</value></node>
+ <node>MET:CG<value>MET:CG</value></node>
+ <node>MET:HG2<value>MET:1HG</value></node>
+ <node>MET:HG3<value>MET:2HG</value></node>
+ <node>MET:SD<value>MET:SD</value></node>
+ <node>MET:CE<value>MET:CE</value></node>
+ <node>MET:HE1<value>MET:1HE</value></node>
+ <node>MET:HE2<value>MET:2HE</value></node>
+ <node>MET:HE3<value>MET:3HE</value></node>
+ <node>PHE:CA<value>PHE:CA</value></node>
+ <node>PHE:HA<value>PHE:HA</value></node>
+ <node>PHE:CB<value>PHE:CB</value></node>
+ <node>PHE:HB2<value>PHE:1HB</value></node>
+ <node>PHE:HB3<value>PHE:2HB</value></node>
+ <node>PHE:CG<value>PHE:CG</value></node>
+ <node>PHE:CD1<value>PHE:CD1</value></node>
+ <node>PHE:HD1<value>PHE:HD1</value></node>
+ <node>PHE:CE1<value>PHE:CE1</value></node>
+ <node>PHE:HE1<value>PHE:HE1</value></node>
+ <node>PHE:CZ<value>PHE:CZ</value></node>
+ <node>PHE:HZ<value>PHE:HZ</value></node>
+ <node>PHE:CE2<value>PHE:CE2</value></node>
+ <node>PHE:HE2<value>PHE:HE2</value></node>
+ <node>PHE:CD2<value>PHE:CD2</value></node>
+ <node>PHE:HD2<value>PHE:HD2</value></node>
+ <node>PRO:CA<value>PRO:CA</value></node>
+ <node>PRO:HA<value>PRO:HA</value></node>
+ <node>PRO:CD<value>PRO:CD</value></node>
+ <node>PRO:HD2<value>PRO:1HD</value></node>
+ <node>PRO:HD3<value>PRO:2HD</value></node>
+ <node>PRO:CG<value>PRO:CG</value></node>
+ <node>PRO:HG2<value>PRO:1HG</value></node>
+ <node>PRO:HG3<value>PRO:2HG</value></node>
+ <node>PRO:CB<value>PRO:CB</value></node>
+ <node>PRO:HB2<value>PRO:1HB</value></node>
+ <node>PRO:HB3<value>PRO:2HB</value></node>
+ <node>SER:CA<value>SER:CA</value></node>
+ <node>SER:HA<value>SER:HA</value></node>
+ <node>SER:CB<value>SER:CB</value></node>
+ <node>SER:HB2<value>SER:1HB</value></node>
+ <node>SER:HB3<value>SER:2HB</value></node>
+ <node>SER:OG<value>SER:OG</value></node>
+ <node>SER:HG<value>SER:HG</value></node>
+ <node>THR:CA<value>THR:CA</value></node>
+ <node>THR:HA<value>THR:HA</value></node>
+ <node>THR:CB<value>THR:CB</value></node>
+ <node>THR:HB<value>THR:HB</value></node>
+ <node>THR:CG2<value>THR:CG2</value></node>
+ <node>THR:HG21<value>THR:1HG2</value></node>
+ <node>THR:HG22<value>THR:2HG2</value></node>
+ <node>THR:HG23<value>THR:3HG2</value></node>
+ <node>THR:OG1<value>THR:OG1</value></node>
+ <node>THR:HG1<value>THR:HG1</value></node>
+ <node>TRP:CA<value>TRP:CA</value></node>
+ <node>TRP:HA<value>TRP:HA</value></node>
+ <node>TRP:CB<value>TRP:CB</value></node>
+ <node>TRP:HB2<value>TRP:1HB</value></node>
+ <node>TRP:HB3<value>TRP:2HB</value></node>
+ <node>TRP:CG<value>TRP:CG</value></node>
+ <node>TRP:CD1<value>TRP:CD1</value></node>
+ <node>TRP:HD1<value>TRP:HD1</value></node>
+ <node>TRP:NE1<value>TRP:NE1</value></node>
+ <node>TRP:HE1<value>TRP:HE1</value></node>
+ <node>TRP:CE2<value>TRP:CE2</value></node>
+ <node>TRP:CZ2<value>TRP:CZ2</value></node>
+ <node>TRP:HZ2<value>TRP:HZ2</value></node>
+ <node>TRP:CH2<value>TRP:CH2</value></node>
+ <node>TRP:HH2<value>TRP:HH2</value></node>
+ <node>TRP:CZ3<value>TRP:CZ3</value></node>
+ <node>TRP:HZ3<value>TRP:HZ3</value></node>
+ <node>TRP:CE3<value>TRP:CE3</value></node>
+ <node>TRP:HE3<value>TRP:HE3</value></node>
+ <node>TRP:CD2<value>TRP:CD2</value></node>
+ <node>TYR:CA<value>TYR:CA</value></node>
+ <node>TYR:HA<value>TYR:HA</value></node>
+ <node>TYR:CB<value>TYR:CB</value></node>
+ <node>TYR:HB2<value>TYR:1HB</value></node>
+ <node>TYR:HB3<value>TYR:2HB</value></node>
+ <node>TYR:CG<value>TYR:CG</value></node>
+ <node>TYR:CD1<value>TYR:CD1</value></node>
+ <node>TYR:HD1<value>TYR:HD1</value></node>
+ <node>TYR:CE1<value>TYR:CE1</value></node>
+ <node>TYR:HE1<value>TYR:HE1</value></node>
+ <node>TYR:CZ<value>TYR:CZ</value></node>
+ <node>TYR:OH<value>TYR:OH</value></node>
+ <node>TYR:HH<value>TYR:HH</value></node>
+ <node>TYR:CE2<value>TYR:CE2</value></node>
+ <node>TYR:HE2<value>TYR:HE2</value></node>
+ <node>TYR:CD2<value>TYR:CD2</value></node>
+ <node>TYR:HD2<value>TYR:HD2</value></node>
+ <node>VAL:CA<value>VAL:CA</value></node>
+ <node>VAL:HA<value>VAL:HA</value></node>
+ <node>VAL:CB<value>VAL:CB</value></node>
+ <node>VAL:HB<value>VAL:HB</value></node>
+ <node>VAL:CG1<value>VAL:CG1</value></node>
+ <node>VAL:HG11<value>VAL:1HG1</value></node>
+ <node>VAL:HG12<value>VAL:2HG1</value></node>
+ <node>VAL:HG13<value>VAL:3HG1</value></node>
+ <node>VAL:CG2<value>VAL:CG2</value></node>
+ <node>VAL:HG21<value>VAL:1HG2</value></node>
+ <node>VAL:HG22<value>VAL:2HG2</value></node>
+ <node>VAL:HG23<value>VAL:3HG2</value></node>
+ <node>DC:P<value>C:P</value></node>
+ <node>DC:O1P<value>C:O1P</value></node>
+ <node>DC:O2P<value>C:O2P</value></node>
+ <node>DC:O5'<value>C:O5*</value></node>
+ <node>DC:C5'<value>C:C5*</value></node>
+ <node>DC:H5'1<value>C:1H5*</value></node>
+ <node>DC:H5'2<value>C:2H5*</value></node>
+ <node>DC:C4'<value>C:C4*</value></node>
+ <node>DC:H4'<value>C:H4*</value></node>
+ <node>DC:O4'<value>C:O4*</value></node>
+ <node>DC:C1'<value>C:C1*</value></node>
+ <node>DC:H1'<value>C:H1*</value></node>
+ <node>DC:N1<value>C:N1</value></node>
+ <node>DC:C6<value>C:C6</value></node>
+ <node>DC:H6<value>C:H6</value></node>
+ <node>DC:C5<value>C:C5</value></node>
+ <node>DC:H5<value>C:H5</value></node>
+ <node>DC:C4<value>C:C4</value></node>
+ <node>DC:N4<value>C:N4</value></node>
+ <node>DC:H41<value>C:1H4</value></node>
+ <node>DC:H42<value>C:2H4</value></node>
+ <node>DC:N3<value>C:N3</value></node>
+ <node>DC:C2<value>C:C2</value></node>
+ <node>DC:O2<value>C:O2</value></node>
+ <node>DC:C3'<value>C:C3*</value></node>
+ <node>DC:H3'<value>C:H3*</value></node>
+ <node>DC:C2'<value>C:C2*</value></node>
+ <node>DC:H2'1<value>C:1H2*</value></node>
+ <node>DC:H2'2<value>C:2H2*</value></node>
+ <node>DC:O3'<value>C:O3*</value></node>
+ <node>DA:P<value>A:P</value></node>
+ <node>DA:O1P<value>A:O1P</value></node>
+ <node>DA:O2P<value>A:O2P</value></node>
+ <node>DA:O5'<value>A:O5*</value></node>
+ <node>DA:C5'<value>A:C5*</value></node>
+ <node>DA:H5'1<value>A:1H5*</value></node>
+ <node>DA:H5'2<value>A:2H5*</value></node>
+ <node>DA:C4'<value>A:C4*</value></node>
+ <node>DA:H4'<value>A:H4*</value></node>
+ <node>DA:O4'<value>A:O4*</value></node>
+ <node>DA:C1'<value>A:C1*</value></node>
+ <node>DA:H1'<value>A:H1*</value></node>
+ <node>DA:N9<value>A:N9</value></node>
+ <node>DA:C8<value>A:C8</value></node>
+ <node>DA:H8<value>A:H8</value></node>
+ <node>DA:N7<value>A:N7</value></node>
+ <node>DA:C5<value>A:C5</value></node>
+ <node>DA:C6<value>A:C6</value></node>
+ <node>DA:N6<value>A:N6</value></node>
+ <node>DA:H61<value>A:1H6</value></node>
+ <node>DA:H62<value>A:2H6</value></node>
+ <node>DA:N1<value>A:N1</value></node>
+ <node>DA:C2<value>A:C2</value></node>
+ <node>DA:H2<value>A:2H</value></node>
+ <node>DA:N3<value>A:N3</value></node>
+ <node>DA:C4<value>A:C4</value></node>
+ <node>DA:C3'<value>A:C3*</value></node>
+ <node>DA:H3'<value>A:H3*</value></node>
+ <node>DA:C2'<value>A:C2*</value></node>
+ <node>DA:H2'1<value>A:1H2*</value></node>
+ <node>DA:H2'2<value>A:2H2*</value></node>
+ <node>DA:O3'<value>A:O3*</value></node>
+ <node>DT:P<value>T:P</value></node>
+ <node>DT:O1P<value>T:O1P</value></node>
+ <node>DT:O2P<value>T:O2P</value></node>
+ <node>DT:O5'<value>T:O5*</value></node>
+ <node>DT:C5'<value>T:C5*</value></node>
+ <node>DT:H5'1<value>T:1H5*</value></node>
+ <node>DT:H5'2<value>T:2H5*</value></node>
+ <node>DT:C4'<value>T:C4*</value></node>
+ <node>DT:H4'<value>T:H4*</value></node>
+ <node>DT:O4'<value>T:O4*</value></node>
+ <node>DT:C1'<value>T:C1*</value></node>
+ <node>DT:H1'<value>T:H1*</value></node>
+ <node>DT:N1<value>T:N1</value></node>
+ <node>DT:C6<value>T:C6</value></node>
+ <node>DT:H6<value>T:H6</value></node>
+ <node>DT:C5<value>T:C5</value></node>
+ <node>DT:C7<value>T:C5M</value></node>
+ <node>DT:H71<value>T:1H5M</value></node>
+ <node>DT:H72<value>T:2H5M</value></node>
+ <node>DT:H73<value>T:3H5M</value></node>
+ <node>DT:C4<value>T:C4</value></node>
+ <node>DT:O4<value>T:O4</value></node>
+ <node>DT:N3<value>T:N3</value></node>
+ <node>DT:H3<value>T:3H</value></node>
+ <node>DT:C2<value>T:C2</value></node>
+ <node>DT:O2<value>T:O2</value></node>
+ <node>DT:C3'<value>T:C3*</value></node>
+ <node>DT:H3'<value>T:H3*</value></node>
+ <node>DT:C2'<value>T:C2*</value></node>
+ <node>DT:H2'1<value>T:1H2*</value></node>
+ <node>DT:H2'2<value>T:2H2*</value></node>
+ <node>DT:O3'<value>T:O3*</value></node>
+ <node>DG:P<value>G:P</value></node>
+ <node>DG:O1P<value>G:O1P</value></node>
+ <node>DG:O2P<value>G:O2P</value></node>
+ <node>DG:O5'<value>G:O5*</value></node>
+ <node>DG:C5'<value>G:C5*</value></node>
+ <node>DG:H5'1<value>G:1H5*</value></node>
+ <node>DG:H5'2<value>G:2H5*</value></node>
+ <node>DG:C4'<value>G:C4*</value></node>
+ <node>DG:H4'<value>G:H4*</value></node>
+ <node>DG:O4'<value>G:O4*</value></node>
+ <node>DG:C1'<value>G:C1*</value></node>
+ <node>DG:H1'<value>G:H1*</value></node>
+ <node>DG:N9<value>G:N9</value></node>
+ <node>DG:C8<value>G:C8</value></node>
+ <node>DG:H8<value>G:H8</value></node>
+ <node>DG:N7<value>G:N7</value></node>
+ <node>DG:C5<value>G:C5</value></node>
+ <node>DG:C6<value>G:C6</value></node>
+ <node>DG:O6<value>G:O6</value></node>
+ <node>DG:N1<value>G:N1</value></node>
+ <node>DG:H1<value>G:1H</value></node>
+ <node>DG:C2<value>G:C2</value></node>
+ <node>DG:N2<value>G:N2</value></node>
+ <node>DG:H21<value>G:1H2</value></node>
+ <node>DG:H22<value>G:2H2</value></node>
+ <node>DG:N3<value>G:N3</value></node>
+ <node>DG:C4<value>G:C4</value></node>
+ <node>DG:C3'<value>G:C3*</value></node>
+ <node>DG:H3'<value>G:H3*</value></node>
+ <node>DG:C2'<value>G:C2*</value></node>
+ <node>DG:H2'1<value>G:1H2*</value></node>
+ <node>DG:H2'2<value>G:2H2*</value></node>
+ <node>DG:O3'<value>G:O3*</value></node>
+
+ <node>*:OXT<value>*:OXT</value></node>
+
+ <node>GLH:CA<value>GLH:CA</value></node>
+ <node>GLH:HA<value>GLH:HA</value></node>
+ <node>GLH:CB<value>GLH:CB</value></node>
+ <node>GLH:HB2<value>GLH:1HB</value></node>
+ <node>GLH:HB3<value>GLH:2HB</value></node>
+ <node>GLH:CG<value>GLH:CG</value></node>
+ <node>GLH:HG2<value>GLH:1HG</value></node>
+ <node>GLH:HG3<value>GLH:2HG</value></node>
+ <node>GLH:CD<value>GLH:CD</value></node>
+ <node>GLH:OE1<value>GLH:OE1</value></node>
+ <node>GLH:OE2<value>GLH:OE2</value></node>
+ <node>GLH:HE2<value>GLH:2HE</value></node>
+
+ <node>HID:CA<value>HID:CA</value></node>
+ <node>HID:HA<value>HID:HA</value></node>
+ <node>HID:CB<value>HID:CB</value></node>
+ <node>HID:HB2<value>HID:1HB</value></node>
+ <node>HID:HB3<value>HID:2HB</value></node>
+ <node>HID:CG<value>HID:CG</value></node>
+ <node>HID:ND1<value>HID:ND1</value></node>
+ <node>HID:HD1<value>HID:HD1</value></node>
+ <node>HID:CE1<value>HID:CE1</value></node>
+ <node>HID:HE1<value>HID:HE1</value></node>
+ <node>HID:NE2<value>HID:NE2</value></node>
+ <node>HID:HE2<value>HID:HE2</value></node>
+ <node>HID:CD2<value>HID:CD2</value></node>
+ <node>HID:HD2<value>HID:HD2</value></node>
+
+ <node>HIE:CA<value>HIE:CA</value></node>
+ <node>HIE:HA<value>HIE:HA</value></node>
+ <node>HIE:CB<value>HIE:CB</value></node>
+ <node>HIE:HB2<value>HIE:1HB</value></node>
+ <node>HIE:HB3<value>HIE:2HB</value></node>
+ <node>HIE:CG<value>HIE:CG</value></node>
+ <node>HIE:ND1<value>HIE:ND1</value></node>
+ <node>HIE:HD1<value>HIE:HD1</value></node>
+ <node>HIE:CE1<value>HIE:CE1</value></node>
+ <node>HIE:HE1<value>HIE:HE1</value></node>
+ <node>HIE:NE2<value>HIE:NE2</value></node>
+ <node>HIE:HE2<value>HIE:HE2</value></node>
+ <node>HIE:CD2<value>HIE:CD2</value></node>
+ <node>HIE:HD2<value>HIE:HD2</value></node>
+
+ <node>HIP:CA<value>HIP:CA</value></node>
+ <node>HIP:HA<value>HIP:HA</value></node>
+ <node>HIP:CB<value>HIP:CB</value></node>
+ <node>HIP:HB2<value>HIP:1HB</value></node>
+ <node>HIP:HB3<value>HIP:2HB</value></node>
+ <node>HIP:CG<value>HIP:CG</value></node>
+ <node>HIP:ND1<value>HIP:ND1</value></node>
+ <node>HIP:HD1<value>HIP:HD1</value></node>
+ <node>HIP:CE1<value>HIP:CE1</value></node>
+ <node>HIP:HE1<value>HIP:HE1</value></node>
+ <node>HIP:NE2<value>HIP:NE2</value></node>
+ <node>HIP:HE2<value>HIP:HE2</value></node>
+ <node>HIP:CD2<value>HIP:CD2</value></node>
+ <node>HIP:HD2<value>HIP:HD2</value></node>
+
+ <node>CYM:CA<value>CYM:CA</value></node>
+ <node>CYM:CB<value>CYM:CB</value></node>
+ <node>CYM:HA<value>CYM:HA</value></node>
+ <node>CYM:HB2<value>CYM:1HB</value></node>
+ <node>CYM:HB3<value>CYM:2HB</value></node>
+ <node>CYM:SG<value>CYM:SG</value></node>
+ <node>CYM:HN<value>CYM:HN</value></node>
+
+ <node>CYX:CA<value>CYX:CA</value></node>
+ <node>CYX:CB<value>CYX:CB</value></node>
+ <node>CYX:HA<value>CYX:HA</value></node>
+ <node>CYX:HB2<value>CYX:1HB</value></node>
+ <node>CYX:HB3<value>CYX:2HB</value></node>
+ <node>CYX:SG<value>CYX:SG</value></node>
+
+ <node>ACE:CH3<value>ACE:CH3</value></node>
+ <node>ACE:HH31<value>ACE:1HH3</value></node>
+ <node>ACE:HH32<value>ACE:2HH3</value></node>
+ <node>ACE:HH33<value>ACE:3HH3</value></node>
+ <node>NME:CH3<value>NME:CH3</value></node>
+ <node>NME:HH31<value>NME:1HH3</value></node>
+ <node>NME:HH32<value>NME:2HH3</value></node>
+ <node>NME:HH33<value>NME:3HH3</value></node>
+
+ <node>LYN:NZ<value>LYN:NZ</value></node>
+ <node>LYN:CA<value>LYN:CA</value></node>
+ <node>LYN:CB<value>LYN:CB</value></node>
+ <node>LYN:CG<value>LYN:CG</value></node>
+ <node>LYN:CD<value>LYN:CD</value></node>
+ <node>LYN:CE<value>LYN:CE</value></node>
+ <node>LYN:HA<value>LYN:HA</value></node>
+ <node>LYN:HB2<value>LYN:1HB</value></node>
+ <node>LYN:HB3<value>LYN:2HB</value></node>
+ <node>LYN:HD2<value>LYN:1HD</value></node>
+ <node>LYN:HD3<value>LYN:2HD</value></node>
+ <node>LYN:HE2<value>LYN:1HE</value></node>
+ <node>LYN:HE3<value>LYN:2HE</value></node>
+ <node>LYN:HG2<value>LYN:1HG</value></node>
+ <node>LYN:HG3<value>LYN:2HG</value></node>
+ <node>LYN:HZ2<value>LYN:2HZ</value></node>
+ <node>LYN:HZ3<value>LYN:3HZ</value></node>
+</node>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.CHARMM.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,279 @@
+<node>CHARMM<value>PDB</value>
+ <node>*:H1<value>*:1H</value></node>
+ <node>*:H2<value>*:2H</value></node>
+ <node>*:H3<value>*:3H</value></node>
+ <node>*:N<value>*:N</value></node>
+ <node>*:C<value>*:C</value></node>
+ <node>*:CA<value>*:CA</value></node>
+ <node>*:O<value>*:O</value></node>
+ <node>*:H<value>*:H</value></node>
+ <node>*:OT1<value>*:O</value></node>
+ <node>*:OT2<value>*:OXT</value></node>
+ <node>*:OCT1<value>*:O</value></node>
+ <node>*:OCT2<value>*:OXT</value></node>
+ <node>*:HT1<value>*:1H</value></node>
+ <node>*:HT2<value>*:2H</value></node>
+ <node>*:HT3<value>*:3H</value></node>
+ <node>ALA:HB1<value>ALA:1HB</value></node>
+ <node>ALA:HB2<value>ALA:2HB</value></node>
+ <node>ALA:HB3<value>ALA:3HB</value></node>
+ <node>ARG:HB2<value>ARG:1HB</value></node>
+ <node>ARG:HB3<value>ARG:2HB</value></node>
+ <node>ARG:HG2<value>ARG:1HG</value></node>
+ <node>ARG:HG3<value>ARG:2HG</value></node>
+ <node>ARG:HD2<value>ARG:1HD</value></node>
+ <node>ARG:HD3<value>ARG:2HD</value></node>
+ <node>ARG:HH1<value>ARG:1HH1</value></node>
+ <node>ARG:HH2<value>ARG:1HH2</value></node>
+ <node>ARG:HH11<value>ARG:1HH1</value></node>
+ <node>ARG:HH12<value>ARG:2HH1</value></node>
+ <node>ARG:HH21<value>ARG:1HH2</value></node>
+ <node>ARG:HH22<value>ARG:2HH2</value></node>
+ <node>ASN:HB2<value>ASN:1HB</value></node>
+ <node>ASN:HB3<value>ASN:2HB</value></node>
+ <node>ASN:HD1<value>ASN:1HD1</value></node>
+ <node>ASN:HD2<value>ASN:1HD2</value></node>
+ <node>ASN:HD21<value>ASN:1HD2</value></node>
+ <node>ASN:HD22<value>ASN:2HD2</value></node>
+ <node>ASP:HB2<value>ASP:1HB</value></node>
+ <node>ASP:HB3<value>ASP:2HB</value></node>
+ <node>CYS:HB2<value>CYS:1HB</value></node>
+ <node>CYS:HB3<value>CYS:2HB</value></node>
+ <node>GLU:HB2<value>GLU:1HB</value></node>
+ <node>GLU:HB3<value>GLU:2HB</value></node>
+ <node>GLU:HG2<value>GLU:1HG</value></node>
+ <node>GLU:HG3<value>GLU:2HG</value></node>
+ <node>GLN:HB2<value>GLN:1HB</value></node>
+ <node>GLN:HB3<value>GLN:2HB</value></node>
+ <node>GLN:HG2<value>GLN:1HG</value></node>
+ <node>GLN:HG3<value>GLN:2HG</value></node>
+ <node>GLN:HE21<value>GLN:1HE2</value></node>
+ <node>GLN:HE22<value>GLN:2HE2</value></node>
+ <node>GLN:HE1<value>GLN:1HE1</value></node>
+ <node>GLN:HE2<value>GLN:1HE2</value></node>
+ <node>GLY:HA2<value>GLY:1HA</value></node>
+ <node>GLY:HA3<value>GLY:2HA</value></node>
+ <node>HIS:HB2<value>HIS:1HB</value></node>
+ <node>HIS:HB3<value>HIS:2HB</value></node>
+ <node>HIE:*<value>HIS:*</value></node>
+ <node>HID:*<value>HIS:*</value></node>
+ <node>HIP:*<value>HIS:*</value></node>
+ <node>ILE:HG21<value>ILE:1HG2</value></node>
+ <node>ILE:HG22<value>ILE:2HG2</value></node>
+ <node>ILE:HG23<value>ILE:3HG2</value></node>
+ <node>ILE:HG12<value>ILE:1HG1</value></node>
+ <node>ILE:HG13<value>ILE:2HG1</value></node>
+ <node>ILE:HD11<value>ILE:1HD1</value></node>
+ <node>ILE:HD12<value>ILE:2HD1</value></node>
+ <node>ILE:HD13<value>ILE:3HD1</value></node>
+ <node>ILE:CD<value>ILE:CD1</value></node>
+ <node>LEU:HB2<value>LEU:1HB</value></node>
+ <node>LEU:HB3<value>LEU:2HB</value></node>
+ <node>LEU:HD11<value>LEU:1HD1</value></node>
+ <node>LEU:HD12<value>LEU:2HD1</value></node>
+ <node>LEU:HD13<value>LEU:3HD1</value></node>
+ <node>LEU:HD21<value>LEU:1HD2</value></node>
+ <node>LEU:HD22<value>LEU:2HD2</value></node>
+ <node>LEU:HD23<value>LEU:3HD2</value></node>
+ <node>LYS:HB2<value>LYS:1HB</value></node>
+ <node>LYS:HB3<value>LYS:2HB</value></node>
+ <node>LYS:HG2<value>LYS:1HG</value></node>
+ <node>LYS:HG3<value>LYS:2HG</value></node>
+ <node>LYS:HD2<value>LYS:1HD</value></node>
+ <node>LYS:HD3<value>LYS:2HD</value></node>
+ <node>LYS:HE2<value>LYS:1HE</value></node>
+ <node>LYS:HE3<value>LYS:2HE</value></node>
+ <node>LYS:HZ1<value>LYS:1HZ</value></node>
+ <node>LYS:HZ2<value>LYS:2HZ</value></node>
+ <node>LYS:HZ3<value>LYS:3HZ</value></node>
+ <node>MET:HB2<value>MET:1HB</value></node>
+ <node>MET:HB3<value>MET:2HB</value></node>
+ <node>MET:HG2<value>MET:1HG</value></node>
+ <node>MET:HG3<value>MET:2HG</value></node>
+ <node>MET:HE1<value>MET:1HE</value></node>
+ <node>MET:HE2<value>MET:2HE</value></node>
+ <node>MET:HE3<value>MET:3HE</value></node>
+ <node>PHE:HB2<value>PHE:1HB</value></node>
+ <node>PHE:HB3<value>PHE:2HB</value></node>
+ <node>PRO:HD2<value>PRO:1HD</value></node>
+ <node>PRO:HD3<value>PRO:2HD</value></node>
+ <node>PRO:HG2<value>PRO:1HG</value></node>
+ <node>PRO:HG3<value>PRO:2HG</value></node>
+ <node>PRO:HB2<value>PRO:1HB</value></node>
+ <node>PRO:HB3<value>PRO:2HB</value></node>
+ <node>SER:HB2<value>SER:1HB</value></node>
+ <node>SER:HB3<value>SER:2HB</value></node>
+ <node>THR:HG21<value>THR:1HG2</value></node>
+ <node>THR:HG22<value>THR:2HG2</value></node>
+ <node>THR:HG23<value>THR:3HG2</value></node>
+ <node>TRP:HB2<value>TRP:1HB</value></node>
+ <node>TRP:HB3<value>TRP:2HB</value></node>
+ <node>TYR:HB2<value>TYR:1HB</value></node>
+ <node>TYR:HB3<value>TYR:2HB</value></node>
+ <node>VAL:HG11<value>VAL:1HG1</value></node>
+ <node>VAL:HG12<value>VAL:2HG1</value></node>
+ <node>VAL:HG13<value>VAL:3HG1</value></node>
+ <node>VAL:HG21<value>VAL:1HG2</value></node>
+ <node>VAL:HG22<value>VAL:2HG2</value></node>
+ <node>VAL:HG23<value>VAL:3HG2</value></node>
+ <node>ACE:HH31<value>ACE:1HH3</value></node>
+ <node>ACE:HH32<value>ACE:2HH3</value></node>
+ <node>ACE:HH33<value>ACE:3HH3</value></node>
+ <node>NME:HH31<value>NME:1HH3</value></node>
+ <node>NME:HH32<value>NME:2HH3</value></node>
+ <node>NME:HH33<value>NME:3HH3</value></node>
+ <node>ALA:CA<value>ALA:CA</value></node>
+ <node>ALA:HA<value>ALA:HA</value></node>
+ <node>ALA:CB<value>ALA:CB</value></node>
+ <node>ARG:CA<value>ARG:CA</value></node>
+ <node>ARG:HA<value>ARG:HA</value></node>
+ <node>ARG:CB<value>ARG:CB</value></node>
+ <node>ARG:CG<value>ARG:CG</value></node>
+ <node>ARG:CD<value>ARG:CD</value></node>
+ <node>ARG:NE<value>ARG:NE</value></node>
+ <node>ARG:HE<value>ARG:HE</value></node>
+ <node>ARG:CZ<value>ARG:CZ</value></node>
+ <node>ARG:NH1<value>ARG:NH1</value></node>
+ <node>ARG:NH2<value>ARG:NH2</value></node>
+ <node>ASN:CA<value>ASN:CA</value></node>
+ <node>ASN:HA<value>ASN:HA</value></node>
+ <node>ASN:CB<value>ASN:CB</value></node>
+ <node>ASN:CG<value>ASN:CG</value></node>
+ <node>ASN:OD1<value>ASN:OD1</value></node>
+ <node>ASN:ND2<value>ASN:ND2</value></node>
+ <node>ASP:CA<value>ASP:CA</value></node>
+ <node>ASP:HA<value>ASP:HA</value></node>
+ <node>ASP:CB<value>ASP:CB</value></node>
+ <node>ASP:CG<value>ASP:CG</value></node>
+ <node>ASP:OD1<value>ASP:OD1</value></node>
+ <node>ASP:OD2<value>ASP:OD2</value></node>
+ <node>CYS:CA<value>CYS:CA</value></node>
+ <node>CYS:HA<value>CYS:HA</value></node>
+ <node>CYS:CB<value>CYS:CB</value></node>
+ <node>CYS:SG<value>CYS:SG</value></node>
+ <node>CYS:HG<value>CYS:HG</value></node>
+ <node>GLU:CA<value>GLU:CA</value></node>
+ <node>GLU:HA<value>GLU:HA</value></node>
+ <node>GLU:CB<value>GLU:CB</value></node>
+ <node>GLU:CG<value>GLU:CG</value></node>
+ <node>GLU:CD<value>GLU:CD</value></node>
+ <node>GLU:OE1<value>GLU:OE1</value></node>
+ <node>GLU:OE2<value>GLU:OE2</value></node>
+ <node>GLN:CA<value>GLN:CA</value></node>
+ <node>GLN:HA<value>GLN:HA</value></node>
+ <node>GLN:CB<value>GLN:CB</value></node>
+ <node>GLN:CG<value>GLN:CG</value></node>
+ <node>GLN:CD<value>GLN:CD</value></node>
+ <node>GLN:OE1<value>GLN:OE1</value></node>
+ <node>GLN:NE2<value>GLN:NE2</value></node>
+ <node>GLY:CA<value>GLY:CA</value></node>
+ <node>HIS:CA<value>HIS:CA</value></node>
+ <node>HIS:HA<value>HIS:HA</value></node>
+ <node>HIS:CB<value>HIS:CB</value></node>
+ <node>HIS:CG<value>HIS:CG</value></node>
+ <node>HIS:ND1<value>HIS:ND1</value></node>
+ <node>HIS:HD1<value>HIS:HD1</value></node>
+ <node>HIS:CE1<value>HIS:CE1</value></node>
+ <node>HIS:HE1<value>HIS:HE1</value></node>
+ <node>HIS:NE2<value>HIS:NE2</value></node>
+ <node>HIS:HE2<value>HIS:HE2</value></node>
+ <node>HIS:CD2<value>HIS:CD2</value></node>
+ <node>HIS:HD2<value>HIS:HD2</value></node>
+ <node>ILE:CA<value>ILE:CA</value></node>
+ <node>ILE:HA<value>ILE:HA</value></node>
+ <node>ILE:CB<value>ILE:CB</value></node>
+ <node>ILE:HB<value>ILE:HB</value></node>
+ <node>ILE:CG2<value>ILE:CG2</value></node>
+ <node>ILE:CG1<value>ILE:CG1</value></node>
+ <node>ILE:CD1<value>ILE:CD1</value></node>
+ <node>LEU:CA<value>LEU:CA</value></node>
+ <node>LEU:HA<value>LEU:HA</value></node>
+ <node>LEU:CB<value>LEU:CB</value></node>
+ <node>LEU:CG<value>LEU:CG</value></node>
+ <node>LEU:HG<value>LEU:HG</value></node>
+ <node>LEU:CD1<value>LEU:CD1</value></node>
+ <node>LEU:CD2<value>LEU:CD2</value></node>
+ <node>LYS:CA<value>LYS:CA</value></node>
+ <node>LYS:HA<value>LYS:HA</value></node>
+ <node>LYS:CB<value>LYS:CB</value></node>
+ <node>LYS:CG<value>LYS:CG</value></node>
+ <node>LYS:CD<value>LYS:CD</value></node>
+ <node>LYS:CE<value>LYS:CE</value></node>
+ <node>LYS:NZ<value>LYS:NZ</value></node>
+ <node>MET:CA<value>MET:CA</value></node>
+ <node>MET:HA<value>MET:HA</value></node>
+ <node>MET:CB<value>MET:CB</value></node>
+ <node>MET:CG<value>MET:CG</value></node>
+ <node>MET:SD<value>MET:SD</value></node>
+ <node>MET:CE<value>MET:CE</value></node>
+ <node>PHE:CA<value>PHE:CA</value></node>
+ <node>PHE:HA<value>PHE:HA</value></node>
+ <node>PHE:CB<value>PHE:CB</value></node>
+ <node>PHE:CG<value>PHE:CG</value></node>
+ <node>PHE:CD1<value>PHE:CD1</value></node>
+ <node>PHE:HD1<value>PHE:HD1</value></node>
+ <node>PHE:CE1<value>PHE:CE1</value></node>
+ <node>PHE:HE1<value>PHE:HE1</value></node>
+ <node>PHE:CZ<value>PHE:CZ</value></node>
+ <node>PHE:HZ<value>PHE:HZ</value></node>
+ <node>PHE:CE2<value>PHE:CE2</value></node>
+ <node>PHE:HE2<value>PHE:HE2</value></node>
+ <node>PHE:CD2<value>PHE:CD2</value></node>
+ <node>PHE:HD2<value>PHE:HD2</value></node>
+ <node>PRO:CA<value>PRO:CA</value></node>
+ <node>PRO:HA<value>PRO:HA</value></node>
+ <node>PRO:CD<value>PRO:CD</value></node>
+ <node>PRO:CG<value>PRO:CG</value></node>
+ <node>PRO:CB<value>PRO:CB</value></node>
+ <node>SER:CA<value>SER:CA</value></node>
+ <node>SER:HA<value>SER:HA</value></node>
+ <node>SER:CB<value>SER:CB</value></node>
+ <node>SER:OG<value>SER:OG</value></node>
+ <node>SER:HG<value>SER:HG</value></node>
+ <node>THR:CA<value>THR:CA</value></node>
+ <node>THR:HA<value>THR:HA</value></node>
+ <node>THR:CB<value>THR:CB</value></node>
+ <node>THR:HB<value>THR:HB</value></node>
+ <node>THR:CG2<value>THR:CG2</value></node>
+ <node>THR:OG1<value>THR:OG1</value></node>
+ <node>THR:HG1<value>THR:HG1</value></node>
+ <node>TRP:CA<value>TRP:CA</value></node>
+ <node>TRP:HA<value>TRP:HA</value></node>
+ <node>TRP:CB<value>TRP:CB</value></node>
+ <node>TRP:CG<value>TRP:CG</value></node>
+ <node>TRP:CD1<value>TRP:CD1</value></node>
+ <node>TRP:HD1<value>TRP:HD1</value></node>
+ <node>TRP:NE1<value>TRP:NE1</value></node>
+ <node>TRP:HE1<value>TRP:HE1</value></node>
+ <node>TRP:CE2<value>TRP:CE2</value></node>
+ <node>TRP:CZ2<value>TRP:CZ2</value></node>
+ <node>TRP:HZ2<value>TRP:HZ2</value></node>
+ <node>TRP:CH2<value>TRP:CH2</value></node>
+ <node>TRP:HH2<value>TRP:HH2</value></node>
+ <node>TRP:CZ3<value>TRP:CZ3</value></node>
+ <node>TRP:HZ3<value>TRP:HZ3</value></node>
+ <node>TRP:CE3<value>TRP:CE3</value></node>
+ <node>TRP:HE3<value>TRP:HE3</value></node>
+ <node>TRP:CD2<value>TRP:CD2</value></node>
+ <node>TYR:CA<value>TYR:CA</value></node>
+ <node>TYR:HA<value>TYR:HA</value></node>
+ <node>TYR:CB<value>TYR:CB</value></node>
+ <node>TYR:CG<value>TYR:CG</value></node>
+ <node>TYR:CD1<value>TYR:CD1</value></node>
+ <node>TYR:HD1<value>TYR:HD1</value></node>
+ <node>TYR:CE1<value>TYR:CE1</value></node>
+ <node>TYR:HE1<value>TYR:HE1</value></node>
+ <node>TYR:CZ<value>TYR:CZ</value></node>
+ <node>TYR:OH<value>TYR:OH</value></node>
+ <node>TYR:HH<value>TYR:HH</value></node>
+ <node>TYR:CE2<value>TYR:CE2</value></node>
+ <node>TYR:HE2<value>TYR:HE2</value></node>
+ <node>TYR:CD2<value>TYR:CD2</value></node>
+ <node>TYR:HD2<value>TYR:HD2</value></node>
+ <node>VAL:CA<value>VAL:CA</value></node>
+ <node>VAL:HA<value>VAL:HA</value></node>
+ <node>VAL:CB<value>VAL:CB</value></node>
+ <node>VAL:HB<value>VAL:HB</value></node>
+ <node>VAL:CG1<value>VAL:CG1</value></node>
+ <node>VAL:CG2<value>VAL:CG2</value></node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.DNA.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,174 @@
+<node>DNA<value>PDB</value>
+ <node>C:P<value>C:P</value></node>
+ <node>DC:OP1<value>C:O1P</value></node>
+ <node>DC:OP2<value>C:O2P</value></node>
+ <node>DC:*<value>C:*</value></node>
+ <node>C:OP1<value>C:O1P</value></node>
+ <node>C:OP2<value>C:O2P</value></node>
+ <node>C:O5'<value>C:O5*</value></node>
+ <node>C:C5'<value>C:C5*</value></node>
+ <node>C:H5'<value>C:1H5*</value></node>
+ <node>C:H5''<value>C:2H5*</value></node>
+ <node>C:C4'<value>C:C4*</value></node>
+ <node>C:H4'<value>C:H4*</value></node>
+ <node>C:O4'<value>C:O4*</value></node>
+ <node>C:C1'<value>C:C1*</value></node>
+ <node>C:H1'<value>C:H1*</value></node>
+ <node>C:N1<value>C:N1</value></node>
+ <node>C:C6<value>C:C6</value></node>
+ <node>C:H6<value>C:H6</value></node>
+ <node>C:C5<value>C:C5</value></node>
+ <node>C:H5<value>C:H5</value></node>
+ <node>C:C4<value>C:C4</value></node>
+ <node>C:N4<value>C:N4</value></node>
+ <node>C:H41<value>C:1H4</value></node>
+ <node>C:H42<value>C:2H4</value></node>
+ <node>C:N3<value>C:N3</value></node>
+ <node>C:C2<value>C:C2</value></node>
+ <node>C:O2<value>C:O2</value></node>
+ <node>C:O2'<value>C:O2*</value></node>
+ <node>C:HO2'<value>C:HO3*</value></node>
+ <node>C:C3'<value>C:C3*</value></node>
+ <node>C:H3'<value>C:H3*</value></node>
+ <node>C:C2'<value>C:C2*</value></node>
+ <node>C:H2'<value>C:1H2*</value></node>
+ <node>C:H2''<value>C:2H2*</value></node>
+ <node>C:O3'<value>C:O3*</value></node>
+ <node>A:P<value>A:P</value></node>
+ <node>DA:OP1<value>A:O1P</value></node>
+ <node>DA:OP2<value>A:O2P</value></node>
+ <node>DA:*<value>A:*</value></node>
+ <node>A:OP1<value>A:O1P</value></node>
+ <node>A:OP2<value>A:O2P</value></node>
+ <node>A:O5'<value>A:O5*</value></node>
+ <node>A:C5'<value>A:C5*</value></node>
+ <node>A:H5'<value>A:1H5*</value></node>
+ <node>A:H5''<value>A:2H5*</value></node>
+ <node>A:C4'<value>A:C4*</value></node>
+ <node>A:H4'<value>A:H4*</value></node>
+ <node>A:O4'<value>A:O4*</value></node>
+ <node>A:C1'<value>A:C1*</value></node>
+ <node>A:H1'<value>A:H1*</value></node>
+ <node>A:N9<value>A:N9</value></node>
+ <node>A:C8<value>A:C8</value></node>
+ <node>A:H8<value>A:H8</value></node>
+ <node>A:N7<value>A:N7</value></node>
+ <node>A:C5<value>A:C5</value></node>
+ <node>A:C6<value>A:C6</value></node>
+ <node>A:N6<value>A:N6</value></node>
+ <node>A:H61<value>A:1H6</value></node>
+ <node>A:H62<value>A:2H6</value></node>
+ <node>A:N1<value>A:N1</value></node>
+ <node>A:C2<value>A:C2</value></node>
+ <node>A:H2<value>A:2H</value></node>
+ <node>A:N3<value>A:N3</value></node>
+ <node>A:C4<value>A:C4</value></node>
+ <node>A:C3'<value>A:C3*</value></node>
+ <node>A:H3'<value>A:H3*</value></node>
+ <node>A:C2'<value>A:C2*</value></node>
+ <node>A:H2'<value>A:1H2*</value></node>
+ <node>A:H2''<value>A:2H2*</value></node>
+ <node>A:O3'<value>A:O3*</value></node>
+ <node>U:P<value>U:P</value></node>
+ <node>U:OP1<value>U:O1P</value></node>
+ <node>U:OP2<value>U:O2P</value></node>
+ <node>U:O5'<value>U:O5*</value></node>
+ <node>U:C5'<value>U:C5*</value></node>
+ <node>U:H5'<value>U:1H5*</value></node>
+ <node>U:H5''<value>U:2H5*</value></node>
+ <node>U:C4'<value>U:C4*</value></node>
+ <node>U:H4'<value>U:H4*</value></node>
+ <node>U:O4'<value>U:O4*</value></node>
+ <node>U:C1'<value>U:C1*</value></node>
+ <node>U:H1'<value>U:H1*</value></node>
+ <node>U:N1<value>U:N1</value></node>
+ <node>U:C6<value>U:C6</value></node>
+ <node>U:H6<value>U:H6</value></node>
+ <node>U:C5<value>U:C5</value></node>
+ <node>U:C4<value>U:C4</value></node>
+ <node>U:O4<value>U:O4</value></node>
+ <node>U:N3<value>U:N3</value></node>
+ <node>U:H3<value>U:H3</value></node>
+ <node>U:C2<value>U:C2</value></node>
+ <node>U:O2<value>U:O2</value></node>
+ <node>U:O2'<value>U:O2*</value></node>
+ <node>U:HO2'<value>U:HO2*</value></node>
+ <node>U:C3'<value>U:C3*</value></node>
+ <node>U:H3'<value>U:H3*</value></node>
+ <node>U:C2'<value>U:C2*</value></node>
+ <node>U:H2'<value>U:1H2*</value></node>
+ <node>U:H2''<value>U:2H2*</value></node>
+ <node>U:O3'<value>U:O3*</value></node>
+ 
+ <node>T:P<value>T:P</value></node>
+ <node>DT:OP1<value>T:O1P</value></node>
+ <node>DT:OP2<value>T:O2P</value></node>
+ <node>DT:*<value>T:*</value></node>
+ <node>T:OP1<value>T:O1P</value></node>
+ <node>T:OP2<value>T:O2P</value></node>
+ <node>T:O5'<value>T:O5*</value></node>
+ <node>T:C5'<value>T:C5*</value></node>
+ <node>T:H5'<value>T:1H5*</value></node>
+ <node>T:H5''<value>T:2H5*</value></node>
+ <node>T:C4'<value>T:C4*</value></node>
+ <node>T:H4'<value>T:H4*</value></node>
+ <node>T:O4'<value>T:O4*</value></node>
+ <node>T:C1'<value>T:C1*</value></node>
+ <node>T:H1'<value>T:H1*</value></node>
+ <node>T:N1<value>T:N1</value></node>
+ <node>T:C6<value>T:C6</value></node>
+ <node>T:H6<value>T:H6</value></node>
+ <node>T:C5<value>T:C5</value></node>
+ <node>T:C7<value>T:C5M</value></node>
+ <node>T:H71<value>T:1H5M</value></node>
+ <node>T:H72<value>T:2H5M</value></node>
+ <node>T:H73<value>T:3H5M</value></node>
+ <node>T:C4<value>T:C4</value></node>
+ <node>T:O4<value>T:O4</value></node>
+ <node>T:N3<value>T:N3</value></node>
+ <node>T:C2<value>T:C2</value></node>
+ <node>T:O2<value>T:O2</value></node>
+ <node>T:C3'<value>T:C3*</value></node>
+ <node>T:H3'<value>T:H3*</value></node>
+ <node>T:C2'<value>T:C2*</value></node>
+ <node>T:H2'<value>T:1H2*</value></node>
+ <node>T:H2''<value>T:2H2*</value></node>
+ <node>T:O3'<value>T:O3*</value></node>
+ <node>T:H3<value>T:3H</value></node>
+ <node>G:P<value>G:P</value></node>
+ <node>DG:OP1<value>G:O1P</value></node>
+ <node>DG:OP2<value>G:O2P</value></node>
+ <node>DG:*<value>G:*</value></node>
+ <node>G:OP1<value>G:O1P</value></node>
+ <node>G:OP2<value>G:O2P</value></node>
+ <node>G:O5'<value>G:O5*</value></node>
+ <node>G:C5'<value>G:C5*</value></node>
+ <node>G:H5'<value>G:1H5*</value></node>
+ <node>G:H5''<value>G:2H5*</value></node>
+ <node>G:C4'<value>G:C4*</value></node>
+ <node>G:H4'<value>G:H4*</value></node>
+ <node>G:O4'<value>G:O4*</value></node>
+ <node>G:C1'<value>G:C1*</value></node>
+ <node>G:H1'<value>G:H1*</value></node>
+ <node>G:N9<value>G:N9</value></node>
+ <node>G:C8<value>G:C8</value></node>
+ <node>G:H8<value>G:H8</value></node>
+ <node>G:N7<value>G:N7</value></node>
+ <node>G:C5<value>G:C5</value></node>
+ <node>G:C6<value>G:C6</value></node>
+ <node>G:O6<value>G:O6</value></node>
+ <node>G:N1<value>G:N1</value></node>
+ <node>G:H1<value>G:1H</value></node>
+ <node>G:C2<value>G:C2</value></node>
+ <node>G:N2<value>G:N2</value></node>
+ <node>G:H21<value>G:1H2</value></node>
+ <node>G:H22<value>G:2H2</value></node>
+ <node>G:N3<value>G:N3</value></node>
+ <node>G:C4<value>G:C4</value></node>
+ <node>G:C3'<value>G:C3*</value></node>
+ <node>G:H3'<value>G:H3*</value></node>
+ <node>G:C2'<value>G:C2*</value></node>
+ <node>G:H2'<value>G:1H2*</value></node>
+ <node>G:H2''<value>G:2H2*</value></node>
+ <node>G:O3'<value>G:O3*</value></node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.Discover.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,255 @@
+<node>Discover<value>PDB</value>
+ <node>*:H1<value>*:1H</value></node>
+ <node>*:H2<value>*:2H</value></node>
+ <node>*:H3<value>*:3H</value></node>
+ <node>*:N<value>*:N</value></node>
+ <node>*:O<value>*:O</value></node>
+ <node>*:C<value>*:C</value></node>
+ <node>*:HN<value>*:H</value></node>
+ <node>ALA:CA<value>ALA:CA</value></node>
+ <node>ALA:HA<value>ALA:HA</value></node>
+ <node>ALA:CB<value>ALA:CB</value></node>
+ <node>ALA:HB1<value>ALA:1HB</value></node>
+ <node>ALA:HB2<value>ALA:2HB</value></node>
+ <node>ALA:HB3<value>ALA:3HB</value></node>
+ <node>ARG:CA<value>ARG:CA</value></node>
+ <node>ARG:HA<value>ARG:HA</value></node>
+ <node>ARG:CB<value>ARG:CB</value></node>
+ <node>ARG:HB1<value>ARG:1HB</value></node>
+ <node>ARG:HB2<value>ARG:2HB</value></node>
+ <node>ARG:CG<value>ARG:CG</value></node>
+ <node>ARG:HG1<value>ARG:1HG</value></node>
+ <node>ARG:HG2<value>ARG:2HG</value></node>
+ <node>ARG:CD<value>ARG:CD</value></node>
+ <node>ARG:HD1<value>ARG:1HD</value></node>
+ <node>ARG:HD2<value>ARG:2HD</value></node>
+ <node>ARG:NE<value>ARG:NE</value></node>
+ <node>ARG:HE<value>ARG:HE</value></node>
+ <node>ARG:CZ<value>ARG:CZ</value></node>
+ <node>ARG:NH1<value>ARG:NH1</value></node>
+ <node>ARG:HH11<value>ARG:1HH1</value></node>
+ <node>ARG:HH12<value>ARG:2HH1</value></node>
+ <node>ARG:NH2<value>ARG:NH2</value></node>
+ <node>ARG:HH21<value>ARG:1HH2</value></node>
+ <node>ARG:HH22<value>ARG:2HH2</value></node>
+ <node>ASN:CA<value>ASN:CA</value></node>
+ <node>ASN:HA<value>ASN:HA</value></node>
+ <node>ASN:CB<value>ASN:CB</value></node>
+ <node>ASN:HB1<value>ASN:1HB</value></node>
+ <node>ASN:HB2<value>ASN:2HB</value></node>
+ <node>ASN:CG<value>ASN:CG</value></node>
+ <node>ASN:OD1<value>ASN:OD1</value></node>
+ <node>ASN:ND2<value>ASN:ND2</value></node>
+ <node>ASN:HD21<value>ASN:1HD2</value></node>
+ <node>ASN:HD22<value>ASN:2HD2</value></node>
+ <node>ASP:CA<value>ASP:CA</value></node>
+ <node>ASP:HA<value>ASP:HA</value></node>
+ <node>ASP:CB<value>ASP:CB</value></node>
+ <node>ASP:HB1<value>ASP:1HB</value></node>
+ <node>ASP:HB2<value>ASP:2HB</value></node>
+ <node>ASP:CG<value>ASP:CG</value></node>
+ <node>ASP:OD1<value>ASP:OD1</value></node>
+ <node>ASP:OD2<value>ASP:OD2</value></node>
+ <node>CYS:CA<value>CYS:CA</value></node>
+ <node>CYS:HA<value>CYS:HA</value></node>
+ <node>CYS:CB<value>CYS:CB</value></node>
+ <node>CYS:HB1<value>CYS:1HB</value></node>
+ <node>CYS:HB2<value>CYS:2HB</value></node>
+ <node>CYS:SG<value>CYS:SG</value></node>
+ <node>CYS:HG<value>CYS:HG</value></node>
+ <node>GLU:CA<value>GLU:CA</value></node>
+ <node>GLU:HA<value>GLU:HA</value></node>
+ <node>GLU:CB<value>GLU:CB</value></node>
+ <node>GLU:HB1<value>GLU:1HB</value></node>
+ <node>GLU:HB2<value>GLU:2HB</value></node>
+ <node>GLU:CG<value>GLU:CG</value></node>
+ <node>GLU:HG1<value>GLU:1HG</value></node>
+ <node>GLU:HG2<value>GLU:2HG</value></node>
+ <node>GLU:CD<value>GLU:CD</value></node>
+ <node>GLU:OE1<value>GLU:OE1</value></node>
+ <node>GLU:OE2<value>GLU:OE2</value></node>
+ <node>GLN:CA<value>GLN:CA</value></node>
+ <node>GLN:HA<value>GLN:HA</value></node>
+ <node>GLN:CB<value>GLN:CB</value></node>
+ <node>GLN:HB1<value>GLN:1HB</value></node>
+ <node>GLN:HB2<value>GLN:2HB</value></node>
+ <node>GLN:CG<value>GLN:CG</value></node>
+ <node>GLN:HG1<value>GLN:1HG</value></node>
+ <node>GLN:HG2<value>GLN:2HG</value></node>
+ <node>GLN:CD<value>GLN:CD</value></node>
+ <node>GLN:OE1<value>GLN:OE1</value></node>
+ <node>GLN:NE2<value>GLN:NE2</value></node>
+ <node>GLN:HE21<value>GLN:1HE2</value></node>
+ <node>GLN:HE22<value>GLN:2HE2</value></node>
+ <node>GLY:CA<value>GLY:CA</value></node>
+ <node>GLY:HA1<value>GLY:1HA</value></node>
+ <node>GLY:HA2<value>GLY:2HA</value></node>
+ <node>HIS:CA<value>HIS:CA</value></node>
+ <node>HIS:HA<value>HIS:HA</value></node>
+ <node>HIS:CB<value>HIS:CB</value></node>
+ <node>HIS:HB1<value>HIS:1HB</value></node>
+ <node>HIS:HB2<value>HIS:2HB</value></node>
+ <node>HIS:CG<value>HIS:CG</value></node>
+ <node>HIS:ND1<value>HIS:ND1</value></node>
+ <node>HIS:HD1<value>HIS:HD1</value></node>
+ <node>HIS:CE1<value>HIS:CE1</value></node>
+ <node>HIS:HE1<value>HIS:HE1</value></node>
+ <node>HIS:NE2<value>HIS:NE2</value></node>
+ <node>HIS:HE2<value>HIS:HE2</value></node>
+ <node>HIS:CD2<value>HIS:CD2</value></node>
+ <node>HIS:HD2<value>HIS:HD2</value></node>
+ <node>ILE:CA<value>ILE:CA</value></node>
+ <node>ILE:HA<value>ILE:HA</value></node>
+ <node>ILE:CB<value>ILE:CB</value></node>
+ <node>ILE:HB<value>ILE:HB</value></node>
+ <node>ILE:CG2<value>ILE:CG2</value></node>
+ <node>ILE:HG21<value>ILE:1HG2</value></node>
+ <node>ILE:HG22<value>ILE:2HG2</value></node>
+ <node>ILE:HG23<value>ILE:3HG2</value></node>
+ <node>ILE:CG1<value>ILE:CG1</value></node>
+ <node>ILE:HG11<value>ILE:1HG1</value></node>
+ <node>ILE:HG12<value>ILE:2HG1</value></node>
+ <node>ILE:CD1<value>ILE:CD1</value></node>
+ <node>ILE:HD11<value>ILE:1HD1</value></node>
+ <node>ILE:HD12<value>ILE:2HD1</value></node>
+ <node>ILE:HD13<value>ILE:3HD1</value></node>
+ <node>LEU:CA<value>LEU:CA</value></node>
+ <node>LEU:HA<value>LEU:HA</value></node>
+ <node>LEU:CB<value>LEU:CB</value></node>
+ <node>LEU:HB1<value>LEU:1HB</value></node>
+ <node>LEU:HB2<value>LEU:2HB</value></node>
+ <node>LEU:CG<value>LEU:CG</value></node>
+ <node>LEU:HG<value>LEU:HG</value></node>
+ <node>LEU:CD1<value>LEU:CD1</value></node>
+ <node>LEU:HD11<value>LEU:1HD1</value></node>
+ <node>LEU:HD12<value>LEU:2HD1</value></node>
+ <node>LEU:HD13<value>LEU:3HD1</value></node>
+ <node>LEU:CD2<value>LEU:CD2</value></node>
+ <node>LEU:HD21<value>LEU:1HD2</value></node>
+ <node>LEU:HD22<value>LEU:2HD2</value></node>
+ <node>LEU:HD23<value>LEU:3HD2</value></node>
+ <node>LYS:CA<value>LYS:CA</value></node>
+ <node>LYS:HA<value>LYS:HA</value></node>
+ <node>LYS:CB<value>LYS:CB</value></node>
+ <node>LYS:HB1<value>LYS:1HB</value></node>
+ <node>LYS:HB2<value>LYS:2HB</value></node>
+ <node>LYS:CG<value>LYS:CG</value></node>
+ <node>LYS:HG1<value>LYS:1HG</value></node>
+ <node>LYS:HG2<value>LYS:2HG</value></node>
+ <node>LYS:CD<value>LYS:CD</value></node>
+ <node>LYS:HD1<value>LYS:1HD</value></node>
+ <node>LYS:HD2<value>LYS:2HD</value></node>
+ <node>LYS:CE<value>LYS:CE</value></node>
+ <node>LYS:HE1<value>LYS:1HE</value></node>
+ <node>LYS:HE2<value>LYS:2HE</value></node>
+ <node>LYS:NZ<value>LYS:NZ</value></node>
+ <node>LYS:HZ1<value>LYS:1HZ</value></node>
+ <node>LYS:HZ2<value>LYS:2HZ</value></node>
+ <node>LYS:HZ3<value>LYS:3HZ</value></node>
+ <node>MET:CA<value>MET:CA</value></node>
+ <node>MET:HA<value>MET:HA</value></node>
+ <node>MET:CB<value>MET:CB</value></node>
+ <node>MET:HB1<value>MET:1HB</value></node>
+ <node>MET:HB2<value>MET:2HB</value></node>
+ <node>MET:CG<value>MET:CG</value></node>
+ <node>MET:HG1<value>MET:1HG</value></node>
+ <node>MET:HG2<value>MET:2HG</value></node>
+ <node>MET:SD<value>MET:SD</value></node>
+ <node>MET:CE<value>MET:CE</value></node>
+ <node>MET:HE1<value>MET:1HE</value></node>
+ <node>MET:HE2<value>MET:2HE</value></node>
+ <node>MET:HE3<value>MET:3HE</value></node>
+ <node>PHE:CA<value>PHE:CA</value></node>
+ <node>PHE:HA<value>PHE:HA</value></node>
+ <node>PHE:CB<value>PHE:CB</value></node>
+ <node>PHE:HB1<value>PHE:1HB</value></node>
+ <node>PHE:HB2<value>PHE:2HB</value></node>
+ <node>PHE:CG<value>PHE:CG</value></node>
+ <node>PHE:CD1<value>PHE:CD1</value></node>
+ <node>PHE:HD1<value>PHE:HD1</value></node>
+ <node>PHE:CE1<value>PHE:CE1</value></node>
+ <node>PHE:HE1<value>PHE:HE1</value></node>
+ <node>PHE:CZ<value>PHE:CZ</value></node>
+ <node>PHE:HZ<value>PHE:HZ</value></node>
+ <node>PHE:CE2<value>PHE:CE2</value></node>
+ <node>PHE:HE2<value>PHE:HE2</value></node>
+ <node>PHE:CD2<value>PHE:CD2</value></node>
+ <node>PHE:HD2<value>PHE:HD2</value></node>
+ <node>PRO:CA<value>PRO:CA</value></node>
+ <node>PRO:HA<value>PRO:HA</value></node>
+ <node>PRO:CD<value>PRO:CD</value></node>
+ <node>PRO:HD1<value>PRO:1HD</value></node>
+ <node>PRO:HD2<value>PRO:2HD</value></node>
+ <node>PRO:CG<value>PRO:CG</value></node>
+ <node>PRO:HG1<value>PRO:1HG</value></node>
+ <node>PRO:HG2<value>PRO:2HG</value></node>
+ <node>PRO:CB<value>PRO:CB</value></node>
+ <node>PRO:HB1<value>PRO:1HB</value></node>
+ <node>PRO:HB2<value>PRO:2HB</value></node>
+ <node>SER:CA<value>SER:CA</value></node>
+ <node>SER:HA<value>SER:HA</value></node>
+ <node>SER:CB<value>SER:CB</value></node>
+ <node>SER:HB1<value>SER:1HB</value></node>
+ <node>SER:HB2<value>SER:2HB</value></node>
+ <node>SER:OG<value>SER:OG</value></node>
+ <node>SER:HG<value>SER:HG</value></node>
+ <node>THR:CA<value>THR:CA</value></node>
+ <node>THR:HA<value>THR:HA</value></node>
+ <node>THR:CB<value>THR:CB</value></node>
+ <node>THR:HB<value>THR:HB</value></node>
+ <node>THR:CG2<value>THR:CG2</value></node>
+ <node>THR:HG21<value>THR:1HG2</value></node>
+ <node>THR:HG22<value>THR:2HG2</value></node>
+ <node>THR:HG23<value>THR:3HG2</value></node>
+ <node>THR:OG1<value>THR:OG1</value></node>
+ <node>THR:HG1<value>THR:HG1</value></node>
+ <node>TRP:CA<value>TRP:CA</value></node>
+ <node>TRP:HA<value>TRP:HA</value></node>
+ <node>TRP:CB<value>TRP:CB</value></node>
+ <node>TRP:HB1<value>TRP:1HB</value></node>
+ <node>TRP:HB2<value>TRP:2HB</value></node>
+ <node>TRP:CG<value>TRP:CG</value></node>
+ <node>TRP:CD1<value>TRP:CD1</value></node>
+ <node>TRP:HD1<value>TRP:HD1</value></node>
+ <node>TRP:NE1<value>TRP:NE1</value></node>
+ <node>TRP:HE1<value>TRP:HE1</value></node>
+ <node>TRP:CE2<value>TRP:CE2</value></node>
+ <node>TRP:CZ2<value>TRP:CZ2</value></node>
+ <node>TRP:HZ2<value>TRP:HZ2</value></node>
+ <node>TRP:CH2<value>TRP:CH2</value></node>
+ <node>TRP:HH2<value>TRP:HH2</value></node>
+ <node>TRP:CZ3<value>TRP:CZ3</value></node>
+ <node>TRP:HZ3<value>TRP:HZ3</value></node>
+ <node>TRP:CE3<value>TRP:CE3</value></node>
+ <node>TRP:HE3<value>TRP:HE3</value></node>
+ <node>TRP:CD2<value>TRP:CD2</value></node>
+ <node>TYR:CA<value>TYR:CA</value></node>
+ <node>TYR:HA<value>TYR:HA</value></node>
+ <node>TYR:CB<value>TYR:CB</value></node>
+ <node>TYR:HB1<value>TYR:1HB</value></node>
+ <node>TYR:HB2<value>TYR:2HB</value></node>
+ <node>TYR:CG<value>TYR:CG</value></node>
+ <node>TYR:CD1<value>TYR:CD1</value></node>
+ <node>TYR:HD1<value>TYR:HD1</value></node>
+ <node>TYR:CE1<value>TYR:CE1</value></node>
+ <node>TYR:HE1<value>TYR:HE1</value></node>
+ <node>TYR:CZ<value>TYR:CZ</value></node>
+ <node>TYR:OH<value>TYR:OH</value></node>
+ <node>TYR:HH<value>TYR:HH</value></node>
+ <node>TYR:CE2<value>TYR:CE2</value></node>
+ <node>TYR:HE2<value>TYR:HE2</value></node>
+ <node>TYR:CD2<value>TYR:CD2</value></node>
+ <node>TYR:HD2<value>TYR:HD2</value></node>
+ <node>VAL:CA<value>VAL:CA</value></node>
+ <node>VAL:HA<value>VAL:HA</value></node>
+ <node>VAL:CB<value>VAL:CB</value></node>
+ <node>VAL:HB<value>VAL:HB</value></node>
+ <node>VAL:CG1<value>VAL:CG1</value></node>
+ <node>VAL:HG11<value>VAL:1HG1</value></node>
+ <node>VAL:HG12<value>VAL:2HG1</value></node>
+ <node>VAL:HG13<value>VAL:3HG1</value></node>
+ <node>VAL:CG2<value>VAL:CG2</value></node>
+ <node>VAL:HG21<value>VAL:1HG2</value></node>
+ <node>VAL:HG22<value>VAL:2HG2</value></node>
+ <node>VAL:HG23<value>VAL:3HG2</value></node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.Star.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,261 @@
+<node>Star<value>PDB</value>
+ <node>*:H1<value>*:1H</value></node>
+ <node>*:H2<value>*:2H</value></node>
+ <node>*:H3<value>*:3H</value></node>
+ <node>*:HT1<value>*:1H</value></node>
+ <node>*:HT2<value>*:2H</value></node>
+ <node>*:HT3<value>*:3H</value></node>
+ <node>*:OT1<value>*:O</value></node>
+ <node>*:OT2<value>*:OXT</value></node>
+ <node>*:N<value>*:N</value></node>
+ <node>*:O<value>*:O</value></node>
+ <node>*:C<value>*:C</value></node>
+ <node>*:HN<value>*:H</value></node>
+ <node>*:H<value>*:H</value></node>
+ <node>ALA:CA<value>ALA:CA</value></node>
+ <node>ALA:HA<value>ALA:HA</value></node>
+ <node>ALA:CB<value>ALA:CB</value></node>
+ <node>ALA:HB1<value>ALA:1HB</value></node>
+ <node>ALA:HB2<value>ALA:2HB</value></node>
+ <node>ALA:HB3<value>ALA:3HB</value></node>
+ <node>ARG:CA<value>ARG:CA</value></node>
+ <node>ARG:HA<value>ARG:HA</value></node>
+ <node>ARG:CB<value>ARG:CB</value></node>
+ <node>ARG:HB2<value>ARG:1HB</value></node>
+ <node>ARG:HB3<value>ARG:2HB</value></node>
+ <node>ARG:CG<value>ARG:CG</value></node>
+ <node>ARG:HG2<value>ARG:1HG</value></node>
+ <node>ARG:HG3<value>ARG:2HG</value></node>
+ <node>ARG:CD<value>ARG:CD</value></node>
+ <node>ARG:HD2<value>ARG:1HD</value></node>
+ <node>ARG:HD3<value>ARG:2HD</value></node>
+ <node>ARG:NE<value>ARG:NE</value></node>
+ <node>ARG:HE<value>ARG:HE</value></node>
+ <node>ARG:CZ<value>ARG:CZ</value></node>
+ <node>ARG:NH1<value>ARG:NH1</value></node>
+ <node>ARG:HH11<value>ARG:1HH1</value></node>
+ <node>ARG:HH12<value>ARG:2HH1</value></node>
+ <node>ARG:NH2<value>ARG:NH2</value></node>
+ <node>ARG:HH21<value>ARG:1HH2</value></node>
+ <node>ARG:HH22<value>ARG:2HH2</value></node>
+ <node>ASN:CA<value>ASN:CA</value></node>
+ <node>ASN:HA<value>ASN:HA</value></node>
+ <node>ASN:CB<value>ASN:CB</value></node>
+ <node>ASN:HB2<value>ASN:1HB</value></node>
+ <node>ASN:HB3<value>ASN:2HB</value></node>
+ <node>ASN:CG<value>ASN:CG</value></node>
+ <node>ASN:OD1<value>ASN:OD1</value></node>
+ <node>ASN:ND2<value>ASN:ND2</value></node>
+ <node>ASN:HD21<value>ASN:1HD2</value></node>
+ <node>ASN:HD22<value>ASN:2HD2</value></node>
+ <node>ASP:CA<value>ASP:CA</value></node>
+ <node>ASP:HA<value>ASP:HA</value></node>
+ <node>ASP:CB<value>ASP:CB</value></node>
+ <node>ASP:HB2<value>ASP:1HB</value></node>
+ <node>ASP:HB3<value>ASP:2HB</value></node>
+ <node>ASP:CG<value>ASP:CG</value></node>
+ <node>ASP:OD1<value>ASP:OD1</value></node>
+ <node>ASP:OD2<value>ASP:OD2</value></node>
+ <node>CYS:CA<value>CYS:CA</value></node>
+ <node>CYS:HA<value>CYS:HA</value></node>
+ <node>CYS:CB<value>CYS:CB</value></node>
+ <node>CYS:HB2<value>CYS:1HB</value></node>
+ <node>CYS:HB3<value>CYS:2HB</value></node>
+ <node>CYS:SG<value>CYS:SG</value></node>
+ <node>CYS:HG<value>CYS:HG</value></node>
+ <node>GLU:CA<value>GLU:CA</value></node>
+ <node>GLU:HA<value>GLU:HA</value></node>
+ <node>GLU:CB<value>GLU:CB</value></node>
+ <node>GLU:HB2<value>GLU:1HB</value></node>
+ <node>GLU:HB3<value>GLU:2HB</value></node>
+ <node>GLU:CG<value>GLU:CG</value></node>
+ <node>GLU:HG2<value>GLU:1HG</value></node>
+ <node>GLU:HG3<value>GLU:2HG</value></node>
+ <node>GLU:CD<value>GLU:CD</value></node>
+ <node>GLU:OE1<value>GLU:OE1</value></node>
+ <node>GLU:OE2<value>GLU:OE2</value></node>
+ <node>GLN:CA<value>GLN:CA</value></node>
+ <node>GLN:HA<value>GLN:HA</value></node>
+ <node>GLN:CB<value>GLN:CB</value></node>
+ <node>GLN:HB2<value>GLN:1HB</value></node>
+ <node>GLN:HB3<value>GLN:2HB</value></node>
+ <node>GLN:CG<value>GLN:CG</value></node>
+ <node>GLN:HG2<value>GLN:1HG</value></node>
+ <node>GLN:HG3<value>GLN:2HG</value></node>
+ <node>GLN:CD<value>GLN:CD</value></node>
+ <node>GLN:OE1<value>GLN:OE1</value></node>
+ <node>GLN:NE2<value>GLN:NE2</value></node>
+ <node>GLN:HE21<value>GLN:1HE2</value></node>
+ <node>GLN:HE22<value>GLN:2HE2</value></node>
+ <node>GLY:CA<value>GLY:CA</value></node>
+ <node>GLY:HA2<value>GLY:1HA</value></node>
+ <node>GLY:HA3<value>GLY:2HA</value></node>
+ <node>HIS:CA<value>HIS:CA</value></node>
+ <node>HIS:HA<value>HIS:HA</value></node>
+ <node>HIS:CB<value>HIS:CB</value></node>
+ <node>HIS:HB2<value>HIS:1HB</value></node>
+ <node>HIS:HB3<value>HIS:2HB</value></node>
+ <node>HIS:CG<value>HIS:CG</value></node>
+ <node>HIS:ND1<value>HIS:ND1</value></node>
+ <node>HIS:HD1<value>HIS:HD1</value></node>
+ <node>HIS:CE1<value>HIS:CE1</value></node>
+ <node>HIS:HE1<value>HIS:HE1</value></node>
+ <node>HIS:NE2<value>HIS:NE2</value></node>
+ <node>HIS:HE2<value>HIS:HE2</value></node>
+ <node>HIS:CD2<value>HIS:CD2</value></node>
+ <node>HIS:HD2<value>HIS:HD2</value></node>
+ <node>ILE:CA<value>ILE:CA</value></node>
+ <node>ILE:HA<value>ILE:HA</value></node>
+ <node>ILE:CB<value>ILE:CB</value></node>
+ <node>ILE:HB<value>ILE:HB</value></node>
+ <node>ILE:CG2<value>ILE:CG2</value></node>
+ <node>ILE:HG21<value>ILE:1HG2</value></node>
+ <node>ILE:HG22<value>ILE:2HG2</value></node>
+ <node>ILE:HG23<value>ILE:3HG2</value></node>
+ <node>ILE:CG1<value>ILE:CG1</value></node>
+ <node>ILE:HG12<value>ILE:1HG1</value></node>
+ <node>ILE:HG13<value>ILE:2HG1</value></node>
+ <node>ILE:CD1<value>ILE:CD1</value></node>
+ <node>ILE:HD11<value>ILE:1HD1</value></node>
+ <node>ILE:HD12<value>ILE:2HD1</value></node>
+ <node>ILE:HD13<value>ILE:3HD1</value></node>
+ <node>LEU:CA<value>LEU:CA</value></node>
+ <node>LEU:HA<value>LEU:HA</value></node>
+ <node>LEU:CB<value>LEU:CB</value></node>
+ <node>LEU:HB2<value>LEU:1HB</value></node>
+ <node>LEU:HB3<value>LEU:2HB</value></node>
+ <node>LEU:CG<value>LEU:CG</value></node>
+ <node>LEU:HG<value>LEU:HG</value></node>
+ <node>LEU:CD1<value>LEU:CD1</value></node>
+ <node>LEU:HD11<value>LEU:1HD1</value></node>
+ <node>LEU:HD12<value>LEU:2HD1</value></node>
+ <node>LEU:HD13<value>LEU:3HD1</value></node>
+ <node>LEU:CD2<value>LEU:CD2</value></node>
+ <node>LEU:HD21<value>LEU:1HD2</value></node>
+ <node>LEU:HD22<value>LEU:2HD2</value></node>
+ <node>LEU:HD23<value>LEU:3HD2</value></node>
+ <node>LYS:CA<value>LYS:CA</value></node>
+ <node>LYS:HA<value>LYS:HA</value></node>
+ <node>LYS:CB<value>LYS:CB</value></node>
+ <node>LYS:HB2<value>LYS:1HB</value></node>
+ <node>LYS:HB3<value>LYS:2HB</value></node>
+ <node>LYS:CG<value>LYS:CG</value></node>
+ <node>LYS:HG2<value>LYS:1HG</value></node>
+ <node>LYS:HG3<value>LYS:2HG</value></node>
+ <node>LYS:CD<value>LYS:CD</value></node>
+ <node>LYS:HD2<value>LYS:1HD</value></node>
+ <node>LYS:HD3<value>LYS:2HD</value></node>
+ <node>LYS:CE<value>LYS:CE</value></node>
+ <node>LYS:HE2<value>LYS:1HE</value></node>
+ <node>LYS:HE3<value>LYS:2HE</value></node>
+ <node>LYS:NZ<value>LYS:NZ</value></node>
+ <node>LYS:HZ1<value>LYS:1HZ</value></node>
+ <node>LYS:HZ2<value>LYS:2HZ</value></node>
+ <node>LYS:HZ3<value>LYS:3HZ</value></node>
+ <node>MET:CA<value>MET:CA</value></node>
+ <node>MET:HA<value>MET:HA</value></node>
+ <node>MET:CB<value>MET:CB</value></node>
+ <node>MET:HB2<value>MET:1HB</value></node>
+ <node>MET:HB3<value>MET:2HB</value></node>
+ <node>MET:CG<value>MET:CG</value></node>
+ <node>MET:HG2<value>MET:1HG</value></node>
+ <node>MET:HG3<value>MET:2HG</value></node>
+ <node>MET:SD<value>MET:SD</value></node>
+ <node>MET:CE<value>MET:CE</value></node>
+ <node>MET:HE1<value>MET:1HE</value></node>
+ <node>MET:HE2<value>MET:2HE</value></node>
+ <node>MET:HE3<value>MET:3HE</value></node>
+ <node>PHE:CA<value>PHE:CA</value></node>
+ <node>PHE:HA<value>PHE:HA</value></node>
+ <node>PHE:CB<value>PHE:CB</value></node>
+ <node>PHE:HB2<value>PHE:1HB</value></node>
+ <node>PHE:HB3<value>PHE:2HB</value></node>
+ <node>PHE:CG<value>PHE:CG</value></node>
+ <node>PHE:CD1<value>PHE:CD1</value></node>
+ <node>PHE:HD1<value>PHE:HD1</value></node>
+ <node>PHE:CE1<value>PHE:CE1</value></node>
+ <node>PHE:HE1<value>PHE:HE1</value></node>
+ <node>PHE:CZ<value>PHE:CZ</value></node>
+ <node>PHE:HZ<value>PHE:HZ</value></node>
+ <node>PHE:CE2<value>PHE:CE2</value></node>
+ <node>PHE:HE2<value>PHE:HE2</value></node>
+ <node>PHE:CD2<value>PHE:CD2</value></node>
+ <node>PHE:HD2<value>PHE:HD2</value></node>
+ <node>PRO:CA<value>PRO:CA</value></node>
+ <node>PRO:HA<value>PRO:HA</value></node>
+ <node>PRO:CD<value>PRO:CD</value></node>
+ <node>PRO:HD2<value>PRO:1HD</value></node>
+ <node>PRO:HD3<value>PRO:2HD</value></node>
+ <node>PRO:CG<value>PRO:CG</value></node>
+ <node>PRO:HG2<value>PRO:1HG</value></node>
+ <node>PRO:HG3<value>PRO:2HG</value></node>
+ <node>PRO:CB<value>PRO:CB</value></node>
+ <node>PRO:HB2<value>PRO:1HB</value></node>
+ <node>PRO:HB3<value>PRO:2HB</value></node>
+ <node>SER:CA<value>SER:CA</value></node>
+ <node>SER:HA<value>SER:HA</value></node>
+ <node>SER:CB<value>SER:CB</value></node>
+ <node>SER:HB2<value>SER:1HB</value></node>
+ <node>SER:HB3<value>SER:2HB</value></node>
+ <node>SER:OG<value>SER:OG</value></node>
+ <node>SER:HG<value>SER:HG</value></node>
+ <node>THR:CA<value>THR:CA</value></node>
+ <node>THR:HA<value>THR:HA</value></node>
+ <node>THR:CB<value>THR:CB</value></node>
+ <node>THR:HB<value>THR:HB</value></node>
+ <node>THR:CG2<value>THR:CG2</value></node>
+ <node>THR:HG21<value>THR:1HG2</value></node>
+ <node>THR:HG22<value>THR:2HG2</value></node>
+ <node>THR:HG23<value>THR:3HG2</value></node>
+ <node>THR:OG1<value>THR:OG1</value></node>
+ <node>THR:HG1<value>THR:HG1</value></node>
+ <node>TRP:CA<value>TRP:CA</value></node>
+ <node>TRP:HA<value>TRP:HA</value></node>
+ <node>TRP:CB<value>TRP:CB</value></node>
+ <node>TRP:HB2<value>TRP:1HB</value></node>
+ <node>TRP:HB3<value>TRP:2HB</value></node>
+ <node>TRP:CG<value>TRP:CG</value></node>
+ <node>TRP:CD1<value>TRP:CD1</value></node>
+ <node>TRP:HD1<value>TRP:HD1</value></node>
+ <node>TRP:NE1<value>TRP:NE1</value></node>
+ <node>TRP:HE1<value>TRP:HE1</value></node>
+ <node>TRP:CE2<value>TRP:CE2</value></node>
+ <node>TRP:CZ2<value>TRP:CZ2</value></node>
+ <node>TRP:HZ2<value>TRP:HZ2</value></node>
+ <node>TRP:CH2<value>TRP:CH2</value></node>
+ <node>TRP:HH2<value>TRP:HH2</value></node>
+ <node>TRP:CZ3<value>TRP:CZ3</value></node>
+ <node>TRP:HZ3<value>TRP:HZ3</value></node>
+ <node>TRP:CE3<value>TRP:CE3</value></node>
+ <node>TRP:HE3<value>TRP:HE3</value></node>
+ <node>TRP:CD2<value>TRP:CD2</value></node>
+ <node>TYR:CA<value>TYR:CA</value></node>
+ <node>TYR:HA<value>TYR:HA</value></node>
+ <node>TYR:CB<value>TYR:CB</value></node>
+ <node>TYR:HB2<value>TYR:1HB</value></node>
+ <node>TYR:HB3<value>TYR:2HB</value></node>
+ <node>TYR:CG<value>TYR:CG</value></node>
+ <node>TYR:CD1<value>TYR:CD1</value></node>
+ <node>TYR:HD1<value>TYR:HD1</value></node>
+ <node>TYR:CE1<value>TYR:CE1</value></node>
+ <node>TYR:HE1<value>TYR:HE1</value></node>
+ <node>TYR:CZ<value>TYR:CZ</value></node>
+ <node>TYR:OH<value>TYR:OH</value></node>
+ <node>TYR:HH<value>TYR:HH</value></node>
+ <node>TYR:CE2<value>TYR:CE2</value></node>
+ <node>TYR:HE2<value>TYR:HE2</value></node>
+ <node>TYR:CD2<value>TYR:CD2</value></node>
+ <node>TYR:HD2<value>TYR:HD2</value></node>
+ <node>VAL:CA<value>VAL:CA</value></node>
+ <node>VAL:HA<value>VAL:HA</value></node>
+ <node>VAL:CB<value>VAL:CB</value></node>
+ <node>VAL:HB<value>VAL:HB</value></node>
+ <node>VAL:CG1<value>VAL:CG1</value></node>
+ <node>VAL:HG11<value>VAL:1HG1</value></node>
+ <node>VAL:HG12<value>VAL:2HG1</value></node>
+ <node>VAL:HG13<value>VAL:3HG1</value></node>
+ <node>VAL:CG2<value>VAL:CG2</value></node>
+ <node>VAL:HG21<value>VAL:1HG2</value></node>
+ <node>VAL:HG22<value>VAL:2HG2</value></node>
+ <node>VAL:HG23<value>VAL:3HG2</value></node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.XPLOR.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,256 @@
+<node>XPLOR<value>PDB</value>
+ <node>*:H1<value>*:1H</value></node>
+ <node>*:H2<value>*:2H</value></node>
+ <node>*:H3<value>*:3H</value></node>
+ <node>*:N<value>*:N</value></node>
+ <node>*:O<value>*:O</value></node>
+ <node>*:C<value>*:C</value></node>
+ <node>*:HN<value>*:H</value></node>
+ <node>*:H<value>*:H</value></node>
+ <node>ALA:CA<value>ALA:CA</value></node>
+ <node>ALA:HA<value>ALA:HA</value></node>
+ <node>ALA:CB<value>ALA:CB</value></node>
+ <node>ALA:HB1<value>ALA:1HB</value></node>
+ <node>ALA:HB2<value>ALA:2HB</value></node>
+ <node>ALA:HB3<value>ALA:3HB</value></node>
+ <node>ARG:CA<value>ARG:CA</value></node>
+ <node>ARG:HA<value>ARG:HA</value></node>
+ <node>ARG:CB<value>ARG:CB</value></node>
+ <node>ARG:HB1<value>ARG:1HB</value></node>
+ <node>ARG:HB2<value>ARG:2HB</value></node>
+ <node>ARG:CG<value>ARG:CG</value></node>
+ <node>ARG:HG1<value>ARG:1HG</value></node>
+ <node>ARG:HG2<value>ARG:2HG</value></node>
+ <node>ARG:CD<value>ARG:CD</value></node>
+ <node>ARG:HD1<value>ARG:1HD</value></node>
+ <node>ARG:HD2<value>ARG:2HD</value></node>
+ <node>ARG:NE<value>ARG:NE</value></node>
+ <node>ARG:HE<value>ARG:HE</value></node>
+ <node>ARG:CZ<value>ARG:CZ</value></node>
+ <node>ARG:NH1<value>ARG:NH1</value></node>
+ <node>ARG:HH11<value>ARG:1HH1</value></node>
+ <node>ARG:HH12<value>ARG:2HH1</value></node>
+ <node>ARG:NH2<value>ARG:NH2</value></node>
+ <node>ARG:HH21<value>ARG:1HH2</value></node>
+ <node>ARG:HH22<value>ARG:2HH2</value></node>
+ <node>ASN:CA<value>ASN:CA</value></node>
+ <node>ASN:HA<value>ASN:HA</value></node>
+ <node>ASN:CB<value>ASN:CB</value></node>
+ <node>ASN:HB1<value>ASN:1HB</value></node>
+ <node>ASN:HB2<value>ASN:2HB</value></node>
+ <node>ASN:CG<value>ASN:CG</value></node>
+ <node>ASN:OD1<value>ASN:OD1</value></node>
+ <node>ASN:ND2<value>ASN:ND2</value></node>
+ <node>ASN:HD21<value>ASN:1HD2</value></node>
+ <node>ASN:HD22<value>ASN:2HD2</value></node>
+ <node>ASP:CA<value>ASP:CA</value></node>
+ <node>ASP:HA<value>ASP:HA</value></node>
+ <node>ASP:CB<value>ASP:CB</value></node>
+ <node>ASP:HB1<value>ASP:1HB</value></node>
+ <node>ASP:HB2<value>ASP:2HB</value></node>
+ <node>ASP:CG<value>ASP:CG</value></node>
+ <node>ASP:OD1<value>ASP:OD1</value></node>
+ <node>ASP:OD2<value>ASP:OD2</value></node>
+ <node>CYS:CA<value>CYS:CA</value></node>
+ <node>CYS:HA<value>CYS:HA</value></node>
+ <node>CYS:CB<value>CYS:CB</value></node>
+ <node>CYS:HB1<value>CYS:1HB</value></node>
+ <node>CYS:HB2<value>CYS:2HB</value></node>
+ <node>CYS:SG<value>CYS:SG</value></node>
+ <node>CYS:HG<value>CYS:HG</value></node>
+ <node>GLU:CA<value>GLU:CA</value></node>
+ <node>GLU:HA<value>GLU:HA</value></node>
+ <node>GLU:CB<value>GLU:CB</value></node>
+ <node>GLU:HB1<value>GLU:1HB</value></node>
+ <node>GLU:HB2<value>GLU:2HB</value></node>
+ <node>GLU:CG<value>GLU:CG</value></node>
+ <node>GLU:HG1<value>GLU:1HG</value></node>
+ <node>GLU:HG2<value>GLU:2HG</value></node>
+ <node>GLU:CD<value>GLU:CD</value></node>
+ <node>GLU:OE1<value>GLU:OE1</value></node>
+ <node>GLU:OE2<value>GLU:OE2</value></node>
+ <node>GLN:CA<value>GLN:CA</value></node>
+ <node>GLN:HA<value>GLN:HA</value></node>
+ <node>GLN:CB<value>GLN:CB</value></node>
+ <node>GLN:HB1<value>GLN:1HB</value></node>
+ <node>GLN:HB2<value>GLN:2HB</value></node>
+ <node>GLN:CG<value>GLN:CG</value></node>
+ <node>GLN:HG1<value>GLN:1HG</value></node>
+ <node>GLN:HG2<value>GLN:2HG</value></node>
+ <node>GLN:CD<value>GLN:CD</value></node>
+ <node>GLN:OE1<value>GLN:OE1</value></node>
+ <node>GLN:NE2<value>GLN:NE2</value></node>
+ <node>GLN:HE21<value>GLN:1HE2</value></node>
+ <node>GLN:HE22<value>GLN:2HE2</value></node>
+ <node>GLY:CA<value>GLY:CA</value></node>
+ <node>GLY:HA1<value>GLY:1HA</value></node>
+ <node>GLY:HA2<value>GLY:2HA</value></node>
+ <node>HIS:CA<value>HIS:CA</value></node>
+ <node>HIS:HA<value>HIS:HA</value></node>
+ <node>HIS:CB<value>HIS:CB</value></node>
+ <node>HIS:HB1<value>HIS:1HB</value></node>
+ <node>HIS:HB2<value>HIS:2HB</value></node>
+ <node>HIS:CG<value>HIS:CG</value></node>
+ <node>HIS:ND1<value>HIS:ND1</value></node>
+ <node>HIS:HD1<value>HIS:HD1</value></node>
+ <node>HIS:CE1<value>HIS:CE1</value></node>
+ <node>HIS:HE1<value>HIS:HE1</value></node>
+ <node>HIS:NE2<value>HIS:NE2</value></node>
+ <node>HIS:HE2<value>HIS:HE2</value></node>
+ <node>HIS:CD2<value>HIS:CD2</value></node>
+ <node>HIS:HD2<value>HIS:HD2</value></node>
+ <node>ILE:CA<value>ILE:CA</value></node>
+ <node>ILE:HA<value>ILE:HA</value></node>
+ <node>ILE:CB<value>ILE:CB</value></node>
+ <node>ILE:HB<value>ILE:HB</value></node>
+ <node>ILE:CG2<value>ILE:CG2</value></node>
+ <node>ILE:HG21<value>ILE:1HG2</value></node>
+ <node>ILE:HG22<value>ILE:2HG2</value></node>
+ <node>ILE:HG23<value>ILE:3HG2</value></node>
+ <node>ILE:CG1<value>ILE:CG1</value></node>
+ <node>ILE:HG11<value>ILE:1HG1</value></node>
+ <node>ILE:HG12<value>ILE:2HG1</value></node>
+ <node>ILE:CD1<value>ILE:CD1</value></node>
+ <node>ILE:HD11<value>ILE:1HD1</value></node>
+ <node>ILE:HD12<value>ILE:2HD1</value></node>
+ <node>ILE:HD13<value>ILE:3HD1</value></node>
+ <node>LEU:CA<value>LEU:CA</value></node>
+ <node>LEU:HA<value>LEU:HA</value></node>
+ <node>LEU:CB<value>LEU:CB</value></node>
+ <node>LEU:HB1<value>LEU:1HB</value></node>
+ <node>LEU:HB2<value>LEU:2HB</value></node>
+ <node>LEU:CG<value>LEU:CG</value></node>
+ <node>LEU:HG<value>LEU:HG</value></node>
+ <node>LEU:CD1<value>LEU:CD1</value></node>
+ <node>LEU:HD11<value>LEU:1HD1</value></node>
+ <node>LEU:HD12<value>LEU:2HD1</value></node>
+ <node>LEU:HD13<value>LEU:3HD1</value></node>
+ <node>LEU:CD2<value>LEU:CD2</value></node>
+ <node>LEU:HD21<value>LEU:1HD2</value></node>
+ <node>LEU:HD22<value>LEU:2HD2</value></node>
+ <node>LEU:HD23<value>LEU:3HD2</value></node>
+ <node>LYS:CA<value>LYS:CA</value></node>
+ <node>LYS:HA<value>LYS:HA</value></node>
+ <node>LYS:CB<value>LYS:CB</value></node>
+ <node>LYS:HB1<value>LYS:1HB</value></node>
+ <node>LYS:HB2<value>LYS:2HB</value></node>
+ <node>LYS:CG<value>LYS:CG</value></node>
+ <node>LYS:HG1<value>LYS:1HG</value></node>
+ <node>LYS:HG2<value>LYS:2HG</value></node>
+ <node>LYS:CD<value>LYS:CD</value></node>
+ <node>LYS:HD1<value>LYS:1HD</value></node>
+ <node>LYS:HD2<value>LYS:2HD</value></node>
+ <node>LYS:CE<value>LYS:CE</value></node>
+ <node>LYS:HE1<value>LYS:1HE</value></node>
+ <node>LYS:HE2<value>LYS:2HE</value></node>
+ <node>LYS:NZ<value>LYS:NZ</value></node>
+ <node>LYS:HZ1<value>LYS:1HZ</value></node>
+ <node>LYS:HZ2<value>LYS:2HZ</value></node>
+ <node>LYS:HZ3<value>LYS:3HZ</value></node>
+ <node>MET:CA<value>MET:CA</value></node>
+ <node>MET:HA<value>MET:HA</value></node>
+ <node>MET:CB<value>MET:CB</value></node>
+ <node>MET:HB1<value>MET:1HB</value></node>
+ <node>MET:HB2<value>MET:2HB</value></node>
+ <node>MET:CG<value>MET:CG</value></node>
+ <node>MET:HG1<value>MET:1HG</value></node>
+ <node>MET:HG2<value>MET:2HG</value></node>
+ <node>MET:SD<value>MET:SD</value></node>
+ <node>MET:CE<value>MET:CE</value></node>
+ <node>MET:HE1<value>MET:1HE</value></node>
+ <node>MET:HE2<value>MET:2HE</value></node>
+ <node>MET:HE3<value>MET:3HE</value></node>
+ <node>PHE:CA<value>PHE:CA</value></node>
+ <node>PHE:HA<value>PHE:HA</value></node>
+ <node>PHE:CB<value>PHE:CB</value></node>
+ <node>PHE:HB1<value>PHE:1HB</value></node>
+ <node>PHE:HB2<value>PHE:2HB</value></node>
+ <node>PHE:CG<value>PHE:CG</value></node>
+ <node>PHE:CD1<value>PHE:CD1</value></node>
+ <node>PHE:HD1<value>PHE:HD1</value></node>
+ <node>PHE:CE1<value>PHE:CE1</value></node>
+ <node>PHE:HE1<value>PHE:HE1</value></node>
+ <node>PHE:CZ<value>PHE:CZ</value></node>
+ <node>PHE:HZ<value>PHE:HZ</value></node>
+ <node>PHE:CE2<value>PHE:CE2</value></node>
+ <node>PHE:HE2<value>PHE:HE2</value></node>
+ <node>PHE:CD2<value>PHE:CD2</value></node>
+ <node>PHE:HD2<value>PHE:HD2</value></node>
+ <node>PRO:CA<value>PRO:CA</value></node>
+ <node>PRO:HA<value>PRO:HA</value></node>
+ <node>PRO:CD<value>PRO:CD</value></node>
+ <node>PRO:HD1<value>PRO:1HD</value></node>
+ <node>PRO:HD2<value>PRO:2HD</value></node>
+ <node>PRO:CG<value>PRO:CG</value></node>
+ <node>PRO:HG1<value>PRO:1HG</value></node>
+ <node>PRO:HG2<value>PRO:2HG</value></node>
+ <node>PRO:CB<value>PRO:CB</value></node>
+ <node>PRO:HB1<value>PRO:1HB</value></node>
+ <node>PRO:HB2<value>PRO:2HB</value></node>
+ <node>SER:CA<value>SER:CA</value></node>
+ <node>SER:HA<value>SER:HA</value></node>
+ <node>SER:CB<value>SER:CB</value></node>
+ <node>SER:HB1<value>SER:1HB</value></node>
+ <node>SER:HB2<value>SER:2HB</value></node>
+ <node>SER:OG<value>SER:OG</value></node>
+ <node>SER:HG<value>SER:HG</value></node>
+ <node>THR:CA<value>THR:CA</value></node>
+ <node>THR:HA<value>THR:HA</value></node>
+ <node>THR:CB<value>THR:CB</value></node>
+ <node>THR:HB<value>THR:HB</value></node>
+ <node>THR:CG2<value>THR:CG2</value></node>
+ <node>THR:HG21<value>THR:1HG2</value></node>
+ <node>THR:HG22<value>THR:2HG2</value></node>
+ <node>THR:HG23<value>THR:3HG2</value></node>
+ <node>THR:OG1<value>THR:OG1</value></node>
+ <node>THR:HG1<value>THR:HG1</value></node>
+ <node>TRP:CA<value>TRP:CA</value></node>
+ <node>TRP:HA<value>TRP:HA</value></node>
+ <node>TRP:CB<value>TRP:CB</value></node>
+ <node>TRP:HB1<value>TRP:1HB</value></node>
+ <node>TRP:HB2<value>TRP:2HB</value></node>
+ <node>TRP:CG<value>TRP:CG</value></node>
+ <node>TRP:CD1<value>TRP:CD1</value></node>
+ <node>TRP:HD1<value>TRP:HD1</value></node>
+ <node>TRP:NE1<value>TRP:NE1</value></node>
+ <node>TRP:HE1<value>TRP:HE1</value></node>
+ <node>TRP:CE2<value>TRP:CE2</value></node>
+ <node>TRP:CZ2<value>TRP:CZ2</value></node>
+ <node>TRP:HZ2<value>TRP:HZ2</value></node>
+ <node>TRP:CH2<value>TRP:CH2</value></node>
+ <node>TRP:HH2<value>TRP:HH2</value></node>
+ <node>TRP:CZ3<value>TRP:CZ3</value></node>
+ <node>TRP:HZ3<value>TRP:HZ3</value></node>
+ <node>TRP:CE3<value>TRP:CE3</value></node>
+ <node>TRP:HE3<value>TRP:HE3</value></node>
+ <node>TRP:CD2<value>TRP:CD2</value></node>
+ <node>TYR:CA<value>TYR:CA</value></node>
+ <node>TYR:HA<value>TYR:HA</value></node>
+ <node>TYR:CB<value>TYR:CB</value></node>
+ <node>TYR:HB1<value>TYR:1HB</value></node>
+ <node>TYR:HB2<value>TYR:2HB</value></node>
+ <node>TYR:CG<value>TYR:CG</value></node>
+ <node>TYR:CD1<value>TYR:CD1</value></node>
+ <node>TYR:HD1<value>TYR:HD1</value></node>
+ <node>TYR:CE1<value>TYR:CE1</value></node>
+ <node>TYR:HE1<value>TYR:HE1</value></node>
+ <node>TYR:CZ<value>TYR:CZ</value></node>
+ <node>TYR:OH<value>TYR:OH</value></node>
+ <node>TYR:HH<value>TYR:HH</value></node>
+ <node>TYR:CE2<value>TYR:CE2</value></node>
+ <node>TYR:HE2<value>TYR:HE2</value></node>
+ <node>TYR:CD2<value>TYR:CD2</value></node>
+ <node>TYR:HD2<value>TYR:HD2</value></node>
+ <node>VAL:CA<value>VAL:CA</value></node>
+ <node>VAL:HA<value>VAL:HA</value></node>
+ <node>VAL:CB<value>VAL:CB</value></node>
+ <node>VAL:HB<value>VAL:HB</value></node>
+ <node>VAL:CG1<value>VAL:CG1</value></node>
+ <node>VAL:HG11<value>VAL:1HG1</value></node>
+ <node>VAL:HG12<value>VAL:2HG1</value></node>
+ <node>VAL:HG13<value>VAL:3HG1</value></node>
+ <node>VAL:CG2<value>VAL:CG2</value></node>
+ <node>VAL:HG21<value>VAL:1HG2</value></node>
+ <node>VAL:HG22<value>VAL:2HG2</value></node>
+ <node>VAL:HG23<value>VAL:3HG2</value></node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/PCA.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,58 @@
+<node>PCA
+  <node>Names
+		<node>Pyroglutamate</node>
+		<node>Pyroglutamat</node>
+		<node>PCA</node>
+  </node>
+  <node>Atoms
+    <node>N<value>N 0.633233 -0.738520 0.753950</value></node>
+    <node>H<value>H 0.354342 -1.687937 0.623119</value></node>
+    <node>CA<value>C -0.480480 0.254947 0.696080</value></node>
+    <node>C<value>C -1.757691 -0.270758 -0.060790</value></node>
+    <node>O<value>O -1.739275 -1.432777 -0.530185</value></node>
+    <node>CB<value>C 0.102054 1.514384 0.035819</value></node>
+    <node>CG<value>C 1.511340 1.164025 -0.440294</value></node>
+    <node>CD<value>C 1.725147 -0.277577 -0.025832</value></node>
+    <node>OE<value>O 2.716615 -0.966582 -0.238284</value></node>
+    <node>HA<value>H -0.765277 0.458788 1.753344</value></node>
+    <node>1HB<value>H -0.540287 1.847529 -0.801287</value></node>
+    <node>2HB<value>H 0.122684 2.361261 0.746090</value></node>
+    <node>1HG<value>H 1.616550 1.265144 -1.535904</value></node>
+    <node>2HG<value>H 2.282434 1.821242 0.000860</value></node>
+    <node>OXT<value>O -2.740502 0.498543 -0.143251</value></node>
+  </node>
+  <node>Bonds
+    <node>4<value>H N s</value></node>
+    <node>5<value>C CA s</value></node>
+    <node>8<value>O C d</value></node>
+    <node>11<value>CB CA s</value></node>
+    <node>13<value>CG CB s</value></node>
+    <node>17<value>CD CG s</value></node>
+    <node>19<value>CD N s</value></node>
+    <node>20<value>OE CD d</value></node>
+    <node>21<value>HA CA s</value></node>
+    <node>22<value>1HB CB s</value></node>
+    <node>23<value>2HB CB s</value></node>
+    <node>24<value>1HG CG s</value></node>
+    <node>25<value>2HG CG s</value></node>
+    <node>26<value>OXT C s</value></node>
+		<node>27<value>N CA s</value></node>
+  </node>
+	<node>Connections
+    <node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+	</node>
+	<node>Variants
+		<node>Default
+		</node>
+		<node>PCA-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/PHE.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,103 @@
+<node>PHE
+	<node>Names
+		<node>Phenylalanine</node>
+		<node>Phenylalanin</node>
+		<node>Phe</node>
+		<node>F</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.1341407 1.351202 -0.07911759</value></node>
+		<node>3H<value>H 0.803193 2.035005 0.2534044</value></node>
+		<node>CA<value>C -0.7211604 2.001838 -1.087341</value></node>
+		<node>HA<value>H -0.07892336 2.270821 -1.926756</value></node>
+		<node>C<value>C -1.300131 3.307535 -0.5325462</value></node>
+		<node>O<value>O -0.4477309 4.171679 -0.229457</value></node>
+		<node>CB<value>C -1.791856 1.027805 -1.599674</value></node>
+		<node>1HB<value>H -1.28636 0.160502 -2.026756</value></node>
+		<node>2HB<value>H -2.380364 0.6727667 -0.7525354</value></node>
+		<node>CG<value>C -2.70873 1.607533 -2.661208</value></node>
+		<node>CD1<value>C -4.074711 1.815559 -2.387768</value></node>
+		<node>HD1<value>H -4.496757 1.527902 -1.435336</value></node>
+		<node>CD2<value>C -2.185439 1.971959 -3.916095</value></node>
+		<node>HD2<value>H -1.142983 1.801105 -4.144545</value></node>
+		<node>CE1<value>C -4.90709 2.399215 -3.358655</value></node>
+		<node>HE1<value>H -5.955226 2.557371 -3.147432</value></node>
+		<node>CE2<value>C -3.019025 2.554821 -4.88633</value></node>
+		<node>HE2<value>H -2.61471 2.832835 -5.84938</value></node>
+		<node>CZ<value>C -4.379117 2.771946 -4.606688</value></node>
+		<node>HZ<value>H -5.020426 3.217529 -5.354036</value></node>
+		<node>1H<value>H -0.4341985 1.034029 0.6931909</value></node>
+		<node>2H<value>H 0.6169096 0.5661594 -0.4922875</value></node>
+		<node>OXT<value>O -2.460581 3.26509 -0.06804343</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>1HB CB s</value></node>
+    <node>20<value>2HB CB s</value></node>
+    <node>21<value>CG CB s</value></node>
+    <node>24<value>CD1 CG a</value></node>
+    <node>27<value>HD1 CD1 s</value></node>
+    <node>28<value>CD2 CG a</value></node>
+    <node>31<value>HD2 CD2 s</value></node>
+    <node>32<value>CE1 CD1 a</value></node>
+    <node>35<value>HE1 CE1 s</value></node>
+    <node>36<value>CE2 CD2 a</value></node>
+    <node>39<value>HE2 CE2 s</value></node>
+    <node>40<value>CZ CE1 a</value></node>
+    <node>41<value>CZ CE2 a</value></node>
+    <node>43<value>HZ CZ s</value></node>
+    <node>44<value>1H N s</value></node>
+    <node>45<value>2H N s</value></node>
+    <node>46<value>OXT C s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>PHE-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>PHE-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>PHE-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/PRO.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,85 @@
+<node>PRO
+	<node>Names
+ 		<node>Proline</node>
+		<node>Prolin</node>
+		<node>Pro</node>
+		<node>P</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.03190848 1.374047 -0.2465853</value></node>
+		<node>CA<value>C 0.4437964 0.4522487 -1.313841</value></node>
+		<node>HA<value>H -0.4329885 0.1122399 -1.866649</value></node>
+		<node>C<value>C 1.153984 -0.7795747 -0.7384319</value></node>
+		<node>O<value>O 2.396496 -0.7261156 -0.5988901</value></node>
+		<node>CB<value>C 1.34565 1.283736 -2.23033</value></node>
+		<node>1HB<value>H 2.062533 0.6767905 -2.785621</value></node>
+		<node>2HB<value>H 0.7182986 1.840951 -2.927554</value></node>
+		<node>CG<value>C 2.02933 2.275858 -1.278275</value></node>
+		<node>1HG<value>H 3.057449 1.966999 -1.081919</value></node>
+		<node>2HG<value>H 2.018846 3.280874 -1.702292</value></node>
+		<node>CD<value>C 1.21179 2.210818 0.01815094</value></node>
+		<node>1HD<value>H 0.9135454 3.204023 0.3557259</value></node>
+		<node>2HD<value>H 1.815136 1.733186 0.791898</value></node>
+		<node>OXT<value>O 0.4228693 -1.712297 -0.3395816</value></node>
+		<node>1H<value>H -0.2823305 0.8858488 0.5799416</value></node>
+		<node>2H<value>H -0.7056003 1.96474 -0.6034356</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>CA N s</value></node>
+    <node>9<value>HA CA s</value></node>
+    <node>10<value>C CA s</value></node>
+    <node>13<value>O C d</value></node>
+    <node>14<value>CB CA s</value></node>
+    <node>18<value>1HB CB s</value></node>
+    <node>19<value>2HB CB s</value></node>
+    <node>20<value>CG CB s</value></node>
+    <node>24<value>1HG CG s</value></node>
+    <node>25<value>2HG CG s</value></node>
+    <node>26<value>CD N s</value></node>
+    <node>27<value>CD CG s</value></node>
+    <node>30<value>1HD CD s</value></node>
+    <node>31<value>2HD CD s</value></node>
+    <node>32<value>OXT C s</value></node>
+    <node>33<value>1H N s</value></node>
+    <node>34<value>2H N s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+ 		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+		</node>
+		<node>PRO-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+ 			</node>
+		</node>
+		<node>PRO-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+ 			</node>
+		</node>
+ 		<node>PRO-N
+ 			<node>Delete
+	 			<node>OXT</node>
+ 			</node>
+ 			<node>Properties
+ 				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Pyrrole-Skeleton.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,21 @@
+<node>Pyrrole-Skeleton
+	<node>Names
+		<node>Pyrrole-Skeleton</node>
+	</node>
+	<node>Atoms
+		<node>C1<value>C -0.028662 -0.037639 1.451927</value></node>
+		<node>N2<value>N -0.002221 -1.136686 0.619895</value></node>
+		<node>C3<value>C 0.0447 -0.76844 -0.708243</value></node>
+		<node>C4<value>C 0.046187 0.65781 -0.681334</value></node>
+		<node>C5<value>C -0.008647 1.094253 0.712146</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>C1 N2 s</value></node>
+		<node>2<value>N2 C3 d</value></node>
+		<node>3<value>C3 C4 s</value></node>
+		<node>4<value>C4 C5 d</value></node>
+		<node>5<value>C5 C1 s</value></node>
+	</node>
+	<node>Properties
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/SER.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,84 @@
+<node>SER
+	<node>Names
+		<node>Serine</node>
+		<node>Serin</node>
+		<node>Ser</node>
+		<node>S</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.1130663 1.226434 -0.1468897</value></node>
+		<node>3H<value>H 0.8968111 1.837972 0.05464922</value></node>
+		<node>CA<value>C -0.7048293 1.905604 -1.168307</value></node>
+		<node>HA<value>H -0.2017423 1.780946 -2.128185</value></node>
+		<node>C<value>C -0.7701361 3.410257 -0.8778276</value></node>
+		<node>O<value>O 0.1488766 3.858471 -0.1539113</value></node>
+		<node>CB<value>C -2.088618 1.24965 -1.250489</value></node>
+		<node>1HB<value>H -1.956628 0.1725609 -1.368818</value></node>
+		<node>2HB<value>H -2.637483 1.435655 -0.3253672</value></node>
+		<node>OG<value>O -2.817839 1.744102 -2.356831</value></node>
+		<node>HG<value>H -3.648096 1.264079 -2.429246</value></node>
+		<node>OXT<value>O -1.487331 4.10633 -1.629405</value></node>
+		<node>1H<value>H -0.4311985 1.10388 0.6950446</value></node>
+		<node>2H<value>H 0.4303224 0.3296314 -0.4862972</value></node>
+	</node>
+	<node>Bonds
+		<node>5<value>3H N s</value></node>
+		<node>6<value>CA N s</value></node>
+		<node>10<value>HA CA s</value></node>
+		<node>11<value>C CA s</value></node>
+		<node>14<value>O C d</value></node>
+		<node>15<value>CB CA s</value></node>
+		<node>19<value>1HB CB s</value></node>
+		<node>20<value>2HB CB s</value></node>
+		<node>21<value>OG CB s</value></node>
+		<node>23<value>HG OG s</value></node>
+		<node>24<value>OXT C s</value></node>
+		<node>25<value>1H N s</value></node>
+		<node>26<value>2H N s</value></node>
+	</node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>SER-M
+			<node>Properties
+				<node>N_TERMINAL</node>
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>SER-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>SER-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/T.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,106 @@
+<node>T
+	<node>Names
+		<node>Thymine</node>
+		<node>Thymin</node>
+		<node>T</node> 
+	</node>
+	<node>Atoms
+		<node>P<value>P 38.566 27.407 37.821</value></node>
+		<node>O1P<value>O 38.595 26.254 36.889</value></node>
+		<node>O2P<value>O 39.157 27.302 39.179</value></node>
+		<node>O5*<value>O 37.072 27.912 37.957</value></node>
+		<node>C5*<value>C 36.632 28.815 38.965</value></node>
+		<node>1H5*<value>H 37.233 29.724 38.959</value></node>
+		<node>2H5*<value>H 36.702 28.339 39.943</value></node>
+		<node>C4*<value>C 35.191 29.171 38.689</value></node>
+		<node>H4*<value>H 34.765 29.830 39.445</value></node>
+		<node>O4*<value>O 35.114 29.926 37.469</value></node>
+		<node>C3*<value>C 34.331 27.906 38.457</value></node>
+		<node>H3*<value>H 34.825 26.944 38.594</value></node>
+		<node>O3*<value>O 33.163 27.975 39.270</value></node>
+		<node>C2*<value>C 33.920 28.064 36.992</value></node>
+		<node>1H2*<value>H 34.360 27.260 36.402</value></node>
+		<node>2H2*<value>H 32.834 28.020 36.912</value></node>
+		<node>C1*<value>C 33.860 29.573 36.906</value></node>
+		<node>H1*<value>H 33.070 30.098 37.443</value></node>
+		<node>N1<value>N 33.730 30.096 35.526</value></node>
+		<node>C6<value>C 34.405 29.543 34.472</value></node>
+		<node>H6<value>H 35.056 28.699 34.642</value></node>
+		<node>C5<value>C 34.237 29.984 33.219</value></node>
+		<node>C5M<value>C 35.018 29.323 32.073</value></node>
+		<node>1H5M<value>H 34.762 28.265 32.021</value></node>
+		<node>2H5M<value>H 34.759 29.806 31.130</value></node>
+		<node>3H5M<value>H 36.088 29.429 32.253</value></node>
+		<node>C4<value>C 33.326 31.071 32.932</value></node>
+		<node>O4<value>O 33.094 31.529 31.816</value></node>
+		<node>N3<value>N 32.681 31.586 34.053</value></node>
+		<node>3H<value>H 31.993 32.416 33.893</value></node>
+		<node>C2<value>C 32.839 31.151 35.352</value></node>
+		<node>O2<value>O 32.225 31.690 36.276</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>P O1P s</value></node>
+		<node>2<value>P O2P d</value></node>
+		<node>3<value>P O5* s</value></node>		
+		<node>4<value>O5* C5* s</value></node>
+		<node>5<value>C5* C4* s</value></node>
+		<node>6<value>C4* O4* s</value></node>	
+		<node>7<value>C4* C3* s</value></node>
+		<node>8<value>C3* O3* s</value></node>
+		<node>9<value>C3* C2* s</value></node>
+		<node>10<value>C2* C1* s</value></node>
+		<node>11<value>C1* O4* s</value></node>
+		<node>12<value>C1* N1 s</value></node>
+		<node>13<value>N1 C6 s</value></node>
+		<node>14<value>C6 C5 d</value></node>
+		<node>15<value>C5 C5M s</value></node>
+		<node>16<value>C5 C4 s</value></node>
+		<node>17<value>C4 O4 d</value></node>
+		<node>18<value>C4 N3 s</value></node>
+		<node>19<value>N3 C2 s</value></node>
+		<node>20<value>C2 O2 d</value></node>
+		<node>21<value>C2 N1 s</value></node>
+		<node>22<value>C5* 1H5* s</value></node>
+		<node>23<value>C5* 2H5* s</value></node>
+		<node>24<value>C4* H4* s</value></node>
+		<node>25<value>C1* H1* s</value></node>
+		<node>26<value>C3* H3* s</value></node>
+		<node>27<value>C2* 1H2* s</value></node>
+	        <node>28<value>C2* 2H2* s</value></node>
+		<node>29<value>C6 H6 s</value></node>
+		<node>30<value>C5M 1H5M s</value></node>
+		<node>31<value>C5M 2H5M s</value></node>
+		<node>32<value>C5M 3H5M s</value></node>
+		<node>33<value>N3 3H s</value></node>
+ 	</node>
+	<node>Connections
+       		<node>5-term<value>P 3-term s 1.62 0.5</value></node>
+    		<node>3-term<value>O3* 5-term s 1.62 0.5</value></node>
+	</node>
+  	<node>Properties
+    		<node>NUCLEOTIDE</node>
+  	</node>
+  	<node>Variants
+    		<node>T-M
+      			<node>Properties
+        			<node>5_PRIME</node>
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>Default
+      			<node>Properties
+      			</node>
+    		</node>
+    		<node>T-3
+      			<node>Properties
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>T-5
+      			<node>Properties
+        			<node>5_PRIME</node>
+      			</node>
+    		</node>
+  	</node>
+</node>
+	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/THR.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,90 @@
+<node>THR
+	<node>Names
+		<node>Threonine</node>
+		<node>Threonin</node>
+		<node>Thr</node>
+		<node>T</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.07944571 1.265783 -0.06982248</value></node>
+		<node>3H<value>H 0.9103429 1.833856 0.0462634</value></node>
+		<node>CA<value>C -0.730729 1.899472 -1.127707</value></node>
+		<node>HA<value>H -0.2399387 1.69489 -2.079941</value></node>
+		<node>C<value>C -0.7224239 3.419906 -0.9435946</value></node>
+		<node>O<value>O 0.3746189 3.909003 -0.5883108</value></node>
+		<node>CB<value>C -2.153607 1.314487 -1.182294</value></node>
+		<node>HB<value>H -2.679771 1.729994 -2.044027</value></node>
+		<node>OG1<value>O -2.862524 1.651035 -0.00717756</value></node>
+		<node>HG1<value>H -3.698466 1.178201 0.002366092</value></node>
+		<node>CG2<value>C -2.126356 -0.2100642 -1.334626</value></node>
+		<node>1HG2<value>H -3.140605 -0.5875605 -1.466431</value></node>
+		<node>2HG2<value>H -1.532317 -0.4833375 -2.207111</value></node>
+		<node>3HG2<value>H -1.690858 -0.6725402 -0.448057</value></node>
+		<node>1H<value>H -0.4419178 1.260401 0.7952214</value></node>
+		<node>2H<value>H 0.324596 0.3214647 -0.3308986</value></node>
+		<node>OXT<value>O -1.661421 4.065769 -1.458723</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>HB CB s</value></node>
+    <node>20<value>OG1 CB s</value></node>
+    <node>22<value>HG1 OG1 s</value></node>
+    <node>23<value>CG2 CB s</value></node>
+    <node>27<value>1HG2 CG2 s</value></node>
+    <node>28<value>2HG2 CG2 s</value></node>
+    <node>29<value>3HG2 CG2 s</value></node>
+    <node>30<value>1H N s</value></node>
+    <node>31<value>2H N s</value></node>
+    <node>32<value>OXT C s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>THR-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>THR-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>THR-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+			<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/TRP.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,112 @@
+<node>TRP
+	<node>Names
+		<node>Tryptophane</node>
+		<node>Tryptophan</node>
+		<node>Trp</node>
+		<node>W</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.06601259 1.26337 0.1174229</value></node>
+		<node>3H<value>H 0.6980239 1.889212 0.6011554</value></node>
+		<node>CA<value>C -0.7641827 2.069947 -0.7944807</value></node>
+		<node>HA<value>H -0.09635611 2.49911 -1.541994</value></node>
+		<node>C<value>C -1.398304 3.240995 -0.03709874</value></node>
+		<node>O<value>O -0.5874859 4.036549 0.4871631</value></node>
+		<node>CB<value>C -1.786919 1.186925 -1.524096</value></node>
+		<node>1HB<value>H -1.239827 0.4012884 -2.046958</value></node>
+		<node>2HB<value>H -2.428179 0.7027346 -0.7858279</value></node>
+		<node>CG<value>C -2.643165 1.884437 -2.539373</value></node>
+		<node>CD1<value>C -3.982776 2.050424 -2.457166</value></node>
+		<node>HD1<value>H -4.607287 1.697167 -1.648804</value></node>
+		<node>CD2<value>C -2.239992 2.518021 -3.792893</value></node>
+		<node>NE1<value>N -4.432695 2.747722 -3.558181</value></node>
+		<node>HE1<value>H -5.40488 2.982779 -3.697329</value></node>
+		<node>CE2<value>C -3.401079 3.062783 -4.417417</value></node>
+		<node>CE3<value>C -1.011219 2.68937 -4.467488</value></node>
+		<node>HE3<value>H -0.1073443 2.284464 -4.037195</value></node>
+		<node>CZ2<value>C -3.347395 3.744152 -5.642442</value></node>
+		<node>HZ2<value>H -4.246768 4.143939 -6.087246</value></node>
+		<node>CZ3<value>C -0.945238 3.371593 -5.697227</value></node>
+		<node>HZ3<value>H 0.006688994 3.489207 -6.194728</value></node>
+		<node>CH2<value>C -2.108581 3.899702 -6.284111</value></node>
+		<node>HH2<value>H -2.049103 4.422244 -7.228023</value></node>
+		<node>OXT<value>O -2.601413 3.132993 0.2872543</value></node>
+		<node>1H<value>H 0.590273 0.5789365 -0.4086703</value></node>
+		<node>2H<value>H -0.5252197 0.7968075 0.7903904</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>1HB CB s</value></node>
+    <node>20<value>2HB CB s</value></node>
+    <node>21<value>CG CB s</value></node>
+    <node>24<value>CD1 CG a</value></node>
+    <node>27<value>HD1 CD1 s</value></node>
+    <node>28<value>CD2 CG a</value></node>
+    <node>31<value>NE1 CD1 a</value></node>
+    <node>34<value>HE1 NE1 s</value></node>
+    <node>35<value>CE2 CD2 a</value></node>
+    <node>36<value>CE2 NE1 a</value></node>
+    <node>39<value>CE3 CD2 a</value></node>
+    <node>41<value>HE3 CE3 s</value></node>
+    <node>42<value>CZ2 CE2 a</value></node>
+    <node>45<value>HZ2 CZ2 s</value></node>
+    <node>47<value>CZ3 CE3 a</value></node>
+    <node>49<value>HZ3 CZ3 s</value></node>
+    <node>50<value>CH2 CZ2 a</value></node>
+    <node>51<value>CH2 CZ3 a</value></node>
+    <node>53<value>HH2 CH2 s</value></node>
+    <node>54<value>OXT C s</value></node>
+    <node>55<value>1H N s</value></node>
+    <node>56<value>2H N s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+		<node>Variants
+			<node>Default
+				<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>TRP-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>TRP-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>TRP-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/TYR.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,105 @@
+<node>TYR
+	<node>Names
+		<node>Tyrosine</node>
+		<node>Tyrosin</node>
+		<node>Tyr</node>
+		<node>Y</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.0892698 1.397582 0.01951128</value></node>
+		<node>3H<value>H 0.7468582 2.066645 0.3997705</value></node>
+		<node>CA<value>C -0.7022205 2.069859 -1.026261</value></node>
+		<node>HA<value>H -0.008099081 2.359834 -1.816127</value></node>
+		<node>C<value>C -1.325588 3.357111 -0.4775957</value></node>
+		<node>O<value>O -0.5109698 4.260831 -0.1874116</value></node>
+		<node>CB<value>C -1.734457 1.10693 -1.63201</value></node>
+		<node>1HB<value>H -1.201299 0.2395796 -2.0242</value></node>
+		<node>2HB<value>H -2.395853 0.7504926 -0.8408001</value></node>
+		<node>CG<value>C -2.557806 1.696825 -2.76258</value></node>
+		<node>CD1<value>C -3.932589 1.947373 -2.588092</value></node>
+		<node>HD1<value>H -4.418424 1.704676 -1.654011</value></node>
+		<node>CD2<value>C -1.942974 2.007092 -3.98996</value></node>
+		<node>HD2<value>H -0.8916094 1.806731 -4.138027</value></node>
+		<node>CE1<value>C -4.68326 2.520281 -3.629397</value></node>
+		<node>HE1<value>H -5.736402 2.710342 -3.483602</value></node>
+		<node>CE2<value>C -2.6951 2.579179 -5.030118</value></node>
+		<node>HE2<value>H -2.222162 2.818849 -5.971263</value></node>
+		<node>CZ<value>C -4.063968 2.83503 -4.851168</value></node>
+		<node>OH<value>O -4.785331 3.388967 -5.865766</value></node>
+		<node>HH<value>H -5.709894 3.51796 -5.645833</value></node>
+		<node>OXT<value>O -2.492483 3.282188 -0.03387626</value></node>
+		<node>1H<value>H -0.5246789 1.074702 0.7536617</value></node>
+		<node>2H<value>H 0.5865244 0.613409 -0.3778604</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>1HB CB s</value></node>
+    <node>20<value>2HB CB s</value></node>
+    <node>21<value>CG CB s</value></node>
+    <node>24<value>CD1 CG a</value></node>
+    <node>27<value>HD1 CD1 s</value></node>
+    <node>28<value>CD2 CG a</value></node>
+    <node>31<value>HD2 CD2 s</value></node>
+    <node>32<value>CE1 CD1 a</value></node>
+    <node>35<value>HE1 CE1 s</value></node>
+    <node>36<value>CE2 CD2 a</value></node>
+    <node>39<value>HE2 CE2 s</value></node>
+    <node>40<value>CZ CE1 a</value></node>
+    <node>41<value>CZ CE2 a</value></node>
+    <node>43<value>OH CZ s</value></node>
+    <node>45<value>HH OH s</value></node>
+    <node>46<value>OXT C s</value></node>
+    <node>47<value>1H N s</value></node>
+    <node>48<value>2H N s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>TYR-M
+			<node>Properties
+				<node>C_TERMINAL</node>
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+		<node>TYR-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>TYR-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/U.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,99 @@
+<node>U
+	<node>Names
+		<node>Uracil</node>
+		<node>U</node> 
+	</node>
+	<node>Atoms
+		<node>P<value>P 38.566 27.407 37.821</value></node>
+		<node>O1P<value>O 38.595 26.254 36.889</value></node>
+		<node>O2P<value>O 39.157 27.302 39.179</value></node>
+		<node>O5*<value>O 37.072 27.912 37.957</value></node>
+		<node>C5*<value>C 36.632 28.815 38.965</value></node>
+		<node>1H5*<value>H 37.233 29.724 38.959</value></node>
+		<node>2H5*<value>H 36.702 28.339 39.943</value></node>
+		<node>C4*<value>C 35.191 29.171 38.689</value></node>
+		<node>H4*<value>H 34.765 29.830 39.445</value></node>
+		<node>O4*<value>O 35.114 29.926 37.469</value></node>
+		<node>C3*<value>C 34.331 27.906 38.457</value></node>
+		<node>H3*<value>H 34.825 26.944 38.594</value></node>
+		<node>O3*<value>O 33.163 27.975 39.270</value></node>
+		<node>C2*<value>C 33.920 28.064 36.992</value></node>
+		<node>1H2*<value>H 34.360 27.260 36.402</value></node>
+		<node>2H2*<value>H 32.834 28.020 36.912</value></node>
+		<node>C1*<value>C 33.860 29.573 36.906</value></node>
+		<node>H1*<value>H 33.070 30.098 37.443</value></node>
+		<node>N1<value>N 33.730 30.096 35.526</value></node>
+		<node>C6<value>C 34.405 29.543 34.472</value></node>
+		<node>H6<value>H 35.056 28.699 34.642</value></node>
+		<node>C5<value>C 34.237 29.984 33.219</value></node>
+		<node>H5<value>H 35.018 29.323 32.073</value></node>
+		<node>C4<value>C 33.326 31.071 32.932</value></node>
+		<node>O4<value>O 33.094 31.529 31.816</value></node>
+		<node>N3<value>N 32.681 31.586 34.053</value></node>
+		<node>H3<value>H 31.993 32.416 33.893</value></node>
+		<node>C2<value>C 32.839 31.151 35.352</value></node>
+		<node>O2<value>O 32.225 31.690 36.276</value></node>
+	</node>
+	<node>Bonds
+		<node>1<value>P O1P s</value></node>
+		<node>2<value>P O2P d</value></node>
+		<node>3<value>P O5* s</value></node>		
+		<node>4<value>O5* C5* s</value></node>
+		<node>5<value>C5* C4* s</value></node>
+		<node>6<value>C4* O4* s</value></node>	
+		<node>7<value>C4* C3* s</value></node>
+		<node>8<value>C3* O3* s</value></node>
+		<node>9<value>C3* C2* s</value></node>
+		<node>10<value>C2* C1* s</value></node>
+		<node>11<value>C1* O4* s</value></node>
+		<node>12<value>C1* N1 s</value></node>
+		<node>13<value>N1 C6 s</value></node>
+		<node>14<value>C6 C5 d</value></node>
+		<node>15<value>C5 H5 s</value></node>
+		<node>16<value>C5 C4 s</value></node>
+		<node>17<value>C4 O4 d</value></node>
+		<node>18<value>C4 N3 s</value></node>
+		<node>19<value>N3 C2 s</value></node>
+		<node>20<value>C2 O2 d</value></node>
+		<node>21<value>C2 N1 s</value></node>
+		<node>22<value>C5* 1H5* s</value></node>
+		<node>23<value>C5* 2H5* s</value></node>
+		<node>24<value>C4* H4* s</value></node>
+		<node>25<value>C1* H1* s</value></node>
+		<node>26<value>C3* H3* s</value></node>
+		<node>27<value>C2* 1H2* s</value></node>
+	        <node>28<value>C2* 2H2* s</value></node>
+		<node>29<value>C6 H6 s</value></node>
+		<node>30<value>N3 H3 s</value></node>
+ 	</node>
+	<node>Connections
+       		<node>5-term<value>P 3-term s 1.62 0.5</value></node>
+    		<node>3-term<value>O3* 5-term s 1.62 0.5</value></node>
+	</node>
+  	<node>Properties
+    		<node>NUCLEOTIDE</node>
+  	</node>
+  	<node>Variants
+    		<node>U-M
+      			<node>Properties
+        			<node>5_PRIME</node>
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>Default
+      			<node>Properties
+      			</node>
+    		</node>
+    		<node>U-3
+      			<node>Properties
+        			<node>3_PRIME</node>
+      			</node>
+    		</node>
+    		<node>U-5
+      			<node>Properties
+        			<node>5_PRIME</node>
+      			</node>
+    		</node>
+  	</node>
+</node>
+	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/VAL.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,94 @@
+<node>VAL
+	<node>Names
+		<node>Valine</node>
+		<node>Valin</node>
+		<node>Val</node>
+		<node>V</node>
+	</node>
+	<node>Atoms
+		<node>N<value>N 0.08111785 1.2013 -0.133711</value></node>
+		<node>3H<value>H 0.9032491 1.762717 0.06032801</value></node>
+		<node>CA<value>C -0.698245 1.931722 -1.152099</value></node>
+		<node>HA<value>H -0.2125321 1.7346 -2.108571</value></node>
+		<node>C<value>C -0.5967644 3.443358 -0.9052255</value></node>
+		<node>O<value>O 0.3370198 3.799585 -0.1501447</value></node>
+		<node>CB<value>C -2.141793 1.389981 -1.219405</value></node>
+		<node>HB<value>H -2.073082 0.3006792 -1.23859</value></node>
+		<node>CG1<value>C -2.976131 1.780723 0.008393872</value></node>
+		<node>1HG1<value>H -3.953726 1.301327 -0.05053521</value></node>
+		<node>2HG1<value>H -2.483032 1.448739 0.9220271</value></node>
+		<node>3HG1<value>H -3.118463 2.860577 0.05077193</value></node>
+		<node>CG2<value>C -2.878923 1.800528 -2.501579</value></node>
+		<node>1HG2<value>H -3.809818 1.237256 -2.575363</value></node>
+		<node>2HG2<value>H -3.122159 2.862025 -2.496346</value></node>
+		<node>3HG2<value>H -2.266089 1.572718 -3.374182</value></node>
+		<node>OXT<value>O -1.142181 4.189281 -1.746952</value></node>
+		<node>1H<value>H -0.4588342 1.115157 0.7148547</value></node>
+		<node>2H<value>H 0.3376986 0.2854735 -0.4735033</value></node>
+	</node>
+  <node>Bonds
+    <node>5<value>3H N s</value></node>
+    <node>6<value>CA N s</value></node>
+    <node>10<value>HA CA s</value></node>
+    <node>11<value>C CA s</value></node>
+    <node>14<value>O C d</value></node>
+    <node>15<value>CB CA s</value></node>
+    <node>19<value>HB CB s</value></node>
+    <node>20<value>CG1 CB s</value></node>
+    <node>24<value>1HG1 CG1 s</value></node>
+    <node>25<value>2HG1 CG1 s</value></node>
+    <node>26<value>3HG1 CG1 s</value></node>
+    <node>27<value>CG2 CB s</value></node>
+    <node>31<value>1HG2 CG2 s</value></node>
+    <node>32<value>2HG2 CG2 s</value></node>
+    <node>33<value>3HG2 CG2 s</value></node>
+    <node>34<value>OXT C s</value></node>
+    <node>35<value>1H N s</value></node>
+    <node>36<value>2H N s</value></node>
+  </node>
+	<node>Connections
+		<node>N-term<value>N C-term s 1.33 0.5</value></node>
+		<node>C-term<value>C N-term s 1.33 0.5</value></node>
+	</node>
+	<node>Properties
+		<node>AMINO_ACID</node>
+	</node>
+	<node>Variants
+		<node>Default
+			<node>Delete
+				<node>OXT</node>
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+		</node>
+		<node>VAL-M
+			<node>Properties
+				<node>N_TERMINAL</node>
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>VAL-C
+			<node>Delete
+				<node>1H</node>
+				<node>2H</node>
+			</node>
+			<node>Rename
+				<node>3H<value>H</value></node>
+			</node>
+			<node>Properties
+				<node>C_TERMINAL</node>
+			</node>
+		</node>
+		<node>VAL-N
+			<node>Delete
+				<node>OXT</node>
+			</node>
+			<node>Properties
+				<node>N_TERMINAL</node>
+			</node>
+		</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ZN.db	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,18 @@
+<node>ZN
+	<node>Names
+ 		<node>Zinc ion</node>
+ 		<node>Zn2+</node>
+	</node>
+	<node>Atoms
+		<node>ZN<value>Zn 0.0 0.0 0.0</value></node>
+	</node>
+	<node>Bonds
+	</node>
+	<node>Connections
+	</node>
+	<node>Properties
+	</node>
+	<node>Variants
+		<node>Default</node>
+	</node>
+</node>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/functionalGroups.smarts	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,133 @@
+C[*X1](C)([*X1])[*X1]	terminal primary C(sp3)
+[C,c]([C,c])([C,c])(*)*	 total secondary C(sp3)
+[C,c]([C,c])([C,c])([C,c])*	total tertiary C(sp3)
+[C,c]([C,c])([C,c])([C,c])[C,c]	total quaternary C(sp3)
+[$([Cr,cr]([Cr,cr])([Cr,cr])(*)*),$([Cr,cr]([Cr,cr])([C,c])([*r])*)]		ring secondary C(sp3)
+[$([Cr,cr]([Cr,cr])([Cr,cr])([C,c])*),$([Cr,cr]([Cr,cr])([C,c])([C,c])[*r])]	ring tertiary C(sp3)
+[Cr,cr]([Cr,cr])([Cr,cr])([C,c])[C,c]	ring quaternary C(sp3)
+[cX3]		aromatic C(sp2)
+[Ch1,ch1]1[C,c][C,c][C,c][C,c][C,c]1	unsubstituted benzene C(sp2)
+[Ch0,ch0]1[C,c][C,c][C,c][C,c][C,c]1	substituted benzene C(sp2)
+O=CC1=CCCC=C1		non-aromatic conjugated C(sp2)
+[C,c]=[C,c](*)(*)		terminal primary C(sp2)
+C=C(C)(*)	aliphatic secondary C(sp2)
+C=C(C)(C)	aliphatic tertiary C(sp2)
+[C,c]=[C,c]=[C,c]		allenes groups
+[*X1][C,c]#C	terminal C(sp)
+**[C,c]#C	non-terminal C(sp)
+OC#N		cyanates
+O=C=N	isocyanates
+SC#N		thiocyanates
+N=C=S	isothiocyanates
+[OH,Oh]C=O	carboxylic acids
+[*;!H]OC=O	 esters
+[NH2,Nh2]C=O		primary amides
+[*;!H][NH,Nh]C=O		secondary amides
+[*;!H]N([*;!H])C=O	tertiary amides
+*N(*)C([O,S]*)=[O,S]		(thio-)carbamates
+[F,Cl,Br,I,At]C(*)=O		acyl halogenides
+[$([OH,Oh]C(*)=S),$([SH,Sh]C(*)=O)]		thioacids
+[SH,Sh]C(*)=S		dithioacids
+[$([*;!H]OC(*)=S),$([*;!H]SC(*)=O)]		thioesters
+[*;!H]SC(*)=S		dithioesters
+[CH,Ch](*)=O	aldehydes
+*C(*)=O		ketones
+[NX3]C([NX3])=[O,S]		urea (-thio) derivatives
+[OX2,SX2]C([OX2,SX2])=[O,S]	carbonate (-thio) derivatives
+[NX2]C([C,H])[NX3]	amidine derivatives
+[NX3]C(=[NX2])[NX3]	guanidine derivatives
+*C(*)=N[N,C,H]		imines
+*C(*)=NO*	oximes
+[NH2X3,Nh2X3]		primary amines
+[NH1X3,Nh1X3]		secondary amines
+[NH0X3;Nh0X3]	 tertiary amines
+[C,H][NX3][NX3][C,H]		N hydrazines
+[C,H][NX2]=[NX2][C,H]	N azo-derivatives
+N#C*	nitriles
+[N+n]	positive charged N
+[NX4]	quaternary N
+*N(*)O*	hydroxylamines
+*N(*)N=O		nitrosamine
+*N=O	nitroso groups
+*N(O)=O		nitro groups
+[CX3](=[O,S])[NX3]([H,C])[CX3]=[O,S]	imides
+[C,H]C([C,H])=NN([C,H])[C,H]	hydrazones
+A[OX2h1,OX2H1]		hydroxyl groups
+a[OX2h1,OX2H1]		aromatic hydroxyls
+C[CH2,Ch2][OH,Oh]		primary alcohols
+C[CH,Ch](C)[OH,Oh]	secondary alcohols
+CC(C)(C)[OH,Oh]	tertiary alcohols
+*O*	 ethers
+*O[F,Cl,Br,I,At]	hypohalogenides
+[CX3](=[O,S])O[CX3][O,S]	anhydrides
+[OH2,Oh2]	water
+C[SH,Sh]	thiols
+S=C(C)C	thioketones
+C[SX2]C	sulfides
+C[SX2][SX2]C	disulfides
+[$(CS(C)=O),$(C=S=O),$(S=S=O)]	sulfoxides
+[$(O=[SX4]=O),$(O=S(=[C,S])=O)]	sulfones
+[SX2][Oh1,OH1,Sh1,SH1]		sulfenic acids
+[SX3](=[O,S])[Oh1,OH1,Sh1,SH1]		sulfinic acids
+[SX4](=[O,S])(=[O,S])[Oh1,OH1,Sh1,SH1]		sulfonic acids
+[OX2,SX2][SX4](=[O,S])(=[O,S])[Oh1,OH1,Sh1,SH1]		sulfuric acids
+[SX3](=[O,S])[OX2,SX2]		sulfites
+[SX4](=[O,S])(=[O,S])[OX2,SX2]	sulfonates
+[OX2,SX2][SX4](=[O,S])(=[O,S])[OX2,SX2]	sulfates
+[$(C[SX4](=O)(=O)[NX3]),$(C[SX4](=S)(=O)[NX3]),$(C[SX3](=O)[NX3]),$(C[SX3](=S)[NX3]),$(CS[NX3])]	sulfonamides/sulfinamides/sulfenamides
+[O,S]P([O,S])[O,S]	phosphites/thiophosphites
+[O,S]P(=[O,S])([O,S])[O,S]		phosphates/thiophosphates
+[O,S]P([O,S])[O,S]	phosphanes
+[H,S,F,Cl,Br,I,At][PX4](=[S,O])([SX2,OX2])[SX2,OX2]	phosphonates/thiophosphonates
+[$([H,S,F,Cl,Br,I,At][PX4](=[S,O])([H,S,F,Cl,Br,I,At])[H,S,F,Cl,Br,I,At]),$([H,S,F,Cl,Br,I,At][PX5]([H,S,F,Cl,Br,I,At])([H,S,F,Cl,Br,I,At])([H,S,F,Cl,Br,I,At])[H,S,F,Cl,Br,I,At])]		phosphoranes/thiophosphoranes
+[F,Cl,Br,I,At][CX4h2,CX4H2,cx4h2,cx4H2][C,c]		CH2RX
+[F,Cl,Br,I,At][CX4h1,CX4H1,cX4h1,cX4H1]([C,c])[C,c]	CHR2X
+[F,Cl,Br,I,At][C,c]([C,c])([C,c])[C,c]		CR3X
+[C,c]=[CX3h1,cX3h1,CX3H1,cX3H1][F,Cl,Br,I,At]	R=CHX
+[C,c]=[C,c]([C,c])[F,Cl,Br,I,At]		R=CRX
+[F,Cl,Br,I,At]C#C		R#CX
+[F,Cl,Br,I,At][CX4h1,CX4H1,cX4h1,cX4H1]([C,c])[F,Cl,Br,I,At]	 CHRX2
+[F,Cl,Br,I,At][C,c]([C,c])([C,c])[F,Cl,Br,I,At]	CR2X2
+[C,c]=[C,c]([F,Cl,Br,I,At])[F,Cl,Br,I,At]	 R=CX2
+[F,Cl,Br,I,At][C,c]([C,c])([F,Cl,Br,I,At])[F,Cl,Br,I,At]	CRX3
+[F,Cl,Br,I,At][ar]	halogene on aromatic ring
+[CrX4,crX4][F,Cl,Br,I,At]	X on ring C(sp3)
+[CrX3,crX3][F,Cl,Br,I,At]	X on ring C(sp2)
+[C,c]=[C,c]([F,Cl,Br,I,At])[C,c]=[C,c]	 halogene on exo-conjugated C
+[N,n]1@[C,c]@[C,c]1	Aziridines
+[O,o]1@[C,c]@[C,c]1	Oxiranes
+[S,s]1@[C,c]@[C,c]1	Thiranes
+[N,n]1@[C,c]@[C,c]@[C,c]1	Azetidines
+[O,o]1@[C,c]@[C,c]@[C,c]1	Oxetanes
+[S,s]1@[C,c]@[C,c]@[C,c]1	Thioethanes
+[N,n]12@[C,c]@[C,c]@[C,c]@[C,c]@[C,c]1(@[C,c]@C2(=O))	Beta-Lactams
+[N,n]1@[C,c]@[C,c]@[C,c]1		Pyrrolidines
+[O,o]1[C,c][C,c][C,c][C,c]1	Oxolanes
+[S,s]1[C,c][C,c][C,c][C,c]1	tetrahydro-Thiophenes
+[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]1	Pyrroles
+[N,n]1@[N,n]@[C,c]@[C,c]@[C,c]1	Pyrazoles
+[N,n]1@[C,c]@[N,n]@[C,c]@[C,c]1	Imidazoles
+[O,o]1[C,c]=[C,c][C,c]=[C,c]1	Furanes
+[S,s]1[C,c]=[C,c][C,c]=[C,c]1	Thiophenes
+[O,o]1@[C,c]@[N,n]@[C,c]@[C,c]1	Oxazoles
+[O,o]1@[N,n]@[C,c]@[C,c]@[C,c]1	Isoxazoles
+[S,s]1@[C,c]@[N,n]@[C,c]@[C,c]1	Thiazoles
+[S,s]1@[N,n]@[C,c]@[C,c]@[C,c]1	Isothiazoles
+[$([N,n]1@[N,n]@[C,c]@[N,n]@C1),$([N,n]1@[N,n]@[N,n]@[C,c]@[C,c]1)]	Triazoles
+[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]@[C,c]1	Pyridines
+[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]@[N,n]1	Pyridazines
+[N,n]1@[C,c]@[C,c]@[C,c]@[N,n]@[C,c]1	Pyrimidines
+[N,n]1@[C,c]@[C,c]@[N,n]@[C,c]@[C,c]1	Pyrazines
+[N,n]1@[C,c]@[N,n]@[C,c]@[N,n]@[C,c]1	135-Triazines
+[N,n]1@[C,c]@[N,n]@[N,n]@[C,c]@[C,c]1	124-Triazines
+[C,c]1([Oh1,OH1])[C,c][C,c][C,c][C,c][C,c]1	Phenoles
+[C,c]1([C])[C,c][C,c][C,c][C,c][C,c]1	Phenyles
+[C,c]1([CH3,ch3])[C,c][C,c][C,c][C,c][C,c]1	Toluenes
+OC[C,c]1@[C,c](O)@[C,c](O)@[C,c](O)@[C,c](O)@[O,o]1	Glucose
+OC[C,c]1(O)@[C,c](O)@[C,c](O)@[C,c](CO)[O,o]1	Fructose
+[CH3,Ch3]	Methyl
+[F,Cl,Br,I,At]		Halogenides
+[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2,Ch3,CH3]	Propyl
+[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2][CH2,Ch2,Ch3,CH3]	Butyl
+[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2][CH2,Ch2][CH2,Ch2,Ch3,CH3]	Pentyl
+CC=C([CH3,Ch3])([CH3,Ch3])	Prenyl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/confFiles.py	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,32 @@
+# -*- coding: utf-8 -*-
+"""
+XML format classes
+"""
+import data
+import logging
+from galaxy.datatypes.sniff import *
+import commands
+
+log = logging.getLogger(__name__)
+
+
+class ini( data.Text ):
+	file_ext = "ini"
+	def sniff( self, filename ):
+		self.no_sections = commands.getstatusoutput("grep -c \"\[Docking-Settings\]\" "+filename)
+		if (self.no_sections[0] == 0) & (self.no_sections[1] > 0):
+			return True
+		else:
+			self.no_sections = commands.getstatusoutput("grep -c \"\[ReferenceArea\" "+filename)
+			if (self.no_sections[0] == 0) & (self.no_sections[1] > 0):
+				return True
+			else:
+				self.no_sections = commands.getstatusoutput("grep -c \"\[PharmacophoreConstraint\" "+filename)
+				if (self.no_sections[0] == 0) & (self.no_sections[1] > 0):
+					return True
+				else:
+					return False
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/countResidues.sh	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,64 @@
+#!/bin/bash
+
+IFS=$'\n';
+residue_list=""
+hetsys_list=""
+hoh_list=""
+
+for line in $(cat $1); do
+	if [ "${line:0:4}" = "ATOM"  ];then
+		residue_list+="${line:23:6}\n"
+	else
+		if [ "${line:0:6}" = "HETATM"  ];then
+			s2=`echo $line | grep HOH`
+			if [ "$s2" != "" ];then
+				hoh_list+="${line:21:8}\n"
+			else
+				s3=`echo $line | grep WAT`
+				if [ "$s3" != "" ];then
+					hoh_list+="${line:21:8}\n"
+				else
+					hetsys_list+="${line:21:8}\n"
+				fi
+			fi
+		fi
+	fi
+done
+
+IFS=$' ';
+let num_res=`echo -e "\n"$residue_list | uniq | wc -l`
+let num_hoh=`echo -e "\n"$hoh_list | uniq | wc -l`
+let num_hetsys=`echo -e "\n"$hetsys_list | uniq | wc -l`
+
+# empty line at begin and end of lists -> substract 2
+let num_res-=2
+let num_hoh-=2
+let num_hetsys-=2
+if [ $num_res -lt 0 ]; then
+	let num_res=0
+fi
+if [ $num_hoh -lt 0 ]; then
+	let num_hoh=0
+fi
+if [ $num_hetsys -lt 0 ]; then
+	let num_hetsys=0
+fi
+
+echo -n "$num_res "
+if [ $num_res -eq 1 ]; then
+	echo "residue"
+else
+	echo "residues"
+fi
+echo -n "$num_hoh water "
+if [ $num_hoh -eq 1 ]; then
+	echo "molecule"
+else
+	echo "molecules"
+fi
+echo -n "$num_hetsys "
+if [ $num_hetsys -eq 1 ]; then
+	echo "heterosystem"
+else
+	echo "heterosystems"
+fi
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/datatypes_conf.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<datatypes>
+    <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
+			<datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/>
+			<datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
+			<datatype extension="jpg" type="galaxy.datatypes.images:Image" mimetype="image/jpeg"/>
+			<datatype extension="gif" type="galaxy.datatypes.images:Image" mimetype="image/gif"/>
+			<datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/>
+
+			<datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
+			<datatype extension="grd.tgz" type="galaxy.datatypes.molFiles:grdtgz" display_in_upload="true"/>
+			<datatype extension="mol2" type="galaxy.datatypes.molFiles:MOL2" display_in_upload="true"/>
+			<datatype extension="sdf" type="galaxy.datatypes.molFiles:SDF" display_in_upload="true"/>
+			<datatype extension="pdb" type="galaxy.datatypes.molFiles:PDB" display_in_upload="true"/>
+			<datatype extension="drf" type="galaxy.datatypes.molFiles:DRF" display_in_upload="true"/>
+			<datatype extension="mol2/sdf/drf" type="galaxy.datatypes.molFiles:GenericMolFile" display_in_upload="true"/>
+			<datatype extension="bvp" type="galaxy.datatypes.data:Data" display_in_upload="true"/>
+			<datatype extension="ini" type="galaxy.datatypes.confFiles:ini" display_in_upload="true"/>
+
+		<!-- Datatypes for QuEasy -->
+			<datatype extension="dat" type="galaxy.datatypes.data:Text" display_in_upload="false"/>
+			<datatype extension="csv" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
+			<datatype extension="mod" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
+    </registration>
+
+    <sniffers>
+		<sniffer type="galaxy.datatypes.confFiles:ini"/>
+		<sniffer type="galaxy.datatypes.molFiles:SDF"/>
+		<sniffer type="galaxy.datatypes.molFiles:MOL2"/>
+		<sniffer type="galaxy.datatypes.molFiles:DRF"/>
+		<sniffer type="galaxy.datatypes.molFiles:PDB"/>
+    </sniffers>
+</datatypes>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/molFiles.py	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,128 @@
+# -*- coding: utf-8 -*-
+
+import data
+import logging
+from galaxy.datatypes.sniff import *
+import commands
+
+log = logging.getLogger(__name__)
+
+class GenericMolFile( data.Text ):
+	file_ext = "mol2/sdf/drf"
+	def check_filetype( self,filename ):
+		self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			self.file_ext="sdf"
+			return True
+		self.no_mols = commands.getstatusoutput("grep -c @\<TRIPOS\>MOLECULE "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			self.file_ext="mol2"
+			return True
+		self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			self.file_ext="drf"
+			return True
+		self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			self.file_ext="pdb"
+			return True
+		return False
+
+	def set_peek( self, dataset, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			if(self.check_filetype(dataset.file_name)) :
+				if (self.no_mols[1] == '1'):
+					dataset.blurb = "1 molecule"
+				else:
+					dataset.blurb = "%s molecules"%self.no_mols[1]
+			dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+		else:
+			dataset.peek = 'file does not exist'
+			dataset.blurb = 'file purged from disk'
+
+	def get_mime(self):
+		return 'text/plain'
+
+
+class GenericMultiMolFile( GenericMolFile ):
+	def set_peek( self, dataset, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			self.sniff(dataset.file_name)
+			if (self.no_mols[1] == '1'):
+				dataset.blurb = "1 molecule"
+			else:
+				dataset.blurb = "%s molecules"%self.no_mols[1]
+			dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+		else:
+			dataset.peek = 'file does not exist'
+			dataset.blurb = 'file purged from disk'
+
+class SDF( GenericMultiMolFile ):
+	file_ext = "sdf"
+	def sniff( self, filename ):
+		self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			return True
+		else:
+			return False
+
+class MOL2( GenericMultiMolFile ):
+	file_ext = "mol2"
+	def sniff( self, filename ):
+		self.no_mols = commands.getstatusoutput("grep -c @\<TRIPOS\>MOLECULE "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			return True
+		else:
+			return False
+
+class DRF( GenericMultiMolFile ):
+	file_ext = "drf"
+	def sniff( self, filename ):
+		self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			return True
+		else:
+			return False
+
+class PDB( GenericMolFile ):
+	file_ext = "pdb"
+	def sniff( self, filename ):
+		self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename)
+		if (self.no_mols[0] == 0) & (self.no_mols[1] > 0):
+			return True
+		else:
+			return False
+	def set_peek( self, dataset, is_multi_byte=False ):
+	#def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			res = commands.getstatusoutput("lib/galaxy/datatypes/countResidues.sh "+dataset.file_name)
+			dataset.peek = res[1]
+			self.sniff(dataset.file_name)
+			if (self.no_mols[1] == '1'):
+				dataset.blurb = "1 protein structure"
+			else:
+				dataset.blurb = "%s protein structures"%self.no_mols[1]
+		else:
+			dataset.peek = 'file does not exist'
+			dataset.blurb = 'file purged from disk'
+
+class grd ( data.Text ) :
+	file_ext = "grd"
+	def set_peek( self, dataset, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			#dataset.peek = ""
+			dataset.blurb = "score-grids for docking"
+		else:
+			dataset.peek = 'file does not exist'
+			dataset.blurb = 'file purged from disk'
+
+class grdtgz ( data.Text ) :
+	file_ext = "grd.tgz"
+	def set_peek( self, dataset, is_multi_byte=False ):
+		if not dataset.dataset.purged:
+			#dataset.peek = ""
+			dataset.blurb = "compressed score-grids for docking"
+		else:
+			dataset.peek = 'file does not exist'
+			dataset.blurb = 'file purged from disk'
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tool_conf.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,71 @@
+<?xml version="1.0"?>
+<toolbox>
+  <label text="CADDSuite" id="cadds" />
+
+  <section name="Get Data" id="getext">
+    <tool file="data_source/upload.xml"/>
+    <tool file="CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml"/>
+    <tool file="CADDSuite/galaxyconfigs/tools/PDBDownload.xml"/>
+    <tool file="CADDSuite/galaxyconfigs/tools/DBExporter.xml"/>
+  </section>
+
+  <section name="Data preparation" id="dataPrep">
+	<tool file="CADDSuite/galaxyconfigs/tools/PDBCutter.xml" />
+	<tool file="CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml" />
+	<tool file="CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml" />
+	<tool file="CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml" />
+   <tool file="CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml"/>
+   <tool file="CADDSuite/galaxyconfigs/tools/EvenSplit.xml"/>
+   <tool file="CADDSuite/galaxyconfigs/tools/PropertyModifier.xml"/>
+   <tool file="CADDSuite/galaxyconfigs/tools/MolFilter.xml"/>
+  </section>
+
+  <section name="Checks and evaluations" id="checks">
+	<tool file="CADDSuite/galaxyconfigs/tools/ProteinCheck.xml" />
+	<tool file="CADDSuite/galaxyconfigs/tools/LigCheck.xml" />
+  </section>
+
+  <section name="Docking" id="dockingTools">
+	 <tool file="CADDSuite/galaxyconfigs/tools/WaterFinder.xml" />
+	 <tool file="CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml" />
+	 <tool file="CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml" />
+	 <tool file="CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml"/>
+	 <tool file="CADDSuite/galaxyconfigs/tools/PocketDetector.xml"/>
+    <tool file="CADDSuite/galaxyconfigs/tools/GridBuilder.xml" />
+    <tool file="CADDSuite/galaxyconfigs/tools/IMeedyDock.xml" />
+  </section>
+
+  <section name="Rescoring" id="rescoringsection">
+	<tool file="CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml"/>
+	<tool file="CADDSuite/galaxyconfigs/tools/TaGRes-train.xml"/>
+	<tool file="CADDSuite/galaxyconfigs/tools/TaGRes.xml"/>
+	<tool file="CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml" />
+  </section>
+
+	<section name="QuEasy (QSAR)" id="queasy">
+		<tool file="CADDSuite/galaxyconfigs/tools/InputReader.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/ModelCreator.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/FeatureSelector.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/Validator.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/MolPredictor.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/AutoModel.xml" />
+	</section>
+
+	<section name="Analysis" id="analysis">
+		<tool file="CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml"/>
+		<tool file="CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml"/>
+		<tool file="CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml"/>
+		<tool file="CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml"/>
+	</section>
+
+	<section name="Convert, combine and store" id="storeData">
+		<tool file="CADDSuite/galaxyconfigs/tools/Converter.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/MolCombine.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/DockResultMerger.xml"/>
+		<tool file="CADDSuite/galaxyconfigs/tools/Filter.xml"/>
+		<tool file="CADDSuite/galaxyconfigs/tools/MolDepict.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/DBImporter.xml" />
+		<tool file="CADDSuite/galaxyconfigs/tools/VendorFinder.xml" />
+	</section>
+
+</toolbox>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,32 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.94">
+    <description>rescore w/ anti-target dock-results</description>
+    <command interpreter="bash"><![CDATA[../../AntitargetRescorer 
+#if str( $t ) != ''  and str( $t ) != 'None' :
+   -t "$t"
+#end if
+#if str( $at ) != ''  and str( $at ) != 'None' :
+   -at "$at"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="t" label="input file w/ target dock-results" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="at" label="input file w/ anti-target dock-results" optional="false" type="data" format="mol2/sdf/drf"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="t"/>
+    </outputs>
+    <help>This tool rescores docking output poses.
+AntitargetRescoring can be used to try to enhance target specificity. Therefore, dock your compounds into your target of interest and into a (very) different protein and supply the docking results here. All compounds that received a very good antitarget-score will thus be penalized, i.e. they will have a much worse score within the output file.
+
+As input we need:
+    * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docket into the specified protein (i.e. the target).
+    * a file containing the same compounds docked into the antitarget.
+
+Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 'antitarget_rescore'.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/AutoModel.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,27 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="automodel" name="AutoModel" version="1.1">
+    <description>automatically find best QSAR model</description>
+    <command interpreter="bash"><![CDATA[../../AutoModel 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $min_quality ) != ''  and str( $min_quality ) != 'None' :
+   -min_quality "$min_quality"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input data-file" optional="false" type="data" format="dat"/>
+        <param name="min_quality" label="minimal desired quality (default: 0.3)" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value="0.3"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mod"/>
+    </outputs>
+    <help>This tool tries to automatically find the best QSAR model for a given data set. 
+
+It therefore applies nested validation, including feature selection, for each available model-type. The model with the best nested prediction quality is saved to the specified output file. However, if the best obtained nested prediction quality is smaller than the value specified by '-min_quality', an error will be shown and no model will be saved.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,36 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.94">
+    <description>fix bindingdb.org downloads</description>
+    <command interpreter="bash"><![CDATA[../../BindingDBCleaner 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $type ) != ''  and str( $type ) != 'None' :
+   -type "$type"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $target ) != ''  and str( $target ) != 'None' :
+   -target "$target"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="type" label="type of contained activity values: 'Ki' or 'IC50'" optional="false" type="select">
+            <option value="IC50">IC50</option>
+            <option value="Ki">Ki</option>
+        </param>
+        <param name="target" label="binding-DB target name" optional="false" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool cleans up the sd-properties contained in sd-files downloaded from bindingdb.org.
+
+For all compounds in the input file, the affinity value for the specified target is searched and retained but all other properties are removed. Furthermore, the IC50 or Ki value of each compound is converted to a binding-free-energy value in units of [kJ/mol] that is added as a property-tag named 'binding_free_energy'.
+
+All compounds in the input file for which no IC50 resp. Ki value for the specified target can found, are ignored and not written to the output file.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,33 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="combilibgenerator" name="CombiLibGenerator" version="0.94">
+    <description>generate combinatorial lib</description>
+    <command interpreter="bash"><![CDATA[../../CombiLibGenerator 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input combi-lib file" optional="false" type="data" format="data"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf"/>
+    </outputs>
+    <help>This tool generates a combinatorial library by combining the given molecule scaffolds with possible combinations of moieties.
+
+As input we need a text file specifying SMARTS expressions for the desired scaffolds and R-groups. Its format should look like the following example, although you may specify as many scaffolds and as many SMARTS expressions per R-group as you need:
+
+&lt;scaffold&gt;
+      Fc1ccc(cc1)C2=C(C([R1])=NO2)c3ccnc([R2])c3
+      Fc1ccc(cc1)C2=NOC([R1])=C2cccnc([R2])c3
+&lt;moietyR1&gt;
+      [R1]C(C)(C)C
+&lt;moietyR2&gt;
+      [R2]OC(C)(C)C
+
+Output of CombiLibGenerator is a file containing created topologies. Note that this tool does *not* generate any conformations but only topologies, so that all coordinates in the output file will be zero. Thus, apply Ligand3DGenerator to the output generated by CombiLibGenerator if you need 3D conformations.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,38 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="constraintsfinder" name="ConstraintsFinder" version="0.94">
+    <description>find strongly interacting residues</description>
+    <command interpreter="bash"><![CDATA[../../ConstraintsFinder 
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="ini"/>
+    </outputs>
+    <help>This tool searches protein residues with which the reference ligand interacts strongly.
+Therefore the interaction of the reference ligand to each residue is evaluated. Residues with a score worse (i.e. larger) than -2 are ignored. A maximum of 3 constraints are created for the most strongly interacting residues that met the above criterion.
+
+As input we need:
+    * a file containing a protonated protein in pdb-format
+    * a file containing a reference ligand.
+      This reference ligand should be located in the binding pocket.
+      Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+
+Output of this tool is a docking configuration file containing the created constraints. This file should in following pipeline steps be specified for grid precalculation and docking.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Converter.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,50 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="converter" name="Converter" version="0.94">
+    <description>interconvert molecular file-formats</description>
+    <command interpreter="bash"><![CDATA[../../Converter 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $f ) != ''  and str( $f ) != 'None' :
+   -f "$f"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="f" label="output format" optional="true" type="select">
+            <option value="mol2">mol2</option>
+            <option value="sdf">sdf</option>
+            <option value="drf">drf</option>
+            <option value="pdb">pdb</option>
+            <option value="ac">ac</option>
+            <option value="ent">ent</option>
+            <option value="brk">brk</option>
+            <option value="hin">hin</option>
+            <option value="mol">mol</option>
+            <option value="xyz">xyz</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf">
+            <change_format>
+                <when input="f" value="mol2" format="mol2"/>
+                <when input="f" value="sdf" format="sdf"/>
+                <when input="f" value="drf" format="drf"/>
+                <when input="f" value="pdb" format="pdb"/>
+                <when input="f" value="ac" format="ac"/>
+                <when input="f" value="ent" format="ent"/>
+                <when input="f" value="brk" format="brk"/>
+                <when input="f" value="hin" format="hin"/>
+                <when input="f" value="mol" format="mol"/>
+                <when input="f" value="xyz" format="xyz"/>
+            </change_format>
+        </data>
+    </outputs>
+    <help>This tool can be used to convert between different molecular file-formats.
+Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/DBExporter.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,97 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="dbexporter" name="DBExporter" version="0.94 (ob)">
+    <description>export molecules from data base</description>
+    <command interpreter="bash"><![CDATA[../../DBExporter 
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $start_id ) != ''  and str( $start_id ) != 'None' :
+   -start_id "$start_id"
+#end if
+#if str( $end_id ) != ''  and str( $end_id ) != 'None' :
+   -end_id "$end_id"
+#end if
+#if str( $min_logP ) != ''  and str( $min_logP ) != 'None' :
+   -min_logP "$min_logP"
+#end if
+#if str( $max_logP ) != ''  and str( $max_logP ) != 'None' :
+   -max_logP "$max_logP"
+#end if
+#if str( $min_MW ) != ''  and str( $min_MW ) != 'None' :
+   -min_MW "$min_MW"
+#end if
+#if str( $max_MW ) != ''  and str( $max_MW ) != 'None' :
+   -max_MW "$max_MW"
+#end if
+#if str( $max_mols ) != ''  and str( $max_mols ) != 'None' :
+   -max_mols "$max_mols"
+#end if
+#if str( $target ) != ''  and str( $target ) != 'None' :
+   -target "$target"
+#end if
+#if str( $q ) != ''  and str( $q ) != 'None' :
+   -q "$q"
+#end if
+#if str( $min_sim ) != ''  and str( $min_sim ) != 'None' :
+   -min_sim "$min_sim"
+#end if
+#if str( $max_sim ) != ''  and str( $max_sim ) != 'None' :
+   -max_sim "$max_sim"
+#end if
+#if str( $smarts ) != ''  and str( $smarts ) != 'None' :
+   -smarts "$smarts"
+#end if
+#if str( $smarts_file ) != ''  and str( $smarts_file ) != 'None' :
+   -smarts_file "$smarts_file"
+#end if
+#if str( $uck ) != ''  and str( $uck ) != 'None' :
+   -uck "$uck"
+#end if
+#if str( $d ) != ''  and str( $d ) != 'None' :
+   -d "$d"
+#end if
+#if str( $u ) != ''  and str( $u ) != 'None' :
+   -u "$u"
+#end if
+#if str( $h ) != ''  and str( $h ) != 'None' :
+   -h "$h"
+#end if
+#if str( $port ) != ''  and str( $port ) != 'None' :
+   -port "$port"
+#end if
+#if str( $p ) != ''  and str( $p ) != 'None' :
+   -p "$p"
+#end if
+#if str( $s ) != ''  and str( $s ) != 'None' :
+   -s
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="mol2/sdf/drf"/>
+        <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/>
+        <param name="start_id" label="ID of the first conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="end_id" label="ID of the last conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="min_logP" label="minimal logP value" optional="true" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/>
+        <param name="max_logP" label="maximal logP value" optional="true" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/>
+        <param name="min_MW" label="minimal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="max_MW" label="maximal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="max_mols" label="max. number of molecules to be exported" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="target" label="target/dataset name whose molecules should be exported" optional="true" area="true" type="text" size="1x15"/>
+        <param name="min_sim" label="minimal average similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/>
+        <param name="max_sim" label="maximal similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/>
+        <param name="smarts" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/>
+        <param name="uck" label="UCK key" optional="true" area="true" type="text" size="1x15"/>
+        <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/>
+        <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/>
+        <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/>
+        <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/>
+        <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/>
+        <param name="s" label="show summary of datasets in database" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf"/>
+    </outputs>
+    <help>This tool exports compounds from a database to a molecular file. Compounds can be filtered according to (among others) SMARTS expressions, logP, molecular weight, or similarity to query molecule(s) and dataset name.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/DBImporter.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,57 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="dbimporter" name="DBImporter" version="0.94 (ob)">
+    <description>import molecules into data base</description>
+    <command interpreter="bash"><![CDATA[../../DBImporter 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $target ) != ''  and str( $target ) != 'None' :
+   -target "$target"
+#end if
+#if str( $d ) != ''  and str( $d ) != 'None' :
+   -d "$d"
+#end if
+#if str( $u ) != ''  and str( $u ) != 'None' :
+   -u "$u"
+#end if
+#if str( $h ) != ''  and str( $h ) != 'None' :
+   -h "$h"
+#end if
+#if str( $port ) != ''  and str( $port ) != 'None' :
+   -port "$port"
+#end if
+#if str( $p ) != ''  and str( $p ) != 'None' :
+   -p "$p"
+#end if
+#if str( $vn ) != ''  and str( $vn ) != 'None' :
+   -vn "$vn"
+#end if
+#if str( $vid ) != ''  and str( $vid ) != 'None' :
+   -vid "$vid"
+#end if
+#if str( $vd ) != ''  and str( $vd ) != 'None' :
+   -vd "$vd"
+#end if
+#if str( $vu ) != ''  and str( $vu ) != 'None' :
+   -vu "$vu"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="target" label="target/dataset name whose molecules should be exported" optional="true" area="true" type="text" size="1x15"/>
+        <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/>
+        <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/>
+        <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/>
+        <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/>
+        <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/>
+        <param name="vn" label="name of compound vendor" optional="true" area="true" type="text" size="1x15"/>
+        <param name="vid" label="name of vendor's compound-ID tag in sd-file" optional="true" area="true" type="text" size="1x15"/>
+        <param name="vd" label="vendor library date or version" optional="true" area="true" type="text" size="1x15"/>
+        <param name="vu" label="url from wich vendor library was obtained" optional="true" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs/>
+    <help>This tool imports molecules into a database.
+As input we need the file containing the molecules to be imported in sd-, mol2- or drf-format.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,49 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="dockresultmerger" name="DockResultMerger" version="0.94">
+    <description>merge docking output files</description>
+    <command interpreter="bash"><![CDATA[../../DockResultMerger 
+#for $s in $series_i 
+   #if str( "${s.i.file_name}" ) != ''  and str( "${s.i.file_name}" ) != 'None' :
+      -i "${s.i.file_name}"
+   #end if
+#end for 
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $score ) != ''  and str( $score ) != 'None' :
+   -score "$score"
+#end if
+#if str( $min ) != ''  and str( $min ) != 'None' :
+   -min "$min"
+#end if
+#if str( $max ) != ''  and str( $max ) != 'None' :
+   -max "$max"
+#end if
+#if str( $k ) != ''  and str( $k ) != 'None' :
+   -k "$k"
+#end if
+#if str( $rm ) != ''  and str( $rm ) != 'None' :
+   -rm
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <repeat name="series_i" title="input files" min="1">
+            <param name="i" label="input files" optional="false" type="data" format="mol2/sdf/drf"/>
+        </repeat>
+        <param name="score" label="score property name" optional="true" area="true" type="text" size="1x15" value="score"/>
+        <param name="min" label="minimal score value" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="max" label="maximal score value" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="k" label="number of output molecules" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="rm" label="remove input files after merging" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool merges and sorts molecule files as generated by docking or rescoring.
+
+You need to specify the property-tag name of the scores according to which the molecules should be sorted. Optionally you can filter those compounds that were assigned a score above and/or below specified thresholds. If desired, you can furthermore choose to have only the compounds with the k best scores written to the output file.
+
+ Output of DockResultMerger is one molecule containing the molecules found in input-files (that matched all filter criteria, if any), sorted ascendingly according to their scores.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/EvenSplit.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,41 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="evensplit" name="EvenSplit" version="0.94">
+    <description>generate splits w/ equal property range</description>
+    <command interpreter="bash"><![CDATA[../../EvenSplit 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o1 ) != ''  and str( $o1 ) != 'None' :
+   -o1 "$o1"
+#end if
+#if str( $o2 ) != ''  and str( $o2 ) != 'None' :
+   -o2 "$o2"
+#end if
+#if str( $n ) != ''  and str( $n ) != 'None' :
+   -n "$n"
+#end if
+#if str( $offset ) != ''  and str( $offset ) != 'None' :
+   -offset "$offset"
+#end if
+#if str( $k ) != ''  and str( $k ) != 'None' :
+   -k "$k"
+#end if
+#if str( $prop ) != ''  and str( $prop ) != 'None' :
+   -prop "$prop"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="n" label="number of compounds to use from input file" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="offset" label="extract each (i+offset)%k == 0 for o2" optional="true" type="text" area="true" size="1x5" value="0"/>
+        <param name="k" label="extract each k'th compound for 2nd output file" optional="true" type="text" area="true" size="1x5" value="2"/>
+        <param name="prop" label="property name" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/>
+    </inputs>
+    <outputs>
+        <data name="o1" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o2" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool splits a molecule file into two subsets in such a way that each of them convers an equal range of a property. The property with respect to which this is to be done should be specified with '-prop'.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/FeatureSelector.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,41 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="featureselector" name="FeatureSelector" version="1.1">
+    <description>run feature-selection on a QSAR model</description>
+    <command interpreter="bash"><![CDATA[../../FeatureSelector 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $dat ) != ''  and str( $dat ) != 'None' :
+   -dat "$dat"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $type ) != ''  and str( $type ) != 'None' :
+   -type "$type"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input mod-file" optional="false" type="data" format="mod"/>
+        <param name="dat" label="data-file" optional="false" type="data" format="dat"/>
+        <param name="type" label="feature-selection type" optional="false" type="select">
+            <option value="remove_correlated">remove_correlated</option>
+            <option value="forward_selection">forward_selection</option>
+            <option value="backward_selection">backward_selection</option>
+            <option value="stepwise_selection">stepwise_selection</option>
+            <option value="twinscan">twinscan</option>
+            <option value="removeLowResponseCorrelation">removeLowResponseCorrelation</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="o" format="mod"/>
+    </outputs>
+    <help>FeatureSelector runs a feature-selection for a given QSAR model.
+
+The type of feature-selection to be done is specified by '-type'. Input of this tool is a data file as generated by InputReader containing the training data for feature-selection and a QSAR model file as generated by ModelCreator (or this tool itself). Note that you can apply several feature-selection methods in succession by using the output of one call of this tool as input for the next call.
+Model- and kernel-parameters (if any) will be automatically optimized by cross-validation after applying the desired feature-selection.
+
+Output of this tool is a model-file that can be used by other QuEasy tools (e.g. Validator).</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,30 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.94">
+    <description>generate galaxy tool-config files</description>
+    <command interpreter="bash"><![CDATA[../../GalaxyConfigGenerator 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ignore ) != ''  and str( $ignore ) != 'None' :
+   -ignore "$ignore"
+#end if
+#if str( $s ) != ''  and str( $s ) != 'None' :
+   -s "$s"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input par-file" optional="false" type="data" format="data"/>
+        <param name="ignore" label="tool-parameter to be ignored, i.e. those for which no galaxy config entry should be created" optional="true" area="true" size="1x5"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="xml"/>
+        <data name="s" format="data"/>
+    </outputs>
+    <help>This tool can be used to create galaxy tool-configuration files.
+As input, please supply a parameter-file as written by '-write_par' by all of our tools.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/GridBuilder.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,38 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="gridbuilder" name="GridBuilder" version="0.94">
+    <description>create score-grids for docking</description>
+    <command interpreter="bash"><![CDATA[../../GridBuilder 
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $grd ) != ''  and str( $grd ) != 'None' :
+   -grd "$grd"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+    </inputs>
+    <outputs>
+        <data name="grd" format="grd.tgz"/>
+    </outputs>
+    <help>This tool precalculates a score-grid for a binding pocket of a given receptor.
+
+As input we need:
+    * a file containing a protonated protein in pdb-format
+    * a file containing a reference ligand.
+      This reference ligand should be located in the binding pocket, 
+      so that a grid can be precalculated around it.
+      Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+
+Output of this tool is a file containing the score-grids that can be used by docking-/scoring-tools (e.g. IMeedyDock).</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/IMGDock.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,47 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="imeedydock" name="IMGDock" version="0.94">
+    <description>Iterative Multi-Greedy Docking</description>
+    <command interpreter="bash"><![CDATA[../../IMGDock 
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $grd ) != ''  and str( $grd ) != 'None' :
+   -grd "$grd"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+        <param name="i" label="compounds to be docked" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="grd" label="ScoreGrid file" optional="false" type="data" format="grd.tgz"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>IMGDock docks compounds into the binding pocket of a receptor using an iterative multi-greedy approach.
+As input we need:
+
+    * a file containing a protonated protein in pdb-format
+    * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+    * a score-grid file generated by GridBuilder. This grid must have been precalculated for the same receptor and reference ligand as those that are to be used here.
+    * a file containing the compounds that are to be docked. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). These molecules must have been assigned 3D coordinates (e.g. by Ligand3DGenerator) and should have been checked for errors using LigCheck.
+
+Output of this tool is a file containing all compounds docked into the binding pocket, with a property-tag named 'score' indicating the score obtained for each compound.
+
+Tip: If you want to parallelize docking, use LigandFileSplitter to separate your input file containing the compounds to be docked into several batches, dock each batch with this tool and merge the output files with DockResultMerger.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/InputPartitioner.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,28 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="inputpartitioner" name="InputPartitioner" version="1.1">
+    <description>split QSAR data set</description>
+    <command interpreter="bash"><![CDATA[../../InputPartitioner 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $n ) != ''  and str( $n ) != 'None' :
+   -n "$n"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input data-file" optional="false" type="data" format="dat"/>
+        <param name="n" label="number of partitions" optional="false" type="text" area="true" size="1x5" value=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="dat"/>
+    </outputs>
+    <help>InputPartitioner partitions a given QSAR data set into n partitions with evenly distributed response values.
+Thus, this tool can be useful as part of a nested validation pipeline.
+Input is a data file as generated by InputReader.
+Output will be written to n files postfixed '_TRAIN&lt;i&gt;.dat' and '_TEST&lt;i&gt;.dat', where &lt;i&gt; is the ID of the resp. partition. For each of these partitions, the training set contains only those compounds that were not selected for the resp. test set.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/InputReader.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,68 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="inputreader" name="InputReader" version="1.1">
+    <description>generate QSAR data set</description>
+    <command interpreter="bash"><![CDATA[../../InputReader 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $act ) != ''  and str( $act ) != 'None' :
+   -act "$act"
+#end if
+#if str( $csv ) != ''  and str( $csv ) != 'None' :
+   -csv "$csv"
+#end if
+#if str( $csv_nr ) != ''  and str( $csv_nr ) != 'None' :
+   -csv_nr "$csv_nr"
+#end if
+#if str( $csv_sep ) != ''  and str( $csv_sep ) != 'None' :
+   -csv_sep "$csv_sep"
+#end if
+#if str( $sdp ) != ''  and str( $sdp ) != 'None' :
+   -sdp
+#end if
+#if str( $no_cd ) != ''  and str( $no_cd ) != 'None' :
+   -no_cd
+#end if
+#if str( $no_cr ) != ''  and str( $no_cr ) != 'None' :
+   -no_cr
+#end if
+#if str( $csv_cl ) != ''  and str( $csv_cl ) != 'None' :
+   -csv_cl
+#end if
+#if str( $csv_dl ) != ''  and str( $csv_dl ) != 'None' :
+   -csv_dl
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input sd-file" optional="false" type="data" format="sdf"/>
+        <param name="csv" label="input csv-file w/ additional descriptors" optional="true" type="data" format="csv"/>
+        <param name="act" label="sd-property containing response values" optional="true" area="true" type="text" size="1x15"/>
+        <param name="csv_nr" label="no. of response variables in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="csv_sep" label="separator symbol in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="sdp" label="use sd-properties as additional descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="no_cd" label="do not center descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="no_cr" label="do not center response values" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="csv_cl" label="csv-file has compound (row) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="csv_dl" label="csv-file has descriptor (column) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="dat"/>
+    </outputs>
+    <help>This tool reads input from sd-files and generate features for QSAR analysis.
+Activity data (response values) for a training set are taken from sd-properties of the input file; the name of this property can be specified by option '-act'.
+The following number of features will be automatically created for each molecule in your sd-file:
+
+    * 40 atom and bond count descriptors
+    * 2 connectivity indices (Balaban and Zagreb index)
+    * 4 partial charge descriptors
+    * 14 surface descriptors
+    * 133 topological descriptors (functional group counts)
+
+If desired, you can also read additional descriptors from a csv-file; in this case you need to specify the file with the above options.
+Output of this tool is a data file that can be used by other QuEasy tools (e.g. ModelCreator).</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,37 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.94">
+    <description>define interaction constraint</description>
+    <command interpreter="bash"><![CDATA[../../InteractionConstraintDefiner 
+#if str( $res ) != ''  and str( $res ) != 'None' :
+   -res "$res"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $s ) != ''  and str( $s ) != 'None' :
+   -s "$s"
+#end if
+#if str( $p ) != ''  and str( $p ) != 'None' :
+   -p "$p"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="ini" label="input configuration file" optional="true" type="data" format="ini"/>
+        <param name="res" label="residue ID" optional="false" area="true" type="text" size="1x15"/>
+        <param name="s" label="desired minimal interation (score) between ligand and specified residue(s)" optional="false" type="text" area="true" size="1x5" value="-2.0"/>
+        <param name="p" label="penalty value" optional="false" type="text" area="true" size="1x5" value="10"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="ini"/>
+    </outputs>
+    <help>This tool allows to define interaction constraints for docking or scoring.
+
+The constraint to be created will enforce a specified minimal interaction between ligands and the specified residue(s) of the receptor. Please specify residue IDs in the following manner: &lt;chain-ID&gt;:&lt;residue-ID&gt;, e.g. A:57. If you want to use more than one residue, separate their IDs by commas, e.g. A:57,B:17.
+
+Output of this tool is a ini-file that contains the desired interaction constraint.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/LigCheck.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,45 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="ligcheck" name="LigCheck" version="0.94">
+    <description>check molecules for errors</description>
+    <command interpreter="bash"><![CDATA[../../LigCheck 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ef ) != ''  and str( $ef ) != 'None' :
+   -ef "$ef"
+#end if
+#if str( $ri ) != ''  and str( $ri ) != 'None' :
+   -ri
+#end if
+#if str( $ut ) != ''  and str( $ut ) != 'None' :
+   -ut
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ef" label="error fraction; print error if fraction of invalid mols is larger" optional="true" type="text" area="true" size="1x5" value="0.5"/>
+        <param name="ri" label="remove invalid molecules." optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="ut" label="check for unique topologies (default: check only for unique conformation)" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+
+The following checks are done for each molecule:
+
+    * bond-lengths may not be completely senseless (i.e. &lt;0.7 or &gt;2.5 Angstroem)
+    * each 'molecule' in the input file may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments.
+    * each atom must have a valid assigned element
+    * the molecule must be protonated (since this is necessary for docking/(re-)scoring).
+    * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
+    * partial charges may not contain completely senseless values (&gt;5 or &lt;-5).
+    * each conformation should appear only once within the given file, otherwise it is rejected and not written to the output file. However, if option '-ut' is used, molecules will instead be checked for unique topologies.
+
+If option '-ri' is used, only those molecules that pass all those tests are written to the output file. If this option is not used, all molecules are written to output containing a property 'score_ligcheck' with a value of 1 if the molecule passed all tests or with a value of 0 if it did not pass them.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,30 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.94">
+    <description>generate 3D coordinates for small molecules</description>
+    <command interpreter="bash"><![CDATA[../../Ligand3DGenerator 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ph ) != ''  and str( $ph ) != 'None' :
+   -ph "$ph"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ph" label="pH-value for pH-dep. protonation" optional="true" type="text" area="true" size="1x5" value="7.0"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool generates 3D conformations for small molecules and adds hydrogens to them.
+As input we only a chemical file containing valid topologies. Any 2D or 3D conformations in the input file are ignored, but the existence of the correct bond-orders is necessary.
+
+Note however, that the main purpose of this tool is to generate feasible start-conformations for docking or other optimization procedures. Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules) different fragments might still overlap with each other.
+
+Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,84 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.94">
+    <description>split molecule files</description>
+    <command interpreter="bash"><![CDATA[../../LigandFileSplitter 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $no ) != ''  and str( $no ) != 'None' :
+   -no "$no"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $o2 ) != ''  and str( $o2 ) != 'None' :
+   -o "$o2"
+#end if
+#if str( $o3 ) != ''  and str( $o3 ) != 'None' :
+   -o "$o3"
+#end if
+#if str( $o4 ) != ''  and str( $o4 ) != 'None' :
+   -o "$o4"
+#end if
+#if str( $o5 ) != ''  and str( $o5 ) != 'None' :
+   -o "$o5"
+#end if
+#if str( $o6 ) != ''  and str( $o6 ) != 'None' :
+   -o "$o6"
+#end if
+#if str( $o7 ) != ''  and str( $o7 ) != 'None' :
+   -o "$o7"
+#end if
+#if str( $o8 ) != ''  and str( $o8 ) != 'None' :
+   -o "$o8"
+#end if
+#if str( $o9 ) != ''  and str( $o9 ) != 'None' :
+   -o "$o9"
+#end if
+#if str( $o10 ) != ''  and str( $o10 ) != 'None' :
+   -o "$o10"
+#end if
+#if str( $o11 ) != ''  and str( $o11 ) != 'None' :
+   -o "$o11"
+#end if
+#if str( $o12 ) != ''  and str( $o12 ) != 'None' :
+   -o "$o12"
+#end if
+#if str( $o13 ) != ''  and str( $o13 ) != 'None' :
+   -o "$o13"
+#end if
+#if str( $o14 ) != ''  and str( $o14 ) != 'None' :
+   -o "$o14"
+#end if
+#if str( $o15 ) != ''  and str( $o15 ) != 'None' :
+   -o "$o15"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="no" label="no. of splits to be created" optional="false" type="hidden" area="true" size="1x5" value="15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o2" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o3" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o4" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o5" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o6" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o7" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o8" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o9" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o10" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o11" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o12" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o13" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o14" format="mol2/sdf/drf" format_source="i"/>
+        <data name="o15" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>LigandFileSplitter splits a molecule file into a given number of subsets.
+Note that the molecules are not sorted in any way for this.
+
+Since Galaxy does not support a flexible number of output-files, we will create 15 output files when you use LigandFileSplitter in Galaxy.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ModelCreator.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,52 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="modelcreator" name="ModelCreator" version="1.1">
+    <description>create a QSAR model</description>
+    <command interpreter="bash"><![CDATA[../../ModelCreator 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $type ) != ''  and str( $type ) != 'None' :
+   -type "$type"
+#end if
+#if str( $kernel ) != ''  and str( $kernel ) != 'None' :
+   -kernel "$kernel"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input dat-file" optional="false" type="data" format="dat"/>
+        <param name="type" label="model type" optional="false" type="select">
+            <option value="MLR">MLR</option>
+            <option value="RR">RR</option>
+            <option value="PCR">PCR</option>
+            <option value="PLS">PLS</option>
+            <option value="OPLS">OPLS</option>
+            <option value="ALL">ALL</option>
+            <option value="KNN">KNN</option>
+            <option value="KPLS">KPLS</option>
+            <option value="KPCR">KPCR</option>
+            <option value="GP">GP</option>
+            <option value="LDA">LDA</option>
+            <option value="snB">snB</option>
+            <option value="nB">nB</option>
+        </param>
+        <param name="kernel" label="kernel type (in case of kernel-model)" optional="true" type="select">
+            <option value="none">none</option>
+            <option value="polynomial">polynomial</option>
+            <option value="rbf">rbf</option>
+            <option value="sigmoidal">sigmoidal</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="o" format="mod"/>
+    </outputs>
+    <help>ModelCreator creates a QSAR model using an input data set as generated by InputReader.
+
+The type of QSAR model to be used can be specified by '-type', the type of kernel-function (if any) can be chosen by '-kernel'. Optimization of model- and kernel-parmeters will be done automatically using cross-validation.
+
+Output of this tool is a model-file that can be used by other QuEasy tools (e.g. FeatureSelector).</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolCombine.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,45 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="molcombine" name="MolCombine" version="0.94">
+    <description>combine molecular files</description>
+    <command interpreter="bash"><![CDATA[../../MolCombine 
+#if str( $i1 ) != ''  and str( $i1 ) != 'None' :
+   -i1 "$i1"
+#end if
+#if str( $i2 ) != ''  and str( $i2 ) != 'None' :
+   -i2 "$i2"
+#end if
+#if str( $mode ) != ''  and str( $mode ) != 'None' :
+   -mode "$mode"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ignH ) != ''  and str( $ignH ) != 'None' :
+   -ignH
+#end if
+#if str( $replace_prop ) != ''  and str( $replace_prop ) != 'None' :
+   -replace_prop
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i1" label="input molecule file A" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="i2" label="input molecule file B" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="mode" label="'intersection', 'union' or 'b_not_a'" optional="false" type="select">
+            <option value="intersection">intersection</option>
+            <option value="union">union</option>
+            <option value="b_not_a">b_not_a</option>
+        </param>
+        <param name="ignH" label="ignore hydrogens, i.e. match molecules to any protonation state." optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="replace_prop" label="replace properties from file 1 w/ those from file 2" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i1"/>
+    </outputs>
+    <help>This tool generates the intersection or union of two given chemical files. Property-tags of molecules that appear in both input files are automatically merged.
+
+If you want to match molecules regardless of their protonation state, use option '-ignH'.
+
+Output of this tool is a file containing the union resp. intersection of all molecules of input A and B.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolDepict.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,28 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="moldepict" name="MolDepict" version="0.94">
+    <description>create structure diagrams</description>
+    <command interpreter="bash"><![CDATA[../../MolDepict 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $max ) != ''  and str( $max ) != 'None' :
+   -max "$max"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="max" label="maximal number of pictures (default=60, 0=unlimited)" optional="true" type="text" area="true" size="1x5" value="60"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="pdf"/>
+    </outputs>
+    <help>This tool create structure diagrams for small molecules.
+Supported input-formats are mol, mol2, sdf, drf.
+
+Output of this tool is one pdf-file containing the structure diagrams for all molecules in the input-file.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolFilter.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,60 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="molfilter" name="MolFilter" version="0.9">
+    <description>filter molecule files</description>
+    <command interpreter="bash"><![CDATA[../../MolFilter 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $min_logP ) != ''  and str( $min_logP ) != 'None' :
+   -min_logP "$min_logP"
+#end if
+#if str( $max_logP ) != ''  and str( $max_logP ) != 'None' :
+   -max_logP "$max_logP"
+#end if
+#if str( $min_MW ) != ''  and str( $min_MW ) != 'None' :
+   -min_MW "$min_MW"
+#end if
+#if str( $max_MW ) != ''  and str( $max_MW ) != 'None' :
+   -max_MW "$max_MW"
+#end if
+#if str( $q ) != ''  and str( $q ) != 'None' :
+   -q "$q"
+#end if
+#if str( $min_sim ) != ''  and str( $min_sim ) != 'None' :
+   -min_sim "$min_sim"
+#end if
+#if str( $max_sim ) != ''  and str( $max_sim ) != 'None' :
+   -max_sim "$max_sim"
+#end if
+#if str( $smarts ) != ''  and str( $smarts ) != 'None' :
+   -smarts "$smarts"
+#end if
+#if str( $smarts_file ) != ''  and str( $smarts_file ) != 'None' :
+   -smarts_file "$smarts_file"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+-quiet 
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input molecule-file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="txt"/>
+        <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/>
+        <param name="min_logP" label="minimal logP value" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="max_logP" label="maximal logP value" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="min_MW" label="minimal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="max_MW" label="maximal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="min_sim" label="minimal average similarity" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="max_sim" label="maximal similarity" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="smarts" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>MolFilter can filter molecules from a molecule input file according to SMARTS expressions, logP, molecular weight, or similarity to query molecule(s).
+
+Output of this tool is a molecule file that contains all compounds that fulfilled the specified search criteria.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolPredictor.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,50 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="molpredictor" name="MolPredictor" version="1.1">
+    <description>predict molecule activities with QSAR model</description>
+    <command interpreter="bash"><![CDATA[../../MolPredictor 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $mod ) != ''  and str( $mod ) != 'None' :
+   -mod "$mod"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $csv ) != ''  and str( $csv ) != 'None' :
+   -csv "$csv"
+#end if
+#if str( $csv_nr ) != ''  and str( $csv_nr ) != 'None' :
+   -csv_nr "$csv_nr"
+#end if
+#if str( $csv_sep ) != ''  and str( $csv_sep ) != 'None' :
+   -csv_sep "$csv_sep"
+#end if
+#if str( $csv_cl ) != ''  and str( $csv_cl ) != 'None' :
+   -csv_cl
+#end if
+#if str( $csv_dl ) != ''  and str( $csv_dl ) != 'None' :
+   -csv_dl
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input sd-file" optional="false" type="data" format="sdf"/>
+        <param name="mod" label="file containing QSAR model" optional="false" type="data" format="mod"/>
+        <param name="csv" label="input csv-file w/ additional descriptors" optional="true" type="data" format="csv"/>
+        <param name="csv_nr" label="no. of response variables in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="csv_sep" label="separator symbol in csv-file" optional="true" type="text" area="true" size="1x5" value=""/>
+        <param name="csv_cl" label="csv-file has compound (row) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+        <param name="csv_dl" label="csv-file has descriptor (column) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="sdf"/>
+    </outputs>
+    <help>This tool predictes the response values of compounds in the given molecule file using the specified QSAR model.
+
+Input of this tool is a molecule file (sdf,mol2,drf) and a model-file as generated by ModelCreator or FeatureSelector.
+Features for all molecules in the input file are generated automatically. However, if you used an additional, externally generated feature-set to generate your QSAR model, make sure to generate features in the same manner (i.e. using the same external tool with the same settings) for the molecule file to be used here and specify the csv-file with the above options.
+
+Output of this tool (as specified by '-o') is a molecule file containing the predicted values as a property tag named 'predicted_activity'.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PDBCutter.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,46 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="pdbcutter" name="PDBCutter" version="0.94">
+    <description>separate ligand and receptor</description>
+    <command interpreter="bash"><![CDATA[../../PDBCutter 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $lig ) != ''  and str( $lig ) != 'None' :
+   -lig "$lig"
+#end if
+#if str( $lig_chain ) != ''  and str( $lig_chain ) != 'None' :
+   -lig_chain "$lig_chain"
+#end if
+#if str( $lig_name ) != ''  and str( $lig_name ) != 'None' :
+   -lig_name "$lig_name"
+#end if
+#if str( $rm_ch ) != ''  and str( $rm_ch ) != 'None' :
+   -rm_ch "$rm_ch"
+#end if
+#if str( $rm_res ) != ''  and str( $rm_res ) != 'None' :
+   -rm_res "$rm_res"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="lig_chain" label="chain-name of ligand" optional="false" area="true" type="text" size="1x15"/>
+        <param name="lig_name" label="ligand name" optional="false" area="true" type="text" size="1x15"/>
+        <param name="rm_ch" label="protein chains that are to be deleted" optional="true" area="true" type="text" size="1x15"/>
+        <param name="rm_res" label="pdb-residues that are to be deleted (e.g. water or ions)" optional="true" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="rec" format="pdb"/>
+        <data name="lig" format="pdb"/>
+    </outputs>
+    <help>This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively.
+
+The name of the reference ligand (exactly as it appears in the pdb-file) and the name of its chain need to be specified by '-lig_name' and '-lig_chain'.
+Optionally, chains (e.g. in case of multimers) or pdb-residues (e.g. water or ions) that you don't need can be deleted from the receptor. In this case, specify their names with '-rm_ch' or '-rm_res'.
+
+Output of this tool is one pdb-file containing the receptor-structure, i.e. the protein w/o reference ligand and w/o undesired chains/residues (if any were specified), and one pdb-file containing the reference ligand.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PDBDownload.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,25 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="pdbdownload" name="PDBDownload" version="0.94">
+    <description>retrieve pdb-file from pdb.org</description>
+    <command interpreter="bash"><![CDATA[../../PDBDownload 
+#if str( $id ) != ''  and str( $id ) != 'None' :
+   -id "$id"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $p ) != ''  and str( $p ) != 'None' :
+   -p "$p"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="id" label="PDB ID for desired structure" optional="false" area="true" type="text" size="1x15"/>
+        <param name="p" label="proxy" optional="true" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="pdb"/>
+    </outputs>
+    <help>Download a pdb-file from the pdb data bank (http://www.pdb.org/) using the specified ID of the desired protein structure.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,26 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="partialchargescopy" name="PartialChargesCopy" version="0.94">
+    <description>transfer part. charges between files</description>
+    <command interpreter="bash"><![CDATA[../../PartialChargesCopy 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $chr ) != ''  and str( $chr ) != 'None' :
+   -chr "$chr"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="chr" label="file containing the same molecules as the input file, but with (different) partial charges" optional="false" type="data" format="mol2"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2" format_source="i"/>
+    </outputs>
+    <help>This tool copies partial charges from a given file to the conformations read from a different file.
+This can be useful when computing partial charges with external tools, most of which write output as mol2-files *without* support for storing molecular properties. By use of this tool we can thus assign the computed partial charges to the original molecules, thus retaining all properties.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PocketDetector.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,38 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="pocketdetector" name="PocketDetector" version="0.94">
+    <description>detect binding pocket</description>
+    <command interpreter="bash"><![CDATA[../../PocketDetector 
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="input ini file" optional="true" type="data" format="ini"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="ini"/>
+    </outputs>
+    <help>This tool tries to detect the binding pocket in which the reference ligand is located.
+Therefore, probe atoms are placed above the protein surface at positions of relative deep burial. The cluster of probe atoms around the geometric center of the reference ligand is used for the description of the binding pocket.
+
+As input we need:
+    * a file containing a protonated protein in pdb-format. Furthermore, it should contain only relevant (i.e. strongly bound) water molecules as detected by WaterFinder.
+    * a file containing a reference ligand.
+      This reference ligand should be located in the binding pocket.
+      Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+
+Output of this tool is a docking configuration file that contains the description of the detected binding pocket. This file should in following pipeline steps be specified for docking and rescoring.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Predictor.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,30 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="predictor" name="Predictor" version="1.1">
+    <description>predict activities with QSAR model</description>
+    <command interpreter="bash"><![CDATA[../../Predictor 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $dat ) != ''  and str( $dat ) != 'None' :
+   -dat "$dat"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input mod-file" optional="false" type="data" format="mod"/>
+        <param name="dat" label="data-file containing prediction data set" optional="false" type="data" format="dat"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="txt"/>
+    </outputs>
+    <help>This tool predictes the response values of compounds in the given data-file using the specified QSAR model.
+
+Input of this tool is a model-file as generated by ModelCreator or FeatureSelector and a data-file generated by InputReader.
+
+Output of this tool (as specified by '-o') is a text file containing the predicted and, if any, the expected response values in one column each.
+If you would prefer to use molecule files (sdf,mol2,drf) for input and output, please use the tool MolPredictor instead of this one.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,43 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="propertymodifier" name="PropertyModifier" version="0.94">
+    <description>modify molecule property tags</description>
+    <command interpreter="bash"><![CDATA[../../PropertyModifier 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $mode ) != ''  and str( $mode ) != 'None' :
+   -mode "$mode"
+#end if
+#if str( $name ) != ''  and str( $name ) != 'None' :
+   -name "$name"
+#end if
+#if str( $value ) != ''  and str( $value ) != 'None' :
+   -value "$value"
+#end if
+#if str( $new_name ) != ''  and str( $new_name ) != 'None' :
+   -new_name "$new_name"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="mode" label="'delete', 'add' or 'rename' properties" optional="false" type="select">
+            <option value="add">add</option>
+            <option value="rename">rename</option>
+            <option value="delete">delete</option>
+        </param>
+        <param name="name" label="property name ('all' will erase all properties if in delete-mode)" optional="false" area="true" type="text" size="1x15"/>
+        <param name="value" label="property value (in case of prop. adding only)" optional="true" area="true" type="text" size="1x15"/>
+        <param name="new_name" label="new property name (in case of renaming only)" optional="true" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>With this tools you can add, rename or delete molecule property tags.
+These tags can for example contain information about scores, binding-free-energy, IDs or names for the resp. molecule.
+The output of this tool is a molecule file in which the desired property tags have been added/renamed/deleted (as chosen).</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,35 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="propertyplotter" name="PropertyPlotter" version="0.94">
+    <description>plot molecule properties</description>
+    <command interpreter="bash"><![CDATA[../../PropertyPlotter 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $p1 ) != ''  and str( $p1 ) != 'None' :
+   -p1 "$p1"
+#end if
+#if str( $p2 ) != ''  and str( $p2 ) != 'None' :
+   -p2 "$p2"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+-quiet 
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="p1" label="name of property 1" optional="false" area="true" type="text" size="1x15"/>
+        <param name="p2" label="name of property 2" optional="true" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="png"/>
+    </outputs>
+    <help>PropertyPlotter can be used to generate distribution- or scatter-plots of data contained in molecule property-tags.
+
+In case you want to create a scatter-plot, specify the name of both property-tags to be used with '-p1' and '-p2'. If you want to generate a distribution plot, just specify '-p1'.
+The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
+
+The output of this tool is a plot in form of an eps or png-file (as chosen).</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,34 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="proteincheck" name="ProteinCheck" version="0.94">
+    <description>quality check for proteins structures</description>
+    <command interpreter="bash"><![CDATA[../../ProteinCheck 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $bc ) != ''  and str( $bc ) != 'None' :
+   -bc
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="bc" label="ignore broken chains" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="pdf"/>
+    </outputs>
+    <help>Check a given protein structure for the following errors:
+    * bond-lengths may not be completely senseless (i.e. &lt;0.7 or &gt;2.5 Angstroem)
+    * each chain may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments. This test is skipped if the above box is checked.
+    * each atom must have a valid assigned element
+    * the protein must be protonated (since this is necessary for docking/(re-)scoring).
+    * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring)
+    * there may be no senseless temperature factors (&lt;1 or &gt;100)
+    * there may be no sterical clashes between atoms
+
+A protein structure quality report, containing the results of those tests and a secondary structure prediction, a Ramachandran plot and a temperature factor plot will be generated and saved as a pdf-file.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,29 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="proteinprotonator" name="ProteinProtonator" version="0.94">
+    <description>protonate protein structures</description>
+    <command interpreter="bash"><![CDATA[../../ProteinProtonator 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ph ) != ''  and str( $ph ) != 'None' :
+   -ph "$ph"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="pdb"/>
+        <param name="ph" label="pH-value for pH-dep. protonation" optional="true" type="text" area="true" size="1x5" value="7.0"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="pdb" format_source="i"/>
+    </outputs>
+    <help>ProteinProtonator allows you add hydrogens to a protein structure.
+
+Note that all hydrogen atoms already present in the input file will be ignored. If desired, you can specify a specific pH value, for which protonation is to be done; otherwise a neutral pH will be assumed.
+
+Output of this tool is one pdb-file containing the input protein structure with added hydrogens atoms.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,31 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="rmsdcalculator" name="RMSDCalculator" version="0.94">
+    <description>calculate RMSD between poses</description>
+    <command interpreter="bash"><![CDATA[../../RMSDCalculator 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $org ) != ''  and str( $org ) != 'None' :
+   -org "$org"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+-quiet 
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="org" label="molecule file containing the original ('true') poses" optional="false" type="data" format="mol2/sdf/drf"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool calculates the RMSD between different conformations of the same molecule.
+
+Therefore this tool can for example be used to evaluate the different between ligands taken from co-crystal structures and their poses generated by a docking.
+Molecules may be sorted differently in the two input files; a topology hashkey will be used to match molecules to each other.
+
+Output of this tool is a molecule file which will for each molecule contain a property-tag 'RMSD' holding the calculated RMSD value.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,55 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.94">
+    <description>generate ROC or enrichment plots</description>
+    <command interpreter="bash"><![CDATA[../../ScoreAnalyzer 
+#if str( $mode ) != ''  and str( $mode ) != 'None' :
+   -mode "$mode"
+#end if
+#if str( $title ) != ''  and str( $title ) != 'None' :
+   -title "$title"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $s ) != ''  and str( $s ) != 'None' :
+   -s "$s"
+#end if
+#if str( $e ) != ''  and str( $e ) != 'None' :
+   -e "$e"
+#end if
+#if str( $t ) != ''  and str( $t ) != 'None' :
+   -t "$t"
+#end if
+#if str( $b ) != ''  and str( $b ) != 'None' :
+   -b
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="mode" label="'roc', 'top50', 'scatter' or 'enrichment'" optional="false" type="select">
+            <option value="roc">roc</option>
+            <option value="top50">top50</option>
+            <option value="scatter">scatter</option>
+            <option value="enrichment">enrichment</option>
+        </param>
+        <param name="title" label="plot title" optional="true" area="true" type="text" size="1x15"/>
+        <param name="s" label="score label" optional="false" area="true" type="text" size="1x15" value="score"/>
+        <param name="e" label="binding-free-energy/class label name" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/>
+        <param name="t" label="only in case of non-binary act. data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder" optional="true" area="true" type="text" size="1x15"/>
+        <param name="b" label="binary experimental activity data" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="png"/>
+    </outputs>
+    <help>This tool can be used generate plots that allow to evaluate the quality of docking or (re-)scoring.
+
+The type of plot to be generated must be chosen by either '-roc', '-top50', '-scatter' or '-enrichment'. The name of the property-tag that contains the scores to be evaluated (e.g. obtained by docking) is to be specified by '-s'; the name of the property-tag containing experimental data (e.g. binding-free-energy measurements or binder/non-binder info) by use '-e'. If the experimental reference data is not binary, then a threshold below which compound will be considered binders must be given with '-t'.
+The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
+
+The output of this tool is a plot in form of an eps or png-file (as chosen).</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,35 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="similarityanalyzer" name="SimilarityAnalyzer" version="0.9">
+    <description>analyze similarity between molecule files</description>
+    <command interpreter="bash"><![CDATA[../../SimilarityAnalyzer 
+#if str( $i1 ) != ''  and str( $i1 ) != 'None' :
+   -i1 "$i1"
+#end if
+#if str( $i2 ) != ''  and str( $i2 ) != 'None' :
+   -i2 "$i2"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $title ) != ''  and str( $title ) != 'None' :
+   -title "$title"
+#end if
+-quiet 
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i1" label="input molecule file 1" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="i2" label="input molecule file 2" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="title" label="plot title" optional="true" area="true" type="text" size="1x15"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="png"/>
+    </outputs>
+    <help>This tool evaluates the similarity between molecules in two input files and creates a distribution plot to visualize the result.
+
+Therefore, for each molecule a pathway-based, hashed binary fingerprint is generated and compared to the fingerprint of other molecules by use of the Tanimoto similarity measure.
+The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
+
+The resulting plot (in form of an eps-, png- or pdf-file; as chosen) shows the distribution of similarity values obtained by comparing each molecule in input file 1 against each molecule in input file 2.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,49 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="simplerescorer" name="SimpleRescorer" version="0.94">
+    <description>rescore docking results</description>
+    <command interpreter="bash"><![CDATA[../../SimpleRescorer 
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $function ) != ''  and str( $function ) != 'None' :
+   -function "$function"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+        <param name="i" label="compounds to be rescored" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="function" label="scoring function: 'MM', 'PLP' or 'PB'" optional="true" type="select">
+            <option value="MM">MM</option>
+            <option value="PLP">PLP</option>
+            <option value="PB">PB</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool rescores docking output poses.
+A scoring function is used to evaluate the binding-free-energy of each compound. This is similar to the scoring done during docking; details depend on the config-file (if one is specified).
+
+As input we need:
+    * a file containing a protonated protein in pdb-format
+    * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+    * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein.
+
+Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,45 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.94">
+    <description>define spatial constraint</description>
+    <command interpreter="bash"><![CDATA[../../SpatialConstraintDefiner 
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $type ) != ''  and str( $type ) != 'None' :
+   -type "$type"
+#end if
+#if str( $n ) != ''  and str( $n ) != 'None' :
+   -n "$n"
+#end if
+#if str( $p ) != ''  and str( $p ) != 'None' :
+   -p "$p"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="ini" label="input configuration file" optional="true" type="data" format="ini"/>
+        <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="type" label="'fraction' or 'number' of compound atoms" optional="false" type="select">
+            <option value="fraction">fraction</option>
+            <option value="number">number</option>
+        </param>
+        <param name="n" label="desired number/fraction of atoms in spatial area" optional="false" type="text" area="true" size="1x5" value=""/>
+        <param name="p" label="penalty value" optional="false" type="text" area="true" size="1x5" value="1e11"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="ini"/>
+    </outputs>
+    <help>This tool allows to define spatial constraints for docking or scoring.
+
+For convenience, we use a molecule file as input and generate a boundary box around the contained compound. This molecule can therefore for example contain the reference ligand (obtained from a co-crystal structure), or a docked compound, or just a set of dummy atoms used to manually define the boundaries of the desired spatial constraint.
+Furthermore, you need to specify how many atoms of the compound to be docked (or scored) should be located inside the spatial area. You can either specify a number of atoms or a fraction of molecule atoms for this.
+
+Output of this tool is a ini-file that contains the desired spatial constraint.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,61 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="tagres-train" name="TaGRes-train" version="0.94">
+    <description>Target-specific Grid-Rescoring, training</description>
+    <command interpreter="bash"><![CDATA[../../TaGRes-train 
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $method ) != ''  and str( $method ) != 'None' :
+   -method "$method"
+#end if
+#if str( $function ) != ''  and str( $function ) != 'None' :
+   -function "$function"
+#end if
+#if str( $exp ) != ''  and str( $exp ) != 'None' :
+   -exp "$exp"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+        <param name="i" label="training compound data set" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select">
+            <option value="Rescoring3D">Rescoring3D</option>
+            <option value="Rescoring4D">Rescoring4D</option>
+            <option value="Rescoring1D">Rescoring1D</option>
+        </param>
+        <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select">
+            <option value="MM">MM</option>
+            <option value="PLP">PLP</option>
+        </param>
+        <param name="exp" label="property-tag name containing experimentally determined binding-free-energies" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/>
+    </inputs>
+    <outputs>
+        <data name="o" format="mod"/>
+    </outputs>
+    <help>This tool generates a model for Target-specific Grid-Rescoring (TaGRes).
+As input we need:
+
+    * a file containing a protonated protein in pdb-format
+    * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+    * a file containing a training data set, i.e. compounds whose binding-free-energy to the specified target is known and annotated in this file. Those compounds should have been docked into the specified protein.
+
+A scoring function is applied and an interaction-grid thereby generated for each input compound. Together with the known binding-free-energy, those grids are used to automatically search for the best linear or non-linear regression model that can approximate the binding-free-energy. After this model has been generated, you can pass it to the tool TaGRes and rescore (different) compounds with it.
+
+The output of this TaGRes-train is a file that contains the generated regression model. However, if no model with suitable prediction quality was found, an error will be shown and no model-file will be written.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/TaGRes.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,63 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="tagres" name="TaGRes" version="0.94">
+    <description>Target-specific Grid-Rescoring</description>
+    <command interpreter="bash"><![CDATA[../../TaGRes 
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $mod ) != ''  and str( $mod ) != 'None' :
+   -mod "$mod"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $method ) != ''  and str( $method ) != 'None' :
+   -method "$method"
+#end if
+#if str( $function ) != ''  and str( $function ) != 'None' :
+   -function "$function"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+        <param name="i" label="compounds to be rescored" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="mod" label="model-file generated by TaGRes-train" optional="false" type="data" format="data"/>
+        <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select">
+            <option value="Rescoring3D">Rescoring3D</option>
+            <option value="Rescoring4D">Rescoring4D</option>
+            <option value="Rescoring1D">Rescoring1D</option>
+        </param>
+        <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select">
+            <option value="MM">MM</option>
+            <option value="PLP">PLP</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="o" format="mol2/sdf/drf" format_source="i"/>
+    </outputs>
+    <help>This tool rescores docking output poses using Target-specific Grid-Rescoring.
+Please generate a regression model for binding-affinity approximation for your protein target by use of the tool TaGRes-train before using this tool.
+As input TaGRes needs:
+
+    * a file containing a protonated protein in pdb-format
+    * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+    * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein.
+    * a regression model file as generated by TaGRes-train for same protein target than the one specified here.
+
+TaGRes will evaluate each given input pose with a scoring function and apply the specified regression model to the score contributions generated this way, resulting in a re-score value, i.e. a (probably) enhanced approximation of the compound's binding-free-energy.
+
+Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Validator.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,36 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="validator" name="Validator" version="1.1">
+    <description>evaluate quality of a QSAR model</description>
+    <command interpreter="bash"><![CDATA[../../Validator 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $dat ) != ''  and str( $dat ) != 'None' :
+   -dat "$dat"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $type ) != ''  and str( $type ) != 'None' :
+   -type "$type"
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input mod-file" optional="false" type="data" format="mod"/>
+        <param name="dat" label="data-file" optional="false" type="data" format="dat"/>
+        <param name="type" label="feature-selection type" optional="false" type="select">
+            <option value="cross validation">cross validation</option>
+            <option value="bootstrapping">bootstrapping</option>
+            <option value="response permutation">response permutation</option>
+            <option value="evaluate fit to test data">evaluate fit to test data</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="o" format="txt"/>
+    </outputs>
+    <help>Validator evaluates the quality of a QSAR model.
+
+The validation technique to be used for this can selected by '-type'. As input this tools need a model-file as generate by InputReader or FeatureSelector and a data-file generated by InputReader containing the prediction data set. Note that the latter must contain response values so that predictions done by the supplied model can be compared to those values by the validation method.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/VendorFinder.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,49 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="vendorfinder" name="VendorFinder" version="0.94">
+    <description>search vendors for compounds</description>
+    <command interpreter="bash"><![CDATA[../../VendorFinder 
+#if str( $i ) != ''  and str( $i ) != 'None' :
+   -i "$i"
+#end if
+#if str( $d ) != ''  and str( $d ) != 'None' :
+   -d "$d"
+#end if
+#if str( $u ) != ''  and str( $u ) != 'None' :
+   -u "$u"
+#end if
+#if str( $h ) != ''  and str( $h ) != 'None' :
+   -h "$h"
+#end if
+#if str( $port ) != ''  and str( $port ) != 'None' :
+   -port "$port"
+#end if
+#if str( $p ) != ''  and str( $p ) != 'None' :
+   -p "$p"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $opt ) != ''  and str( $opt ) != 'None' :
+   -opt
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="i" label="input file containing compounds" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/>
+        <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/>
+        <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/>
+        <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/>
+        <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/>
+        <param name="opt" label="optimize purchase, i.e. select cheapest sources and sort by vendor" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="txt"/>
+    </outputs>
+    <help>This tool can be used to fetch information about vendors for each compound in the given input file from a data base.
+
+Of course, vendors can only be found if they have been stored in the database that is to be used here. Use DBImporter with molecules files obtained from the compound vendors of your choice in order to create such a database.
+
+Output of this tool is a text-file containing a list of vendor-name and vendor's compound-ID for each compound in the input file for which vendor-information was found in the database.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/WaterFinder.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,55 @@
+
+<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
+<tool id="waterfinder" name="WaterFinder" version="0.94">
+    <description>find strongly bound waters</description>
+    <command interpreter="bash"><![CDATA[../../WaterFinder 
+#if str( $rec ) != ''  and str( $rec ) != 'None' :
+   -rec "$rec"
+#end if
+#if str( $rl ) != ''  and str( $rl ) != 'None' :
+   -rl "$rl"
+#end if
+#if str( $ini ) != ''  and str( $ini ) != 'None' :
+   -ini "$ini"
+#end if
+#if str( $wat ) != ''  and str( $wat ) != 'None' :
+   -wat "$wat"
+#end if
+#if str( $o ) != ''  and str( $o ) != 'None' :
+   -o "$o"
+#end if
+#if str( $ai ) != ''  and str( $ai ) != 'None' :
+   -ai
+#end if
+ | tail -n 5
+]]></command>
+    <inputs>
+        <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/>
+        <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/>
+        <param name="ini" label="configuration file" optional="true" type="data" format="ini"/>
+        <param name="wat" label="input pdb-file containing water molecules (if not part of rec.-file)" optional="true" type="data" format="pdb"/>
+        <param name="ai" label="use ab-initio water search (ignore water in pdb-file), experimental!" optional="true" type="boolean" truevalue="true" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="o" format="pdb"/>
+    </outputs>
+    <help>This tool searches for crystal waters that
+    * either interact very strongly with the receptor
+    * or that interact strongly with receptor and reference ligand, 
+      thus functioning as a water bridge.
+
+Water molecules in the pdb-structure (i.e. single oxygens) are automatically protonated and rotationally optimized before the search is done.
+
+As input we need:
+    * a file containing a protonated protein in pdb-format.
+      This file should contain water molecules that are to be evaluated by this tool.
+      However, you can also use a separate pdb-file as input for the water molecules (see below).
+    * a file containing a reference ligand.
+      This reference ligand should be located in the binding pocket.
+      Supported formats are mol2, sdf or drf (DockResultFile, xml-based).
+    * optionally a file in pdb-format containing water molecules.
+      If you specify such a file , all water molecules appearing in the
+      protein input-file (if any) will be ignored.
+
+Output of this tool is a pdb-file containing the protein and all detected strongly bound water molecules.</help>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/upload.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,46 @@
+<?xml version="1.0"?>
+
+<tool name="Upload File" id="cadds_upload" version="1.1.2">
+  <description>
+    from your computer  
+  </description>
+  <action module="galaxy.tools.actions.upload" class="UploadToolAction"/>
+  <command interpreter="python">
+      ../../../data_source/upload.py $GALAXY_ROOT_DIR $GALAXY_DATATYPES_CONF_FILE $paramfile
+    #set $outnum = 0
+    #while $varExists('output%i' % $outnum):
+        #set $output = $getVar('output%i' % $outnum)
+        #set $outnum += 1
+        ${output.dataset.dataset.id}:${output.files_path}:${output}
+    #end while
+  </command>
+  <inputs nginx_upload="true">
+    <param name="file_type" type="select" label="File Format" help="Which format? See help below">
+      <options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ &quot;%s%s%s&quot; % ( line, self.separator, line ) for line in obj ]">
+        <column name="value" index="1"/>
+        <column name="name" index="0"/>
+        <filter type="sort_by" column="0"/>
+        <filter type="add_value" name="Auto-detect" value="auto" index="0"/>
+      </options>
+    </param>
+    <param name="async_datasets" type="hidden" value="None"/>
+    <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata">
+      <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: For NGS and other large files (>~2GB), uploading via HTTP/FTP URL (below) is the most reliable method.">
+        <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator> <!-- use validator to post message to user about needing to reselect the file, since most browsers won't accept the value attribute for file inputs -->
+      </param>
+      <param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/> 
+      <param name="ftp_files" type="ftpfile" label="Files uploaded via FTP"/>
+      <!--
+      <param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand."> 
+        <option value="Yes">Yes</option>
+      </param>
+      -->
+    </upload_dataset>
+    <!--<param name="dbkey" type="genomebuild" label="Genome" />-->
+    <conditional name="files_metadata" title="Specify metadata" value_from="self:app.datatypes_registry.get_upload_metadata_params" value_ref="file_type" value_ref_in_group="False" />
+    <!-- <param name="other_dbkey" type="text" label="Or user-defined Genome" /> -->
+  </inputs>
+  <help>
+
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/install.sh	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,84 @@
+#!/bin/bash
+
+QT_DIR=""
+INSTALL_DIR=""
+#OPT="Linux_x86_64"
+
+
+checkDir()
+{
+	echo -n "checking for "$1" ... "
+	if [ -f $QT_DIR/$1 ]; then
+		echo $QT_DIR/$1
+		return 1
+	else
+		echo "not found!"
+		return 0
+	fi
+}
+
+echo
+cat license.txt
+echo
+echo -n "Do you agree to this license?! (y/n) "
+read license_accepted
+echo
+
+if [ "$license_accepted" != "y" ] && [ "$license_accepted" != "yes" ]; then
+	echo "License was not accepted, aborting."
+	exit 1
+fi
+
+echo -n "Please enter *absolute* path to install target-directory: "
+
+read INSTALL_DIR
+if [ ! -d $INSTALL_DIR ]; then 
+	mkdir $INSTALL_DIR
+fi
+
+if [ ! -d $INSTALL_DIR ]; then
+	echo
+	echo "[Error:] The desired install-directory does not exist and could also not be created!"
+	echo "Perhaps there was a typo or you do not have permission to create this folder."
+	echo "Aborting install."
+	echo
+	exit 1
+fi
+
+# if [ -f /usr/lib/libQtCore.so.4 ] && [ -f  /usr/lib/libQtGui.so.4 ]; then
+# 	QT_DIR=/usr/lib 
+# else 
+# 	echo "Please enter absolute path to the directory containing"
+# 	echo -n "your Qt4 libraries (version>=4.3.5): "
+# 	read QT_DIR
+# fi
+
+# checkDir libQtCore.so.4; ok=$?;
+# checkDir libQtGui.so.4;  if [ $ok = 1 ]; then let ok $?; fi
+# #checkDir libQtOpenGL.so; if [ $ok = 1 ]; then ok=$?; fi
+# 
+# if [ $ok != 1 ]; then
+# 	echo "Aborting installation due to missing Qt4!"
+# 	exit 1
+# fi
+
+cd bin
+programs=`ls *.bin`
+cd ..
+for i in $programs; do
+	chmod +x ${i:0:${#i}-4}
+done
+
+
+mv * $INSTALL_DIR/
+
+if [ -f $INSTALL_DIR/CADDSuite-description.txt ]; then
+	echo
+	echo
+	cat $INSTALL_DIR/CADDSuite-description.txt
+fi
+
+echo
+echo "Installation finished."
+echo "You can find all installed programs in $INSTALL_DIR."
+echo
Binary file CADDSuite/lib/libBALL.so.1.4 has changed
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/license.txt	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,20 @@
+-------------------------------------------------------------------------------
+   CADDSuite - A flexible and open framework and workflow system
+               for computer-aided drug design
+-------------------------------------------------------------------------------
+
+Copyright (C) 2011  Marcel Schumann
+
+CADDSuite is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 3 of the License, or (at
+your option) any later version.
+
+CADDSuite is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, see <http://www.gnu.org/licenses/>.
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/rescoring_common	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,4 @@
+#!/bin/bash
+	export BASE_DIR=`dirname "$0"`
+	. "$BASE_DIR"/setPathes.sh
+	"$BASE_DIR"/bin/rescoring_common.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/setPathes.sh	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,10 @@
+#!/bin/bash
+export LD_LIBRARY_PATH="$BASE_DIR"/lib
+export DYLD_LIBRARY_PATH="$BASE_DIR"/lib
+export BALL_DATA_PATH="$BASE_DIR"/data
+export BABEL_DATADIR="$BASE_DIR"/data/OpenBabel/
+export QT_PLUGIN_PATH="$BASE_DIR"/lib/plugins/
+export PATH="$BASE_DIR"/bin:$PATH
+export GDFONTPATH="$BASE_DIR"/data/fonts
+export GNUPLOT_DEFAULT_GDFONT=FreeSans
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/suite_config.xml	Sun Jun 26 13:53:57 2011 -0400
@@ -0,0 +1,140 @@
+<suite id="CADDSuite_toolsuite" name="CADDSuite" version="0.94">
+
+<description>
+CADDSuite: A flexible and open framework for Computer-Aided Drug Design
+</description>
+<tool id="cadds_upload" name="Upload File" version="1.1.2">
+    <description>from your computer</description>
+</tool>
+<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.94">
+    <description>rescore w/ anti-target dock-results</description>
+</tool>
+<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.94">
+    <description>fix bindingdb.org downloads</description>
+</tool>
+<tool id="combilibgenerator" name="CombiLibGenerator" version="0.94">
+    <description>generate combinatorial lib</description>
+</tool>
+<tool id="constraintsfinder" name="ConstraintsFinder" version="0.94">
+    <description>find strongly interacting residues</description>
+</tool>
+<tool id="converter" name="Converter" version="0.94">
+    <description>interconvert molecular file-formats</description>
+</tool>
+<tool id="dbexporter" name="DBExporter" version="0.94 (ob)">
+    <description>export molecules from data base</description>
+</tool>
+<tool id="dbimporter" name="DBImporter" version="0.94 (ob)">
+    <description>import molecules into data base</description>
+</tool>
+<tool id="dockresultmerger" name="DockResultMerger" version="0.94">
+    <description>merge docking output files</description>
+</tool>
+<tool id="evensplit" name="EvenSplit" version="0.94">
+    <description>generate splits w/ equal property range</description>
+</tool>
+<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.94">
+    <description>generate galaxy tool-config files</description>
+</tool>
+<tool id="gridbuilder" name="GridBuilder" version="0.94">
+    <description>create score-grids for docking</description>
+</tool>
+<tool id="imeedydock" name="IMGDock" version="0.94">
+    <description>Iterative Multi-Greedy Docking</description>
+</tool>
+<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.94">
+    <description>define interaction constraint</description>
+</tool>
+<tool id="ligcheck" name="LigCheck" version="0.94">
+    <description>check molecules for errors</description>
+</tool>
+<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.94">
+    <description>generate 3D coordinates for small molecules</description>
+</tool>
+<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.94">
+    <description>split molecule files</description>
+</tool>
+<tool id="molcombine" name="MolCombine" version="0.94">
+    <description>combine molecular files</description>
+</tool>
+<tool id="moldepict" name="MolDepict" version="0.94">
+    <description>create structure diagrams</description>
+</tool>
+<tool id="molfilter" name="MolFilter" version="0.9">
+    <description>filter molecule files</description>
+</tool>
+<tool id="pdbcutter" name="PDBCutter" version="0.94">
+    <description>separate ligand and receptor</description>
+</tool>
+<tool id="pdbdownload" name="PDBDownload" version="0.94">
+    <description>retrieve pdb-file from pdb.org</description>
+</tool>
+<tool id="partialchargescopy" name="PartialChargesCopy" version="0.94">
+    <description>transfer part. charges between files</description>
+</tool>
+<tool id="pocketdetector" name="PocketDetector" version="0.94">
+    <description>detect binding pocket</description>
+</tool>
+<tool id="propertymodifier" name="PropertyModifier" version="0.94">
+    <description>modify molecule property tags</description>
+</tool>
+<tool id="propertyplotter" name="PropertyPlotter" version="0.94">
+    <description>plot molecule properties</description>
+</tool>
+<tool id="proteincheck" name="ProteinCheck" version="0.94">
+    <description>quality check for proteins structures</description>
+</tool>
+<tool id="proteinprotonator" name="ProteinProtonator" version="0.94">
+    <description>protonate protein structures</description>
+</tool>
+<tool id="rmsdcalculator" name="RMSDCalculator" version="0.94">
+    <description>calculate RMSD between poses</description>
+</tool>
+<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.94">
+    <description>generate ROC or enrichment plots</description>
+</tool>
+<tool id="similarityanalyzer" name="SimilarityAnalyzer" version="0.9">
+    <description>analyze similarity between molecule files</description>
+</tool>
+<tool id="simplerescorer" name="SimpleRescorer" version="0.94">
+    <description>rescore docking results</description>
+</tool>
+<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.94">
+    <description>define spatial constraint</description>
+</tool>
+<tool id="tagres-train" name="TaGRes-train" version="0.94">
+    <description>Target-specific Grid-Rescoring, training</description>
+</tool>
+<tool id="tagres" name="TaGRes" version="0.94">
+    <description>Target-specific Grid-Rescoring</description>
+</tool>
+<tool id="vendorfinder" name="VendorFinder" version="0.94">
+    <description>search vendors for compounds</description>
+</tool>
+<tool id="waterfinder" name="WaterFinder" version="0.94">
+    <description>find strongly bound waters</description>
+</tool>
+<tool id="automodel" name="AutoModel" version="1.1">
+    <description>automatically find best QSAR model</description>
+</tool>
+<tool id="featureselector" name="FeatureSelector" version="1.1">
+    <description>run feature-selection on a QSAR model</description>
+</tool>
+<tool id="inputpartitioner" name="InputPartitioner" version="1.1">
+    <description>split QSAR data set</description>
+</tool>
+<tool id="inputreader" name="InputReader" version="1.1">
+    <description>generate QSAR data set</description>
+</tool>
+<tool id="modelcreator" name="ModelCreator" version="1.1">
+    <description>create a QSAR model</description>
+</tool>
+<tool id="molpredictor" name="MolPredictor" version="1.1">
+    <description>predict molecule activities with QSAR model</description>
+</tool>
+<tool id="predictor" name="Predictor" version="1.1">
+    <description>predict activities with QSAR model</description>
+</tool>
+<tool id="validator" name="Validator" version="1.1">
+    <description>evaluate quality of a QSAR model</description>
+</tool></suite>