Galaxy |

Changeset 0:bac3c274238f (2011-06-07)

Next changeset 1:867bf9f815a0 (2011-06-26)

Commit message:
Migrated tool version 0.93 from old tool shed archive to new tool shed repository

diff -r 000000000000 -r bac3c274238f CADDSuite/AntitargetRescorer
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/AntitargetRescorer Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/AntitargetRescorer.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/AutoModel
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/AutoModel Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/AutoModel.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/BindingDBCleaner
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/BindingDBCleaner Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/BindingDBCleaner.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/CADDSuite-description.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/CADDSuite-description.txt Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,59 @@
+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
+ - 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').

diff -r 000000000000 -r bac3c274238f CADDSuite/CombiLibGenerator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/CombiLibGenerator Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/CombiLibGenerator.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/ConstraintsFinder
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ConstraintsFinder Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/ConstraintsFinder.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/Converter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Converter Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/Converter.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/DBExporter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/DBExporter Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/DBExporter.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/DBImporter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/DBImporter Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/DBImporter.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/DockResultMerger
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/DockResultMerger Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/DockResultMerger.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/EvenSplit
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/EvenSplit Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/EvenSplit.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/FeatureSelector
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/FeatureSelector Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/FeatureSelector.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/GalaxyConfigGenerator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/GalaxyConfigGenerator Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/GalaxyConfigGenerator.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/GridBuilder
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/GridBuilder Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/GridBuilder.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/IMeedyDock
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/IMeedyDock Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/IMeedyDock.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/InputPartitioner
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/InputPartitioner Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/InputPartitioner.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/InputReader
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/InputReader Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/InputReader.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/LigCheck
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/LigCheck Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/LigCheck.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/Ligand3DGenerator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Ligand3DGenerator Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/Ligand3DGenerator.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/LigandFileSplitter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/LigandFileSplitter Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/LigandFileSplitter.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/ModelCreator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ModelCreator Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/ModelCreator.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/MolCombine
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolCombine Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/MolCombine.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/MolDepict
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolDepict Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/MolDepict.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/MolFilter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolFilter Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/MolFilter.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/MolPredictor
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/MolPredictor Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/MolPredictor.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/PDBCutter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PDBCutter Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/PDBCutter.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/PDBDownload
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PDBDownload Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/PDBDownload.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/PartialChargesCopy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PartialChargesCopy Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/PartialChargesCopy.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/PocketDetector
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PocketDetector Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/PocketDetector.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/Predictor
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Predictor Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/Predictor.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/PropertyModifier
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PropertyModifier Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/PropertyModifier.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/PropertyPlotter
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/PropertyPlotter Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/PropertyPlotter.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/ProteinCheck
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ProteinCheck Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/ProteinCheck.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/ProteinProtonator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ProteinProtonator Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/ProteinProtonator.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/QuEasyRun
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/QuEasyRun Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/QuEasyRun.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/README Tue Jun 07 16:43:30 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.
+
+

diff -r 000000000000 -r bac3c274238f CADDSuite/RMSDCalculator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/RMSDCalculator Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/RMSDCalculator.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/ScoreAnalyzer
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/ScoreAnalyzer Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/ScoreAnalyzer.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/SideChainGridBuilder
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/SideChainGridBuilder Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/SideChainGridBuilder.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/SimilarityAnalyzer
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/SimilarityAnalyzer Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/SimilarityAnalyzer.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/SimpleRescorer
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/SimpleRescorer Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/SimpleRescorer.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/TaGRes
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/TaGRes Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/TaGRes.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/TaGRes-train
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/TaGRes-train Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/TaGRes-train.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/Validator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/Validator Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/Validator.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/VendorFinder
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/VendorFinder Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/VendorFinder.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/WaterFinder
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/WaterFinder Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/WaterFinder.bin "$@"

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diff -r 000000000000 -r bac3c274238f CADDSuite/bin/GridBuilder.bin

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diff -r 000000000000 -r bac3c274238f CADDSuite/changelog.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/changelog.txt Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,38 @@
+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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/Amber/amber96-docking.ini
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/Amber/amber96-docking.ini Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,1666 @@\n+; This file contains parameter needed for nonbonded ScoringComponents.\n+; The parameters were converted from parm96.dat using amber2ini and all sections for bonded parameters were removed since are not needed for docking.\n+; 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.\n+\n+[Options]\n+key:0\n+@SCEE=1.2\n+; please check the settings for SCEE! AMBER91/89a requires a value of 2.0 here!\n+\n+\n+\n+\n+[HydrophilicTypes]\n+; ignored\n+;\n+C H HO N NA NB NC N2 NT N2 N3 N* O OH OS P O2 \n+\n+\n+[HydrogenBonds]\n+ver:version key:I key:J value:A value:B\n+@unit_A=kcal/mol*A^12\n+@unit_B=kcal/mol*A^10\n+;\n+;\n+; Rev I J A B\n+; --- --- --- ---------- ----------\n+ 1.0 HW OW 0.0000 0.0000\n+\n+\n+[AtomTypes]\n+value:ver key:type value:mass value:comment\n+@unit=g/mol\n+;\n+;\n+; Rev Type mass comment\n+; --- ---- ---------- ----------------------------------\n+ 1.0 BR 79.90000 "bromine"\n+ 1.0 C 12.01000 "sp2 C carbonyl group "\n+ 1.0 F 19.00000 "fluorine"\n+ 1.0 I 126.90000 "iodine"\n+ 1.0 H 1.00800 "H bonded to nitrogen atoms"\n+ 1.0 IM 35.45000 "assumed to be Cl-"\n+ 1.0 IP 22.99000 "assumed to be Na+"\n+ 1.0 IB 131.00000 "\'big ion w/ waters\' for vacuum (Na+, 6H2O)"\n+ 1.0 N 14.01000 "sp2 nitrogen in amide groups"\n+ 1.0 O 16.00000 "carbonyl group oxygen"\n+ 1.0 P 30.97000 "phosphate"\n+ 1.0 S 32.06000 "sulphur in disulfide linkage"\n+ 1.0 Cu 63.55000 "copper"\n+ 1.0 Fe 55.00000 "iron"\n+ 1.0 Li 6.94000 "lithium"\n+ 1.0 K 39.10000 "potassium"\n+ 1.0 Rb 85.47000 "rubidium"\n+ 1.0 Cs 132.91000 "cesium"\n+ ant Cl 35.450 "same as cl"\n+ 2.0 Ca 40.08000 "calcium"\n+ 1.0 Mg 24.30500 "magnesium"\n+ ant Zn 65.4 "Zn2+, taken from parm99.dat (antechamber)"\n+\n+\n+[LennardJones]\n+ver:version key:I value:R value:epsilon\n+@unit_R=Angstrom\n+@unit_epsilon=kcal/mol\n+@format=RE\n+;\n+;\n+; Rev I R epsilon comment\n+; --- --- ---------- ---------- -------------------------\n+ 1.0 Ca 1.600000 0.100000 " calcium from parm91.dat"\n+ 1.0 H 0.600000 0.015700 " !Ferguson base pair geom."\n+ 1.0 O 1.661200 0.210000 " OPLS"\n+ 1.0 C 1.908000 0.086000 " OPLS"\n+ 1.0 N 1.824000 0.170000 " OPLS"\n+ 1.0 S 2.000000 0.250000 " W. Cornell CH3SH and CH3SCH3 FEP\'s"\n+ 1.0 P 2.100000 0.200000 " JCC,7,(1986),230;"\n+ 1.0 IM 2.470000 0.100000 " Cl- Smith & Dang, JCP 1994,100:5,3757"\n+ 1.0 IB 5.000000 0.100000 " solvated ion for vacuum approximation"\n+ 1.0 Li 1.137000 0.018300 " Li+ Aqvist JPC 1990,94,8021. (adapted)"\n+ 1.0 IP 1.868000 0.002770 " Na+ Aqvist JPC 1990,94,8021. (adapted)"\n+ 1.0 K 2.658000 0.000328 " K+ Aqvist JPC 1990,94,8021. (adapted)"\n+ 1.0 Rb 2.956000 0.000170 " Rb+ Aqvist JPC 1990,94,8021. (adapted)"\n+ 1.0 Cs 3.395000 0.000081 " Cs+ Aqvist JPC 1990,94,8021. (adapted)"\n+ 1.0 I 2.350000 0.400000 " JCC,7,(1986),230;"\n+ 1.0 F 1.750000 0.061000 " Gough et al. JCC 13,(1992),963."\n+ ant Cl 2.47 0.1 " Cl- Smith & Dang, JCP 1994,100:5,3757, taken from parm99.dat (antechamber)"\n+ ant Zn 1.10 0.0125 " Zn2+, Merz,PAK, JACS,113,8262,(1991), taken from parm99.dat (antechamber)"\n+ ant Mg 0.7926 0.8947 " Mg2+ Aqvist JPC 1990,94,8021.(adapted), taken from parm99.dat (antechamber)"\n+; ant Cl 1.9480 0.2650 "same as cl"\n+; 1.0 Mg 1.170000 0.100000 " magnesium from parm91.dat"\n+\n+\n+[ResidueImproperTorsions]\n+key:name\n+;\n+;\n+; res:atom\n+; -------------\n+ ALA:N\n+ ALA:C\n+ GLY:N\n+ GLY:C\n+ SER:N\n+ SER:C\n+ THR:N\n+ THR:C\n+ LEU:N\n+ LEU:C\n+ ILE:N\n+ ILE:C\n+ VAL:N\n+ VAL:C\n+ ASN:N\n+ ASN:C\n+ ASN:CG\n+ ASN:ND2\n+ GLN:N\n+ GLN:C\n+ GLN:CD\n+ GLN:NE2\n+ ARG:N\n+ ARG:C\n+ ARG:CZ\n+ ARG:N'..b'0.03920 CT \n+ 1.0 LYS-C:1HD 0.06110 HC \n+ 1.0 LYS-C:2HD 0.06110 HC \n+ 1.0 LYS-C:CE -0.01760 CT \n+ 1.0 LYS-C:1HE 0.11210 HP \n+ 1.0 LYS-C:2HE 0.11210 HP \n+ 1.0 LYS-C:NZ -0.37410 N3 \n+ 1.0 LYS-C:1HZ 0.33740 H \n+ 1.0 LYS-C:2HZ 0.33740 H \n+ 1.0 LYS-C:3HZ 0.33740 H \n+ 1.0 LYS-C:C 0.84880 C \n+ 1.0 LYS-C:O -0.82520 O2 \n+ 1.0 LYS-C:OXT -0.82520 O2 \n+ 1.0 PRO-C:N -0.28020 N \n+ 1.0 PRO-C:CD 0.04340 CT \n+ 1.0 PRO-C:1HD 0.03310 H1 \n+ 1.0 PRO-C:2HD 0.03310 H1 \n+ 1.0 PRO-C:CG 0.04660 CT \n+ 1.0 PRO-C:1HG 0.01720 HC \n+ 1.0 PRO-C:2HG 0.01720 HC \n+ 1.0 PRO-C:CB -0.05430 CT \n+ 1.0 PRO-C:1HB 0.03810 HC \n+ 1.0 PRO-C:2HB 0.03810 HC \n+ 1.0 PRO-C:CA -0.13360 CT \n+ 1.0 PRO-C:HA 0.07760 H1 \n+ 1.0 PRO-C:C 0.66310 C \n+ 1.0 PRO-C:O -0.76970 O2 \n+ 1.0 PRO-C:OXT -0.76970 O2 \n+ 1.0 CYS-C:N -0.38210 N \n+ 1.0 CYS-C:H 0.26810 H \n+ 1.0 CYS-C:CA -0.16350 CT \n+ 1.0 CYS-C:HA 0.13960 H1 \n+ 1.0 CYS-C:CB -0.19960 CT \n+ 1.0 CYS-C:1HB 0.14370 H1 \n+ 1.0 CYS-C:2HB 0.14370 H1 \n+ 1.0 CYS-C:SG -0.31020 SH \n+ 1.0 CYS-C:HSG 0.20680 HS \n+ 1.0 CYS-C:C 0.74970 C \n+ 1.0 CYS-C:O -0.79810 O2 \n+ 1.0 CYS-C:OXT -0.79810 O2 \n+ 1.0 CYS-CS:N -0.38210 N \n+ 1.0 CYS-CS:H 0.26810 H \n+ 1.0 CYS-CS:CA -0.13180 CT \n+ 1.0 CYS-CS:HA 0.09380 H1 \n+ 1.0 CYS-CS:CB -0.19430 CT \n+ 1.0 CYS-CS:1HB 0.12280 H1 \n+ 1.0 CYS-CS:2HB 0.12280 H1 \n+ 1.0 CYS-CS:SG -0.05290 S \n+ 1.0 CYS-CS:C 0.76180 C \n+ 1.0 CYS-CS:O -0.80410 O2 \n+ 1.0 CYS-CS:OXT -0.80410 O2 \n+ 1.0 MET-C:N -0.38210 N \n+ 1.0 MET-C:H 0.26810 H \n+ 1.0 MET-C:CA -0.25970 CT \n+ 1.0 MET-C:HA 0.12770 H1 \n+ 1.0 MET-C:CB -0.02360 CT \n+ 1.0 MET-C:1HB 0.04800 HC \n+ 1.0 MET-C:2HB 0.04800 HC \n+ 1.0 MET-C:CG 0.04920 CT \n+ 1.0 MET-C:1HG 0.03170 H1 \n+ 1.0 MET-C:2HG 0.03170 H1 \n+ 1.0 MET-C:SD -0.26920 S \n+ 1.0 MET-C:CE -0.03760 CT \n+ 1.0 MET-C:1HE 0.06250 H1 \n+ 1.0 MET-C:2HE 0.06250 H1 \n+ 1.0 MET-C:3HE 0.06250 H1 \n+ 1.0 MET-C:C 0.80130 C \n+ 1.0 MET-C:O -0.81050 O2 \n+ 1.0 MET-C:OXT -0.81050 O2 \n+ 1.0 CA:CA 2.00000 C0\n+ 1.0 MG:MG 2.00000 MG\n+ 1.0 CH4-M:C 0.00000 CT\n+ 1.0 CH4-M:1H 0.00000 H1\n+ 1.0 CH4-M:2H 0.00000 H1\n+ 1.0 CH4-M:3H 0.00000 H1\n+ 1.0 CH4-M:4H 0.00000 H1\n+ 1.0 PCA:N -0.720984 N\n+ 1.0 PCA:H 0.374677 H\n+ 1.0 PCA:CA -0.025874 CT\n+ 1.0 PCA:C 0.865161 C\n+ 1.0 PCA:O -0.798202 O\n+ 1.0 PCA:CB 0.114954 CT\n+ 1.0 PCA:CG -0.126748 CT\n+ 1.0 PCA:CD 0.770356 C\n+ 1.0 PCA:OE -0.682912 O\n+ 1.0 PCA:HA 0.039708 H1\n+ 1.0 PCA:1HB 0.000266 HC\n+ 1.0 PCA:2HB -0.031861 HC\n+ 1.0 PCA:1HG 0.034072 HC\n+ 1.0 PCA:2HG 0.025655 HC\n+ 1.0 PCA:OXT -0.838268 O\n+ 1.0 PCA-N:N -0.720984 N\n+ 1.0 PCA-N:H 0.374677 H\n+ 1.0 PCA-N:CA -0.025874 CT\n+ 1.0 PCA-N:C 0.865161 C\n+ 1.0 PCA-N:O -0.798202 O\n+ 1.0 PCA-N:CB 0.114954 CT\n+ 1.0 PCA-N:CG -0.126748 CT\n+ 1.0 PCA-N:CD 0.770356 C\n+ 1.0 PCA-N:OE -0.682912 O\n+ 1.0 PCA-N:HA 0.039708 H1\n+ 1.0 PCA-N:1HB 0.000266 HC\n+ 1.0 PCA-N:2HB -0.031861 HC\n+ 1.0 PCA-N:1HG 0.034072 HC\n+ 1.0 PCA-N:2HG 0.025655 HC\n+ 1.0 PCA-M:N -0.720984 N\n+ 1.0 PCA-M:H 0.374677 H\n+ 1.0 PCA-M:CA -0.025874 CT\n+ 1.0 PCA-M:C 0.865161 C\n+ 1.0 PCA-M:O -0.798202 O\n+ 1.0 PCA-M:CB 0.114954 CT\n+ 1.0 PCA-M:CG -0.126748 CT\n+ 1.0 PCA-M:CD 0.770356 C\n+ 1.0 PCA-M:OE -0.682912 O\n+ 1.0 PCA-M:HA 0.039708 H1\n+ 1.0 PCA-M:1HB 0.000266 HC\n+ 1.0 PCA-M:2HB -0.031861 HC\n+ 1.0 PCA-M:1HG 0.034072 HC\n+ 1.0 PCA-M:2HG 0.025655 HC\n+ 1.0 PCA-M:OXT -0.838268 O\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/CMakeLists.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/CMakeLists.txt Tue Jun 07 16:43:30 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)

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/MACCS.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/MACCS.txt Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,205 @@\n+#Comments after SMARTS\n+# Extracted from RDKit Jul 2008 release (r747) Python/Chem/MACCSKeys.py\n+#\n+# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC\n+#\n+# @@ All Rights Reserved @@\n+#\n+#Redistribution and use in source and binary forms, with or without\n+#modification, are permitted provided that the following conditions are\n+#met: \n+#\n+# * Redistributions of source code must retain the above copyright \n+# notice, this list of conditions and the following disclaimer.\n+# * Redistributions in binary form must reproduce the above\n+# copyright notice, this list of conditions and the following \n+# disclaimer in the documentation and/or other materials provided \n+# with the distribution.\n+# * Neither the name of Rational Discovery nor the names of its \n+# contributors may be used to endorse or promote products derived \n+# from this software without specific prior written permission.\n+#\n+#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS\n+#"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT\n+#LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR\n+#A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT\n+#OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\n+#SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT\n+#LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,\n+#DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY\n+#THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT\n+#(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\n+#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n+\n+# these are SMARTS patterns corresponding to the MDL MACCS keys\n+ 1:(\'?\',0), # ISOTOPE\n+ #2:(\'[#103,#104,#105,#106,#107,#106,#109,#110,#111,#112]\',0), # ISOTOPE Not complete\n+ 2:(\'[#103,#104]\',0), # ISOTOPE Not complete\n+ 3:(\'[Ge,As,Se,Sn,Sb,Te,Tl,Pb,Bi]\',0), # Group IVa,Va,VIa Periods 4-6 (Ge...) *NOTE* spec wrong\n+ 4:(\'[Ac,Th,Pa,U,Np,Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr]\',0), # actinide\n+ 5:(\'[Sc,Ti,Y,Zr,Hf]\',0), # Group IIIB,IVB (Sc...) *NOTE* spec wrong\n+ 6:(\'[La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu]\',0), # Lanthanide\n+ 7:(\'[V,Cr,Mn,Nb,Mo,Tc,Ta,W,Re]\',0), # Group VB,VIB,VIIB (V...) *NOTE* spec wrong\n+ 8:(\'[!C;!c;!#1]1~*~*~*~*1\',0), # QAAA@1\n+ 9:(\'[Fe,Co,Ni,Ru,Rh,Pd,Os,Ir,Pt]\',0), # Group VIII (Fe...)\n+ 10:(\'[Be,Mg,Ca,Sr,Ba,Ra]\',0), # Group IIa (Alkaline earth)\n+ 11:(\'*1~*~*~*~*1\',0), # 4M Ring *NOTE* Was \'*1~*~*~*~1\' This and 9 others changed by CM because OB didn\'t like it\n+ 12:(\'[Cu,Zn,Ag,Cd,Au,Hg]\',0), # Group IB,IIB (Cu..)\n+ 13:(\'[O,o]~[N,n](~[C,c])~[C,c]\',0), # ON(C)C\n+ 14:(\'[S,s]-[S,s]\',0), # S-S\n+ 15:(\'[O,o]~[C,c](~[O,o])~[O,o]\',0), # OC(O)O\n+ 16:(\'[!C;!c;!#1]1~*~*~*1\',0), # QAA@1\n+ 17:(\'[C,c]#[C,c]\',0), #CTC\n+ 18:(\'[B,Al,Ga,In,Tl]\',0), # Group IIIA (B...) *NOTE* spec wrong\n+ 19:(\'*1~*~*~*~*~*~*~*1\',0), # 7M Ring\n+ 20:(\'[Si]\',0), #Si\n+ 21:(\'[C,c]=[C,c](~[!C;!c;!#1])~[!C;!c;!#1]\',0), # C=C(Q)Q\n+ 22:(\'*1~*~*~*1\',0), # 3M Ring\n+ 23:(\'[N,n]~[C,c](~[O,o])~[O,o]\',0), # NC(O)O\n+ 24:(\'[N,n]-[O,o]\',0), # N-O\n+ 25:(\'[N,n]~[C,c](~[N,n])~[N,n]\',0), # NC(N)N\n+ 26:(\'[C,c]=;@[C,c](@*)@*\',0), # C$=C($A)$A\n+ 27:(\'[I]\',0), # I\n+ 28:(\'[!C;!c;!#1]~[CH2]~[!C;!c;!#1]\',0), # QCH2Q\n+ 29:(\'P\',0),# P\n+ 30:(\'[C,c]~[!C;!c;!#1](~[C,c])(~[C,c])~*\',0), # CQ(C)(C)A\n+ 31:(\'[!C;!c;!#1]~[F,Cl,Br,I]\',0), # QX\n+ 32:(\'[C,c]~[S,s]~[N,n]\',0), # CSN\n+ 33:(\'[N,n]~[S,s]\',0), # NS\n+ 34:(\'[CH2]=*\',0), # CH2=A\n+ 35:(\'[Li,Na,K,Rb,Cs,Fr]\',0), # Group IA (Alkali Metal)\n+ 36:(\'[$(S@*),$(s@*)]\',0), # S Heterocycle\n+ 37:(\'[N,n]~[C,c](~[O,o])~[N,n]\',0), # NC(O)N\n+ 38:(\'[N,n]~[C,c](~[C,c])~[N,n]\',0), # NC(C)N\n+ 39:(\'[O,o]~[S,s](~[O,o])~[O,o]\',0), # OS(O)O\n+ 40:(\'[S,s]-[O,o]\',0), # S-O\n+ 41:(\'[C,c]#[N,n]\',0), # CTN\n+ 42:(\'F\',0), # F\n+ 43:(\'[!C;!c;!#1;H,H2,H3,H4]~*~[!C;!c;!#1;H,H2,H3,H4]\',0), # QHAQH FIX: pos'..b'ete\n+ 70:(\'[!C;!c;!#1]~[N,n]~[!C;!c;!#1]\',0), # QNQ\n+ 71:(\'[N,n]~[O,o]\',0), # NO\n+ 72:(\'[O,o]~*~*~[O,o]\',0), # OAAO\n+ 73:(\'[S,s]=*\',0), # S=A\n+ 74:(\'[CH3]~*~[CH3]\',0), # CH3ACH3\n+ 75:(\'*!@[N,n]@*\',0), # A!N$A\n+ 76:(\'[C,c]=[C,c](~*)~*\',0), # C=C(A)A\n+ 77:(\'[N,n]~*~[N,n]\',0), # NAN\n+ 78:(\'[C,c]=[N,n]\',0), # C=N\n+ 79:(\'[N,n]~*~*~[N,n]\',0), # NAAN\n+ 80:(\'[N,n]~*~*~*~[N,n]\',0), # NAAAN\n+ 81:(\'[S,s]~*(~*)~*\',0), # SA(A)A\n+ 82:(\'*~[CH2]~[!#6;!#1;!H0]\',0), # ACH2QH\n+ 83:(\'[!C;!c;!#1]1~*~*~*~*~*1\',0), # QAAAA@1\n+ 84:(\'[NH2]\',0), #NH2\n+ 85:(\'[C,c]~[N,n](~[C,c])~[C,c]\',0), # CN(C)C\n+ 86:(\'[CH2][!C;!c;!#1][CH2]\',0), # CH2QCH2\n+ 87:(\'[F,Cl,Br,I]!@*@*\',0), # X!A$A\n+ 88:(\'[S,s]\',0), # S\n+ 89:(\'[O,o]~*~*~*~[O,o]\',0), # OAAAO\n+ 90:(\'[!#6;!#1;!H0]~*~*~[CH2]~*\',0), # QHAACH2A\n+ 91:(\'[!#6;!#1;!H0]~*~*~*~[CH2]~*\',0), # QHAAACH2A\n+ 92:(\'[O,o]~[C,c](~[N,n])~[C,c]\',0), # OC(N)C\n+ 93:(\'[!C;!c;!#1]~[CH3]\',0), # QCH3\n+ 94:(\'[!C;!c;!#1]~[N,n]\',0), # QN\n+ 95:(\'[N,n]~*~*~[O,o]\',0), # NAAO\n+ 96:(\'*1~*~*~*~*~*1\',0), # 5 M ring\n+ 97:(\'[N,n]~*~*~*~[O,o]\',0), # NAAAO\n+ 98:(\'[!C;!c;!#1]1~*~*~*~*~*~*1\',0), # QAAAAA@1\n+ 99:(\'[C,c]=[C,c]\',0), # C=C\n+ 100:(\'*~[CH2]~[N,n]\',0), # ACH2N\n+ 101:(\'[r8,r9,r10,r11,r12]\',0), # 8M Ring or larger FIX: This is not exhaustive and it appears that oelib doesn\'t do this right\n+ 102:(\'[!C;!c;!#1]~[O,o]\',0), # QO\n+ 103:(\'Cl\',0), # CL\n+ 104:(\'[!#6;!#1;!H0]~*~[CH2]~*\',0), # QHACH2A\n+ 105:(\'[!C;!c;!#1]@*(@*)@*\',0), # A$A($A)$A\n+ 106:(\'[!C;!c;!#1]~*(~[!C;!c;!#1])~[!C;!c;!#1]\',0), # QA(Q)Q\n+ 107:(\'[F,Cl,Br,I]~*(~*)~*\',0), # XA(A)A\n+ 108:(\'[CH3]~*~*~*~[CH2]~*\',0), # CH3AAACH2A\n+ 109:(\'*~[CH2]~[O,o]\',0), # ACH2O\n+ 110:(\'[N,n]~[C,c]~[O,o]\',0), # NCO\n+ 111:(\'[N,n]~*~[CH2]~*\',0), # NACH2A\n+ 112:(\'*~*(~*)(~*)~*\',0), # AA(A)(A)A\n+ 113:(\'[O,o]!:*:*\',0), # Onot%A%A\n+ 114:(\'[CH3]~[CH2]~*\',0), # CH3CH2A\n+ 115:(\'[CH3]~*~[CH2]~*\',0), # CH3ACH2A\n+ 116:(\'[CH3]~*~*~[CH2]~*\',0), # CH3AACH2A\n+ 117:(\'[N,n]~*~[O,o]\',0), # NAO\n+ 118:(\'*~[CH2]~[CH2]~*\',1), # ACH2CH2A > 1\n+ 119:(\'[N,n]=*\',0), # N=A\n+ 120:(\'[!C;!c;R]\',1), # Heterocyclic atom > 1\n+ 121:(\'[$(N@*),$(n@*)]\',0), # N Heterocycle\n+ 122:(\'*~[N,n](~*)~*\',0), # AN(A)A\n+ 123:(\'[O,o]~[C,c]~[O,o]\',0), # OCO\n+ 124:(\'[!C;!c;!#1]~[!C;!c;!#1]\',0), # QQ\n+ 125:(\'?\',0), # Aromatic Ring > 1\n+ 126:(\'*!@[O,o]!@*\',0), # A!O!A\n+ 127:(\'*@*!@[O,o]\',1), # A$A!O > 1\n+ 128:(\'*~[CH2]~*~*~*~[CH2]~*\',0), # ACH2AAACH2A\n+ 129:(\'*~[CH2]~*~*~[CH2]~*\',0), # ACH2AACH2A\n+ 130:(\'[!C;!c;!#1]~[!C;!c;!#1]\',1), # QQ > 1 (&...)\n+ 131:(\'[!#6;!#1;!H0]\',1), # QH > 1\n+ 132:(\'[O,o]~*~[CH2]~*\',0), # OACH2A\n+ 133:(\'*@*!:[N,n]\',0), # A$A!N\n+ 134:(\'[F,Cl,Br,I]\',0), # X (HALOGEN)\n+ 135:(\'[N,n]!:*:*\',0), # Nnot%A%A\n+ 136:(\'[O,o]=*\',1), # O=A>1 FIX: maybe not right key\n+ 137:(\'[!C;!c;R]\',0), # Heterocycle\n+ 138:(\'[!C;!c;!#1]~[CH2]~*\',1), # QCH2A>1 (&...)\n+ 139:(\'[OH,OH2,OH3]\',0), # OH\n+ 140:(\'[O,o]\',3), # O > 3\n+ 141:(\'[CH3]\',2), # CH3 > 2\n+ 142:(\'[N,n]\',1), # N > 1\n+ 143:(\'*@*!@[O,o]\',0), # A$A!O\n+ 144:(\'*!:*:*!:*\',0), # Anot%A%Anot%A\n+ 145:(\'*1~*~*~*~*~*~*1\',1), # 6M ring > 1\n+ 146:(\'[O,o]\',2), # O > 2\n+ 147:(\'*~[CH2]~[CH2]~*\',0), # ACH2CH2A\n+ 148:(\'*~[!C;!c;!#1](~*)~*\',0), # AQ(A)A\n+ 149:(\'[CH3]\',1), # CH3 > 1\n+ 150:(\'*!@*@*!@*\',0), # A!A$A!A\n+ 151:(\'[N!H0]\',0), # NH\n+ 152:(\'[O,o]~[C,c](~[C,c])~[C,c]\',0), # OC(C)C\n+ 153:(\'[!C;!c;!#1]~[CH2]~*\',0), # QCH2A\n+ 154:(\'[C,c]=[O,o]\',0), # C=O\n+ 155:(\'*!@[CH2]!@*\',0), # A!CH2!A\n+ 156:(\'[N,n]~*(~*)~*\',0), # NA(A)A\n+ 157:(\'[C,c]-[O,o]\',0), # C-O\n+ 158:(\'[C,c]-[N,n]\',0), # C-N\n+ 159:(\'[O,o]\',1), # O>1\n+ 160:(\'[CH3]\',0), #CH3\n+ 161:(\'[N,n]\',0), # N\n+ 162:(\'a\',0), # Aromatic\n+ 163:(\'*1~*~*~*~*~*~*1\',0), # 6M Ring\n+ 164:(\'[O,o]\',0), # O\n+ 165:(\'[R]\',0), # Ring\n+ 166:(\'?\',0), # Fragments FIX: this should be (*).(*), but that doesn\'t work properly in oelib\n+\n+# Output with SMILES "CNO"\n+#>\t24: N-O\t68: QHQH \t69: QQH \t71: NO\t93: QCH3\t94: QN\t102: QO\t\n+#124: QQ\t131: QH > 1*2\t139: OH\t151: NH\t158: C-N\t160: CH3\t161: N\t164: O\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/Makefile
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/Makefile Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,178 @@
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diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/SMARTS_InteLigand.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/SMARTS_InteLigand.txt Tue Jun 07 16:43:30 2011 -0400

[

b"@@ -0,0 +1,983 @@\n+#\n+# SMARTS Patterns for Functional Group Classification \n+#\n+# written by Christian Laggner \n+# Copyright 2005 Inte:Ligand Software-Entwicklungs und Consulting GmbH\n+#\n+# Released under the Lesser General Public License (LGPL license)\n+# see http://www.gnu.org/copyleft/lesser.html\n+# Modified from Version 221105\n+#####################################################################################################\n+\n+# General Stuff:\n+# These patters were written in an attempt to represent the classification of organic compounds \n+# from the viewpoint of an organic chemist.\n+# They are often very restrictive. This may be generally a good thing, but it also takes some time\n+# for filtering/indexing large compound sets. \n+# For filtering undesired groups (in druglike compounds) one will want to have more general patterns \n+# (e.g. you don't want *any* halide of *any* acid, *neither* aldehyde *nor* formyl esters and amides, ...). \n+#\n+\n+# Part I: Carbon \n+# ==============\n+\n+\n+# I.1: Carbon-Carbon Bonds\n+# ------------------------\n+\n+# I.1.1 Alkanes:\n+\n+Primary_carbon: [CX4H3][#6]\n+\n+Secondary_carbon: [CX4H2]([#6])[#6]\n+\n+Tertiary_carbon: [CX4H1]([#6])([#6])[#6]\n+\n+Quaternary_carbon: [CX4]([#6])([#6])([#6])[#6]\n+\n+\n+# I.1.2 C-C double and Triple Bonds\n+\n+Alkene: [CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])] \n+# sp2 C may be substituted only by C or H - \n+# does not hit ketenes and allenes, nor enamines, enols and the like\n+\n+Alkyne: [CX2]#[CX2]\n+# non-carbon substituents (e.g. alkynol ethers) are rather rare, thus no further discrimination\n+\n+Allene: [CX3]=[CX2]=[CX3]\n+\n+\n+# I.2: One Carbon-Hetero Bond\n+# ---------------------------\n+\n+\n+# I.2.1 Alkyl Halogenides\n+\n+Alkylchloride: [ClX1][CX4]\n+# will also hit chloromethylethers and the like, but no chloroalkenes, -alkynes or -aromats \n+# a more restrictive version can be obtained by modifying the Alcohol string.\n+\n+Alkylfluoride: [FX1][CX4]\n+\n+Alkylbromide: [BrX1][CX4]\n+\n+Alkyliodide: [IX1][CX4]\n+\n+\n+# I.2.2 Alcohols and Ethers\n+\n+Alcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])]\n+# nonspecific definition, no acetals, aminals, and the like\n+\n+Primary_alcohol: [OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])]\n+\n+Secondary_alcohol: [OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])]\n+\n+Tertiary_alcohol: [OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])]\n+\n+Dialkylether: [OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]\n+# no acetals and the like; no enolethers\n+\n+Dialkylthioether: [SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]\n+# no acetals and the like; no enolethers\n+\n+Alkylarylether: [OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]\n+# no acetals and the like; no enolethers\n+\n+Diarylether: [c][OX2][c]\n+\n+Alkylarylthioether: [SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]\n+\n+Diarylthioether: [c][SX2][c]\n+\n+Oxonium: [O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])]\n+# can't be aromatic, thus O and not #8\n+\n+# I.2.3 Amines\n+\n+Amine: [NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])]\n+# hits all amines (prim/sec/tert/quart), including ammonium salts, also enamines, but not amides, imides, aminals, ...\n+\n+# the following amines include also the protonated forms \n+\n+Primary_aliph_amine: [NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]\n+\n+Secondary_aliph_amine: [NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]\n+\n+Tertiary_aliph_amine: [NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]\n+\n+Quaternary_aliph_ammonium: [NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]\n+\n+Primary_arom_amine: [NX3H2+0,NX4H3+]c\n+\n+Secondary_arom_amine: [NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]\n+\n+Tertiary_arom_amine: [NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]\n+\n+Quaternary_arom_ammonium: [NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]\n+\n+Secondary_mixed_amine: [NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])]\n+\n+Tertiary_mixed"..b'X1,IX1])@C@C@C@C1)])\n+# pattern2 occours more than once (in same molecule, but moieties don\'t have to be adjacent!)\n+\n+\n+# III.4 Everything else...\n+# ------------------------\n+\n+Conjugated_double_bond: *=*[*]=,#,:[*]\n+\n+Conjugated_tripple_bond: *#*[*]=,#,:[*]\n+\n+Cis_double_bond: */[D2]=[D2]\\*\n+# only one single-bonded substituent on each DB-atom. no aromats. \n+# only found when character of DB is explicitely stated.\n+\n+Trans_double_bond: */[D2]=[D2]/*\n+# analog\n+\n+Mixed_anhydrides: [$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))]\n+# should hits all combinations of two acids\n+\n+Halogen_on_hetero: [FX1,ClX1,BrX1,IX1][!#6]\n+\n+Halogen_multi_subst: [F,Cl,Br,I;!$([X1]);!$([X0-])]\n+# Halogen which is not mono-substituted nor an anion, e.g. chlorate.\n+# Most of these cases should be also filtered by Halogen_on_hetero.\n+\n+Trifluoromethyl: [FX1][CX4;!$([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1])\n+# C with three F attached, connected to anything which is not another halogen\n+\n+C_ONS_bond: [#6]~[#7,#8,#16]\n+# probably all drug-like molecules have at least one O, N, or S connected to a C -> nice filter\n+\n+## Mixture: (*).(*)\n+# two or more seperate parts, may also be salt\n+# component-level grouping is not yet supported in Open Babel Version 2.0\n+\n+\n+Charged: [!+0]\n+\n+Anion: [-1,-2,-3,-4,-5,-6,-7]\n+\n+Kation: [+1,+2,+3,+4,+5,+6,+7]\n+\n+Salt: ([-1,-2,-3,-4,-5,-6,-7]).([+1,+2,+3,+4,+5,+6,+7])\n+# two or more seperate components with opposite charges\n+\n+##Zwitterion: ([-1,-2,-3,-4,-5,-6,-7].[+1,+2,+3,+4,+5,+6,+7])\n+# both negative and positive charges somewhere within the same molecule. \n+\n+1,3-Tautomerizable: [$([#7X2,OX1,SX1]=*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=*),$([#7X3,OX2,SX2;!H0]*:n)]\n+# 1,3 migration of H allowed. Includes keto/enol and amide/enamide. \n+# Aromatic rings must stay aromatic - no keto form of phenol \n+\n+1,5-Tautomerizable: [$([#7X2,OX1,SX1]=,:**=,:*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=**=*),$([#7X3,OX2,SX2;!H0]*=,:**:n)]\n+\n+Rotatable_bond: [!$(*#*)&!D1]-!@[!$(*#*)&!D1]\n+# taken from http://www.daylight.com/support/contrib/smarts/content.html\n+\n+Michael_acceptor: [CX3]=[CX3][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])]\n+# the classical case: C=C near carbonyl, nitrile, nitro, or similar\n+# Oxo-heteroaromats and similar are not included.\n+\n+Dicarbodiazene: [CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1])\n+# Michael-like acceptor, see Mitsunobu reaction\n+\n+# H-Bond_donor:\n+\n+# H-Bond_acceptor:\n+\n+# Pos_ionizable:\n+\n+# Neg_ionizable:\n+\n+# Unlikely_ions: \n+# O+,N-,C+,C-, ...\n+\n+CH-acidic: [$([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;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)]\n+# C-H alpha to carbony, nitro or similar, C is not double-bonded, only C, H, S,P=O and nitro substituents allowed. \n+# pentadiene is included. acids, their salts, prim./sec. amides, and imides are excluded. \n+# hits also CH-acidic_strong\n+\n+CH-acidic_strong: [CX4;!$([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]);!$([*+0][S,O;X1-])]\n+# same as above (without pentadiene), but carbonyl or similar on two or three sides\n+\n+Chiral_center_specified: [$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)]\n+# Hits atoms with tetrahedral chirality, if chiral center is specified in the SMILES string\n+# depictmach does not find oxonium, sulfonium, or sulfoxides!\n+\n+# Chiral_center_unspecified: [$([*@?](~*)(~*)(*)*),$([*@?H](*)(*)*),$([*@?](~*)(*)*),$([*@?H](~*)~*)]\n+# Hits atoms with tetrahedral chirality, if chiral center is not specified in the SMILES string\n+# "@?" (unspecified chirality) is not yet supported in Open Babel Version 2.0 \n+ \n\\ No newline at end of file\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/UFF.prm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/UFF.prm Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,274 @@\n+#\n+# Open Babel file: UFF.prm\n+#\n+# Force field parameters for UFF, the Universal Force Field\n+# Used by OBForceField and OBUFFForceField\n+#\n+# J. Am. Chem. Soc. (1992) 114(25) p. 10024-10035.\n+# The parameters in this file are taken from the UFF implementation in RDKit\n+# http://rdkit.org/\n+#\n+# Atom typing rules are based on UFF published atom descriptions\n+# atom [SMARTS] [atomtype] [description]\n+# These must be sorted according to the element and complexity\n+# of the type rule (i.e., generic rules first, more specific rules later)\n+#\n+# Parameters follow later\n+# param Atom\tr1\ttheta0\tx1\tD1\tzeta\tZ1\tVi\tUj\tXi\tHard\tRadius\n+\n+atom [#1] H_ Generic hydrogen\n+atom [#1D2] H_b Bridging hydrogen\n+atom [#2] He4+4 Helium\n+atom [#3] Li Lithium\n+atom [#4] Be3+2 Generic Be\n+atom [#5] B_2 Trigonal planar boron\n+atom [#5D4] B_3 Tetrahedral boron\n+atom [#6] C_3 Generic sp3 C\n+atom [C^2] C_2 sp2 non-aromatic C\n+atom [C^1] C_1 sp hybridized C\n+atom [c] C_R aromatic C\n+atom [#7] N_3 Generic sp3 N\n+atom [N^2] N_2 sp2 non-aromatic N\n+atom [N^1] N_1 sp hybridized N\n+atom [n] N_R aromatic N\n+atom [#8] O_3 generic, sp3 hybridized O\n+atom [#8][#14] O_3_z sp3 hybridized O for zeolites\n+atom [O^2] O_2 sp2 hybridized O\n+atom [O^1] O_1 sp hybridized O\n+atom [o] O_R aromatic O\n+atom [#9] F_ generic F\n+atom [#10] Ne4+4 \n+atom [#11] Na \n+atom [#12] Mg3+2\n+atom [#13] Al3\n+atom [#14] Si3\n+#atom [#15] P_3+q Organometallic phosphine ligands\n+atom [#15] P_3+3 generic phosphorus\n+atom [#15D5] P_3+5 formal charge +5\n+atom [#16] S_3+2 generic S \n+atom [#16+4] S_3+4 S+4 ( SO2 )\n+atom [#16+6] S_3+6 S+6 ( SO3 / H2SO4 )\n+atom [S^2] S_2 non-aromatic sp2 S\n+atom [s] S_R aromatic S\n+atom [#17] Cl\n+atom [#18] Ar4+4\n+atom [#19] K_\n+atom [#20] Ca6+2\n+atom [#21] Sc3+3\n+atom [#22] Ti6+4 generic Ti (6-valent)\n+atom [#22D3] Ti3+4\n+atom [#23] V_3+5\n+atom [#24] Cr6+3\n+atom [#25] Mn6+2\n+atom [#26] Fe6+2 generic Fe (6-valent)\n+atom [#26D3] Fe3+2\n+atom [#27] Co6+3\n+atom [#28] Ni4+2\n+atom [#29] Cu3+1\n+atom [#30] Zn3+2\n+atom [#31] Ga3+3\n+atom [#32] Ge3\n+atom [#33] As3+3\n+atom [#34] Se3+2\n+atom [#35] Br\n+atom [#36] Kr4+4\n+atom [#37] Rb\n+atom [#38] Sr6+2\n+atom [#39] Y_3+3\n+atom [#40] Zr3+4\n+atom [#41] Nb3+5\n+atom [#42] Mo6+6 generic Mo (6-valent)\n+atom [#42D3] Mo3+6 trivalent Mo\n+atom [#43] Tc6+5\n+atom [#44] Ru6+2\n+atom [#45] Rh6+3\n+atom [#46] Pd4+2\n+atom [#47] Ag1+1\n+atom [#48] Cd3+2\n+atom [#49] In3+3\n+atom [#50] Sn3\n+atom [#51] Sb3+3\n+atom [#52] Te3+2\n+atom [#53] I_\n+atom [#54] Xe4+4\n+atom [#55] Cs\n+atom [#56] Ba6+2\n+atom [#57] La3+3\n+atom [#58] Ce6+3\n+atom [#59] Pr6+3\n+atom [#60] Nd6+3\n+atom [#61] Pm6+3\n+atom [#62] Sm6+3\n+atom [#63] Eu6+3\n+atom [#64] Gd6+3\n+atom [#65] Tb6+3\n+atom [#66] Dy6+3\n+atom [#67] Ho6+3\n+atom [#68] Er6+3\n+atom [#69] Tm6+3\n+atom [#70] Yb6+3\n+atom [#71] Lu6+3\n+atom [#72] Hf3+4\n+atom [#73] Ta3+5\n+atom [#74] W_6+6 generic W (6-valent)\n+atom [#74D3+4] W_3+4\n+atom [#74D3+6] W_3+6\n+atom [#75] Re6+5 generic Re (6-valent)\n+atom [#75D3] Re3+7 trivalent Re\n+atom [#76] Os6+6\n+atom [#77] Ir6+3\n+atom [#78] Pt4+2\n+atom [#79] Au4+3\n+atom [#80] Hg1+2\n+atom [#81] Tl3+3\n+atom [#82] Pb3\n+atom [#83] Bi3+3\n+atom [#84] Po3+2\n+atom [#85] At\n+atom [#86] Rn4+4\n+atom [#87] Fr\n+atom [#88] Ra6+2\n+atom [#89] Ac6+3\n+atom [#90] Th6+4\n+atom [#91] Pa6+4\n+atom [#92] U_6+4\n+atom [#93] Np6+4\n+atom [#94] Pu6+4\n+atom [#95] Am6'..b'12\t3.4\t0\t0.2\t3.575\t4.015\t1.5\n+param Rh6+3\t1.332\t90\t2.929\t0.053\t12\t3.5\t0\t0.2\t3.975\t4.005\t1.509\n+param Pd4+2\t1.338\t90\t2.899\t0.048\t12\t3.21\t0\t0.2\t4.32\t4\t1.544\n+param Ag1+1\t1.386\t180\t3.148\t0.036\t12\t1.956\t0\t0.2\t4.436\t3.134\t1.622\n+param Cd3+2\t1.403\t109.47\t2.848\t0.228\t12\t1.65\t0\t0.2\t5.034\t3.957\t1.6\n+param In3+3\t1.459\t109.47\t4.463\t0.599\t11\t2.07\t0\t0.2\t3.506\t2.896\t1.404\n+param Sn3\t1.398\t109.47\t4.392\t0.567\t12\t2.961\t0.199\t0.2\t3.987\t3.124\t1.354\n+param Sb3+3\t1.407\t91.6\t4.42\t0.449\t13\t2.704\t1.1\t0.2\t4.899\t3.342\t1.404\n+param Te3+2\t1.386\t90.25\t4.47\t0.398\t14\t2.882\t0.3\t0.2\t5.816\t3.526\t1.38\n+param I_\t1.382\t180\t4.5\t0.339\t15\t2.65\t0\t0.2\t6.822\t3.762\t1.333\n+param Xe4+4\t1.267\t90\t4.404\t0.332\t12\t0.556\t0\t0.2\t7.595\t4.975\t2.459\n+param Cs\t2.57\t180\t4.517\t0.045\t12\t1.573\t0\t0.1\t2.183\t1.711\t2.984\n+param Ba6+2\t2.277\t90\t3.703\t0.364\t12\t2.727\t0\t0.1\t2.814\t2.396\t2.442\n+param La3+3\t1.943\t109.47\t3.522\t0.017\t12\t3.3\t0\t0.1\t2.8355\t2.7415\t2.071\n+param Ce6+3\t1.841\t90\t3.556\t0.013\t12\t3.3\t0\t0.1\t2.774\t2.692\t1.925\n+param Pr6+3\t1.823\t90\t3.606\t0.01\t12\t3.3\t0\t0.1\t2.858\t2.564\t2.007\n+param Nd6+3\t1.816\t90\t3.575\t0.01\t12\t3.3\t0\t0.1\t2.8685\t2.6205\t2.007\n+param Pm6+3\t1.801\t90\t3.547\t0.009\t12\t3.3\t0\t0.1\t2.881\t2.673\t2\n+param Sm6+3\t1.78\t90\t3.52\t0.008\t12\t3.3\t0\t0.1\t2.9115\t2.7195\t1.978\n+param Eu6+3\t1.771\t90\t3.493\t0.008\t12\t3.3\t0\t0.1\t2.8785\t2.7875\t2.227\n+param Gd6+3\t1.735\t90\t3.368\t0.009\t12\t3.3\t0\t0.1\t3.1665\t2.9745\t1.968\n+param Tb6+3\t1.732\t90\t3.451\t0.007\t12\t3.3\t0\t0.1\t3.018\t2.834\t1.954\n+param Dy6+3\t1.71\t90\t3.428\t0.007\t12\t3.3\t0\t0.1\t3.0555\t2.8715\t1.934\n+param Ho6+3\t1.696\t90\t3.409\t0.007\t12\t3.416\t0\t0.1\t3.127\t2.891\t1.925\n+param Er6+3\t1.673\t90\t3.391\t0.007\t12\t3.3\t0\t0.1\t3.1865\t2.9145\t1.915\n+param Tm6+3\t1.66\t90\t3.374\t0.006\t12\t3.3\t0\t0.1\t3.2514\t2.9329\t2\n+param Yb6+3\t1.637\t90\t3.355\t0.228\t12\t2.618\t0\t0.1\t3.2889\t2.965\t2.158\n+param Lu6+3\t1.671\t90\t3.64\t0.041\t12\t3.271\t0\t0.1\t2.9629\t2.4629\t1.896\n+param Hf3+4\t1.611\t109.47\t3.141\t0.072\t12\t3.921\t0\t0.1\t3.7\t3.4\t1.759\n+param Ta3+5\t1.511\t109.47\t3.17\t0.081\t12\t4.075\t0\t0.1\t5.1\t2.85\t1.605\n+param W_6+6\t1.392\t90\t3.069\t0.067\t12\t3.7\t0\t0.1\t4.63\t3.31\t1.538\n+param W_3+4\t1.526\t109.47\t3.069\t0.067\t12\t3.7\t0\t0.1\t4.63\t3.31\t1.538\n+param W_3+6\t1.38\t109.47\t3.069\t0.067\t12\t3.7\t0\t0.1\t4.63\t3.31\t1.538\n+param Re6+5\t1.372\t90\t2.954\t0.066\t12\t3.7\t0\t0.1\t3.96\t3.92\t1.6\n+param Re3+7\t1.314\t109.47\t2.954\t0.066\t12\t3.7\t0\t0.1\t3.96\t3.92\t1.6\n+param Os6+6\t1.372\t90\t3.12\t0.037\t12\t3.7\t0\t0.1\t5.14\t3.63\t1.7\n+param Ir6+3\t1.371\t90\t2.84\t0.073\t12\t3.731\t0\t0.1\t5\t4\t1.866\n+param Pt4+2\t1.364\t90\t2.754\t0.08\t12\t3.382\t0\t0.1\t4.79\t4.43\t1.557\n+param Au4+3\t1.262\t90\t3.293\t0.039\t12\t2.625\t0\t0.1\t4.894\t2.586\t1.618\n+param Hg1+2\t1.34\t180\t2.705\t0.385\t12\t1.75\t0\t0.1\t6.27\t4.16\t1.6\n+param Tl3+3\t1.518\t120\t4.347\t0.68\t11\t2.068\t0\t0.1\t3.2\t2.9\t1.53\n+param Pb3\t1.459\t109.47\t4.297\t0.663\t12\t2.846\t0.1\t0.1\t3.9\t3.53\t1.444\n+param Bi3+3\t1.512\t90\t4.37\t0.518\t13\t2.47\t1\t0.1\t4.69\t3.74\t1.514\n+param Po3+2\t1.5\t90\t4.709\t0.325\t14\t2.33\t0.3\t0.1\t4.21\t4.21\t1.48\n+param At\t1.545\t180\t4.75\t0.284\t15\t2.24\t0\t0.1\t4.75\t4.75\t1.47\n+param Rn4+4\t1.42\t90\t4.765\t0.248\t16\t0.583\t0\t0.1\t5.37\t5.37\t2.2\n+param Fr\t2.88\t180\t4.9\t0.05\t12\t1.847\t0\t0\t2\t2\t2.3\n+param Ra6+2\t2.512\t90\t3.677\t0.404\t12\t2.92\t0\t0\t2.843\t2.434\t2.2\n+param Ac6+3\t1.983\t90\t3.478\t0.033\t12\t3.9\t0\t0\t2.835\t2.835\t2.108\n+param Th6+4\t1.721\t90\t3.396\t0.026\t12\t4.202\t0\t0\t3.175\t2.905\t2.018\n+param Pa6+4\t1.711\t90\t3.424\t0.022\t12\t3.9\t0\t0\t2.985\t2.905\t1.8\n+param U_6+4\t1.684\t90\t3.395\t0.022\t12\t3.9\t0\t0\t3.341\t2.853\t1.713\n+param Np6+4\t1.666\t90\t3.424\t0.019\t12\t3.9\t0\t0\t3.549\t2.717\t1.8\n+param Pu6+4\t1.657\t90\t3.424\t0.016\t12\t3.9\t0\t0\t3.243\t2.819\t1.84\n+param Am6+4\t1.66\t90\t3.381\t0.014\t12\t3.9\t0\t0\t2.9895\t3.0035\t1.942\n+param Cm6+3\t1.801\t90\t3.326\t0.013\t12\t3.9\t0\t0\t2.8315\t3.1895\t1.9\n+param Bk6+3\t1.761\t90\t3.339\t0.013\t12\t3.9\t0\t0\t3.1935\t3.0355\t1.9\n+param Cf6+3\t1.75\t90\t3.313\t0.013\t12\t3.9\t0\t0\t3.197\t3.101\t1.9\n+param Es6+3\t1.724\t90\t3.299\t0.012\t12\t3.9\t0\t0\t3.333\t3.089\t1.9\n+param Fm6+3\t1.712\t90\t3.286\t0.012\t12\t3.9\t0\t0\t3.4\t3.1\t1.9\n+param Md6+3\t1.689\t90\t3.274\t0.011\t12\t3.9\t0\t0\t3.47\t3.11\t1.9\n+param No6+3\t1.679\t90\t3.248\t0.011\t12\t3.9\t0\t0\t3.475\t3.175\t1.9\n+param Lw6+3\t1.698\t90\t3.236\t0.011\t12\t3.9\t0\t0\t3.5\t3.2\t1.9\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/aromatic.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/aromatic.h Tue Jun 07 16:43:30 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
+

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/aromatic.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/aromatic.txt Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/atomtyp.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/atomtyp.h Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,306 @@\n+/***************************************************************\n+This file is part of the Open Babel project.\n+This is copyright under the GNU General Public License (GPL)\n+For more information, see <http://openbabel.org/>\n+\n+This file contains a binary representation of data tables\n+ used by Open Babel. It is used as a fallback if the textual\n+ data table is not found at runtime. It is not a normal header.\n+***************************************************************/\n+\n+\n+#ifndef OB_ATOMTYP_H\n+#define OB_ATOMTYP_H\n+\n+namespace OpenBabel\n+{\n+static const char AtomTypeData[] = {\n+ 0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x44,0x34,0x5D,0x20,0x33,0x20,0x23,\n+ 0x61,0x6E,0x79,0x20,0x34,0x2D,0x76,0x61,0x6C,0x65,0x6E,0x74,0x20,0x61,0x74,\n+ 0x6F,0x6D,0x20,0x2D,0x2D,0x20,0x74,0x65,0x74,0x72,0x61,0x68,0x65,0x64,0x72,\n+ 0x61,0x6C,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x44,0x35,0x5D,0x20,\n+ 0x35,0x20,0x23,0x61,0x6E,0x79,0x20,0x35,0x2D,0x76,0x61,0x6C,0x65,0x6E,0x74,\n+ 0x20,0x61,0x74,0x6F,0x6D,0x20,0x2D,0x2D,0x20,0x74,0x72,0x69,0x67,0x62,0x69,\n+ 0x70,0x79,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x44,0x36,0x5D,0x20,\n+ 0x36,0x20,0x23,0x61,0x6E,0x79,0x20,0x36,0x2D,0x76,0x61,0x6C,0x65,0x6E,0x74,\n+ 0x20,0x61,0x74,0x6F,0x6D,0x20,0x2D,0x2D,0x20,0x6F,0x63,0x74,0x0A,0x49,0x4E,\n+ 0x54,0x48,0x59,0x42,0x20,0x5B,0x43,0x5D,0x20,0x33,0x20,0x23,0x73,0x70,0x33,\n+ 0x20,0x63,0x61,0x72,0x62,0x6F,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,\n+ 0x5B,0x63,0x2C,0x24,0x28,0x43,0x3D,0x2A,0x29,0x5D,0x20,0x32,0x20,0x23,0x73,\n+ 0x70,0x32,0x20,0x63,0x61,0x72,0x62,0x6F,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,\n+ 0x42,0x20,0x5B,0x24,0x28,0x43,0x23,0x2A,0x29,0x2C,0x24,0x28,0x43,0x28,0x3D,\n+ 0x2A,0x29,0x3D,0x2A,0x29,0x5D,0x20,0x31,0x20,0x23,0x73,0x70,0x20,0x63,0x61,\n+ 0x72,0x62,0x6F,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x4E,0x5D,\n+ 0x20,0x33,0x20,0x23,0x73,0x70,0x33,0x20,0x6E,0x69,0x74,0x72,0x6F,0x67,0x65,\n+ 0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x6E,0x2C,0x24,0x28,0x4E,\n+ 0x3D,0x2A,0x29,0x2C,0x24,0x28,0x4E,0x5B,0x23,0x36,0x2C,0x23,0x37,0x2C,0x23,\n+ 0x38,0x5D,0x3D,0x2C,0x3A,0x2C,0x23,0x2A,0x29,0x5D,0x20,0x32,0x20,0x23,0x73,\n+ 0x70,0x32,0x20,0x6E,0x69,0x74,0x72,0x6F,0x67,0x65,0x6E,0x0A,0x49,0x4E,0x54,\n+ 0x48,0x59,0x42,0x20,0x5B,0x4E,0x44,0x31,0x2C,0x4E,0x44,0x32,0x2C,0x4E,0x44,\n+ 0x33,0x5D,0x61,0x20,0x32,0x20,0x23,0x73,0x70,0x32,0x20,0x6E,0x69,0x74,0x72,\n+ 0x6F,0x67,0x65,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x24,0x28,\n+ 0x4E,0x23,0x2A,0x29,0x2C,0x24,0x28,0x5B,0x4E,0x44,0x32,0x5D,0x28,0x3D,0x2A,\n+ 0x29,0x3D,0x2A,0x29,0x5D,0x20,0x31,0x20,0x23,0x73,0x70,0x20,0x6E,0x69,0x74,\n+ 0x72,0x6F,0x67,0x65,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x4F,\n+ 0x5D,0x20,0x33,0x20,0x23,0x73,0x70,0x33,0x20,0x6F,0x78,0x79,0x67,0x65,0x6E,\n+ 0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x6F,0x2C,0x24,0x28,0x4F,0x3D,\n+ 0x2A,0x29,0x2C,0x24,0x28,0x4F,0x5B,0x23,0x36,0x2C,0x23,0x37,0x2C,0x23,0x38,\n+ 0x5D,0x3D,0x2C,0x3A,0x2A,0x29,0x5D,0x20,0x32,0x20,0x23,0x73,0x70,0x32,0x20,\n+ 0x6F,0x78,0x79,0x67,0x65,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,\n+ 0x24,0x28,0x5B,0x23,0x38,0x44,0x31,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x38,\n+ 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0x4F,0x33,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x38,0x5E,0x32,\n+ 0x5D,0x20,0x4F,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x24,0x28,\n+ 0x4F,0x61,0x29,0x5D,0x20,0x4F,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,\n+ 0x5B,0x24,0x28,0x5B,0x4F,0x44,0x32,0x5D,0x43,0x3D,0x5B,0x4F,0x2C,0x53,0x5D,\n+ 0x29,0x5D,0x20,0x4F,0x33,0x20,0x23,0x65,0x73,0x74,0x65,0x72,0x20,0x6F,0x78,\n+ 0x79,0x67,0x65,0x6E,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x24,0x28,\n+ 0x4F,0x61,0x29,0x5D,0x20,0x4F,0x33,0x20,0x23,0x61,0x72,0x6F,0x6D,0x61,0x74,\n+ 0x69,0x63,0x20,0x65,0x74,0x68,0x65,0x72,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,\n+ 0x20,0x5B,0x23,0x38,0x2D,0x5D,0x20,0x4F,0x2D,0x0A,0x45,0x58,0x54,0x54,0x59,\n+ 0x50,0x20,0x5B,0x24,0x28,0x5B,0x23,0x38,0x44,0x31,0x5D,0x7E,0x5B,0x23,0x36,\n+ 0x5E,0x32,0x5D,0x7E,0x5B,0x23,0x38,0x44,0x31,0x5D,0x29,0x5D,0x20,0x4F,0x2E,\n+ 0x63,0x6F,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x31,0x35,\n+ 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0x3D,0x2A,0x29,0x5D,0x20,0x53,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,\n+ 0x5B,0x23,0x31,0x36,0x44,0x34,0x3B,0x24,0x28,0x53,0x28,0x3D,0x4F,0x29,0x28,\n+ 0x3D,0x4F,0x29,0x29,0x5D,0x20,0x53,0x6F,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,\n+ 0x50,0x20,0x5B,0x23,0x31,0x36,0x44,0x33,0x3B,0x24,0x28,0x53,0x28,0x3D,0x4F,\n+ 0x29,0x29,0x5D,0x20,0x53,0x6F,0x78,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,\n+ 0x5B,0x23,0x31,0x36,0x3B,0x24,0x28,0x5B,0x23,0x31,0x36,0x44,0x34,0x5D,0x28,\n+ 0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,\n+ 0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5D,0x20,0x53,0x61,0x63,0x0A,0x45,0x58,\n+ 0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x31,0x36,0x3B,0x24,0x28,0x5B,0x23,0x31,\n+ 0x36,0x44,0x33,0x5D,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,0x4F,\n+ 0x44,0x31,0x5D,0x29,0x5D,0x20,0x53,0x61,0x63,0x0A,0x45,0x58,0x54,0x54,0x59,\n+ 0x50,0x20,0x5B,0x23,0x35,0x5D,0x20,0x42,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,\n+ 0x50,0x20,0x5B,0x23,0x35,0x44,0x34,0x5D,0x20,0x42,0x33,0x0A,0x00};\n+\n+} // namespace OpenBabel\n+#endif // OB_ATOMTYP_H\n+\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/atomtyp.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/atomtyp.txt Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,249 @@\n+##############################################################################\n+# #\n+# Open Babel file: atomtyp.txt #\n+# #\n+# #\n+# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #\n+# Some portions Copyright (c) 2001-2008 Geoffrey R. Hutchison #\n+# Part of the Open Babel package, under the GNU General Public License (GPL)#\n+# #\n+# SMARTS patterns for atom typing (used by typer.cpp:OBAtomTyper) #\n+# #\n+# INTHYB: used to assign the internal hybridization values for atoms #\n+# IMPVAL: used to assign the implicit valence of an atom #\n+# EXTTYP: used to assign the external type of an atom for translation to #\n+# package specific types (i.e. Sybyl Mol2) #\n+# (these should correspond to INT type names in types.txt too.) #\n+# #\n+# The LAST PATTERN MATCHED is used to assign values with the corresponding #\n+# INTHYB, IMPVAL, and EXTTYP values. Additions to this file should be placed #\n+# in the EXTRA DEFINITIONS section (to separate from original patterns.) #\n+# #\n+##############################################################################\n+\n+INTHYB [D4] 3 #any 4-valent atom -- tetrahedral\n+INTHYB [D5] 5 #any 5-valent atom -- trigbipy\n+INTHYB [D6] 6 #any 6-valent atom -- oct\n+INTHYB [C] 3 #sp3 carbon\n+INTHYB [c,$(C=*)] 2 #sp2 carbon\n+# INTHYB [$([#6]([#8D1])[#8D1])] 2 # Commented out after PR#3089597\n+INTHYB [$(C#*),$(C(=*)=*)] 1 #sp carbon\n+\n+INTHYB [N] 3 #sp3 nitrogen\n+INTHYB [n,$(N=*),$(N[#6,#7,#8]=,:,#*)] 2 #sp2 nitrogen\n+INTHYB [ND1,ND2,ND3]a 2 #sp2 nitrogen\n+INTHYB [$(N#*),$([ND2](=*)=*)] 1 #sp nitrogen\n+\n+INTHYB [O] 3 #sp3 oxygen\n+INTHYB [o,$(O=*),$(O[#6,#7,#8]=,:*)] 2 #sp2 oxygen\n+INTHYB [$([#8D1][#6][#8D1])] 2 #sp2 oxygen\n+INTHYB [$(O#*)] 1 #sp oxygen\n+\n+INTHYB [P] 3 #sp3 phosphorus\n+INTHYB [#15;$([PD1]=*)] 2 #sp2 phosphorus\n+INTHYB [PD5]\t\t\t 5\t #sp3d phosphorus, as in PF5\n+INTHYB [Pv5]\t\t\t 5\t #sp3d phosphorus, as in H3PO4\n+INTHYB [S] 3 #sp3 sulfur\n+INTHYB [#16;s,$([SD1]=*)] 2 #sp2 sulfur\n+INTHYB [SD6]\t\t\t 6\t #sp3d2 sulfur, as in SF6\n+INTHYB [B] 2 #sp2 boron\n+INTHYB [BD4] 3 #sp3 boron\n+\n+INTHYB [Al] 2 # typical sp2 Al (and family)\n+INTHYB [Ga] 2\n+INTHYB [In] 2\n+INTHYB [Tl] 2\n+INTHYB [AlD4] 3 # sp3 Al\n+INTHYB [Si] 3 # sp3 Si (and family)\n+INTHYB [Ge] 3\n+INTHYB [Sn] 3\n+INTHYB [Pb] 3\n+INTHYB [As] 3 # sp3 hybridization As (and family)\n+INTHYB [Sb] 3\n+INTHYB [Bi] 3\n+\n+INTHYB [se] 2 # aromatic sp2 Se\n+INTHYB [Se] 3 # sp3 hybridization Se (and family)\n+INTHYB [Te] 3\n+INTHYB [Po] 3\n+\n+INTHYB [Be] '..b'*)] 2\n+\n+IMPVAL [$([#8+]#*)] 1\n+\n+IMPVAL [#8] 2 # Generic O\n+IMPVAL [#8-] 1\n+IMPVAL [#8-2] 0\n+IMPVAL [#8+] 3\n+IMPVAL [$([#8]=*)] 1\n+IMPVAL [#8^1+] 1 # carbon monoxide\n+\n+IMPVAL [#9D0] 1\n+IMPVAL [#9D0-] 0 #[F-]\n+\n+IMPVAL [#13] 3 # generic Al\n+\n+IMPVAL [#14] 4 # regular sp3 Si\n+IMPVAL [#14^2] 2 # silylenes\n+IMPVAL [$([#14]=*)] 3 # e.g., Si=O\n+IMPVAL [$([#14](=*)=*)] 0 # e.g., Si(=O)=O\n+IMPVAL [$([#14+]#*)]\t\t 1 # just for InChI Si2\n+IMPVAL [$([#14-]#*)]\t\t 1 # just for InChI Si2\n+\n+IMPVAL [#15D4] 4\n+IMPVAL [#15D3] 3\n+IMPVAL [#15D2] 3\n+IMPVAL [#15D1^3] 3\n+IMPVAL [#15D1^2] 3\n+IMPVAL [#15D0] 3\n+IMPVAL [$([#15]=[#6])] 2\n+IMPVAL [pD2] 2\n+IMPVAL [$([#15]=[#8])] 4 # phosphinate (double bond = one valence)\n+IMPVAL [$([#15](=[#8])=[#8])] 3 # metaphosphate (double bond = one valence)\n+IMPVAL [$([#15+](=[#8])([#8]))] 0 # R-P+O2\n+\n+IMPVAL [#16] 2 #revised CM April 2008\n+IMPVAL [$([#16D1]=*)] 1\n+IMPVAL [$([#16D3](=O)(=O)-O)] 4 #e.g. O[S](=O)=O\n+IMPVAL [$([#16D2](=O)-O)] 3 # e.g. O[S]=O\n+IMPVAL [#16D1-] 1\n+\n+IMPVAL [#17D0] 1\n+IMPVAL [#17D0-] 0 #[Cl-]\n+\n+IMPVAL [#31] 3\n+IMPVAL [#32] 4\n+\n+IMPVAL [#33] 3\n+IMPVAL [as] 3\n+\n+IMPVAL [#34] 2\n+\n+IMPVAL [#35D0] 1\n+IMPVAL [#35D0-] 0 #[Br-]\n+\n+#IMPVAL [#49,#81] 3 # In, Tl, like Ga\n+#IMPVAL [#50,#82] 4 # Sn, Pb, like Ge\n+#IMPVAL [#51,#83] 3 # Sb, Bi, like As\n+\n+IMPVAL [#52] 2\n+IMPVAL [#53D0] 1\n+IMPVAL [#53D0-] 0 #[I-]\n+\n+#\n+#EXTERNAL TYPE RULES\n+#\n+\n+# Tinker OH hydrogens for MM2\n+# Fixes PR# 1839274\n+EXTTYP [#1][#8] HO\n+\n+EXTTYP [#7^3] N3\n+EXTTYP [#7X4] N3+\n+EXTTYP [#7^2] Npl\n+EXTTYP [#7^1] N1\n+EXTTYP [$(N=*)] N2\n+EXTTYP [$([Nr0]C(=[Nr0])[Nr0])] Ng+\n+EXTTYP [$([Nr0]=C([Nr0])[Nr0])] Ng+\n+EXTTYP [$([ND1]=C[ND1])] Ng+\n+EXTTYP [$([ND1]C=[ND1])] Ng+\n+EXTTYP [$(N(O)*)] Nox\n+EXTTYP [$(NC=[O,S])] Nam\n+EXTTYP [$(N(~[OD1])~[OD1])] Ntr\n+EXTTYP [n] Nar\n+\n+EXTTYP [#6^3] C3\n+EXTTYP [#6^2] C2\n+EXTTYP [$(C(=O)[OD1])] Cac\n+EXTTYP [c] Car\n+EXTTYP [#6^1] C1\n+EXTTYP [#6+] C+\n+EXTTYP [#6-] C-\n+\n+EXTTYP [#8^3] O3\n+EXTTYP [#8^2] O2\n+EXTTYP [$(Oa)] O2\n+#The following 2 lines used for correct Sybyl atom typing\n+EXTTYP [$([OD2]C=[O,S])] O3 #ester oxygen\n+EXTTYP [$(Oa)] O3 #aromatic ether\n+EXTTYP [#8-] O-\n+EXTTYP [$([#8D1]~[#6^2]~[#8D1])] O.co2\n+\n+EXTTYP [#15] P\n+EXTTYP [#15X4+] P3+\n+EXTTYP [#15;$([#15D4](~[OD1])(~[OD1])~[OD1])] Pac\n+EXTTYP [#15;$([#15D3](~[OD1])~[OD1])] Pac\n+\n+EXTTYP [#16] S3\n+EXTTYP [#16D3+,#16X3+] S3+\n+EXTTYP [#16;s,$([SD1]=*)] S2\n+EXTTYP [#16D4;$(S(=O)(=O))] So2\n+EXTTYP [#16D3;$(S(=O))] Sox\n+EXTTYP [#16;$([#16D4](~[OD1])(~[OD1])~[OD1])] Sac\n+EXTTYP [#16;$([#16D3](~[OD1])~[OD1])] Sac\n+\n+EXTTYP [#5] B2\n+EXTTYP [#5D4] B3\n+\n+######################## Add Extra Definitions Here ##########################\n+\n+#INTHYB [U] 3\n+#INTHYB [W] 3\n+#INTHYB [Mo]\t\t\t 6 # for development\n+#INTHYB [Cr]\t\t\t 5 # for development\n+\n+############################# End Extra Definitions ##########################\n+\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/babel_povray3.inc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/babel_povray3.inc Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,1229 @@\n+//Include for Babel\n+//Copyright (c) by Steffen Reith and Oliver Weichold 1996-2002\n+// This program is free software; you can redistribute it and/or modify\n+// it under the terms of the GNU General Public License as published by\n+// the Free Software Foundation version 2 of the License.\n+//EMail: streit@streit.cc\n+//For chemical questions send mail to\n+//weichold@sas.upenn.edu\n+\n+//$Id: babel_povray3.inc 3895 2010-07-22 10:36:05Z baoilleach $\n+\n+#include "colors.inc"\n+#include "metals.inc"\n+\n+//Do a ball and sticks model as default (nothing defined)\n+#ifndef (BAS)\n+ #ifndef (SPF)\n+ #ifndef (CST)\n+ #declare BAS = true;\n+ #declare SPF = false;\n+ #declare CST = false;\n+ #end\n+ #end\n+#end\n+\n+//Default: No Ball and Sticks-model (if undefined)\n+#ifndef (BAS)\n+ #declare BAS = false;\n+#end\n+\n+//Default: No Spacefill-model (if undefined)\n+#ifndef (SPF)\n+ #declare SPF = false;\n+#end\n+\n+//Default: No capped sticks-model (if undefined)\n+#ifndef (CST)\n+ #declare CST = false;\n+#end\n+\n+//Is a model (BAS, SPF or CST) selected ?\n+#if (!((BAS | SPF) | CST))\n+\n+ //Terminate parsing\n+ #error "You have to select BAS (default), SPF or CST" \n+\n+#end\n+\n+//Select only one model\n+#if ((BAS & SPF) | ((BAS & CST) | (SPF & CST)))\n+\n+ //Terminate parsing\n+ #error "You have to select only one model-type" \n+\n+#end\n+\n+//Display copyright\n+#render "\\n\\n"\n+#render "\\nbabel31.inc (C) 1996-2002 by\\n"\n+#render "Oliver Weichold (weichold@sas.upenn.edu)\\n"\n+#render "and Steffen Reith (streit@streit.cc)\\n"\n+#render "\\n\\n"\n+\n+//TRANS mode off by default (only needed for transparent textures)\n+#ifndef (TRANS)\n+#declare TRANS = false;\n+#end \n+\n+#if (TRANS)\n+#include "glass.inc"\n+#end\n+\n+//Finishs for atoms (Nonmetals, Transmetals, Halfmetals and Metals)\n+#if (TRANS)\n+\n+ #declare TransFinish = finish {\n+ ambient 0.1\n+ diffuse 0.1\n+ specular 0.8\n+ reflection 0.1\n+ roughness 0.0003\n+ phong 1 phong_size 400\n+ } \n+\n+ //Transparent finishs\n+ #declare MetalFinish = finish {TransFinish}\n+ #declare HalfMetalFinish = finish {TransFinish}\n+ #declare NonMetalFinish = finish {TransFinish}\n+ #declare TransMetalFinish = finish {TransFinish}\n+ #declare Bond_0_Finish = finish {TransFinish}\n+ #declare Bond_1_Finish = finish {TransFinish}\n+ #declare Bond_2_Finish = finish {TransFinish}\n+ #declare Bond_3_Finish = finish {TransFinish}\n+ #declare Bond_4_Finish = finish {TransFinish}\n+ #declare Bond_5_Finish = finish {TransFinish}\n+\n+ //Filter values for transparent finishs \n+ #declare MetalFilter = 1.00;\n+ #declare HalfMetalFilter = 0.95;\n+ #declare NonMetalFilter = 1.00;\n+ #declare TransMetalFilter = 0.95;\n+ #declare Bond_0_Filter = 0.00;\n+ #declare Bond_1_Filter = 0.90;\n+ #declare Bond_2_Filter = 0.90;\n+ #declare Bond_3_Filter = 0.90;\n+ #declare Bond_4_Filter = 0.90;\n+ #declare Bond_5_Filter = 0.90;\n+\n+#else\n+\n+ //Solid finishs\n+ #declare MetalFinish = finish {F_MetalA}\n+ #declare HalfMetalFinish = finish {F_MetalD}\n+ #declare NonMetalFinish = finish {\n+\n+ ambient 0.2\n+ diffuse 0.8\n+ brilliance 1.0 \n+ phong 1.0 \n+ phong_size 80\n+ reflection 0.25\n+\n+ }\n+ #declare TransMetalFinish = finish {F_MetalD}\n+ #declare Bond_0_Finish = finish {F_MetalC}\n+ #declare Bond_1_Finish = finish {F_MetalC}\n+ #declare Bond_2_Finish = finish {F_MetalC}\n+ #declare Bond_3_Finish = finish {F_MetalC}\n+ #declare Bond_4_Finish = finish {F_MetalC}\n+ #declare Bond_5_Finish = finish {F_MetalC}\n+\n+ //No additional filter (texture is not transparent)\n+ #declare MetalFilter ='..b' finish {TransMetalFinish}\n+\n+ }\n+#if (TRANS)\n+\t interior{ I_Glass}\n+#end\n+ }\n+\n+#declare Color_Cu = rgbf <0.50,0.25,0.15,TransMetalFilter>;\n+#declare Atom_Cu = object { \n+\n+ atom\n+ scale Radius_Cu\n+\n+ texture {\n+\n+ pigment {color Color_Cu}\n+ finish {TransMetalFinish}\n+\n+ }\n+#if (TRANS)\n+\t interior{ I_Glass}\n+#end\n+ }\n+\n+#declare Color_Mn = Color_TransMetal;\n+#declare Atom_Mn = object { \n+\n+ atom\n+ scale Radius_Mn\n+ texture {\n+\n+ pigment {color Color_Mn}\n+ finish {TransMetalFinish}\n+\n+ }\n+#if (TRANS)\n+\t interior{ I_Glass}\n+#end\n+ }\n+\n+#declare Color_Fe = Color_TransMetal;\n+#declare Atom_Fe = object { \n+\n+ atom\n+ scale Radius_Fe\n+\n+ texture {\n+\n+ pigment {color Color_Fe}\n+ finish {TransMetalFinish}\n+\n+ }\n+#if (TRANS)\n+\t interior{ I_Glass}\n+#end\n+ }\n+\n+\n+#declare Color_V = Color_TransMetal;\n+#declare Atom_V = object {\n+ \n+ atom\n+ scale Radius_V\n+ texture {\n+ \n+ pigment {color Color_V}\n+ finish {TransMetalFinish}\n+ \n+ } \n+#if (TRANS)\n+\t interior{ I_Glass}\n+#end\n+ }\n+\n+#declare Atom_V2 = object {\n+ \n+ atom\n+ scale Radius_V2\n+ texture {\n+ \n+ pigment {color Color_V}\n+ finish {TransMetalFinish}\n+ \n+ } \n+#if (TRANS)\n+\t interior{ I_Glass}\n+#end\n+ } \n+\n+#declare Atom_V3 = object {\n+ \n+ atom\n+ scale Radius_V3\n+ texture {\n+ \n+ pigment {color Color_V}\n+ finish {TransMetalFinish}\n+ \n+ } \n+#if (TRANS)\n+\t interior{ I_Glass}\n+#end\n+ } \n+\n+#declare Atom_V4 = object {\n+ \n+ atom\n+ scale Radius_V4\n+ texture {\n+ \n+ pigment {color Color_V}\n+ finish {TransMetalFinish}\n+ \n+ } \n+#if (TRANS)\n+\t interior{ I_Glass}\n+#end\n+ } \n+\n+#declare Atom_V5 = object {\n+ \n+ atom\n+ scale Radius_V5\n+ texture {\n+ \n+ pigment {color Color_V}\n+ finish {TransMetalFinish}\n+ \n+ } \n+#if (TRANS)\n+\t interior{ I_Glass}\n+#end\n+ } \n+\n+\n+#declare Color_Zn = Color_TransMetal;\n+#declare Atom_Zn = object {\n+ \n+ atom\n+ scale Radius_Zn\n+ texture {\n+ \n+ pigment {color Color_Zn} \n+ finish {TransMetalFinish}\n+ \n+ }\n+#if (TRANS)\n+\t interior{ I_Glass}\n+#end\n+ } \n+\n+#declare Atom_Zn2 = object {\n+ \n+ atom\n+ scale Radius_Zn2\n+ texture {\n+ \n+ pigment {color Color_Zn} \n+ finish {TransMetalFinish}\n+ \n+ }\n+#if (TRANS)\n+\t interior{ I_Glass}\n+#end\n+ } \n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/bin2hex.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/bin2hex.pl Tue Jun 07 16:43:30 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;
+

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/bondtyp.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/bondtyp.h Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,132 @@\n+/***************************************************************\n+This file is part of the Open Babel project.\n+This is copyright under the GNU General Public License (GPL)\n+For more information, see <http://openbabel.org/>\n+\n+This file contains a binary representation of data tables\n+ used by Open Babel. It is used as a fallback if the textual\n+ data table is not found at runtime. It is not a normal header.\n+***************************************************************/\n+\n+\n+#ifndef OB_BONDTYP_H\n+#define OB_BONDTYP_H\n+\n+namespace OpenBabel\n+{\n+static const char BondTypeData[] = {\n+ 0x2A,0x31,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x32,0x29,\n+ 0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x32,0x2A,0x5B,\n+ 0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x33,0x29,0x5B,0x23,0x36,\n+ 0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x33,0x2A,0x5B,0x23,0x36,0x5D,\n+ 0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x34,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,\n+ 0x36,0x5D,0x5B,0x23,0x36,0x5D,0x34,0x2A,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,\n+ 0x37,0x44,0x33,0x5D,0x35,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,\n+ 0x23,0x36,0x5D,0x35,0x31,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,0x32,\n+ 0x20,0x31,0x20,0x31,0x20,0x33,0x20,0x31,0x20,0x33,0x20,0x34,0x20,0x32,0x20,\n+ 0x34,0x20,0x35,0x20,0x31,0x20,0x35,0x20,0x32,0x20,0x31,0x20,0x35,0x20,0x36,\n+ 0x20,0x32,0x20,0x36,0x20,0x37,0x20,0x31,0x20,0x37,0x20,0x38,0x20,0x32,0x20,\n+ 0x37,0x20,0x39,0x20,0x31,0x20,0x39,0x20,0x31,0x30,0x20,0x32,0x20,0x31,0x30,\n+ 0x20,0x31,0x31,0x20,0x31,0x20,0x31,0x31,0x20,0x38,0x20,0x31,0x20,0x31,0x31,\n+ 0x20,0x31,0x32,0x20,0x32,0x20,0x31,0x32,0x20,0x31,0x33,0x20,0x31,0x20,0x31,\n+ 0x33,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x33,0x20,0x31,0x35,0x20,0x32,0x20,\n+ 0x31,0x35,0x20,0x31,0x36,0x20,0x31,0x20,0x31,0x36,0x20,0x31,0x37,0x20,0x32,\n+ 0x20,0x31,0x37,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x37,0x20,0x31,0x38,0x20,\n+ 0x31,0x20,0x31,0x38,0x20,0x31,0x39,0x20,0x32,0x20,0x31,0x39,0x20,0x32,0x30,\n+ 0x20,0x31,0x20,0x31,0x39,0x20,0x32,0x31,0x20,0x31,0x20,0x32,0x31,0x20,0x32,\n+ 0x32,0x20,0x32,0x20,0x32,0x32,0x20,0x32,0x33,0x20,0x31,0x20,0x32,0x33,0x20,\n+ 0x32,0x30,0x20,0x32,0x0A,0x2A,0x31,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,\n+ 0x44,0x33,0x5D,0x32,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,\n+ 0x36,0x5D,0x32,0x2A,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x5D,0x33,0x29,\n+ 0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x33,0x2A,0x5B,\n+ 0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x34,0x29,0x5B,0x23,0x36,\n+ 0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x34,0x2A,0x5B,0x23,0x36,0x5D,\n+ 0x28,0x5B,0x23,0x37,0x5D,0x35,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,\n+ 0x5B,0x23,0x36,0x5D,0x35,0x31,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,\n+ 0x32,0x20,0x31,0x20,0x31,0x20,0x33,0x20,0x31,0x20,0x33,0x20,0x34,0x20,0x32,\n+ 0x20,0x34,0x20,0x35,0x20,0x31,0x20,0x35,0x20,0x32,0x20,0x31,0x20,0x35,0x20,\n+ 0x36,0x20,0x32,0x20,0x36,0x20,0x37,0x20,0x31,0x20,0x37,0x20,0x38,0x20,0x32,\n+ 0x20,0x37,0x20,0x39,0x20,0x31,0x20,0x39,0x20,0x31,0x30,0x20,0x32,0x20,0x31,\n+ 0x30,0x20,0x31,0x31,0x20,0x31,0x20,0x31,0x31,0x20,0x38,0x20,0x31,0x20,0x31,\n+ 0x31,0x20,0x31,0x32,0x20,0x32,0x20,0x31,0x32,0x20,0x31,0x33,0x20,0x31,0x20,\n+ 0x31,0x33,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x33,0x20,0x31,0x35,0x20,0x32,\n+ 0x20,0x31,0x35,0x20,0x31,0x36,0x20,0x31,0x20,0x31,0x36,0x20,0x31,0x37,0x20,\n+ 0x32,0x20,0x31,0x37,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x37,0x20,0x31,0x38,\n+ 0x20,0x31,0x20,0x31,0x38,0x20,0x31,0x39,0x20,0x32,0x20,0x31,0x39,0x20,0x32,\n+ 0x30,0x20,0x31,0x20,0x31,0x39,0x20,0x32,0x31,0x20,0x31,0x20,0x32,0x31,0x20,\n+ 0x32,0x32,0x20,0x32,0x20,0x32,0x32,0x20,0x32,0x33,0x20,0x31,0x20,0x32,0x33,\n+ 0x20,0x32,0x30,0x20,0x32,0x0A,0x2A,0x31,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,\n+ 0x37,0x5D,0x32,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,\n+ 0x5D,0x32,0x2A,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x5D,0x33,0x29,0x5B,\n+ 0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D'..b'0x20,0x32,0x30,\n+ 0x20,0x32,0x0A,0x5B,0x23,0x37,0x44,0x32,0x5D,0x5B,0x23,0x37,0x44,0x32,0x5E,\n+ 0x31,0x5D,0x5B,0x23,0x37,0x44,0x31,0x5D,0x09,0x09,0x30,0x20,0x31,0x20,0x32,\n+ 0x20,0x31,0x20,0x32,0x20,0x32,0x0A,0x5B,0x23,0x38,0x44,0x31,0x5D,0x5B,0x23,\n+ 0x37,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x38,0x44,0x31,0x5D,0x29,0x2A,\n+ 0x09,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,0x32,0x20,0x32,0x20,0x31,\n+ 0x20,0x33,0x20,0x31,0x0A,0x5B,0x23,0x31,0x36,0x44,0x34,0x5D,0x28,0x5B,0x23,\n+ 0x38,0x44,0x31,0x5D,0x29,0x28,0x5B,0x23,0x38,0x44,0x31,0x5D,0x29,0x28,0x2A,\n+ 0x29,0x28,0x2A,0x29,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,\n+ 0x32,0x20,0x30,0x20,0x33,0x20,0x31,0x20,0x30,0x20,0x34,0x20,0x31,0x0A,0x5B,\n+ 0x23,0x31,0x35,0x44,0x34,0x5D,0x28,0x5B,0x23,0x38,0x44,0x31,0x5D,0x29,0x28,\n+ 0x2A,0x29,0x28,0x2A,0x29,0x28,0x2A,0x29,0x09,0x30,0x20,0x31,0x20,0x32,0x20,\n+ 0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,0x20,0x30,0x20,0x34,\n+ 0x20,0x31,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x38,\n+ 0x44,0x31,0x5D,0x29,0x28,0x5B,0x23,0x38,0x5D,0x29,0x2A,0x09,0x09,0x30,0x20,\n+ 0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,\n+ 0x0A,0x5B,0x23,0x38,0x44,0x31,0x5D,0x5B,0x23,0x36,0x44,0x32,0x5E,0x31,0x5D,\n+ 0x5B,0x23,0x38,0x44,0x31,0x5D,0x09,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,\n+ 0x20,0x32,0x20,0x32,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,\n+ 0x23,0x38,0x44,0x31,0x5D,0x29,0x28,0x5B,0x23,0x37,0x5D,0x29,0x2A,0x09,0x09,\n+ 0x30,0x20,0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,\n+ 0x20,0x31,0x0A,0x5B,0x23,0x33,0x34,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,\n+ 0x38,0x44,0x31,0x5D,0x29,0x28,0x5B,0x23,0x38,0x5D,0x29,0x2A,0x09,0x09,0x30,\n+ 0x20,0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,\n+ 0x31,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x38,0x44,\n+ 0x31,0x5D,0x29,0x28,0x5B,0x23,0x31,0x36,0x5D,0x29,0x2A,0x09,0x09,0x30,0x20,\n+ 0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,\n+ 0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x31,0x36,0x44,\n+ 0x31,0x5D,0x29,0x28,0x5B,0x23,0x31,0x36,0x5D,0x29,0x2A,0x09,0x09,0x30,0x20,\n+ 0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,\n+ 0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x31,0x36,0x44,\n+ 0x31,0x5D,0x29,0x28,0x5B,0x23,0x37,0x5D,0x29,0x2A,0x09,0x09,0x30,0x20,0x31,\n+ 0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,0x0A,\n+ 0x5B,0x23,0x36,0x5E,0x32,0x5D,0x5B,0x23,0x36,0x44,0x32,0x5E,0x31,0x5D,0x5B,\n+ 0x23,0x36,0x5E,0x32,0x5D,0x09,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,\n+ 0x32,0x20,0x32,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,0x5D,\n+ 0x28,0x5B,0x23,0x37,0x44,0x31,0x48,0x30,0x3B,0x21,0x52,0x5D,0x29,0x28,0x5B,\n+ 0x23,0x37,0x3B,0x21,0x52,0x5D,0x29,0x2A,0x09,0x30,0x20,0x31,0x20,0x32,0x20,\n+ 0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,0x0A,0x5B,0x23,0x36,\n+ 0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,0x5D,0x28,0x5B,0x23,0x37,0x44,0x32,0x48,\n+ 0x31,0x3B,0x21,0x52,0x5D,0x29,0x28,0x5B,0x23,0x37,0x3B,0x21,0x52,0x5D,0x29,\n+ 0x2A,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,\n+ 0x20,0x33,0x20,0x31,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,\n+ 0x5D,0x28,0x5B,0x23,0x37,0x44,0x33,0x48,0x32,0x3B,0x21,0x52,0x5D,0x29,0x28,\n+ 0x5B,0x23,0x37,0x3B,0x21,0x52,0x5D,0x29,0x2A,0x09,0x30,0x20,0x31,0x20,0x32,\n+ 0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,0x0A,0x5B,0x23,\n+ 0x36,0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,0x5D,0x28,0x5B,0x23,0x31,0x2C,0x23,\n+ 0x36,0x5D,0x29,0x28,0x5B,0x23,0x31,0x2C,0x23,0x36,0x5D,0x29,0x5B,0x23,0x37,\n+ 0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,0x5D,0x28,0x5B,0x23,0x31,0x5D,0x29,0x5B,\n+ 0x23,0x36,0x5D,0x09,0x30,0x20,0x31,0x20,0x31,0x20,0x30,0x20,0x32,0x20,0x31,\n+ 0x20,0x30,0x20,0x33,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x31,0x20,0x33,0x20,\n+ 0x35,0x20,0x31,0x0A,0x00};\n+\n+} // namespace OpenBabel\n+#endif // OB_BONDTYP_H\n+\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/bondtyp.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/bondtyp.txt Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/cmake_install.cmake
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/cmake_install.cmake Tue Jun 07 16:43:30 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")
+

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/element.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/element.h Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,616 @@\n+/***************************************************************\n+This file is part of the Open Babel project.\n+This is copyright under the GNU General Public License (GPL)\n+For more information, see <http://openbabel.org/>\n+\n+This file contains a binary representation of data tables\n+ used by Open Babel. It is used as a fallback if the textual\n+ data table is not found at runtime. It is not a normal header.\n+***************************************************************/\n+\n+\n+#ifndef OB_ELEMENT_H\n+#define OB_ELEMENT_H\n+\n+namespace OpenBabel\n+{\n+static const char ElementData[] = {\n+ 0x30,0x09,0x58,0x78,0x09,0x30,0x2E,0x30,0x30,0x09,0x30,0x2E,0x30,0x30,0x09,\n+ 0x30,0x2E,0x30,0x30,0x09,0x30,0x2E,0x30,0x30,0x09,0x30,0x09,0x30,0x09,0x30,\n+ 0x2E,0x30,0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x2E,0x30,0x37,0x09,0x30,0x2E,\n+ 0x35,0x30,0x09,0x30,0x2E,0x37,0x30,0x09,0x44,0x75,0x6D,0x6D,0x79,0x0A,0x31,\n+ 0x09,0x48,0x09,0x32,0x2E,0x32,0x30,0x09,0x30,0x2E,0x33,0x31,0x09,0x30,0x2E,\n+ 0x33,0x31,0x09,0x31,0x2E,0x31,0x30,0x09,0x31,0x09,0x31,0x2E,0x30,0x30,0x37,\n+ 0x39,0x34,0x09,0x32,0x2E,0x32,0x30,0x09,0x31,0x33,0x2E,0x35,0x39,0x38,0x34,\n+ 0x09,0x30,0x2E,0x37,0x35,0x34,0x32,0x30,0x33,0x37,0x35,0x09,0x30,0x2E,0x37,\n+ 0x35,0x09,0x30,0x2E,0x37,0x35,0x09,0x30,0x2E,0x37,0x35,0x09,0x48,0x79,0x64,\n+ 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0x31,0x2E,0x36,0x30,0x09,0x31,0x2E,0x36,0x30,0x09,0x32,0x2E,0x30,0x30,0x09,\n+ 0x36,0x09,0x32,0x39,0x33,0x09,0x30,0x2E,0x30,0x30,0x09,0x30,0x09,0x30,0x09,\n+ 0x30,0x2E,0x39,0x39,0x09,0x30,0x2E,0x30,0x30,0x09,0x30,0x2E,0x30,0x38,0x09,\n+ 0x55,0x6E,0x75,0x6E,0x68,0x65,0x78,0x69,0x75,0x6D,0x0A,0x31,0x31,0x37,0x09,\n+ 0x55,0x75,0x68,0x09,0x30,0x2E,0x30,0x30,0x09,0x31,0x2E,0x36,0x30,0x09,0x31,\n+ 0x2E,0x36,0x30,0x09,0x32,0x2E,0x30,0x30,0x09,0x36,0x09,0x32,0x39,0x34,0x09,\n+ 0x30,0x2E,0x30,0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x2E,0x39,0x39,0x09,0x30,\n+ 0x2E,0x30,0x30,0x09,0x30,0x2E,0x30,0x37,0x09,0x55,0x6E,0x75,0x6E,0x73,0x65,\n+ 0x70,0x74,0x69,0x75,0x6D,0x0A,0x31,0x31,0x38,0x09,0x55,0x75,0x68,0x09,0x30,\n+ 0x2E,0x30,0x30,0x09,0x31,0x2E,0x36,0x30,0x09,0x31,0x2E,0x36,0x30,0x09,0x32,\n+ 0x2E,0x30,0x30,0x09,0x36,0x09,0x32,0x39,0x34,0x09,0x30,0x2E,0x30,0x30,0x09,\n+ 0x30,0x09,0x30,0x09,0x30,0x2E,0x39,0x39,0x09,0x30,0x2E,0x30,0x30,0x09,0x30,\n+ 0x2E,0x30,0x36,0x09,0x55,0x6E,0x75,0x6E,0x6F,0x63,0x74,0x69,0x75,0x6D,0x0A,\n+0x00};\n+\n+} // namespace OpenBabel\n+#endif // OB_ELEMENT_H\n+\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/element.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/element.txt Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,153 @@\n+##############################################################################\n+# #\n+#\t Open Babel file: element.txt #\n+# #\n+# Some portions Copyright (c) 2001-2009 Geoffrey R. Hutchison #\n+# Part of the Open Babel package, under the GNU General Public License (GPL)#\n+# #\n+# Created from the Blue Obelisk Cheminformatics Data Repository #\n+# Direct Source: http://www.blueobelisk.org/ #\n+# http://www.blueobelisk.org/repos/blueobelisk/elements.xml #\n+# (includes furhter bibliographic citation information) #\n+# #\n+# Allred and Rochow Electronegativity from: #\n+# http://www.hull.ac.uk/chemistry/electroneg.php?type=Allred-Rochow #\n+# #\n+# Columns represent: (used by data.cpp:OBElementTable and OBElement) #\n+# - atomic number (used as an index to the vector as well) #\n+# - elemental symbol\t\t\t\t\t\t\t #\n+# - Allred and Rochow electronegativity 0.0 if unknown\t\t #\n+# - covalent radii (in Angstrom) 1.6 if unknown\t\t #\n+# from http://dx.doi.org/10.1039/b801115j #\n+# - "bond order" radii -- ignored, but included for compatibility #\n+# - van der Waals radii (in Angstrom)\t 2.0 if unknown\t\t #\n+# from http://dx.doi.org/10.1021/jp8111556 #\n+# - maximum bond valence\t\t 6 if unknown\t\t\t #\n+# - IUPAC recommended atomic masses (in amu)\t\t\t\t #\n+# - Pauling electronegativity\t\t 0.0 if unknown\t\t #\n+# - ionization potential (in eV) 0.0 if unknown #\n+# - electron affinity (in eV) 0.0 if unknown #\n+# - RGB values (defaults for visualization)\t\t\t\t #\n+# - element name (in English)\t\t\t\t\t\t #\n+# #\n+##############################################################################\n+#Num\tSymb\tARENeg\tRCov\tRBO\tRVdW\tMaxBnd\tMass\tElNeg.\tIonization\tElAffinity\tRed\tGreen\tBlue\tName\n+0\tXx\t0.00\t0.00\t0.00\t0.00\t0\t0\t0.00\t0\t0\t0.07\t0.50\t0.70\tDummy\n+1\tH\t2.20\t0.31\t0.31\t1.10\t1\t1.00794\t2.20\t13.5984\t0.75420375\t0.75\t0.75\t0.75\tHydrogen\n+2\tHe\t0.00\t0.28\t0.28\t1.40\t0\t4.002602\t0.00\t24.5874\t0\t0.85\t1.00\t1.00\tHelium\n+3\tLi\t0.97\t1.28\t1.28\t1.81\t1\t6.941\t0.98\t5.3917\t0.618049\t0.80\t0.50\t1.00\tLithium\n+4\tBe\t1.47\t0.96\t0.96\t1.53\t2\t9.012182\t1.57\t9.3227\t0\t0.76\t1.00\t0.00\tBeryllium\n+5\tB\t2.01\t0.84\t0.84\t1.92\t4\t10.811\t2.04\t8.298\t0.279723\t1.00\t0.71\t0.71\tBoron\n+6\tC\t2.50\t0.76\t0.76\t1.70\t4\t12.0107\t2.55\t11.2603\t1.262118\t0.40\t0.40\t0.40\tCarbon\n+7\tN\t3.07\t0.71\t0.71\t1.55\t4\t14.0067\t3.04\t14.5341\t-0.07\t0.05\t0.05\t1.00\tNitrogen\n+8\tO\t3.50\t0.66\t0.66\t1.52\t2\t15.9994\t3.44\t13.6181\t1.461112\t1.00\t0.05\t0.05\tOxygen\n+9\tF\t4.10\t0.57\t0.57\t1.47\t1\t18.9984032\t3.98\t17.4228\t3.4011887\t0.50\t0.70\t1.00\tFluorine\n+10\tNe\t0.00\t0.58\t0.58\t1.54\t0\t20.1797\t0.00\t21.5645\t0\t0.70\t0.89\t0.96\tNeon\n+11\tNa\t1.01\t1.66\t1.66\t2.27\t1\t22.98977\t0.93\t5.1391\t0.547926\t0.67\t0.36\t0.95\tSodium\n+12\tMg\t1.23\t1.41\t1.41\t1.73\t2\t24.3050\t1.31\t7.6462\t0\t0.54\t1.00\t0.00\tMagnesium\n+13\tAl\t1.47\t1.21\t1.21\t1.84\t6\t26.981538\t1.61\t5.9858\t0.43283\t0.75\t0.65\t0.65\tAluminium\n+14\tSi\t1.74\t1.11\t1.11\t2.10\t6\t28.0855\t1.90\t8.1517\t1.389521\t0.50\t0.60\t0.60\tSilicon\n+15\tP\t2.06\t1.07\t1.07\t1.80\t6\t30.973761\t2.19\t10.4867\t0.7465\t1.00\t0.50\t0.00\tPhosphorus\n+16\tS\t2.44\t1.05\t1.05\t1.80\t6\t32.065\t2.58\t10.36\t2.0771029\t0.70\t0.70\t0.00\tSulfur\n+17\tCl\t2.83\t1.02\t1.02\t1.75\t1\t35.453\t3.16\t12.9676\t3.612724\t0.12\t0.94\t0.12\tChlorine\n+18\tAr\t0.00\t1.06\t1.06\t1.88\t0\t39.948\t0.00\t15.7596\t0\t0.50\t0'..b'\t6\t157.25\t1.20\t6.1498\t0.5\t0.27\t1.00\t0.78\tGadolinium\n+65\tTb\t0.00\t1.94\t1.94\t2.37\t6\t158.92534\t0.00\t5.8638\t0.5\t0.19\t1.00\t0.78\tTerbium\n+66\tDy\t0.00\t1.92\t1.92\t2.35\t6\t162.500\t1.22\t5.9389\t0.5\t0.12\t1.00\t0.78\tDysprosium\n+67\tHo\t0.00\t1.92\t1.92\t2.33\t6\t164.93032\t1.23\t6.0215\t0.5\t0.00\t1.00\t0.61\tHolmium\n+68\tEr\t0.00\t1.89\t1.89\t2.32\t6\t167.259\t1.24\t6.1077\t0.5\t0.00\t0.90\t0.46\tErbium\n+69\tTm\t0.00\t1.90\t1.90\t2.30\t6\t168.93421\t1.25\t6.1843\t0.5\t0.00\t0.83\t0.32\tThulium\n+70\tYb\t0.00\t1.87\t1.87\t2.28\t6\t173.054\t0.00\t6.2542\t0.5\t0.00\t0.75\t0.22\tYtterbium\n+71\tLu\t0.00\t1.87\t1.87\t2.27\t6\t174.9668\t1.27\t5.4259\t0.5\t0.00\t0.67\t0.14\tLutetium\n+72\tHf\t1.23\t1.75\t1.75\t2.25\t6\t178.49\t1.30\t6.8251\t0\t0.30\t0.76\t1.00\tHafnium\n+73\tTa\t1.33\t1.70\t1.70\t2.20\t6\t180.9479\t1.50\t7.5496\t0.322\t0.30\t0.65\t1.00\tTantalum\n+74\tW\t1.40\t1.62\t1.62\t2.10\t6\t183.84\t2.36\t7.864\t0.815\t0.13\t0.58\t0.84\tTungsten\n+75\tRe\t1.46\t1.51\t1.51\t2.05\t6\t186.207\t1.90\t7.8335\t0.15\t0.15\t0.49\t0.67\tRhenium\n+76\tOs\t1.52\t1.44\t1.44\t2.00\t6\t190.23\t2.20\t8.4382\t1.0778\t0.15\t0.40\t0.59\tOsmium\n+77\tIr\t1.55\t1.41\t1.41\t2.00\t6\t192.217\t2.20\t8.967\t1.56436\t0.09\t0.33\t0.53\tIridium\n+78\tPt\t1.44\t1.36\t1.36\t2.05\t6\t195.078\t2.28\t8.9588\t2.1251\t0.96\t0.93\t0.82\tPlatinum\n+79\tAu\t1.42\t1.36\t1.36\t2.10\t6\t196.96655\t2.54\t9.2255\t2.30861\t0.80\t0.82\t0.12\tGold\n+80\tHg\t1.44\t1.32\t1.32\t2.05\t6\t200.59\t2.00\t10.4375\t0\t0.71\t0.71\t0.76\tMercury\n+81\tTl\t1.44\t1.45\t1.45\t1.96\t3\t204.3833\t1.62\t6.1082\t0.377\t0.65\t0.33\t0.30\tThallium\n+82\tPb\t1.55\t1.46\t1.46\t2.02\t4\t207.2\t2.33\t7.4167\t0.364\t0.34\t0.35\t0.38\tLead\n+83\tBi\t1.67\t1.48\t1.48\t2.07\t3\t208.98040\t2.02\t7.2855\t0.942363\t0.62\t0.31\t0.71\tBismuth\n+84\tPo\t1.76\t1.40\t1.40\t1.97\t2\t209\t2.00\t8.414\t1.9\t0.67\t0.36\t0.00\tPolonium\n+85\tAt\t1.90\t1.50\t1.50\t2.02\t1\t210\t2.20\t0\t2.8\t0.46\t0.31\t0.27\tAstatine\n+86\tRn\t0.00\t1.50\t1.50\t2.20\t0\t222\t0.00\t10.7485\t0\t0.26\t0.51\t0.59\tRadon\n+87\tFr\t0.00\t2.60\t2.60\t3.48\t1\t223\t0.70\t4.0727\t0\t0.26\t0.00\t0.40\tFrancium\n+88\tRa\t0.00\t2.21\t2.21\t2.83\t2\t226\t0.90\t5.2784\t0\t0.00\t0.49\t0.00\tRadium\n+89\tAc\t0.00\t2.15\t2.15\t2.00\t6\t227\t1.10\t5.17\t0\t0.44\t0.67\t0.98\tActinium\n+90\tTh\t0.00\t2.06\t2.06\t2.40\t6\t232.0381\t1.30\t6.3067\t0\t0.00\t0.73\t1.00\tThorium\n+91\tPa\t0.00\t2.00\t2.00\t2.00\t6\t231.03588\t1.50\t5.89\t0\t0.00\t0.63\t1.00\tProtactinium\n+92\tU\t0.00\t1.96\t1.96\t2.30\t6\t238.02891\t1.38\t6.1941\t0\t0.00\t0.56\t1.00\tUranium\n+93\tNp\t0.00\t1.90\t1.90\t2.00\t6\t237\t1.36\t6.2657\t0\t0.00\t0.50\t1.00\tNeptunium\n+94\tPu\t0.00\t1.87\t1.87\t2.00\t6\t244\t1.28\t6.026\t0\t0.00\t0.42\t1.00\tPlutonium\n+95\tAm\t0.00\t1.80\t1.80\t2.00\t6\t243\t1.30\t5.9738\t0\t0.33\t0.36\t0.95\tAmericium\n+96\tCm\t0.00\t1.69\t1.69\t2.00\t6\t247\t1.30\t5.9914\t0\t0.47\t0.36\t0.89\tCurium\n+97\tBk\t0.00\t1.60\t1.60\t2.00\t6\t247\t1.30\t6.1979\t0\t0.54\t0.31\t0.89\tBerkelium\n+98\tCf\t0.00\t1.60\t1.60\t2.00\t6\t251\t1.30\t6.2817\t0\t0.63\t0.21\t0.83\tCalifornium\n+99\tEs\t0.00\t1.60\t1.60\t2.00\t6\t252\t1.30\t6.42\t0\t0.70\t0.12\t0.83\tEinsteinium\n+100\tFm\t0.00\t1.60\t1.60\t2.00\t6\t257\t1.30\t6.5\t0\t0.70\t0.12\t0.73\tFermium\n+101\tMd\t0.00\t1.60\t1.60\t2.00\t6\t258\t1.30\t6.58\t0\t0.70\t0.05\t0.65\tMendelevium\n+102\tNo\t0.00\t1.60\t1.60\t2.00\t6\t259\t1.30\t6.65\t0\t0.74\t0.05\t0.53\tNobelium\n+103\tLr\t0.00\t1.60\t1.60\t2.00\t6\t262\t0.00\t4.9\t0\t0.78\t0.00\t0.40\tLawrencium\n+104\tRf\t0.00\t1.60\t1.60\t2.00\t6\t267\t0.00\t6\t0\t0.80\t0.00\t0.35\tRutherfordium\n+105\tDb\t0.00\t1.60\t1.60\t2.00\t6\t268\t0.00\t0\t0\t0.82\t0.00\t0.31\tDubnium\n+106\tSg\t0.00\t1.60\t1.60\t2.00\t6\t271\t0.00\t0\t0\t0.85\t0.00\t0.27\tSeaborgium\n+107\tBh\t0.00\t1.60\t1.60\t2.00\t6\t272\t0.00\t0\t0\t0.88\t0.00\t0.22\tBohrium\n+108\tHs\t0.00\t1.60\t1.60\t2.00\t6\t270\t0.00\t0\t0\t0.90\t0.00\t0.18\tHassium\n+109\tMt\t0.00\t1.60\t1.60\t2.00\t6\t268\t0.00\t0\t0\t0.92\t0.00\t0.15\tMeitnerium\n+110\tDs\t0.00\t1.60\t1.60\t2.00\t6\t281\t0.00\t0\t0\t0.93\t0.00\t0.14\tDarmstadtium\n+111\tRg\t0.00\t1.60\t1.60\t2.00\t6\t280\t0.00\t0\t0\t0.94\t0.00\t0.13\tRoentgenium\n+112\tCn\t0.00\t1.60\t1.60\t2.00\t6\t285\t0.00\t0\t0\t0.95\t0.00\t0.12\tCopernicium\n+113\tUut\t0.00\t1.60\t1.60\t2.00\t6\t284\t0.00\t0\t0\t0.96\t0.00\t0.11\tUnuntrium\n+114\tUuq\t0.00\t1.60\t1.60\t2.00\t6\t289\t0.00\t0\t0\t0.97\t0.00\t0.10\tUnunquadium\n+115\tUup\t0.00\t1.60\t1.60\t2.00\t6\t288\t0.00\t0\t0\t0.98\t0.00\t0.09\tUnunpentium\n+116\tUuh\t0.00\t1.60\t1.60\t2.00\t6\t293\t0.00\t0\t0\t0.99\t0.00\t0.08\tUnunhexium\n+117\tUuh\t0.00\t1.60\t1.60\t2.00\t6\t294\t0.00\t0\t0\t0.99\t0.00\t0.07\tUnunseptium\n+118\tUuh\t0.00\t1.60\t1.60\t2.00\t6\t294\t0.00\t0\t0\t0.99\t0.00\t0.06\tUnunoctium\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/fragments.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/fragments.txt Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,33785 @@\n+#\n+# Open Babel file: fragments.txt\n+#\n+# Copyright (c) 2007-2008 by Geoffrey R Hutchison\n+# Part of the Open Babel package, under the GNU General Public License (GPL)\n+#\n+# Fragments for OBBuilder coordinate generation \n+# These consist of a generic SMARTS pattern\n+# followed by the 3D coordinates of all heavy atoms\n+# \n+# Fragments are ordered by length of SMARTS pattern\n+# (i.e., most complicated will match first)\n+#\n+# This file contains ~1000 of the most common ring fragments\n+# from analysis over the NCI database and ZINC\n+#\n+# NCI: http://cactus.nci.nih.gov/ncidb2/download.html\n+# ZINC: http://zinc.docking.org/\n+#\n+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\n+ -6.211 -1.460 -0.030\n+ -5.943 -0.593 1.206\n+ -5.091 0.648 0.864\n+ -3.994 0.300 -0.169\n+ -4.538 -0.250 -1.367\n+ -5.898 -0.674 -1.321\n+ -3.111 1.535 -0.461\n+ -1.792 1.261 0.318\n+ -2.126 0.038 1.158\n+ -0.839 -0.820 1.272\n+ 0.215 0.187 0.788\n+ -0.505 0.862 -0.397\n+ 0.361 2.038 -0.842\n+ 1.787 1.544 -1.206\n+ 2.492 0.838 -0.023\n+ 1.643 -0.352 0.504\n+ 1.731 -1.601 -0.389\n+ 3.140 -1.884 -0.874\n+ 4.220 -1.079 -0.124\n+ 5.652 -1.521 -0.524\n+ 6.711 -0.431 -0.189\n+ 6.283 0.453 0.974\n+ 4.934 1.171 0.717\n+ 3.983 0.435 -0.283\n+ -3.106 -0.636 0.409\n+A1A=A2AA3AA[A@@]45[A@@H]3A[A@@H]2[A@H]2[A@@H](A1)AAA(a1aaaaa51)[A@H]42\n+ -3.888 0.914 0.115\n+ -3.459 -0.469 0.519\n+ -2.450 -1.056 -0.087\n+ -1.962 -2.361 0.428\n+ -0.673 -2.830 -0.062\n+ 0.191 -3.047 1.144\n+ 0.602 -1.615 1.554\n+ 0.598 -0.812 0.219\n+ 0.084 -1.793 -0.806\n+ -0.800 -1.233 -1.901\n+ -1.848 -0.330 -1.263\n+ -1.065 0.868 -0.767\n+ -1.865 2.101 -0.431\n+ -2.873 1.838 0.542\n+ -0.974 3.251 0.020\n+ 0.403 2.844 0.453\n+ 0.828 1.570 0.379\n+ 2.076 1.022 0.182\n+ 3.313 1.677 0.144\n+ 4.435 0.913 -0.126\n+ 4.355 -0.449 -0.358\n+ 3.133 -1.117 -0.307\n+ 2.013 -0.363 -0.016\n+ -0.183 0.472 0.416\n+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\n+ -3.053 1.785 1.205\n+ -3.252 1.888 -0.289\n+ -3.572 0.529 -0.878\n+ -2.734 -0.643 -0.356\n+ -2.599 -0.629 1.153\n+ -2.102 0.714 1.691\n+ -1.649 -1.724 1.640\n+ -0.276 -1.515 1.004\n+ -0.364 -1.639 -0.513\n+ -1.409 -0.720 -1.105\n+ -0.879 0.699 -1.318\n+ 0.352 0.642 -2.224\n+ 1.470 -0.096 -1.492\n+ 1.030 -1.511 -1.133\n+ 2.052 -2.232 -0.252\n+ 2.597 -1.407 0.910\n+ 3.123 -0.085 0.382\n+ 3.542 0.917 1.473\n+ 3.414 2.288 0.758\n+ 2.384 2.093 -0.385\n+ 1.927 0.647 -0.270\n+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\n+ 3.192 1.390 -1.579\n+ 3.326 1.929 -0.176\n+ 3.606 0.809 0.807\n+ 2.782 -0.467 0.617\n+ 2.739 -0.906 -0.833\n+ 2.271 0.207 -1.774\n+ 1.821 -2.114 -1.014\n+ 0.409 -1.749 -0.560\n+ 0.383 -1.369 0.915\n+ 1.409 -0.313 1.261\n+ 0.898 1.103 1.000\n+ -0.408 1.331 1.764\n+ -1.489 0.408 1.193\n+ -1.036 -1.032 1.362\n+ -2.064 -1.979 0.744\n+ -2.348 -1.673 -0.709\n+ -2.655 -0.233 -0.998\n+ -4.130 0.114 -0.711\n+ -4.114 1.655 -0.837\n+ -2.743 2.073 -0.254\n+ -1.849 0.815 -0.219\n+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\n+ -4.909 1.704 0.237\n+ -5.602 0.484 -0.347\n+ -4.965 -0.840 0.089\n+ -3.459 -0.788 -0.071\n+ -2.722 -2.033 0.391\n+ -1.349 -2.083 -0.288\n+ -0.780 -0.715 -0.608\n+ 0.775 -0.747 -0.577\n+ 1.278 -2.064 -0.018\n+ 2.758 -2.058 0.366\n+ 3.462 -0.795 -0.085\n+ 4.973 -0.838 0.090\n+ 5.614 0.482 -0.346\n+ 4.916 1.704 0.231\n+ 3.424 1.697 -0.102\n+ 2.786 0.438 0.476\n+ 1.277 0.412 0.258\n+ 0.759 1.750 -0.252\n+ -0.771 1.761 -0.165\n+ -1.271 0.391 0.297\n+ -2.784 0.440 0.505\n+ -3.412 1.699 -0.083\n+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\n+ 5.502 0.333 0.526\n+ 4.863 1.616 0.014\n+ 3.371 1.639 0.334\n+ 2.674 0.469 -0.391\n+ 3.298 -0.826 0.113\n+ 4.802 -0.921 0.003\n+ 2.574 -2.029 -0.485\n+ 1.135 -2.027 0.055\n+ 0.416 -0.753 -0.389\n+ 1.198 0.486 0.015\n+ 0.496 1.755 -0.457\n+ -0.920 1.813 0.128\n+ -1.706 0.560 -0.258\n+ -0.984 '..b'0.060\n+ -0.418 1.330 -0.066\n+ -1.444 0.252 0.129\n+ -0.838 -1.108 -0.064\n+ 0.463 -1.294 -0.062\n+a1aaa[a+]1\n+ -0.489 0.963 -0.002\n+ -1.091 -0.089 0.001\n+ -0.220 -1.113 0.001\n+ 1.016 -0.545 -0.002\n+ 0.784 0.784 0.002\n+A1AA=AA=A1\n+ 0.278 -1.309 0.000\n+ -1.004 -0.899 0.002\n+ -1.301 0.431 -0.003\n+ -0.294 1.335 0.002\n+ 1.039 0.873 -0.000\n+ 1.280 -0.431 -0.001\n+A1=AA=AAA1\n+ -1.351 -0.236 -0.002\n+ -0.915 1.019 0.003\n+ 0.536 1.245 -0.002\n+ 1.337 0.201 -0.000\n+ 0.858 -0.993 0.001\n+ -0.463 -1.234 0.000\n+A1AAA=AAA1\n+ 0.074 1.446 -0.516\n+ 0.925 0.916 0.601\n+ 1.387 -0.337 0.584\n+ 0.929 -1.251 -0.368\n+ -0.386 -1.428 -0.540\n+ -1.518 -0.517 0.461\n+ -1.413 1.172 -0.222\n+[aH]1aaaa1\n+ -1.144 0.000 -0.002\n+ -0.328 -1.082 0.003\n+ 0.901 -0.643 -0.002\n+ 0.901 0.643 0.001\n+ -0.328 1.082 0.001\n+A1AAAA=AA1\n+ 1.536 -0.516 0.070\n+ 0.539 -1.634 -0.136\n+ -0.826 -1.408 0.492\n+ -1.697 -0.080 -0.367\n+ -0.948 1.318 0.430\n+ 0.290 1.574 0.200\n+ 1.109 0.744 -0.692\n+A1A[A-]AA1\n+ 0.570 1.100 0.002\n+ -0.917 0.805 -0.002\n+ -1.022 -0.539 0.001\n+ 0.179 -1.128 0.001\n+ 1.188 -0.238 -0.002\n+[A-]1AAAA1\n+ -1.179 -0.279 -0.052\n+ -0.722 0.985 -0.054\n+ 0.779 0.995 0.133\n+ 1.209 -0.459 -0.168\n+ -0.087 -1.241 0.140\n+A1AA2AA1A2\n+ -1.213 0.790 0.037\n+ -1.230 -0.768 0.057\n+ 0.313 -1.035 0.009\n+ 0.993 0.015 0.975\n+ 0.335 1.022 -0.017\n+ 0.802 -0.025 -1.060\n+a1aaa[a]a1\n+ -0.679 1.193 0.001\n+ -1.389 0.001 -0.002\n+ -0.681 -1.192 0.001\n+ 0.700 -1.155 0.001\n+ 1.346 -0.001 -0.002\n+ 0.701 1.155 0.001\n+[At]1AAAA1\n+ 1.635 -0.001 -0.014\n+ 0.191 -1.568 -0.036\n+ -1.028 -0.712 0.201\n+ -0.986 0.726 -0.320\n+ 0.187 1.555 0.171\n+a1aaa[aH]1\n+ -0.108 1.131 0.003\n+ -1.094 0.277 -0.002\n+ -0.599 -0.970 0.001\n+ 0.745 -0.884 0.001\n+ 1.057 0.448 -0.002\n+A1AAA=AA1\n+ 0.368 1.292 0.000\n+ 1.330 0.353 0.001\n+ 1.004 -0.957 0.000\n+ -0.418 -1.329 -0.002\n+ -1.349 -0.330 0.003\n+ -0.936 0.972 -0.002\n+A1AAAAAA1\n+ -1.502 0.713 0.149\n+ -0.279 1.437 -0.451\n+ 0.904 1.202 0.450\n+ 1.756 -0.000 0.000\n+ 0.903 -1.202 -0.450\n+ -0.280 -1.437 0.450\n+ -1.502 -0.712 -0.148\n+A1=AA=AA1\n+ 1.105 0.356 0.001\n+ 0.743 -0.916 0.001\n+ -0.743 -0.916 -0.002\n+ -1.105 0.356 0.002\n+ 0.000 1.119 -0.002\n+A1AA=AAA1\n+ -0.501 -1.306 0.067\n+ 0.972 -1.099 -0.133\n+ 1.352 0.339 0.069\n+ 0.450 1.315 0.065\n+ -0.906 1.031 -0.124\n+ -1.369 -0.279 0.056\n+A1AAAA=A1\n+ -0.796 -1.155 -0.085\n+ 0.528 -1.381 -0.153\n+ 1.659 -0.075 0.201\n+ 0.671 1.332 -0.380\n+ -0.729 1.203 0.152\n+ -1.334 0.077 0.264\n+A1=AAA=A1\n+ -0.218 -1.305 0.001\n+ 0.921 -0.631 -0.000\n+ 0.930 0.633 -0.002\n+ -0.244 1.311 0.003\n+ -1.387 -0.009 -0.001\n+A1AA21AA2\n+ -1.325 -0.708 -0.290\n+ -1.325 0.708 0.290\n+ 0.000 0.000 0.000\n+ 1.325 0.290 -0.708\n+ 1.325 -0.290 0.708\n+A1AA=AA1\n+ -1.305 0.000 -0.163\n+ -0.372 1.197 0.136\n+ 1.025 0.652 -0.055\n+ 1.024 -0.653 -0.055\n+ -0.372 -1.197 0.136\n+A1A=AAA1\n+ -0.028 1.145 0.002\n+ 1.132 0.340 -0.001\n+ 0.653 -0.934 -0.001\n+ -0.688 -0.851 0.002\n+ -1.068 0.298 -0.002\n+A1AAA=A1\n+ 0.590 -1.000 -0.001\n+ 1.227 0.192 0.001\n+ 0.124 1.233 -0.001\n+ -1.148 0.410 0.000\n+ -0.792 -0.834 0.000\n+A1AAAAA1\n+ 0.703 1.247 -0.255\n+ 1.446 -0.001 0.233\n+ 0.702 -1.248 -0.255\n+ -0.743 -1.199 0.247\n+ -1.367 0.000 -0.216\n+ -0.742 1.199 0.247\n+a1aaaaa1\n+ 1.200 -0.692 0.003\n+ -0.000 -1.381 -0.002\n+ -1.200 -0.691 -0.000\n+ -1.207 0.688 0.001\n+ 0.000 1.389 -0.000\n+ 1.207 0.687 -0.002\n+A1AA=A1\n+ 0.294 0.987 0.001\n+ 1.011 -0.311 -0.001\n+ -0.312 -0.951 0.002\n+ -0.992 0.275 -0.002\n+A1AAAA1\n+ -0.783 -1.009 -0.200\n+ 0.734 -1.068 0.074\n+ 1.238 0.386 0.074\n+ 0.009 1.278 -0.200\n+ -1.198 0.413 0.251\n+a1aaaa1\n+ -0.188 -1.354 -0.002\n+ 1.002 -0.639 0.003\n+ 0.908 0.730 -0.002\n+ -0.322 1.311 0.000\n+ -1.401 -0.046 0.000\n+A1AAA1\n+ 0.334 1.006 -0.173\n+ -1.007 0.333 0.173\n+ -0.333 -1.005 -0.173\n+ 1.006 -0.334 0.173\n+A1AA1\n+ -0.029 0.883 0.000\n+ 0.779 -0.417 0.000\n+ -0.751 -0.466 0.000\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/gaff.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/gaff.dat Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,5169 @@\n+AMBER General Force Field for organic mol., add. info. at the end (June, 2003)\n+c 12.01 0.616 Sp2 C carbonyl group \n+c1 12.01 0.360 Sp C\n+c2 12.01 0.360 Sp2 C \n+c3 12.01 0.878 Sp3 C\n+ca 12.01 0.360 Sp2 C in pure aromatic systems\n+cp 12.01 0.360 Head Sp2 C that connect two rings in biphenyl sys. \n+cq 12.01 0.360 Head Sp2 C that connect two rings in biphenyl sys. identical to cp \n+cc 12.01 0.360 Sp2 carbons in non-pure aromatic systems\n+cd 12.01 0.360 Sp2 carbons in non-pure aromatic systems, identical to cc\n+ce 12.01 0.360 Inner Sp2 carbons in conjugated systems\n+cf 12.01 0.360 Inner Sp2 carbons in conjugated systems, identical to ce\n+cg 12.01 0.360 Inner Sp carbons in conjugated systems\n+ch 12.01 0.360 Inner Sp carbons in conjugated systems, identical to cg\n+cx 12.01 0.360 Sp3 carbons in triangle systems\n+cy 12.01 0.360 Sp3 carbons in square systems\n+cu 12.01 0.360 Sp2 carbons in triangle systems\n+cv 12.01 0.360 Sp2 carbons in square systems\n+h1 1.008 0.135 H bonded to aliphatic carbon with 1 electrwd. group \n+h2 1.008 0.135 H bonded to aliphatic carbon with 2 electrwd. group \n+h3 1.008 0.135 H bonded to aliphatic carbon with 3 electrwd. group \n+h4 1.008 0.135 H bonded to non-sp3 carbon with 1 electrwd. group \n+h5 1.008 0.135 H bonded to non-sp3 carbon with 2 electrwd. group \n+ha 1.008 0.135 H bonded to aromatic carbon \n+hc 1.008 0.135 H bonded to aliphatic carbon without electrwd. group \n+hn 1.008 0.161 H bonded to nitrogen atoms\n+ho 1.008 0.135 Hydroxyl group\n+hp 1.008 0.135 H bonded to phosphate \n+hs 1.008 0.135 Hydrogen bonded to sulphur \n+hw 1.008 0.135 Hydrogen in water \n+hx 1.008 0.135 H bonded to C next to positively charged group \n+f 19.00 0.320 Fluorine\n+cl 35.45 1.910 Chlorine \n+br 79.90 2.880 Bromine \n+i 126.9 4.690 Iodine \n+n 14.01 0.530 Sp2 nitrogen in amide groups\n+n1 14.01 0.530 Sp N \n+n2 14.01 0.530 aliphatic Sp2 N with two connected atoms \n+n3 14.01 0.530 Sp3 N with three connected atoms\n+n4 14.01 0.530 Sp3 N with four connected atoms \n+na 14.01 0.530 Sp2 N with three connected atoms \n+nb 14.01 0.530 Sp2 N in pure aromatic systems \n+nc 14.01 0.530 Sp2 N in non-pure aromatic systems\n+nd 14.01 0.530 Sp2 N in non-pure aromatic systems, identical to nc\n+ne 14.01 0.530 Inner Sp2 N in conjugated systems\n+nf 14.01 0.530 Inner Sp2 N in conjugated systems, identical to ne\n+nh 14.01 0.530 Amine N connected one or more aromatic rings \n+no 14.01 0.530 Nitro N \n+o 16.00 0.434 Oxygen with one connected atom\n+oh 16.00 0.465 Oxygen in hydroxyl group\n+os 16.00 0.465 Ether and ester oxygen\n+ow 16.00 0.465 Oxygen in water \n+p2 30.97 1.538 Phosphate with two connected atoms \n+p3 30.97 1.538 Phosphate with three connected atoms, such as PH3\n+p4 30.97 1.538 Phosphate with three connected atoms, such as O=P(CH3)2\n+p5 30.97 1.53'..b"a et al JCC,8,(1992),963\n+ o 1.6612 0.2100 OPLS\n+ oh 1.7210 0.2104 OPLS \n+ os 1.6837 0.1700 OPLS ether\n+ ow 1.7683 0.1520 TIP3P water model\n+ c 1.9080 0.0860 OPLS\n+ c1 1.9080 0.0860 cp C \n+ c2 1.9080 0.0860 sp2 atom in the middle of C=CD-CD=C\n+ c3 1.9080 0.1094 OPLS\n+ ca 1.9080 0.0860 OPLS\n+ cc 1.9080 0.0860 OPLS\n+ cd 1.9080 0.0860 OPLS\n+ ce 1.9080 0.0860 OPLS\n+ cf 1.9080 0.0860 OPLS\n+ cg 1.9080 0.0860 OPLS\n+ ch 1.9080 0.0860 OPLS\n+ cp 1.9080 0.0860 OPLS\n+ cq 1.9080 0.0860 OPLS\n+ cu 1.9080 0.0860 OPLS\n+ cv 1.9080 0.0860 OPLS\n+ cx 1.9080 0.0860 OPLS\n+ cy 1.9080 0.0860 OPLS\n+ n 1.8240 0.1700 OPLS\n+ n1 1.8240 0.1700 OPLS\n+ n2 1.8240 0.1700 OPLS\n+ n3 1.8240 0.1700 OPLS\n+ n4 1.8240 0.1700 OPLS\n+ na 1.8240 0.1700 OPLS\n+ nb 1.8240 0.1700 OPLS\n+ nc 1.8240 0.1700 OPLS\n+ nd 1.8240 0.1700 OPLS\n+ ne 1.8240 0.1700 OPLS\n+ nf 1.8240 0.1700 OPLS\n+ nh 1.8240 0.1700 OPLS\n+ no 1.8240 0.1700 OPLS\n+ s 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's\n+ s2 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's\n+ s4 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's\n+ s6 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's\n+ sx 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's\n+ sy 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's\n+ sh 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's\n+ ss 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's\n+ p2 2.1000 0.2000 JCC,7,(1986),230; \n+ p3 2.1000 0.2000 JCC,7,(1986),230; \n+ p4 2.1000 0.2000 JCC,7,(1986),230; \n+ p5 2.1000 0.2000 JCC,7,(1986),230; \n+ pb 2.1000 0.2000 JCC,7,(1986),230; \n+ px 2.1000 0.2000 JCC,7,(1986),230; \n+ py 2.1000 0.2000 JCC,7,(1986),230; \n+ f 1.75 0.061 Gough et al. JCC 13,(1992),963.\n+ cl 1.948 0.265 Fox, JPCB,102,8070,(98),flex.mdl CHCl3\n+ br 2.22 0.320 Junmei\n+ i 2.35 0.40 JCC,7,(1986),230; \n+\n+END\n+\n+\n+\n+----------------------------------------------------------------------------\n+\t\tMiscellaneous \n+\t!!!! gaff is still in development, for some molecules, the current version \n+\tmay have some problems. Please find the latest parameter file from \n+\twww.amber.ucsf.edu/antechamber.html\n+\n+(1)\tParameters for p4 are not enough\n+(2) For bond lengty, bond angle and torsional angle parameters, hc and ha \n+ are the generic names of aliphatic and aromatic hydrogen connected \n+ to carbon, respectively.\n+(3) \tDefination priority of nitrogen: n>n3, n>n4, n>nh, n2>n, no>n, na>n\n+ n4>nh\n+(5) Although the four atom types are same, maybe there are several different\n+ parameters correspond to different bond types. You may need to use \n+ additional atom types to apply them correctly (with antechamber package,\n+ you can easily do this). \n+(4) \tPolarizabilities: mg2+ 0.120, f- 0.9743\n+----------------------------------------------------------------------------\n"

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/gaff.prm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/gaff.prm Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,222 @@\n+//\n+// Copyright (C) 2009 by Frank Peters <e.a.j.f.peters@tue.nl>\n+// \n+// This is a SMARTS template-file for GAFF-atom types\n+//\n+// It is attempted to obey the typing given in the "ATOMTYPE_GFF.DEF"\n+// file included with the antechamber package of amber10.\n+// There is no 1-to-1 correspondence between the ATD format and SMARTS.\n+// Therefore the current definitions need to be tested and possibly changed\n+//\n+//\n+//\n+// GAFF atomtypes defined using SMARTS \n+// [SMARTS] [atomtype id number] [description]\n+// must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE!\n+//\n+// Be careful lines do not exceed the maximum length of 80!\n+\n+atom [*] X\n+atom [#1X1] ha "other hydrogen e.g. on aromatic C"\n+atom [#1X1][CX4] hc "hydrogen on aliphatic C"\n+// "hydrogen on aliphatic C with 1 ewd"\n+atom [#1X1][CX4][#7,#8,#16,#17,#35,#53] h1 \n+// "hydrogen on aliphatic C with 2 ewd"\n+atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53] h2 \n+// "hydrogen on aliphatic C with 3 ewd"\n+atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#7,#8] h3\n+atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#16,#17] h3\n+atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#35,#53] h3\n+// "hydrogen on sp2 C with 1 ewd"\n+atom [#1X1][#6X3][#7,#8,#16,#17,#35,#53] h4 \n+// "hydrogen on sp2 C with 2 ewd"\n+atom [#1X1][#6X3]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53] h5 \n+atom [#1X1][#6](N)(N)(N)N hx ""\n+atom [#1X1]O ho "hydrogen on oxygen"\n+atom [#1X1][Oh1] hw "hydrogen on water"\n+atom [#1X1]N hn "nitrogen"\n+atom [#1X1]S hs "sulphur"\n+atom [#1X1]P hp "phosphor"\n+atom [#6X4] c3 "other sp3 C"\n+atom [#6X4r3] cx "3-membered ring atom"\n+atom [#6X4r4] cy "4-membered ring atom"\n+atom [#6X3] c2 "other sp2 C"\n+atom [#6X3]=[O,S] c "C=O or C=S"\n+atom [#6X3](N)(N)N cz ""\n+atom [#6X3;R](=*)-*=* cc "inner sp2 C of conjugated ring systems"\n+atom [#6X3;R](=*)-*#* cc "inner sp2 C of conjugated ring systems"\n+atom [#6X3;R](#*)-*#* cc "inner sp2 C of conjugated ring systems"\n+atom [#6X3;!R](=*)-*=* ce "inner sp2 C of conjugated ring systems"\n+atom [#6X3;!R](#*)-*=* ce "inner sp2 C of conjugated ring systems"\n+atom [#6X3;!R](#*)-*#* ce "inner sp2 C of conjugated ring systems"\n+atom [cr6](c)(c)c cp "bridge aromatic c in byphenyl system"\n+atom [#6X3r3] cu "sp2 carbon in a 3-membered ring"\n+atom [#6X3r4] cv "sp2 carbon in a 4-membered ring"\n+atom [c] ca "pure aromatic atom"\n+atom [#6X2] c1 "other sp C"\n+atom [#6X2](=*)-*=* cg "sp C of conjugated system"\n+atom [#6X2](#*)-*=* cg "sp C of conjugated system"\n+atom [#6X2](#*)-*#* cg "sp C of conjugated system"\n+atom [#6X1] c1 "other sp C"\n+\n+atom [F]* f (-*) "general fluorine"\n+atom [Cl]* cl (-*) "general chlorine"\n+atom [Br]* br (-*) "general bromine"\n+atom [I]* i (-*) "general iodine"\n+\n+atom [#15X1] p2 "other sp2 P"\n+atom [#15X2] p2 "other sp2 P"\n+atom [#15X2;R](=*)-*=* pc "inner sp2 P of conjugated ring systems"\n+atom [#15X2;R](=*)-*#* pc "inner sp2 P of conjugated ring systems"\n+atom [#15X2;R](#*)-*#* pc "inner sp2 P of conjugated ring systems"\n+atom [#15X2;!R](=*)-*=* pe "inner sp2 P of conjugated chain system"\n+atom [#15X2;!R](=*)-*#* pe "inner sp2 P of conjugated chain system"\n+atom [#15X2;!R](#*)-*#* pe "inner sp2 P of conjugated chain system"\n+atom [#15;a] pb "aromatic P"\n+atom [#15X3] p3 "other sp3 P"\n+atom [#15X3](=*)-*=* px "sp2 P of conjugated system"\n+atom [#15X3](=*)-*#* px "sp2 P of conjugated system"\n+atom [#15X3]=[O,S] p4 "hype'..b' "sp2 O"\n+atom [OX2] os "sp3 O in esters and ethers"\n+atom [OX3] os "sp3 O in esters and ethers"\n+atom [OX2H] oh "sp3 O in hydroxyl group"\n+atom [OX3H] oh "sp3 O in hydroxyl group"\n+\n+atom [SX1] s ""\n+atom [SX2] ss "sp3 sulphur"\n+atom [SX2]=* s2 "sp2 sulphur"\n+atom [SX2]#* s2 "sp2 sulphur"\n+atom [SX2H] sh "sp3 S in thiol"\n+atom [SX3] s4 "hypervalent S"\n+atom [SX3](=*)-*=* sx "conjugated S"\n+atom [SX3](=*)-*#* sx "conjugated S"\n+atom [SX4] s6 "hypervalent S"\n+atom [SX4](=*)-*=* sy "conjugated S"\n+atom [SX4](=*)-*#* sy "conjugated S"\n+atom [SX5] s6 "hypervalent S"\n+atom [SX6] s6 "hypervalent S"\n+\n+atom [He] He ""\n+atom [Li] Li ""\n+atom [Be] Be ""\n+atom [B] B ""\n+atom [Ne] Ne ""\n+atom [Na] Na ""\n+atom [Mg] Mg ""\n+atom [Al] Al ""\n+atom [Si] Si ""\n+atom [Ar] Ar ""\n+atom [K] K ""\n+atom [Ca] Ca ""\n+atom [Sc] Sc ""\n+atom [Ti] Ti ""\n+atom [V] V ""\n+atom [Cr] Cr ""\n+atom [Mn] Mn ""\n+atom [Fe] Fe ""\n+atom [Co] Co ""\n+atom [Ni] Ni ""\n+atom [Cu] Cu ""\n+atom [Zn] Zn ""\n+atom [Ga] Ga ""\n+atom [Ge] Ge ""\n+atom [As] As ""\n+atom [Se] Se ""\n+atom [Kr] Kr ""\n+atom [Rb] Rb ""\n+atom [Sr] Sr ""\n+atom [Y] Y ""\n+atom [Zr] Zr ""\n+atom [Nb] Nb ""\n+atom [Mo] Mo ""\n+atom [Tc] Tc ""\n+atom [Ru] Ru ""\n+atom [Rh] Rh ""\n+atom [Pd] Pd ""\n+atom [Ag] Ag ""\n+atom [Cd] Cd ""\n+atom [In] In ""\n+atom [Sn] Sn ""\n+atom [Sb] Sb ""\n+atom [Te] Te ""\n+atom [Xe] Xe ""\n+atom [Cs] Cs ""\n+atom [Ba] Ba ""\n+atom [La] La ""\n+atom [Ce] Ce ""\n+atom [Pr] Pr ""\n+atom [Nd] Nd ""\n+atom [Pm] Pm ""\n+atom [Sm] Sm ""\n+atom [Eu] Eu ""\n+atom [Gd] Gd ""\n+atom [Tb] Tb ""\n+atom [Dy] Dy ""\n+atom [Ho] Ho ""\n+atom [Er] Er ""\n+atom [Tm] Tm ""\n+atom [Yb] Yb ""\n+atom [Lu] Lu ""\n+atom [Hf] Hf ""\n+atom [Ta] Ta ""\n+atom [W] W ""\n+atom [Re] Re ""\n+atom [Os] Os ""\n+atom [Ir] Ir ""\n+atom [Pt] Pt ""\n+atom [Au] Au ""\n+atom [Hg] Hg ""\n+atom [Tl] Tl ""\n+atom [Pb] Pb ""\n+atom [Bi] Bi ""\n+atom [Po] Po ""\n+atom [At] At ""\n+atom [Rn] Rn ""\n+atom [Fr] Fr ""\n+atom [Ra] Ra ""\n+atom [Ac] Ac ""\n+atom [Th] Th ""\n+atom [Pa] Pa ""\n+atom [U] U ""\n+atom [Np] Np ""\n+atom [Pu] Pu ""\n+atom [Am] Am ""\n+atom [Cm] Cm ""\n+atom [Bk] Bk ""\n+atom [Cf] Cf ""\n+atom [Es] Es ""\n+atom [Fm] Fm ""\n+atom [Md] Md ""\n+atom [No] No ""\n+atom [Lr] Lr ""\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/genheaders.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/genheaders.sh Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/ghemical.prm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/ghemical.prm Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,476 @@\n+//\n+// The parameters int his file are taken from ghemical.\n+//\n+\n+// atomtypes and typerules 09.05.2000 (based on Tripos 5.2 and MMFF94)\n+// [SMARTS] [atomtype id number] [typerule] [description]\n+//\n+// must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE!!!\n+\n+atom [*] FFFF\n+atom [#1] 0100 (-*) "general hydrogen"\n+atom [#6] 0600 (-*) "general sp3 carbon"\n+atom [#6]=* 0601 (=*) "general sp2 carbon"\n+atom [#6]#* 0602 (#*) "general sp carbon"\n+atom [#6](=*)=* 0602 (=*,=*) "allenic sp carbon"\n+atom [c] 0603 (~*,~*) "aromatic sp2 carbon"\n+//atom [#6^3r3] 0604 ([-*?*-]) "sp3 carbon in a 3-membered ring"\n+//atom [#6^3r4] 0605 ([-*?*?*-]) "sp3 carbon in a 4-membered ring"\n+atom [N] 0700 (-*) "general sp3 nitrogen"\n+atom [N]=* 0701 (=*) "general sp2 nitrogen"\n+atom [N]#* 0702 (#*) "general sp nitrogen"\n+atom [n] 0703 (~*,~*) "aromatic sp2 nitrogen"\n+atom [ND4] 0704 (-*,-*,-*,-*) "ammonium nitrogen"\n+atom [#7][C]=O 0705 (-C(=O)) "amide nitrogen"\n+atom [O] 0800 (-*) "general sp3 oxygen"\n+atom [O]=* 0801 (=*) "general sp2 oxygen"\n+atom [F]* 0900 (-*) "general fluorine"\n+atom [P] 0F00 (-*) "general sp3 phosphorus"\n+atom [S] 1000 (-*) "general sp3 sulphur"\n+atom [S]=* 1001 (=*) "general sp2 sulphur"\n+atom [S]=[#8] 1002 (=O) "sulfoxide sulphur"\n+atom [S](=O)=O 1003 (=O,=O) "sulfone sulphur"\n+atom [Cl]* 1100 (-*) "general chlorine"\n+atom [Br]* 2300 (-*) "general bromine"\n+atom [I]* 3500 (-*) "general iodine"\n+\n+// bond stretching parameters 09.05.2000 (based on Tripos 5.2 and MMFF94)\n+// [id #1] [id #2] [bondtype] [opt] [fc]\n+//\n+// wildcard atomtype is FFFF !!!!!!!!!!!!!!!!!!!!!!!!!!!\n+// wildcard atomtype is FFFF !!!!!!!!!!!!!!!!!!!!!!!!!!!\n+// wildcard atomtype is FFFF !!!!!!!!!!!!!!!!!!!!!!!!!!!\n+//\n+// parameters containing those should be left last since the first matching\n+// one is chosen. that is, choose normal parameters if there is any matching\n+// one, and take wildcarded one only if there is no better choice...\n+//\n+// [opt] = \xc5\n+// [fc] = kcal/(mol * \xc5^2)\n+\n+bond \t0602 0602 T 1.204 1400.0\n+bond \t0602 0602 S 1.380 700.0\n+bond\t2300 0601 S 1.890 500.0\n+bond\t0602 0601 S 1.440 1340.0\n+bond\t0602 0601 D 1.440 1340.0\n+bond\t0601 0601 D 1.335 1340.0\n+bond\t0601 0601 S 1.470 700.0\n+bond\t0602 0600 S 1.458 640.0\n+bond\t0601 0600 S 1.501 639.0\n+bond\t0600 0600 S 1.540 633.6\n+bond\t2300 0603 S 1.850 500.0\n+bond\t0602 0603 S 1.440 1340.0\n+bond\t0601 0603 S 1.510 1340.0\n+bond\t0600 0603 S 1.525 640.0\n+bond\t0603 0603 C 1.395 1400.0\n+bond\t0603 0603 S 1.480 1000.0\n+bond\t0601 1100 S 1.750 520.0\n+bond\t0600 1100 S 1.767 600.0\n+bond\t0603 1100 S 1.750 513.4\n+bond\t0601 2300 S 1.850 520.0\n+bond\t0600 2300 S 1.867 600.0\n+bond\t0603 2300 S 1.850 513.4\n+bond\t0601 0900 S 1.330 1200.0\n+bond\t0600 0900 S 1.360 600.0\n+bond\t0603 0900 S 1.330 500.0\n+bond\t0602 0100 S 1.056 700.0\n+bond\t0601 0100 S 1.089 692.0\n+bond\t0600 0100 S 1.100 662.4\n+bond\t0603 0100 S 1.084 692.0\n+bond\t0600 3500 S 2.050 490.0\t//added 20050225\n+bond\t0601 3500 S 2.050 490.0\t//added 20050225\n+bond\t0602 3500 S 2.050 490.0\t//added 20050225\n+bond\t0603 3500 S 2.050 490.0\n+bond\t0602 0702 T 1.158 1600.0\n+bond\t0602 0701 S 1.330 1300.0\n+bond\t0602 0701 D 1.330 1300.0\n+bond\t0601 0701 D 1.270 1305.9\n+bond\t0601 0701 S 1.444 1300.0\n+bond\t0600 0701 S 1.440 760.2\n+bond\t0603 0701 S 1.346 1305.9\n+bond\t0701 0701 D 1.346 1305.9\n+bond\t0701 0701 S 1.418 1300.0\n+bond\t0601 0700 S 1.330 1300.0\n+bond\t0600 0700 S 1.470 760.0\n+bond\t0603 0700 S 1.410 720.0\n+bond\t0100 0700 S 1.080 692.0\n+bond\t0601 0704 S 1.330 1300.0\n+bond\t0600 0704 S 1.470 760.0\n+bond\t0603 0704 S 1.410 720.0\n+bond\t0601 0705 S 1.345 870.1\n+bond\t0600 0705 S 1.450 677.6\n+bond\t0603 0705 S 1.416 1090.1\n+bond\t0100 0705 S 1.000 700.0\n+bond\t0701 0705 S 1.440 667.6\n+bond\t0705 0705 S 1.450 744.5\n+bond\t0603 0703 C 1.346 1305.9\n+bond\t0703 0703 C 1.330 1400.0\n+bo'..b'0.320 + 3.0\n+torsion\t0601 0601 0600 FFFF ?S? 0.126 - 3.0\n+torsion\t0600 0601 0600 FFFF ?S? 0.126 + 3.0\n+torsion\t0100 0601 0600 FFFF ?S? 0.274 + 3.0\n+torsion\tFFFF 0602 0602 FFFF ?T? 0.000 + 1.0\n+torsion\tFFFF 0602 0602 FFFF ?S? 0.000 + 1.0\n+torsion\tFFFF 0602 0601 FFFF ?S? 0.000 + 1.0\n+torsion\tFFFF 0602 0601 FFFF ?D? 0.000 + 1.0\n+torsion\tFFFF 0601 0601 FFFF ?D? 12.500 - 2.0\n+torsion\tFFFF 0601 0601 FFFF ?S? 1.424 - 2.0\n+torsion\tFFFF 0602 0600 FFFF ?S? 0.000 + 1.0\n+torsion\tFFFF 0601 0600 FFFF ?S? 0.120 - 3.0\n+torsion\tFFFF 0600 0600 FFFF ?S? 0.200 + 3.0\n+torsion\tFFFF 0602 0603 FFFF ?S? 0.000 + 1.0\n+torsion\tFFFF 0601 0603 FFFF ?S? 1.600 - 2.0\n+torsion\tFFFF 0600 0603 FFFF ?S? 0.120 - 3.0\n+torsion\tFFFF 0603 0603 FFFF ?C? 2.000 - 2.0\n+torsion\tFFFF 0603 0603 FFFF ?S? 0.600 - 2.0\n+torsion\tFFFF 0602 0701 FFFF ?S? 0.000 + 1.0\n+torsion\tFFFF 0602 0701 FFFF ?D? 0.000 + 1.0\n+torsion\tFFFF 0601 0701 FFFF ?D? 12.000 - 2.0\n+torsion\tFFFF 0601 0701 FFFF ?S? 12.000 - 2.0\n+torsion\tFFFF 0600 0701 FFFF ?S? 0.400 - 3.0\n+torsion\tFFFF 0603 0701 FFFF ?S? 1.600 - 2.0\n+torsion\tFFFF 0701 0701 FFFF ?D? 1.600 - 2.0\n+torsion\tFFFF 0701 0701 FFFF ?S? 1.600 - 2.0\n+torsion\tFFFF 0601 0700 FFFF ?S? 0.120 - 3.0\n+torsion\tFFFF 0600 0700 FFFF ?S? 0.200 + 3.0\n+torsion\tFFFF 0603 0700 FFFF ?S? 0.120 - 3.0\n+torsion\tFFFF 0700 0700 FFFF ?S? 0.200 + 3.0\n+torsion\tFFFF 0601 0705 FFFF ?S? 6.460 - 2.0\n+torsion\tFFFF 0600 0705 FFFF ?S? 0.200 + 3.0\n+torsion\tFFFF 0603 0705 FFFF ?S? 1.600 - 2.0\n+torsion\tFFFF 0701 0705 FFFF ?S? 1.600 - 2.0\n+torsion\tFFFF 0700 0705 FFFF ?S? 0.120 - 3.0\n+torsion\tFFFF 0705 0705 FFFF ?S? 1.600 - 2.0\n+torsion\tFFFF 0603 0703 FFFF ?C? 1.600 - 2.0\n+torsion\tFFFF 0601 0800 FFFF ?S? 5.800 - 2.0\n+torsion\tFFFF 0600 0800 FFFF ?S? 1.200 + 3.0\n+torsion\tFFFF 0603 0800 FFFF ?S? 1.200 - 2.0\n+torsion\tFFFF 0701 0800 FFFF ?S? 1.000 + 2.0\n+torsion\tFFFF 0700 0800 FFFF ?S? 0.200 + 3.0\n+torsion\tFFFF 0601 0F00 FFFF ?S? 1.000 - 2.0\n+torsion\tFFFF 0600 0F00 FFFF ?S? 0.400 + 3.0\n+torsion\tFFFF 0603 0F00 FFFF ?S? 1.000 + 3.0\n+torsion\tFFFF 0800 0F00 FFFF ?S? 0.400 + 3.0\n+torsion\tFFFF 0601 1001 FFFF ?D? 1.000 - 2.0\n+torsion\tFFFF 0600 1001 FFFF ?S? 0.400 + 3.0\n+torsion\tFFFF 0603 1001 FFFF ?S? 1.000 + 3.0\n+torsion\tFFFF 0700 1001 FFFF ?S? 0.400 + 3.0\n+torsion\tFFFF 0601 1000 FFFF ?S? 1.000 - 2.0\n+torsion\tFFFF 0600 1000 FFFF ?S? 0.400 + 3.0\n+torsion\tFFFF 0603 1000 FFFF ?S? 1.000 + 3.0\n+torsion\tFFFF 1000 1000 FFFF ?S? 4.000 + 3.0\n+\n+// lenjon-parameters 09.05.2000 (based on Tripos 5.2 and MMFF94)\n+// [id] [r] [k]\n+//\n+// [r] = \xc5\n+// [k] = kcal/mol\n+\n+vdw\t0100 1.50 0.042\n+vdw\t0600 1.70 0.107\n+vdw\t0601 1.70 0.107\n+vdw\t0602 1.70 0.107\n+vdw\t0603 1.70 0.107\n+vdw\t0604 1.70 0.107\n+vdw\t0605 1.70 0.107\n+vdw\t0700 1.55 0.095\n+vdw\t0701 1.55 0.095\n+vdw\t0702 1.55 0.095\n+vdw\t0703 1.55 0.095\n+vdw\t0704 1.55 0.095\n+vdw\t0705 1.55 0.095\n+vdw\t0800 1.52 0.116\n+vdw\t0801 1.52 0.116\n+vdw\t0900 1.47 0.109\n+vdw\t0F00 1.80 0.314\n+vdw\t1000 1.80 0.314\n+vdw\t1001 1.80 0.314\n+vdw\t1002 1.80 0.314\n+vdw\t1003 1.80 0.314\n+vdw\t1100 1.75 0.314\n+vdw\t2300 1.85 0.434\n+vdw\t3500 1.98 0.623\n+vdw\tFFFF 1.50 0.042\n+\n+// atomic charge parameters 09.05.2000 (based on Tripos 5.2 and MMFF94)\n+// [id #1] [id #2] [delta]\n+//\n+// THE NUMERICAL VALUES HERE ARE NOT PROPERLY CHECKED!!!\n+//\n+// sign of [delta] is inverted if order of atoms is switched...\n+// sign of [delta] is inverted if order of atoms is switched...\n+// sign of [delta] is inverted if order of atoms is switched...\n+\n+charge 0601 0100 S +0.100\n+charge 0602 0100 S +0.200\n+charge 0603 0100 S +0.100\n+charge 0604 0100 S +0.050\n+charge 0700 0100 S +0.100\n+charge 0701 0100 S +0.200\n+charge 0702 0100 S +0.250\n+charge 0703 0100 S +0.250\n+charge 0704 0100 S +0.200\n+charge 0705 0100 S +0.150\n+charge 0800 0100 S +0.250\n+charge 0801 0601 D +0.100\n+charge 0900 0100 S +0.500\n+charge 0900 0600 S +0.125\n+charge 1002 0801 D +0.200\n+charge 1003 0801 D +0.200\n+charge 1100 0600 S +0.150\n+charge 2300 0600 S +0.175\n+charge 3500 0600 S +0.200\n+\n+\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/isotope-small.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/isotope-small.txt Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,141 @@\n+##############################################################################\n+# #\n+#\t Open Babel file: isotope-small.txt #\n+# #\n+# Copyright (c) 2002-2003 by Geoffrey R. Hutchison #\n+# Part of the Open Babel package, under the GNU General Public License (GPL)#\n+# #\n+# Small isotope table with most frequently-used isotopes (as default data) #\n+# (GRH currently trimmed up to atomic # 40 and #100+) #\n+# Note that this is only used when data files are not available #\n+# and hence is not as likely to be updated frequently--it is hand-edited! #\n+# #\n+# This file has a series of lines, one for each element #\n+# (i.e. line 0 = neutron, line 1 = hydrogen, line 2 = helium, etc.) #\n+# Each line: Atomic #, 0 then exact mass of most abundant isotope #\n+# then a list of isotopes as int, float pairs corresponding to masses #\n+# #\n+# CAUTION: Masses have been zero-padded to 6 decimal places #\n+# (we don\'t currently have a math package that can deal with sig. fig.) #\n+# so trailing zeros may not be significant and/or useful #\n+# #\n+# Values are compiled from "The 1995 update to the atomic mass evaluation" #\n+# by G.Audi and A.H.Wapstra #\n+# Nuclear Physics A595 vol. 4 p.409-480, December 25, 1995. #\n+# as made available in the mass_rmd.mas95 file #\n+# #\n+# Currently: 110 lines (neutron, H to Mt) #\n+# (note that since element 0 often represents a dummy atom, the default #\n+# mass is 0 amu, *not* the mass of a neutron, accessible as isotope 1) #\n+# #\n+##############################################################################\n+0 0 0.000000 1 1.008664\n+1 0 1.007825 1 1.007825 2 2.014101 3 3.016049\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+11 0 22.989769 19 19.013879 20 20.007348 21 20.99765'..b'47500 236 236.049710 237 237.053890\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+106 0 263.118310 259 259.114650 260 260.114440 261 261.116200 263 263.118310 265 265.121070 266 266.121930\n+107 0 264.124730 261 261.121800 262 262.123010 264 264.124730\n+108 0 265.130000 263 263.128710 264 264.128410 265 265.130000\n+109 0 268.138820 266 266.137940 268 268.138820\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/isotope.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/isotope.h Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,2551 @@\n+/***************************************************************\n+This file is part of the Open Babel project.\n+This is copyright under the GNU General Public License (GPL)\n+For more information, see <http://openbabel.org/>\n+\n+This file contains a binary representation of data tables\n+ used by Open Babel. It is used as a fallback if the textual\n+ data table is not found at runtime. It is not a normal header.\n+***************************************************************/\n+\n+\n+#ifndef OB_ISOTOPE_H\n+#define OB_ISOTOPE_H\n+\n+namespace OpenBabel\n+{\n+static const char IsotopeData[] = {\n+ 0x30,0x20,0x30,0x20,0x30,0x2E,0x30,0x30,0x30,0x30,0x30,0x30,0x20,0x31,0x20,\n+ 0x31,0x2E,0x30,0x30,0x38,0x36,0x36,0x34,0x0A,0x31,0x20,0x30,0x20,0x31,0x2E,\n+ 0x30,0x30,0x37,0x38,0x32,0x35,0x20,0x31,0x20,0x31,0x2E,0x30,0x30,0x37,0x38,\n+ 0x32,0x35,0x20,0x32,0x20,0x32,0x2E,0x30,0x31,0x34,0x31,0x30,0x31,0x20,0x33,\n+ 0x20,0x33,0x2E,0x30,0x31,0x36,0x30,0x34,0x39,0x0A,0x32,0x20,0x30,0x20,0x34,\n+ 0x2E,0x30,0x30,0x32,0x36,0x30,0x33,0x20,0x33,0x20,0x33,0x2E,0x30,0x31,0x36,\n+ 0x30,0x32,0x39,0x20,0x34,0x20,0x34,0x2E,0x30,0x30,0x32,0x36,0x30,0x33,0x20,\n+ 0x35,0x20,0x35,0x2E,0x30,0x31,0x32,0x32,0x32,0x30,0x20,0x36,0x20,0x36,0x2E,\n+ 0x30,0x31,0x38,0x38,0x38,0x38,0x20,0x37,0x20,0x37,0x2E,0x30,0x32,0x38,0x30,\n+ 0x33,0x30,0x20,0x38,0x20,0x38,0x2E,0x30,0x33,0x33,0x39,0x32,0x32,0x20,0x39,\n+ 0x20,0x39,0x2E,0x30,0x34,0x33,0x38,0x32,0x30,0x20,0x31,0x30,0x20,0x31,0x30,\n+ 0x2E,0x30,0x35,0x32,0x34,0x30,0x30,0x0A,0x33,0x20,0x30,0x20,0x37,0x2E,0x30,\n+ 0x31,0x36,0x30,0x30,0x34,0x20,0x35,0x20,0x35,0x2E,0x30,0x31,0x32,0x35,0x34,\n+ 0x30,0x20,0x36,0x20,0x36,0x2E,0x30,0x31,0x35,0x31,0x32,0x32,0x20,0x37,0x20,\n+ 0x37,0x2E,0x30,0x31,0x36,0x30,0x30,0x34,0x20,0x38,0x20,0x38,0x2E,0x30,0x32,\n+ 0x32,0x34,0x38,0x36,0x20,0x39,0x20,0x39,0x2E,0x30,0x32,0x36,0x37,0x38,0x39,\n+ 0x20,0x31,0x30,0x20,0x31,0x30,0x2E,0x30,0x33,0x35,0x34,0x38,0x31,0x20,0x31,\n+ 0x31,0x20,0x31,0x31,0x2E,0x30,0x34,0x33,0x37,0x39,0x36,0x0A,0x34,0x20,0x30,\n+ 0x20,0x39,0x2E,0x30,0x31,0x32,0x31,0x38,0x32,0x20,0x36,0x20,0x36,0x2E,0x30,\n+ 0x31,0x39,0x37,0x32,0x36,0x20,0x37,0x20,0x37,0x2E,0x30,0x31,0x36,0x39,0x32,\n+ 0x39,0x20,0x38,0x20,0x38,0x2E,0x30,0x30,0x35,0x33,0x30,0x35,0x20,0x39,0x20,\n+ 0x39,0x2E,0x30,0x31,0x32,0x31,0x38,0x32,0x20,0x31,0x30,0x20,0x31,0x30,0x2E,\n+ 0x30,0x31,0x33,0x35,0x33,0x33,0x20,0x31,0x31,0x20,0x31,0x31,0x2E,0x30,0x32,\n+ 0x31,0x36,0x35,0x38,0x20,0x31,0x32,0x20,0x31,0x32,0x2E,0x30,0x32,0x36,0x39,\n+ 0x32,0x31,0x20,0x31,0x34,0x20,0x31,0x34,0x2E,0x30,0x34,0x32,0x38,0x32,0x30,\n+ 0x0A,0x35,0x20,0x30,0x20,0x31,0x31,0x2E,0x30,0x30,0x39,0x33,0x30,0x35,0x20,\n+ 0x37,0x20,0x37,0x2E,0x30,0x32,0x39,0x39,0x32,0x30,0x20,0x38,0x20,0x38,0x2E,\n+ 0x30,0x32,0x34,0x36,0x30,0x36,0x20,0x39,0x20,0x39,0x2E,0x30,0x31,0x33,0x33,\n+ 0x32,0x38,0x20,0x31,0x30,0x20,0x31,0x30,0x2E,0x30,0x31,0x32,0x39,0x33,0x37,\n+ 0x20,0x31,0x31,0x20,0x31,0x31,0x2E,0x30,0x30,0x39,0x33,0x30,0x35,0x20,0x31,\n+ 0x32,0x20,0x31,0x32,0x2E,0x30,0x31,0x34,0x33,0x35,0x32,0x20,0x31,0x33,0x20,\n+ 0x31,0x33,0x2E,0x30,0x31,0x37,0x37,0x38,0x30,0x20,0x31,0x34,0x20,0x31,0x34,\n+ 0x2E,0x30,0x32,0x35,0x34,0x30,0x34,0x20,0x31,0x35,0x20,0x31,0x35,0x2E,0x30,\n+ 0x33,0x31,0x30,0x39,0x37,0x20,0x31,0x37,0x20,0x31,0x37,0x2E,0x30,0x34,0x36,\n+ 0x39,0x33,0x30,0x20,0x31,0x39,0x20,0x31,0x39,0x2E,0x30,0x36,0x33,0x37,0x33,\n+ 0x30,0x0A,0x36,0x20,0x30,0x20,0x31,0x32,0x2E,0x30,0x30,0x30,0x30,0x30,0x30,\n+ 0x20,0x38,0x20,0x38,0x2E,0x30,0x33,0x37,0x36,0x37,0x35,0x20,0x39,0x20,0x39,\n+ 0x2E,0x30,0x33,0x31,0x30,0x34,0x30,0x20,0x31,0x30,0x20,0x31,0x30,0x2E,0x30,\n+ 0x31,0x36,0x38,0x35,0x33,0x20,0x31,0x31,0x20,0x31,0x31,0x2E,0x30,0x31,0x31,\n+ 0x34,0x33,0x33,0x20,0x31,0x32,0x20,0x31,0x32,0x2E,0x30,0x30,0x30,0x30,0x30,\n+ 0x30,0x20,0x31,0x33,0x20,0x31,0x33,0x2E,0x30,0x30,0x33,0x33,0x35,0x34,0x20,\n+ 0x31,0x34,0x20,0x31,0x34,0x2E,0x30,0x30,0x33,0x32,0x34,0x31,0x20,0x31,0x35,\n+ 0x20,0x31,0x35,0x2E,0x30,0x31,0x30,0x35,0x39,0x39,0x20,0x31,0x36,0x20,0x31,\n+ 0x36,0x2E,0x30,0x31,0x34,0x37,0x30'..b'0x36,0x32,\n+ 0x2E,0x31,0x30,0x39,0x36,0x39,0x30,0x20,0x32,0x35,0x33,0x20,0x32,0x35,0x33,\n+ 0x2E,0x30,0x39,0x35,0x32,0x36,0x30,0x20,0x32,0x35,0x34,0x20,0x32,0x35,0x34,\n+ 0x2E,0x30,0x39,0x36,0x35,0x39,0x30,0x20,0x32,0x35,0x35,0x20,0x32,0x35,0x35,\n+ 0x2E,0x30,0x39,0x36,0x37,0x37,0x30,0x20,0x32,0x35,0x36,0x20,0x32,0x35,0x36,\n+ 0x2E,0x30,0x39,0x38,0x37,0x36,0x30,0x20,0x32,0x35,0x37,0x20,0x32,0x35,0x37,\n+ 0x2E,0x30,0x39,0x39,0x36,0x31,0x30,0x20,0x32,0x35,0x38,0x20,0x32,0x35,0x38,\n+ 0x2E,0x31,0x30,0x31,0x38,0x38,0x30,0x20,0x32,0x35,0x39,0x20,0x32,0x35,0x39,\n+ 0x2E,0x31,0x30,0x32,0x39,0x39,0x30,0x20,0x32,0x36,0x30,0x20,0x32,0x36,0x30,\n+ 0x2E,0x31,0x30,0x35,0x35,0x37,0x30,0x20,0x32,0x36,0x31,0x20,0x32,0x36,0x31,\n+ 0x2E,0x31,0x30,0x36,0x39,0x34,0x30,0x20,0x32,0x36,0x32,0x20,0x32,0x36,0x32,\n+ 0x2E,0x31,0x30,0x39,0x36,0x39,0x30,0x0A,0x31,0x30,0x34,0x20,0x30,0x20,0x32,\n+ 0x36,0x31,0x2E,0x31,0x30,0x38,0x37,0x35,0x30,0x20,0x32,0x35,0x33,0x20,0x32,\n+ 0x35,0x33,0x2E,0x31,0x30,0x30,0x36,0x38,0x30,0x20,0x32,0x35,0x34,0x20,0x32,\n+ 0x35,0x34,0x2E,0x31,0x30,0x30,0x31,0x37,0x30,0x20,0x32,0x35,0x35,0x20,0x32,\n+ 0x35,0x35,0x2E,0x31,0x30,0x31,0x34,0x39,0x30,0x20,0x32,0x35,0x36,0x20,0x32,\n+ 0x35,0x36,0x2E,0x31,0x30,0x31,0x31,0x38,0x30,0x20,0x32,0x35,0x37,0x20,0x32,\n+ 0x35,0x37,0x2E,0x31,0x30,0x33,0x30,0x37,0x30,0x20,0x32,0x35,0x38,0x20,0x32,\n+ 0x35,0x38,0x2E,0x31,0x30,0x33,0x35,0x37,0x30,0x20,0x32,0x35,0x39,0x20,0x32,\n+ 0x35,0x39,0x2E,0x31,0x30,0x35,0x36,0x33,0x30,0x20,0x32,0x36,0x30,0x20,0x32,\n+ 0x36,0x30,0x2E,0x31,0x30,0x36,0x34,0x33,0x30,0x20,0x32,0x36,0x31,0x20,0x32,\n+ 0x36,0x31,0x2E,0x31,0x30,0x38,0x37,0x35,0x30,0x20,0x32,0x36,0x32,0x20,0x32,\n+ 0x36,0x32,0x2E,0x31,0x30,0x39,0x39,0x32,0x30,0x20,0x32,0x36,0x33,0x20,0x32,\n+ 0x36,0x33,0x2E,0x31,0x31,0x32,0x35,0x34,0x30,0x0A,0x31,0x30,0x35,0x20,0x30,\n+ 0x20,0x32,0x36,0x32,0x2E,0x31,0x31,0x34,0x31,0x35,0x30,0x20,0x32,0x35,0x35,\n+ 0x20,0x32,0x35,0x35,0x2E,0x31,0x30,0x37,0x34,0x30,0x30,0x20,0x32,0x35,0x37,\n+ 0x20,0x32,0x35,0x37,0x2E,0x31,0x30,0x37,0x38,0x36,0x30,0x20,0x32,0x35,0x38,\n+ 0x20,0x32,0x35,0x38,0x2E,0x31,0x30,0x39,0x34,0x34,0x30,0x20,0x32,0x35,0x39,\n+ 0x20,0x32,0x35,0x39,0x2E,0x31,0x30,0x39,0x37,0x32,0x30,0x20,0x32,0x36,0x30,\n+ 0x20,0x32,0x36,0x30,0x2E,0x31,0x31,0x31,0x34,0x33,0x30,0x20,0x32,0x36,0x31,\n+ 0x20,0x32,0x36,0x31,0x2E,0x31,0x31,0x32,0x31,0x31,0x30,0x20,0x32,0x36,0x32,\n+ 0x20,0x32,0x36,0x32,0x2E,0x31,0x31,0x34,0x31,0x35,0x30,0x20,0x32,0x36,0x33,\n+ 0x20,0x32,0x36,0x33,0x2E,0x31,0x31,0x35,0x30,0x38,0x30,0x0A,0x31,0x30,0x36,\n+ 0x20,0x30,0x20,0x32,0x36,0x33,0x2E,0x31,0x31,0x38,0x33,0x31,0x30,0x20,0x32,\n+ 0x35,0x39,0x20,0x32,0x35,0x39,0x2E,0x31,0x31,0x34,0x36,0x35,0x30,0x20,0x32,\n+ 0x36,0x30,0x20,0x32,0x36,0x30,0x2E,0x31,0x31,0x34,0x34,0x34,0x30,0x20,0x32,\n+ 0x36,0x31,0x20,0x32,0x36,0x31,0x2E,0x31,0x31,0x36,0x32,0x30,0x30,0x20,0x32,\n+ 0x36,0x33,0x20,0x32,0x36,0x33,0x2E,0x31,0x31,0x38,0x33,0x31,0x30,0x20,0x32,\n+ 0x36,0x35,0x20,0x32,0x36,0x35,0x2E,0x31,0x32,0x31,0x30,0x37,0x30,0x20,0x32,\n+ 0x36,0x36,0x20,0x32,0x36,0x36,0x2E,0x31,0x32,0x31,0x39,0x33,0x30,0x0A,0x31,\n+ 0x30,0x37,0x20,0x30,0x20,0x32,0x36,0x34,0x2E,0x31,0x32,0x34,0x37,0x33,0x30,\n+ 0x20,0x32,0x36,0x31,0x20,0x32,0x36,0x31,0x2E,0x31,0x32,0x31,0x38,0x30,0x30,\n+ 0x20,0x32,0x36,0x32,0x20,0x32,0x36,0x32,0x2E,0x31,0x32,0x33,0x30,0x31,0x30,\n+ 0x20,0x32,0x36,0x34,0x20,0x32,0x36,0x34,0x2E,0x31,0x32,0x34,0x37,0x33,0x30,\n+ 0x0A,0x31,0x30,0x38,0x20,0x30,0x20,0x32,0x36,0x35,0x2E,0x31,0x33,0x30,0x30,\n+ 0x30,0x30,0x20,0x32,0x36,0x33,0x20,0x32,0x36,0x33,0x2E,0x31,0x32,0x38,0x37,\n+ 0x31,0x30,0x20,0x32,0x36,0x34,0x20,0x32,0x36,0x34,0x2E,0x31,0x32,0x38,0x34,\n+ 0x31,0x30,0x20,0x32,0x36,0x35,0x20,0x32,0x36,0x35,0x2E,0x31,0x33,0x30,0x30,\n+ 0x30,0x30,0x0A,0x31,0x30,0x39,0x20,0x30,0x20,0x32,0x36,0x38,0x2E,0x31,0x33,\n+ 0x38,0x38,0x32,0x30,0x20,0x32,0x36,0x36,0x20,0x32,0x36,0x36,0x2E,0x31,0x33,\n+ 0x37,0x39,0x34,0x30,0x20,0x32,0x36,0x38,0x20,0x32,0x36,0x38,0x2E,0x31,0x33,\n+ 0x38,0x38,0x32,0x30,0x0A,0x00};\n+\n+} // namespace OpenBabel\n+#endif // OB_ISOTOPE_H\n+\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/isotope.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/isotope.txt Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,147 @@\n+##############################################################################\n+# #\n+# Open Babel file: isotope.txt #\n+# #\n+# Copyright (c) 2002-2004 by Geoffrey R. Hutchison #\n+# Part of the Open Babel package, under the GNU General Public License (GPL)#\n+# #\n+# This file has a series of lines, one for each element #\n+# (i.e. line 0 = neutron, line 1 = hydrogen, line 2 = helium, etc.) #\n+# Each line: Atomic #, 0 then exact mass of most abundant isotope #\n+# then a list of isotopes as int, float pairs corresponding to masses #\n+# #\n+# CAUTION: Masses have been zero-padded to 9 decimal places #\n+# (we don\'t currently have a math package that can deal with sig. fig.) #\n+# so trailing zeros may not be significant and/or useful #\n+# #\n+# Values are compiled from: #\n+# "The Ame2003 atomic mass evaluation (II)" #\n+# by G.Audi, A.H.Wapstra and C.Thibault #\n+# Nuclear Physics A729 p. 337-676, December 22, 2003. #\n+# as made available in the mass.mas03round file #\n+# (these are values for publication) #\n+# #\n+# Currently: 110 lines (neutron, H to Mt) #\n+# (note that since element 0 often represents a dummy atom, the default #\n+# mass is 0 amu, *not* the mass of a neutron, accessible as isotope 1) #\n+# #\n+##############################################################################\n+0 0 0.000000000 1 1.008664915\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+9 0 18.998403220 14 14.035060000 15 15.018010000 '..b' 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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+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\n+110 0 281.162061 281 281.162061\n+111 0 280.164473 280 280.164473\n+112 0 285.174105 285 285.174105\n+113 0 284.178080 284 284.178080\n+114 0 289.187279 289 289.187279\n+115 0 288.192492 288 288.192492\n+116 0 292.199786 292 292.199786\n+117 0 292.207550 291 291.206560 292 292.207550\n+118 0 293.214670 293 293.214670\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/logp.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/logp.txt Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mm2.prm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mm2.prm Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,2028 @@\n+\n+ ##############################\n+ ## ##\n+ ## Force Field Definition ##\n+ ## ##\n+ ##############################\n+\n+\n+forcefield MM2-1991\n+\n+bondunit 71.94\n+bond-cubic -2.0\n+bond-quartic 1.25 !! keeps Ebond positive; not in "real" MM2\n+angleunit 0.02191418\n+angle-sextic 0.00000007\n+strbndunit 2.51118\n+mm2-strbnd\n+opbendunit 0.02191418\n+torsionunit 0.5\n+vdwtype BUCKINGHAM\n+radiusrule ARITHMETIC\n+radiustype R-MIN\n+radiussize RADIUS\n+epsilonrule GEOMETRIC\n+a-expterm 290000.0\n+b-expterm 12.5\n+c-expterm 2.25\n+vdw-14-scale 1.0\n+chg-14-scale 1.0\n+dielectric 1.5\n+\n+\n+ #############################\n+ ## ##\n+ ## Literature References ##\n+ ## ##\n+ #############################\n+\n+\n+N. L. Allinger, "Conformational Analysis. 130. MM2. A Hydrocarbon\n+Force Field Utilizing V1 and V2 Torsional Terms", J. Am. Chem. Soc.,\n+99, 8127-8134 (1977)\n+\n+J. T. Sprague, J. C. Tai, Y. Yuh and N. L. Allinger, "The MMP2\n+Calculational Method", J. Comput. Chem., 8, 581-603 (1987)\n+\n+N. L. Allinger, R. A. Kok and M. R. Imam, "Hydrogen Bonding in MM2",\n+J. Comput. Chem., 9, 591-595 (1988)\n+\n+All parameters in this file are from the "MM2 (1991) Parameter Set",\n+as provided by Prof. N. L. Allinger, University of Georgia\n+\n+\n+ #############################\n+ ## ##\n+ ## Atom Type Definitions ##\n+ ## ##\n+ #############################\n+\n+\n+atom 1 C "CSP3 ALKANE" 6 12.000 4\n+atom 2 C "CSP2 ALKENE" 6 12.000 3\n+atom 3 C "CSP2 CARBONYL" 6 12.000 3\n+atom 4 C "CSP ALKYNE, C=C=O" 6 12.000 2\n+atom 5 H "NONPOLAR HYDROGEN" 1 1.008 1\n+atom 6 O "-O- ALCOHOL, ETHER" 8 15.995 4\n+atom 7 O "=O CARBONYL" 8 15.995 1\n+atom 8 N "NSP3" 7 14.003 4\n+atom 9 N "NSP2 AMIDE" 7 14.003 3\n+atom 10 N "NSP" 7 14.003 1\n+atom 11 F "FLUORIDE" 9 18.998 1\n+atom 12 Cl "CHLORIDE" 17 34.969 1\n+atom 13 Br "BROMIDE" 35 78.918 1\n+atom 14 I "IODIDE" 53 126.900 1\n+atom 15 S "-S- SULFIDE" 16 31.972 2\n+atom 16 S+ ">S+ SULFONIUM" 16 31.972 2\n+atom 17 S ">S=O SULFOXIDE" 16 31.972 3\n+atom 18 S ">SO2 SULFONE" 16 31.972 4\n+atom 19 Si "SILANE" 14 27.977 4\n+atom 20 Lp "LONE PAIR" 0 0.000 1\n+atom 21 H "-OH ALCOHOL" 1 1.008 1\n+atom 22 C "CYCLOPROPANE" 6 12.000 4\n+atom 23 H "NH AMINE" 1 1.008 1\n+atom 24 H "COOH CARBOXYL" 1 1.008 1\n+atom 25 P ">P- PHOSPHINE" 15 30.994 3\n+atom 26 B ">B- TRIGONAL" 5 11.009 3\n+atom 27 B ">B< TETRAHEDRAL" 5 11.009 4\n+atom 28 H "-H AMIDE, ENOL" 1 1.008 1\n+atom 29 C* "CARBON RADICAL" 6 12.000 3\n+atom 30 C+ "CARBONIUM ION" 6 12.000 3\n+atom 31 Ge "GERMANIUM" 32 73.922 2\n+atom 32 Sn "TIN" 50 117.902 2\n+atom 33 Pb '..b'.200 0.500\n+dipole 3 7 2.600 0.500\n+dipole 3 9 -0.290 0.500\n+dipole 3 11 1.480 0.500\n+dipole 3 12 1.580 0.500\n+dipole 3 13 1.560 0.500\n+dipole 3 14 1.400 0.500\n+dipole 3 22 0.300 0.500\n+dipole 3 72 0.583 0.500\n+dipole 4 10 3.400 0.500\n+dipole 5 15 0.900 0.500\n+dipole 5 25 0.500 0.500\n+dipole 5 34 0.700 0.500\n+dipole 5 35 0.800 0.500\n+dipole 6 19 -0.400 0.500\n+dipole 6 20 0.900 0.500\n+dipole 6 21 -1.115 0.500\n+dipole 6 24 -0.700 0.500\n+dipole 6 25 0.970 0.500\n+dipole 6 28 -0.700 0.500\n+dipole 7 17 -3.030 0.500\n+dipole 7 18 -2.930 0.500\n+dipole 7 43 -2.600 0.500\n+dipole 7 46 -2.530 0.500\n+dipole 8 20 0.600 0.500\n+dipole 8 23 -0.760 0.500\n+dipole 9 18 0.800 0.500\n+dipole 9 28 -1.310 0.500\n+dipole 20 37 -0.600 0.500\n+dipole 20 41 -0.750 0.500\n+dipole 20 72 -0.600 0.500\n+dipole 22 46 1.700 0.500\n+dipole 23 37 0.600 0.500\n+dipole 23 40 0.550 0.500\n+dipole 23 72 0.600 0.500\n+dipole 28 41 0.700 0.500\n+dipole 37 40 0.300 0.500\n+dipole 70 71 -2.800 0.500\n+\n+\n+ ##############################################\n+ ## ##\n+ ## Bond Dipole Moment Parameters (3-Ring) ##\n+ ## ##\n+ ##############################################\n+\n+\n+dipole3 22 49 0.735 0.500\n+\n+\n+ ###########################################\n+ ## ##\n+ ## Conjugated Pisystem Atom Parameters ##\n+ ## ##\n+ ###########################################\n+\n+\n+piatom 2 1.0 -11.160 11.134\n+piatom 3 1.0 -11.160 11.134\n+piatom 4 1.0 -11.160 11.134\n+piatom 6 2.0 -17.600 19.342\n+piatom 7 1.0 -17.210 14.520\n+piatom 9 2.0 -13.145 17.210\n+piatom 10 1.0 -14.120 12.340\n+piatom 37 1.0 -14.120 12.340\n+piatom 40 2.0 -13.145 17.210\n+piatom 41 2.0 -17.600 19.342\n+piatom 42 2.0 -15.800 11.920\n+piatom 72 1.0 -14.120 12.340\n+\n+\n+ ###########################################\n+ ## ##\n+ ## Conjugated Pisystem Bond Parameters ##\n+ ## ##\n+ ###########################################\n+\n+\n+pibond 2 2 4.600 0.166\n+pibond 2 3 4.600 0.166\n+pibond 2 4 7.790 0.156\n+pibond 2 37 10.880 0.196\n+pibond 2 40 10.880 0.196\n+pibond 2 41 5.440 0.196\n+pibond 2 42 4.861 0.397\n+pibond 2 72 10.880 0.196\n+pibond 3 3 4.600 0.140\n+pibond 3 4 4.600 0.166\n+pibond 3 7 4.600 0.105\n+pibond 3 72 10.880 0.196\n+pibond 4 4 4.600 0.238\n+pibond 37 37 10.500 0.170\n+pibond 37 40 10.880 0.196\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmff94.ff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmff94.ff Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmff94s.ff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmff94s.ff Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmffang.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffang.par Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,2354 @@\n+*\n+* Copyright (c) Merck and Co., Inc., 1994\n+* All Rights Reserved\n+*\n+* MMFF ANGLE PARAMETERS- Rev: 26-Oct-94 Source: MMFF94\n+* C94 = CORE MMFF94 parameter - obtained from ab initio data\n+* X94 = EXTD MMFF94 parameter - fit to additional ab initio data\n+* E94 = theta0 from fit to X-ray data, ka from empirical rule\n+* #E94 = theta0 and ka both from empirical rules\n+*\n+* types ka theta0 Comment/origin\n+0 0 1 0 0.000 108.900 0:*-1-* MMFF94 DEF\n+0 1 1 1 0.851 109.608 C94\n+0 1 1 2 0.736 109.445 C94\n+0 1 1 3 0.777 107.517 C94\n+0 1 1 4 1.006 110.265 E94\n+0 1 1 5 0.636 110.549 C94\n+0 1 1 6 0.992 108.133 C94\n+0 1 1 8 0.777 108.290 C94\n+0 1 1 9 1.136 108.194 E94\n+0 1 1 10 1.050 109.960 C94\n+0 1 1 11 1.225 108.313 C94\n+0 1 1 12 1.056 108.679 C94\n+0 1 1 13 1.078 106.820 E94\n+0 1 1 14 0.980 109.945 E94\n+0 1 1 15 0.743 107.397 C94\n+0 1 1 17 1.089 108.578 E94\n+0 1 1 18 1.093 109.315 E94\n+0 1 1 19 0.755 115.436 E94\n+0 1 1 20 1.021 108.659 E94\n+0 1 1 22 1.001 110.125 E94\n+0 1 1 25 0.803 112.356 X94\n+0 1 1 26 0.833 109.879 E94\n+0 1 1 34 1.179 106.493 C94\n+0 1 1 37 0.756 108.617 C94\n+0 1 1 39 0.927 109.170 C94\n+0 1 1 40 1.130 108.678 E94\n+0 1 1 41 0.330 98.422 C94\n+0 1 1 43 1.135 108.019 E94\n+0 1 1 45 1.197 105.028 E94\n+0 1 1 54 1.173 106.424 E94\n+0 1 1 55 1.150 107.604 E94\n+0 1 1 56 1.199 110.371 C94\n+0 1 1 57 1.012 109.900 E94\n+0 1 1 58 1.179 106.327 E94\n+0 1 1 61 1.125 109.311 E94\n+0 1 1 63 1.006 110.058 E94\n+0 1 1 64 0.988 111.064 E94\n+0 1 1 67 1.216 104.557 E94\n+0 1 1 68 1.018 107.195 C94\n+0 1 1 73 1.160 104.658 E94\n+0 1 1 78 1.012 109.850 E94\n+0 1 1 80 0.947 113.327 E94\n+0 1 1 81 1.108 109.837 E94\n+0 2 1 2 1.113 111.453 C94\n+0 2 1 3 0.667 104.829 C94\n+0 2 1 4 1.022 109.873 E94\n+0 2 1 5 0.632 110.292 C94\n+0 2 1 6 1.074 108.699 C94\n+0 2 1 8 0.884 111.553 C94\n+0 2 1 9 1.118 109.577 E94\n+0 2 1 10 1.160 107.963 E94\n+0 2 1 11 1.192 110.419 E94\n+0 2 1 12 1.070 109.410 E94\n+0 2 1 15 1.078 109.560 E94\n+0 2 1 17 1.077 109.434 E94\n+0 2 1 18 1.188 105.110 E94\n+0 2 1 20 1.053 107.448 E94\n+0 2 1 22 0.942 114.020 E94\n+0 2 1 25 0.893 106.815 E94\n+0 2 1 26 1.029 99.065 E94\n+0 2 1 34 1.066 111.817 E94\n+0 2 1 37 0.985 111.446 E94\n+0 2 1 39 1.124 109.513 E94\n+0 2 1 40 1.149 108.270 E94\n+0 2 1 45 1.232 103.978 E94\n+0 2 1 63 0.935 114.692 E94\n+0 2 1 67 1.224 104.687 E94\n+0 3 1 3 0.974 111.746 E94\n+0 3 1 4 1.019 109.850 E94\n+0 3 1 5 0.650 108.385 C94\n+0 3 1 6 0.528 104.112 C94\n+0 3 1 8 1.197 105.837 E94\n+0 3 1 9 1.201 105.535 E94\n+0 3 1 10 0.634 102.655 C94\n+0 3 1 11 1.189 110.328 E94\n+0 3 1 12 1.136 106.064 E94\n+0 3 1 13 1.147 103.645 E94\n+0 3 1 14 1.048 106.404 E94\n+0 3 1 15 1.125 107.192 E94\n+0 3 1 17 1.092 108.602 E94\n+0 3 1 18 1.120 108.119 E94\n+0 3 '..b'09.500 0:*-77-* MMFF94 DEF\n+0 32 77 32 1.652 109.472 X94\n+0 0 78 0 0.000 121.900 0:*-78-* MMFF94 DEF\n+1 0 78 0 0.000 126.100 1:*-78-* MMFF94 DEF\n+0 1 78 78 0.744 130.960 E94\n+0 1 78 81 0.938 121.477 E94\n+1 3 78 78 0.827 125.468 E94\n+1 3 78 81 0.922 123.748 E94\n+0 5 78 76 0.584 123.407 X94\n+0 5 78 78 0.546 128.000 C94\n+0 5 78 79 0.617 122.000 #E94\n+0 5 78 81 0.542 109.881 C94\n+1 9 78 78 0.863 129.501 E94\n+1 9 78 81 0.991 125.857 E94\n+0 37 78 76 0.770 137.282 E94\n+0 37 78 78 0.803 128.249 E94\n+0 37 78 81 0.864 128.714 E94\n+0 38 78 78 0.844 130.617 E94\n+0 38 78 81 1.023 123.532 E94\n+0 39 78 64 0.734 138.714 E94\n+0 39 78 78 1.202 109.426 E94\n+0 40 78 76 0.930 130.150 E94\n+0 40 78 78 0.778 135.746 E94\n+0 40 78 81 1.058 121.251 E94\n+0 44 78 63 0.677 141.902 E94\n+0 44 78 64 0.663 142.589 E94\n+0 44 78 66 0.816 134.701 E94\n+0 44 78 78 1.089 111.702 E94\n+0 45 78 76 1.199 114.467 E94\n+0 45 78 78 0.915 125.050 E94\n+0 45 78 81 1.216 112.926 E94\n+0 59 78 64 0.963 128.471 E94\n+0 59 78 65 1.097 128.375 E94\n+0 59 78 78 1.443 105.916 E94\n+0 63 78 64 0.942 117.779 E94\n+0 64 78 65 0.835 131.530 E94\n+0 64 78 78 1.038 111.834 E94\n+0 66 78 78 1.030 118.376 E94\n+0 76 78 76 1.245 113.179 X94\n+0 76 78 78 1.159 111.900 E94\n+0 78 78 78 1.336 99.459 E94\n+0 78 78 81 1.302 105.130 C94\n+0 79 78 81 1.217 114.792 E94\n+0 0 79 0 0.000 103.400 0:*-79-* MMFF94 DEF\n+0 78 79 81 1.569 102.043 E94\n+0 79 79 81 1.625 104.857 E94\n+0 0 80 0 0.000 121.900 0:*-80-* MMFF94 DEF\n+1 0 80 0 0.000 128.200 1:*-80-* MMFF94 DEF\n+0 1 80 81 0.864 127.147 E94\n+1 3 80 81 0.886 128.181 E94\n+0 5 80 81 0.651 125.682 C94\n+0 18 80 81 1.032 120.869 E94\n+0 41 80 81 0.909 125.057 E94\n+0 44 80 55 0.918 127.755 E94\n+0 44 80 81 1.184 112.411 E94\n+0 55 80 59 1.254 120.263 E94\n+0 55 80 81 0.991 127.612 E94\n+0 56 80 81 1.003 126.038 E94\n+0 59 80 81 1.439 112.030 E94\n+0 81 80 81 1.205 108.609 C94\n+0 0 81 0 0.000 119.500 0:*-81-* MMFF94 DEF\n+0 1 81 63 0.996 120.129 E94\n+0 1 81 64 0.978 119.970 E94\n+0 1 81 78 0.879 126.535 E94\n+0 1 81 79 1.144 116.113 E94\n+0 1 81 80 0.895 126.324 E94\n+1 2 81 78 0.927 125.080 E94\n+1 2 81 80 0.895 128.399 E94\n+1 9 81 78 1.015 124.270 E94\n+1 9 81 80 1.106 120.028 E94\n+0 36 81 64 0.522 130.295 E94\n+0 36 81 66 0.583 128.738 E94\n+0 36 81 78 0.578 124.658 C94\n+0 36 81 80 0.575 124.787 C94\n+0 37 81 64 0.929 122.408 E94\n+1 37 81 64 0.983 119.722 E94\n+0 37 81 65 1.184 114.158 E94\n+1 37 81 65 1.281 110.477 E94\n+1 37 81 78 0.884 126.208 E94\n+1 37 81 80 0.940 123.333 E94\n+0 63 81 64 1.115 114.945 E94\n+0 64 81 65 1.075 122.099 E94\n+0 64 81 80 1.143 113.176 E94\n+0 66 81 80 1.067 122.250 E94\n+0 78 81 80 0.957 110.556 C94\n+0 79 81 80 1.379 107.936 E94\n+0 32 82 59 1.666 114.660 E94\n+0 32 82 64 1.075 131.706 E94\n+0 32 82 65 1.238 129.293 E94\n+0 59 82 64 1.563 105.660 E94\n+0 64 82 65 1.281 112.955 E94\n+$\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmffbndk.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffbndk.par Tue Jun 07 16:43:30 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
+$

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmffbond.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffbond.par Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,507 @@\n+*\n+* Copyright (c) Merck and Co., Inc., 1994\n+* All Rights Reserved\n+*\n+* MMFF BOND PARAMETERS- Rev: 26-OCT-94 Source: MMFF94\n+* C94 = CORE MMFF94 parameter - obtained from ab initio data\n+* X94 = EXTD MMFF94 parameter - fit to additional ab initio data\n+* E94 = r0 from fit to X-ray data, kb from empirical rule\n+* #C94 = r0 lies between C94 and E94 values, kb from empirical rule\n+* #X94 = r0 lies between X94 and E94 values, kb from empirical rule\n+* #E94 = r0 and k both from empirical rules\n+*\n+* types kb r0 Source\n+0 1 1 4.258 1.508 C94\n+0 1 2 4.539 1.482 C94\n+0 1 3 4.190 1.492 C94\n+0 1 4 4.707 1.459 X94\n+0 1 5 4.766 1.093 C94\n+0 1 6 5.047 1.418 C94\n+0 1 8 5.084 1.451 C94\n+0 1 9 4.763 1.458 C94\n+0 1 10 4.664 1.436 C94\n+0 1 11 6.011 1.360 #C94\n+0 1 12 2.974 1.773 C94\n+0 1 13 2.529 1.949 E94\n+0 1 14 1.706 2.090 E94\n+0 1 15 2.893 1.805 C94\n+0 1 17 2.841 1.813 X94\n+0 1 18 3.258 1.772 X94\n+0 1 19 2.866 1.830 #X94\n+0 1 20 4.650 1.504 C94\n+0 1 22 4.286 1.482 E94\n+0 1 25 2.980 1.810 #X94\n+0 1 26 2.790 1.830 #X94\n+0 1 34 3.844 1.480 #C94\n+0 1 35 7.915 1.307 X94\n+0 1 37 4.957 1.486 C94\n+0 1 39 6.114 1.445 C94\n+0 1 40 4.922 1.446 C94\n+0 1 41 3.830 1.510 #C94\n+0 1 43 3.971 1.472 X94\n+0 1 45 3.844 1.480 X94\n+0 1 46 3.813 1.482 X94\n+0 1 54 4.267 1.461 C94\n+0 1 55 4.646 1.454 C94\n+0 1 56 4.166 1.453 C94\n+0 1 57 4.669 1.461 E94\n+0 1 58 4.329 1.451 E94\n+0 1 61 4.845 1.424 X94\n+0 1 62 4.456 1.444 X94\n+0 1 63 4.481 1.471 E94\n+0 1 64 4.518 1.469 E94\n+0 1 67 4.188 1.459 E94\n+0 1 68 4.217 1.479 C94\n+0 1 72 2.956 1.801 X94\n+0 1 73 2.608 1.839 X94\n+0 1 75 2.547 1.858 E94\n+0 1 78 4.593 1.465 E94\n+0 1 80 4.373 1.477 E94\n+0 1 81 4.512 1.441 E94\n+0 2 2 9.505 1.333 C94\n+1 2 2 5.310 1.430 #C94\n+1 2 3 4.565 1.468 C94\n+0 2 4 9.538 1.297 E94\n+1 2 4 5.657 1.415 E94\n+0 2 5 5.170 1.083 C94\n+0 2 6 5.520 1.373 C94\n+1 2 9 6.385 1.360 E94\n+0 2 10 6.329 1.362 E94\n+0 2 11 6.283 1.350 #X94\n+0 2 12 3.390 1.720 #X94\n+0 2 13 3.413 1.854 E94\n+0 2 14 2.062 2.025 E94\n+0 2 15 3.896 1.720 E94\n+0 2 17 3.247 1.773 E94\n+0 2 18 3.789 1.728 E94\n+0 2 19 3.052 1.811 E94\n+0 2 20 4.593 1.465 E94\n+0 2 22 4.926 1.448 E94\n+0 2 25 3.750 1.742 E94\n+0 2 30 8.166 1.331 E94\n+0 2 34 5.207 1.407 E94\n+0 2 35 10.343 1.250 #X94\n+1 2 37 5.007 1.449 C94\n+1 2 39 6.164 1.368 E94\n+0 2 40 6.110 1.370 #C94\n+0 2 41 3.746 1.505 C94\n+0 2 43 4.928 1.420 E94\n+0 2 45 4.725 1.430 #X94\n+0 2 46 7.466 1.325 E94\n+0 2 55 6.164 1.368 E94\n+0 2 56 6.246 1.365 E94\n+0 2 62 7.105 1.336 X94\n+1 2 63 6.030 1.400 E94\n+1 2 64 5.754 1.411 E94\n+1 2 67 4.685 1.432 E94\n+0 2 72 4.179 1.700 #X94\n+1 2 81 6.357 1.361 E94\n+1 3 3 4.418 1.489 C94\n+1 3 4 5.135 1.438 E94\n+0 3 5 4.650 1.101 C94\n+0 3 6 5.801 1.355 C9'..b'E94\n+0 37 55 6.615 1.352 E94\n+0 37 56 5.055 1.414 E94\n+1 37 57 5.092 1.440 E94\n+0 37 58 7.432 1.326 E94\n+1 37 58 5.055 1.414 E94\n+0 37 61 5.724 1.385 E94\n+0 37 62 7.137 1.335 E94\n+0 37 63 6.095 1.372 C94\n+1 37 63 5.178 1.436 E94\n+0 37 64 6.161 1.379 C94\n+1 37 64 5.265 1.432 E94\n+1 37 67 4.725 1.430 E94\n+0 37 69 5.396 1.352 C94\n+0 37 78 6.719 1.375 E94\n+0 37 81 3.987 1.471 E94\n+1 37 81 4.531 1.440 E94\n+0 38 38 5.002 1.246 C94\n+0 38 63 7.299 1.330 E94\n+0 38 64 6.978 1.340 E94\n+0 38 69 5.036 1.321 E94\n+0 38 78 6.218 1.366 E94\n+0 39 40 4.101 1.367 E94\n+0 39 45 3.524 1.402 E94\n+0 39 63 6.301 1.364 C94\n+1 39 63 6.137 1.369 E94\n+0 39 64 6.357 1.361 E94\n+1 39 64 5.482 1.395 E94\n+0 39 65 5.513 1.339 C94\n+0 39 78 6.137 1.369 E94\n+0 40 40 4.248 1.359 E94\n+0 40 45 4.305 1.356 E94\n+0 40 46 4.727 1.335 E94\n+0 40 54 6.817 1.256 E94\n+0 40 63 6.733 1.348 E94\n+0 40 64 6.644 1.351 E94\n+0 40 78 5.900 1.378 E94\n+0 41 41 5.029 1.443 E94\n+0 41 55 5.577 1.391 E94\n+0 41 62 7.137 1.335 E94\n+0 41 72 4.519 1.678 X94\n+0 41 80 5.222 1.434 E94\n+0 42 61 16.223 1.087 E94\n+0 43 43 4.211 1.361 E94\n+0 43 45 3.710 1.390 E94\n+0 43 64 5.389 1.399 E94\n+0 44 63 3.589 1.717 C94\n+0 44 65 3.374 1.684 C94\n+0 44 78 3.711 1.734 E94\n+0 44 80 3.910 1.719 E94\n+0 45 63 5.119 1.411 E94\n+0 45 64 5.076 1.413 E94\n+0 45 78 5.724 1.385 E94\n+0 47 53 12.192 1.140 #X94\n+0 49 50 6.812 0.991 C94\n+0 51 52 7.100 0.987 X94\n+0 55 57 7.227 1.319 C94\n+0 55 62 3.977 1.374 E94\n+0 55 64 5.529 1.393 E94\n+0 55 80 7.500 1.324 E94\n+0 56 57 4.137 1.383 C94\n+0 56 63 5.900 1.378 E94\n+0 56 80 6.470 1.357 E94\n+1 57 63 5.400 1.426 E94\n+1 57 64 5.135 1.438 E94\n+0 58 63 6.794 1.346 E94\n+0 58 64 6.164 1.368 E94\n+0 59 63 5.787 1.360 C94\n+0 59 65 4.756 1.388 C94\n+0 59 78 6.127 1.364 E94\n+0 59 80 7.064 1.332 E94\n+0 59 82 3.855 1.431 E94\n+0 60 61 15.749 1.170 #X94\n+0 62 63 6.947 1.341 E94\n+0 62 64 6.273 1.364 E94\n+1 63 63 5.729 1.412 E94\n+0 63 64 7.118 1.377 C94\n+0 63 66 8.326 1.313 C94\n+0 63 72 4.503 1.679 E94\n+0 63 78 7.434 1.352 E94\n+0 63 81 7.778 1.316 E94\n+0 64 64 4.313 1.418 C94\n+1 64 64 4.926 1.448 E94\n+0 64 65 8.258 1.335 C94\n+0 64 66 4.456 1.369 C94\n+0 64 78 5.492 1.422 E94\n+0 64 81 5.824 1.381 E94\n+0 64 82 6.794 1.346 E94\n+0 65 66 7.243 1.323 C94\n+0 65 78 8.447 1.298 E94\n+0 65 81 5.223 1.313 E94\n+0 65 82 5.622 1.297 E94\n+0 66 66 3.874 1.368 C94\n+0 66 78 6.385 1.360 E94\n+0 66 81 3.960 1.375 E94\n+0 67 67 6.085 1.280 E94\n+0 71 75 2.852 1.423 X94\n+0 72 73 2.628 2.035 X94\n+0 76 76 4.286 1.357 X94\n+0 76 78 6.824 1.345 X94\n+0 78 78 5.573 1.374 C94\n+0 78 79 8.890 1.287 E94\n+0 78 81 5.046 1.381 C94\n+0 79 79 6.408 1.269 E94\n+0 79 81 4.305 1.356 E94\n+0 80 81 8.237 1.335 C94\n+$\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmffchg.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffchg.par Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,512 @@\n+*\n+* Copyright (c) Merck and Co., Inc., 1994\n+* All Rights Reserved\n+*\n+* MMFF BOND-CHARGE INCREMENTS - Rev: 26-OCT-94 Source: MMFF94\n+* C94 - CORE MMFF94 parameter, obtained from fit to dipole moments\n+* #C94 - CORE MMFF94 parameter, either fixed or adjusted to fit \n+* HF/6-31G* interaction energies\n+* X94 - EXTD MMFF94 parameter, obtained from fit to dipole moments\n+* #X94 - EXTD MMFF94 parameter, fixed in the fit to dipole moments\n+* E94 - derived from partial bond charge increments (empirical rule)\n+*\n+* types bci Source\n+0 1 1 0.0000 #C94\n+0 1 2 -0.1382 C94\n+0 1 3 -0.0610 #C94\n+0 1 4 -0.2000 #X94\n+0 1 5 0.0000 #C94\n+0 1 6 -0.2800 #C94\n+0 1 8 -0.2700 #C94\n+0 1 9 -0.2460 #C94\n+0 1 10 -0.3001 C94\n+0 1 11 -0.3400 #C94\n+0 1 12 -0.2900 #C94\n+0 1 13 -0.2300 #X94\n+0 1 14 -0.1900 #X94\n+0 1 15 -0.2300 #C94\n+0 1 17 -0.1935 X94\n+0 1 18 -0.1052 X94\n+0 1 19 0.0805 X94\n+0 1 20 0.0000 #C94\n+0 1 22 -0.0950 E94\n+0 1 25 0.0000 #X94\n+0 1 26 -0.1669 X94\n+0 1 34 -0.5030 C94\n+0 1 35 -0.4274 X94\n+0 1 37 -0.1435 C94\n+0 1 39 -0.2556 C94\n+0 1 40 -0.3691 C94\n+0 1 41 0.1060 #C94\n+0 1 43 -0.3557 X94\n+0 1 45 -0.2402 X94\n+0 1 46 -0.3332 X94\n+0 1 54 -0.3461 C94\n+0 1 55 -0.4895 C94\n+0 1 56 -0.3276 C94\n+0 1 57 -0.1050 E94\n+0 1 58 -0.4880 E94\n+0 1 61 -0.2657 X94\n+0 1 62 -0.2000 #X94\n+0 1 63 -0.1800 E94\n+0 1 64 -0.1810 E94\n+0 1 67 -0.0990 E94\n+0 1 68 -0.2560 #C94\n+0 1 72 -0.5500 #X94\n+0 1 73 -0.0877 X94\n+0 1 75 -0.2550 E94\n+0 1 78 -0.1680 E94\n+0 1 80 -0.1440 E94\n+0 1 81 -0.5140 E94\n+0 2 2 0.0000 #C94\n+1 2 2 0.0000 #C94\n+1 2 3 -0.0144 C94\n+0 2 4 -0.0650 E94\n+1 2 4 -0.0650 E94\n+0 2 5 0.1500 #C94\n+0 2 6 -0.0767 C94\n+1 2 9 -0.1710 E94\n+0 2 10 -0.1090 E94\n+0 2 11 -0.1495 X94\n+0 2 12 -0.1400 #X94\n+0 2 13 -0.1100 #X94\n+0 2 14 -0.0900 #X94\n+0 2 15 -0.1010 E94\n+0 2 17 -0.0560 E94\n+0 2 18 0.0170 E94\n+0 2 19 0.2290 E94\n+0 2 20 0.1160 E94\n+0 2 22 0.0400 E94\n+0 2 25 0.1470 E94\n+0 2 30 -0.0310 E94\n+0 2 34 -0.3560 E94\n+0 2 35 -0.3500 #X94\n+1 2 37 0.0284 C94\n+1 2 39 0.0310 E94\n+0 2 40 -0.1000 #C94\n+0 2 41 0.2500 #C94\n+0 2 43 -0.1910 E94\n+0 2 45 -0.2044 X94\n+0 2 46 -0.2940 E94\n+0 2 55 -0.3410 E94\n+0 2 56 -0.3030 E94\n+0 2 62 -0.0500 #X94\n+1 2 63 -0.0450 E94\n+1 2 64 -0.0460 E94\n+1 2 67 0.0360 E94\n+0 2 72 -0.4500 #X94\n+1 2 81 -0.3790 E94\n+1 3 3 0.0000 #C94\n+1 3 4 -0.1050 E94\n+0 3 5 0.0600 #C94\n+0 3 6 -0.1500 #C94\n+0 3 7 -0.5700 #C94\n+0 3 9 -0.4500 #C94\n+1 3 9 -0.2110 E94\n+0 3 10 -0.0600 C94\n+0 3 11 -0.2220 E94\n+0 3 12 -0.2090 E94\n+0 3 15 -0.1410 E94\n+0 3 16 -0.3800 #X94\n+0 3 17 -0.0960 E94\n+0 3 18 -0.0230 E94\n+0 3 20 0.0530 #C94\n+0 3 22 0.0000 E94\n+0 3 25 0.1070 E94\n+1 3 30 -0.0710 E94\n+0 3 35 -0.3610 E94\n+1 3 37 0.0862 C94\n+1 3 39 -0.0090 E94\n+0 3 40 -0.0500 #C94\n+0 3 41 0.1470 E94\n+0 3 43 -0.2363 X94\n+0 3 45 -0.1650 E94\n+0 3 48 -0.4300 E94\n+0 3 51 -0.9500 #X94\n+0 3 53 -0.0134 X94\n+0 3 54 -0.4000 #C94\n+1 3 54 -0.3290 E94\n+0 3 55 -0.3810 E94\n+0 3 56 -0.3430 E94\n+1 3 57 -0.0100 E94\n+1 3 58 -0.3930 E94\n+0 3 62 -0.'..b'+0 28 48 -0.4000 #X94\n+0 30 30 0.0000 #C94\n+0 30 40 -0.0980 E94\n+1 30 67 0.0670 E94\n+0 31 70 -0.4300 #C94\n+0 32 41 0.6500 #C94\n+0 32 45 0.5200 #X94\n+0 32 67 0.6330 E94\n+0 32 68 0.7500 #C94\n+0 32 69 0.7500 #C94\n+0 32 73 0.3500 #X94\n+0 32 77 0.4500 #X94\n+0 32 82 0.6330 E94\n+0 34 36 0.4500 #C94\n+0 34 37 0.3640 E94\n+0 34 43 0.1650 E94\n+0 35 37 0.3290 E94\n+0 35 63 0.2760 E94\n+0 36 54 -0.4000 #C94\n+0 36 55 -0.4500 #C94\n+0 36 56 -0.4500 #C94\n+0 36 58 -0.4570 E94\n+4 36 58 -0.4500 #C94\n+0 36 81 -0.4500 #C94\n+0 37 37 0.0000 #C94\n+1 37 37 0.0000 #C94\n+0 37 38 -0.3100 #C94\n+0 37 39 0.0230 E94\n+1 37 39 0.0230 E94\n+0 37 40 -0.1000 #C94\n+0 37 41 0.1790 E94\n+0 37 43 -0.1990 E94\n+0 37 45 -0.1330 E94\n+0 37 46 -0.3020 E94\n+0 37 55 -0.3490 E94\n+0 37 56 -0.3110 E94\n+1 37 57 0.0220 E94\n+0 37 58 -0.3610 E94\n+1 37 58 -0.3610 E94\n+4 37 58 -0.3500 #C94\n+0 37 61 -0.1380 E94\n+0 37 62 0.0020 E94\n+0 37 63 0.0000 #C94\n+1 37 63 -0.0530 E94\n+0 37 64 0.0000 #C94\n+1 37 64 -0.0540 E94\n+1 37 67 0.0280 E94\n+0 37 69 -0.0895 C94\n+0 37 78 -0.0410 E94\n+0 37 81 -0.3870 E94\n+1 37 81 -0.3870 E94\n+0 38 38 0.0000 #C94\n+0 38 63 0.2570 E94\n+0 38 64 0.2560 E94\n+0 38 69 0.3380 E94\n+0 38 78 0.2690 E94\n+1 39 39 0.0000 #C94\n+0 39 40 -0.1600 E94\n+0 39 45 -0.1560 E94\n+0 39 63 -0.1516 C94\n+1 39 63 -0.0760 E94\n+0 39 64 -0.0770 E94\n+1 39 64 -0.0770 E94\n+0 39 65 -0.4180 C94\n+0 39 78 -0.0640 E94\n+0 40 40 0.0000 #C94\n+0 40 45 0.0040 E94\n+0 40 46 -0.1650 E94\n+0 40 54 -0.1600 E94\n+0 40 63 0.0840 E94\n+0 40 64 0.0830 E94\n+0 40 78 0.0960 E94\n+0 41 41 0.0000 #C94\n+0 41 55 -0.5280 E94\n+0 41 62 -0.1770 E94\n+0 41 72 -0.5000 #X94\n+0 41 80 -0.1960 E94\n+0 42 61 0.4920 E94\n+0 43 43 0.0000 #X94\n+0 43 45 0.0660 E94\n+0 43 64 0.1450 E94\n+0 44 63 0.0400 #C94\n+0 44 65 -0.2207 C94\n+0 44 78 0.0690 E94\n+0 44 80 0.0930 E94\n+0 45 63 0.0800 E94\n+0 45 64 0.0790 E94\n+0 45 78 0.0920 E94\n+0 47 53 0.3700 #X94\n+0 49 50 0.5673 C94\n+0 51 52 0.5000 #X94\n+0 55 57 0.3544 C94\n+0 55 62 0.3510 E94\n+0 55 64 0.2950 E94\n+0 55 80 0.3320 E94\n+0 56 57 0.4000 #C94\n+0 56 63 0.2580 E94\n+0 56 80 0.2700 E94\n+4 57 58 -0.4000 #C94\n+1 57 63 -0.0750 E94\n+1 57 64 -0.0760 E94\n+0 58 63 0.3080 E94\n+0 58 64 0.3070 E94\n+0 59 63 0.1400 #C94\n+0 59 65 -0.1209 C94\n+0 59 78 0.1690 E94\n+0 59 80 0.1930 E94\n+0 59 82 0.2380 E94\n+0 60 61 0.3700 #X94\n+0 62 63 -0.0550 E94\n+0 62 64 -0.0560 E94\n+0 63 63 0.0000 #C94\n+1 63 63 0.0000 #C94\n+0 63 64 0.0000 #C94\n+0 63 66 -0.3381 C94\n+0 63 72 -0.4000 E94\n+0 63 78 0.0120 E94\n+0 63 81 -0.3340 E94\n+0 64 64 0.0000 #C94\n+0 64 65 -0.2888 C94\n+0 64 66 -0.2272 C94\n+0 64 78 0.0130 E94\n+0 64 81 -0.3330 E94\n+0 64 82 0.0820 E94\n+0 65 66 0.0000 #C94\n+0 65 78 0.3070 E94\n+0 65 81 -0.0390 E94\n+0 65 82 0.3760 E94\n+0 66 66 0.0000 #C94\n+0 66 78 0.2990 E94\n+0 66 81 -0.0470 E94\n+0 71 75 -0.0958 X94\n+0 72 73 0.4500 #X94\n+0 76 76 0.0000 #X94\n+0 76 78 0.4000 #X94\n+0 78 78 0.0000 #C94\n+1 78 78 0.0000 #C94\n+0 78 79 -0.3030 E94\n+0 78 81 -0.3500 #C94\n+0 79 81 -0.0430 E94\n+0 80 81 -0.4000 #C94\n+$\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmffdef.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffdef.par Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,192 @@\n+*\n+* Copyright (c) Merck and Co., Inc., 1994\n+* All Rights Reserved\n+*\n+* PRIMARY\n+* MMFF MMFF \n+*SYMBOL TYPE DEFAULT TYPES DEFINITION \n+*\n+ CR 1 1 1 1 0 ALKYL CARBON \n+ C=C 2 2 2 1 0 VINYLIC \n+* CSP2 2 2 2 1 0 GENERIC CSP2 \n+* CGD 2 2 2 1 0 GUANIDINE CARBON \n+ C=O 3 3 3 1 0 GENERAL CARBONYL C \n+* C=N 3 3 3 1 0 C=N \n+* C=OR 3 3 3 1 0 KETONE OR ALDEHYDE CO \n+* C=ON 3 3 3 1 0 AMIDE CARBONYL \n+* COO 3 3 3 1 0 CARBOXYLIC ACID OF EST \n+* COON 3 3 3 1 0 CARBAMATE CARBONYL \n+* COOO 3 3 3 1 0 CARBONIC ACID OR ESTER \n+* C=OS 3 3 3 1 0 THIOESTER, C=O \n+* C=S 3 3 3 1 0 THIOESTER, C=S \n+* C=SN 3 3 3 1 0 THIOAMIDE \n+* CSO2 3 3 3 1 0 CARBON IN >C=SO2 \n+ CSP 4 4 4 1 0 ACETYLENIC C \n+* =C= 4 4 4 1 0 ALLENIC C \n+ HC 5 5 5 5 0 H-C \n+* HSI 5 5 5 5 0 H-SI \n+* HP 5 5 5 5 0 H-P \n+ OR 6 6 6 6 0 O-CSP3 \n+* OH2 6 6 6 6 0 OXYGEN IN H2O \n+* OC=O 6 6 6 6 0 ESTER OR ACID -O- \n+* OC=C 6 6 6 6 0 ENOL OR PHEMOLIC O \n+* OC=N 6 6 6 6 0 OXYGEN IN -O-C=N MOIETY\n+* OSO3 6 6 6 6 0 DIVALENT O IN SULFATE\n+* OSO2 6 6 6 6 0 DIVALENT O IN SULFITE\n+* OSO 6 6 6 6 0 PAIR OF DIVALENT O ON S\n+* -OS 6 6 6 6 0 OTHER DIVALENT O ON S\n+* OPO3 6 6 6 6 0 DIVALENT O IN PHOSPHATE\n+* OPO2 6 6 6 6 0 DIVALENT O IN PHOSPHITE\n+* OPO 6 6 6 6 0 PAIR OF DIVALENT O ON P\n+* -OP 6 6 6 6 0 OTHER DIVALENT O ON P\n+* -O- 6 6 6 6 0 GENERAL DIVALENT OX \n+ O=C 7 7 7 6 0 O=C, GENERIC \n+* O=CN 7 7 7 6 0 O=C IN AMIDES \n+* O=CR 7 7 7 6 0 O=C IN KET, ALD \n+* O=CO 7 7 7 6 0 O=C IN ACIDS, ESTERS \n+* O=S 7 7 7 6 0 TERMINAL O SULFOXIDES \n+* O=N 7 7 7 6 0 NITROSO-GROUP OXYGEN \n+ NR 8 8 8 8 0 AMINE N \n+ N=C 9 9 9 8 0 N=C, IMINES \n+* N=N 9 9 9 8 0 N=N, AZO COMPOUNDS \n+ NC=O 10 10 10 8 0 N-C=O, AMIDES \n+* NC=S 10 10 10 8 0 N-C=S (DELOC LP) \n+* NN=C 10 10 10 8 0 N-N=C (DELOC LP) \n+* NN=N 10 10 10 8 0 N-N=N (DELOC LP) \n+ F 11 11 11 11 0 FLUORINE \n+ CL 12 12 12 12 0 CHLORINE \n+ BR 13 13 13 13 0 BROMINE \n+ I 14 14 14 14 0 IODINE \n+ S 15 15 15 15 0 THIOL, SULFIDE \n+ S=C 16 16 16 15 0 S DOUBLY BONDED TO C \n+ S=O 17 17 17 15 0 SULFOXIDE S \n+ SO2 18 18 18 15 0 SULFONE S \n+* SO2N 18 18 18 15 0 SULFONAMIDE S \n+* SO3 18 18 18 15 0 SULFONATE S \n+* =SO2 18 18 18 15 0 OXYGENATED SULFONE S \n+* SNO 18 18 18 15 0 NITROGEN ANALOG OF SO2 \n+ SI 19 19 19 19 0 SILICON \n+ CR4R 20 20 1 1 0 C IN CYCLOBUTYL \n+ HOR 21 21 21 5 '..b' \n+ CO2M 41 41 3 1 0 C IN CO2- ANION \n+* CS2M 41 41 3 1 0 THIOCARBOXYLATE C \n+ NSP 42 42 42 8 0 N TRIPLE BONDED \n+ NSO2 43 43 10 8 0 N, SULFONAMIDES \n+ STHI 44 44 16 15 0 S IN THIOPHENE \n+ NO2 45 45 10 8 0 NITRO GROUP N \n+* NO3 45 45 10 8 0 NITRATE GROUP N \n+ N=O 46 46 9 8 0 NITROSO GROUP N \n+ NAZT 47 47 42 8 0 TERMINAL N, AZIDE \n+ NSO 48 48 9 8 0 DIVAL. N IN S(N)(O) GP \n+ O+ 49 49 6 6 0 OXONIUM (TRICOORD) O \n+ HO+ 50 50 21 5 0 H ON OXONIUM OXYGEN \n+ O=+ 51 51 7 6 0 OXENIUM OXYGEN+ \n+ HO=+ 52 52 21 5 0 H ON OXENIUM O+ \n+ =N= 53 53 42 8 0 N TWICE DOUBLE BONDED \n+ N+=C 54 54 9 8 0 IMINIUM NITROGEN \n+* N+=N 54 54 9 8 0 AZONIUM NITROGEN \n+ NCN+ 55 55 10 8 0 N IN +N=C-N: ; Q=1/2 \n+ NGD+ 56 56 10 8 0 GUANIDINIUM N; Q=1/3 \n+ CGD+ 57 57 2 1 0 GUANIDINIUM CARBON \n+* CNN+ 57 57 2 1 0 C IN +N=C-N RESONANCE \n+ NPD+ 58 58 10 8 0 N PYRIDINIUM ION \n+ OFUR 59 59 6 6 0 AROMATIC O, FURAN \n+ C% 60 60 4 1 0 ISONITRILE CARBON \n+ NR% 61 61 42 8 0 ISONITRILE N \n+ NM 62 62 10 8 0 SULFONAMIDE N- \n+ C5A 63 63 2 1 0 ALPHA AROM 5-RING C \n+ C5B 64 64 2 1 0 BETA AROM 5-RING C \n+ N5A 65 65 9 8 0 ALPHA AROM 5-RING N \n+ N5B 66 66 9 8 0 ALPHA AROM 5-RING N \n+ N2OX 67 67 9 8 0 NITROGEN IN N-OXIDE \n+ N3OX 68 68 8 8 0 NITROGEN IN N-OXIDE \n+ NPOX 69 69 9 8 0 NITROGEN IN N-OXIDE \n+ OH2 70 70 70 70 70 OXYGEN IN WATER \n+ HS 71 71 5 5 0 H-S \n+ S2CM 72 72 16 15 0 THIOCARBOXYLATE S \n+* S-P 72 72 16 15 0 TERMINAL SULFUR ON P \n+* SM 72 72 16 15 0 TERMINAL SULFUR ON C \n+* SSMO 72 72 16 15 0 TERM S, THIOSULFINATE \n+ SO2M 73 73 18 15 0 SULFUR IN SULFINATE \n+* SSOM 73 73 18 15 0 SULFUR, THIOSULFINATE \n+ =S=O 74 74 17 15 0 SULFINYL SULFUR, C=S=O \n+ -P=C 75 75 26 25 0 P DOUBLY BONDED TO C\n+ N5M 76 76 9 8 0 NEG N IN TETRAZOLE AN \n+ CLO4 77 77 12 12 0 CHLORINE IN CLO4(-) \n+ C5 78 78 2 1 0 GENERAL AROM 5-RING C \n+ N5 79 79 9 8 0 GENERAL AROM 5-RING N \n+ CIM+ 80 80 2 1 0 C IN N-C-N, IM+ ION \n+ NIM+ 81 81 10 8 0 N IN N-C-N, IM+ ION \n+ N5AX 82 82 9 8 0 5R NITROGEN IN N-OXIDE \n+* N5BX 82 82 9 8 0 5R NITROGEN IN N-OXIDE \n+* N5OX 82 82 9 8 0 5R NITROGEN IN N-OXIDE \n+ FE+2 87 87 87 87 87 IRON +2 CATION\n+ FE+3 88 88 88 88 88 IRON +3 CATION\n+ F- 89 89 89 89 89 FLUORIDE ANION\n+ CL- 90 90 90 90 90 CHLORIDE ANION\n+ BR- 91 91 91 91 91 BROMIDE ANION\n+ LI+ 92 92 92 92 92 LITHIUM CATION \n+ NA+ 93 93 93 93 93 SODIUM CATION \n+ K+ 94 94 94 94 94 POTASSIUM CATION \n+ ZN+2 95 95 95 95 95 DIPOSITIVE ZINC CATION \n+* ZINC 95 95 95 95 95 DIPOSITIVE ZINC CATION \n+ CA+2 96 96 96 96 96 DIPOSITIVE CALCIUM CATION\n+ CU+1 97 97 97 97 97 MONOPOSITIVE COPPER CATION\n+ CU+2 98 98 98 98 98 DIPOSITIVE COPPER CATION\n+ MG+2 99 99 99 99 99 DIPOSITIVE MAGNESIUM CATION\n+$\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmffdfsb.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffdfsb.par Tue Jun 07 16:43:30 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
+$

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmffoop.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffoop.par Tue Jun 07 16:43:30 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
+$

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmffpbci.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffpbci.par Tue Jun 07 16:43:30 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
+$

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmffprop.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffprop.par Tue Jun 07 16:43:30 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
+$

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmffs_oop.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffs_oop.par Tue Jun 07 16:43:30 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
+$

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmffs_tor.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffs_tor.par Tue Jun 07 16:43:30 2011 -0400

b"@@ -0,0 +1,939 @@\n+*\n+* Copyright (c) Merck and Co., Inc., 1994,1995,1996,1997,1998,1999\n+* All Rights Reserved\n+*\n+* MMFF94s TORSION PARAMETERS\n+* C94 - CORE MMFF94 parameter - from fits to conformational energies\n+* C94S - CORE MMFF94s parameter - from fits to conformational energies\n+* X94 - EXTD MMFF94 parameter - also from fits to conformational E's\n+* E94 - EXTD MMFF94 parameter - from empirical rule\n+* #E94 - Adjusted from empirical rule value\n+*\n+* atom types V1 V2 V3 Source\n+0 0 1 1 0 0.000 0.000 0.300 C94 0:*-1-1-* Def\n+5 0 1 1 0 0.200 -0.800 1.500 C94 5:*-1-1-* Def\n+0 1 1 1 1 0.103 0.681 0.332 C94\n+5 1 1 1 1 0.144 -0.547 1.126 C94\n+0 1 1 1 2 -0.295 0.438 0.584 C94\n+0 1 1 1 3 0.066 -0.156 0.143 C94\n+0 1 1 1 5 0.639 -0.630 0.264 C94\n+0 1 1 1 6 -0.688 1.757 0.477 C94\n+5 1 1 1 6 0.000 0.000 0.054 C94\n+0 1 1 1 8 -1.420 -0.092 1.101 C94\n+5 1 1 1 8 0.000 -0.158 0.323 C94\n+0 1 1 1 11 0.593 0.662 1.120 C94\n+0 1 1 1 12 -0.678 0.417 0.624 C94\n+0 1 1 1 15 -0.714 0.698 0.000 C94\n+0 1 1 1 34 -0.647 0.550 0.590 C94\n+0 2 1 1 5 0.321 -0.411 0.144 C94\n+0 3 1 1 3 0.443 0.000 -1.140 C94\n+0 3 1 1 5 -0.256 0.058 0.000 C94\n+0 3 1 1 6 -0.679 -0.029 0.000 C94\n+0 5 1 1 5 0.284 -1.386 0.314 C94\n+0 5 1 1 6 -0.654 1.072 0.279 C94\n+0 5 1 1 8 -0.744 -1.235 0.337 C94\n+0 5 1 1 10 0.000 0.000 0.418 C94S\n+0 5 1 1 11 0.000 0.516 0.291 C94\n+0 5 1 1 12 0.678 -0.602 0.398 C94\n+0 5 1 1 15 1.142 -0.644 0.367 C94\n+0 5 1 1 25 0.000 0.000 0.295 X94\n+0 5 1 1 34 0.692 -0.530 0.278 C94\n+0 5 1 1 37 0.000 0.000 0.389 C94\n+0 5 1 1 39 0.000 0.000 0.278 C94\n+0 5 1 1 41 0.000 0.000 -0.141 C94\n+0 5 1 1 56 0.000 0.000 0.324 C94\n+0 5 1 1 68 0.000 0.000 0.136 C94\n+0 6 1 1 6 0.408 1.397 0.961 C94\n+5 6 1 1 6 0.313 -1.035 1.631 C94\n+0 8 1 1 8 1.055 0.834 0.000 C94\n+0 11 1 1 11 -0.387 -0.543 1.405 C94\n+0 12 1 1 12 0.000 0.000 0.893 C94\n+0 15 1 1 15 -0.177 0.000 0.049 C94\n+0 0 1 2 0 0.000 0.000 0.000 C94 0:*-1-2-* Def\n+2 0 1 2 0 0.000 0.000 0.000 E94 2:*1-2-* Def\n+5 0 1 2 0 0.000 0.000 0.000 C94 5:*-1-2-* Def\n+0 0 1 2 2 0.000 0.000 -0.650 C94 0:*-1-2=2 Def\n+5 0 1 2 2 0.000 0.000 -0.650 C94 5:*-1-2=2 Def\n+0 1 1 2 1 0.419 0.296 0.282 C94\n+0 1 1 2 2 -0.494 0.274 -0.630 C94\n+0 1 1 2 5 0.075 0.000 0.358 C94\n+0 2 1 2 2 -0.293 0.115 -0.508 C94\n+0 2 1 2 5 0.301 0.104 0.507 C94\n+0 3 1 2 1 0.565 -0.554 0.234 C94\n+0 3 1 2 2 -0.577 -0.482 -0.427 C94\n+0 3 1 2 5 0.082 0.000 0.123 C94\n+0 5 1 2 1 0.000 -0.184 0.220 C94\n+0 5 1 2 2 0.501 -0.410 -0.535 C94\n+2 5 1 2 2 0.000 0.000 0.055 C94\n+2 5 1 2 3 0.000 0.000 -0.108 C94\n+0 5 1 2 5 -0.523 -0.228 0.208 C94\n+2 5 1 2 37 0.000 0.000 0.000 C94\n+0 6 1 2 1 -0.467 0.000 0.490 C94\n+0 6 1 2 2 0.425 0.168 -0.875 C94\n+0 6 1 2 5 0.000 0.136 0.396 C94\n+0 8 1 2 1 -0.504 0.371 0.557 C94\n+0 8 1 2 2 0.541 0.539 -1.009 C94\n+0 8 1 2 5 0.000 0.204 0.464 C94\n+0 0 1 3 0 0.000"..b' 57 0 0.000 4.800 0.000 E94 2:*-55-57-* Def\n+5 0 55 57 0 0.000 4.800 0.000 E94 5:*-55-57-* Def\n+0 1 55 57 5 0.423 12.064 0.090 C94\n+0 1 55 57 55 -0.428 12.044 0.000 C94\n+0 36 55 57 5 -0.268 8.077 -0.806 C94\n+0 36 55 57 55 0.273 8.025 0.692 C94\n+0 0 55 62 0 0.000 3.600 0.000 E94 0:*-55-62-* Def\n+0 0 55 64 0 0.000 4.800 0.000 E94 0:*-55-64-* Def\n+0 0 55 80 0 0.000 4.800 0.000 E94 0:*-55-80-* Def\n+0 0 56 57 0 0.000 6.000 0.000 C94 0:*-56-57-* Def\n+0 1 56 57 56 0.000 6.886 -0.161 C94\n+0 36 56 57 56 0.000 4.688 0.107 C94\n+0 0 56 63 0 0.000 4.800 0.000 E94 0:*-56-63-* Def\n+0 0 56 80 0 0.000 4.800 0.000 E94 0:*-56-80-* Def\n+1 0 57 63 0 0.000 1.800 0.000 E94 1:*-57-63-* Def\n+1 0 57 64 0 0.000 1.800 0.000 E94 1:*-57-64-* Def\n+0 0 58 63 0 0.000 6.000 0.000 E94 0:*-58-63-* Def\n+0 0 58 64 0 0.000 6.000 0.000 E94 0:*-58-64-* Def\n+0 0 59 63 0 0.000 7.000 0.000 C94 0:*-59-63-* Def\n+0 0 59 65 0 0.000 7.000 0.000 C94 0:*-59-65-* Def\n+0 0 59 78 0 0.000 3.600 0.000 E94 0:*-59-78-* Def\n+0 0 59 80 0 0.000 3.600 0.000 E94 0:*-59-80-* Def\n+0 0 59 82 0 0.000 3.600 0.000 E94 0:*-59-82-* Def\n+0 0 62 63 0 0.000 3.600 0.000 E94 0:*-62-63-* Def\n+0 0 62 64 0 0.000 3.600 0.000 E94 0:*-62-64-* Def\n+1 0 63 63 0 0.000 1.800 0.000 E94 1:*-63-63-* Def\n+0 0 63 64 0 0.000 7.000 0.000 C94 0:*-63-64-* Def\n+0 5 63 64 5 0.000 7.000 0.000 C94\n+0 5 63 64 64 0.000 7.000 0.000 C94\n+0 39 63 64 5 0.000 7.000 0.000 C94\n+0 39 63 64 64 0.000 7.000 0.000 C94\n+0 0 63 66 0 0.000 7.000 0.000 C94 0:*-63-66-* Def\n+0 0 63 78 0 0.000 6.000 0.000 E94 0:*-63-78-* Def\n+0 0 63 81 0 0.000 6.000 0.000 E94 0:*-63-81-* Def\n+0 0 64 64 0 0.000 7.000 0.000 C94 0:*-64-64-* Def\n+1 0 64 64 0 0.000 1.800 0.000 E94 1:*-64-64-* Def\n+0 5 64 64 5 0.000 7.000 0.000 C94\n+0 5 64 64 63 0.000 7.000 0.000 C94\n+0 63 64 64 63 0.000 7.000 0.000 C94\n+0 0 64 65 0 0.000 7.000 0.000 C94 0:*-64-65-* Def\n+0 0 64 66 0 0.000 7.000 0.000 C94 0:*-64-66-* Def\n+0 0 64 78 0 0.000 6.000 0.000 E94 0:*-64-78-* Def\n+0 0 64 81 0 0.000 6.000 0.000 E94 0:*-64-81-* Def\n+5 0 64 81 0 0.000 6.000 0.000 E94 5:*-64-81-* Def\n+0 0 64 82 0 0.000 6.000 0.000 E94 0:*-64-82-* Def\n+0 0 65 66 0 0.000 7.000 0.000 C94 0:*-65-66-* Def\n+0 0 65 78 0 0.000 6.000 0.000 E94 0:*-65-78-* Def\n+0 0 65 81 0 0.000 6.000 0.000 E94 0:*-65-81-* Def\n+0 0 65 82 0 0.000 6.000 0.000 E94 0:*-65-82-* Def\n+0 0 66 66 0 0.000 7.000 0.000 C94 0:*-66-66-* Def\n+0 0 66 78 0 0.000 6.000 0.000 E94 0:*-66-78-* Def\n+0 0 66 81 0 0.000 6.000 0.000 E94 0:*-66-81-* Def\n+0 0 67 67 0 0.000 12.000 0.000 E94 0:*-67-67-* Def\n+5 0 67 67 0 0.000 12.000 0.000 E94 5:*-67-67-* Def\n+0 0 76 76 0 0.000 3.600 0.000 E94 0:*-76-76-* Def\n+0 0 76 78 0 0.000 3.600 0.000 E94 0:*-76-78-* Def\n+0 0 78 78 0 0.000 7.000 0.000 C94 0:*-78-78-* Def\n+0 0 78 79 0 0.000 6.000 0.000 E94 0:*-78-79-* Def\n+0 0 78 81 0 0.000 4.000 0.000 C94 0:*-78-81-* Def\n+0 0 79 79 0 0.000 6.000 0.000 E94 0:*-79-79-* Def\n+0 0 79 81 0 0.000 6.000 0.000 E94 0:*-79-81-* Def\n+0 0 80 81 0 0.000 4.000 0.000 C94 0:*-80-81-* Def\n+$\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmffstbn.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffstbn.par Tue Jun 07 16:43:30 2011 -0400

b"@@ -0,0 +1,292 @@\n+*\n+* Copyright (c) Merck and Co., Inc., 1994\n+* All Rights Reserved\n+*\n+* MMFF STRETCH-BEND PARAMETERS- Rev: 23-FEB-93 Source: MMFF94\n+* C94 - CORE MMFF94 parameter, from fits to HF/6-31G* 2nd D's\n+* X94 - EXTD MMFF94 parameter, also from fits to HF/6-31G* 2nd D's\n+*\n+* types I, J, K kbaIJK kbaKJI Source\n+0 1 1 1 0.206 0.206 C94\n+0 1 1 2 0.136 0.197 C94\n+0 1 1 3 0.211 0.092 C94\n+0 1 1 5 0.227 0.070 C94\n+0 1 1 6 0.173 0.417 C94\n+0 1 1 8 0.136 0.282 C94\n+0 1 1 10 0.187 0.338 C94\n+0 1 1 11 0.209 0.633 C94\n+0 1 1 12 0.176 0.386 C94\n+0 1 1 15 0.139 0.217 C94\n+0 1 1 34 0.236 0.436 C94\n+0 1 1 37 0.152 0.260 C94\n+0 1 1 39 0.144 0.595 C94\n+0 1 1 41 0.122 0.051 C94\n+0 1 1 56 0.262 0.451 C94\n+0 1 1 68 0.186 0.125 C94\n+0 2 1 2 0.282 0.282 C94\n+0 2 1 3 0.206 0.022 C94\n+0 2 1 5 0.234 0.088 C94\n+0 2 1 6 0.183 0.387 C94\n+0 2 1 8 0.214 0.363 C94\n+0 3 1 5 0.157 0.115 C94\n+0 3 1 6 -0.036 0.456 C94\n+0 3 1 10 0.038 0.195 C94\n+0 5 1 5 0.115 0.115 C94\n+0 5 1 6 0.013 0.436 C94\n+0 5 1 8 0.027 0.358 C94\n+0 5 1 9 0.040 0.418 C94\n+0 5 1 10 0.043 0.261 C94\n+0 5 1 11 0.003 0.452 C94\n+0 5 1 12 -0.018 0.380 C94\n+0 5 1 15 0.018 0.255 C94\n+0 5 1 18 0.121 0.218 X94\n+0 5 1 20 0.069 0.327 C94\n+0 5 1 22 0.055 0.267 X94\n+0 5 1 34 -0.003 0.342 C94\n+0 5 1 37 0.074 0.287 C94\n+0 5 1 39 0.092 0.607 C94\n+0 5 1 40 0.023 0.335 C94\n+0 5 1 41 0.093 0.118 C94\n+0 5 1 54 0.016 0.343 C94\n+0 5 1 55 0.030 0.397 C94\n+0 5 1 56 0.031 0.384 C94\n+0 5 1 68 0.041 0.216 C94\n+0 6 1 6 0.320 0.320 C94\n+0 6 1 37 0.310 0.160 C94\n+0 11 1 11 0.586 0.586 C94\n+0 12 1 12 0.508 0.508 C94\n+0 1 2 1 0.250 0.250 C94\n+0 1 2 2 0.203 0.207 C94\n+2 1 2 2 0.222 0.269 C94\n+2 1 2 3 0.244 0.292 C94\n+0 1 2 5 0.215 0.128 C94\n+2 1 2 37 0.246 0.260 C94\n+1 2 2 2 0.250 0.219 C94\n+2 2 2 3 0.155 0.112 C94\n+0 2 2 5 0.207 0.157 C94\n+1 2 2 5 0.267 0.159 C94\n+0 2 2 6 0.118 0.576 C94\n+2 2 2 37 0.143 0.172 C94\n+0 2 2 40 0.289 0.390 C94\n+0 2 2 41 0.191 -0.047 C94\n+1 3 2 5 0.264 0.156 C94\n+0 5 2 5 0.140 0.140 C94\n+0 5 2 6 0.213 0.502 C94\n+2 5 2 37 0.153 0.288 C94\n+0 5 2 40 0.070 0.463 C94\n+0 5 2 41 0.191 0.005 C94\n+0 1 3 1 0.358 0.358 C94\n+2 1 3 2 0.246 0.409 C94\n+2 1 3 3 0.303 0.145 C94\n+0 1 3 5 0.321 0.183 C94\n+0 1 3 6 0.338 0.732 C94\n+0 1 3 7 0.154 0.856 C94\n+0 1 3 10 0.223 0.732 C94\n+2 1 3 37 0.217 0.207 C94\n+1 2 3 5 0.407 0.159 C94\n+1 2 3 6 0.429 0.473 C94\n+1 2 3 7 0.214 0.794 C94\n+1 2 3 9 0.227 0.610 C94\n+1 2 3 10 0.298 0.600 C94\n+1 3 3 5 0.251 0.133 C94\n+1 3 3 6 0.066 0.668 C94\n+1 3 3 7 -0.093 0.866 C94\n+0 5 3 "..b' 37 37 40 0.429 0.901 C94\n+0 37 37 63 -0.173 -0.215 C94\n+0 37 37 64 -0.229 -0.229 C94\n+0 37 37 69 -0.244 -0.555 C94\n+0 38 37 38 -0.516 -0.516 C94\n+0 37 38 37 -0.342 -0.342 C94\n+0 37 38 38 -0.164 -1.130 C94\n+0 1 39 63 0.313 0.500 C94\n+0 23 39 63 -0.131 0.422 C94\n+0 23 39 65 -0.122 0.281 C94\n+0 63 39 63 0.469 0.469 C94\n+0 63 39 65 0.741 0.506 C94\n+0 65 39 65 0.706 0.706 C94\n+0 1 40 28 0.238 0.091 C94\n+0 1 40 37 0.153 0.590 C94\n+0 2 40 28 0.342 0.156 C94\n+0 3 40 28 0.228 0.104 C94\n+0 28 40 28 0.094 0.094 C94\n+0 28 40 37 0.186 0.423 C94\n+0 1 41 32 0.503 0.943 C94\n+0 2 41 32 0.594 0.969 C94\n+0 5 41 32 0.276 0.852 C94\n+0 32 41 32 0.652 0.652 C94\n+0 18 43 23 0.377 0.057 X94\n+0 23 43 23 0.082 0.082 X94\n+0 63 44 63 0.591 0.591 C94\n+0 63 44 65 0.857 0.978 C94\n+0 50 49 50 0.072 0.072 C94\n+0 1 54 3 0.192 -0.051 C94\n+0 1 54 36 0.240 0.079 C94\n+0 3 54 36 0.005 0.127 C94\n+0 36 54 36 0.148 0.148 C94\n+0 1 55 36 0.189 0.033 C94\n+0 1 55 57 0.166 0.211 C94\n+0 36 55 36 0.106 0.106 C94\n+0 36 55 57 0.093 0.080 C94\n+0 1 56 36 0.211 -0.040 C94\n+0 1 56 57 0.026 0.386 C94\n+0 36 56 36 0.101 0.101 C94\n+0 36 56 57 0.108 0.068 C94\n+0 5 57 55 0.043 0.420 C94\n+0 55 57 55 0.125 0.125 C94\n+0 56 57 56 0.431 0.431 C94\n+0 58 57 58 0.732 0.732 C94\n+0 63 59 63 0.497 0.497 C94\n+0 63 59 65 0.723 0.874 C94\n+0 5 63 39 0.009 0.654 C94\n+0 5 63 44 -0.015 0.446 C94\n+0 5 63 59 0.067 0.588 C94\n+0 5 63 64 0.055 0.370 C94\n+0 5 63 66 0.110 0.464 C94\n+0 37 63 39 0.178 0.523 C94\n+0 37 63 64 -0.045 0.497 C94\n+0 39 63 64 0.422 0.409 C94\n+0 39 63 66 0.436 0.525 C94\n+0 44 63 64 0.581 0.426 C94\n+0 44 63 66 0.542 0.365 C94\n+0 59 63 64 0.852 0.332 C94\n+0 59 63 66 0.775 0.300 C94\n+0 5 64 63 0.086 0.345 C94\n+0 5 64 64 0.085 0.369 C94\n+0 5 64 65 0.051 0.436 C94\n+0 5 64 66 0.113 0.452 C94\n+0 37 64 63 0.059 0.299 C94\n+0 37 64 64 0.277 0.377 C94\n+0 63 64 64 0.206 0.030 C94\n+0 63 64 66 0.171 0.078 C94\n+0 64 64 65 0.079 0.403 C94\n+0 65 64 66 0.406 0.066 C94\n+0 39 65 64 0.528 0.644 C94\n+0 39 65 66 0.397 0.258 C94\n+0 44 65 64 0.816 0.543 C94\n+0 59 65 64 1.177 0.594 C94\n+0 63 66 64 0.213 -0.173 C94\n+0 63 66 66 0.234 0.077 C94\n+0 64 66 65 -0.149 0.383 C94\n+0 65 66 66 0.199 0.101 C94\n+0 1 68 1 0.217 0.217 C94\n+0 1 68 23 0.285 0.050 C94\n+0 1 68 32 -0.047 0.503 C94\n+0 23 68 23 0.145 0.145 C94\n+0 23 68 32 -0.182 0.504 C94\n+0 32 69 37 1.018 0.418 C94\n+0 37 69 37 -0.169 -0.169 C94\n+0 31 70 31 0.210 0.210 C94\n+0 5 78 78 0.279 0.250 C94\n+0 5 78 81 0.083 0.250 C94\n+0 78 78 81 -0.398 0.314 C94\n+0 5 80 81 -0.101 0.691 C94\n+0 81 80 81 0.732 0.732 C94\n+0 36 81 78 0.021 0.368 C94\n+0 36 81 80 0.018 0.422 C94\n+0 78 81 80 0.366 0.419 C94\n+$\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmfftor.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmfftor.par Tue Jun 07 16:43:30 2011 -0400

b"@@ -0,0 +1,938 @@\n+*\n+* Copyright (c) Merck and Co., Inc., 1994\n+* All Rights Reserved\n+*\n+* MMFF TORSION PARAMETERS- Rev: 26-OCT-94 Source: MMFF94\n+* C94 - CORE MMFF94 parameter - from fits to conformational energies\n+* X94 - EXTD MMFF94 parameter - also from fits to conformational E's\n+* E94 - EXTD MMFF94 parameter - from empirical rule\n+* #E94 - Adjusted from empirical rule value\n+*\n+* atom types V1 V2 V3 Source\n+0 0 1 1 0 0.000 0.000 0.300 C94 0:*-1-1-* Def\n+5 0 1 1 0 0.200 -0.800 1.500 C94 5:*-1-1-* Def\n+0 1 1 1 1 0.103 0.681 0.332 C94\n+5 1 1 1 1 0.144 -0.547 1.126 C94\n+0 1 1 1 2 -0.295 0.438 0.584 C94\n+0 1 1 1 3 0.066 -0.156 0.143 C94\n+0 1 1 1 5 0.639 -0.630 0.264 C94\n+0 1 1 1 6 -0.688 1.757 0.477 C94\n+5 1 1 1 6 0.000 0.000 0.054 C94\n+0 1 1 1 8 -1.420 -0.092 1.101 C94\n+5 1 1 1 8 0.000 -0.158 0.323 C94\n+0 1 1 1 11 0.593 0.662 1.120 C94\n+0 1 1 1 12 -0.678 0.417 0.624 C94\n+0 1 1 1 15 -0.714 0.698 0.000 C94\n+0 1 1 1 34 -0.647 0.550 0.590 C94\n+0 2 1 1 5 0.321 -0.411 0.144 C94\n+0 3 1 1 3 0.443 0.000 -1.140 C94\n+0 3 1 1 5 -0.256 0.058 0.000 C94\n+0 3 1 1 6 -0.679 -0.029 0.000 C94\n+0 5 1 1 5 0.284 -1.386 0.314 C94\n+0 5 1 1 6 -0.654 1.072 0.279 C94\n+0 5 1 1 8 -0.744 -1.235 0.337 C94\n+0 5 1 1 10 0.000 0.000 0.427 C94\n+0 5 1 1 11 0.000 0.516 0.291 C94\n+0 5 1 1 12 0.678 -0.602 0.398 C94\n+0 5 1 1 15 1.142 -0.644 0.367 C94\n+0 5 1 1 25 0.000 0.000 0.295 X94\n+0 5 1 1 34 0.692 -0.530 0.278 C94\n+0 5 1 1 37 0.000 0.000 0.389 C94\n+0 5 1 1 39 0.000 0.000 0.278 C94\n+0 5 1 1 41 0.000 0.000 -0.141 C94\n+0 5 1 1 56 0.000 0.000 0.324 C94\n+0 5 1 1 68 0.000 0.000 0.136 C94\n+0 6 1 1 6 0.408 1.397 0.961 C94\n+5 6 1 1 6 0.313 -1.035 1.631 C94\n+0 8 1 1 8 1.055 0.834 0.000 C94\n+0 11 1 1 11 -0.387 -0.543 1.405 C94\n+0 12 1 1 12 0.000 0.000 0.893 C94\n+0 15 1 1 15 -0.177 0.000 0.049 C94\n+0 0 1 2 0 0.000 0.000 0.000 C94 0:*-1-2-* Def\n+2 0 1 2 0 0.000 0.000 0.000 E94 2:*-1-2-* Def\n+5 0 1 2 0 0.000 0.000 0.000 C94 5:*-1-2-* Def\n+0 0 1 2 2 0.000 0.000 -0.650 C94 0:*-1-2=2 Def\n+5 0 1 2 2 0.000 0.000 -0.650 C94 5:*-1-2=2 Def\n+0 1 1 2 1 0.419 0.296 0.282 C94\n+0 1 1 2 2 -0.494 0.274 -0.630 C94\n+0 1 1 2 5 0.075 0.000 0.358 C94\n+0 2 1 2 2 -0.293 0.115 -0.508 C94\n+0 2 1 2 5 0.301 0.104 0.507 C94\n+0 3 1 2 1 0.565 -0.554 0.234 C94\n+0 3 1 2 2 -0.577 -0.482 -0.427 C94\n+0 3 1 2 5 0.082 0.000 0.123 C94\n+0 5 1 2 1 0.000 -0.184 0.220 C94\n+0 5 1 2 2 0.501 -0.410 -0.535 C94\n+2 5 1 2 2 0.000 0.000 0.055 C94\n+2 5 1 2 3 0.000 0.000 -0.108 C94\n+0 5 1 2 5 -0.523 -0.228 0.208 C94\n+2 5 1 2 37 0.000 0.000 0.000 C94\n+0 6 1 2 1 -0.467 0.000 0.490 C94\n+0 6 1 2 2 0.425 0.168 -0.875 C94\n+0 6 1 2 5 0.000 0.136 0.396 C94\n+0 8 1 2 1 -0.504 0.371 0.557 C94\n+0 8 1 2 2 0.541 0.539 -1.009 C94\n+0 8 1 2 5 0.000 0.204 0.464 C94\n+0 0 1 3 0 0.000 0.400 0.300 C94 0:*-1-3-* Def\n+2 0 1 "..b' 57 0 0.000 4.800 0.000 E94 2:*-55-57-* Def\n+5 0 55 57 0 0.000 4.800 0.000 E94 5:*-55-57-* Def\n+0 1 55 57 5 0.423 12.064 0.090 C94\n+0 1 55 57 55 -0.428 12.044 0.000 C94\n+0 36 55 57 5 -0.268 8.077 -0.806 C94\n+0 36 55 57 55 0.273 8.025 0.692 C94\n+0 0 55 62 0 0.000 3.600 0.000 E94 0:*-55-62-* Def\n+0 0 55 64 0 0.000 4.800 0.000 E94 0:*-55-64-* Def\n+0 0 55 80 0 0.000 4.800 0.000 E94 0:*-55-80-* Def\n+0 0 56 57 0 0.000 6.000 0.000 C94 0:*-56-57-* Def\n+0 1 56 57 56 0.000 6.886 -0.161 C94\n+0 36 56 57 56 0.000 4.688 0.107 C94\n+0 0 56 63 0 0.000 4.800 0.000 E94 0:*-56-63-* Def\n+0 0 56 80 0 0.000 4.800 0.000 E94 0:*-56-80-* Def\n+1 0 57 63 0 0.000 1.800 0.000 E94 1:*-57-63-* Def\n+1 0 57 64 0 0.000 1.800 0.000 E94 1:*-57-64-* Def\n+0 0 58 63 0 0.000 6.000 0.000 E94 0:*-58-63-* Def\n+0 0 58 64 0 0.000 6.000 0.000 E94 0:*-58-64-* Def\n+0 0 59 63 0 0.000 7.000 0.000 C94 0:*-59-63-* Def\n+0 0 59 65 0 0.000 7.000 0.000 C94 0:*-59-65-* Def\n+0 0 59 78 0 0.000 3.600 0.000 E94 0:*-59-78-* Def\n+0 0 59 80 0 0.000 3.600 0.000 E94 0:*-59-80-* Def\n+0 0 59 82 0 0.000 3.600 0.000 E94 0:*-59-82-* Def\n+0 0 62 63 0 0.000 3.600 0.000 E94 0:*-62-63-* Def\n+0 0 62 64 0 0.000 3.600 0.000 E94 0:*-62-64-* Def\n+1 0 63 63 0 0.000 1.800 0.000 E94 1:*-63-63-* Def\n+0 0 63 64 0 0.000 7.000 0.000 C94 0:*-63-64-* Def\n+0 5 63 64 5 0.000 7.000 0.000 C94\n+0 5 63 64 64 0.000 7.000 0.000 C94\n+0 39 63 64 5 0.000 7.000 0.000 C94\n+0 39 63 64 64 0.000 7.000 0.000 C94\n+0 0 63 66 0 0.000 7.000 0.000 C94 0:*-63-66-* Def\n+0 0 63 78 0 0.000 6.000 0.000 E94 0:*-63-78-* Def\n+0 0 63 81 0 0.000 6.000 0.000 E94 0:*-63-81-* Def\n+0 0 64 64 0 0.000 7.000 0.000 C94 0:*-64-64-* Def\n+1 0 64 64 0 0.000 1.800 0.000 E94 1:*-64-64-* Def\n+0 5 64 64 5 0.000 7.000 0.000 C94\n+0 5 64 64 63 0.000 7.000 0.000 C94\n+0 63 64 64 63 0.000 7.000 0.000 C94\n+0 0 64 65 0 0.000 7.000 0.000 C94 0:*-64-65-* Def\n+0 0 64 66 0 0.000 7.000 0.000 C94 0:*-64-66-* Def\n+0 0 64 78 0 0.000 6.000 0.000 E94 0:*-64-78-* Def\n+0 0 64 81 0 0.000 6.000 0.000 E94 0:*-64-81-* Def\n+5 0 64 81 0 0.000 6.000 0.000 E94 5:*-64-81-* Def\n+0 0 64 82 0 0.000 6.000 0.000 E94 0:*-64-82-* Def\n+0 0 65 66 0 0.000 7.000 0.000 C94 0:*-65-66-* Def\n+0 0 65 78 0 0.000 6.000 0.000 E94 0:*-65-78-* Def\n+0 0 65 81 0 0.000 6.000 0.000 E94 0:*-65-81-* Def\n+0 0 65 82 0 0.000 6.000 0.000 E94 0:*-65-82-* Def\n+0 0 66 66 0 0.000 7.000 0.000 C94 0:*-66-66-* Def\n+0 0 66 78 0 0.000 6.000 0.000 E94 0:*-66-78-* Def\n+0 0 66 81 0 0.000 6.000 0.000 E94 0:*-66-81-* Def\n+0 0 67 67 0 0.000 12.000 0.000 E94 0:*-67-67-* Def\n+5 0 67 67 0 0.000 12.000 0.000 E94 5:*-67-67-* Def\n+0 0 76 76 0 0.000 3.600 0.000 E94 0:*-76-76-* Def\n+0 0 76 78 0 0.000 3.600 0.000 E94 0:*-76-78-* Def\n+0 0 78 78 0 0.000 7.000 0.000 C94 0:*-78-78-* Def\n+0 0 78 79 0 0.000 6.000 0.000 E94 0:*-78-79-* Def\n+0 0 78 81 0 0.000 4.000 0.000 C94 0:*-78-81-* Def\n+0 0 79 79 0 0.000 6.000 0.000 E94 0:*-79-79-* Def\n+0 0 79 81 0 0.000 6.000 0.000 E94 0:*-79-81-* Def\n+0 0 80 81 0 0.000 4.000 0.000 C94 0:*-80-81-* Def\n+$\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mmffvdw.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mmffvdw.par Tue Jun 07 16:43:30 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
+$

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/mr.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/mr.txt Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/patterns.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/patterns.txt Tue Jun 07 16:43:30 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
+

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/phmodel.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/phmodel.txt Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/phmodeldata.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/phmodeldata.h Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,248 @@\n+/***************************************************************\n+This file is part of the Open Babel project.\n+This is copyright under the GNU General Public License (GPL)\n+For more information, see <http://openbabel.org/>\n+\n+This file contains a binary representation of data tables\n+ used by Open Babel. It is used as a fallback if the textual\n+ data table is not found at runtime. It is not a normal header.\n+***************************************************************/\n+\n+\n+#ifndef OB_PHMODELDATA_H\n+#define OB_PHMODELDATA_H\n+\n+namespace OpenBabel\n+{\n+static const char PhModelData[] = {\n+ 0x54,0x52,0x41,0x4E,0x53,0x46,0x4F,0x52,0x4D,0x20,0x4F,0x3D,0x43,0x5B,0x4F,\n+ 0x44,0x31,0x2D,0x30,0x3A,0x31,0x5D,0x20,0x3E,0x3E,0x20,0x4F,0x3D,0x43,0x5B,\n+ 0x4F,0x2D,0x3A,0x31,0x5D,0x09,0x09,0x09,0x09,0x09,0x34,0x2E,0x30,0x20,0x23,\n+ 0x20,0x70,0x4B,0x61,0x20,0x66,0x72,0x6F,0x6D,0x20,0x61,0x63,0x69,0x64,0x20,\n+ 0x28,0x41,0x48,0x29,0x0A,0x54,0x52,0x41,0x4E,0x53,0x46,0x4F,0x52,0x4D,0x20,\n+ 0x5B,0x4F,0x3A,0x31,0x5D,0x3D,0x5B,0x43,0x3A,0x32,0x5D,0x5B,0x43,0x3A,0x33,\n+ 0x5D,0x3D,0x5B,0x43,0x3A,0x34,0x5D,0x5B,0x4F,0x3A,0x35,0x5D,0x20,0x3E,0x3E,\n+ 0x20,0x5B,0x4F,0x2D,0x3A,0x31,0x5D,0x5B,0x43,0x3A,0x32,0x5D,0x3D,0x5B,0x43,\n+ 0x3A,0x33,0x5D,0x5B,0x43,0x3A,0x34,0x5D,0x3D,0x5B,0x4F,0x3A,0x35,0x5D,0x09,\n+ 0x34,0x2E,0x30,0x20,0x23,0x20,0x70,0x4B,0x61,0x20,0x66,0x72,0x6F,0x6D,0x20,\n+ 0x61,0x63,0x69,0x64,0x20,0x28,0x41,0x48,0x29,0x0A,0x54,0x52,0x41,0x4E,0x53,\n+ 0x46,0x4F,0x52,0x4D,0x20,0x5B,0x4E,0x5E,0x33,0x3B,0x21,0x24,0x28,0x4E,0x7E,\n+ 0x5B,0x21,0x23,0x36,0x3B,0x21,0x23,0x31,0x5D,0x29,0x3A,0x31,0x5D,0x20,0x3E,\n+ 0x3E,0x20,0x5B,0x4E,0x2B,0x3A,0x31,0x5D,0x09,0x09,0x09,0x09,0x31,0x30,0x2E,\n+ 0x30,0x20,0x23,0x20,0x70,0x4B,0x61,0x20,0x66,0x72,0x6F,0x6D,0x20,0x63,0x6F,\n+ 0x6E,0x6A,0x75,0x67,0x61,0x74,0x65,0x64,0x20,0x61,0x63,0x69,0x64,0x20,0x28,\n+ 0x42,0x48,0x2B,0x29,0x0A,0x54,0x52,0x41,0x4E,0x53,0x46,0x4F,0x52,0x4D,0x20,\n+ 0x5B,0x6E,0x44,0x32,0x3A,0x31,0x5D,0x31,0x63,0x5B,0x6E,0x48,0x5D,0x63,0x63,\n+ 0x31,0x20,0x3E,0x3E,0x20,0x5B,0x6E,0x2B,0x3A,0x31,0x5D,0x31,0x63,0x5B,0x6E,\n+ 0x48,0x5D,0x63,0x63,0x31,0x09,0x09,0x09,0x09,0x37,0x2E,0x30,0x0A,0x54,0x52,\n+ 0x41,0x4E,0x53,0x46,0x4F,0x52,0x4D,0x20,0x5B,0x4E,0x44,0x33,0x2B,0x30,0x3A,\n+ 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0x5D,0x28,0x5B,0x23,0x31,0x3A,0x32,0x5D,0x29,0x5B,0x6E,0x44,0x32,0x2D,0x30,\n+ 0x5D,0x5B,0x6E,0x44,0x32,0x2D,0x30,0x5D,0x63,0x31,0x20,0x3E,0x3E,0x20,0x6E,\n+ 0x31,0x5B,0x6E,0x2D,0x3A,0x31,0x5D,0x6E,0x6E,0x63,0x31,0x09,0x34,0x2E,0x38,\n+ 0x39,0x20,0x23,0x70,0x4B,0x61,0x20,0x66,0x72,0x6F,0x6D,0x20,0x61,0x63,0x69,\n+ 0x64,0x20,0x28,0x41,0x48,0x29,0x0A,0x54,0x52,0x41,0x4E,0x53,0x46,0x4F,0x52,\n+ 0x4D,0x20,0x5B,0x6E,0x44,0x32,0x2D,0x30,0x3A,0x31,0x5D,0x31,0x5B,0x6E,0x44,\n+ 0x32,0x2D,0x30,0x5D,0x5B,0x6E,0x44,0x32,0x2D,0x30,0x5D,0x5B,0x6E,0x44,0x32,\n+ 0x2D,0x30,0x5D,0x63,0x31,0x20,0x3E,0x3E,0x20,0x5B,0x6E,0x2D,0x3A,0x31,0x5D,\n+ 0x31,0x6E,0x6E,0x6E,0x63,0x31,0x09,0x09,0x34,0x2E,0x38,0x39,0x20,0x23,0x70,\n+ 0x4B,0x61,0x20,0x66,0x72,0x6F,0x6D,0x20,0x61,0x63,0x69,0x64,0x20,0x28,0x41,\n+ 0x48,0x29,0x0A,0x54,0x52,0x'..b'x47,0x45,0x09,0x5B,0x4E,0x2B,0x5D,0x09,0x09,0x31,0x2E,\n+ 0x30,0x0A,0x53,0x45,0x45,0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x5B,0x6E,\n+ 0x44,0x32,0x5D,0x31,0x5B,0x6E,0x44,0x32,0x5D,0x5B,0x6E,0x44,0x32,0x5D,0x5B,\n+ 0x6E,0x44,0x32,0x5D,0x63,0x31,0x09,0x2D,0x30,0x2E,0x32,0x09,0x2D,0x30,0x2E,\n+ 0x32,0x09,0x2D,0x30,0x2E,0x32,0x20,0x2D,0x30,0x2E,0x32,0x20,0x2D,0x30,0x2E,\n+ 0x32,0x0A,0x53,0x45,0x45,0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x5B,0x53,\n+ 0x44,0x33,0x5D,0x28,0x3D,0x4F,0x29,0x5B,0x4F,0x2D,0x5D,0x09,0x09,0x30,0x2E,\n+ 0x30,0x09,0x2D,0x30,0x2E,0x35,0x09,0x2D,0x30,0x2E,0x35,0x0A,0x53,0x45,0x45,\n+ 0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x5B,0x53,0x44,0x34,0x5D,0x28,0x3D,\n+ 0x4F,0x29,0x28,0x3D,0x4F,0x29,0x28,0x5B,0x4F,0x2D,0x5D,0x29,0x5B,0x4F,0x48,\n+ 0x31,0x5D,0x09,0x30,0x2E,0x30,0x09,0x2D,0x30,0x2E,0x33,0x33,0x09,0x2D,0x30,\n+ 0x2E,0x33,0x33,0x09,0x2D,0x30,0x2E,0x33,0x33,0x09,0x30,0x2E,0x30,0x0A,0x53,\n+ 0x45,0x45,0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x5B,0x53,0x44,0x34,0x5D,\n+ 0x28,0x5B,0x44,0x32,0x5D,0x29,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x28,\n+ 0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x09,0x30,\n+ 0x2E,0x30,0x09,0x30,0x2E,0x30,0x09,0x2D,0x30,0x2E,0x33,0x33,0x09,0x2D,0x30,\n+ 0x2E,0x33,0x33,0x09,0x2D,0x30,0x2E,0x33,0x33,0x0A,0x53,0x45,0x45,0x44,0x43,\n+ 0x48,0x41,0x52,0x47,0x45,0x09,0x5B,0x23,0x37,0x5E,0x32,0x5D,0x7E,0x5B,0x43,\n+ 0x5E,0x32,0x5D,0x28,0x7E,0x5B,0x4E,0x5E,0x32,0x5D,0x29,0x7E,0x5B,0x4E,0x5E,\n+ 0x32,0x5D,0x09,0x30,0x2E,0x33,0x33,0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,0x33,\n+ 0x33,0x09,0x30,0x2E,0x33,0x33,0x0A,0x53,0x45,0x45,0x44,0x43,0x48,0x41,0x52,\n+ 0x47,0x45,0x09,0x5B,0x23,0x36,0x5D,0x7E,0x5B,0x43,0x5E,0x32,0x5D,0x28,0x7E,\n+ 0x5B,0x4E,0x5E,0x32,0x5D,0x29,0x7E,0x5B,0x4E,0x5E,0x32,0x5D,0x09,0x30,0x2E,\n+ 0x30,0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,0x35,0x09,0x30,0x2E,0x35,0x0A,0x53,\n+ 0x45,0x45,0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x5B,0x50,0x44,0x34,0x5D,\n+ 0x28,0x3D,0x4F,0x29,0x28,0x5B,0x4F,0x44,0x32,0x5D,0x29,0x28,0x5B,0x4F,0x44,\n+ 0x32,0x5D,0x29,0x5B,0x4F,0x44,0x31,0x5D,0x09,0x30,0x2E,0x30,0x09,0x2D,0x30,\n+ 0x2E,0x35,0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,0x30,0x09,0x2D,0x30,0x2E,0x35,\n+ 0x0A,0x53,0x45,0x45,0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x4F,0x3D,0x50,\n+ 0x28,0x5B,0x21,0x44,0x31,0x5D,0x29,0x28,0x5B,0x4F,0x2D,0x5D,0x29,0x5B,0x4F,\n+ 0x2D,0x5D,0x09,0x2D,0x30,0x2E,0x36,0x36,0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,\n+ 0x30,0x09,0x2D,0x30,0x2E,0x36,0x36,0x09,0x2D,0x30,0x2E,0x36,0x36,0x0A,0x53,\n+ 0x45,0x45,0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x50,0x28,0x3D,0x4F,0x29,\n+ 0x28,0x3D,0x4F,0x29,0x28,0x5B,0x4F,0x2D,0x5D,0x29,0x5B,0x4F,0x2D,0x5D,0x09,\n+ 0x30,0x2E,0x30,0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,0x30,0x20,0x2D,0x30,0x2E,\n+ 0x35,0x09,0x2D,0x30,0x2E,0x35,0x0A,0x53,0x45,0x45,0x44,0x43,0x48,0x41,0x52,\n+ 0x47,0x45,0x09,0x5B,0x23,0x36,0x5D,0x50,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,\n+ 0x29,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,\n+ 0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,0x30,0x09,0x2D,0x30,0x2E,0x33,0x33,0x20,\n+ 0x2D,0x30,0x2E,0x33,0x33,0x20,0x2D,0x30,0x2E,0x33,0x33,0x0A,0x53,0x45,0x45,\n+ 0x44,0x43,0x48,0x41,0x52,0x47,0x45,0x09,0x4F,0x3D,0x43,0x5B,0x4E,0x3B,0x21,\n+ 0x24,0x28,0x4E,0x28,0x43,0x3D,0x4F,0x29,0x43,0x3D,0x4F,0x29,0x5D,0x5B,0x4F,\n+ 0x44,0x31,0x5D,0x09,0x2D,0x30,0x2E,0x35,0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,\n+ 0x30,0x09,0x2D,0x30,0x2E,0x35,0x0A,0x53,0x45,0x45,0x44,0x43,0x48,0x41,0x52,\n+ 0x47,0x45,0x09,0x4F,0x3D,0x43,0x4E,0x28,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x4E,\n+ 0x43,0x3D,0x4F,0x09,0x09,0x2D,0x30,0x2E,0x33,0x33,0x09,0x30,0x2E,0x30,0x09,\n+ 0x30,0x2E,0x30,0x09,0x2D,0x30,0x2E,0x33,0x33,0x09,0x30,0x2E,0x30,0x20,0x30,\n+ 0x2E,0x30,0x09,0x2D,0x30,0x2E,0x33,0x33,0x0A,0x53,0x45,0x45,0x44,0x43,0x48,\n+ 0x41,0x52,0x47,0x45,0x09,0x5B,0x6E,0x2B,0x48,0x5D,0x31,0x63,0x5B,0x6E,0x48,\n+ 0x5D,0x63,0x63,0x31,0x09,0x09,0x30,0x2E,0x35,0x09,0x30,0x2E,0x30,0x09,0x30,\n+ 0x2E,0x35,0x09,0x30,0x2E,0x30,0x09,0x30,0x2E,0x30,0x0A,0x00};\n+\n+} // namespace OpenBabel\n+#endif // OB_PHMODELDATA_H\n+\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/plugindefines.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/plugindefines.txt Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/psa.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/psa.txt Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/qeq.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/qeq.txt Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/resdata.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/resdata.h Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,920 @@\n+/***************************************************************\n+This file is part of the Open Babel project.\n+This is copyright under the GNU General Public License (GPL)\n+For more information, see <http://openbabel.org/>\n+\n+This file contains a binary representation of data tables\n+ used by Open Babel. It is used as a fallback if the textual\n+ data table is not found at runtime. It is not a normal header.\n+***************************************************************/\n+\n+\n+#ifndef OB_RESDATA_H\n+#define OB_RESDATA_H\n+\n+namespace OpenBabel\n+{\n+static const char ResidueData[] = {\n+ 0x52,0x45,0x53,0x20,0x41,0x4C,0x41,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x41,\n+ 0x20,0x43,0x33,0x20,0x33,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x4E,0x20,0x4E,0x61,\n+ 0x6D,0x20,0x32,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x42,0x20,0x43,0x33,0x20,\n+ 0x33,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x20,0x43,0x61,0x63,0x20,0x32,0x0A,\n+ 0x41,0x54,0x4F,0x4D,0x20,0x4F,0x20,0x4F,0x32,0x20,0x32,0x0A,0x42,0x4F,0x4E,\n+ 0x44,0x20,0x43,0x41,0x20,0x4E,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,\n+ 0x41,0x20,0x43,0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x41,0x20,\n+ 0x43,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x20,0x4F,0x20,0x32,0x0A,\n+ 0x42,0x4F,0x4E,0x44,0x20,0x4E,0x20,0x48,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,\n+ 0x20,0x4E,0x20,0x48,0x4E,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x48,0x41,\n+ 0x20,0x43,0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x31,0x48,0x42,0x20,\n+ 0x43,0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x32,0x48,0x42,0x20,0x43,\n+ 0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x33,0x48,0x42,0x20,0x43,0x42,\n+ 0x20,0x31,0x0A,0x45,0x4E,0x44,0x0A,0x52,0x45,0x53,0x20,0x41,0x52,0x47,0x0A,\n+ 0x41,0x54,0x4F,0x4D,0x20,0x43,0x41,0x20,0x43,0x33,0x20,0x33,0x0A,0x41,0x54,\n+ 0x4F,0x4D,0x20,0x4E,0x20,0x4E,0x61,0x6D,0x20,0x32,0x0A,0x41,0x54,0x4F,0x4D,\n+ 0x20,0x43,0x42,0x20,0x43,0x33,0x20,0x33,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,\n+ 0x20,0x43,0x61,0x63,0x20,0x32,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x4F,0x20,0x4F,\n+ 0x32,0x20,0x32,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x47,0x20,0x43,0x33,0x20,\n+ 0x33,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x44,0x20,0x43,0x33,0x20,0x33,0x0A,\n+ 0x41,0x54,0x4F,0x4D,0x20,0x4E,0x45,0x20,0x4E,0x67,0x2B,0x20,0x32,0x0A,0x41,\n+ 0x54,0x4F,0x4D,0x20,0x43,0x5A,0x20,0x43,0x2B,0x20,0x32,0x0A,0x41,0x54,0x4F,\n+ 0x4D,0x20,0x4E,0x48,0x32,0x20,0x4E,0x67,0x2B,0x20,0x32,0x0A,0x41,0x54,0x4F,\n+ 0x4D,0x20,0x4E,0x48,0x31,0x20,0x4E,0x67,0x2B,0x20,0x32,0x0A,0x42,0x4F,0x4E,\n+ 0x44,0x20,0x43,0x41,0x20,0x4E,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,\n+ 0x41,0x20,0x43,0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x41,0x20,\n+ 0x43,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x20,0x4F,0x20,0x32,0x0A,\n+ 0x42,0x4F,0x4E,0x44,0x20,0x43,0x42,0x20,0x43,0x47,0x20,0x31,0x0A,0x42,0x4F,\n+ 0x4E,0x44,0x20,0x43,0x47,0x20,0x43,0x44,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,\n+ 0x20,0x43,0x44,0x20,0x4E,0x45,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,\n+ 0x45,0x20,0x43,0x5A,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x5A,0x20,\n+ 0x4E,0x48,0x32,0x20,0x32,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x5A,0x20,0x4E,\n+ 0x48,0x31,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,0x20,0x48,0x20,0x31,\n+ 0x0A,0x42,0x4F,0x4E,0x44,0x20,0x48,0x4E,0x20,0x4E,0x20,0x31,0x0A,0x42,0x4F,\n+ 0x4E,0x44,0x20,0x4E,0x48,0x31,0x20,0x31,0x48,0x48,0x31,0x20,0x31,0x0A,0x42,\n+ 0x4F,0x4E,0x44,0x20,0x4E,0x48,0x31,0x20,0x32,0x48,0x48,0x31,0x20,0x31,0x0A,\n+ 0x42,0x4F,0x4E,0x44,0x20,0x4E,0x45,0x20,0x48,0x45,0x20,0x31,0x0A,0x42,0x4F,\n+ 0x4E,0x44,0x20,0x4E,0x48,0x32,0x20,0x31,0x48,0x48,0x32,0x20,0x31,0x0A,0x42,\n+ 0x4F,0x4E,0x44,0x20,0x4E,0x48,0x32,0x20,0x32,0x48,0x48,0x32,0x20,0x31,0x0A,\n+ 0x42,0x4F,0x4E,0x44,0x20,0x4E,0x48,0x31,0x20,0x48,0x48,0x31,0x20,0x31,0x0A,\n+ 0x42,0x4F,0x4E,0x44,0x20,0x4E,0x48,0x32,0x20,0x48,0x48,0x32,0x20,0x31,0x0A,\n+ 0x42,0x4F,0x4E,0x44,0x20,0x48,0x41,0x20,0x43,0x41,0x20,0x31,0x09,0x0A,0x42,\n+ 0x4F,0x4E,0x44,0x20,0x31,0x48,0x42,0x20,0x43,0x42,0x20,0x31,0x0A,0x42,0x4F,\n+ 0x4E,0x44,0x20,0x32,0x48,0x42,0x20,'..b'0x0A,0x41,0x54,0x4F,0x4D,\n+ 0x20,0x4F,0x31,0x44,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x4F,0x32,0x44,0x0A,0x42,\n+ 0x4F,0x4E,0x44,0x20,0x46,0x45,0x20,0x4E,0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,\n+ 0x44,0x20,0x46,0x45,0x20,0x4E,0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,\n+ 0x46,0x45,0x20,0x4E,0x43,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x46,0x45,\n+ 0x20,0x4E,0x44,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x41,0x20,\n+ 0x43,0x31,0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x41,0x20,\n+ 0x43,0x34,0x44,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x42,0x20,\n+ 0x43,0x34,0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x42,0x20,\n+ 0x43,0x31,0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x43,0x20,\n+ 0x43,0x34,0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x43,0x20,\n+ 0x43,0x31,0x43,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x44,0x20,\n+ 0x43,0x34,0x43,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x48,0x44,0x20,\n+ 0x43,0x31,0x44,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,0x41,0x20,0x43,\n+ 0x31,0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,0x41,0x20,0x43,0x34,\n+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x31,0x41,0x20,0x43,0x32,\n+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x32,0x41,0x20,0x43,0x33,\n+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x32,0x41,0x20,0x43,0x41,\n+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x33,0x41,0x20,0x43,0x34,\n+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x33,0x41,0x20,0x43,0x4D,\n+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x41,0x41,0x20,0x43,0x42,\n+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x42,0x41,0x20,0x43,0x47,\n+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x47,0x41,0x20,0x4F,0x31,\n+ 0x41,0x20,0x32,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x47,0x41,0x20,0x4F,0x32,\n+ 0x41,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,0x42,0x20,0x43,0x31,0x42,\n+ 0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,0x42,0x20,0x43,0x34,0x42,0x20,\n+ 0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x31,0x42,0x20,0x43,0x32,0x42,0x20,\n+ 0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x32,0x42,0x20,0x43,0x33,0x42,0x20,\n+ 0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x32,0x42,0x20,0x43,0x4D,0x42,0x20,\n+ 0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x33,0x42,0x20,0x43,0x34,0x42,0x20,\n+ 0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x33,0x42,0x20,0x43,0x41,0x42,0x20,\n+ 0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x41,0x42,0x20,0x43,0x42,0x42,0x20,\n+ 0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,0x43,0x20,0x43,0x31,0x43,0x20,0x31,\n+ 0x0A,0x42,0x4F,0x4E,0x44,0x20,0x4E,0x43,0x20,0x43,0x34,0x43,0x20,0x31,0x0A,\n+ 0x42,0x4F,0x4E,0x44,0x20,0x43,0x31,0x43,0x20,0x43,0x32,0x43,0x20,0x31,0x0A,\n+ 0x42,0x4F,0x4E,0x44,0x20,0x43,0x32,0x43,0x20,0x43,0x33,0x43,0x20,0x31,0x0A,\n+ 0x42,0x4F,0x4E,0x44,0x20,0x43,0x32,0x43,0x20,0x43,0x4D,0x43,0x20,0x31,0x0A,\n+ 0x42,0x4F,0x4E,0x44,0x20,0x43,0x33,0x43,0x20,0x43,0x34,0x43,0x20,0x31,0x0A,\n+ 0x42,0x4F,0x4E,0x44,0x20,0x43,0x33,0x43,0x20,0x43,0x41,0x43,0x20,0x31,0x0A,\n+ 0x42,0x4F,0x4E,0x44,0x20,0x43,0x41,0x43,0x20,0x43,0x42,0x43,0x20,0x31,0x0A,\n+ 0x42,0x4F,0x4E,0x44,0x20,0x4E,0x44,0x20,0x43,0x31,0x44,0x20,0x31,0x0A,0x42,\n+ 0x4F,0x4E,0x44,0x20,0x4E,0x44,0x20,0x43,0x34,0x44,0x20,0x31,0x0A,0x42,0x4F,\n+ 0x4E,0x44,0x20,0x43,0x31,0x44,0x20,0x43,0x32,0x44,0x20,0x31,0x0A,0x42,0x4F,\n+ 0x4E,0x44,0x20,0x43,0x32,0x44,0x20,0x43,0x33,0x44,0x20,0x31,0x0A,0x42,0x4F,\n+ 0x4E,0x44,0x20,0x43,0x32,0x44,0x20,0x43,0x4D,0x44,0x20,0x31,0x0A,0x42,0x4F,\n+ 0x4E,0x44,0x20,0x43,0x33,0x44,0x20,0x43,0x34,0x44,0x20,0x31,0x0A,0x42,0x4F,\n+ 0x4E,0x44,0x20,0x43,0x33,0x44,0x20,0x43,0x41,0x44,0x20,0x31,0x0A,0x42,0x4F,\n+ 0x4E,0x44,0x20,0x43,0x41,0x44,0x20,0x43,0x42,0x44,0x20,0x31,0x0A,0x42,0x4F,\n+ 0x4E,0x44,0x20,0x43,0x42,0x44,0x20,0x43,0x47,0x44,0x20,0x31,0x0A,0x42,0x4F,\n+ 0x4E,0x44,0x20,0x43,0x47,0x44,0x20,0x4F,0x31,0x44,0x20,0x32,0x0A,0x42,0x4F,\n+ 0x4E,0x44,0x20,0x43,0x47,0x44,0x20,0x4F,0x32,0x44,0x20,0x31,0x0A,0x45,0x4E,\n+ 0x44,0x0A,0x00};\n+\n+} // namespace OpenBabel\n+#endif // OB_RESDATA_H\n+\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/resdata.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/resdata.txt Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,1139 @@\n+##############################################################################\n+# #\n+# Open Babel file: resdata.txt #\n+# #\n+# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #\n+# Some portions Copyright (c) 2001-2003 by Geoffrey R. Hutchison #\n+# Part of the Open Babel package, under the GNU General Public License (GPL)#\n+# #\n+# Residue records are specified as follows: (used by data.cpp:OBResidueData)#\n+# RES <name> #\n+# ATOM Name Type Hybridization (hydrogens are implicit) #\n+# BOND Name1 Name2 BondOrder (where Name1, Name2 are ATOM records) #\n+# END #\n+# #\n+##############################################################################\n+\n+RES ALA\n+ATOM CA C3 3\n+ATOM N Nam 2\n+ATOM CB C3 3\n+ATOM C Cac 2\n+ATOM O O2 2\n+BOND CA N 1\n+BOND CA CB 1\n+BOND CA C 1\n+BOND C O 2\n+BOND N H 1\n+BOND N HN 1\n+BOND HA CA 1\n+BOND 1HB CB 1\n+BOND 2HB CB 1\n+BOND 3HB CB 1\n+END\n+\n+RES ARG\n+ATOM CA C3 3\n+ATOM N Nam 2\n+ATOM CB C3 3\n+ATOM C Cac 2\n+ATOM O O2 2\n+ATOM CG C3 3\n+ATOM CD C3 3\n+ATOM NE Ng+ 2\n+ATOM CZ C+ 2\n+ATOM NH2 Ng+ 2\n+ATOM NH1 Ng+ 2\n+BOND CA N 1\n+BOND CA CB 1\n+BOND CA C 1\n+BOND C O 2\n+BOND CB CG 1\n+BOND CG CD 1\n+BOND CD NE 1\n+BOND NE CZ 1\n+BOND CZ NH2 2\n+BOND CZ NH1 1\n+BOND N H 1\n+BOND HN N 1\n+BOND NH1 1HH1 1\n+BOND NH1 2HH1 1\n+BOND NE HE 1\n+BOND NH2 1HH2 1\n+BOND NH2 2HH2 1\n+BOND NH1 HH1 1\n+BOND NH2 HH2 1\n+BOND HA CA 1\t\n+BOND 1HB CB 1\n+BOND 2HB CB 1\n+BOND 1HD CD 1\n+BOND 2HD CD 1\n+BOND 1HG CG 1\n+BOND 2HG CG 1\n+END\n+\n+RES ARZ\n+ATOM CA C3 3\n+ATOM N Nam 2\n+ATOM CB C3 3\n+ATOM C Cac 2\n+ATOM O O2 2\n+ATOM CG C3 3\n+ATOM CD C3 3\n+ATOM NE Ng+ 2\n+ATOM CZ C+ 2\n+ATOM NH2 Ng+ 2\n+ATOM NH1 Ng+ 2\n+BOND CA N 1\n+BOND CA CB 1\n+BOND CA C 1\n+BOND C O 2\n+BOND CB CG 1\n+BOND CG CD 1\n+BOND CD NE 1\n+BOND NE CZ 1\n+BOND CZ NH2 1\n+BOND CZ NH1 2\n+BOND N H 1\n+BOND N HN 1\n+BOND NH1 HH1 1\n+BOND NE HE 1\n+BOND NH2 1HH2 1\n+BOND NH2 2HH2 1\n+END\n+\n+RES ASN\n+ATOM CA C3 3\n+ATOM N Nam 2\n+ATOM CB C3 3\n+ATOM C Cac 2\n+ATOM O O2 2\n+ATOM CG C3 3\n+ATOM ND2 Nam 2\n+ATOM OD1 O2 2\n+BOND CA N 1\n+BOND CA CB 1\n+BOND CA C 1\n+BOND C O 2\n+BOND CB CG 1\n+BOND CG ND2 1\n+BOND CG OD1 2\n+BOND N H 1\n+BOND N HN 1\n+BOND HA CA 1\n+BOND 1HB CB 1\n+BOND 2HB CB 1\n+BOND ND2 1HD2 1\n+BOND ND2 2HD2 1\n+BOND ND2 HD2 1\n+END\n+\n+RES ASP\n+ATOM CA C3 3\n+ATOM N Nam 2\n+ATOM CB C3 3\n+ATOM C Cac 2\n+ATOM O O2 2\n+ATOM CG C2 2\n+ATOM OD2 O2 2\n+ATOM OD1 O3 3\n+BOND CA N 1\n+BOND CA CB 1\n+BOND CA C 1\n+BOND C O 2\n+BOND CB CG 1\n+BOND CG OD2 2\n+BOND CG OD1 1\n+BOND N H 1\n+BOND N HN 1\n+BOND HA CA 1\n+BOND 1HB CB 1\n+BOND 2HB CB 1\n+END\n+\n+RES ASH\n+ATOM CA C3 3\n+ATOM N Nam 2\n+ATOM CB C3 3\n+ATOM C Cac 2\n+ATOM O O2 2\n+ATOM CG C2 2\n+ATOM OD2 O3 3\n+ATOM OD1 O2 2\n+BOND CA N 1\n+BOND CA CB 1\n+BOND CA C 1\n+BOND C O 2\n+BOND CB CG 1\n+BOND CG OD2 1\n+BOND CG OD1 2\n+BOND N H 1\n+BOND N HN 1\n+BOND OD2 HD2 1\n+END\n+\n+RES CYS\n+ATOM CA C3 3\n+ATOM N Nam 2\n+ATOM CB C3 3\n+ATOM C Cac 2\n+ATOM O O2 2\n+ATOM SG S3 3\n+BOND SG CB 1\n+BOND CA N 1\n+BOND CA CB 1\n+BOND CA C 1\n+BOND C O 2\n+BOND CB SG 1\n+BOND N H 1\n+BOND N HN 1\n+BOND CA HA 1\n+BOND 1HB CB 1\n+BOND 2HB CB 1\n+BOND SG HG 1\n+END\n+\n+RES CYX\n+ATOM CA C3 3\n+ATOM N Nam 2\n+ATOM CB C3 3\n+ATOM C Cac 2\n+ATOM O O2 2\n+ATOM SG S3 3\n+BOND CA N 1\n+BOND CA CB 1\n+BOND CA C 1\n+BOND C O 2\n+BOND CB SG 1\n+BOND N H 1\n+END\n+\n+RES GLN\n+ATOM CA C3 3\n+ATOM N Nam 2\n+ATOM CB C3 3\n+ATOM C Cac 2\n+ATOM O O2 2\n+ATOM CG C3 3\n+ATOM CD C2 2\n+ATOM NE2 Nam 2\n+ATOM OE1 O2 2\n+BOND CA N 1\n+BOND CA CB 1\n+BOND CA C 1\n+BOND C O 2\n+BOND CB CG 1\n+BOND CG CD 1\n+BOND CD NE2 1\n+BOND CD OE1 2\n+BOND N H'..b'+BOND CZ2 CH2 1\n+BOND CH2 CZ3 2\n+BOND CZ3 CE3 1\n+BOND N H 1\n+BOND N HN 1\n+BOND HA CA 1\n+BOND 1HB CB 1\n+BOND 2HB CB 1\n+BOND 1HD CD1 1\n+BOND 1HE CE1 1\n+BOND 2HZ CZ2 1\n+BOND 3HZ CZ3 1\n+BOND 3HE CE3 1\n+BOND 2HH CH2 1\n+BOND NE1 HE1 1\n+BOND NE1 1HE 1\n+END\n+\n+RES TYR\n+ATOM CA C3 3\n+ATOM N Nam 2\n+ATOM CB C3 3\n+ATOM C Cac 2\n+ATOM O O2 2\n+ATOM CG Car 2\n+ATOM CD1 Car 2\n+ATOM CD2 Car 2\n+ATOM CE2 Car 2\n+ATOM CZ Car 2\n+ATOM OH O3 3\n+ATOM CE1 Car 2\n+BOND CA N 1\n+BOND CA CB 1\n+BOND CA C 1\n+BOND C O 2\n+BOND CB CG 1\n+BOND CG CD1 2\n+BOND CG CD2 1\n+BOND CD2 CE2 2\n+BOND CE2 CZ 1\n+BOND CZ OH 1\n+BOND CZ CE1 2\n+BOND CE1 CD1 1\n+BOND N H 1\n+BOND OH HH 1\n+BOND N HN 1\n+BOND HA CA 1\n+BOND 1HB CB 1\n+BOND 2HB CB 1\n+BOND 1HD CD1 1\n+BOND 2HD CD2 1\n+BOND 1HE CE1 1\n+BOND 2HE CE2 1\n+BOND HZ CZ 1\n+END\n+\n+RES VAL\n+ATOM CA C3 3\n+ATOM N Nam 2\n+ATOM CB C3 3\n+ATOM C Cac 2\n+ATOM O O2 2\n+ATOM CG2 C3 3\n+ATOM CG1 C3 3\n+BOND CA N 1\n+BOND CA CB 1\n+BOND CA C 1\n+BOND C O 2\n+BOND CB CG2 1\n+BOND CB CG1 1\n+BOND N H 1\n+BOND N HN 1\n+BOND HA CA 1\n+BOND HB CB 1\n+BOND 1HG1 CG1 1\n+BOND 2HG1 CG1 1\n+BOND 3HG1 CG1 1\n+BOND 1HG2 CG2 1\n+BOND 2HG2 CG2 1\n+BOND 3HG2 CG2 1\n+END\n+\n+RES TIP\n+ATOM OH2 O3 3\n+BOND OH2 H1 1\n+BOND OH2 H2 1\n+END\n+\n+RES HOH\n+ATOM O O3 3\n+ATOM 1H\n+ATOM 2H\n+BOND O 1H 1\n+BOND O 2H 1\n+END\n+\n+RES WAT\n+ATOM O O3 3\n+ATOM H1\n+ATOM H2\n+BOND O H1 1\n+BOND O H2 1\n+END\n+\n+RES INH\n+ATOM P\n+ATOM O1P\n+ATOM O2P\n+ATOM O3P\n+ATOM O5\n+ATOM C5\n+ATOM C4\n+ATOM O4\n+ATOM C3\n+ATOM C1\n+ATOM O3\n+ATOM C2\n+ATOM O2\n+ATOM N9\n+ATOM C8\n+ATOM N7\n+ATOM C6\n+ATOM O6\n+ATOM N1\n+ATOM N3\n+BOND P O1P 2\n+BOND P O2P 1\n+BOND P O3P 1\n+BOND P O5 1\n+BOND O5 C5 1\n+BOND C5 C4 1\n+BOND C4 O4 1\n+BOND C4 C3 1\n+BOND O4 C1 1\n+BOND C3 O3 1\n+BOND C3 C2 1\n+BOND O3 H1 1\n+BOND C2 O2 1\n+BOND C2 C1 1\n+BOND O2 H2 1\n+BOND C1 N9 1\n+BOND N9 C8 1\n+BOND N9 C4 1\n+BOND C8 N7 2\n+BOND N7 C5 1\n+BOND C5 C6 1\n+BOND C6 O6 2\n+BOND C6 N1 1\n+BOND N1 C2 1\n+BOND N1 H3 1\n+BOND C2 N3 2\n+BOND N3 C4 1\n+END\n+\n+RES UMP\n+ATOM N1\n+ATOM C2\n+ATOM C6\n+ATOM C1\n+ATOM N3\n+ATOM O2\n+ATOM C4\n+ATOM C5\n+ATOM O4\n+ATOM C3\n+ATOM O3\n+ATOM O5\n+ATOM P\n+ATOM O1P\n+ATOM O2P\n+ATOM O3P\n+BOND N1 C2 1\n+BOND N1 C6 1\n+BOND N1 C1 1\n+BOND C2 N3 1\n+BOND C2 O2 1\n+BOND C2 H5 1\n+BOND N3 C4 1\n+BOND N3 H1 1\n+BOND C4 C5 1\n+BOND C4 O4 1\n+BOND C4 H6 1\n+BOND C5 C6 1\n+BOND C5 H7 1\n+BOND C5 H8 1\n+BOND C6 H9 1\n+BOND C6 H10 1\n+BOND O2 H2 1\n+BOND O4 H3 1\n+BOND C1 C2 1\n+BOND C1 O4 1\n+BOND C1 H11 1\n+BOND C2 C3 1\n+BOND C2 H12 1\n+BOND C2 H13 1\n+BOND C3 C4 1\n+BOND C3 O3 1\n+BOND C3 H14 1\n+BOND C4 H15 1\n+BOND O3 H4 1\n+BOND C5 O5 1\n+BOND C5 H16 1\n+BOND C5 H17 1\n+BOND O5 P 1\n+BOND P O1P 2\n+BOND P O2P 2\n+BOND P O3P 2\n+END\n+\n+RES HED\n+ATOM C1\n+ATOM O1\n+ATOM C2\n+ATOM S3\n+ATOM S4\n+ATOM C5\n+ATOM C6\n+ATOM O6\n+BOND C1 O1 2\n+BOND C1 C2 1\n+BOND C2 S3 1\n+BOND S3 S4 1\n+BOND S4 C5 1\n+BOND C5 C6 1\n+BOND C6 O6 2\n+END\n+\n+RES HEM\n+ATOM FE\n+ATOM NA\n+ATOM NB\n+ATOM NC\n+ATOM ND\n+ATOM CHA\n+ATOM C1A\n+ATOM C4D\n+ATOM CHB\n+ATOM C4A\n+ATOM C1B\n+ATOM CHC\n+ATOM C4B\n+ATOM C1C\n+ATOM CHD\n+ATOM C4C\n+ATOM C1D\n+ATOM C2A\n+ATOM C3A\n+ATOM CAA\n+ATOM CMA\n+ATOM CBA\n+ATOM CGA\n+ATOM O1A\n+ATOM O2A\n+ATOM C2B\n+ATOM C3B\n+ATOM CMB\n+ATOM CAB\n+ATOM CBB\n+ATOM C2C\n+ATOM C3C\n+ATOM CMC\n+ATOM CAC C3 3\n+ATOM CBC\n+ATOM C2D\n+ATOM C3D\n+ATOM CMD\n+ATOM CAD\n+ATOM CBD\n+ATOM CGD\n+ATOM O1D\n+ATOM O2D\n+BOND FE NA 1\n+BOND FE NB 1\n+BOND FE NC 1\n+BOND FE ND 1\n+BOND CHA C1A 1\n+BOND CHA C4D 1\n+BOND CHB C4A 1\n+BOND CHB C1B 1\n+BOND CHC C4B 1\n+BOND CHC C1C 1\n+BOND CHD C4C 1\n+BOND CHD C1D 1\n+BOND NA C1A 1\n+BOND NA C4A 1\n+BOND C1A C2A 1\n+BOND C2A C3A 1\n+BOND C2A CAA 1\n+BOND C3A C4A 1\n+BOND C3A CMA 1\n+BOND CAA CBA 1\n+BOND CBA CGA 1\n+BOND CGA O1A 2\n+BOND CGA O2A 1\n+BOND NB C1B 1\n+BOND NB C4B 1\n+BOND C1B C2B 1\n+BOND C2B C3B 1\n+BOND C2B CMB 1\n+BOND C3B C4B 1\n+BOND C3B CAB 1\n+BOND CAB CBB 1\n+BOND NC C1C 1\n+BOND NC C4C 1\n+BOND C1C C2C 1\n+BOND C2C C3C 1\n+BOND C2C CMC 1\n+BOND C3C C4C 1\n+BOND C3C CAC 1\n+BOND CAC CBC 1\n+BOND ND C1D 1\n+BOND ND C4D 1\n+BOND C1D C2D 1\n+BOND C2D C3D 1\n+BOND C2D CMD 1\n+BOND C3D C4D 1\n+BOND C3D CAD 1\n+BOND CAD CBD 1\n+BOND CBD CGD 1\n+BOND CGD O1D 2\n+BOND CGD O2D 1\n+END\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/ringtyp.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/ringtyp.txt Tue Jun 07 16:43:30 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
+#

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/space-groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/space-groups.txt Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,9508 @@\n+1\n+P 1\n+P 1\n+x,y,z\n+\n+2\n+-P 1\n+P -1\n+x,y,z\n+-x,-y,-z\n+\n+3\n+P 2y\n+P 2,P 1 2 1\n+x,y,z\n+-x,y,-z\n+\n+3\n+P 2x\n+P 2 1 1\n+x,y,z\n+x,-y,-z\n+\n+3\n+P 2\n+P 1 1 2\n+x,y,z\n+-x,-y,z\n+\n+4\n+P 2yb\n+P 21,P 1 21 1\n+x,y,z\n+-x,1/2+y,-z\n+\n+4\n+P 2xa\n+P 21 1 1\n+x,y,z\n+1/2+x,-y,-z\n+\n+4\n+P 2c\n+P 1 1 21\n+x,y,z\n+-x,-y,1/2+z\n+\n+5\n+C 2y\n+C 2,C 1 2 1\n+x,y,z\n+-x,y,-z\n+1/2+x,1/2+y,z\n+1/2-x,1/2+y,-z\n+\n+5\n+A 2y\n+A 1 2 1\n+x,y,z\n+-x,y,-z\n+x,1/2+y,1/2+z\n+-x,1/2+y,1/2-z\n+\n+5\n+I 2y\n+I 1 2 1\n+x,y,z\n+-x,y,-z\n+1/2+x,1/2+y,1/2+z\n+1/2-x,1/2+y,1/2-z\n+\n+5\n+A 2\n+A 1 1 2\n+x,y,z\n+-x,-y,z\n+x,1/2+y,1/2+z\n+-x,1/2-y,1/2+z\n+\n+5\n+B 2\n+B 1 1 2\n+x,y,z\n+-x,-y,z\n+1/2+x,y,1/2+z\n+1/2-x,-y,1/2+z\n+\n+5\n+I 2\n+I 1 1 2\n+x,y,z\n+-x,-y,z\n+1/2+x,1/2+y,1/2+z\n+1/2-x,1/2-y,1/2+z\n+\n+5\n+B 2x\n+B 2 1 1\n+x,y,z\n+x,-y,-z\n+1/2+x,y,1/2+z\n+1/2+x,-y,1/2-z\n+\n+5\n+C 2x\n+C 2 1 1\n+x,y,z\n+x,-y,-z\n+1/2+x,1/2+y,z\n+1/2+x,1/2-y,-z\n+\n+5\n+I 2x\n+I 2 1 1\n+x,y,z\n+x,-y,-z\n+1/2+x,1/2+y,1/2+z\n+1/2+x,1/2-y,1/2-z\n+\n+6\n+P -2y\n+P m,P 1 m 1\n+x,y,z\n+x,-y,z\n+\n+6\n+P -2\n+P 1 1 m\n+x,y,z\n+x,y,-z\n+\n+6\n+P -2x\n+P m 1 1\n+x,y,z\n+-x,y,z\n+\n+7\n+P -2yc\n+P c,P 1 c 1\n+x,y,z\n+x,-y,1/2+z\n+\n+7\n+P -2yac\n+P 1 n 1\n+x,y,z\n+1/2+x,y,1/2+z\n+\n+7\n+P -2ya\n+P 1 a 1\n+x,y,z\n+1/2+x,-y,z\n+\n+7\n+P -2a\n+P 1 1 a\n+x,y,z\n+1/2+x,y,-z\n+\n+7\n+P -2ab\n+P 1 1 n\n+x,y,z\n+1/2+x,1/2+y,-z\n+\n+7\n+P -2b\n+P b,P 1 1 b\n+x,y,z\n+x,1/2+y,-z\n+\n+7\n+P -2xb\n+P b 1 1\n+x,y,z\n+-x,1/2+y,z\n+\n+7\n+P -2xbc\n+P n 1 1\n+x,y,z\n+-x,1/2+y,1/2+z\n+\n+7\n+P -2xc\n+P c 1 1\n+x,y,z\n+-x,y,1/2+z\n+\n+8\n+C -2y\n+C m,C 1 m 1\n+x,y,z\n+x,-y,z\n+1/2+x,1/2+y,z\n+1/2+x,1/2-y,z\n+\n+8\n+A -2y\n+A 1 m 1\n+x,y,z\n+x,-y,z\n+x,1/2+y,1/2+z\n+x,1/2-y,1/2+z\n+\n+8\n+I -2y\n+I 1 m 1\n+x,y,z\n+x,-y,z\n+1/2+x,1/2+y,1/2+z\n+1/2+x,1/2-y,1/2+z\n+\n+8\n+A -2\n+A 1 1 m\n+x,y,z\n+x,y,-z\n+x,1/2+y,1/2+z\n+x,1/2+y,1/2-z\n+\n+8\n+B -2\n+B m,B 1 1 m\n+x,y,z\n+x,y,-z\n+1/2+x,y,1/2+z\n+1/2+x,y,1/2-z\n+\n+8\n+I -2\n+I 1 1 m\n+x,y,z\n+x,y,-z\n+1/2+x,1/2+y,1/2+z\n+1/2+x,1/2+y,1/2-z\n+\n+8\n+B -2x\n+B m 1 1\n+x,y,z\n+-x,y,z\n+1/2+x,y,1/2+z\n+1/2-x,y,1/2+z\n+\n+8\n+C -2x\n+C m 1 1\n+x,y,z\n+-x,y,z\n+1/2+x,1/2+y,z\n+1/2-x,1/2+y,z\n+\n+8\n+I -2x\n+I m 1 1\n+x,y,z\n+-x,y,z\n+1/2+x,1/2+y,1/2+z\n+1/2-x,1/2+y,1/2+z\n+\n+9\n+C -2yc\n+C c,C 1 c 1\n+x,y,z\n+x,-y,1/2+z\n+1/2+x,1/2+y,z\n+1/2+x,1/2-y,1/2+z\n+\n+9\n+A -2yac\n+A 1 n 1\n+x,y,z\n+1/2+x,-y,1/2+z\n+x,1/2+y,1/2+z\n+1/2+x,1/2-y,z\n+\n+9\n+I -2ya\n+I 1 a 1\n+x,y,z\n+1/2+x,-y,z\n+1/2+x,1/2+y,1/2+z\n+x,1/2-y,1/2+z\n+\n+9\n+A -2ya\n+A 1 a 1\n+x,y,z\n+1/2+x,-y,z\n+x,1/2+y,1/2+z\n+1/2+x,1/2-y,1/2+z\n+\n+9\n+C -2ybc\n+C 1 n 1\n+x,y,z\n+1/2+x,-y,1/2+z\n+1/2+x,1/2+y,z\n+x,1/2-y,1/2+z\n+\n+9\n+I -2yc\n+I 1 c 1\n+x,y,z\n+x,-y,1/2+z\n+1/2+x,1/2+y,1/2+z\n+1/2+x,1/2-y,z\n+\n+9\n+A -2a\n+A 1 1 a\n+x,y,z\n+1/2+x,y,-z\n+x,1/2+y,1/2+z\n+1/2+x,1/2+y,1/2-z\n+\n+9\n+B -2bc\n+B 1 1 n\n+x,y,z\n+x,1/2+y,-z\n+1/2+x,y,1/2+z\n+1/2+x,1/2+y,1/2-z\n+\n+9\n+I -2b\n+I 1 1 b\n+x,y,z\n+x,1/2+y,-z\n+1/2+x,1/2+y,1/2+z\n+1/2+x,y,1/2-z\n+\n+9\n+B -2b\n+B b,B 1 1 b\n+x,y,z\n+x,1/2+y,-z\n+1/2+x,y,1/2+z\n+1/2+x,1/2+y,1/2-z\n+\n+9\n+A -2ac\n+A 1 1 n\n+x,y,z\n+1/2+x,1/2+y,-z\n+x,1/2+y,1/2+z\n+1/2+x,y,1/2-z\n+\n+9\n+I -2a\n+I 1 1 a\n+x,y,z\n+1/2+x,y,-z\n+1/2+x,1/2+y,1/2+z\n+x,1/2+y,1/2-z\n+\n+9\n+B -2xb\n+B b 1 1\n+x,y,z\n+-x,1/2+y,z\n+1/2+x,y,1/2+z\n+1/2-x,1/2+y,1/2+z\n+\n+9\n+C -2xbc\n+C n 1 1\n+x,y,z\n+-x,1/2+y,1/2+z\n+1/2+x,1/2+y,z\n+1/2-x,y,1/2+z\n+\n+9\n+I -2xc\n+I c 1 1\n+x,y,z\n+-x,y,1/2+z\n+1/2+x,1/2+y,1/2+z\n+1/2-x,1/2+y,z\n+\n+9\n+C -2xc\n+C c 1 1\n+x,y,z\n+-x,y,1/2+z\n+1/2+x,1/2+y,z\n+1/2-x,1/2+y,1/2+z\n+\n+9\n+B -2xbc\n+B n 1 1\n+x,y,z\n+-x,1/2+y,1/2+z\n+1/2+x,y,1/2+z\n+1/2-x,1/2+y,z\n+\n+9\n+I -2xb\n+I b 1 1\n+x,y,z\n+-x,1/2+y,z\n+1/2+x,1/2+y,1/2+z\n+1/2-x,y,1/2+z\n+\n+10\n+-P 2y\n+P 2/m,P 1 2/m 1\n+x,y,z\n+-x,y,-z\n+-x,-y,-z\n+x,-y,z\n+\n+10\n+-P 2\n+P 1 1 2/m\n+x,y,z\n+-x,-y,z\n+-x,-y,-z\n+x,y,-z\n+\n+10\n+-P 2x\n+P 2/m 1 1\n+x,y,z\n+x,-y,-z\n+-x,-y,-z\n+-x,y,z\n+\n+11\n+-P 2yb\n+P 21/m,P 1 21/m 1\n+x,y,z\n+-x,1/2+y,-z\n+-x,-y,-z\n+x,1/2-y,z\n+\n+11\n+-P 2c\n+P 1 1 21/m\n+x,y,z\n+-x,-y,1/2+z\n+-x,-y,-z\n+x,y,1/2-z\n+\n+11\n+-P 2xa\n+P 21/m 1 1\n+x,y,z\n+1/2+x,-y,-z\n+-x,-y,-z\n+1/2-x,y,z\n+\n+12\n+-C 2y\n+C 2/m,C 1 2/m 1\n+x,y,z\n+-x,y,-z\n+-x,-y,-z\n+x,-y,z\n+1/2+x,1/2+y,z\n+1/2-x,1/2+y,-z\n+1/2-x,1/2-y,-z\n+1/2+x,1/2-y,z\n+\n+12\n+-A 2y\n+A 1 2/m 1\n+x,y,z\n+-x,y,-z\n+-x,-y,-z\n+x,-y,z\n+x,1/2+y,1'..b'/4-y,3/4-x,1/2+z\n+y,1/2+x,z\n+1/4-y,x,3/4-z\n+1/2+y,1/4-x,1/4-z\n+3/4-x,3/4-z,1/2+y\n+1/2+x,1/4-z,1/4-y\n+x,1/2+z,y\n+1/4-x,z,3/4-y\n+3/4-z,3/4-y,1/2+x\n+1/4-z,y,3/4-x\n+1/2+z,1/4-y,1/4-x\n+z,1/2+y,x\n+1/2+x,1/2+y,z\n+3/4-x,1/4-y,1/2+z\n+1/4-x,y,1/4-z\n+x,3/4-y,3/4-z\n+1/2+z,1/2+x,y\n+z,3/4-x,3/4-y\n+3/4-z,1/4-x,1/2+y\n+1/4-z,x,1/4-y\n+1/2+y,1/2+z,x\n+1/4-y,z,1/4-x\n+y,3/4-z,3/4-x\n+3/4-y,1/4-z,1/2+x\n+1/4+y,3/4+x,-z\n+-y,-x,1/2-z\n+3/4+y,1/2-x,3/4+z\n+1/2-y,1/4+x,1/4+z\n+1/4+x,3/4+z,-y\n+1/2-x,1/4+z,1/4+y\n+-x,-z,1/2-y\n+3/4+x,1/2-z,3/4+y\n+1/4+z,3/4+y,-x\n+3/4+z,1/2-y,3/4+x\n+1/2-z,1/4+y,1/4+x\n+-z,-y,1/2-x\n+1/2-x,1/2-y,-z\n+1/4+x,3/4+y,1/2-z\n+3/4+x,-y,3/4+z\n+-x,1/4+y,1/4+z\n+1/2-z,1/2-x,-y\n+-z,1/4+x,1/4+y\n+1/4+z,3/4+x,1/2-y\n+3/4+z,-x,3/4+y\n+1/2-y,1/2-z,-x\n+3/4+y,-z,3/4+x\n+-y,1/4+z,1/4+x\n+1/4+y,3/4+z,1/2-x\n+3/4-y,1/4-x,z\n+y,x,1/2+z\n+1/4-y,1/2+x,1/4-z\n+1/2+y,3/4-x,3/4-z\n+3/4-x,1/4-z,y\n+1/2+x,3/4-z,3/4-y\n+x,z,1/2+y\n+1/4-x,1/2+z,1/4-y\n+3/4-z,1/4-y,x\n+1/4-z,1/2+y,1/4-x\n+1/2+z,3/4-y,3/4-x\n+z,y,1/2+x\n+\n+229\n+-I 4 2 3\n+I m -3 m\n+x,y,z\n+-y,x,z\n+-x,-y,z\n+y,-x,z\n+x,-y,-z\n+y,x,-z\n+-x,y,-z\n+-y,-x,-z\n+z,x,y\n+-x,z,y\n+-z,-x,y\n+x,-z,y\n+z,-x,-y\n+x,z,-y\n+-z,x,-y\n+-x,-z,-y\n+y,z,x\n+y,-z,-x\n+z,y,-x\n+-y,z,-x\n+-z,-y,-x\n+-y,-z,x\n+z,-y,x\n+-z,y,x\n+-x,-y,-z\n+y,-x,-z\n+x,y,-z\n+-y,x,-z\n+-x,y,z\n+-y,-x,z\n+x,-y,z\n+y,x,z\n+-z,-x,-y\n+x,-z,-y\n+z,x,-y\n+-x,z,-y\n+-z,x,y\n+-x,-z,y\n+z,-x,y\n+x,z,y\n+-y,-z,-x\n+-y,z,x\n+-z,-y,x\n+y,-z,x\n+z,y,x\n+y,z,-x\n+-z,y,-x\n+z,-y,-x\n+x+1/2,y+1/2,z+1/2\n+-y+1/2,x+1/2,z+1/2\n+-x+1/2,-y+1/2,z+1/2\n+y+1/2,-x+1/2,z+1/2\n+x+1/2,-y+1/2,-z+1/2\n+y+1/2,x+1/2,-z+1/2\n+-x+1/2,y+1/2,-z+1/2\n+-y+1/2,-x+1/2,-z+1/2\n+z+1/2,x+1/2,y+1/2\n+-x+1/2,z+1/2,y+1/2\n+-z+1/2,-x+1/2,y+1/2\n+x+1/2,-z+1/2,y+1/2\n+z+1/2,-x+1/2,-y+1/2\n+x+1/2,z+1/2,-y+1/2\n+-z+1/2,x+1/2,-y+1/2\n+-x+1/2,-z+1/2,-y+1/2\n+y+1/2,z+1/2,x+1/2\n+y+1/2,-z+1/2,-x+1/2\n+z+1/2,y+1/2,-x+1/2\n+-y+1/2,z+1/2,-x+1/2\n+-z+1/2,-y+1/2,-x+1/2\n+-y+1/2,-z+1/2,x+1/2\n+z+1/2,-y+1/2,x+1/2\n+-z+1/2,y+1/2,x+1/2\n+-x+1/2,-y+1/2,-z+1/2\n+y+1/2,-x+1/2,-z+1/2\n+x+1/2,y+1/2,-z+1/2\n+-y+1/2,x+1/2,-z+1/2\n+-x+1/2,y+1/2,z+1/2\n+-y+1/2,-x+1/2,z+1/2\n+x+1/2,-y+1/2,z+1/2\n+y+1/2,x+1/2,z+1/2\n+-z+1/2,-x+1/2,-y+1/2\n+x+1/2,-z+1/2,-y+1/2\n+z+1/2,x+1/2,-y+1/2\n+-x+1/2,z+1/2,-y+1/2\n+-z+1/2,x+1/2,y+1/2\n+-x+1/2,-z+1/2,y+1/2\n+z+1/2,-x+1/2,y+1/2\n+x+1/2,z+1/2,y+1/2\n+-y+1/2,-z+1/2,-x+1/2\n+-y+1/2,z+1/2,x+1/2\n+-z+1/2,-y+1/2,x+1/2\n+y+1/2,-z+1/2,x+1/2\n+z+1/2,y+1/2,x+1/2\n+y+1/2,z+1/2,-x+1/2\n+-z+1/2,y+1/2,-x+1/2\n+z+1/2,-y+1/2,-x+1/2\n+\n+230\n+-I 4bd 2c 3\n+I a -3 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diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/space-groups.xsl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/space-groups.xsl Tue Jun 07 16:43:30 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>
</xsl:text>
+     <xsl:value-of select="@Hall"/>
+     <xsl:text>
</xsl:text>
+     <xsl:if test="@HMs">
+          <xsl:value-of select="@HMs"/>
+          <xsl:text>,</xsl:text>
+     </xsl:if>
+     <xsl:value-of select="@HM"/>
+     <xsl:text>
</xsl:text>
+     <xsl:apply-templates select="transform"/>
+     <xsl:text>
</xsl:text>
+</xsl:template>
+
+<xsl:template match="transform">
+     <xsl:value-of select="."/>
+     <xsl:text>
</xsl:text>
+</xsl:template>
+
+</xsl:stylesheet>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/superatom.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/superatom.txt Tue Jun 07 16:43:30 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]

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/svgformat.script
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/svgformat.script Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/templates.sdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/templates.sdf Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/torlib.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/torlib.h Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,479 @@\n+/***************************************************************\n+This file is part of the Open Babel project.\n+This is copyright under the GNU General Public License (GPL)\n+For more information, see <http://openbabel.org/>\n+\n+This file contains a binary representation of data tables\n+ used by Open Babel. It is used as a fallback if the textual\n+ data table is not found at runtime. It is not a normal header.\n+***************************************************************/\n+\n+\n+#ifndef OB_TORLIB_H\n+#define OB_TORLIB_H\n+\n+namespace OpenBabel\n+{\n+static const char TorsionDefaults[] = {\n+ 0x53,0x50,0x33,0x2D,0x53,0x50,0x33,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,\n+ 0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x20,0x0A,0x53,0x50,0x32,0x2D,\n+ 0x53,0x50,0x32,0x20,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x20,0x2D,\n+ 0x33,0x30,0x2E,0x30,0x20,0x33,0x30,0x2E,0x30,0x20,0x31,0x35,0x30,0x2E,0x30,\n+ 0x20,0x2D,0x31,0x35,0x30,0x2E,0x30,0x20,0x0A,0x53,0x50,0x33,0x2D,0x53,0x50,\n+ 0x32,0x20,0x30,0x2E,0x30,0x20,0x33,0x30,0x2E,0x30,0x20,0x2D,0x33,0x30,0x2E,\n+ 0x30,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,0x30,0x2E,0x30,0x20,0x31,0x32,\n+ 0x30,0x2E,0x30,0x20,0x2D,0x31,0x32,0x30,0x2E,0x30,0x20,0x2D,0x31,0x35,0x30,\n+ 0x2E,0x30,0x20,0x31,0x35,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x20,\n+ 0x2D,0x39,0x30,0x2E,0x30,0x20,0x39,0x30,0x2E,0x30,0x0A,0x4F,0x40,0x5B,0x43,\n+ 0x44,0x33,0x5D,0x4F,0x5B,0x43,0x44,0x33,0x5D,0x28,0x5B,0x23,0x31,0x5D,0x29,\n+ 0x40,0x43,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x35,0x20,0x30,0x2E,0x30,0x20,\n+ 0x33,0x30,0x2E,0x30,0x20,0x2D,0x33,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,\n+ 0x30,0x0A,0x4F,0x40,0x5B,0x43,0x44,0x33,0x5D,0x28,0x5B,0x23,0x31,0x5D,0x29,\n+ 0x4F,0x5B,0x43,0x44,0x33,0x5D,0x28,0x5B,0x23,0x31,0x5D,0x29,0x40,0x43,0x20,\n+ 0x33,0x20,0x32,0x20,0x34,0x20,0x35,0x20,0x30,0x2E,0x30,0x20,0x33,0x30,0x2E,\n+ 0x30,0x20,0x2D,0x33,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x0A,0x5B,\n+ 0x4F,0x44,0x31,0x5D,0x7E,0x43,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5B,\n+ 0x43,0x58,0x34,0x5D,0x28,0x2A,0x29,0x2A,0x20,0x31,0x20,0x32,0x20,0x34,0x20,\n+ 0x35,0x20,0x33,0x30,0x2E,0x30,0x20,0x2D,0x33,0x30,0x2E,0x30,0x20,0x2D,0x36,\n+ 0x30,0x2E,0x30,0x20,0x36,0x30,0x2E,0x30,0x20,0x39,0x30,0x2E,0x30,0x20,0x2D,\n+ 0x39,0x30,0x2E,0x30,0x20,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x0A,\n+ 0x5B,0x61,0x5D,0x63,0x43,0x28,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x3D,0x4F,0x20,\n+ 0x31,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x30,0x2E,0x30,0x20,0x32,0x30,0x2E,\n+ 0x30,0x20,0x2D,0x32,0x30,0x2E,0x30,0x0A,0x5B,0x4F,0x44,0x31,0x5D,0x43,0x28,\n+ 0x3D,0x4F,0x29,0x5B,0x43,0x44,0x32,0x5D,0x43,0x20,0x31,0x20,0x32,0x20,0x34,\n+ 0x20,0x35,0x20,0x30,0x2E,0x30,0x20,0x34,0x35,0x2E,0x30,0x20,0x39,0x30,0x2E,\n+ 0x30,0x0A,0x4E,0x53,0x28,0x3D,0x4F,0x29,0x28,0x3D,0x4F,0x29,0x63,0x31,0x5B,\n+ 0x63,0x44,0x32,0x5D,0x5B,0x63,0x44,0x32,0x5D,0x61,0x5B,0x63,0x44,0x32,0x5D,\n+ 0x5B,0x63,0x44,0x32,0x5D,0x31,0x20,0x31,0x20,0x32,0x20,0x35,0x20,0x36,0x20,\n+ 0x39,0x30,0x2E,0x30,0x0A,0x63,0x28,0x5B,0x61,0x44,0x32,0x5D,0x29,0x53,0x28,\n+ 0x3D,0x4F,0x29,0x28,0x3D,0x4F,0x29,0x5B,0x4E,0x44,0x32,0x5D,0x5B,0x43,0x44,\n+ 0x32,0x5D,0x20,0x31,0x20,0x33,0x20,0x36,0x20,0x37,0x20,0x36,0x30,0x2E,0x30,\n+ 0x20,0x2D,0x36,0x30,0x2E,0x30,0x0A,0x4F,0x3D,0x53,0x28,0x3D,0x4F,0x29,0x4E,\n+ 0x5B,0x43,0x58,0x34,0x44,0x33,0x5D,0x2A,0x20,0x32,0x20,0x34,0x20,0x35,0x20,\n+ 0x36,0x20,0x2D,0x39,0x30,0x2E,0x30,0x20,0x39,0x30,0x2E,0x30,0x20,0x31,0x32,\n+ 0x30,0x2E,0x30,0x20,0x2D,0x31,0x32,0x30,0x2E,0x30,0x0A,0x4F,0x3D,0x53,0x28,\n+ 0x3D,0x4F,0x29,0x4E,0x5B,0x43,0x58,0x34,0x44,0x32,0x5D,0x2A,0x20,0x32,0x20,\n+ 0x34,0x20,0x35,0x20,0x36,0x20,0x2D,0x39,0x30,0x2E,0x30,0x20,0x39,0x30,0x2E,\n+ 0x30,0x20,0x31,0x32,0x30,0x2E,0x30,0x20,0x2D,0x31,0x32,0x30,0x2E,0x30,0x0A,\n+ 0x5B,0x63,0x5D,0x53,0x28,0x3D,0x4F,0x29,0x28,0x3D,0x4F,0x29,0x4E,0x43,0x20,\n+ 0x31,0x20,0x32,0x20,0x35,0x20,0x36,0x20,0x2D,0x37,0x30,0x2E,0x30,0x20,0x37,\n+ 0x30,0x2E,0x30,0x20,0x39,0x30,0x2E,0x30,0x20,0x2D,0x39,0x30,0x2E,0x30,0x20,\n+ 0x35,0x30,0x2E,0x30,0x20,0x2D,0x3'..b',\n+ 0x30,0x2E,0x30,0x20,0x31,0x36,0x30,0x2E,0x30,0x20,0x2D,0x31,0x36,0x30,0x2E,\n+ 0x30,0x20,0x31,0x32,0x30,0x2E,0x30,0x20,0x2D,0x31,0x32,0x30,0x2E,0x30,0x0A,\n+ 0x5B,0x2A,0x44,0x32,0x5D,0x5B,0x43,0x44,0x32,0x5D,0x5B,0x43,0x52,0x48,0x5D,\n+ 0x28,0x5B,0x2A,0x52,0x5D,0x29,0x5B,0x2A,0x52,0x5D,0x20,0x31,0x20,0x32,0x20,\n+ 0x33,0x20,0x34,0x20,0x33,0x30,0x2E,0x30,0x20,0x2D,0x33,0x30,0x2E,0x30,0x20,\n+ 0x31,0x32,0x30,0x2E,0x30,0x20,0x2D,0x31,0x32,0x30,0x2E,0x30,0x20,0x31,0x35,\n+ 0x30,0x2E,0x30,0x20,0x2D,0x31,0x35,0x30,0x2E,0x30,0x20,0x36,0x30,0x2E,0x30,\n+ 0x20,0x2D,0x36,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x20,0x30,0x2E,\n+ 0x30,0x0A,0x5B,0x2A,0x44,0x32,0x5D,0x5B,0x43,0x44,0x32,0x5D,0x5B,0x43,0x58,\n+ 0x34,0x44,0x33,0x5D,0x5B,0x2A,0x44,0x32,0x5D,0x20,0x31,0x20,0x32,0x20,0x33,\n+ 0x20,0x34,0x20,0x33,0x30,0x2E,0x30,0x20,0x2D,0x33,0x30,0x2E,0x30,0x20,0x31,\n+ 0x32,0x30,0x2E,0x30,0x20,0x2D,0x31,0x32,0x30,0x2E,0x30,0x20,0x31,0x35,0x30,\n+ 0x2E,0x30,0x20,0x2D,0x31,0x35,0x30,0x2E,0x30,0x20,0x36,0x30,0x2E,0x30,0x20,\n+ 0x2D,0x36,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x0A,0x2A,0x5B,0x43,\n+ 0x48,0x44,0x33,0x5D,0x5B,0x43,0x48,0x32,0x44,0x32,0x5D,0x2A,0x20,0x31,0x20,\n+ 0x32,0x20,0x33,0x20,0x34,0x20,0x31,0x35,0x30,0x2E,0x30,0x20,0x2D,0x31,0x35,\n+ 0x30,0x2E,0x30,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,0x30,0x2E,0x30,0x20,\n+ 0x31,0x38,0x30,0x2E,0x30,0x20,0x2D,0x39,0x30,0x2E,0x30,0x20,0x39,0x30,0x2E,\n+ 0x30,0x20,0x30,0x2E,0x30,0x20,0x33,0x30,0x2E,0x30,0x20,0x2D,0x33,0x30,0x2E,\n+ 0x30,0x0A,0x5B,0x43,0x44,0x31,0x5D,0x43,0x28,0x5B,0x43,0x44,0x31,0x5D,0x29,\n+ 0x5B,0x43,0x44,0x32,0x5D,0x2A,0x20,0x31,0x20,0x32,0x20,0x34,0x20,0x35,0x20,\n+ 0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,\n+ 0x30,0x20,0x38,0x30,0x2E,0x30,0x20,0x2D,0x38,0x30,0x2E,0x30,0x20,0x33,0x30,\n+ 0x2E,0x30,0x20,0x2D,0x33,0x30,0x2E,0x30,0x0A,0x5B,0x43,0x44,0x33,0x5D,0x5B,\n+ 0x4F,0x44,0x32,0x5D,0x5B,0x43,0x44,0x32,0x5D,0x5B,0x4F,0x44,0x32,0x5D,0x20,\n+ 0x31,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,\n+ 0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x20,0x31,0x30,0x30,0x2E,0x30,\n+ 0x20,0x2D,0x31,0x30,0x30,0x2E,0x30,0x0A,0x5B,0x43,0x44,0x31,0x5D,0x5B,0x43,\n+ 0x44,0x32,0x5D,0x5B,0x43,0x44,0x32,0x5D,0x5B,0x2A,0x44,0x32,0x5D,0x5B,0x2A,\n+ 0x44,0x32,0x5D,0x5B,0x2A,0x44,0x32,0x5D,0x20,0x32,0x20,0x33,0x20,0x34,0x20,\n+ 0x35,0x20,0x31,0x38,0x30,0x2E,0x30,0x0A,0x5B,0x43,0x44,0x31,0x5D,0x5B,0x43,\n+ 0x44,0x32,0x5D,0x5B,0x43,0x44,0x32,0x5D,0x5B,0x2A,0x44,0x32,0x5D,0x5B,0x2A,\n+ 0x44,0x32,0x5D,0x5B,0x2A,0x44,0x32,0x5D,0x20,0x31,0x20,0x32,0x20,0x33,0x20,\n+ 0x34,0x20,0x31,0x38,0x30,0x2E,0x30,0x0A,0x5B,0x2A,0x44,0x32,0x5E,0x33,0x5D,\n+ 0x5B,0x2A,0x44,0x32,0x5E,0x33,0x5D,0x5B,0x2A,0x44,0x32,0x5E,0x33,0x5D,0x5B,\n+ 0x2A,0x44,0x32,0x5E,0x33,0x5D,0x5B,0x2A,0x44,0x32,0x5E,0x33,0x5D,0x5B,0x2A,\n+ 0x44,0x32,0x5E,0x33,0x5D,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x35,0x20,0x31,\n+ 0x38,0x30,0x2E,0x30,0x0A,0x5B,0x61,0x44,0x33,0x5D,0x63,0x4E,0x28,0x7E,0x5B,\n+ 0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x20,0x31,0x20,0x32,\n+ 0x20,0x33,0x20,0x34,0x20,0x30,0x2E,0x30,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,\n+ 0x36,0x30,0x2E,0x30,0x0A,0x5B,0x61,0x5D,0x63,0x4E,0x28,0x7E,0x5B,0x4F,0x44,\n+ 0x31,0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x20,0x31,0x20,0x32,0x20,0x33,\n+ 0x20,0x34,0x20,0x30,0x2E,0x30,0x0A,0x2A,0x2A,0x43,0x28,0x46,0x29,0x28,0x46,\n+ 0x29,0x46,0x20,0x31,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x30,0x2E,0x30,0x0A,\n+ 0x5B,0x61,0x5D,0x63,0x43,0x28,0x43,0x6C,0x29,0x28,0x43,0x6C,0x29,0x43,0x6C,\n+ 0x20,0x31,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x30,0x2E,0x30,0x0A,0x61,0x5B,\n+ 0x50,0x44,0x33,0x5D,0x28,0x61,0x29,0x2D,0x5B,0x50,0x44,0x33,0x5D,0x28,0x61,\n+ 0x29,0x61,0x20,0x31,0x20,0x32,0x20,0x34,0x20,0x35,0x20,0x31,0x38,0x30,0x2E,\n+ 0x30,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,0x30,0x2E,0x30,0x0A,0x50,0x50,\n+ 0x63,0x63,0x20,0x31,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x36,0x30,0x2E,0x30,\n+ 0x20,0x2D,0x36,0x30,0x2E,0x30,0x0A,0x00};\n+\n+} // namespace OpenBabel\n+#endif // OB_TORLIB_H\n+\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/torlib.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/torlib.txt Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,224 @@\n+##############################################################################\n+# #\n+# Open Babel file: torlib.txt #\n+# #\n+# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #\n+# Some portions Copyright (c) 2001-2005 by Geoffrey R. Hutchison #\n+# Part of the Open Babel package, under the GNU General Public License (GPL)#\n+# #\n+# First three lines represent: (used by rotor.cpp::OBRotorRules #\n+# Hybridization pair (atom types around a rotatable bond) #\n+# followed by a list of default bond rotation angles (in degrees) #\n+# #\n+# Later lines should specify: #\n+# * A SMARTS pattern for the rotor rule #\n+# * A set of 4 "reference atoms" (as integers, numbered from 1 #\n+# in the specified SMARTS pattern #\n+# * At least one torsion value (in degrees) #\n+# * Optionally ending with "Delta" and a delta value #\n+# (i.e., the resolution of a dihedral step #\n+# #\n+# SMARTS rules will be attempted first, then hybridization #\n+# #\n+##############################################################################\n+\n+SP3-SP3 60.0 -60.0 180.0 \n+SP2-SP2 0.0 180.0 -30.0 30.0 150.0 -150.0 \n+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\n+\n+# Many of these rules came from the Supporting Information\n+# from Irwin, et. al., J. Med. Chem. (2006) 49(23) 6789-6801\n+\n+#polysaccaride bridges\n+O@[CD3]O[CD3]([#1])@C 2 3 4 5 0.0 30.0 -30.0 180.0\n+O@[CD3]([#1])O[CD3]([#1])@C 3 2 4 5 0.0 30.0 -30.0 180.0\n+\n+#acids\n+[OD1]~C(~[OD1])[CX4](*)* 1 2 4 5 30.0 -30.0 -60.0 60.0 90.0 -90.0 0.0 180.0\n+[a]cC([OD1])=O 1 2 3 4 0.0 20.0 -20.0\n+[OD1]C(=O)[CD2]C 1 2 4 5 0.0 45.0 90.0\n+\n+#sulfonamides\n+NS(=O)(=O)c1[cD2][cD2]a[cD2][cD2]1 1 2 5 6 90.0\n+c([aD2])S(=O)(=O)[ND2][CD2] 1 3 6 7 60.0 -60.0\n+O=S(=O)N[CX4D3]* 2 4 5 6 -90.0 90.0 120.0 -120.0\n+O=S(=O)N[CX4D2]* 2 4 5 6 -90.0 90.0 120.0 -120.0\n+[c]S(=O)(=O)NC 1 2 5 6 -70.0 70.0 90.0 -90.0 50.0 -50.0\n+*=*-S(=O)(=O)C 1 2 3 6 90.0 -90.0 60.0 -60.0\n+O=S(=O)N[CH2] 1 2 4 5 -60.0 60.0 180.0 0.0 30.0 -30.0\n+[aD2]c([aD2])S(=O)(=O)[ND2^3] 1 2 4 7 90.0 -90.0 120.0 -120.0 60.0 -60.0\n+[aD2]c([aD3])S(=O)(=O)[ND2^3] 1 2 4 7 80.0 -80.0 110.0 -110.0\n+[aD3]c([aD3])S(=O)(=O)[ND2^3] 1 2 4 7 70.0 -70.0 110.0 -110.0\n+[aD2]c([aD2])S(=O)(=O)[CD2^3] 1 2 4 7 90.0 -90.0 110.0 -110.0 70.0 -70.0\n+[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\n+aS(=O)(=O)[ND2]a 1 2 5 6 90.0 -90.0\n+aaNS(=O)(=O) 1 2 3 4 90.0 -90.0\n+\n+#sulfone\n+O=S(=O)[CD2][CD3][#1] 2 4 5 6 30.0 -30.0\n+\n+#hydrazides\n+[O,S]=C[ND2][ND2] 1 2 3 4 0.0 180.0\n+[O,S]=C[ND2][ND2]-,=* 2 3 4 5 180.0 90.0 -90.0\n+\n+#cyclopropyl-ketones\n+O=CC1([#1])[CD2][CD2]1 1 2 3 4 180.0\n+O=CC1([#1])CC1 1 2 3 4 180.0 160.0 -160.0 0.0 20.0 -20.0\n+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\n+\n+#epoxy-ketone\n+O=C([*D2])C1([#1])O[CD2,CD3]1 1 2 4 5 0.0 180.0\n+\n+#opposite end of tert amide\n+O=C([ND3])[CD2]* 1 2 4 5 0.0 30.0 -30.0 100.0 -100.0 80.0 -80.0\n+O=C([CD3^3])[CD2]* 1 2 4 5 0.0 30.0 -30.0\n+O=C([ND3])[CD3][#1] 1 2 4 5 180.0 150.0 -150.0 120.0 -120.0\n+\n+#misc\n+[CD2]C(=O)[ND2]-!@[CD3][#1] 2 4 5 6 0.0 30.0 -30.0 60.0 -60.0 180.0\n+[cD2]c([cD2])-!@[CD2^3][CD3^3] 1 2 4 5 90.0 -90.0 70.0 -70.0 110.'..b'D2][CD2X4][CD2X4] 1 2 3 4 180.0 160.0 -160.0 80.0 -80.0 60.0 -60.0\n+[ND1]C(=O)c([aD3]) 1 2 4 5 0.0 180.0 30.0 -30.0 150.0 -150.0\n+[aD2]c([aD2])c([aD2])[aD2] 1 2 4 5 -150.0 -30.0 30.0 150.0\n+[a]c[CD2][*D2] 1 2 3 4 -90.0 90.0 180.0 0.0 30.0 -30.0 150.0 -150.0\n+[a]cC(=O)c[a] 1 2 3 4 -150.0 -30.0 0.0 30.0 150.0 180.0\n+[a]cC(=O)[*D2] 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0\n+[a]cOC 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0\n+\n+#borderline low-res\n+[CD2]C(=O)[ND2][CD3][#1] 2 4 5 6 90.0 -90.0 60.0 -60.0 120.0 -120.0\n+\n+#conjugated substituents\n+a[CD2]C=* 1 2 3 4 150.0 -150.0 180.0 30.0 -30.0 0.0\n+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\n+cO[CD2]* 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 90.0 -90.0 180.0\n+C=N[ND2]*=,:* 2 3 4 5 0.0 30.0 -30.0 150.0 -150.0 180.0\n+c[CD2][ND2]c 1 2 3 4 60.0 -60.0 80.0 -80.0 180.0\n+C=[CD3][ND3]* 1 2 3 4 30.0 -30.0 60.0 -60.0 90.0 -90.0 0.0 180.0\n+\n+#ureas\n+[ND2]C(=O)Nc[nD2] 2 4 5 6 0.0 180.0\n+[ND2]C(=O)[ND2]* 1 2 4 5 0.0 180.0\n+\n+#carbamates\n+C[ND2]C(=O)O 1 2 3 4 0.0 180.0\n+[ND2]C(=O)OC 3 2 4 5 0.0\n+OC(=O)N* 3 2 4 5 0.0 20.0 -20.0 120.0 -120.0 160.0 -160.0 180.0\n+\n+#piperidine amide\n+O=CN1[CD2][CD2][CD2][CD2][CD2]1 1 2 3 4 0.0\n+\n+#amides and esters\n+[*D2]C(=O)O[CD3][#1] 2 4 5 6 0.0 30.0 -30.0\n+[OD2]C(=O)[CD2][CD2^3] 3 2 4 5 0.0 30.0 -30.0 120.0 -120.0 180.0\n+[O,SD1]=C(C)[ND2]C=[O,S] 1 2 4 5 0.0 180.0\n+[O,SD1]=C(C)[ND2][#7,#8]=* 1 2 4 5 0.0 180.0\n+[O,SD1]=C(C)[ND2]N 1 2 4 5 0.0 180.0\n+[O,SD1]=C(C)cn 1 2 4 5 0.0 180.0\n+[O,SD1]=C([#6])[ND2]* 1 2 4 5 0.0 20.0 -20.0\n+[O,SD1]=C[ND2]* 1 2 3 4 0.0 20.0 -20.0 180\n+O=C[ND3][CD3X4][#1] 2 3 4 5 0.0 180.0 20.0 -20.0\n+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\n+O=CNc[a] 2 3 4 5 -20.0 20.0 90.0 -90.0 -160.0 160.0\n+O=C([CD2,CD3])O[CD2] 1 2 4 5 0.0\n+O=C([CD1])O[CD1] 1 2 4 5 0.0\n+[O,S]=CO[CD1] 1 2 3 4 0.0 20.0 -20.0 180.0\n+O=CO[CD2][CD1] 2 3 4 5 180.0\n+O=CO[CD2]* 2 3 4 5 180.0 60.0 -60.0 90.0 -90.0\n+O=CO[CD3]* 2 3 4 5 120.0 -120.0 180.0 0.0 60.0 -60.0\n+O=CO[CD4]* 2 3 4 5 -60.0 60.0 120.0 80.0 -80.0\n+O=CO[CD3,CD4] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0\n+O=CO* 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0\n+O=C[ND3]([*D3])[*D3] 1 2 3 4 20.0 -20.0 0.0 180 150.0 -150.0\n+O=C[ND3]* 1 2 3 4 0.0 180.0\n+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\n+[a][CD2][CD2][ND3] 1 2 3 4 90.0 -90.0 180.0 60.0 -60.0\n+[ND3]C(=O)[nD3]* 1 2 4 5 90.0 -90.0 60.0 -60.0 120.0 -120.0\n+[CD2]OC(=O)[CD2][CD3] 4 3 5 6 0.0 150.0 -150.0\n+\n+#t-butyl\n+C([CD1])([CD1])([CD1])c[a] 2 1 5 6 90.0 30.0\n+**C([CD1])([CD1])[CD1] 1 2 3 4 180.0 150.0\n+\n+#propyl\n+[CD1]C([CD1])([#1])[CD2]* 4 2 5 6 60.0 -60.0\n+\n+#highly substituted alkane\n+#[CD2]C(=O)[ND2]-!@[CD3][#1] 2 4 5 6\n+*[CD2X4][CD3X4]([#1])[CD3] 1 2 3 4 180.0 60.0 -60.0 40.0 -40.0\n+c[CD2^3][CD3^3][#1] 1 2 3 4 180.0 60.0 -60.0\n+[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\n+[*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\n+[*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\n+*[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\n+[CD1]C([CD1])[CD2]* 1 2 4 5 60.0 -60.0 180.0 80.0 -80.0 30.0 -30.0\n+\n+#long unsubstituted alkanes\n+[CD3][OD2][CD2][OD2] 1 2 3 4 60.0 -60.0 180.0 100.0 -100.0\n+[CD1][CD2][CD2][*D2][*D2][*D2] 2 3 4 5 180.0\n+[CD1][CD2][CD2][*D2][*D2][*D2] 1 2 3 4 180.0\n+[*D2^3][*D2^3][*D2^3][*D2^3][*D2^3][*D2^3] 2 3 4 5 180.0\n+\n+#nitro\n+[aD3]cN(~[OD1])~[OD1] 1 2 3 4 0.0 60.0 -60.0\n+[a]cN(~[OD1])~[OD1] 1 2 3 4 0.0\n+\n+#trifluoromethyl\n+**C(F)(F)F 1 2 3 4 0.0\n+\n+#trichloromethyl\n+[a]cC(Cl)(Cl)Cl 1 2 3 4 0.0\n+\n+#CSD SPECIFIC RULES\n+a[PD3](a)-[PD3](a)a 1 2 4 5 180.0 60.0 -60.0\n+PPcc 1 2 3 4 60.0 -60.0\n+\n+#phosphorus containing groups\n+#[OD1]~PO* 1 2 3 4 0.0 -30.0 30.0 -60.0 60.0 120.0 -120.0\n+#[OD1]~P(~[OD1])(~[OD1])[OD2][CD2]* 2 5 6 7 0.0 60.0 120.0 180.0 -120.0 -60.0\n+#S=POc 1 2 3 4 0.0 -60.0 60.0 90.0 -90.0\n+#[a]cCP(c)(c)c 1 2 3 4 90.0 -90.0\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/types.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/types.h Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,709 @@\n+/***************************************************************\n+This file is part of the Open Babel project.\n+This is copyright under the GNU General Public License (GPL)\n+For more information, see <http://openbabel.org/>\n+\n+This file contains a binary representation of data tables\n+ used by Open Babel. It is used as a fallback if the textual\n+ data table is not found at runtime. It is not a normal header.\n+***************************************************************/\n+\n+\n+#ifndef OB_TYPES_H\n+#define OB_TYPES_H\n+\n+namespace OpenBabel\n+{\n+static const char TypesData[] = {\n+ 0x31,0x39,0x34,0x09,0x32,0x30,0x0A,0x49,0x4E,0x54,0x09,0x41,0x54,0x4E,0x09,\n+ 0x48,0x59,0x42,0x09,0x4D,0x4D,0x44,0x09,0x4D,0x4D,0x32,0x09,0x58,0x59,0x5A,\n+ 0x09,0x41,0x4C,0x43,0x09,0x48,0x41,0x44,0x09,0x4D,0x43,0x4D,0x4C,0x09,0x43,\n+ 0x33,0x44,0x09,0x53,0x59,0x42,0x09,0x4D,0x4F,0x4C,0x09,0x4D,0x41,0x50,0x09,\n+ 0x44,0x52,0x45,0x09,0x58,0x45,0x44,0x09,0x44,0x4F,0x4B,0x09,0x4D,0x33,0x44,\n+ 0x09,0x49,0x44,0x58,0x09,0x53,0x42,0x4E,0x20,0x50,0x43,0x4D,0x0A,0x58,0x09,\n+ 0x30,0x09,0x30,0x09,0x36,0x32,0x09,0x30,0x09,0x58,0x09,0x44,0x75,0x09,0x30,\n+ 0x09,0x58,0x09,0x30,0x09,0x44,0x75,0x09,0x32,0x36,0x09,0x58,0x09,0x58,0x09,\n+ 0x32,0x31,0x09,0x32,0x35,0x09,0x75,0x6E,0x2E,0x30,0x09,0x30,0x09,0x32,0x36,\n+ 0x20,0x30,0x0A,0x4D,0x6E,0x09,0x32,0x35,0x09,0x30,0x09,0x36,0x32,0x09,0x30,\n+ 0x09,0x4D,0x6E,0x09,0x44,0x75,0x09,0x30,0x09,0x4D,0x09,0x32,0x35,0x38,0x09,\n+ 0x4D,0x6E,0x09,0x32,0x36,0x09,0x4D,0x6E,0x09,0x4D,0x6E,0x09,0x32,0x30,0x09,\n+ 0x32,0x35,0x09,0x4D,0x6E,0x2E,0x30,0x09,0x31,0x09,0x32,0x36,0x20,0x4D,0x6E,\n+ 0x0A,0x46,0x65,0x09,0x32,0x36,0x09,0x30,0x09,0x36,0x32,0x09,0x30,0x09,0x46,\n+ 0x65,0x09,0x44,0x75,0x09,0x30,0x09,0x4D,0x09,0x32,0x36,0x36,0x09,0x46,0x65,\n+ 0x09,0x32,0x36,0x09,0x46,0x65,0x09,0x46,0x65,0x09,0x32,0x30,0x09,0x32,0x35,\n+ 0x09,0x46,0x65,0x2E,0x36,0x09,0x32,0x09,0x32,0x36,0x20,0x46,0x65,0x0A,0x44,\n+ 0x75,0x09,0x30,0x09,0x30,0x09,0x36,0x31,0x09,0x30,0x09,0x44,0x75,0x09,0x44,\n+ 0x75,0x09,0x30,0x09,0x5A,0x09,0x30,0x09,0x44,0x75,0x09,0x32,0x36,0x09,0x44,\n+ 0x75,0x09,0x44,0x75,0x09,0x32,0x30,0x09,0x32,0x35,0x09,0x75,0x6E,0x2E,0x30,\n+ 0x09,0x33,0x09,0x32,0x36,0x20,0x30,0x0A,0x43,0x33,0x09,0x36,0x09,0x33,0x09,\n+ 0x33,0x09,0x31,0x09,0x43,0x09,0x43,0x33,0x09,0x34,0x09,0x43,0x09,0x36,0x34,\n+ 0x09,0x43,0x2E,0x33,0x09,0x31,0x09,0x43,0x33,0x09,0x43,0x5F,0x33,0x09,0x31,\n+ 0x09,0x35,0x09,0x43,0x2E,0x34,0x09,0x34,0x09,0x31,0x20,0x31,0x0A,0x43,0x32,\n+ 0x09,0x36,0x09,0x32,0x09,0x32,0x09,0x32,0x09,0x43,0x09,0x43,0x32,0x09,0x33,\n+ 0x09,0x43,0x09,0x36,0x33,0x09,0x43,0x2E,0x32,0x09,0x32,0x09,0x43,0x32,0x09,\n+ 0x43,0x5F,0x32,0x09,0x32,0x09,0x31,0x09,0x43,0x2E,0x33,0x09,0x35,0x09,0x32,\n+ 0x20,0x32,0x0A,0x43,0x32,0x09,0x36,0x09,0x32,0x09,0x32,0x09,0x33,0x38,0x09,\n+ 0x43,0x09,0x43,0x32,0x09,0x33,0x09,0x43,0x09,0x36,0x33,0x09,0x43,0x2E,0x32,\n+ 0x09,0x32,0x09,0x43,0x32,0x09,0x43,0x5F,0x32,0x09,0x32,0x09,0x31,0x09,0x43,\n+ 0x2E,0x33,0x09,0x36,0x09,0x32,0x20,0x32,0x0A,0x43,0x31,0x09,0x36,0x09,0x31,\n+ 0x09,0x31,0x09,0x34,0x09,0x43,0x09,0x43,0x31,0x09,0x32,0x09,0x43,0x09,0x36,\n+ 0x32,0x09,0x43,0x2E,0x31,0x09,0x34,0x09,0x43,0x31,0x09,0x43,0x5F,0x31,0x09,\n+ 0x34,0x09,0x31,0x09,0x43,0x2E,0x32,0x09,0x37,0x09,0x34,0x20,0x34,0x0A,0x43,\n+ 0x61,0x63,0x09,0x36,0x09,0x32,0x09,0x32,0x09,0x33,0x09,0x43,0x09,0x43,0x32,\n+ 0x09,0x30,0x09,0x43,0x09,0x36,0x33,0x09,0x43,0x2E,0x32,0x09,0x32,0x09,0x43,\n+ 0x32,0x09,0x43,0x5F,0x32,0x09,0x32,0x09,0x31,0x09,0x43,0x2E,0x33,0x09,0x38,\n+ 0x09,0x32,0x20,0x33,0x0A,0x43,0x62,0x6C,0x09,0x36,0x09,0x32,0x09,0x32,0x09,\n+ 0x33,0x09,0x43,0x09,0x43,0x32,0x09,0x33,0x09,0x43,0x09,0x36,0x33,0x09,0x43,\n+ 0x2E,0x32,0x09,0x32,0x09,0x43,0x32,0x09,0x43,0x5F,0x32,0x09,0x32,0x09,0x31,\n+ 0x09,0x43,0x2E,0x33,0x09,0x39,0x09,0x32,0x20,0x32,0x0A,0x43,0x2D,0x09,0x36,\n+ 0x09,0x32,0x09,0x31,0x30,0x09,0x32,0x37,0x09,0x43,0x09,0x43,0x33,0x09,0x34,\n+ 0x09,0x43,0x09,0x36,0x34,0x09,0x43,0x2E,0x33,0x09,0x31,0x09,0x43,0x33,0x09,\n+ 0x43,0x5F,0x33,0x09,0x31,0x09,0x31,0x09,0'..b'0x32,0x36,0x20,0x4D,0x74,0x0A,0x41,0x72,0x09,0x31,\n+ 0x38,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x41,0x72,0x09,0x30,0x09,0x30,0x09,\n+ 0x30,0x09,0x30,0x09,0x41,0x72,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x09,\n+ 0x30,0x09,0x30,0x09,0x31,0x38,0x31,0x09,0x32,0x36,0x20,0x41,0x72,0x0A,0x42,\n+ 0x32,0x09,0x35,0x09,0x30,0x09,0x35,0x34,0x09,0x32,0x36,0x09,0x42,0x09,0x42,\n+ 0x09,0x30,0x09,0x42,0x09,0x35,0x33,0x09,0x42,0x09,0x32,0x36,0x09,0x42,0x32,\n+ 0x09,0x42,0x5F,0x32,0x09,0x32,0x30,0x09,0x32,0x30,0x09,0x42,0x2E,0x30,0x09,\n+ 0x31,0x38,0x32,0x09,0x32,0x36,0x20,0x32,0x36,0x0A,0x42,0x33,0x09,0x35,0x09,\n+ 0x30,0x09,0x35,0x35,0x09,0x32,0x37,0x09,0x42,0x09,0x42,0x09,0x30,0x09,0x42,\n+ 0x09,0x35,0x33,0x09,0x42,0x09,0x32,0x36,0x09,0x42,0x33,0x09,0x42,0x5F,0x33,\n+ 0x09,0x32,0x30,0x09,0x32,0x30,0x09,0x42,0x2E,0x30,0x09,0x31,0x38,0x33,0x09,\n+ 0x32,0x36,0x20,0x32,0x37,0x0A,0x4E,0x09,0x37,0x09,0x30,0x09,0x36,0x32,0x09,\n+ 0x33,0x30,0x09,0x4E,0x09,0x4E,0x09,0x33,0x09,0x4E,0x09,0x32,0x09,0x4E,0x2E,\n+ 0x09,0x33,0x33,0x09,0x4E,0x09,0x4E,0x09,0x32,0x09,0x31,0x09,0x4E,0x2E,0x30,\n+ 0x09,0x31,0x38,0x34,0x09,0x32,0x36,0x20,0x38,0x0A,0x48,0x53,0x20,0x31,0x20,\n+ 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0x09,0x31,0x32,0x09,0x4F,0x2E,0x33,0x09,0x31,0x39,0x31,0x09,0x32,0x36,0x20,\n+ 0x34,0x36,0x0A,0x43,0x33,0x09,0x36,0x09,0x33,0x09,0x33,0x09,0x31,0x09,0x43,\n+ 0x09,0x43,0x33,0x09,0x34,0x09,0x43,0x09,0x36,0x34,0x09,0x43,0x2E,0x33,0x09,\n+ 0x31,0x09,0x43,0x33,0x09,0x43,0x5F,0x33,0x09,0x31,0x09,0x35,0x09,0x43,0x2E,\n+ 0x34,0x09,0x31,0x39,0x32,0x09,0x31,0x20,0x32,0x32,0x0A,0x43,0x72,0x09,0x32,\n+ 0x34,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x43,0x72,0x09,0x30,0x09,0x30,0x09,\n+ 0x30,0x09,0x30,0x09,0x43,0x72,0x2E,0x74,0x68,0x09,0x30,0x09,0x30,0x09,0x30,\n+ 0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x31,0x39,0x33,0x09,0x32,0x36,0x20,0x43,\n+ 0x72,0x0A,0x44,0x75,0x09,0x30,0x09,0x30,0x09,0x36,0x31,0x09,0x30,0x09,0x44,\n+ 0x75,0x09,0x44,0x75,0x09,0x30,0x09,0x5A,0x09,0x30,0x09,0x4C,0x70,0x09,0x32,\n+ 0x36,0x09,0x44,0x75,0x09,0x44,0x75,0x09,0x32,0x30,0x09,0x32,0x35,0x09,0x75,\n+ 0x6E,0x2E,0x30,0x09,0x31,0x39,0x34,0x09,0x32,0x36,0x20,0x30,0x0A,0x00};\n+\n+} // namespace OpenBabel\n+#endif // OB_TYPES_H\n+\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/OpenBabel/types.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/OpenBabel/types.txt Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,213 @@\n+##############################################################################\n+# #\n+#\t Open Babel file: types.txt #\n+# #\n+# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. #\n+# Some portions Copyright (c) 2001-2005 Geoffrey R. Hutchison #\n+# Part of the Open Babel package, under the GNU General Public License (GPL)#\n+# #\n+# Conversion between different external atom types #\n+# (used by data.cpp:OBTypeTable) #\n+# #\n+# First line specifies size of the table: # rows # columns #\n+# Second line specifies type names used in the code #\n+# Remaining lines specify equivalent atomic type names in each column #\n+# #\n+##############################################################################\n+194\t20\n+INT\tATN\tHYB\tMMD\tMM2\tXYZ\tALC\tHAD\tMCML\tC3D\tSYB\tMOL\tMAP\tDRE\tXED\tDOK\tM3D\tIDX\tSBN PCM\n+X\t0\t0\t62\t0\tX\tDu\t0\tX\t0\tDu\t26\tX\tX\t21\t25\tun.0\t0\t26 0\n+Mn\t25\t0\t62\t0\tMn\tDu\t0\tM\t258\tMn\t26\tMn\tMn\t20\t25\tMn.0\t1\t26 Mn\n+Fe\t26\t0\t62\t0\tFe\tDu\t0\tM\t266\tFe\t26\tFe\tFe\t20\t25\tFe.6\t2\t26 Fe\n+Du\t0\t0\t61\t0\tDu\tDu\t0\tZ\t0\tDu\t26\tDu\tDu\t20\t25\tun.0\t3\t26 0\n+C3\t6\t3\t3\t1\tC\tC3\t4\tC\t64\tC.3\t1\tC3\tC_3\t1\t5\tC.4\t4\t1 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17\n+Sox\t16\t2\t49\t18\tS\tSO2\t0\tS\t161\tS.O\t30\tS3\tS_3\t12\t14\tS.4\t30\t29 17\n+S\t16\t3\t49\t15\tS\tS3\t0\tS\t164\tS.3\t10\tS3\tS_3\t12\t14\tS.2\t31\t10 15\n+Bac\t5\t0\t54\t27\tB\tB\t0\tB\t53\tB\t26\tB2\tB_2\t20\t20\tB.0\t32\t26 26\n+Box\t5\t0\t54\t26\tB\tB\t0\tB\t53\tB\t26\tB2\tB_2\t20\t20\tB.0\t33\t26 26\n+B\t5\t0\t55\t27\tB\tB\t0\tB\t53\tB\t26\tB3\tB_3\t20\t20\tB.0\t34\t26 26\n+P3\t15\t3\t53\t25\tP\tP3\t0\tP\t159\tP.3\t12\tP3\tP_3\t14\t13\tP.4\t35\t12 25\n+Pac\t15\t2\t53\t25\tP\tP3\t0\tP\t159\tP.3\t12\tP3\tP_3\t14\t13\tP.4\t36\t12 25\n+Pox\t15\t3\t53\t25\tP\tP3\t0\tP\t159\tP.3\t12\tP3\tP_3\t14\t13\tP.4\t37\t12 25\n+P3+\t15\t3\t53\t25\tP\tP3\t0\tP\t154\tP.3\t12\tP3\tP_3\t14\t13\tP.4\t38\t12 25\n+P\t15\t3\t53\t25\tP\tP3\t0\tP\t159\tP.3\t12\tP3\tP_3\t14\t13\tP.4\t39\t12 25\n+HC\t1\t0\t41\t5\tH\tH\t0\tH\t11\tH\t13\tH\tH_\t15\t7\tH.1\t40\t13 5\n+H-\t1\t0\t45\t5\tH\tH\t0\tH\t11\tH\t13\tH\tH_\t15\t6\tH.1\t41\t13 5\n+H\t1\t0\t48\t5\tH\tH\t0\tH\t11\tH\t13\tH\tH_\t15\t6\tH.1\t42\t13 5\n+H\t1\t0\t48\t5\tD\tH\t0\tH\t12\tH\t13\tH\tH_\t15\t6\tH.1\t43\t13 5\n+DC\t1\t0\t48\t36\tD\tH\t0\tD\t19\tH\t13\tD\tH_\t15\t6\tH.1\t44\t13 36\n+D\t1\t0\t48\t36\tD\tH\t0\tD'..b' Ru\n+Rh\t45\t0\t0\t0\tRh\t0\t0\t0\t0\tRh\t0\t0\t0\t0\t0\t0\t123\t26 Rh\n+Ag\t47\t0\t0\t0\tAg\t0\t0\t0\t0\tAg\t0\t0\t0\t0\t0\t0\t124\t26 Ag\n+Cd\t48\t0\t0\t0\tCd\t0\t0\t0\t0\tCd\t0\t0\t0\t0\t0\t0\t125\t26 Cd\n+In\t49\t0\t0\t0\tIn\t0\t0\t0\t0\tIn\t0\t0\t0\t0\t0\t0\t126\t26 In\n+Sb\t51\t0\t0\t0\tSb\t0\t0\t0\t0\tSb\t0\t0\t0\t0\t0\t0\t127\t26 Sb\n+Xe\t54\t0\t0\t0\tXe\t0\t0\t0\t0\tXe\t0\t0\t0\t0\t0\t0\t128\t26 Xe\n+Cs\t55\t0\t0\t0\tCs\t0\t0\t0\t0\tCs\t0\t0\t0\t0\t0\t0\t129\t26 Cs\n+Ba\t56\t0\t0\t0\tBa\t0\t0\t0\t0\tBa\t0\t0\t0\t0\t0\t0\t130\t26 Ba\n+La\t57\t0\t0\t0\tLa\t0\t0\t0\t0\tLa\t0\t0\t0\t0\t0\t0\t131\t26 La\n+Ce\t58\t0\t0\t0\tCe\t0\t0\t0\t0\tCe\t0\t0\t0\t0\t0\t0\t132\t26 Ce\n+Pr\t59\t0\t0\t0\tPr\t0\t0\t0\t0\tPr\t0\t0\t0\t0\t0\t0\t133\t26 Pr\n+Nd\t60\t0\t0\t0\tNd\t0\t0\t0\t0\tNd\t0\t0\t0\t0\t0\t0\t134\t26 Nd\n+Pm\t61\t0\t0\t0\tPm\t0\t0\t0\t0\tPm\t0\t0\t0\t0\t0\t0\t135\t26 Pm\n+Sm\t62\t0\t0\t0\tSm\t0\t0\t0\t0\tSm\t0\t0\t0\t0\t0\t0\t136\t26 Sm\n+Eu\t63\t0\t0\t0\tEu\t0\t0\t0\t0\tEu\t0\t0\t0\t0\t0\t0\t137\t26 Eu\n+Gd\t64\t0\t0\t0\tGd\t0\t0\t0\t0\tGd\t0\t0\t0\t0\t0\t0\t138\t26 Gd\n+Tb\t65\t0\t0\t0\tTb\t0\t0\t0\t0\tTb\t0\t0\t0\t0\t0\t0\t139\t26 Tb\n+Dy\t66\t0\t0\t0\tDy\t0\t0\t0\t0\tDy\t0\t0\t0\t0\t0\t0\t140\t26 Dy\n+Ho\t67\t0\t0\t0\tHo\t0\t0\t0\t0\tHo\t0\t0\t0\t0\t0\t0\t141\t26 Ho\n+Er\t68\t0\t0\t0\tEr\t0\t0\t0\t0\tEr\t0\t0\t0\t0\t0\t0\t142\t26 Er\n+Tm\t69\t0\t0\t0\tTm\t0\t0\t0\t0\tTm\t0\t0\t0\t0\t0\t0\t143\t26 Tm\n+Yb\t70\t0\t0\t0\tYb\t0\t0\t0\t0\tYb\t0\t0\t0\t0\t0\t0\t144\t26 Yb\n+Lu\t71\t0\t0\t0\tLu\t0\t0\t0\t0\tLu\t0\t0\t0\t0\t0\t0\t145\t26 Lu\n+Hf\t72\t0\t0\t0\tHf\t0\t0\t0\t0\tHf\t0\t0\t0\t0\t0\t0\t146\t26 Hf\n+Ta\t73\t0\t0\t0\tTa\t0\t0\t0\t0\tTa\t0\t0\t0\t0\t0\t0\t147\t26 Ta\n+Re\t75\t0\t0\t0\tRe\t0\t0\t0\t0\tRe\t0\t0\t0\t0\t0\t0\t148\t26 Re\n+Os\t76\t0\t0\t0\tOs\t0\t0\t0\t0\tOs\t0\t0\t0\t0\t0\t0\t149\t26 Os\n+Ir\t77\t0\t0\t0\tIr\t0\t0\t0\t0\tIr\t0\t0\t0\t0\t0\t0\t150\t26 Ir\n+Au\t79\t0\t0\t0\tAu\t0\t0\t0\t0\tAu\t0\t0\t0\t0\t0\t0\t151\t26 Au\n+Hg\t80\t0\t0\t0\tHg\t0\t0\t0\t0\tHg\t0\t0\t0\t0\t0\t0\t152\t26 Hg\n+Tl\t81\t0\t0\t0\tTl\t0\t0\t0\t0\tTl\t0\t0\t0\t0\t0\t0\t153\t26 Tl\n+Bi\t83\t0\t0\t0\tBi\t0\t0\t0\t0\tBi\t0\t0\t0\t0\t0\t0\t154\t26 Bi\n+Po\t84\t0\t0\t0\tPo\t0\t0\t0\t0\tPo\t0\t0\t0\t0\t0\t0\t155\t26 Po\n+At\t85\t0\t0\t0\tAt\t0\t0\t0\t0\tAt\t0\t0\t0\t0\t0\t0\t156\t26 At\n+Rn\t86\t0\t0\t0\tRn\t0\t0\t0\t0\tRn\t0\t0\t0\t0\t0\t0\t157\t26 Rn\n+Fr\t87\t0\t0\t0\tFr\t0\t0\t0\t0\tFr\t0\t0\t0\t0\t0\t0\t158\t26 Fr\n+Ra\t88\t0\t0\t0\tRa\t0\t0\t0\t0\tRa\t0\t0\t0\t0\t0\t0\t159\t26 Ra\n+Ac\t89\t0\t0\t0\tAc\t0\t0\t0\t0\tAc\t0\t0\t0\t0\t0\t0\t160\t26 Ac\n+Th\t90\t0\t0\t0\tTh\t0\t0\t0\t0\tTh\t0\t0\t0\t0\t0\t0\t161\t26 Th\n+Pa\t91\t0\t0\t0\tPa\t0\t0\t0\t0\tPa\t0\t0\t0\t0\t0\t0\t162\t26 Pa\n+U\t92\t0\t0\t0\tU\t0\t0\t0\t0\tU\t0\t0\t0\t0\t0\t0\t163\t26 U\n+Np\t93\t0\t0\t0\tNp\t0\t0\t0\t0\tNp\t0\t0\t0\t0\t0\t0\t164\t26 Np\n+Pu\t94\t0\t0\t0\tPu\t0\t0\t0\t0\tPu\t0\t0\t0\t0\t0\t0\t165\t26 Pu\n+Am\t95\t0\t0\t0\tAm\t0\t0\t0\t0\tAm\t0\t0\t0\t0\t0\t0\t166\t26 Am\n+Cm\t96\t0\t0\t0\tCm\t0\t0\t0\t0\tCm\t0\t0\t0\t0\t0\t0\t167\t26 Cm\n+Bk\t97\t0\t0\t0\tBk\t0\t0\t0\t0\tBk\t0\t0\t0\t0\t0\t0\t168\t26 Bk\n+Cf\t98\t0\t0\t0\tCf\t0\t0\t0\t0\tCf\t0\t0\t0\t0\t0\t0\t169\t26 Cf\n+Es\t99\t0\t0\t0\tEs\t0\t0\t0\t0\tEs\t0\t0\t0\t0\t0\t0\t170\t26 Es\n+Fm\t100\t0\t0\t0\tFm\t0\t0\t0\t0\tFm\t0\t0\t0\t0\t0\t0\t171\t26 Fm\n+Md\t101\t0\t0\t0\tMd\t0\t0\t0\t0\tMd\t0\t0\t0\t0\t0\t0\t172\t26 Md\n+No\t102\t0\t0\t0\tNo\t0\t0\t0\t0\tNo\t0\t0\t0\t0\t0\t0\t173\t26 No\n+Lr\t103\t0\t0\t0\tLr\t0\t0\t0\t0\tLr\t0\t0\t0\t0\t0\t0\t174\t26 Lr\n+Rf\t104\t0\t0\t0\tRf\t0\t0\t0\t0\tRf\t0\t0\t0\t0\t0\t0\t175\t26 Rf\n+Db\t105\t0\t0\t0\tDb\t0\t0\t0\t0\tDb\t0\t0\t0\t0\t0\t0\t176\t26 Db\n+Sg\t106\t0\t0\t0\tSg\t0\t0\t0\t0\tSg\t0\t0\t0\t0\t0\t0\t177\t26 Sg\n+Bh\t107\t0\t0\t0\tBh\t0\t0\t0\t0\tBh\t0\t0\t0\t0\t0\t0\t178\t26 Bh\n+Hs\t108\t0\t0\t0\tHs\t0\t0\t0\t0\tHs\t0\t0\t0\t0\t0\t0\t179\t26 Hs\n+Mt\t109\t0\t0\t0\tMt\t0\t0\t0\t0\tMt\t0\t0\t0\t0\t0\t0\t180\t26 Mt\n+Ar\t18\t0\t0\t0\tAr\t0\t0\t0\t0\tAr\t0\t0\t0\t0\t0\t0\t181\t26 Ar\n+B2\t5\t0\t54\t26\tB\tB\t0\tB\t53\tB\t26\tB2\tB_2\t20\t20\tB.0\t182\t26 26\n+B3\t5\t0\t55\t27\tB\tB\t0\tB\t53\tB\t26\tB3\tB_3\t20\t20\tB.0\t183\t26 27\n+N\t7\t0\t62\t30\tN\tN\t3\tN\t2\tN.\t33\tN\tN\t2\t1\tN.0\t184\t26 8\n+HS 1 0 42 21 H H 0 H 11 H 13 H H_HB 15 25 H.1 185 26 5\n+HB 1 0 42 21 H H 0 H 11 H 13 H H_b 15 25 H.1 186 26 5\n+Oar 8 2 15 7 O O2 0 O 81 O.2 9 O2 O_R 11 11 O.3 187 26 7\n+O1 8 0 62 30 O O 3 O 2 O. 33 O O_1 2 1 O.0 188 26 7\n+HO\t1\t0\t42\t24\tH\tH\t0\tH\t11\tH\t13\tH\tH_HB\t15\t6\tH.1\t189\t26 24\n+HO\t1\t0\t42\t24\tH\tH\t0\tH\t11\tH\t13\tH\tH_HB\t15\t6\tH.1\t190\t26 28\n+O\t8\t2\t20\t7\tO\tO3\t0\tO\t86\tO.\t9\tO3\tO_3\t26\t12\tO.3\t191\t26 46\n+C3\t6\t3\t3\t1\tC\tC3\t4\tC\t64\tC.3\t1\tC3\tC_3\t1\t5\tC.4\t192\t1 22\n+Cr\t24\t0\t0\t0\tCr\t0\t0\t0\t0\tCr.th\t0\t0\t0\t0\t0\t0\t193\t26 Cr\n+Du\t0\t0\t61\t0\tDu\tDu\t0\tZ\t0\tLp\t26\tDu\tDu\t20\t25\tun.0\t194\t26 0\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/QSAR/atomic_electron_affinities.data
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/atomic_electron_affinities.data Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/QSAR/atomic_ionization_potentials.data
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/atomic_ionization_potentials.data Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/data/QSAR/atomic_polarizabilities.data
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/atomic_polarizabilities.data Tue Jun 07 16:43:30 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
+

diff -r 000000000000 -r bac3c274238f CADDSuite/data/QSAR/dragon_descriptors.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/QSAR/dragon_descriptors.txt Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,1665 @@\n+MW\tmolecular weight\n+AMW\taverage molecular weight\n+Sv\tsum of atomic van der Waals volumes (scaled on Carbon atom)\n+Se\tsum of atomic Sanderson electronegativities (scaled on Carbon atom)\n+Sp\tsum of atomic polarizabilities (scaled on Carbon atom)\n+Ss\tsum of Kier-Hall electrotopological states\n+Mv\tmean atomic van der Waals volume (scaled on Carbon atom)\n+Me\tmean atomic Sanderson electronegativity (scaled on Carbon atom)\n+Mp\tmean atomic polarizability (scaled on Carbon atom)\n+Ms\tmean electrotopological state\n+nAT\tnumber of atoms\n+nSK\tnumber of non-H atoms\n+nBT\tnumber of bonds\n+nBO\tnumber of non-H bonds\n+nBM\tnumber of multiple bonds\n+SCBO\tsum of conventional bond orders (H-depleted)\n+ARR\taromatic ratio\n+nCIC\tnumber of rings\n+nCIR\tnumber of circuits\n+RBN\tnumber of rotatable bonds\n+RBF\trotatable bond fraction\n+nDB\tnumber of double bonds\n+nTB\tnumber of triple bonds\n+nAB\tnumber of aromatic bonds\n+nH\tnumber of Hydrogen atoms\n+nC\tnumber of Carbon atoms\n+nN\tnumber of Nitrogen atoms\n+nO\tnumber of Oxygen atoms\n+nP\tnumber of Phosphorous atoms\n+nS\tnumber of Sulfur atoms\n+nF\tnumber of Fluorine atoms\n+nCL\tnumber of Chlorine atoms\n+nBR\tnumber of Bromine atoms\n+nI\tnumber of Iodine atoms\n+nB\tnumber of Boron atoms\n+nHM\tnumber of heavy atoms\n+nX\tnumber of halogen atoms\n+nR03\tnumber of 3-membered rings\n+nR04\tnumber of 4-membered rings\n+nR05\tnumber of 5-membered rings\n+nR06\tnumber of 6-membered rings\n+nR07\tnumber of 7-membered rings\n+nR08\tnumber of 8-membered rings\n+nR09\tnumber of 9-membered rings\n+nR10\tnumber of 10-membered rings\n+nR11\tnumber of 11-membered rings\n+nR12\tnumber of 12-membered rings\n+nBnz\tnumber of benzene-like rings\n+ZM1\tfirst Zagreb index M1\n+ZM1V\tfirst Zagreb index by valence vertex degrees\n+ZM2\tsecond Zagreb index M2\n+ZM2V\tsecond Zagreb index by valence vertex degrees\n+Qindex\tQuadratic index\n+SNar\tNarumi simple topological index (log)\n+HNar\tNarumi harmonic topological index\n+GNar\tNarumi geometric topological index\n+Xt\tTotal structure connectivity index\n+Dz\tPogliani index\n+Ram\tramification index\n+Pol\tpolarity number\n+LPRS\tlog of product of row sums (PRS)\n+VDA\taverage vertex distance degree\n+MSD\tmean square distance index (Balaban)\n+SMTI\tSchultz Molecular Topological Index (MTI)\n+SMTIV\tSchultz MTI by valence vertex degrees\n+GMTI\tGutman Molecular Topological Index\n+GMTIV\tGutman MTI by valence vertex degrees\n+Xu\tXu index\n+SPI\tsuperpendentic index\n+W\tWiener W index\n+WA\tmean Wiener index\n+Har\tHarary H index\n+Har2\tsquare reciprocal distance sum index\n+QW\tquasi-Wiener index (Kirchhoff number)\n+TI1\tfirst Mohar index TI1\n+TI2\tsecond Mohar index TI2\n+STN\tspanning tree number (log)\n+HyDp\thyper-distance-path index\n+RHyDp\treciprocal hyper-distance-path index\n+w\tdetour index\n+ww\thyper-detour index\n+Rww\treciprocal hyper-detour index\n+D/D\tdistance/detour index\n+Wap\tall-path Wiener index\n+WhetZ\tWiener-type index from Z weighted distance matrix (Barysz matrix)\n+Whetm\tWiener-type index from mass weighted distance matrix\n+Whetv\tWiener-type index from van der Waals weighted distance matrix\n+Whete\tWiener-type index from electronegativity weighted distance matrix\n+Whetp\tWiener-type index from polarizability weighted distance matrix\n+J\tBalaban distance connectivity index\n+JhetZ\tBalaban-type index from Z weighted distance matrix (Barysz matrix)\n+Jhetm\tBalaban-type index from mass weighted distance matrix\n+Jhetv\tBalaban-type index from van der Waals weighted distance matrix\n+Jhete\tBalaban-type index from electronegativity weighted distance matrix\n+Jhetp\tBalaban-type index from polarizability weighted distance matrix\n+MAXDN\tmaximal electrotopological negative variation\n+MAXDP\tmaximal electrotopological positive variation\n+DELS\tmolecular electrotopological variation\n+TIE\tE-state topological parameter\n+S0K\tKier symmetry index\n+S1K\t1-path Kier alpha-modified shape index\n+S2K\t2-path Kier alpha-modified shape index\n+S3K\t3-path Kier alpha-modified shape index\n+PHI\tKier flexibility index\n+BLI\tKier benzene-likeliness index\n+PW2\tpath/walk 2 - Randi'..b')\n+PCWTe\tpartial charge weighted topological electronic descriptor\n+LDI\tlocal dipole index\n+Ui\tunsaturation index\n+Hy\thydrophilic factor\n+AMR\tmolar refractivity\n+TPSA(NO)\ttopological polar surface area using N, O polar contributions\n+TPSA(tot)\ttopological polar surface area using N, O, S, P polar contributions\n+MLogP\tMoriguchi octanol-water partition coefficient\n+MLOGP2\tSquared Moriguchi octanol-water partition coeff. (logP^2)\n+ALOGP\tGhose-Crippen octanol-water partition coeff. (logP)\n+ALOGP2\tSquared Ghose-Crippen octanol-water partition coeff. (logP^2)\n+LAI\tLipinski alert index\n+GVWAI-80\tGhose-Viswanadhan-Wendoloski drug-like index at 80%\n+GVWAI-50\tGhose-Viswanadhan-Wendoloski drug-like index at 50%\n+Inflammat-80\tGhose-Viswanadhan-Wendoloski antiinflammatory-like index at 80%\n+Inflammat-50\tGhose-Viswanadhan-Wendoloski antiinflammatory-like index at 50%\n+Depressant-80\tGhose-Viswanadhan-Wendoloski antidepressant-like index at 80%\n+Depressant-50\tGhose-Viswanadhan-Wendoloski antidepressant-like index at 50%\n+Psychotic-80\tGhose-Viswanadhan-Wendoloski antipsychotic-like index at 80%\n+Psychotic-50\tGhose-Viswanadhan-Wendoloski antipsychotic-like index at 50%\n+Hypertens-80\tGhose-Viswanadhan-Wendoloski antihypertensive-like index at 80%\n+Hypertens-50\tGhose-Viswanadhan-Wendoloski antihypertensive-like index at 50%\n+Hypnotic-80\tGhose-Viswanadhan-Wendoloski hypnotic-like index at 80%\n+Hypnotic-50\tGhose-Viswanadhan-Wendoloski hypnotic-like index at 50%\n+Neoplastic-80\tGhose-Viswanadhan-Wendoloski antineoplastic-like index at 80%\n+Neoplastic-50\tGhose-Viswanadhan-Wendoloski antineoplastic-like index at 50%\n+Infective-80\tGhose-Viswanadhan-Wendoloski antiinfective-like index at 80%\n+Infective-50\tGhose-Viswanadhan-Wendoloski antiinfective-like index at 50% \n+BLTF96\tVerhaar model of Fish base-line toxicity for Fish (96h) from MLOGP (mmol/l)\n+BLTD48\tVerhaar model of Daphnia base-line toxicity\xc2\xa0 for Daphnia (48h) from MLOGP (mmol/l)\n+BLTA96\tVerhaar model of Algae base-line toxicity for Algae (96h) from MLOGP (mmol/l)\n+B01[C-C]\tpresence/absence of C-C at topological distance 1\n+B01[C-N]\tpresence/absence of C-N at topological distance 1\n+B01[C-O]\tpresence/absence of C-O at topological distance 1\n+B01[C-S]\tpresence/absence of C-S at topological distance 1\n+B01[C-P]\tpresence/absence of C-P at topological distance 1\n+B01[C-F]\tpresence/absence of C-F at topological distance 1\n+B01[C-Cl]\tpresence/absence of C-Cl at topological distance 1\n+B01[C-Br]\tpresence/absence of C-Br at topological distance 1\n+B01[C-I]\tpresence/absence of C-I at topological distance 1\n+B01[C-B]\tpresence/absence of C-B at topological distance 1\n+B01[C-Si]\tpresence/absence of C-Si at topological distance 1\n+B01[C-X]\tpresence/absence of C-X at topological distance 1\n+B01[N-N]\tpresence/absence of N-N at topological distance 1\n+B01[N-O]\tpresence/absence of N-O at topological distance 1\n+.........\t..........................................................\n+B10[Si-X]\tpresence/absence of Si-X at topological distance 10\n+B10[X-X]\tpresence/absence of X-X at topological distance 10\n+F01[C-C]\tfrequency of C-C at topological distance 1\n+F01[C-N]\tfrequency of C-N at topological distance 1\n+F01[C-O]\tfrequency of C-O at topological distance 1\n+F01[C-S]\tfrequency of C-S at topological distance 1\n+F01[C-P]\tfrequency of C-P at topological distance 1\n+F01[C-F]\tfrequency of C-F at topological distance 1\n+F01[C-Cl]\tfrequency of C-Cl at topological distance 1\n+F01[C-Br]\tfrequency of C-Br at topological distance 1\n+F01[C-I]\tfrequency of C-I at topological distance 1\n+F01[C-B]\tfrequency of C-B at topological distance 1\n+F01[C-Si]\tfrequency of C-Si at topological distance 1\n+F01[C-X]\tfrequency of C-X at topological distance 1\n+F01[N-N]\tfrequency of N-N at topological distance 1\n+F01[N-O]\tfrequency of N-O at topological distance 1\n+.........\t..........................................................\n+F10[Si-X]\tfrequency of Si-X at topological distance 10\n+F10[X-X]\tfrequency of X-X at topological distance 10\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/XRAY/spacegroups.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/XRAY/spacegroups.dat Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,4926 @@\n+P 1\t1\n+(X,Y,Z)\n+\n+P 1-\t2\n+(X,Y,Z)\n+(-X,-Y,-Z)\n+\n+P -1\t2\n+(X,Y,Z)\n+(-X,-Y,-Z)\n+\n+P 2\t2\n+(X,Y,Z)\n+(-X,Y,-Z)\n+\n+P 1 21 1\t2\n+(X,Y,Z)\n+(-X,Y+1/2,-Z)\n+\n+P 21\t2\n+(X,Y,Z)\n+(-X,Y+1/2,-Z)\n+\n+C 1 2 1\t4\n+(X,Y,Z)\n+(-X,Y,-Z)\n+(1/2+X,1/2+Y,Z)\n+(1/2-X,1/2+Y,-Z)\n+\n+C 2\t4\n+(X,Y,Z)\n+(-X,Y,-Z)\n+(1/2+X,1/2+Y,Z)\n+(1/2-X,1/2+Y,-Z)\n+\n+P M\t2\n+(X,Y,Z)\n+(X,-Y,Z)\n+\n+P C\t2\n+(X,Y,Z)\n+(X,-Y,1/2+Z)\n+\n+C M\t4\n+(X,Y,Z)\n+(X,-Y,Z)\n+(1/2+X,1/2+Y,Z)\n+(1/2+X,1/2-Y,Z)\n+\n+C C\t4\n+(X,Y,Z)\n+(X,-Y,1/2+Z)\n+(1/2+X,1/2+Y,Z)\n+(1/2+X,1/2-Y,1/2+Z)\n+\n+P 2/M\t4\n+(X,Y,Z)\n+(X,-Y,Z)\n+(-X,Y,-Z)\n+(-X,-Y,-Z)\n+\n+P 21/M\t4\n+(X,Y,Z)\n+(-X,1/2+Y,-Z)\n+(-X,-Y,-Z)\n+(X,1/2-Y,Z)\n+\n+C 2/M\t8\n+(X,Y,Z)\n+(X,-Y,Z)\n+(-X,Y,-Z)\n+(-X,-Y,-Z)\n+(1/2+X,1/2+Y,Z)\n+(1/2+X,1/2-Y,Z)\n+(1/2-X,1/2+Y,-Z)\n+(1/2-X,1/2-Y,-Z)\n+\n+P 2/C\t4\n+(X,Y,Z)\n+(-X,Y,1/2-Z)\n+(-X,-Y,-Z)\n+(X,-Y,1/2+Z)\n+\n+P 21/C\t4\n+(X,Y,Z)\n+(-X,-Y,-Z)\n+(-X,1/2+Y,1/2-Z)\n+(X,1/2-Y,1/2+Z)\n+\n+C 2/C\t8\n+(X,Y,Z)\n+(-X,Y,1/2-Z)\n+(-X,-Y,-Z)\n+(X,-Y,1/2+Z)\n+(1/2+X,1/2+Y,Z)\n+(1/2-X,1/2+Y,1/2-Z)\n+(1/2-X,1/2-Y,-Z)\n+(1/2+X,1/2-Y,1/2+Z)\n+\n+P 2 2 2\t4\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(-X,Y,-Z)\n+(X,-Y,-Z)\n+\n+P 2 2 21\t4\n+(X,Y,Z)\n+(-X,-Y,1/2+Z)\n+(-X,Y,1/2-Z)\n+(X,-Y,-Z)\n+\n+P 21 21 2\t4\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(1/2-X,1/2+Y,-Z)\n+(1/2+X,1/2-Y,-Z)\n+\n+P 21 21 21\t4\n+(X,Y,Z)\n+(1/2-X,-Y,1/2+Z)\n+(-X,1/2+Y,1/2-Z)\n+(1/2+X,1/2-Y,-Z)\n+\n+C 2 2 21\t8\n+(X,Y,Z)\n+(-X,-Y,1/2+Z)\n+(-X,Y,1/2-Z)\n+(X,-Y,-Z)\n+(1/2+X,1/2+Y,Z)\n+(1/2-X,1/2-Y,1/2+Z)\n+(1/2-X,1/2+Y,1/2-Z)\n+(1/2+X,1/2-Y,-Z)\n+\n+C 2 2 2\t8\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(-X,Y,-Z)\n+(X,-Y,-Z)\n+(1/2+X,1/2+Y,Z)\n+(1/2-X,1/2-Y,Z)\n+(1/2-X,1/2+Y,-Z)\n+(1/2+X,1/2-Y,-Z)\n+\n+F 2 2 2\t16\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(-X,Y,-Z)\n+(X,-Y,-Z)\n+(X,1/2+Y,1/2+Z)\n+(-X,1/2-Y,1/2+Z)\n+(-X,1/2+Y,1/2-Z)\n+(X,1/2-Y,1/2-Z)\n+(1/2+X,Y,1/2+Z)\n+(1/2-X,-Y,1/2+Z)\n+(1/2-X,Y,1/2-Z)\n+(1/2+X,-Y,1/2-Z)\n+(1/2+X,1/2+Y,Z)\n+(1/2-X,1/2-Y,Z)\n+(1/2-X,1/2+Y,-Z)\n+(1/2+X,1/2-Y,-Z)\n+\n+I 2 2 2\t8\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(X,-Y,-Z)\n+(-X,Y,-Z)\n+(X+1/2,Y+1/2,Z+1/2)\n+(-X+1/2,-Y+1/2,Z+1/2)\n+(X+1/2,-Y+1/2,-Z+1/2)\n+(-X+1/2,Y+1/2,-Z+1/2)\n+\n+I 21 21 21\t8\n+(X,Y,Z)\n+(1/2-X,-Y,1/2+Z)\n+(-X,1/2+Y,1/2-Z)\n+(1/2+X,1/2-Y,-Z)\n+(1/2+X,1/2+Y,1/2+Z)\n+(-X,1/2-Y,Z)\n+(1/2-X,Y,-Z)\n+(X,-Y,1/2-Z)\n+\n+P M M 2\t4\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(X,-Y,Z)\n+(-X,Y,Z)\n+\n+P M C 21\t4\n+(X,Y,Z)\n+(-X,-Y,1/2+Z)\n+(X,-Y,1/2+Z)\n+(-X,Y,Z)\n+\n+P C C 2\t4\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(X,-Y,1/2+Z)\n+(-X,Y,1/2+Z)\n+\n+P M A 2\t4\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(1/2+X,-Y,Z)\n+(1/2-X,Y,Z)\n+\n+P C A 21\t4\n+(X,Y,Z)\n+(-X,-Y,1/2+Z)\n+(1/2+X,-Y,Z)\n+(1/2-X,Y,1/2+Z)\n+\n+P N C 2\t4\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(X,1/2-Y,1/2+Z)\n+(-X,1/2+Y,1/2+Z)\n+\n+P M N 21\t4\n+(X,Y,Z)\n+(1/2-X,-Y,1/2+Z)\n+(1/2+X,-Y,1/2+Z)\n+(-X,Y,Z)\n+\n+P B A 2\t4\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(1/2+X,1/2-Y,Z)\n+(1/2-X,1/2+Y,Z)\n+\n+P N A 21\t4\n+(X,Y,Z)\n+(-X,-Y,1/2+Z)\n+(1/2+X,1/2-Y,Z)\n+(1/2-X,1/2+Y,1/2+Z)\n+\n+P N N 2\t4\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(1/2+X,1/2-Y,1/2+Z)\n+(1/2-X,1/2+Y,1/2+Z)\n+\n+C M M 2\t8\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(X,-Y,Z)\n+(-X,Y,Z)\n+(1/2+X,1/2+Y,Z)\n+(1/2-X,1/2-Y,Z)\n+(1/2+X,1/2-Y,Z)\n+(1/2-X,1/2+Y,Z)\n+\n+C M C 21\t8\n+(X,Y,Z)\n+(-X,-Y,1/2+Z)\n+(X,-Y,1/2+Z)\n+(-X,Y,Z)\n+(1/2+X,1/2+Y,Z)\n+(1/2-X,1/2-Y,1/2+Z)\n+(1/2+X,1/2-Y,1/2+Z)\n+(1/2-X,1/2+Y,Z)\n+\n+C C C 2\t8\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(X,-Y,1/2+Z)\n+(-X,Y,1/2+Z)\n+(1/2+X,1/2+Y,Z)\n+(1/2-X,1/2-Y,Z)\n+(1/2+X,1/2-Y,1/2+Z)\n+(1/2-X,1/2+Y,1/2+Z)\n+\n+A M M 2\t8\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(X,-Y,Z)\n+(-X,Y,Z)\n+(X,1/2+Y,1/2+Z)\n+(-X,1/2-Y,1/2+Z)\n+(X,1/2-Y,1/2+Z)\n+(-X,1/2+Y,1/2+Z)\n+\n+A B M 2\t8\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(X,1/2-Y,Z)\n+(-X,1/2+Y,Z)\n+(X,1/2+Y,1/2+Z)\n+(-X,1/2-Y,1/2+Z)\n+(X,-Y,1/2+Z)\n+(-X,Y,1/2+Z)\n+\n+A M A 2\t8\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(1/2+X,-Y,Z)\n+(1/2-X,Y,Z)\n+(X,1/2+Y,1/2+Z)\n+(-X,1/2-Y,1/2+Z)\n+(1/2+X,1/2-Y,1/2+Z)\n+(1/2-X,1/2+Y,1/2+Z)\n+\n+A B A 2\t8\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(1/2+X,1/2-Y,Z)\n+(1/2-X,1/2+Y,Z)\n+(X,1/2+Y,1/2+Z)\n+(-X,1/2-Y,1/2+Z)\n+(1/2+X,-Y,1/2+Z)\n+(1/2-X,Y,1/2+Z)\n+\n+F M M 2\t16\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(X,-Y,Z)\n+(-X,Y,Z)\n+(X,1/2+Y,1/2+Z)\n+(-X,1/2-Y,1/2+Z)\n+(X,1/2-Y,1/2+Z)\n+(-X,1/2+Y,1/2+Z)\n+(1/2+X,Y,1/2+Z)\n+(1/2-X,-Y,1/2+Z)\n+(1/2+X,-Y,1/2+Z)\n+(1/2-X,Y,1/2+Z)\n+(1/2+X,1/2+Y,Z)\n+(1/2-X,1/2-Y,Z)\n+(1/2+X,1/2-Y,Z)\n+(1/2-X,1/2+Y,Z)\n+\n+F D D 2\t16\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(1/4+X,1/4-Y,1/4'..b'-X,1/4+Y,1/4+Z)\n+(1/4-Z,1/4-X,3/4-Y)\n+(3/4-Z,1/4+X,1/4+Y)\n+(1/4+Z,3/4+X,1/4-Y)\n+(3/4+Z,3/4-X,3/4+Y)\n+(1/4-Y,1/4-Z,3/4-X)\n+(3/4+Y,3/4-Z,3/4+X)\n+(3/4-Y,1/4+Z,1/4+X)\n+(1/4+Y,3/4+Z,1/4-X)\n+(1/2-Y,-X,Z)\n+(Y,X,1/2+Z)\n+(-Y,1/2+X,-Z)\n+(1/2+Y,1/2-X,1/2-Z)\n+(1/2-X,-Z,Y)\n+(1/2+X,1/2-Z,1/2-Y)\n+(X,Z,1/2+Y)\n+(-X,1/2+Z,-Y)\n+(1/2-Z,-Y,X)\n+(-Z,1/2+Y,-X)\n+(1/2+Z,1/2-Y,1/2-X)\n+(Z,Y,1/2+X)\n+\n+I M -3 M\t96\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(-X,Y,-Z)\n+(X,-Y,-Z)\n+(Z,X,Y)\n+(Z,-X,-Y)\n+(-Z,-X,Y)\n+(-Z,X,-Y)\n+(Y,Z,X)\n+(-Y,Z,-X)\n+(Y,-Z,-X)\n+(-Y,-Z,X)\n+(Y,X,-Z)\n+(-Y,-X,-Z)\n+(Y,-X,Z)\n+(-Y,X,Z)\n+(X,Z,-Y)\n+(-X,Z,Y)\n+(-X,-Z,-Y)\n+(X,-Z,Y)\n+(Z,Y,-X)\n+(Z,-Y,X)\n+(-Z,Y,X)\n+(-Z,-Y,-X)\n+(-X,-Y,-Z)\n+(X,Y,-Z)\n+(X,-Y,Z)\n+(-X,Y,Z)\n+(-Z,-X,-Y)\n+(-Z,X,Y)\n+(Z,X,-Y)\n+(Z,-X,Y)\n+(-Y,-Z,-X)\n+(Y,-Z,X)\n+(-Y,Z,X)\n+(Y,Z,-X)\n+(-Y,-X,Z)\n+(Y,X,Z)\n+(-Y,X,-Z)\n+(Y,-X,-Z)\n+(-X,-Z,Y)\n+(X,-Z,-Y)\n+(X,Z,Y)\n+(-X,Z,-Y)\n+(-Z,-Y,X)\n+(-Z,Y,-X)\n+(Z,-Y,-X)\n+(Z,Y,X)\n+(1/2+X,1/2+Y,1/2+Z)\n+(1/2-X,1/2-Y,1/2+Z)\n+(1/2-X,1/2+Y,1/2-Z)\n+(1/2+X,1/2-Y,1/2-Z)\n+(1/2+Z,1/2+X,1/2+Y)\n+(1/2+Z,1/2-X,1/2-Y)\n+(1/2-Z,1/2-X,1/2+Y)\n+(1/2-Z,1/2+X,1/2-Y)\n+(1/2+Y,1/2+Z,1/2+X)\n+(1/2-Y,1/2+Z,1/2-X)\n+(1/2+Y,1/2-Z,1/2-X)\n+(1/2-Y,1/2-Z,1/2+X)\n+(1/2+Y,1/2+X,1/2-Z)\n+(1/2-Y,1/2-X,1/2-Z)\n+(1/2+Y,1/2-X,1/2+Z)\n+(1/2-Y,1/2+X,1/2+Z)\n+(1/2+X,1/2+Z,1/2-Y)\n+(1/2-X,1/2+Z,1/2+Y)\n+(1/2-X,1/2-Z,1/2-Y)\n+(1/2+X,1/2-Z,1/2+Y)\n+(1/2+Z,1/2+Y,1/2-X)\n+(1/2+Z,1/2-Y,1/2+X)\n+(1/2-Z,1/2+Y,1/2+X)\n+(1/2-Z,1/2-Y,1/2-X)\n+(1/2-X,1/2-Y,1/2-Z)\n+(1/2+X,1/2+Y,1/2-Z)\n+(1/2+X,1/2-Y,1/2+Z)\n+(1/2-X,1/2+Y,1/2+Z)\n+(1/2-Z,1/2-X,1/2-Y)\n+(1/2-Z,1/2+X,1/2+Y)\n+(1/2+Z,1/2+X,1/2-Y)\n+(1/2+Z,1/2-X,1/2+Y)\n+(1/2-Y,1/2-Z,1/2-X)\n+(1/2+Y,1/2-Z,1/2+X)\n+(1/2-Y,1/2+Z,1/2+X)\n+(1/2+Y,1/2+Z,1/2-X)\n+(1/2-Y,1/2-X,1/2+Z)\n+(1/2+Y,1/2+X,1/2+Z)\n+(1/2-Y,1/2+X,1/2-Z)\n+(1/2+Y,1/2-X,1/2-Z)\n+(1/2-X,1/2-Z,1/2+Y)\n+(1/2+X,1/2-Z,1/2-Y)\n+(1/2+X,1/2+Z,1/2+Y)\n+(1/2-X,1/2+Z,1/2-Y)\n+(1/2-Z,1/2-Y,1/2+X)\n+(1/2-Z,1/2+Y,1/2-X)\n+(1/2+Z,1/2-Y,1/2-X)\n+(1/2+Z,1/2+Y,1/2+X)\n+\n+I A -3 D\t96\n+(X,Y,Z)\n+(1/2-X,-Y,1/2+Z)\n+(-X,1/2+Y,1/2-Z)\n+(1/2+X,1/2-Y,-Z)\n+(Z,X,Y)\n+(1/2+Z,1/2-X,-Y)\n+(1/2-Z,-X,1/2+Y)\n+(-Z,1/2+X,1/2-Y)\n+(Y,Z,X)\n+(-Y,1/2+Z,1/2-X)\n+(1/2+Y,1/2-Z,-X)\n+(1/2-Y,-Z,1/2+X)\n+(3/4+Y,1/4+X,1/4-Z)\n+(3/4-Y,3/4-X,3/4-Z)\n+(1/4+Y,1/4-X,3/4+Z)\n+(1/4-Y,3/4+X,1/4+Z)\n+(3/4+X,1/4+Z,1/4-Y)\n+(1/4-X,3/4+Z,1/4+Y)\n+(3/4-X,3/4-Z,3/4-Y)\n+(1/4+X,1/4-Z,3/4+Y)\n+(3/4+Z,1/4+Y,1/4-X)\n+(1/4+Z,1/4-Y,3/4+X)\n+(1/4-Z,3/4+Y,1/4+X)\n+(3/4-Z,3/4-Y,3/4-X)\n+(-X,-Y,-Z)\n+(1/2+X,Y,1/2-Z)\n+(X,1/2-Y,1/2+Z)\n+(1/2-X,1/2+Y,Z)\n+(-Z,-X,-Y)\n+(1/2-Z,1/2+X,Y)\n+(1/2+Z,X,1/2-Y)\n+(Z,1/2-X,1/2+Y)\n+(-Y,-Z,-X)\n+(Y,1/2-Z,1/2+X)\n+(1/2-Y,1/2+Z,X)\n+(1/2+Y,Z,1/2-X)\n+(1/4-Y,3/4-X,3/4+Z)\n+(1/4+Y,1/4+X,1/4+Z)\n+(3/4-Y,3/4+X,1/4-Z)\n+(3/4+Y,1/4-X,3/4-Z)\n+(1/4-X,3/4-Z,3/4+Y)\n+(3/4+X,1/4-Z,3/4-Y)\n+(1/4+X,1/4+Z,1/4+Y)\n+(3/4-X,3/4+Z,1/4-Y)\n+(1/4-Z,3/4-Y,3/4+X)\n+(3/4-Z,3/4+Y,1/4-X)\n+(3/4+Z,1/4-Y,3/4-X)\n+(1/4+Z,1/4+Y,1/4+X)\n+(1/2+X,1/2+Y,1/2+Z)\n+(-X,1/2-Y,Z)\n+(1/2-X,Y,-Z)\n+(X,-Y,1/2-Z)\n+(1/2+Z,1/2+X,1/2+Y)\n+(Z,-X,1/2-Y)\n+(-Z,1/2-X,Y)\n+(1/2-Z,X,-Y)\n+(1/2+Y,1/2+Z,1/2+X)\n+(1/2-Y,Z,-X)\n+(Y,-Z,1/2-X)\n+(-Y,1/2-Z,X)\n+(1/4+Y,3/4+X,3/4-Z)\n+(1/4-Y,1/4-X,1/4-Z)\n+(3/4+Y,3/4-X,1/4+Z)\n+(3/4-Y,1/4+X,3/4+Z)\n+(1/4+X,3/4+Z,3/4-Y)\n+(3/4-X,1/4+Z,3/4+Y)\n+(1/4-X,1/4-Z,1/4-Y)\n+(3/4+X,3/4-Z,1/4+Y)\n+(1/4+Z,3/4+Y,3/4-X)\n+(3/4+Z,3/4-Y,1/4+X)\n+(3/4-Z,1/4+Y,3/4+X)\n+(1/4-Z,1/4-Y,1/4-X)\n+(1/2-X,1/2-Y,1/2-Z)\n+(X,1/2+Y,-Z)\n+(1/2+X,-Y,Z)\n+(-X,Y,1/2+Z)\n+(1/2-Z,1/2-X,1/2-Y)\n+(-Z,X,1/2+Y)\n+(Z,1/2+X,-Y)\n+(1/2+Z,-X,Y)\n+(1/2-Y,1/2-Z,1/2-X)\n+(1/2+Y,-Z,X)\n+(-Y,Z,1/2+X)\n+(Y,1/2+Z,-X)\n+(3/4-Y,1/4-X,1/4+Z)\n+(3/4+Y,3/4+X,3/4+Z)\n+(1/4-Y,1/4+X,3/4-Z)\n+(1/4+Y,3/4-X,1/4-Z)\n+(3/4-X,1/4-Z,1/4+Y)\n+(1/4+X,3/4-Z,1/4-Y)\n+(3/4+X,3/4+Z,3/4+Y)\n+(1/4-X,1/4+Z,3/4-Y)\n+(3/4-Z,1/4-Y,1/4+X)\n+(1/4-Z,1/4+Y,3/4-X)\n+(1/4+Z,3/4-Y,1/4-X)\n+(3/4+Z,3/4+Y,3/4+X)\n+\n+B 2\t4\n+(X,Y,Z)\n+(-X,-Y,Z)\n+(1/2+X,+Y,1/2+Z)\n+(1/2-X,-Y,1/2+Z)\n+\n+P 1 1 21\t2\n+(X,Y,Z)\n+(-X,-Y,1/2+Z)\n+\n+P 2 21 21\t4\n+(X,Y,Z)\n+(X,-Y,-Z)\n+(-X,1/2+Y,1/2-Z)\n+(-X,1/2-Y,1/2+Z)\n+\n+P 21 2 21\t4\n+(X,Y,Z)\n+(-X,Y,-Z)\n+(1/2+X,-Y,1/2-Z)\n+(1/2-X,-Y,1/2+Z)\n+\n+I 1 2 1\t4\n+(X,Y,Z)\n+(-X,Y,-Z)\n+(1/2+X,1/2+Y,1/2+Z)\n+(1/2-X,1/2+Y,1/2-Z)\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/atomtyping/AMBERTypes.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/atomtyping/AMBERTypes.dat Tue Jun 07 16:43:30 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 * * * *

diff -r 000000000000 -r bac3c274238f CADDSuite/data/atomtyping/GAFFTypes.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/atomtyping/GAFFTypes.dat Tue Jun 07 16:43:30 2011 -0400

[

b"@@ -0,0 +1,208 @@\n+cx 6 4 * * [RG3] *\n+cy 6\t\t4 * * [RG4] * \n+c3 6 4 *\t\t*\t\t*\t\t\t\t\t\t*\n+c 6 3 * * [2DL] \t\t(XA1)\t\n+c 6 3 * * [1DB,0DL] \t(XA1)\t\n+c 6 3 * * [3sb] \t\t(XA1)\n+cz 6 3 * * * (N3,N3,N3) \n+cp 6 3 * * [AR1,1RG6] (XX[AR1],XX[AR1],XX[AR1]) \n+ca 6 3 * * [AR1] \t\t*\n+cc 6 3 * * [sb,db,AR2] (C3(C3))\t\n+cc 6 3 * * [sb,db,AR2] (C3(C2))\t\n+cc 6 3 * * [sb,db,AR2] (C3(XB2))\t\n+cc 6 3 * * [sb,db,AR2] (XB2(XB2))\t \n+cc 6 3 * * [sb,db,AR2] (XB2(C2))\t\n+cc 6 3 * * [sb,db,AR2] (XB2(C3))\t\n+cc 6 3 * * [sb,db,AR2] (C3[sb'])\t\n+cc 6 3 * * [sb,db,AR2] (XB2[sb'])\t\n+cc 6 3 * * [sb,db,AR2] (XD3[sb',db])\t\n+cc 6 3 * * [sb,db,AR2] (XD4[sb',db])\t\n+cc 6 3 * * [sb,db,AR3] (C3(C3))\t\n+cc 6 3 * * [sb,db,AR3] (C3(C2))\t\n+cc 6 3 * * [sb,db,AR3] (C3(XB2))\t\n+cc \t6 3 * * [sb,db,AR3] (XB2(XB2)) \t\n+cc 6 3 * * [sb,db,AR3] (XB2(C2))\t\n+cc 6 3 * * [sb,db,AR3] (XB2(C3))\t\n+cc 6 3 * * [sb,db,AR3] (C3[sb'])\t\n+cc 6 3 * * [sb,db,AR3] (XB2[sb'])\t\n+cc 6 3 * * [sb,db,AR3] (XD3[sb',db])\t\n+cc 6 3 * * [sb,db,AR3] (XD4[sb',db])\t\n+ce 6 3 * * [sb,db] (C3[SB'])\t\n+ce 6 3 * * [sb,db] (C2[SB'])\t\n+ce 6 3 * * [sb,db] (XB2[SB'])\t\n+ce 6 3 * * [sb,db] (XD3[SB',db])\t\n+ce 6 3 * * [sb,db] (XD4[SB',db])\t\n+cu 6 3 * * [RG3] *\n+cv 6 3 * * [RG4] *\n+c2 6 3 *\t\t*\t\t*\t\t\t\t\t\t*\n+cg 6 2 * * [sb,tb] (C2[SB'])\t\n+cg 6 2 * * [sb,tb] (C3[SB'])\t\n+cg 6 2 * * [sb,tb] (N1[SB'])\t\n+cg 6 2 * * [sb,tb] (XB2[SB'])\t\n+c1 6 2 *\t\t*\t\t*\t\t\t\t\t\t*\n+c1 6 1 *\t\t*\t\t*\t\t\t\t\t\t*\n+hn 1 1 * * * \t\t(N)\n+ho 1 1 * * * \t\t(O)\n+hs 1 1 * * * \t\t(S)\n+hp 1 1 * * * \t\t(P)\n+hx 1 1 * * * \t\t(C(N4))\n+hw 1 1 * * * \t\t(O(H1))\n+h3 1 1 *\t\t3 * \t\t(C4)\n+h2 1 1 * 2 * \t\t(C4)\n+h1 1 1 * 1 * \t\t(C4)\n+hc 1 1 * * * \t\t(C4)\n+h5 1 1 * 2 * \t\t(C3)\n+h4 1 1 * 1 * \t\t(C3)\n+ha 1 1 *\t\t*\t\t*\t\t\t\t\t\t*\n+f 9 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t*\n+cl 17 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t*\n+br 35 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t*\n+i 53 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t*\n+pc 15 2 * * [sb,db,AR2] (C3(C3))\t\n+pc 15 2 * * [sb,db,AR2] (C3(C2))\t\n+pc 15 2 * * [sb,db,AR2] (C3(XB2))\t\n+pc 15 2 * * [sb,db,AR2] (XB2(C3))\t\n+pc 15 2 * * [sb,db,AR2] (XB2(C2))\t\n+pc 15 2 * * [sb,db,AR2] (XB2(XB2))\t\n+pc 15 2 * * [sb,db,AR2] (C3[sb'])\t\n+pc 15 2 * * [sb,db,AR2] (C2[sb'])\t\n+pc 15 2 * * [sb,db,AR2] (XB2[sb'])\t\n+pc 15 2 * * [sb,db,AR2] (XD3[sb',db])\t\n+pc 15 2 * * [sb,db,AR2] (XD4[sb',db])\t\n+pc 15 2 * * [sb,db,AR3] (C3(C3))\t\n+pc 15 2 * * [sb,db,AR3] (C3(C2))\t\n+pc 15 2 * * [sb,db,AR3] (C3(XB2))\t\n+pc 15 2 * * [sb,db,AR3] (XB2(C3))\t\n+pc 15 2 * * [sb,db,AR3] (XB2(C2))\t\n+pc 15 2 * * [sb,db,AR3] (XB2(XB2))\n+pc \t15 2 * * [sb,db,AR3] (C3[sb'])\t\n+pc 15 2 * * [sb,db,AR3] (C2[sb'])\t\n+pc 15 2 * * [sb,db,AR3] (XB2[sb'])\t\n+pc 15 2 * * [sb,db,AR3] (XD3[sb',db])\t\n+pc 15 2 * * [sb,db,AR3] (XD4[sb',db])\t\n+pb 15 2 * * [AR1] *\n+pe 15 2 * * [sb,db] (C3[sb'])\t\n+pe 15 2 * * [sb,db] (C2[SB'])\t\n+pe 15 2 "..b" * \t\t(O1,O1)\n+na 7 3 * * [AR1.AR2.AR3] *\n+nh 7 3 * * * \t\t(XX[AR1.AR2.AR3]) \n+nh 7 3 * * * \t\t(C3[DB]) \t\n+nh 7 3 * * * \t\t(N2[DB]) \n+nh 7 3 * * * \t\t(P2[DB]) \n+n3 7 3 *\t\t*\t\t*\t\t\t\t\t\t*\n+nb 7 2 * * [AR1] *\n+nc 7 2 * * [sb,db,AR2] (C3(C3))\t\n+nc 7 2 * * [sb,db,AR2] (C3(C2))\t\n+nc 7 2 * * [sb,db,AR2] (C3(XB2))\t\n+nc 7 2 * * [sb,db,AR2] (XB2(C3))\t\n+nc 7 2 * * [sb,db,AR2] (XB2(C2))\t\n+nc 7 2 * * [sb,db,AR2] (XB2(XB2))\t\n+nc 7 2 * * [sb,db,AR2] (C3[sb'])\t\n+nc 7 2 * * [sb,db,AR2] (XB2[sb'])\t\n+nc 7 2 * * [sb,db,AR2] (XD3[sb',db])\t\n+nc 7 2 * * [sb,db,AR2] (XD4[sb',db])\t\n+nc 7 2 * * [sb,db,AR3] (C3(C3))\t\n+nc 7 2 * * [sb,db,AR3] (C3(C2))\t\n+nc 7 2 * * [sb,db,AR3] (C3(XB2))\t\n+nc 7 2 * * [sb,db,AR3] (XB2(C3))\t\n+nc 7 2 * * [sb,db,AR3] (XB2(C2))\t\n+nc 7 2 * * [sb,db,AR3] (XB2(XB2))\t\n+nc 7 2 * * [sb,db,AR3] (C3[sb'])\t\n+nc 7 2 * * [sb,db,AR3] (XB2[sb'])\t\n+nc 7 2 * * [sb,db,AR3] (XD3[sb',db])\n+nc 7 2 * * [sb,db,AR3] (XD4[sb',db])\t\n+ne 7 2 * * [sb,db] (C2[SB'])\n+ne 7 2 * * [sb,db] (C3[SB'])\n+ne 7 2 * * [sb,db] (XA1[SB'])\n+ne 7 2 * * [sb,db] (XB2[SB'])\n+ne 7 2 * * [sb,db] (XD3[SB',db])\n+ne 7 2 * * [sb,db] (XD4[SB',db])\n+n1 7 2 * * [2db] *\n+n1 7 2 * * [tb,sb] *\n+n2 7 2 *\t\t*\t\t*\t\t\t\t\t\t\t\t\t*\n+n1 7 1 *\t\t*\t\t*\t\t\t\t\t\t\t\t\t*\n+o 8 1 *\t\t*\t\t*\t\t\t\t\t\t\t\t\t*\n+oh 8 2 1 *\t\t*\t\t\t\t\t\t\t\t\t*\n+oh 8 2 2 *\t\t*\t\t\t\t\t\t\t\t\t*\n+oh 8 3 1 *\t\t*\t\t\t\t\t\t\t\t\t*\n+oh 8 3 2 *\t\t*\t\t\t\t\t\t\t\t\t*\n+oh 8 3 3 *\t\t*\t\t\t\t\t\t\t\t\t*\n+os 8 2 *\t\t*\t\t*\t\t\t\t\t\t\t\t\t*\n+os 8 3 *\t\t*\t\t*\t\t\t\t\t\t\t\t\t*\n+os 8 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t\t\t\t*\n+s 16 1 *\t\t*\t\t*\t\t\t\t\t\t\t\t\t*\n+s2 16 2 * * [DB] * \n+s2 16 2 * * [TB] * \n+sh 16 2 1 *\t\t*\t\t\t\t\t\t\t\t\t*\n+sh 16 2 2 *\t\t*\t\t\t\t\t\t\t\t\t*\n+ss \t16 2 *\t\t*\t\t*\t\t\t\t\t\t\t\t\t*\n+sx 16 3 * * [db] \t\t(XB2[sb']) \t\n+sx 16 3 * * [db] \t\t(C3[sb']) \n+sx 16 3 * * [db] \t\t(XD3[sb',db]) \n+sx 16 3 * * [db] \t\t(XD4[sb',db]) \n+s4 16 3 *\t\t*\t\t*\t\t\t\t\t\t*\n+sy 16 4 * * [db] \t\t(XB2[sb']) \n+sy 16 4 * * [db] \t\t(C3[sb']) \n+sy 16 4 * * [db] \t\t(XD3[sb',db]) \n+sy 16 4 * * [db] \t\t(XD4[sb',db]) \n+s6 16 4 *\t\t*\t\t*\t\t\t\t\t\t*\n+s6 16 5 *\t\t*\t\t*\t\t\t\t\t\t*\n+s6 16 6 *\t\t*\t\t*\t\t\t\t\t\t*\n+Li 3 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t*\n+Be 4 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+B 5 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Na 11 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t*\n+Mg 12 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t*\t \n+Al 13 -1 \t*\t\t*\t\t*\t\t\t\t\t\t*\n+Si 14 -1 \t*\t\t*\t\t*\t\t\t\t\t\t*\n+K 19 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Ca 20 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Sr 38 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t*\n+Ba \t56 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Sc 21 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Ti 22 -1\t\t*\t\t* \t*\t\t\t\t\t\t*\n+V 23 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t*\n+Cr 24 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Mn 25 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Fe 26 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Co 27 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t*\n+Ni 28 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Cu 29 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Zn 30 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Ga 31 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Ge 32 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+As 33 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Se 34 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Ru 44 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Rh 45 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Pd 46 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Ag 47 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Cd 48 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Pt 78 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Au 79 -1\t\t*\t\t*\t\t*\t\t\t\t\t\t* \n+Hg 80 -1\t *\t\t*\t\t*\t\t\t\t\t\t* \n+Tl 81 -1\t *\t\t*\t\t*\t\t\t\t\t\t* \n+Pb 82 -1\t *\t\t*\t\t*\t\t\t\t\t\t* \n+lp 0 1 * *\t\t*\t\t\t\t\t\t* \n+DU -1 -1\t\t* *\t\t*\t\t\t\t\t\t* \n"

diff -r 000000000000 -r bac3c274238f CADDSuite/data/atomtyping/SYBYLTypes.dat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/atomtyping/SYBYLTypes.dat Tue Jun 07 16:43:30 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 * * * * *

diff -r 000000000000 -r bac3c274238f CADDSuite/data/bond_lengths/BondOrder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/BondOrder.xml Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,366 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<table>\n+\t\t\n+\t\n+\t<entry id="0">\n+\t\t<elementstring>H</elementstring>\n+\t\t<smartstring>SMARTS([#1+])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="1">\n+\t\t<elementstring>H</elementstring>\n+\t\t<smartstring>SMARTS([#1])</smartstring>\n+\t\t<penalty valence="1">0</penalty>\n+\t</entry>\n+\t<entry id="2">\n+\t\t<elementstring>F</elementstring>\n+\t\t<smartstring>SMARTS(F)</smartstring>\n+\t\t<penalty valence="0">64</penalty>\n+\t\t<penalty valence="1">0</penalty>\n+\t\t<penalty valence="2">64</penalty>\n+\t</entry>\t\n+\t<entry id="4">\n+\t\t<elementstring>Br</elementstring>\n+\t\t<smartstring>SMARTS(Br)</smartstring>\n+\t\t<penalty valence="0">64</penalty>\n+\t\t<penalty valence="1">0</penalty>\n+\t\t<penalty valence="2">64</penalty>\n+\t</entry>\n+\t<entry id="5">\n+\t\t<elementstring>I</elementstring>\n+\t\t<smartstring>SMARTS(I)</smartstring>\n+\t\t<penalty valence="0">64</penalty>\n+\t\t<penalty valence="1">0</penalty>\n+\t\t<penalty valence="2">64</penalty>\n+\t</entry>\n+\t<entry id="6"> \n+\t\t<elementstring>C</elementstring>\n+\t\t<smartstring>SMARTS([$([#6D1](~[#7D2]))])</smartstring>\n+\t\t<penalty valence="3">0</penalty>\n+\t\t<penalty valence="4">1</penalty>\n+\t\t<penalty valence="5">32</penalty>\n+\t</entry>\n+\t<entry id="7">\n+\t\t<elementstring>C</elementstring>\n+\t\t<smartstring>SMARTS([#6D1])</smartstring>\n+\t\t<penalty valence="3">1</penalty>\n+\t\t<penalty valence="4">0</penalty>\n+\t\t<penalty valence="5">32</penalty>\n+\t</entry>\n+\t<entry id="9">\n+\t\t<elementstring>C</elementstring>\n+\t\t<smartstring>SMARTS([#6])</smartstring>\n+\t\t<penalty valence="2">64</penalty>\n+\t\t<penalty valence="3">32</penalty>\n+\t\t<penalty valence="4">0</penalty>\n+\t\t<penalty valence="5">32</penalty>\n+\t\t<penalty valence="6">64</penalty>\n+\t</entry>\n+\t<entry id="10">\n+\t\t<elementstring>Si</elementstring>\n+\t\t<smartstring>SMARTS(Si)</smartstring>\n+\t\t<penalty valence="4">0</penalty>\n+\t</entry>\n+\t<entry id="11">\n+\t\t<elementstring>N</elementstring>\n+\t\t<smartstring>SMARTS([$([#7D1](~[#7D2]))])</smartstring> \n+\t\t<penalty valence="2">0</penalty>\n+\t\t<penalty valence="3">0</penalty>\n+\t</entry>\n+\t<entry id="12">\n+\t\t<elementstring>N</elementstring>\n+\t\t<smartstring>SMARTS([#7D1])</smartstring>\n+\t\t<penalty valence="2">3</penalty>\n+\t\t<penalty valence="3">0</penalty>\n+\t\t<penalty valence="4">32</penalty>\n+\t</entry>\n+\t<entry id="13">\n+\t\t<elementstring>N</elementstring>\n+\t\t<smartstring>SMARTS([$([#7D2](~[#7D1]))])</smartstring> \n+\t\t<penalty valence="3">1</penalty>\n+\t\t<penalty valence="4">0</penalty>\n+\t</entry>\n+\t<entry id="14">\n+\t\t<elementstring>N</elementstring>\n+\t\t<smartstring>SMARTS([#7D2])</smartstring>\n+\t\t<penalty valence="2">4</penalty>\n+\t\t<penalty valence="3">0</penalty>\n+\t\t<penalty valence="4">2</penalty>\n+\t</entry>\n+\t<entry id="151">\t\n+\t\t<elementstring>N</elementstring>\n+\t\t<smartstring>SMARTS([$([#7D3](~[#8D1-,#16D1-])~[#8D1,#16D1])])</smartstring>\n+\t\t<penalty valence="3">32</penalty>\n+\t\t<penalty valence="4">0</penalty>\n+\t\t<penalty valence="5">32</penalty>\n+\t\t<penalty valence="6">64</penalty>\n+\t</ent'..b'291">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>SMARTS([$([#16D1](~[#6D3]~[#8D1,#16D1]))])</smartstring>\n+\t\t<penalty valence="1">0</penalty>\n+\t\t<penalty valence="2">0</penalty>\n+\t</entry>\n+\t<entry id="29">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>SMARTS([#16D1])</smartstring>\n+\t\t<penalty valence="1">2</penalty>\n+\t\t<penalty valence="2">0</penalty>\n+\t\t<penalty valence="3">64</penalty>\n+\t</entry>\n+\t<entry id="30">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>SMARTS([#16D2])</smartstring>\n+\t\t<penalty 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id="33">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring>\t\t\n+\t\t<penalty valence="6">32</penalty>\n+\t\t<penalty valence="7">0</penalty>\n+\t</entry>\n+\t<entry id="34">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>\n+\t\t<penalty valence="6">32</penalty>\n+\t\t<penalty valence="7">0</penalty>\n+\t</entry>\n+\t<entry id="35">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>SMARTS([#16D4])</smartstring>\n+\t\t<penalty valence="4">4</penalty>\n+\t\t<penalty valence="5">2</penalty>\n+\t\t<penalty valence="6">0</penalty>\n+\t\t</entry>\t\n+\t<entry id="36">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>SMARTS([#16D5])</smartstring>\n+\t\t<penalty valence="5">2</penalty>\n+\t\t<penalty valence="6">0</penalty>\n+\t</entry>\n+\n+\t<entry id="40">\n+\t\t<elementstring>Li</elementstring>\n+\t\t<smartstring>SMARTS([#3])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="41">\n+\t\t<elementstring>Na</elementstring>\n+\t\t<smartstring>SMARTS([#11])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="42">\n+\t\t<elementstring>Mg</elementstring>\n+\t\t<smartstring>SMARTS([#12])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="43">\n+\t\t<elementstring>K</elementstring>\n+\t\t<smartstring>SMARTS([#19])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="44">\n+\t\t<elementstring>Ca</elementstring>\n+\t\t<smartstring>SMARTS([#20])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="45">\n+\t\t<elementstring>Cu</elementstring>\n+\t\t<smartstring>SMARTS([#29])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="46">\n+\t\t<elementstring>Zn</elementstring>\n+\t\t<smartstring>SMARTS([#30])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="47">\n+\t\t<elementstring>Fe</elementstring>\n+\t\t<smartstring>SMARTS([#26])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="48">\n+\t\t<elementstring>Cl</elementstring>\n+\t\t<smartstring>SMARTS([#17-])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="49">\n+\t\t<elementstring>Cl</elementstring>\n+\t\t<smartstring>SMARTS([#17])</smartstring>\n+\t\t<penalty valence="0">64</penalty>\n+\t\t<penalty valence="1">0</penalty>\n+\t\t<penalty valence="2">64</penalty>\t\n+\t\t<penalty valence="3">128</penalty>\n+\t\t<penalty valence="4">128</penalty>\n+\t</entry>\n+</table>\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/bond_lengths/BondOrderGAFF.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/BondOrderGAFF.xml Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,306 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<table>\n+\t\t\n+\t<entry id="1">\n+\t\t<elementstring>H</elementstring>\n+\t\t<smartstring>SMARTS([#1])</smartstring>\n+\t\t<penalty valence="0">64</penalty>\n+\t\t<penalty valence="1">0</penalty>\n+\t\t<penalty valence="2">64</penalty>\n+\t</entry>\n+\t<entry id="2">\n+\t\t<elementstring>F</elementstring>\n+\t\t<smartstring>SMARTS(F)</smartstring>\n+\t\t<penalty valence="0">64</penalty>\n+\t\t<penalty valence="1">0</penalty>\n+\t\t<penalty valence="2">64</penalty>\n+\t</entry>\n+\t<entry id="3">\n+\t\t<elementstring>Cl</elementstring>\n+\t\t<smartstring>SMARTS(Cl)</smartstring>\n+\t\t<penalty valence="0">64</penalty>\n+\t\t<penalty valence="1">0</penalty>\n+\t\t<penalty valence="2">64</penalty>\n+\t</entry>\n+\t<entry id="4">\n+\t\t<elementstring>Br</elementstring>\n+\t\t<smartstring>SMARTS(Br)</smartstring>\n+\t\t<penalty valence="0">64</penalty>\n+\t\t<penalty valence="1">0</penalty>\n+\t\t<penalty valence="2">64</penalty>\n+\t</entry>\n+\t<entry id="5">\n+\t\t<elementstring>I</elementstring>\n+\t\t<smartstring>SMARTS(I)</smartstring>\n+\t\t<penalty valence="0">64</penalty>\n+\t\t<penalty valence="1">0</penalty>\n+\t\t<penalty valence="2">64</penalty>\n+\t</entry>\n+\t<entry id="6">\n+\t\t<elementstring>C</elementstring>\n+\t\t<smartstring>SMARTS([$([#6D1](~[#7D2]))])</smartstring>\n+\t\t\n+\t\t<penalty valence="3">0</penalty>\n+\t\t<penalty valence="4">1</penalty>\n+\t\t<penalty valence="5">32</penalty>\n+\t</entry>\n+\t<entry id="7">\n+\t\t<elementstring>C</elementstring>\n+\t\t<smartstring>SMARTS([#6D1])</smartstring>\n+\t\t<penalty valence="3">1</penalty>\n+\t\t<penalty valence="4">0</penalty>\n+\t\t<penalty valence="5">32</penalty>\n+\t</entry>\n+\t<entry id="8">\n+\t\t<elementstring>C</elementstring>\n+\t\t<smartstring>SMARTS([$([#6D3](~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>\n+\t\t<penalty valence="4">32</penalty>\n+\t\t<penalty valence="5">0</penalty>\n+\t\t<penalty 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id="13">\n+\t\t<elementstring>N</elementstring>\n+\t\t<smartstring>SMARTS([$([#7D2](~[#7D1]))])</smartstring>\n+\t\t<penalty valence="3">1</penalty>\n+\t\t<penalty valence="4">0</penalty>\n+\t</entry>\n+\t<entry id="14">\n+\t\t<elementstring>N</elementstring>\n+\t\t<smartstring>SMARTS([#7D2])</smartstring>\n+\t\t<penalty valence="2">4</penalty>\n+\t\t<penalty valence="3">0</penalty>\n+\t\t<penalty valence="4">2</penalty>\n+\t</entry>\n+\t<entry id="15">\n+\t\t<elementstr'..b'\t<penalty valence="6">0</penalty>\n+\t\t<penalty valence="7">32</penalty>\n+\t</entry>\n+\t<entry id="26">\n+\t\t<elementstring>P</elementstring>\n+\t\t<smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring>\n+\t\t<penalty valence="6">32</penalty>\n+\t\t<penalty valence="7">0</penalty>\n+\t</entry>\n+\t<entry id="27">\n+\t\t<elementstring>P</elementstring>\n+\t\t\n+\t\t<smartstring>SMARTS(#15D4)</smartstring>\n+\t\t<penalty valence="3">64</penalty>\n+\t\t<penalty valence="4">1</penalty>\n+\t\t<penalty valence="5">0</penalty>\n+\t\t<penalty valence="6">32</penalty>\n+\t</entry>\n+\t<entry id="28">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>SMARTS([#7D3](~[#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])) AND element(S)</smartstring>\n+\t\t<penalty valence="1">0</penalty>\n+\t\t<penalty valence="2">1</penalty>\n+\t</entry>\n+\t<entry id="29">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>SMARTS([#16D1])</smartstring>\n+\t\t<penalty valence="1">2</penalty>\n+\t\t<penalty valence="2">0</penalty>\n+\t\t<penalty valence="3">64</penalty>\n+\t</entry>\n+\t<entry id="30">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>SMARTS([#16D2])</smartstring>\n+\t\t\n+\t\t<penalty valence="1">2</penalty>\n+\t\t<penalty valence="2">0</penalty>\n+\t\t<penalty valence="3">64</penalty>\n+\t</entry>\n+\t<entry id="31">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>SMARTS([#16D3])</smartstring>\n+\t\t<penalty valence="3">1</penalty>\n+\t\t<penalty valence="4">0</penalty>\n+\t\t<penalty valence="5">2</penalty>\n+\t\t<penalty valence="6">2</penalty>\n+\t</entry>\n+\t<entry id="32">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>\tSMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1]))])</smartstring>\n+\t\t<penalty valence="6">0</penalty>\n+\t\t<penalty valence="7">32</penalty>\n+\t</entry>\n+\t<entry id="33">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring>\t\t\n+\t\t<penalty valence="6">32</penalty>\n+\t\t<penalty valence="7">0</penalty>\n+\t</entry>\n+\t<entry id="34">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring>\n+\t\t<penalty valence="6">32</penalty>\n+\t\t<penalty valence="7">0</penalty>\n+\t</entry>\n+\t<entry id="35">\n+\t\t<elementstring>S</elementstring>\n+\t\t<smartstring>SMARTS([#16D4])</smartstring>\n+\t\t<penalty valence="4">4</penalty>\n+\t\t<penalty valence="5">2</penalty>\n+\t\t<penalty valence="6">0</penalty>\n+\t</entry>\n+\t\n+\t<entry id="40">\n+\t\t<elementstring>Li</elementstring>\n+\t\t<smartstring>SMARTS([#3])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="41">\n+\t\t<elementstring>Na</elementstring>\n+\t\t<smartstring>SMARTS([#11])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="42">\n+\t\t<elementstring>Mg</elementstring>\n+\t\t<smartstring>SMARTS([#12])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="43">\n+\t\t<elementstring>K</elementstring>\n+\t\t<smartstring>SMARTS([#19])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="44">\n+\t\t<elementstring>Ca</elementstring>\n+\t\t<smartstring>SMARTS([#20])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="45">\n+\t\t<elementstring>Cu</elementstring>\n+\t\t<smartstring>SMARTS([#29])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\t<entry id="46">\n+\t\t<elementstring>Zn</elementstring>\n+\t\t<smartstring>SMARTS([#30])</smartstring>\n+\t\t<penalty valence="0">0</penalty>\n+\t</entry>\n+\n+</table>\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/bond_lengths/bond_lengths.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/bond_lengths.db Tue Jun 07 16:43:30 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
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+ <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
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+ <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>
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+ <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
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+ <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
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+ <node>max<value>1.95</value></node>
+ <node>single<value>1.8</value></node>
+ <node>min<value>1.7</value></node>
+ </node>
+ </node>
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+ <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
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+ <node>single<value>1.8</value></node>
+ <node>min<value>1.0</value></node>
+ </node>
+ </node>
+ <node>35
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+ <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
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+ <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
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+ <node>double<value>1.22</value></node>
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+ </node>
+ </node>
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+ <node>single<value>1.4</value></node>
+ <node>double<value>1.21</value></node>
+ <node>min<value>1.15</value></node>
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+ </node>
+ <node>9
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+ <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
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+ <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>
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+ <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
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+ <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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/bond_lengths/bond_lengths_mmff94.ini
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/bond_lengths/bond_lengths_mmff94.ini Tue Jun 07 16:43:30 2011 -0400

[

b'@@ -0,0 +1,1505 @@\n+[BondLengths]\n+key:I key:deg_I key:J key:deg_J key:order value:r0\n+@unit_r0=Angstrom\n+;\n+;\n+;\t I deg_I J deg_J order r0 \n+\t--- ------- --- ------- ------- --------- \n+\t C 1 C 1 1 1.508\n+\t C 1 C 2 1 1.508\n+\t C 1 C 3 1 1.508\n+\t C 1 C 4 1 1.5086\n+\t C 2 C 1 1 1.508\n+\t C 2 C 2 1 1.5086\n+\t C 2 C 3 1 1.5072\n+\t C 2 C 4 1 1.5093\n+\t C 3 C 1 1 1.508\n+\t C 3 C 2 1 1.5072\n+\t C 3 C 3 1 1.5066\n+\t C 3 C 4 1 1.51\n+\t C 4 C 1 1 1.5086\n+\t C 4 C 2 1 1.5093\n+\t C 4 C 3 1 1.51\n+\t C 4 C 4 1 1.5121\n+\t C 1 C 1 2 1.333\n+\t C 1 C 2 2 1.333\n+\t C 1 C 3 2 1.3333\n+\t C 1 C 4 2 1.344\n+\t C 2 C 1 2 1.333\n+\t C 2 C 2 2 1.3333\n+\t C 2 C 3 2 1.3341\n+\t C 2 C 4 2 1.3453\n+\t C 3 C 1 2 1.3333\n+\t C 3 C 2 2 1.3341\n+\t C 3 C 3 2 1.3358\n+\t C 3 C 4 2 1.3477\n+\t C 4 C 1 2 1.344\n+\t C 4 C 2 2 1.3453\n+\t C 4 C 3 2 1.3477\n+\t C 4 C 4 2 1.3624\n+\t C 1 C 1 3 1.192\n+\t C 1 C 2 3 1.4529\n+\t C 1 C 3 3 1.192\n+\t C 1 C 4 3 1.1917\n+\t C 2 C 1 3 1.452\n+\t C 2 C 2 3 1.211\n+\t C 2 C 3 3 1.3034\n+\t C 2 C 4 3 1.4768\n+\t C 3 C 1 3 1.192\n+\t C 3 C 2 3 1.299\n+\t C 3 C 3 3 1.3358\n+\t C 3 C 4 3 1.4835\n+\t C 4 C 1 3 1.1917\n+\t C 4 C 2 3 1.468\n+\t C 4 C 3 3 1.4833\n+\t C 4 C 4 3 1.5121\n+\t C 1 N 1 1 1.4556\n+\t C 1 N 2 1 1.4556\n+\t C 1 N 3 1 1.451\n+\t C 1 N 4 1 1.4801\n+\t C 1 N 5 1 1.5343\n+\t C 2 N 1 1 1.4556\n+\t C 2 N 3 1 1.4508\n+\t C 2 N 4 1 1.4808\n+\t C 3 N 1 1 1.4556\n+\t C 3 N 3 1 1.4507\n+\t C 3 N 4 1 1.4814\n+\t C 4 N 1 1 1.4545\n+\t C 4 N 3 1 1.452\n+\t C 4 N 4 1 1.4757\n+\t C 1 N 1 2 1.29\n+\t C 1 N 2 2 1.29\n+\t C 1 N 3 2 1.28\n+\t C 1 N 4 2 1.2913\n+\t C 1 N 5 2 1.2904\n+\t C 2 N 1 2 1.29\n+\t C 2 N 2 2 1.289\n+\t C 2 N 3 2 1.2811\n+\t C 2 N 4 2 1.2904\n+\t C 2 N 5 2 1.2901\n+\t C 3 N 1 2 1.2866\n+\t C 3 N 2 2 1.2868\n+\t C 3 N 3 2 1.2798\n+\t C 3 N 4 2 1.2881\n+\t C 3 N 5 2 1.2904\n+\t C 4 N 1 2 1.3265\n+\t C 4 N 2 2 1.3277\n+\t C 4 N 3 2 1.29\n+\t C 4 N 4 2 1.3347\n+\t C 4 N 5 2 1.3364\n+\t C 1 N 1 3 1.3756\n+\t C 1 N 2 3 1.2075\n+\t C 1 N 3 3 1.3756\n+\t C 1 N 4 3 1.4018\n+\t C 1 N 5 3 1.4163\n+\t C 2 N 1 3 1.1897\n+\t C 3 N 1 3 1.1154\n+\t C 4 N 1 3 1.3758\n+\t C 1 O 1 1 1.402\n+\t C 1'..b' 1 2 1.491\n+\t Cl 1 O 1 3 1.3443\n+\t Cl 1 O 2 3 1.3443\n+\t Cl 1 O 3 3 1.3443\n+\t Cl 2 O 1 3 1.3443\n+\t Cl 3 O 1 3 1.3444\n+\t Cl 4 O 1 3 1.3479\n+\t Cl 1 P 1 1 2.0445\n+\t Cl 1 P 2 1 2.0445\n+\t Cl 1 P 3 1 2.1\n+\t Cl 1 P 4 1 2.0103\n+\t Cl 1 P 5 1 2.0863\n+\t Cl 1 P 6 1 2.1254\n+\t Cl 2 P 1 1 2.0445\n+\t Cl 3 P 1 1 2.0447\n+\t Cl 4 P 1 1 2.0745\n+\t Cl 1 P 1 2 1.8445\n+\t Cl 1 P 2 2 1.8445\n+\t Cl 1 P 3 2 1.8446\n+\t Cl 1 P 4 2 1.8573\n+\t Cl 1 P 5 2 1.8648\n+\t Cl 1 P 6 2 1.8799\n+\t Cl 2 P 1 2 1.8445\n+\t Cl 3 P 1 2 1.8445\n+\t Cl 4 P 1 2 1.8591\n+\t Cl 1 P 1 3 1.7045\n+\t Cl 1 P 2 3 1.7045\n+\t Cl 1 P 3 3 1.7045\n+\t Cl 1 P 4 3 1.7121\n+\t Cl 1 P 5 3 1.7165\n+\t Cl 1 P 6 3 1.7244\n+\t Cl 2 P 1 3 1.7045\n+\t Cl 3 P 1 3 1.7045\n+\t Cl 4 P 1 3 1.7132\n+\t Cl 1 S 1 1 2.031\n+\t Cl 1 S 2 1 2.031\n+\t Cl 1 S 3 1 2.031\n+\t Cl 1 S 4 1 1.9985\n+\t Cl 1 S 5 1 1.9855\n+\t Cl 1 S 6 1 1.9827\n+\t Cl 2 S 1 1 2.031\n+\t Cl 3 S 1 1 2.031\n+\t Cl 4 S 1 1 2.0566\n+\t Cl 1 S 1 2 2.031\n+\t Cl 1 S 2 2 2.031\n+\t Cl 1 S 3 2 2.031\n+\t Cl 1 S 4 2 1.9985\n+\t Cl 1 S 5 2 1.9855\n+\t Cl 1 S 6 2 1.9827\n+\t Cl 2 S 1 2 2.031\n+\t Cl 3 S 1 2 2.031\n+\t Cl 4 S 1 2 2.0566\n+\t Cl 1 S 1 3 2.031\n+\t Cl 1 S 2 3 2.031\n+\t Cl 1 S 3 3 2.031\n+\t Cl 1 S 4 3 1.9985\n+\t Cl 1 S 5 3 1.9855\n+\t Cl 1 S 6 3 1.9827\n+\t Cl 2 S 1 3 2.031\n+\t Cl 3 S 1 3 2.031\n+\t Cl 4 S 1 3 2.0566\n+\t Cl 1 H 1 1 1.3138\n+\t Cl 2 H 1 1 1.3138\n+\t Cl 3 H 1 1 1.3138\n+\t Cl 4 H 1 1 1.3138\n+\t Cl 1 H 1 2 1.3138\n+\t Cl 2 H 1 2 1.3138\n+\t Cl 3 H 1 2 1.3138\n+\t Cl 4 H 1 2 1.3138\n+\t Cl 1 H 1 3 1.3138\n+\t Cl 2 H 1 3 1.3138\n+\t Cl 3 H 1 3 1.3138\n+\t Cl 4 H 1 3 1.3138\n+\t Cl 1 Cl 1 1 2.02\n+\t Cl 1 Cl 2 1 2.02\n+\t Cl 1 Cl 3 1 2.02\n+\t Cl 1 Cl 4 1 2.0439\n+\t Cl 2 Cl 1 1 2.02\n+\t Cl 3 Cl 1 1 2.02\n+\t Cl 4 Cl 1 1 2.0439\n+\t Cl 1 Cl 1 2 1.82\n+\t Cl 1 Cl 2 2 1.82\n+\t Cl 1 Cl 3 2 1.82\n+\t Cl 1 Cl 4 2 1.8317\n+\t Cl 2 Cl 1 2 1.82\n+\t Cl 3 Cl 1 2 1.8201\n+\t Cl 4 Cl 1 2 1.8317\n+\t Cl 1 Cl 1 3 1.68\n+\t Cl 1 Cl 2 3 1.68\n+\t Cl 1 Cl 3 3 1.68\n+\t Cl 1 Cl 4 3 1.6869\n+\t Cl 2 Cl 1 3 1.68\n+\t Cl 3 Cl 1 3 1.68\n+\t Cl 4 Cl 1 3 1.6869\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fonts/FreeSans.ttf

Binary file CADDSuite/data/fonts/FreeSans.ttf has changed

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/A.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/A.db Tue Jun 07 16:43:30 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>
+

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/ACE.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ACE.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/ALA.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ALA.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/ARG.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ARG.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/ASN.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ASN.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/ASP.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ASP.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/Benzene-Skeleton.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Benzene-Skeleton.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/C.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/C.db Tue Jun 07 16:43:30 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>
+

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/CA.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/CA.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/CYS.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/CYS.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/Editing-Fragments.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Editing-Fragments.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/Fragments.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Fragments.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/G.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/G.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/GLN.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/GLN.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/GLU.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/GLU.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/GLY.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/GLY.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/HIS.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/HIS.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/HOH.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/HOH.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/ILE.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ILE.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/Indole-Skeleton.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Indole-Skeleton.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/LEU.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/LEU.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/LYS.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/LYS.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/MET.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/MET.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/MG.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/MG.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/MSE.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/MSE.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/NME.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/NME.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/Names.Amber.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.Amber.db Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,486 @@\n+<node>Amber<value>PDB</value>\n+ <node>*:H1<value>*:1H</value></node>\n+ <node>*:H2<value>*:2H</value></node>\n+ <node>*:H3<value>*:3H</value></node>\n+ <node>*:N<value>*:N</value></node>\n+ <node>*:C<value>*:C</value></node>\n+ <node>*:O<value>*:O</value></node>\n+ <node>*:H<value>*:H</value></node>\n+ <node>ALA:CA<value>ALA:CA</value></node>\n+ <node>ALA:HA<value>ALA:HA</value></node>\n+ <node>ALA:CB<value>ALA:CB</value></node>\n+ <node>ALA:HB1<value>ALA:1HB</value></node>\n+ <node>ALA:HB2<value>ALA:2HB</value></node>\n+ <node>ALA:HB3<value>ALA:3HB</value></node>\n+ <node>ARG:CA<value>ARG:CA</value></node>\n+ <node>ARG:HA<value>ARG:HA</value></node>\n+ <node>ARG:CB<value>ARG:CB</value></node>\n+ <node>ARG:HB2<value>ARG:1HB</value></node>\n+ <node>ARG:HB3<value>ARG:2HB</value></node>\n+ <node>ARG:CG<value>ARG:CG</value></node>\n+ <node>ARG:HG2<value>ARG:1HG</value></node>\n+ <node>ARG:HG3<value>ARG:2HG</value></node>\n+ <node>ARG:CD<value>ARG:CD</value></node>\n+ <node>ARG:HD2<value>ARG:1HD</value></node>\n+ <node>ARG:HD3<value>ARG:2HD</value></node>\n+ <node>ARG:NE<value>ARG:NE</value></node>\n+ <node>ARG:HE<value>ARG:HE</value></node>\n+ <node>ARG:CZ<value>ARG:CZ</value></node>\n+ <node>ARG:NH1<value>ARG:NH1</value></node>\n+ <node>ARG:HH11<value>ARG:1HH1</value></node>\n+ <node>ARG:HH12<value>ARG:2HH1</value></node>\n+ <node>ARG:NH2<value>ARG:NH2</value></node>\n+ <node>ARG:HH21<value>ARG:1HH2</value></node>\n+ <node>ARG:HH22<value>ARG:2HH2</value></node>\n+ <node>ASN:CA<value>ASN:CA</value></node>\n+ <node>ASN:HA<value>ASN:HA</value></node>\n+ <node>ASN:CB<value>ASN:CB</value></node>\n+ <node>ASN:HB2<value>ASN:1HB</value></node>\n+ <node>ASN:HB3<value>ASN:2HB</value></node>\n+ <node>ASN:CG<value>ASN:CG</value></node>\n+ <node>ASN:OD1<value>ASN:OD1</value></node>\n+ <node>ASN:ND2<value>ASN:ND2</value></node>\n+ <node>ASN:HD21<value>ASN:1HD2</value></node>\n+ <node>ASN:HD22<value>ASN:2HD2</value></node>\n+ <node>ASP:CA<value>ASP:CA</value></node>\n+ <node>ASP:HA<value>ASP:HA</value></node>\n+ <node>ASP:CB<value>ASP:CB</value></node>\n+ <node>ASP:HB2<value>ASP:1HB</value></node>\n+ <node>ASP:HB3<value>ASP:2HB</value></node>\n+ <node>ASP:CG<value>ASP:CG</value></node>\n+ <node>ASP:OD1<value>ASP:OD1</value></node>\n+ <node>ASP:OD2<value>ASP:OD2</value></node>\n+ <node>CYS:CA<value>CYS:CA</value></node>\n+ <node>CYS:HA<value>CYS:HA</value></node>\n+ <node>CYS:CB<value>CYS:CB</value></node>\n+ <node>CYS:HB2<value>CYS:1HB</value></node>\n+ <node>CYS:HB3<value>CYS:2HB</value></node>\n+ <node>CYS:SG<value>CYS:SG</value></node>\n+ <node>CYS:HG<value>CYS:HG</value></node>\n+ <node>CYS:HSG<value>CYS:HG</value></node>\n+ <node>GLU:CA<value>GLU:CA</value></node>\n+ <node>GLU:HA<value>GLU:HA</value></node>\n+ <node>GLU:CB<value>GLU:CB</value></node>\n+ <node>GLU:HB2<value>GLU:1HB</value></node>\n+ <node>GLU:HB3<value>GLU:2HB</value></node>\n+ <node>GLU:CG<value>GLU:CG</value></node>\n+ <node>GLU:HG2<value>GLU:1HG</value></node>\n+ <node>GLU:HG3<value>GLU:2HG</value></node>\n+ <node>GLU:CD<value>GLU:CD</value></node>\n+ <node>GLU:OE1<value>GLU:OE1</value></node>\n+ <node>GLU:OE2<value>GLU:OE2</value></node>\n+ <node>GLN:CA<value>GLN:CA</value></node>\n+ <node>GLN:HA<value>GLN:HA</value></node>\n+ <node>GLN:CB<value>GLN:CB</value></node>\n+ <node>GLN:HB2<value>GLN:1HB</value></node>\n+ <node>GLN:HB3<value>GLN:2HB</value></node>\n+ <node>GLN:CG<value>GLN:CG</value></node>\n+ <node>GLN:HG2<value>GLN:1HG</value></node>\n+ <node>GLN:HG3<value>GLN:2HG</value></node>\n+ <node>GLN:CD<value>GLN:CD</value></node>\n+ <node>GLN:OE1<value>GLN:OE1</value></node>\n+ <node>GLN:NE2<value>GLN:NE2</value></node>\n+ <node>GLN:HE21<value>GLN:1HE2</value></node>\n+ <node>GLN:HE22<value>GLN:2HE2</value></node>\n+ <node>GLY:CA<value>GLY:CA</value></node>\n+ <node>GLY:HA2<value>GLY:1HA</value></node>\n+ <node>GLY:HA3<value>GLY:2HA</value></node>\n+ <node>HIS:CA<value>HIS:CA</value></node>\n+ <node>HIS:HA<value>HIS:HA</value></node>\n+ <node>HIS:CB<value>HIS:CB</value></node>\n+ <node>HIS:HB2<value>HIS:1HB</value></node>\n+ <node>HIS'..b'B</value></node>\n+ <node>GLH:HB2<value>GLH:1HB</value></node>\n+ <node>GLH:HB3<value>GLH:2HB</value></node>\n+ <node>GLH:CG<value>GLH:CG</value></node>\n+ <node>GLH:HG2<value>GLH:1HG</value></node>\n+ <node>GLH:HG3<value>GLH:2HG</value></node>\n+ <node>GLH:CD<value>GLH:CD</value></node>\n+ <node>GLH:OE1<value>GLH:OE1</value></node>\n+ <node>GLH:OE2<value>GLH:OE2</value></node>\n+ <node>GLH:HE2<value>GLH:2HE</value></node>\n+\n+ <node>HID:CA<value>HID:CA</value></node>\n+ <node>HID:HA<value>HID:HA</value></node>\n+ <node>HID:CB<value>HID:CB</value></node>\n+ <node>HID:HB2<value>HID:1HB</value></node>\n+ <node>HID:HB3<value>HID:2HB</value></node>\n+ <node>HID:CG<value>HID:CG</value></node>\n+ <node>HID:ND1<value>HID:ND1</value></node>\n+ <node>HID:HD1<value>HID:HD1</value></node>\n+ <node>HID:CE1<value>HID:CE1</value></node>\n+ <node>HID:HE1<value>HID:HE1</value></node>\n+ <node>HID:NE2<value>HID:NE2</value></node>\n+ <node>HID:HE2<value>HID:HE2</value></node>\n+ <node>HID:CD2<value>HID:CD2</value></node>\n+ <node>HID:HD2<value>HID:HD2</value></node>\n+\n+ <node>HIE:CA<value>HIE:CA</value></node>\n+ <node>HIE:HA<value>HIE:HA</value></node>\n+ <node>HIE:CB<value>HIE:CB</value></node>\n+ <node>HIE:HB2<value>HIE:1HB</value></node>\n+ <node>HIE:HB3<value>HIE:2HB</value></node>\n+ <node>HIE:CG<value>HIE:CG</value></node>\n+ <node>HIE:ND1<value>HIE:ND1</value></node>\n+ <node>HIE:HD1<value>HIE:HD1</value></node>\n+ <node>HIE:CE1<value>HIE:CE1</value></node>\n+ <node>HIE:HE1<value>HIE:HE1</value></node>\n+ <node>HIE:NE2<value>HIE:NE2</value></node>\n+ <node>HIE:HE2<value>HIE:HE2</value></node>\n+ <node>HIE:CD2<value>HIE:CD2</value></node>\n+ <node>HIE:HD2<value>HIE:HD2</value></node>\n+\n+ <node>HIP:CA<value>HIP:CA</value></node>\n+ <node>HIP:HA<value>HIP:HA</value></node>\n+ <node>HIP:CB<value>HIP:CB</value></node>\n+ <node>HIP:HB2<value>HIP:1HB</value></node>\n+ <node>HIP:HB3<value>HIP:2HB</value></node>\n+ <node>HIP:CG<value>HIP:CG</value></node>\n+ <node>HIP:ND1<value>HIP:ND1</value></node>\n+ <node>HIP:HD1<value>HIP:HD1</value></node>\n+ <node>HIP:CE1<value>HIP:CE1</value></node>\n+ <node>HIP:HE1<value>HIP:HE1</value></node>\n+ <node>HIP:NE2<value>HIP:NE2</value></node>\n+ <node>HIP:HE2<value>HIP:HE2</value></node>\n+ <node>HIP:CD2<value>HIP:CD2</value></node>\n+ <node>HIP:HD2<value>HIP:HD2</value></node>\n+\n+ <node>CYM:CA<value>CYM:CA</value></node>\n+ <node>CYM:CB<value>CYM:CB</value></node>\n+ <node>CYM:HA<value>CYM:HA</value></node>\n+ <node>CYM:HB2<value>CYM:1HB</value></node>\n+ <node>CYM:HB3<value>CYM:2HB</value></node>\n+ <node>CYM:SG<value>CYM:SG</value></node>\n+ <node>CYM:HN<value>CYM:HN</value></node>\n+\n+ <node>CYX:CA<value>CYX:CA</value></node>\n+ <node>CYX:CB<value>CYX:CB</value></node>\n+ <node>CYX:HA<value>CYX:HA</value></node>\n+ <node>CYX:HB2<value>CYX:1HB</value></node>\n+ <node>CYX:HB3<value>CYX:2HB</value></node>\n+ <node>CYX:SG<value>CYX:SG</value></node>\n+\n+ <node>ACE:CH3<value>ACE:CH3</value></node>\n+ <node>ACE:HH31<value>ACE:1HH3</value></node>\n+ <node>ACE:HH32<value>ACE:2HH3</value></node>\n+ <node>ACE:HH33<value>ACE:3HH3</value></node>\n+ <node>NME:CH3<value>NME:CH3</value></node>\n+ <node>NME:HH31<value>NME:1HH3</value></node>\n+ <node>NME:HH32<value>NME:2HH3</value></node>\n+ <node>NME:HH33<value>NME:3HH3</value></node>\n+\n+ <node>LYN:NZ<value>LYN:NZ</value></node>\n+ <node>LYN:CA<value>LYN:CA</value></node>\n+ <node>LYN:CB<value>LYN:CB</value></node>\n+ <node>LYN:CG<value>LYN:CG</value></node>\n+ <node>LYN:CD<value>LYN:CD</value></node>\n+ <node>LYN:CE<value>LYN:CE</value></node>\n+ <node>LYN:HA<value>LYN:HA</value></node>\n+ <node>LYN:HB2<value>LYN:1HB</value></node>\n+ <node>LYN:HB3<value>LYN:2HB</value></node>\n+ <node>LYN:HD2<value>LYN:1HD</value></node>\n+ <node>LYN:HD3<value>LYN:2HD</value></node>\n+ <node>LYN:HE2<value>LYN:1HE</value></node>\n+ <node>LYN:HE3<value>LYN:2HE</value></node>\n+ <node>LYN:HG2<value>LYN:1HG</value></node>\n+ <node>LYN:HG3<value>LYN:2HG</value></node>\n+ <node>LYN:HZ2<value>LYN:2HZ</value></node>\n+ <node>LYN:HZ3<value>LYN:3HZ</value></node>\n+</node>\n+\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/Names.CHARMM.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.CHARMM.db Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,279 @@\n+<node>CHARMM<value>PDB</value>\n+ <node>*:H1<value>*:1H</value></node>\n+ <node>*:H2<value>*:2H</value></node>\n+ <node>*:H3<value>*:3H</value></node>\n+ <node>*:N<value>*:N</value></node>\n+ <node>*:C<value>*:C</value></node>\n+ <node>*:CA<value>*:CA</value></node>\n+ <node>*:O<value>*:O</value></node>\n+ <node>*:H<value>*:H</value></node>\n+ <node>*:OT1<value>*:O</value></node>\n+ <node>*:OT2<value>*:OXT</value></node>\n+ <node>*:OCT1<value>*:O</value></node>\n+ <node>*:OCT2<value>*:OXT</value></node>\n+ <node>*:HT1<value>*:1H</value></node>\n+ <node>*:HT2<value>*:2H</value></node>\n+ <node>*:HT3<value>*:3H</value></node>\n+ <node>ALA:HB1<value>ALA:1HB</value></node>\n+ <node>ALA:HB2<value>ALA:2HB</value></node>\n+ <node>ALA:HB3<value>ALA:3HB</value></node>\n+ <node>ARG:HB2<value>ARG:1HB</value></node>\n+ <node>ARG:HB3<value>ARG:2HB</value></node>\n+ <node>ARG:HG2<value>ARG:1HG</value></node>\n+ <node>ARG:HG3<value>ARG:2HG</value></node>\n+ <node>ARG:HD2<value>ARG:1HD</value></node>\n+ <node>ARG:HD3<value>ARG:2HD</value></node>\n+ <node>ARG:HH1<value>ARG:1HH1</value></node>\n+ <node>ARG:HH2<value>ARG:1HH2</value></node>\n+ <node>ARG:HH11<value>ARG:1HH1</value></node>\n+ <node>ARG:HH12<value>ARG:2HH1</value></node>\n+ <node>ARG:HH21<value>ARG:1HH2</value></node>\n+ <node>ARG:HH22<value>ARG:2HH2</value></node>\n+ <node>ASN:HB2<value>ASN:1HB</value></node>\n+ <node>ASN:HB3<value>ASN:2HB</value></node>\n+ <node>ASN:HD1<value>ASN:1HD1</value></node>\n+ <node>ASN:HD2<value>ASN:1HD2</value></node>\n+ <node>ASN:HD21<value>ASN:1HD2</value></node>\n+ <node>ASN:HD22<value>ASN:2HD2</value></node>\n+ <node>ASP:HB2<value>ASP:1HB</value></node>\n+ <node>ASP:HB3<value>ASP:2HB</value></node>\n+ <node>CYS:HB2<value>CYS:1HB</value></node>\n+ <node>CYS:HB3<value>CYS:2HB</value></node>\n+ <node>GLU:HB2<value>GLU:1HB</value></node>\n+ <node>GLU:HB3<value>GLU:2HB</value></node>\n+ <node>GLU:HG2<value>GLU:1HG</value></node>\n+ <node>GLU:HG3<value>GLU:2HG</value></node>\n+ <node>GLN:HB2<value>GLN:1HB</value></node>\n+ <node>GLN:HB3<value>GLN:2HB</value></node>\n+ <node>GLN:HG2<value>GLN:1HG</value></node>\n+ <node>GLN:HG3<value>GLN:2HG</value></node>\n+ <node>GLN:HE21<value>GLN:1HE2</value></node>\n+ <node>GLN:HE22<value>GLN:2HE2</value></node>\n+ <node>GLN:HE1<value>GLN:1HE1</value></node>\n+ <node>GLN:HE2<value>GLN:1HE2</value></node>\n+ <node>GLY:HA2<value>GLY:1HA</value></node>\n+ <node>GLY:HA3<value>GLY:2HA</value></node>\n+ <node>HIS:HB2<value>HIS:1HB</value></node>\n+ <node>HIS:HB3<value>HIS:2HB</value></node>\n+ <node>HIE:*<value>HIS:*</value></node>\n+ <node>HID:*<value>HIS:*</value></node>\n+ <node>HIP:*<value>HIS:*</value></node>\n+ <node>ILE:HG21<value>ILE:1HG2</value></node>\n+ <node>ILE:HG22<value>ILE:2HG2</value></node>\n+ <node>ILE:HG23<value>ILE:3HG2</value></node>\n+ <node>ILE:HG12<value>ILE:1HG1</value></node>\n+ <node>ILE:HG13<value>ILE:2HG1</value></node>\n+ <node>ILE:HD11<value>ILE:1HD1</value></node>\n+ <node>ILE:HD12<value>ILE:2HD1</value></node>\n+ <node>ILE:HD13<value>ILE:3HD1</value></node>\n+ <node>ILE:CD<value>ILE:CD1</value></node>\n+ <node>LEU:HB2<value>LEU:1HB</value></node>\n+ <node>LEU:HB3<value>LEU:2HB</value></node>\n+ <node>LEU:HD11<value>LEU:1HD1</value></node>\n+ <node>LEU:HD12<value>LEU:2HD1</value></node>\n+ <node>LEU:HD13<value>LEU:3HD1</value></node>\n+ <node>LEU:HD21<value>LEU:1HD2</value></node>\n+ <node>LEU:HD22<value>LEU:2HD2</value></node>\n+ <node>LEU:HD23<value>LEU:3HD2</value></node>\n+ <node>LYS:HB2<value>LYS:1HB</value></node>\n+ <node>LYS:HB3<value>LYS:2HB</value></node>\n+ <node>LYS:HG2<value>LYS:1HG</value></node>\n+ <node>LYS:HG3<value>LYS:2HG</value></node>\n+ <node>LYS:HD2<value>LYS:1HD</value></node>\n+ <node>LYS:HD3<value>LYS:2HD</value></node>\n+ <node>LYS:HE2<value>LYS:1HE</value></node>\n+ <node>LYS:HE3<value>LYS:2HE</value></node>\n+ <node>LYS:HZ1<value>LYS:1HZ</value></node>\n+ <node>LYS:HZ2<value>LYS:2HZ</value></node>\n+ <node>LYS:HZ3<value>LYS:3HZ</value></node>\n+ <node>MET:HB2<value>MET:1HB</value></node>\n+ <node>MET:HB3<value>MET:2HB</value></no'..b'\n+ <node>ILE:CD1<value>ILE:CD1</value></node>\n+ <node>LEU:CA<value>LEU:CA</value></node>\n+ <node>LEU:HA<value>LEU:HA</value></node>\n+ <node>LEU:CB<value>LEU:CB</value></node>\n+ <node>LEU:CG<value>LEU:CG</value></node>\n+ <node>LEU:HG<value>LEU:HG</value></node>\n+ <node>LEU:CD1<value>LEU:CD1</value></node>\n+ <node>LEU:CD2<value>LEU:CD2</value></node>\n+ <node>LYS:CA<value>LYS:CA</value></node>\n+ <node>LYS:HA<value>LYS:HA</value></node>\n+ <node>LYS:CB<value>LYS:CB</value></node>\n+ <node>LYS:CG<value>LYS:CG</value></node>\n+ <node>LYS:CD<value>LYS:CD</value></node>\n+ <node>LYS:CE<value>LYS:CE</value></node>\n+ <node>LYS:NZ<value>LYS:NZ</value></node>\n+ <node>MET:CA<value>MET:CA</value></node>\n+ <node>MET:HA<value>MET:HA</value></node>\n+ <node>MET:CB<value>MET:CB</value></node>\n+ <node>MET:CG<value>MET:CG</value></node>\n+ <node>MET:SD<value>MET:SD</value></node>\n+ <node>MET:CE<value>MET:CE</value></node>\n+ <node>PHE:CA<value>PHE:CA</value></node>\n+ <node>PHE:HA<value>PHE:HA</value></node>\n+ <node>PHE:CB<value>PHE:CB</value></node>\n+ <node>PHE:CG<value>PHE:CG</value></node>\n+ <node>PHE:CD1<value>PHE:CD1</value></node>\n+ <node>PHE:HD1<value>PHE:HD1</value></node>\n+ <node>PHE:CE1<value>PHE:CE1</value></node>\n+ <node>PHE:HE1<value>PHE:HE1</value></node>\n+ <node>PHE:CZ<value>PHE:CZ</value></node>\n+ <node>PHE:HZ<value>PHE:HZ</value></node>\n+ <node>PHE:CE2<value>PHE:CE2</value></node>\n+ <node>PHE:HE2<value>PHE:HE2</value></node>\n+ <node>PHE:CD2<value>PHE:CD2</value></node>\n+ <node>PHE:HD2<value>PHE:HD2</value></node>\n+ <node>PRO:CA<value>PRO:CA</value></node>\n+ <node>PRO:HA<value>PRO:HA</value></node>\n+ <node>PRO:CD<value>PRO:CD</value></node>\n+ <node>PRO:CG<value>PRO:CG</value></node>\n+ <node>PRO:CB<value>PRO:CB</value></node>\n+ <node>SER:CA<value>SER:CA</value></node>\n+ <node>SER:HA<value>SER:HA</value></node>\n+ <node>SER:CB<value>SER:CB</value></node>\n+ <node>SER:OG<value>SER:OG</value></node>\n+ <node>SER:HG<value>SER:HG</value></node>\n+ <node>THR:CA<value>THR:CA</value></node>\n+ <node>THR:HA<value>THR:HA</value></node>\n+ <node>THR:CB<value>THR:CB</value></node>\n+ <node>THR:HB<value>THR:HB</value></node>\n+ <node>THR:CG2<value>THR:CG2</value></node>\n+ <node>THR:OG1<value>THR:OG1</value></node>\n+ <node>THR:HG1<value>THR:HG1</value></node>\n+ <node>TRP:CA<value>TRP:CA</value></node>\n+ <node>TRP:HA<value>TRP:HA</value></node>\n+ <node>TRP:CB<value>TRP:CB</value></node>\n+ <node>TRP:CG<value>TRP:CG</value></node>\n+ <node>TRP:CD1<value>TRP:CD1</value></node>\n+ <node>TRP:HD1<value>TRP:HD1</value></node>\n+ <node>TRP:NE1<value>TRP:NE1</value></node>\n+ <node>TRP:HE1<value>TRP:HE1</value></node>\n+ <node>TRP:CE2<value>TRP:CE2</value></node>\n+ <node>TRP:CZ2<value>TRP:CZ2</value></node>\n+ <node>TRP:HZ2<value>TRP:HZ2</value></node>\n+ <node>TRP:CH2<value>TRP:CH2</value></node>\n+ <node>TRP:HH2<value>TRP:HH2</value></node>\n+ <node>TRP:CZ3<value>TRP:CZ3</value></node>\n+ <node>TRP:HZ3<value>TRP:HZ3</value></node>\n+ <node>TRP:CE3<value>TRP:CE3</value></node>\n+ <node>TRP:HE3<value>TRP:HE3</value></node>\n+ <node>TRP:CD2<value>TRP:CD2</value></node>\n+ <node>TYR:CA<value>TYR:CA</value></node>\n+ <node>TYR:HA<value>TYR:HA</value></node>\n+ <node>TYR:CB<value>TYR:CB</value></node>\n+ <node>TYR:CG<value>TYR:CG</value></node>\n+ <node>TYR:CD1<value>TYR:CD1</value></node>\n+ <node>TYR:HD1<value>TYR:HD1</value></node>\n+ <node>TYR:CE1<value>TYR:CE1</value></node>\n+ <node>TYR:HE1<value>TYR:HE1</value></node>\n+ <node>TYR:CZ<value>TYR:CZ</value></node>\n+ <node>TYR:OH<value>TYR:OH</value></node>\n+ <node>TYR:HH<value>TYR:HH</value></node>\n+ <node>TYR:CE2<value>TYR:CE2</value></node>\n+ <node>TYR:HE2<value>TYR:HE2</value></node>\n+ <node>TYR:CD2<value>TYR:CD2</value></node>\n+ <node>TYR:HD2<value>TYR:HD2</value></node>\n+ <node>VAL:CA<value>VAL:CA</value></node>\n+ <node>VAL:HA<value>VAL:HA</value></node>\n+ <node>VAL:CB<value>VAL:CB</value></node>\n+ <node>VAL:HB<value>VAL:HB</value></node>\n+ <node>VAL:CG1<value>VAL:CG1</value></node>\n+ <node>VAL:CG2<value>VAL:CG2</value></node>\n+</node>\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/Names.DNA.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.DNA.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/Names.Discover.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.Discover.db Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,255 @@\n+<node>Discover<value>PDB</value>\n+ <node>*:H1<value>*:1H</value></node>\n+ <node>*:H2<value>*:2H</value></node>\n+ <node>*:H3<value>*:3H</value></node>\n+ <node>*:N<value>*:N</value></node>\n+ <node>*:O<value>*:O</value></node>\n+ <node>*:C<value>*:C</value></node>\n+ <node>*:HN<value>*:H</value></node>\n+ <node>ALA:CA<value>ALA:CA</value></node>\n+ <node>ALA:HA<value>ALA:HA</value></node>\n+ <node>ALA:CB<value>ALA:CB</value></node>\n+ <node>ALA:HB1<value>ALA:1HB</value></node>\n+ <node>ALA:HB2<value>ALA:2HB</value></node>\n+ <node>ALA:HB3<value>ALA:3HB</value></node>\n+ <node>ARG:CA<value>ARG:CA</value></node>\n+ <node>ARG:HA<value>ARG:HA</value></node>\n+ <node>ARG:CB<value>ARG:CB</value></node>\n+ <node>ARG:HB1<value>ARG:1HB</value></node>\n+ <node>ARG:HB2<value>ARG:2HB</value></node>\n+ <node>ARG:CG<value>ARG:CG</value></node>\n+ <node>ARG:HG1<value>ARG:1HG</value></node>\n+ <node>ARG:HG2<value>ARG:2HG</value></node>\n+ <node>ARG:CD<value>ARG:CD</value></node>\n+ <node>ARG:HD1<value>ARG:1HD</value></node>\n+ <node>ARG:HD2<value>ARG:2HD</value></node>\n+ <node>ARG:NE<value>ARG:NE</value></node>\n+ <node>ARG:HE<value>ARG:HE</value></node>\n+ <node>ARG:CZ<value>ARG:CZ</value></node>\n+ <node>ARG:NH1<value>ARG:NH1</value></node>\n+ <node>ARG:HH11<value>ARG:1HH1</value></node>\n+ <node>ARG:HH12<value>ARG:2HH1</value></node>\n+ <node>ARG:NH2<value>ARG:NH2</value></node>\n+ <node>ARG:HH21<value>ARG:1HH2</value></node>\n+ <node>ARG:HH22<value>ARG:2HH2</value></node>\n+ <node>ASN:CA<value>ASN:CA</value></node>\n+ <node>ASN:HA<value>ASN:HA</value></node>\n+ <node>ASN:CB<value>ASN:CB</value></node>\n+ <node>ASN:HB1<value>ASN:1HB</value></node>\n+ <node>ASN:HB2<value>ASN:2HB</value></node>\n+ <node>ASN:CG<value>ASN:CG</value></node>\n+ <node>ASN:OD1<value>ASN:OD1</value></node>\n+ <node>ASN:ND2<value>ASN:ND2</value></node>\n+ <node>ASN:HD21<value>ASN:1HD2</value></node>\n+ <node>ASN:HD22<value>ASN:2HD2</value></node>\n+ <node>ASP:CA<value>ASP:CA</value></node>\n+ <node>ASP:HA<value>ASP:HA</value></node>\n+ <node>ASP:CB<value>ASP:CB</value></node>\n+ <node>ASP:HB1<value>ASP:1HB</value></node>\n+ <node>ASP:HB2<value>ASP:2HB</value></node>\n+ <node>ASP:CG<value>ASP:CG</value></node>\n+ <node>ASP:OD1<value>ASP:OD1</value></node>\n+ <node>ASP:OD2<value>ASP:OD2</value></node>\n+ <node>CYS:CA<value>CYS:CA</value></node>\n+ <node>CYS:HA<value>CYS:HA</value></node>\n+ <node>CYS:CB<value>CYS:CB</value></node>\n+ <node>CYS:HB1<value>CYS:1HB</value></node>\n+ <node>CYS:HB2<value>CYS:2HB</value></node>\n+ <node>CYS:SG<value>CYS:SG</value></node>\n+ <node>CYS:HG<value>CYS:HG</value></node>\n+ <node>GLU:CA<value>GLU:CA</value></node>\n+ <node>GLU:HA<value>GLU:HA</value></node>\n+ <node>GLU:CB<value>GLU:CB</value></node>\n+ <node>GLU:HB1<value>GLU:1HB</value></node>\n+ <node>GLU:HB2<value>GLU:2HB</value></node>\n+ <node>GLU:CG<value>GLU:CG</value></node>\n+ <node>GLU:HG1<value>GLU:1HG</value></node>\n+ <node>GLU:HG2<value>GLU:2HG</value></node>\n+ <node>GLU:CD<value>GLU:CD</value></node>\n+ <node>GLU:OE1<value>GLU:OE1</value></node>\n+ <node>GLU:OE2<value>GLU:OE2</value></node>\n+ <node>GLN:CA<value>GLN:CA</value></node>\n+ <node>GLN:HA<value>GLN:HA</value></node>\n+ <node>GLN:CB<value>GLN:CB</value></node>\n+ <node>GLN:HB1<value>GLN:1HB</value></node>\n+ <node>GLN:HB2<value>GLN:2HB</value></node>\n+ <node>GLN:CG<value>GLN:CG</value></node>\n+ <node>GLN:HG1<value>GLN:1HG</value></node>\n+ <node>GLN:HG2<value>GLN:2HG</value></node>\n+ <node>GLN:CD<value>GLN:CD</value></node>\n+ <node>GLN:OE1<value>GLN:OE1</value></node>\n+ <node>GLN:NE2<value>GLN:NE2</value></node>\n+ <node>GLN:HE21<value>GLN:1HE2</value></node>\n+ <node>GLN:HE22<value>GLN:2HE2</value></node>\n+ <node>GLY:CA<value>GLY:CA</value></node>\n+ <node>GLY:HA1<value>GLY:1HA</value></node>\n+ <node>GLY:HA2<value>GLY:2HA</value></node>\n+ <node>HIS:CA<value>HIS:CA</value></node>\n+ <node>HIS:HA<value>HIS:HA</value></node>\n+ <node>HIS:CB<value>HIS:CB</value></node>\n+ <node>HIS:HB1<value>HIS:1HB</value></node>\n+ <node>HIS:HB2<value>HIS:2HB</value></node>\n+ <nod'..b'1<value>PHE:1HB</value></node>\n+ <node>PHE:HB2<value>PHE:2HB</value></node>\n+ <node>PHE:CG<value>PHE:CG</value></node>\n+ <node>PHE:CD1<value>PHE:CD1</value></node>\n+ <node>PHE:HD1<value>PHE:HD1</value></node>\n+ <node>PHE:CE1<value>PHE:CE1</value></node>\n+ <node>PHE:HE1<value>PHE:HE1</value></node>\n+ <node>PHE:CZ<value>PHE:CZ</value></node>\n+ <node>PHE:HZ<value>PHE:HZ</value></node>\n+ <node>PHE:CE2<value>PHE:CE2</value></node>\n+ <node>PHE:HE2<value>PHE:HE2</value></node>\n+ <node>PHE:CD2<value>PHE:CD2</value></node>\n+ <node>PHE:HD2<value>PHE:HD2</value></node>\n+ <node>PRO:CA<value>PRO:CA</value></node>\n+ <node>PRO:HA<value>PRO:HA</value></node>\n+ <node>PRO:CD<value>PRO:CD</value></node>\n+ <node>PRO:HD1<value>PRO:1HD</value></node>\n+ <node>PRO:HD2<value>PRO:2HD</value></node>\n+ <node>PRO:CG<value>PRO:CG</value></node>\n+ <node>PRO:HG1<value>PRO:1HG</value></node>\n+ <node>PRO:HG2<value>PRO:2HG</value></node>\n+ <node>PRO:CB<value>PRO:CB</value></node>\n+ <node>PRO:HB1<value>PRO:1HB</value></node>\n+ <node>PRO:HB2<value>PRO:2HB</value></node>\n+ <node>SER:CA<value>SER:CA</value></node>\n+ <node>SER:HA<value>SER:HA</value></node>\n+ <node>SER:CB<value>SER:CB</value></node>\n+ <node>SER:HB1<value>SER:1HB</value></node>\n+ <node>SER:HB2<value>SER:2HB</value></node>\n+ <node>SER:OG<value>SER:OG</value></node>\n+ <node>SER:HG<value>SER:HG</value></node>\n+ <node>THR:CA<value>THR:CA</value></node>\n+ <node>THR:HA<value>THR:HA</value></node>\n+ <node>THR:CB<value>THR:CB</value></node>\n+ <node>THR:HB<value>THR:HB</value></node>\n+ <node>THR:CG2<value>THR:CG2</value></node>\n+ <node>THR:HG21<value>THR:1HG2</value></node>\n+ <node>THR:HG22<value>THR:2HG2</value></node>\n+ <node>THR:HG23<value>THR:3HG2</value></node>\n+ <node>THR:OG1<value>THR:OG1</value></node>\n+ <node>THR:HG1<value>THR:HG1</value></node>\n+ <node>TRP:CA<value>TRP:CA</value></node>\n+ <node>TRP:HA<value>TRP:HA</value></node>\n+ <node>TRP:CB<value>TRP:CB</value></node>\n+ <node>TRP:HB1<value>TRP:1HB</value></node>\n+ <node>TRP:HB2<value>TRP:2HB</value></node>\n+ <node>TRP:CG<value>TRP:CG</value></node>\n+ <node>TRP:CD1<value>TRP:CD1</value></node>\n+ <node>TRP:HD1<value>TRP:HD1</value></node>\n+ <node>TRP:NE1<value>TRP:NE1</value></node>\n+ <node>TRP:HE1<value>TRP:HE1</value></node>\n+ <node>TRP:CE2<value>TRP:CE2</value></node>\n+ <node>TRP:CZ2<value>TRP:CZ2</value></node>\n+ <node>TRP:HZ2<value>TRP:HZ2</value></node>\n+ <node>TRP:CH2<value>TRP:CH2</value></node>\n+ <node>TRP:HH2<value>TRP:HH2</value></node>\n+ <node>TRP:CZ3<value>TRP:CZ3</value></node>\n+ <node>TRP:HZ3<value>TRP:HZ3</value></node>\n+ <node>TRP:CE3<value>TRP:CE3</value></node>\n+ <node>TRP:HE3<value>TRP:HE3</value></node>\n+ <node>TRP:CD2<value>TRP:CD2</value></node>\n+ <node>TYR:CA<value>TYR:CA</value></node>\n+ <node>TYR:HA<value>TYR:HA</value></node>\n+ <node>TYR:CB<value>TYR:CB</value></node>\n+ <node>TYR:HB1<value>TYR:1HB</value></node>\n+ <node>TYR:HB2<value>TYR:2HB</value></node>\n+ <node>TYR:CG<value>TYR:CG</value></node>\n+ <node>TYR:CD1<value>TYR:CD1</value></node>\n+ <node>TYR:HD1<value>TYR:HD1</value></node>\n+ <node>TYR:CE1<value>TYR:CE1</value></node>\n+ <node>TYR:HE1<value>TYR:HE1</value></node>\n+ <node>TYR:CZ<value>TYR:CZ</value></node>\n+ <node>TYR:OH<value>TYR:OH</value></node>\n+ <node>TYR:HH<value>TYR:HH</value></node>\n+ <node>TYR:CE2<value>TYR:CE2</value></node>\n+ <node>TYR:HE2<value>TYR:HE2</value></node>\n+ <node>TYR:CD2<value>TYR:CD2</value></node>\n+ <node>TYR:HD2<value>TYR:HD2</value></node>\n+ <node>VAL:CA<value>VAL:CA</value></node>\n+ <node>VAL:HA<value>VAL:HA</value></node>\n+ <node>VAL:CB<value>VAL:CB</value></node>\n+ <node>VAL:HB<value>VAL:HB</value></node>\n+ <node>VAL:CG1<value>VAL:CG1</value></node>\n+ <node>VAL:HG11<value>VAL:1HG1</value></node>\n+ <node>VAL:HG12<value>VAL:2HG1</value></node>\n+ <node>VAL:HG13<value>VAL:3HG1</value></node>\n+ <node>VAL:CG2<value>VAL:CG2</value></node>\n+ <node>VAL:HG21<value>VAL:1HG2</value></node>\n+ <node>VAL:HG22<value>VAL:2HG2</value></node>\n+ <node>VAL:HG23<value>VAL:3HG2</value></node>\n+</node>\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/Names.Star.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.Star.db Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,261 @@\n+<node>Star<value>PDB</value>\n+ <node>*:H1<value>*:1H</value></node>\n+ <node>*:H2<value>*:2H</value></node>\n+ <node>*:H3<value>*:3H</value></node>\n+ <node>*:HT1<value>*:1H</value></node>\n+ <node>*:HT2<value>*:2H</value></node>\n+ <node>*:HT3<value>*:3H</value></node>\n+ <node>*:OT1<value>*:O</value></node>\n+ <node>*:OT2<value>*:OXT</value></node>\n+ <node>*:N<value>*:N</value></node>\n+ <node>*:O<value>*:O</value></node>\n+ <node>*:C<value>*:C</value></node>\n+ <node>*:HN<value>*:H</value></node>\n+ <node>*:H<value>*:H</value></node>\n+ <node>ALA:CA<value>ALA:CA</value></node>\n+ <node>ALA:HA<value>ALA:HA</value></node>\n+ <node>ALA:CB<value>ALA:CB</value></node>\n+ <node>ALA:HB1<value>ALA:1HB</value></node>\n+ <node>ALA:HB2<value>ALA:2HB</value></node>\n+ <node>ALA:HB3<value>ALA:3HB</value></node>\n+ <node>ARG:CA<value>ARG:CA</value></node>\n+ <node>ARG:HA<value>ARG:HA</value></node>\n+ <node>ARG:CB<value>ARG:CB</value></node>\n+ <node>ARG:HB2<value>ARG:1HB</value></node>\n+ <node>ARG:HB3<value>ARG:2HB</value></node>\n+ <node>ARG:CG<value>ARG:CG</value></node>\n+ <node>ARG:HG2<value>ARG:1HG</value></node>\n+ <node>ARG:HG3<value>ARG:2HG</value></node>\n+ <node>ARG:CD<value>ARG:CD</value></node>\n+ <node>ARG:HD2<value>ARG:1HD</value></node>\n+ <node>ARG:HD3<value>ARG:2HD</value></node>\n+ <node>ARG:NE<value>ARG:NE</value></node>\n+ <node>ARG:HE<value>ARG:HE</value></node>\n+ <node>ARG:CZ<value>ARG:CZ</value></node>\n+ <node>ARG:NH1<value>ARG:NH1</value></node>\n+ <node>ARG:HH11<value>ARG:1HH1</value></node>\n+ <node>ARG:HH12<value>ARG:2HH1</value></node>\n+ <node>ARG:NH2<value>ARG:NH2</value></node>\n+ <node>ARG:HH21<value>ARG:1HH2</value></node>\n+ <node>ARG:HH22<value>ARG:2HH2</value></node>\n+ <node>ASN:CA<value>ASN:CA</value></node>\n+ <node>ASN:HA<value>ASN:HA</value></node>\n+ <node>ASN:CB<value>ASN:CB</value></node>\n+ <node>ASN:HB2<value>ASN:1HB</value></node>\n+ <node>ASN:HB3<value>ASN:2HB</value></node>\n+ <node>ASN:CG<value>ASN:CG</value></node>\n+ <node>ASN:OD1<value>ASN:OD1</value></node>\n+ <node>ASN:ND2<value>ASN:ND2</value></node>\n+ <node>ASN:HD21<value>ASN:1HD2</value></node>\n+ <node>ASN:HD22<value>ASN:2HD2</value></node>\n+ <node>ASP:CA<value>ASP:CA</value></node>\n+ <node>ASP:HA<value>ASP:HA</value></node>\n+ <node>ASP:CB<value>ASP:CB</value></node>\n+ <node>ASP:HB2<value>ASP:1HB</value></node>\n+ <node>ASP:HB3<value>ASP:2HB</value></node>\n+ <node>ASP:CG<value>ASP:CG</value></node>\n+ <node>ASP:OD1<value>ASP:OD1</value></node>\n+ <node>ASP:OD2<value>ASP:OD2</value></node>\n+ <node>CYS:CA<value>CYS:CA</value></node>\n+ <node>CYS:HA<value>CYS:HA</value></node>\n+ <node>CYS:CB<value>CYS:CB</value></node>\n+ <node>CYS:HB2<value>CYS:1HB</value></node>\n+ <node>CYS:HB3<value>CYS:2HB</value></node>\n+ <node>CYS:SG<value>CYS:SG</value></node>\n+ <node>CYS:HG<value>CYS:HG</value></node>\n+ <node>GLU:CA<value>GLU:CA</value></node>\n+ <node>GLU:HA<value>GLU:HA</value></node>\n+ <node>GLU:CB<value>GLU:CB</value></node>\n+ <node>GLU:HB2<value>GLU:1HB</value></node>\n+ <node>GLU:HB3<value>GLU:2HB</value></node>\n+ <node>GLU:CG<value>GLU:CG</value></node>\n+ <node>GLU:HG2<value>GLU:1HG</value></node>\n+ <node>GLU:HG3<value>GLU:2HG</value></node>\n+ <node>GLU:CD<value>GLU:CD</value></node>\n+ <node>GLU:OE1<value>GLU:OE1</value></node>\n+ <node>GLU:OE2<value>GLU:OE2</value></node>\n+ <node>GLN:CA<value>GLN:CA</value></node>\n+ <node>GLN:HA<value>GLN:HA</value></node>\n+ <node>GLN:CB<value>GLN:CB</value></node>\n+ <node>GLN:HB2<value>GLN:1HB</value></node>\n+ <node>GLN:HB3<value>GLN:2HB</value></node>\n+ <node>GLN:CG<value>GLN:CG</value></node>\n+ <node>GLN:HG2<value>GLN:1HG</value></node>\n+ <node>GLN:HG3<value>GLN:2HG</value></node>\n+ <node>GLN:CD<value>GLN:CD</value></node>\n+ <node>GLN:OE1<value>GLN:OE1</value></node>\n+ <node>GLN:NE2<value>GLN:NE2</value></node>\n+ <node>GLN:HE21<value>GLN:1HE2</value></node>\n+ <node>GLN:HE22<value>GLN:2HE2</value></node>\n+ <node>GLY:CA<value>GLY:CA</value></node>\n+ <node>GLY:HA2<value>GLY:1HA</value></node>\n+ <node>GLY:HA3<value>GLY:2HA</value>'..b'2<value>PHE:1HB</value></node>\n+ <node>PHE:HB3<value>PHE:2HB</value></node>\n+ <node>PHE:CG<value>PHE:CG</value></node>\n+ <node>PHE:CD1<value>PHE:CD1</value></node>\n+ <node>PHE:HD1<value>PHE:HD1</value></node>\n+ <node>PHE:CE1<value>PHE:CE1</value></node>\n+ <node>PHE:HE1<value>PHE:HE1</value></node>\n+ <node>PHE:CZ<value>PHE:CZ</value></node>\n+ <node>PHE:HZ<value>PHE:HZ</value></node>\n+ <node>PHE:CE2<value>PHE:CE2</value></node>\n+ <node>PHE:HE2<value>PHE:HE2</value></node>\n+ <node>PHE:CD2<value>PHE:CD2</value></node>\n+ <node>PHE:HD2<value>PHE:HD2</value></node>\n+ <node>PRO:CA<value>PRO:CA</value></node>\n+ <node>PRO:HA<value>PRO:HA</value></node>\n+ <node>PRO:CD<value>PRO:CD</value></node>\n+ <node>PRO:HD2<value>PRO:1HD</value></node>\n+ <node>PRO:HD3<value>PRO:2HD</value></node>\n+ <node>PRO:CG<value>PRO:CG</value></node>\n+ <node>PRO:HG2<value>PRO:1HG</value></node>\n+ <node>PRO:HG3<value>PRO:2HG</value></node>\n+ <node>PRO:CB<value>PRO:CB</value></node>\n+ <node>PRO:HB2<value>PRO:1HB</value></node>\n+ <node>PRO:HB3<value>PRO:2HB</value></node>\n+ <node>SER:CA<value>SER:CA</value></node>\n+ <node>SER:HA<value>SER:HA</value></node>\n+ <node>SER:CB<value>SER:CB</value></node>\n+ <node>SER:HB2<value>SER:1HB</value></node>\n+ <node>SER:HB3<value>SER:2HB</value></node>\n+ <node>SER:OG<value>SER:OG</value></node>\n+ <node>SER:HG<value>SER:HG</value></node>\n+ <node>THR:CA<value>THR:CA</value></node>\n+ <node>THR:HA<value>THR:HA</value></node>\n+ <node>THR:CB<value>THR:CB</value></node>\n+ <node>THR:HB<value>THR:HB</value></node>\n+ <node>THR:CG2<value>THR:CG2</value></node>\n+ <node>THR:HG21<value>THR:1HG2</value></node>\n+ <node>THR:HG22<value>THR:2HG2</value></node>\n+ <node>THR:HG23<value>THR:3HG2</value></node>\n+ <node>THR:OG1<value>THR:OG1</value></node>\n+ <node>THR:HG1<value>THR:HG1</value></node>\n+ <node>TRP:CA<value>TRP:CA</value></node>\n+ <node>TRP:HA<value>TRP:HA</value></node>\n+ <node>TRP:CB<value>TRP:CB</value></node>\n+ <node>TRP:HB2<value>TRP:1HB</value></node>\n+ <node>TRP:HB3<value>TRP:2HB</value></node>\n+ <node>TRP:CG<value>TRP:CG</value></node>\n+ <node>TRP:CD1<value>TRP:CD1</value></node>\n+ <node>TRP:HD1<value>TRP:HD1</value></node>\n+ <node>TRP:NE1<value>TRP:NE1</value></node>\n+ <node>TRP:HE1<value>TRP:HE1</value></node>\n+ <node>TRP:CE2<value>TRP:CE2</value></node>\n+ <node>TRP:CZ2<value>TRP:CZ2</value></node>\n+ <node>TRP:HZ2<value>TRP:HZ2</value></node>\n+ <node>TRP:CH2<value>TRP:CH2</value></node>\n+ <node>TRP:HH2<value>TRP:HH2</value></node>\n+ <node>TRP:CZ3<value>TRP:CZ3</value></node>\n+ <node>TRP:HZ3<value>TRP:HZ3</value></node>\n+ <node>TRP:CE3<value>TRP:CE3</value></node>\n+ <node>TRP:HE3<value>TRP:HE3</value></node>\n+ <node>TRP:CD2<value>TRP:CD2</value></node>\n+ <node>TYR:CA<value>TYR:CA</value></node>\n+ <node>TYR:HA<value>TYR:HA</value></node>\n+ <node>TYR:CB<value>TYR:CB</value></node>\n+ <node>TYR:HB2<value>TYR:1HB</value></node>\n+ <node>TYR:HB3<value>TYR:2HB</value></node>\n+ <node>TYR:CG<value>TYR:CG</value></node>\n+ <node>TYR:CD1<value>TYR:CD1</value></node>\n+ <node>TYR:HD1<value>TYR:HD1</value></node>\n+ <node>TYR:CE1<value>TYR:CE1</value></node>\n+ <node>TYR:HE1<value>TYR:HE1</value></node>\n+ <node>TYR:CZ<value>TYR:CZ</value></node>\n+ <node>TYR:OH<value>TYR:OH</value></node>\n+ <node>TYR:HH<value>TYR:HH</value></node>\n+ <node>TYR:CE2<value>TYR:CE2</value></node>\n+ <node>TYR:HE2<value>TYR:HE2</value></node>\n+ <node>TYR:CD2<value>TYR:CD2</value></node>\n+ <node>TYR:HD2<value>TYR:HD2</value></node>\n+ <node>VAL:CA<value>VAL:CA</value></node>\n+ <node>VAL:HA<value>VAL:HA</value></node>\n+ <node>VAL:CB<value>VAL:CB</value></node>\n+ <node>VAL:HB<value>VAL:HB</value></node>\n+ <node>VAL:CG1<value>VAL:CG1</value></node>\n+ <node>VAL:HG11<value>VAL:1HG1</value></node>\n+ <node>VAL:HG12<value>VAL:2HG1</value></node>\n+ <node>VAL:HG13<value>VAL:3HG1</value></node>\n+ <node>VAL:CG2<value>VAL:CG2</value></node>\n+ <node>VAL:HG21<value>VAL:1HG2</value></node>\n+ <node>VAL:HG22<value>VAL:2HG2</value></node>\n+ <node>VAL:HG23<value>VAL:3HG2</value></node>\n+</node>\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/Names.XPLOR.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Names.XPLOR.db Tue Jun 07 16:43:30 2011 -0400

b'@@ -0,0 +1,256 @@\n+<node>XPLOR<value>PDB</value>\n+ <node>*:H1<value>*:1H</value></node>\n+ <node>*:H2<value>*:2H</value></node>\n+ <node>*:H3<value>*:3H</value></node>\n+ <node>*:N<value>*:N</value></node>\n+ <node>*:O<value>*:O</value></node>\n+ <node>*:C<value>*:C</value></node>\n+ <node>*:HN<value>*:H</value></node>\n+ <node>*:H<value>*:H</value></node>\n+ <node>ALA:CA<value>ALA:CA</value></node>\n+ <node>ALA:HA<value>ALA:HA</value></node>\n+ <node>ALA:CB<value>ALA:CB</value></node>\n+ <node>ALA:HB1<value>ALA:1HB</value></node>\n+ <node>ALA:HB2<value>ALA:2HB</value></node>\n+ <node>ALA:HB3<value>ALA:3HB</value></node>\n+ <node>ARG:CA<value>ARG:CA</value></node>\n+ <node>ARG:HA<value>ARG:HA</value></node>\n+ <node>ARG:CB<value>ARG:CB</value></node>\n+ <node>ARG:HB1<value>ARG:1HB</value></node>\n+ <node>ARG:HB2<value>ARG:2HB</value></node>\n+ <node>ARG:CG<value>ARG:CG</value></node>\n+ <node>ARG:HG1<value>ARG:1HG</value></node>\n+ <node>ARG:HG2<value>ARG:2HG</value></node>\n+ <node>ARG:CD<value>ARG:CD</value></node>\n+ <node>ARG:HD1<value>ARG:1HD</value></node>\n+ <node>ARG:HD2<value>ARG:2HD</value></node>\n+ <node>ARG:NE<value>ARG:NE</value></node>\n+ <node>ARG:HE<value>ARG:HE</value></node>\n+ <node>ARG:CZ<value>ARG:CZ</value></node>\n+ <node>ARG:NH1<value>ARG:NH1</value></node>\n+ <node>ARG:HH11<value>ARG:1HH1</value></node>\n+ <node>ARG:HH12<value>ARG:2HH1</value></node>\n+ <node>ARG:NH2<value>ARG:NH2</value></node>\n+ <node>ARG:HH21<value>ARG:1HH2</value></node>\n+ <node>ARG:HH22<value>ARG:2HH2</value></node>\n+ <node>ASN:CA<value>ASN:CA</value></node>\n+ <node>ASN:HA<value>ASN:HA</value></node>\n+ <node>ASN:CB<value>ASN:CB</value></node>\n+ <node>ASN:HB1<value>ASN:1HB</value></node>\n+ <node>ASN:HB2<value>ASN:2HB</value></node>\n+ <node>ASN:CG<value>ASN:CG</value></node>\n+ <node>ASN:OD1<value>ASN:OD1</value></node>\n+ <node>ASN:ND2<value>ASN:ND2</value></node>\n+ <node>ASN:HD21<value>ASN:1HD2</value></node>\n+ <node>ASN:HD22<value>ASN:2HD2</value></node>\n+ <node>ASP:CA<value>ASP:CA</value></node>\n+ <node>ASP:HA<value>ASP:HA</value></node>\n+ <node>ASP:CB<value>ASP:CB</value></node>\n+ <node>ASP:HB1<value>ASP:1HB</value></node>\n+ <node>ASP:HB2<value>ASP:2HB</value></node>\n+ <node>ASP:CG<value>ASP:CG</value></node>\n+ <node>ASP:OD1<value>ASP:OD1</value></node>\n+ <node>ASP:OD2<value>ASP:OD2</value></node>\n+ <node>CYS:CA<value>CYS:CA</value></node>\n+ <node>CYS:HA<value>CYS:HA</value></node>\n+ <node>CYS:CB<value>CYS:CB</value></node>\n+ <node>CYS:HB1<value>CYS:1HB</value></node>\n+ <node>CYS:HB2<value>CYS:2HB</value></node>\n+ <node>CYS:SG<value>CYS:SG</value></node>\n+ <node>CYS:HG<value>CYS:HG</value></node>\n+ <node>GLU:CA<value>GLU:CA</value></node>\n+ <node>GLU:HA<value>GLU:HA</value></node>\n+ <node>GLU:CB<value>GLU:CB</value></node>\n+ <node>GLU:HB1<value>GLU:1HB</value></node>\n+ <node>GLU:HB2<value>GLU:2HB</value></node>\n+ <node>GLU:CG<value>GLU:CG</value></node>\n+ <node>GLU:HG1<value>GLU:1HG</value></node>\n+ <node>GLU:HG2<value>GLU:2HG</value></node>\n+ <node>GLU:CD<value>GLU:CD</value></node>\n+ <node>GLU:OE1<value>GLU:OE1</value></node>\n+ <node>GLU:OE2<value>GLU:OE2</value></node>\n+ <node>GLN:CA<value>GLN:CA</value></node>\n+ <node>GLN:HA<value>GLN:HA</value></node>\n+ <node>GLN:CB<value>GLN:CB</value></node>\n+ <node>GLN:HB1<value>GLN:1HB</value></node>\n+ <node>GLN:HB2<value>GLN:2HB</value></node>\n+ <node>GLN:CG<value>GLN:CG</value></node>\n+ <node>GLN:HG1<value>GLN:1HG</value></node>\n+ <node>GLN:HG2<value>GLN:2HG</value></node>\n+ <node>GLN:CD<value>GLN:CD</value></node>\n+ <node>GLN:OE1<value>GLN:OE1</value></node>\n+ <node>GLN:NE2<value>GLN:NE2</value></node>\n+ <node>GLN:HE21<value>GLN:1HE2</value></node>\n+ <node>GLN:HE22<value>GLN:2HE2</value></node>\n+ <node>GLY:CA<value>GLY:CA</value></node>\n+ <node>GLY:HA1<value>GLY:1HA</value></node>\n+ <node>GLY:HA2<value>GLY:2HA</value></node>\n+ <node>HIS:CA<value>HIS:CA</value></node>\n+ <node>HIS:HA<value>HIS:HA</value></node>\n+ <node>HIS:CB<value>HIS:CB</value></node>\n+ <node>HIS:HB1<value>HIS:1HB</value></node>\n+ <node>HIS:HB2<v'..b'1<value>PHE:1HB</value></node>\n+ <node>PHE:HB2<value>PHE:2HB</value></node>\n+ <node>PHE:CG<value>PHE:CG</value></node>\n+ <node>PHE:CD1<value>PHE:CD1</value></node>\n+ <node>PHE:HD1<value>PHE:HD1</value></node>\n+ <node>PHE:CE1<value>PHE:CE1</value></node>\n+ <node>PHE:HE1<value>PHE:HE1</value></node>\n+ <node>PHE:CZ<value>PHE:CZ</value></node>\n+ <node>PHE:HZ<value>PHE:HZ</value></node>\n+ <node>PHE:CE2<value>PHE:CE2</value></node>\n+ <node>PHE:HE2<value>PHE:HE2</value></node>\n+ <node>PHE:CD2<value>PHE:CD2</value></node>\n+ <node>PHE:HD2<value>PHE:HD2</value></node>\n+ <node>PRO:CA<value>PRO:CA</value></node>\n+ <node>PRO:HA<value>PRO:HA</value></node>\n+ <node>PRO:CD<value>PRO:CD</value></node>\n+ <node>PRO:HD1<value>PRO:1HD</value></node>\n+ <node>PRO:HD2<value>PRO:2HD</value></node>\n+ <node>PRO:CG<value>PRO:CG</value></node>\n+ <node>PRO:HG1<value>PRO:1HG</value></node>\n+ <node>PRO:HG2<value>PRO:2HG</value></node>\n+ <node>PRO:CB<value>PRO:CB</value></node>\n+ <node>PRO:HB1<value>PRO:1HB</value></node>\n+ <node>PRO:HB2<value>PRO:2HB</value></node>\n+ <node>SER:CA<value>SER:CA</value></node>\n+ <node>SER:HA<value>SER:HA</value></node>\n+ <node>SER:CB<value>SER:CB</value></node>\n+ <node>SER:HB1<value>SER:1HB</value></node>\n+ <node>SER:HB2<value>SER:2HB</value></node>\n+ <node>SER:OG<value>SER:OG</value></node>\n+ <node>SER:HG<value>SER:HG</value></node>\n+ <node>THR:CA<value>THR:CA</value></node>\n+ <node>THR:HA<value>THR:HA</value></node>\n+ <node>THR:CB<value>THR:CB</value></node>\n+ <node>THR:HB<value>THR:HB</value></node>\n+ <node>THR:CG2<value>THR:CG2</value></node>\n+ <node>THR:HG21<value>THR:1HG2</value></node>\n+ <node>THR:HG22<value>THR:2HG2</value></node>\n+ <node>THR:HG23<value>THR:3HG2</value></node>\n+ <node>THR:OG1<value>THR:OG1</value></node>\n+ <node>THR:HG1<value>THR:HG1</value></node>\n+ <node>TRP:CA<value>TRP:CA</value></node>\n+ <node>TRP:HA<value>TRP:HA</value></node>\n+ <node>TRP:CB<value>TRP:CB</value></node>\n+ <node>TRP:HB1<value>TRP:1HB</value></node>\n+ <node>TRP:HB2<value>TRP:2HB</value></node>\n+ <node>TRP:CG<value>TRP:CG</value></node>\n+ <node>TRP:CD1<value>TRP:CD1</value></node>\n+ <node>TRP:HD1<value>TRP:HD1</value></node>\n+ <node>TRP:NE1<value>TRP:NE1</value></node>\n+ <node>TRP:HE1<value>TRP:HE1</value></node>\n+ <node>TRP:CE2<value>TRP:CE2</value></node>\n+ <node>TRP:CZ2<value>TRP:CZ2</value></node>\n+ <node>TRP:HZ2<value>TRP:HZ2</value></node>\n+ <node>TRP:CH2<value>TRP:CH2</value></node>\n+ <node>TRP:HH2<value>TRP:HH2</value></node>\n+ <node>TRP:CZ3<value>TRP:CZ3</value></node>\n+ <node>TRP:HZ3<value>TRP:HZ3</value></node>\n+ <node>TRP:CE3<value>TRP:CE3</value></node>\n+ <node>TRP:HE3<value>TRP:HE3</value></node>\n+ <node>TRP:CD2<value>TRP:CD2</value></node>\n+ <node>TYR:CA<value>TYR:CA</value></node>\n+ <node>TYR:HA<value>TYR:HA</value></node>\n+ <node>TYR:CB<value>TYR:CB</value></node>\n+ <node>TYR:HB1<value>TYR:1HB</value></node>\n+ <node>TYR:HB2<value>TYR:2HB</value></node>\n+ <node>TYR:CG<value>TYR:CG</value></node>\n+ <node>TYR:CD1<value>TYR:CD1</value></node>\n+ <node>TYR:HD1<value>TYR:HD1</value></node>\n+ <node>TYR:CE1<value>TYR:CE1</value></node>\n+ <node>TYR:HE1<value>TYR:HE1</value></node>\n+ <node>TYR:CZ<value>TYR:CZ</value></node>\n+ <node>TYR:OH<value>TYR:OH</value></node>\n+ <node>TYR:HH<value>TYR:HH</value></node>\n+ <node>TYR:CE2<value>TYR:CE2</value></node>\n+ <node>TYR:HE2<value>TYR:HE2</value></node>\n+ <node>TYR:CD2<value>TYR:CD2</value></node>\n+ <node>TYR:HD2<value>TYR:HD2</value></node>\n+ <node>VAL:CA<value>VAL:CA</value></node>\n+ <node>VAL:HA<value>VAL:HA</value></node>\n+ <node>VAL:CB<value>VAL:CB</value></node>\n+ <node>VAL:HB<value>VAL:HB</value></node>\n+ <node>VAL:CG1<value>VAL:CG1</value></node>\n+ <node>VAL:HG11<value>VAL:1HG1</value></node>\n+ <node>VAL:HG12<value>VAL:2HG1</value></node>\n+ <node>VAL:HG13<value>VAL:3HG1</value></node>\n+ <node>VAL:CG2<value>VAL:CG2</value></node>\n+ <node>VAL:HG21<value>VAL:1HG2</value></node>\n+ <node>VAL:HG22<value>VAL:2HG2</value></node>\n+ <node>VAL:HG23<value>VAL:3HG2</value></node>\n+</node>\n'

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/PCA.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/PCA.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/PHE.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/PHE.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/PRO.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/PRO.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/Pyrrole-Skeleton.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/Pyrrole-Skeleton.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/SER.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/SER.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/T.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/T.db Tue Jun 07 16:43:30 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>
+

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/THR.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/THR.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/TRP.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/TRP.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/TYR.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/TYR.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/U.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/U.db Tue Jun 07 16:43:30 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>
+

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/VAL.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/VAL.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/ZN.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/ZN.db Tue Jun 07 16:43:30 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>

diff -r 000000000000 -r bac3c274238f CADDSuite/data/fragments/functionalGroups.smarts
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/data/fragments/functionalGroups.smarts Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/confFiles.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/confFiles.py Tue Jun 07 16:43:30 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
+
+
+
+

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/countResidues.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/countResidues.sh Tue Jun 07 16:43:30 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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/datatypes_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/datatypes_conf.xml Tue Jun 07 16:43:30 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"/>
+
+ 
+ <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>

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/molFiles.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/molFiles.py Tue Jun 07 16:43:30 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'
+

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tool_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tool_conf.xml Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,69 @@
+<?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/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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,32 @@
+
+
+<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/AutoModel.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/AutoModel.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,27 @@
+
+
+<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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,36 @@
+
+
+<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,33 @@
+
+
+<tool id="combilibgenerator" name="CombiLibGenerator" version="0.93">
+    <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:
+
+<scaffold>
+      Fc1ccc(cc1)C2=C(C([R1])=NO2)c3ccnc([R2])c3
+      Fc1ccc(cc1)C2=NOC([R1])=C2cccnc([R2])c3
+<moietyR1>
+      [R1]C(C)(C)C
+<moietyR2>
+      [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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,38 @@
+
+
+<tool id="constraintsfinder" name="ConstraintsFinder" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/Converter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Converter.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,50 @@
+
+
+<tool id="converter" name="Converter" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/DBExporter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/DBExporter.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,97 @@
+
+
+<tool id="dbexporter" name="DBExporter" version="0.93 (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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/DBImporter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/DBImporter.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,57 @@
+
+
+<tool id="dbimporter" name="DBImporter" version="0.93 (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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/DockResultMerger.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,45 @@
+
+
+<tool id="dockresultmerger" name="DockResultMerger" version="0.93">
+    <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
+ | 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=""/>
+    </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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/EvenSplit.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/EvenSplit.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,41 @@
+
+
+<tool id="evensplit" name="EvenSplit" version="0.93">
+    <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"/>
+    </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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/FeatureSelector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/FeatureSelector.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,41 @@
+
+
+<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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,30 @@
+
+
+<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/GridBuilder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/GridBuilder.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,38 @@
+
+
+<tool id="gridbuilder" name="GridBuilder" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/IMeedyDock.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/IMeedyDock.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,47 @@
+
+
+<tool id="imeedydock" name="IMeedyDock" version="0.93">
+    <description>Iterative Multi-Greedy Docking</description>
+    <command interpreter="bash"><![CDATA[../../IMeedyDock
+#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>IMeedyDock 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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/InputPartitioner.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/InputPartitioner.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,28 @@
+
+
+<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<i>.dat' and '_TEST<i>.dat', where <i> 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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/InputReader.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/InputReader.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,68 @@
+
+
+<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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/LigCheck.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/LigCheck.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,45 @@
+
+
+<tool id="ligcheck" name="LigCheck" version="0.93">
+    <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. <0.7 or >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 (>5 or <-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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,30 @@
+
+
+<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,84 @@
+
+
+<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/ModelCreator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ModelCreator.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,52 @@
+
+
+<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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/MolCombine.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolCombine.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,45 @@
+
+
+<tool id="molcombine" name="MolCombine" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/MolDepict.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolDepict.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,28 @@
+
+
+<tool id="moldepict" name="MolDepict" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/MolFilter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolFilter.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,60 @@
+
+
+<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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/MolPredictor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/MolPredictor.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,50 @@
+
+
+<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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/PDBCutter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PDBCutter.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,46 @@
+
+
+<tool id="pdbcutter" name="PDBCutter" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/PDBDownload.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PDBDownload.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,25 @@
+
+
+<tool id="pdbdownload" name="PDBDownload" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,26 @@
+
+
+<tool id="partialchargescopy" name="PartialChargesCopy" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/PocketDetector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PocketDetector.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,38 @@
+
+
+<tool id="pocketdetector" name="PocketDetector" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/Predictor.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Predictor.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,30 @@
+
+
+<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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/PropertyModifier.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,43 @@
+
+
+<tool id="propertymodifier" name="PropertyModifier" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,35 @@
+
+
+<tool id="propertyplotter" name="PropertyPlotter" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/ProteinCheck.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,34 @@
+
+
+<tool id="proteincheck" name="ProteinCheck" version="0.93">
+    <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. <0.7 or >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 (<1 or >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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,29 @@
+
+
+<tool id="proteinprotonator" name="ProteinProtonator" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,31 @@
+
+
+<tool id="rmsdcalculator" name="RMSDCalculator" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,55 @@
+
+
+<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.93">
+    <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"/>
+        <param name="e" label="binding-free-energy/class label name" optional="false" area="true" type="text" size="1x15"/>
+        <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,35 @@
+
+
+<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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,49 @@
+
+
+<tool id="simplerescorer" name="SimpleRescorer" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/TaGRes-train.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,61 @@
+
+
+<tool id="tagres-train" name="TaGRes-train" version="0.93">
+    <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"/>
+    </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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/TaGRes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/TaGRes.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,63 @@
+
+
+<tool id="tagres" name="TaGRes" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/Validator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/Validator.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,36 @@
+
+
+<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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/VendorFinder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/VendorFinder.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,49 @@
+
+
+<tool id="vendorfinder" name="VendorFinder" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/WaterFinder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/WaterFinder.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,55 @@
+
+
+<tool id="waterfinder" name="WaterFinder" version="0.93">
+    <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

diff -r 000000000000 -r bac3c274238f CADDSuite/galaxyconfigs/tools/upload.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/galaxyconfigs/tools/upload.xml Tue Jun 07 16:43:30 2011 -0400

[

@@ -0,0 +1,46 @@
+<?xml version="1.0"?>
+
+<tool name="Upload File" id="upload1" 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="[ "%s%s%s" % ( 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> 
+      </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"/>
+      
+    </upload_dataset>
+    
+    <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" />
+    
+  </inputs>
+  <help>
+
+  </help>
+</tool>

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diff -r 000000000000 -r bac3c274238f CADDSuite/license.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/license.txt Tue Jun 07 16:43:30 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/>.
+

diff -r 000000000000 -r bac3c274238f CADDSuite/rescoring_common
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/rescoring_common Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,4 @@
+#!/bin/bash
+ export BASE_DIR=`dirname "$0"`
+ . "$BASE_DIR"/setPathes.sh
+ "$BASE_DIR"/bin/rescoring_common.bin "$@"

diff -r 000000000000 -r bac3c274238f CADDSuite/setPathes.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/setPathes.sh Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,10 @@
+#!/bin/bash
+export LD_LIBRARY_PATH=/usr/lib:/lib:$LD_LIBRARY_PATH:"$BASE_DIR"/lib
+export DYLD_LIBRARY_PATH="$BASE_DIR"/lib:$DYLD_LIBRARY_PATH
+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
+

diff -r 000000000000 -r bac3c274238f CADDSuite/suite_config.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite/suite_config.xml Tue Jun 07 16:43:30 2011 -0400

@@ -0,0 +1,135 @@
+<suite id="CADDSuite_Linux_x86_64" name="CADDSuite (Linux x86-64)" version="0.93">
+
+<description>
+CADDSuite: A flexible and open framework for Computer-Aided Drug Design
+</description>
+
+<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.93">
+    <description>rescore w/ anti-target dock-results</description>
+</tool>
+<tool name="Upload File" id="upload1" version="1.1.2">
+<description>upload a file from your computer</description>
+</tool>
+<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.93">
+    <description>fix bindingdb.org downloads</description>
+</tool>
+<tool id="combilibgenerator" name="CombiLibGenerator" version="0.93">
+    <description>generate combinatorial lib</description>
+</tool>
+<tool id="constraintsfinder" name="ConstraintsFinder" version="0.93">
+    <description>find strongly interacting residues</description>
+</tool>
+<tool id="converter" name="Converter" version="0.93">
+    <description>interconvert molecular file-formats</description>
+</tool>
+<tool id="dbexporter" name="DBExporter" version="0.93 (ob)">
+    <description>export molecules from data base</description>
+</tool>
+<tool id="dbimporter" name="DBImporter" version="0.93 (ob)">
+    <description>import molecules into data base</description>
+</tool>
+<tool id="dockresultmerger" name="DockResultMerger" version="0.93">
+    <description>merge docking output files</description>
+</tool>
+<tool id="evensplit" name="EvenSplit" version="0.93">
+    <description>generate splits w/ equal property range</description>
+</tool>
+<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.93">
+    <description>generate galaxy tool-config files</description>
+</tool>
+<tool id="gridbuilder" name="GridBuilder" version="0.93">
+    <description>create score-grids for docking</description>
+</tool>
+<tool id="imeedydock" name="IMeedyDock" version="0.93">
+    <description>Iterative Multi-Greedy Docking</description>
+</tool>
+<tool id="ligcheck" name="LigCheck" version="0.93">
+    <description>check molecules for errors</description>
+</tool>
+<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.93">
+    <description>generate 3D coordinates for small molecules</description>
+</tool>
+<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.93">
+    <description>split molecule files</description>
+</tool>
+<tool id="molcombine" name="MolCombine" version="0.93">
+    <description>combine molecular files</description>
+</tool>
+<tool id="moldepict" name="MolDepict" version="0.93">
+    <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="0.93">
+    <description>separate ligand and receptor</description>
+</tool>
+<tool id="pdbdownload" name="PDBDownload" version="0.93">
+    <description>retrieve pdb-file from pdb.org</description>
+</tool>
+<tool id="partialchargescopy" name="PartialChargesCopy" version="0.93">
+    <description>transfer part. charges between files</description>
+</tool>
+<tool id="pocketdetector" name="PocketDetector" version="0.93">
+    <description>detect binding pocket</description>
+</tool>
+<tool id="propertymodifier" name="PropertyModifier" version="0.93">
+    <description>modify molecule property tags</description>
+</tool>
+<tool id="propertyplotter" name="PropertyPlotter" version="0.93">
+    <description>plot molecule properties</description>
+</tool>
+<tool id="proteincheck" name="ProteinCheck" version="0.93">
+    <description>quality check for proteins structures</description>
+</tool>
+<tool id="proteinprotonator" name="ProteinProtonator" version="0.93">
+    <description>protonate protein structures</description>
+</tool>
+<tool id="rmsdcalculator" name="RMSDCalculator" version="0.93">
+    <description>calculate RMSD between poses</description>
+</tool>
+<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.93">
+    <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="0.93">
+    <description>rescore docking results</description>
+</tool>
+<tool id="tagres-train" name="TaGRes-train" version="0.93">
+    <description>Target-specific Grid-Rescoring, training</description>
+</tool>
+<tool id="tagres" name="TaGRes" version="0.93">
+    <description>Target-specific Grid-Rescoring</description>
+</tool>
+<tool id="vendorfinder" name="VendorFinder" version="0.93">
+    <description>search vendors for compounds</description>
+</tool>
+<tool id="waterfinder" name="WaterFinder" version="0.93">
+    <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>