changeset 5:e30a41af9d2b

Uploaded
author marcel
date Tue, 15 Nov 2011 10:53:16 -0500
parents af446ca2d5c6
children decca54699e3
files CADDSuite-1.0.1/._CADDSuite-description.txt CADDSuite-1.0.1/._changelog.txt CADDSuite-1.0.1/AntitargetRescorer CADDSuite-1.0.1/AutoModel CADDSuite-1.0.1/BindingDBCleaner CADDSuite-1.0.1/CADDSuite-description.txt CADDSuite-1.0.1/CombiLibGenerator CADDSuite-1.0.1/ConstraintsFinder CADDSuite-1.0.1/Converter CADDSuite-1.0.1/DBExporter CADDSuite-1.0.1/DBImporter CADDSuite-1.0.1/DockResultMerger CADDSuite-1.0.1/EvenSplit CADDSuite-1.0.1/FeatureSelector CADDSuite-1.0.1/GalaxyConfigGenerator CADDSuite-1.0.1/GridBuilder CADDSuite-1.0.1/IMGDock CADDSuite-1.0.1/InputPartitioner CADDSuite-1.0.1/InputReader CADDSuite-1.0.1/InteractionConstraintDefiner CADDSuite-1.0.1/LigCheck CADDSuite-1.0.1/Ligand3DGenerator CADDSuite-1.0.1/LigandFileSplitter CADDSuite-1.0.1/ModelCreator CADDSuite-1.0.1/MolCombine CADDSuite-1.0.1/MolDepict CADDSuite-1.0.1/MolFilter CADDSuite-1.0.1/MolPredictor CADDSuite-1.0.1/PDBCutter CADDSuite-1.0.1/PDBDownload CADDSuite-1.0.1/PartialChargesCopy CADDSuite-1.0.1/PocketDetector CADDSuite-1.0.1/Predictor CADDSuite-1.0.1/PropertyModifier CADDSuite-1.0.1/PropertyPlotter CADDSuite-1.0.1/ProteinCheck CADDSuite-1.0.1/ProteinProtonator CADDSuite-1.0.1/README CADDSuite-1.0.1/RMSDCalculator CADDSuite-1.0.1/ScoreAnalyzer CADDSuite-1.0.1/SimilarityAnalyzer CADDSuite-1.0.1/SimpleRescorer CADDSuite-1.0.1/SpatialConstraintDefiner CADDSuite-1.0.1/TaGRes CADDSuite-1.0.1/TaGRes-train CADDSuite-1.0.1/Validator CADDSuite-1.0.1/VendorFinder CADDSuite-1.0.1/WaterFinder CADDSuite-1.0.1/bin/._gnuplot CADDSuite-1.0.1/bin/AntitargetRescorer.bin CADDSuite-1.0.1/bin/AutoModel.bin CADDSuite-1.0.1/bin/BindingDBCleaner.bin CADDSuite-1.0.1/bin/CombiLibGenerator.bin CADDSuite-1.0.1/bin/ConstraintsFinder.bin CADDSuite-1.0.1/bin/Converter.bin CADDSuite-1.0.1/bin/DBExporter.bin CADDSuite-1.0.1/bin/DBImporter.bin CADDSuite-1.0.1/bin/DockResultMerger.bin CADDSuite-1.0.1/bin/EvenSplit.bin CADDSuite-1.0.1/bin/FeatureSelector.bin CADDSuite-1.0.1/bin/GalaxyConfigGenerator.bin CADDSuite-1.0.1/bin/GridBuilder.bin CADDSuite-1.0.1/bin/IMGDock.bin CADDSuite-1.0.1/bin/InputPartitioner.bin CADDSuite-1.0.1/bin/InputReader.bin CADDSuite-1.0.1/bin/InteractionConstraintDefiner.bin CADDSuite-1.0.1/bin/LigCheck.bin CADDSuite-1.0.1/bin/Ligand3DGenerator.bin CADDSuite-1.0.1/bin/LigandFileSplitter.bin CADDSuite-1.0.1/bin/ModelCreator.bin CADDSuite-1.0.1/bin/MolCombine.bin CADDSuite-1.0.1/bin/MolDepict.bin CADDSuite-1.0.1/bin/MolFilter.bin CADDSuite-1.0.1/bin/MolPredictor.bin CADDSuite-1.0.1/bin/PDBCutter.bin CADDSuite-1.0.1/bin/PDBDownload.bin CADDSuite-1.0.1/bin/PartialChargesCopy.bin CADDSuite-1.0.1/bin/PocketDetector.bin CADDSuite-1.0.1/bin/Predictor.bin CADDSuite-1.0.1/bin/PropertyModifier.bin CADDSuite-1.0.1/bin/PropertyPlotter.bin CADDSuite-1.0.1/bin/ProteinCheck.bin CADDSuite-1.0.1/bin/ProteinProtonator.bin CADDSuite-1.0.1/bin/RMSDCalculator.bin CADDSuite-1.0.1/bin/ScoreAnalyzer.bin CADDSuite-1.0.1/bin/SimilarityAnalyzer.bin CADDSuite-1.0.1/bin/SimpleRescorer.bin CADDSuite-1.0.1/bin/SpatialConstraintDefiner.bin CADDSuite-1.0.1/bin/TaGRes-train.bin CADDSuite-1.0.1/bin/TaGRes.bin CADDSuite-1.0.1/bin/Validator.bin CADDSuite-1.0.1/bin/VendorFinder.bin CADDSuite-1.0.1/bin/WaterFinder.bin CADDSuite-1.0.1/bin/convert CADDSuite-1.0.1/bin/gnuplot CADDSuite-1.0.1/changelog.txt CADDSuite-1.0.1/data/Amber/amber96-docking.ini CADDSuite-1.0.1/data/OpenBabel/._CMakeLists.txt CADDSuite-1.0.1/data/OpenBabel/._MACCS.txt CADDSuite-1.0.1/data/OpenBabel/._SMARTS_InteLigand.txt CADDSuite-1.0.1/data/OpenBabel/._UFF.prm CADDSuite-1.0.1/data/OpenBabel/._aromatic.h CADDSuite-1.0.1/data/OpenBabel/._aromatic.txt CADDSuite-1.0.1/data/OpenBabel/._atomtyp.h CADDSuite-1.0.1/data/OpenBabel/._atomtyp.txt CADDSuite-1.0.1/data/OpenBabel/._babel_povray3.inc CADDSuite-1.0.1/data/OpenBabel/._bin2hex.pl CADDSuite-1.0.1/data/OpenBabel/._bondtyp.h CADDSuite-1.0.1/data/OpenBabel/._bondtyp.txt CADDSuite-1.0.1/data/OpenBabel/._element.h CADDSuite-1.0.1/data/OpenBabel/._element.txt CADDSuite-1.0.1/data/OpenBabel/._fragments.txt CADDSuite-1.0.1/data/OpenBabel/._gaff.dat CADDSuite-1.0.1/data/OpenBabel/._gaff.prm CADDSuite-1.0.1/data/OpenBabel/._genheaders.sh CADDSuite-1.0.1/data/OpenBabel/._ghemical.prm CADDSuite-1.0.1/data/OpenBabel/._isotope-small.txt CADDSuite-1.0.1/data/OpenBabel/._isotope.h CADDSuite-1.0.1/data/OpenBabel/._isotope.txt CADDSuite-1.0.1/data/OpenBabel/._logp.txt CADDSuite-1.0.1/data/OpenBabel/._mm2.prm CADDSuite-1.0.1/data/OpenBabel/._mmff94.ff CADDSuite-1.0.1/data/OpenBabel/._mmff94s.ff CADDSuite-1.0.1/data/OpenBabel/._mmffang.par CADDSuite-1.0.1/data/OpenBabel/._mmffbndk.par CADDSuite-1.0.1/data/OpenBabel/._mmffbond.par CADDSuite-1.0.1/data/OpenBabel/._mmffchg.par CADDSuite-1.0.1/data/OpenBabel/._mmffdef.par CADDSuite-1.0.1/data/OpenBabel/._mmffdfsb.par CADDSuite-1.0.1/data/OpenBabel/._mmffoop.par CADDSuite-1.0.1/data/OpenBabel/._mmffpbci.par CADDSuite-1.0.1/data/OpenBabel/._mmffprop.par CADDSuite-1.0.1/data/OpenBabel/._mmffs_oop.par CADDSuite-1.0.1/data/OpenBabel/._mmffs_tor.par CADDSuite-1.0.1/data/OpenBabel/._mmffstbn.par CADDSuite-1.0.1/data/OpenBabel/._mmfftor.par CADDSuite-1.0.1/data/OpenBabel/._mmffvdw.par CADDSuite-1.0.1/data/OpenBabel/._mr.txt CADDSuite-1.0.1/data/OpenBabel/._patterns.txt CADDSuite-1.0.1/data/OpenBabel/._phmodel.txt CADDSuite-1.0.1/data/OpenBabel/._phmodeldata.h CADDSuite-1.0.1/data/OpenBabel/._plugindefines.txt CADDSuite-1.0.1/data/OpenBabel/._psa.txt CADDSuite-1.0.1/data/OpenBabel/._qeq.txt CADDSuite-1.0.1/data/OpenBabel/._resdata.h CADDSuite-1.0.1/data/OpenBabel/._resdata.txt CADDSuite-1.0.1/data/OpenBabel/._ringtyp.txt CADDSuite-1.0.1/data/OpenBabel/._space-groups.txt CADDSuite-1.0.1/data/OpenBabel/._space-groups.xsl CADDSuite-1.0.1/data/OpenBabel/._superatom.txt CADDSuite-1.0.1/data/OpenBabel/._svgformat.script CADDSuite-1.0.1/data/OpenBabel/._templates.sdf CADDSuite-1.0.1/data/OpenBabel/._torlib.h CADDSuite-1.0.1/data/OpenBabel/._torlib.txt CADDSuite-1.0.1/data/OpenBabel/._types.h CADDSuite-1.0.1/data/OpenBabel/._types.txt CADDSuite-1.0.1/data/OpenBabel/CMakeLists.txt CADDSuite-1.0.1/data/OpenBabel/MACCS.txt CADDSuite-1.0.1/data/OpenBabel/Makefile CADDSuite-1.0.1/data/OpenBabel/SMARTS_InteLigand.txt CADDSuite-1.0.1/data/OpenBabel/UFF.prm CADDSuite-1.0.1/data/OpenBabel/aromatic.h CADDSuite-1.0.1/data/OpenBabel/aromatic.txt CADDSuite-1.0.1/data/OpenBabel/atomtyp.h CADDSuite-1.0.1/data/OpenBabel/atomtyp.txt CADDSuite-1.0.1/data/OpenBabel/babel_povray3.inc CADDSuite-1.0.1/data/OpenBabel/bin2hex.pl CADDSuite-1.0.1/data/OpenBabel/bondtyp.h CADDSuite-1.0.1/data/OpenBabel/bondtyp.txt CADDSuite-1.0.1/data/OpenBabel/cmake_install.cmake CADDSuite-1.0.1/data/OpenBabel/element.h CADDSuite-1.0.1/data/OpenBabel/element.txt CADDSuite-1.0.1/data/OpenBabel/fragments.txt CADDSuite-1.0.1/data/OpenBabel/gaff.dat CADDSuite-1.0.1/data/OpenBabel/gaff.prm CADDSuite-1.0.1/data/OpenBabel/genheaders.sh CADDSuite-1.0.1/data/OpenBabel/ghemical.prm CADDSuite-1.0.1/data/OpenBabel/isotope-small.txt CADDSuite-1.0.1/data/OpenBabel/isotope.h CADDSuite-1.0.1/data/OpenBabel/isotope.txt CADDSuite-1.0.1/data/OpenBabel/logp.txt CADDSuite-1.0.1/data/OpenBabel/mm2.prm CADDSuite-1.0.1/data/OpenBabel/mmff94.ff CADDSuite-1.0.1/data/OpenBabel/mmff94s.ff CADDSuite-1.0.1/data/OpenBabel/mmffang.par CADDSuite-1.0.1/data/OpenBabel/mmffbndk.par CADDSuite-1.0.1/data/OpenBabel/mmffbond.par CADDSuite-1.0.1/data/OpenBabel/mmffchg.par CADDSuite-1.0.1/data/OpenBabel/mmffdef.par CADDSuite-1.0.1/data/OpenBabel/mmffdfsb.par CADDSuite-1.0.1/data/OpenBabel/mmffoop.par CADDSuite-1.0.1/data/OpenBabel/mmffpbci.par CADDSuite-1.0.1/data/OpenBabel/mmffprop.par CADDSuite-1.0.1/data/OpenBabel/mmffs_oop.par CADDSuite-1.0.1/data/OpenBabel/mmffs_tor.par CADDSuite-1.0.1/data/OpenBabel/mmffstbn.par CADDSuite-1.0.1/data/OpenBabel/mmfftor.par CADDSuite-1.0.1/data/OpenBabel/mmffvdw.par CADDSuite-1.0.1/data/OpenBabel/mr.txt CADDSuite-1.0.1/data/OpenBabel/patterns.txt CADDSuite-1.0.1/data/OpenBabel/phmodel.txt CADDSuite-1.0.1/data/OpenBabel/phmodeldata.h CADDSuite-1.0.1/data/OpenBabel/plugindefines.txt CADDSuite-1.0.1/data/OpenBabel/psa.txt CADDSuite-1.0.1/data/OpenBabel/qeq.txt CADDSuite-1.0.1/data/OpenBabel/resdata.h CADDSuite-1.0.1/data/OpenBabel/resdata.txt CADDSuite-1.0.1/data/OpenBabel/ringtyp.txt CADDSuite-1.0.1/data/OpenBabel/space-groups.txt CADDSuite-1.0.1/data/OpenBabel/space-groups.xsl CADDSuite-1.0.1/data/OpenBabel/superatom.txt CADDSuite-1.0.1/data/OpenBabel/svgformat.script CADDSuite-1.0.1/data/OpenBabel/templates.sdf CADDSuite-1.0.1/data/OpenBabel/torlib.h CADDSuite-1.0.1/data/OpenBabel/torlib.txt CADDSuite-1.0.1/data/OpenBabel/types.h CADDSuite-1.0.1/data/OpenBabel/types.txt CADDSuite-1.0.1/data/QSAR/atomic_electron_affinities.data CADDSuite-1.0.1/data/QSAR/atomic_ionization_potentials.data CADDSuite-1.0.1/data/QSAR/atomic_polarizabilities.data CADDSuite-1.0.1/data/QSAR/dragon_descriptors.txt CADDSuite-1.0.1/data/XRAY/spacegroups.dat CADDSuite-1.0.1/data/atomtyping/AMBERTypes.dat CADDSuite-1.0.1/data/atomtyping/GAFFTypes.dat CADDSuite-1.0.1/data/atomtyping/SYBYLTypes.dat CADDSuite-1.0.1/data/bond_lengths/BondOrder.xml CADDSuite-1.0.1/data/bond_lengths/BondOrderGAFF.xml CADDSuite-1.0.1/data/bond_lengths/bond_lengths.db CADDSuite-1.0.1/data/bond_lengths/bond_lengths_mmff94.ini CADDSuite-1.0.1/data/fragments/A.db CADDSuite-1.0.1/data/fragments/ACE.db CADDSuite-1.0.1/data/fragments/ALA.db CADDSuite-1.0.1/data/fragments/ARG.db CADDSuite-1.0.1/data/fragments/ASN.db CADDSuite-1.0.1/data/fragments/ASP.db CADDSuite-1.0.1/data/fragments/Benzene-Skeleton.db CADDSuite-1.0.1/data/fragments/C.db CADDSuite-1.0.1/data/fragments/CA.db CADDSuite-1.0.1/data/fragments/CYS.db CADDSuite-1.0.1/data/fragments/Editing-Fragments.db CADDSuite-1.0.1/data/fragments/Fragments.db CADDSuite-1.0.1/data/fragments/G.db CADDSuite-1.0.1/data/fragments/GLN.db CADDSuite-1.0.1/data/fragments/GLU.db CADDSuite-1.0.1/data/fragments/GLY.db CADDSuite-1.0.1/data/fragments/HIS.db CADDSuite-1.0.1/data/fragments/HOH.db CADDSuite-1.0.1/data/fragments/ILE.db CADDSuite-1.0.1/data/fragments/Indole-Skeleton.db CADDSuite-1.0.1/data/fragments/LEU.db CADDSuite-1.0.1/data/fragments/LYS.db CADDSuite-1.0.1/data/fragments/MET.db CADDSuite-1.0.1/data/fragments/MG.db CADDSuite-1.0.1/data/fragments/MSE.db CADDSuite-1.0.1/data/fragments/NME.db CADDSuite-1.0.1/data/fragments/Names.Amber.db CADDSuite-1.0.1/data/fragments/Names.CHARMM.db CADDSuite-1.0.1/data/fragments/Names.DNA.db CADDSuite-1.0.1/data/fragments/Names.Discover.db CADDSuite-1.0.1/data/fragments/Names.Star.db CADDSuite-1.0.1/data/fragments/Names.XPLOR.db CADDSuite-1.0.1/data/fragments/PCA.db CADDSuite-1.0.1/data/fragments/PHE.db CADDSuite-1.0.1/data/fragments/PRO.db CADDSuite-1.0.1/data/fragments/Pyrrole-Skeleton.db CADDSuite-1.0.1/data/fragments/SER.db CADDSuite-1.0.1/data/fragments/T.db CADDSuite-1.0.1/data/fragments/THR.db CADDSuite-1.0.1/data/fragments/TRP.db CADDSuite-1.0.1/data/fragments/TYR.db CADDSuite-1.0.1/data/fragments/U.db CADDSuite-1.0.1/data/fragments/VAL.db CADDSuite-1.0.1/data/fragments/ZN.db CADDSuite-1.0.1/data/fragments/functionalGroups.smarts CADDSuite-1.0.1/data/gnuplot/FreeSans.ttf CADDSuite-1.0.1/data/gnuplot/prologue.ps CADDSuite-1.0.1/galaxyconfigs/confFiles.py CADDSuite-1.0.1/galaxyconfigs/countResidues.sh CADDSuite-1.0.1/galaxyconfigs/datatypes_conf.xml CADDSuite-1.0.1/galaxyconfigs/molFiles.py CADDSuite-1.0.1/galaxyconfigs/tool_conf.xml CADDSuite-1.0.1/galaxyconfigs/tools/AntitargetRescorer.xml CADDSuite-1.0.1/galaxyconfigs/tools/AutoModel.xml CADDSuite-1.0.1/galaxyconfigs/tools/BindingDBCleaner.xml CADDSuite-1.0.1/galaxyconfigs/tools/CombiLibGenerator.xml CADDSuite-1.0.1/galaxyconfigs/tools/ConstraintsFinder.xml CADDSuite-1.0.1/galaxyconfigs/tools/Converter.xml CADDSuite-1.0.1/galaxyconfigs/tools/DBExporter.xml CADDSuite-1.0.1/galaxyconfigs/tools/DBImporter.xml CADDSuite-1.0.1/galaxyconfigs/tools/DockResultMerger.xml CADDSuite-1.0.1/galaxyconfigs/tools/EvenSplit.xml CADDSuite-1.0.1/galaxyconfigs/tools/FeatureSelector.xml CADDSuite-1.0.1/galaxyconfigs/tools/GalaxyConfigGenerator.xml CADDSuite-1.0.1/galaxyconfigs/tools/GridBuilder.xml CADDSuite-1.0.1/galaxyconfigs/tools/IMGDock.xml CADDSuite-1.0.1/galaxyconfigs/tools/InputPartitioner.xml CADDSuite-1.0.1/galaxyconfigs/tools/InputReader.xml CADDSuite-1.0.1/galaxyconfigs/tools/InteractionConstraintDefiner.xml CADDSuite-1.0.1/galaxyconfigs/tools/LigCheck.xml CADDSuite-1.0.1/galaxyconfigs/tools/Ligand3DGenerator.xml CADDSuite-1.0.1/galaxyconfigs/tools/LigandFileSplitter.xml CADDSuite-1.0.1/galaxyconfigs/tools/ModelCreator.xml CADDSuite-1.0.1/galaxyconfigs/tools/MolCombine.xml CADDSuite-1.0.1/galaxyconfigs/tools/MolDepict.xml CADDSuite-1.0.1/galaxyconfigs/tools/MolFilter.xml CADDSuite-1.0.1/galaxyconfigs/tools/MolPredictor.xml CADDSuite-1.0.1/galaxyconfigs/tools/PDBCutter.xml CADDSuite-1.0.1/galaxyconfigs/tools/PDBDownload.xml CADDSuite-1.0.1/galaxyconfigs/tools/PartialChargesCopy.xml CADDSuite-1.0.1/galaxyconfigs/tools/PocketDetector.xml CADDSuite-1.0.1/galaxyconfigs/tools/Predictor.xml CADDSuite-1.0.1/galaxyconfigs/tools/PropertyModifier.xml CADDSuite-1.0.1/galaxyconfigs/tools/PropertyPlotter.xml CADDSuite-1.0.1/galaxyconfigs/tools/ProteinCheck.xml CADDSuite-1.0.1/galaxyconfigs/tools/ProteinProtonator.xml CADDSuite-1.0.1/galaxyconfigs/tools/RMSDCalculator.xml CADDSuite-1.0.1/galaxyconfigs/tools/ScoreAnalyzer.xml CADDSuite-1.0.1/galaxyconfigs/tools/SimilarityAnalyzer.xml CADDSuite-1.0.1/galaxyconfigs/tools/SimpleRescorer.xml CADDSuite-1.0.1/galaxyconfigs/tools/SpatialConstraintDefiner.xml CADDSuite-1.0.1/galaxyconfigs/tools/TaGRes-train.xml CADDSuite-1.0.1/galaxyconfigs/tools/TaGRes.xml CADDSuite-1.0.1/galaxyconfigs/tools/Validator.xml CADDSuite-1.0.1/galaxyconfigs/tools/VendorFinder.xml CADDSuite-1.0.1/galaxyconfigs/tools/WaterFinder.xml CADDSuite-1.0.1/galaxyconfigs/tools/upload.xml CADDSuite-1.0.1/install.sh CADDSuite-1.0.1/lib/._libQtCore.dylib CADDSuite-1.0.1/lib/._libQtNetwork.dylib CADDSuite-1.0.1/lib/._libQtSql.dylib CADDSuite-1.0.1/lib/._libQtXml.dylib CADDSuite-1.0.1/lib/._libboost_iostreams.dylib CADDSuite-1.0.1/lib/._libboost_regex.dylib CADDSuite-1.0.1/lib/._libboost_system.dylib CADDSuite-1.0.1/lib/._libboost_thread.dylib CADDSuite-1.0.1/lib/._libgsl.dylib CADDSuite-1.0.1/lib/._libgslcblas.dylib CADDSuite-1.0.1/lib/._libmysqlclient.18.dylib CADDSuite-1.0.1/lib/._libopenbabel.dylib CADDSuite-1.0.1/lib/libBALL.1.4.dylib CADDSuite-1.0.1/lib/libMagickCore.5.dylib CADDSuite-1.0.1/lib/libMagickWand.5.dylib CADDSuite-1.0.1/lib/libQtCore.dylib CADDSuite-1.0.1/lib/libQtNetwork.dylib CADDSuite-1.0.1/lib/libQtSql.dylib CADDSuite-1.0.1/lib/libQtXml.dylib CADDSuite-1.0.1/lib/libboost_iostreams.dylib CADDSuite-1.0.1/lib/libboost_regex.dylib CADDSuite-1.0.1/lib/libboost_system.dylib CADDSuite-1.0.1/lib/libboost_thread.dylib CADDSuite-1.0.1/lib/libgsl.dylib CADDSuite-1.0.1/lib/libgslcblas.dylib CADDSuite-1.0.1/lib/libmysqlclient.18.dylib CADDSuite-1.0.1/lib/libopenbabel.dylib CADDSuite-1.0.1/license.txt CADDSuite-1.0.1/setPathes.sh CADDSuite-1.0.1/suite_config.xml CADDSuite/AntitargetRescorer CADDSuite/AutoModel CADDSuite/BindingDBCleaner CADDSuite/CADDSuite-description.txt CADDSuite/CombiLibGenerator CADDSuite/ConstraintsFinder CADDSuite/Converter CADDSuite/DBExporter CADDSuite/DBImporter CADDSuite/DockResultMerger CADDSuite/EvenSplit CADDSuite/FeatureSelector CADDSuite/GalaxyConfigGenerator CADDSuite/GridBuilder CADDSuite/IMGDock CADDSuite/InputPartitioner CADDSuite/InputReader CADDSuite/InteractionConstraintDefiner CADDSuite/LigCheck CADDSuite/Ligand3DGenerator CADDSuite/LigandFileSplitter CADDSuite/ModelCreator CADDSuite/MolCombine CADDSuite/MolDepict CADDSuite/MolFilter CADDSuite/MolPredictor CADDSuite/PDBCutter CADDSuite/PDBDownload CADDSuite/PartialChargesCopy CADDSuite/PocketDetector CADDSuite/Predictor CADDSuite/PropertyModifier CADDSuite/PropertyPlotter CADDSuite/ProteinCheck CADDSuite/ProteinProtonator CADDSuite/README CADDSuite/RMSDCalculator CADDSuite/ScoreAnalyzer CADDSuite/SimilarityAnalyzer CADDSuite/SimpleRescorer CADDSuite/SpatialConstraintDefiner CADDSuite/TaGRes CADDSuite/TaGRes-train CADDSuite/Validator CADDSuite/VendorFinder CADDSuite/WaterFinder CADDSuite/bin/AntitargetRescorer.bin CADDSuite/bin/AutoModel.bin CADDSuite/bin/BindingDBCleaner.bin CADDSuite/bin/CombiLibGenerator.bin CADDSuite/bin/ConstraintsFinder.bin CADDSuite/bin/Converter.bin CADDSuite/bin/DBExporter.bin CADDSuite/bin/DBImporter.bin CADDSuite/bin/DockResultMerger.bin CADDSuite/bin/EvenSplit.bin CADDSuite/bin/FeatureSelector.bin CADDSuite/bin/GalaxyConfigGenerator.bin CADDSuite/bin/GridBuilder.bin CADDSuite/bin/IMGDock.bin CADDSuite/bin/InputPartitioner.bin CADDSuite/bin/InputReader.bin CADDSuite/bin/InteractionConstraintDefiner.bin CADDSuite/bin/LigCheck.bin CADDSuite/bin/Ligand3DGenerator.bin CADDSuite/bin/LigandFileSplitter.bin CADDSuite/bin/ModelCreator.bin CADDSuite/bin/MolCombine.bin CADDSuite/bin/MolDepict.bin CADDSuite/bin/MolFilter.bin CADDSuite/bin/MolPredictor.bin CADDSuite/bin/PDBCutter.bin CADDSuite/bin/PDBDownload.bin CADDSuite/bin/PartialChargesCopy.bin CADDSuite/bin/PocketDetector.bin CADDSuite/bin/Predictor.bin CADDSuite/bin/PropertyModifier.bin CADDSuite/bin/PropertyPlotter.bin CADDSuite/bin/ProteinCheck.bin CADDSuite/bin/ProteinProtonator.bin CADDSuite/bin/RMSDCalculator.bin CADDSuite/bin/ScoreAnalyzer.bin CADDSuite/bin/SimilarityAnalyzer.bin CADDSuite/bin/SimpleRescorer.bin CADDSuite/bin/SpatialConstraintDefiner.bin CADDSuite/bin/TaGRes-train.bin CADDSuite/bin/TaGRes.bin CADDSuite/bin/Validator.bin CADDSuite/bin/VendorFinder.bin CADDSuite/bin/WaterFinder.bin CADDSuite/bin/gnuplot CADDSuite/changelog.txt CADDSuite/data/Amber/amber96-docking.ini CADDSuite/data/QSAR/atomic_electron_affinities.data CADDSuite/data/QSAR/atomic_ionization_potentials.data CADDSuite/data/QSAR/atomic_polarizabilities.data CADDSuite/data/QSAR/dragon_descriptors.txt CADDSuite/data/XRAY/spacegroups.dat CADDSuite/data/atomtyping/AMBERTypes.dat CADDSuite/data/atomtyping/GAFFTypes.dat CADDSuite/data/atomtyping/SYBYLTypes.dat CADDSuite/data/bond_lengths/BondOrder.xml CADDSuite/data/bond_lengths/BondOrderGAFF.xml CADDSuite/data/bond_lengths/bond_lengths.db CADDSuite/data/bond_lengths/bond_lengths_mmff94.ini CADDSuite/data/fragments/A.db CADDSuite/data/fragments/ACE.db CADDSuite/data/fragments/ALA.db CADDSuite/data/fragments/ARG.db CADDSuite/data/fragments/ASN.db CADDSuite/data/fragments/ASP.db CADDSuite/data/fragments/Benzene-Skeleton.db CADDSuite/data/fragments/C.db CADDSuite/data/fragments/CA.db CADDSuite/data/fragments/CYS.db CADDSuite/data/fragments/Editing-Fragments.db CADDSuite/data/fragments/Fragments.db CADDSuite/data/fragments/G.db CADDSuite/data/fragments/GLN.db CADDSuite/data/fragments/GLU.db CADDSuite/data/fragments/GLY.db CADDSuite/data/fragments/HIS.db CADDSuite/data/fragments/HOH.db CADDSuite/data/fragments/ILE.db CADDSuite/data/fragments/Indole-Skeleton.db CADDSuite/data/fragments/LEU.db CADDSuite/data/fragments/LYS.db CADDSuite/data/fragments/MET.db CADDSuite/data/fragments/MG.db CADDSuite/data/fragments/MSE.db CADDSuite/data/fragments/NME.db CADDSuite/data/fragments/Names.Amber.db CADDSuite/data/fragments/Names.CHARMM.db CADDSuite/data/fragments/Names.DNA.db CADDSuite/data/fragments/Names.Discover.db CADDSuite/data/fragments/Names.Star.db CADDSuite/data/fragments/Names.XPLOR.db CADDSuite/data/fragments/PCA.db CADDSuite/data/fragments/PHE.db CADDSuite/data/fragments/PRO.db CADDSuite/data/fragments/Pyrrole-Skeleton.db CADDSuite/data/fragments/SER.db CADDSuite/data/fragments/T.db CADDSuite/data/fragments/THR.db CADDSuite/data/fragments/TRP.db CADDSuite/data/fragments/TYR.db CADDSuite/data/fragments/U.db CADDSuite/data/fragments/VAL.db CADDSuite/data/fragments/ZN.db CADDSuite/data/fragments/functionalGroups.smarts CADDSuite/data/gnuplot/FreeSans.ttf CADDSuite/data/gnuplot/prologue.ps CADDSuite/galaxyconfigs/confFiles.py CADDSuite/galaxyconfigs/countResidues.sh CADDSuite/galaxyconfigs/datatypes_conf.xml CADDSuite/galaxyconfigs/molFiles.py CADDSuite/galaxyconfigs/tool_conf.xml CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml CADDSuite/galaxyconfigs/tools/AutoModel.xml CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml CADDSuite/galaxyconfigs/tools/Converter.xml CADDSuite/galaxyconfigs/tools/DBExporter.xml CADDSuite/galaxyconfigs/tools/DBImporter.xml CADDSuite/galaxyconfigs/tools/DockResultMerger.xml CADDSuite/galaxyconfigs/tools/EvenSplit.xml CADDSuite/galaxyconfigs/tools/FeatureSelector.xml CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml CADDSuite/galaxyconfigs/tools/GridBuilder.xml CADDSuite/galaxyconfigs/tools/IMGDock.xml CADDSuite/galaxyconfigs/tools/InputPartitioner.xml CADDSuite/galaxyconfigs/tools/InputReader.xml CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml CADDSuite/galaxyconfigs/tools/LigCheck.xml CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml CADDSuite/galaxyconfigs/tools/ModelCreator.xml CADDSuite/galaxyconfigs/tools/MolCombine.xml CADDSuite/galaxyconfigs/tools/MolDepict.xml CADDSuite/galaxyconfigs/tools/MolFilter.xml CADDSuite/galaxyconfigs/tools/MolPredictor.xml CADDSuite/galaxyconfigs/tools/PDBCutter.xml CADDSuite/galaxyconfigs/tools/PDBDownload.xml CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml CADDSuite/galaxyconfigs/tools/PocketDetector.xml CADDSuite/galaxyconfigs/tools/Predictor.xml CADDSuite/galaxyconfigs/tools/PropertyModifier.xml CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml CADDSuite/galaxyconfigs/tools/ProteinCheck.xml CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml CADDSuite/galaxyconfigs/tools/TaGRes-train.xml CADDSuite/galaxyconfigs/tools/TaGRes.xml CADDSuite/galaxyconfigs/tools/Validator.xml CADDSuite/galaxyconfigs/tools/VendorFinder.xml CADDSuite/galaxyconfigs/tools/WaterFinder.xml CADDSuite/galaxyconfigs/tools/upload.xml CADDSuite/install.sh CADDSuite/lib/Accelerate CADDSuite/lib/QtCore CADDSuite/lib/QtNetwork CADDSuite/lib/QtSql CADDSuite/lib/QtXml CADDSuite/lib/libBALL.1.4.dylib CADDSuite/lib/libBLAS.dylib CADDSuite/lib/libSystem.B.dylib CADDSuite/lib/libboost_iostreams.dylib CADDSuite/lib/libboost_regex.dylib CADDSuite/lib/libboost_system.dylib CADDSuite/lib/libboost_thread.dylib CADDSuite/lib/libgsl.0.dylib CADDSuite/lib/libgslcblas.0.dylib CADDSuite/lib/libmysqlclient.18.dylib CADDSuite/lib/libopenbabel.4.dylib CADDSuite/license.txt CADDSuite/setPathes.sh CADDSuite/suite_config.xml
diffstat 579 files changed, 90401 insertions(+), 19400 deletions(-) [+]
line wrap: on
line diff
Binary file CADDSuite-1.0.1/._CADDSuite-description.txt has changed
Binary file CADDSuite-1.0.1/._changelog.txt has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/AntitargetRescorer	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/AntitargetRescorer.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/AutoModel	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/AutoModel.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/BindingDBCleaner	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/BindingDBCleaner.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/CADDSuite-description.txt	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,61 @@
+This package contains tools belonging to
+CADDSuite: A flexible and open framework for Computer-Aided Drug Design
+
+There are tools for the following tasks:
+
+Get Data:
+	- CombiLibGenerator: generate R-group decorated ligands
+	- DBExporter: fetch (filtered) molecules from DB
+
+Preparation of input:
+	- PDBCutter: separate ligand and receptor
+	- ProteinProtonator: protonate protein structures
+	- BindingDBCleaner: fix data from bindingdb.org
+	- EvenSplit: generate splits w/ equal property range
+	- PropertyModifier: modify property tags
+	- LigandFileSplitter: split molecule files
+	- Ligand3DGenerator: generate 3D coordinates for small molecules
+
+Structure checks and evaluations:
+	- ProteinCheck: evaluate protein quality
+	- LigCheck: chemical sanity check for ligands
+
+QuEasy (QSAR):
+	- InputReader: read molecules and generate features
+	- ModelCreator: create a QSAR model
+	- FeatureSelector: automatically select features of a QSAR model
+	- Validator: evaluate quality of a QSAR model
+	- MolPredictor: predict molecule activities with QSAR model
+	- AutoModel: automatically find best QSAR model
+
+Docking:
+	- WaterFinder: find strongly bound water molecules
+	- SpatialConstraintDefiner: define spatial constraint
+	- InteractionConstraintDefiner: define interaction constraint
+	- ConstraintsFinder: find strongly interacting residues
+	- PocketDetector: detect ligand binding pocket
+	- GridBuilder: precalculate grids for docking
+	- IMGDock: run Iterative Multi-Greedy Docking
+
+Rescoring:
+	- SimpleRescorer: rescore docking results 
+	- TaGRes-train: Target-specific Grid-Rescoring, training
+	- TaGRes: Target-specific Grid-Rescoring
+	- AntitargetRescoring: rescore w/ respect to antitarget
+
+Analysis:
+	- ScoreAnalyzer: generate ROC or enrichment plots
+	- SimilarityAnalyzer: analyze similarity between two molecule sets
+	- PropertyPlotter: plot molecule properties
+	- RMSDCalculator: calculate RMSD between conformations
+	- VendorFinder: search vendors for compounds
+
+Convert, combine and store:
+	- DockResultMerger: merge docking output files and/or filter them
+	- MolCombine: combine molecular files
+	- DBImporter: import molecules into DB
+	- Converter: interconvert molecular file-formats
+	- MolDepict: generate structure diagrams
+	- VendorFinder: search vendors for compounds
+
+For more information about an individual tool, please call the tool without any parameters (or with '-help').
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/CombiLibGenerator	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/CombiLibGenerator.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/ConstraintsFinder	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/ConstraintsFinder.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/Converter	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/Converter.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/DBExporter	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/DBExporter.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/DBImporter	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/DBImporter.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/DockResultMerger	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/DockResultMerger.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/EvenSplit	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/EvenSplit.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/FeatureSelector	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/FeatureSelector.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/GalaxyConfigGenerator	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/GalaxyConfigGenerator.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/GridBuilder	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/GridBuilder.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/IMGDock	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/IMGDock.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/InputPartitioner	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/InputPartitioner.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/InputReader	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/InputReader.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/InteractionConstraintDefiner	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/InteractionConstraintDefiner.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/LigCheck	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/LigCheck.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/Ligand3DGenerator	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/Ligand3DGenerator.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/LigandFileSplitter	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/LigandFileSplitter.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/ModelCreator	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/ModelCreator.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/MolCombine	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/MolCombine.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/MolDepict	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/MolDepict.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/MolFilter	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/MolFilter.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/MolPredictor	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/MolPredictor.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/PDBCutter	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/PDBCutter.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/PDBDownload	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/PDBDownload.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/PartialChargesCopy	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/PartialChargesCopy.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/PocketDetector	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/PocketDetector.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/Predictor	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/Predictor.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/PropertyModifier	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/PropertyModifier.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/PropertyPlotter	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/PropertyPlotter.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/ProteinCheck	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/ProteinCheck.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/ProteinProtonator	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/ProteinProtonator.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/README	Tue Nov 15 10:53:16 2011 -0500
@@ -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 '-help').
+
+
+
+--------------------------------------------------------------------
+Instructions for integration of CADDSuite into the workflow-system
+Galaxy (http://getgalaxy.org)
+--------------------------------------------------------------------
+
+
+In order to install CADDSuite into your Galaxy installation, please to the following:
+
+Let's assume $galaxybase is the base-folder of your Galaxy installation.
+If you don't have a galaxy-installation yet, download a version from http://getgalaxy.org and follow the installation instructions shown there first.
+
+
+-- Extract the CADDSuite archive into a new folder $galaxybase/tools/CADDSuite, or extract it somewhere else and create a link named $galaxybase/tools/CADDSuite that points to this destination.
+
+After this, you need to copy a few files that you find in the galaxyconfig/ subfolder of this archive to the destinations specified below:
+
+-- Copy tool_conf.xml and datatypes_conf.xml to $galaxybase if you want to setup your Galaxy instance for exclusive use of CADDSuite, or copy the contents of those files into the files already existing in $galaxybase if you want to keep using tools that came along with the Galaxy installation.
+
+-- Copy molFiles.py, confFiles.py and countResidues.sh to $galaxybase/lib/galaxy/datatypes/
+
+-- Add "#import molFiles, confFiles.py" to the beginning of the file $galaxybase/lib/galaxy/datatypes/registry.py
+
+
+
+Last but not least, restart Galaxy.
+All CADDSuite tools should now appear in your Galaxy webinterface.
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/RMSDCalculator	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/RMSDCalculator.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/ScoreAnalyzer	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/ScoreAnalyzer.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/SimilarityAnalyzer	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/SimilarityAnalyzer.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/SimpleRescorer	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/SimpleRescorer.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/SpatialConstraintDefiner	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/SpatialConstraintDefiner.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/TaGRes	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/TaGRes.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/TaGRes-train	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/TaGRes-train.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/Validator	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/Validator.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/VendorFinder	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/VendorFinder.bin "$@" 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/WaterFinder	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,4 @@
+#!/bin/bash
+		export BASE_DIR=`dirname "$0"`
+		. "$BASE_DIR"/setPathes.sh
+		"$BASE_DIR"/bin/WaterFinder.bin "$@" 
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/changelog.txt	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,78 @@
+Version 1.0.1, 11-06-2011:
+	- In WaterFinder, remove existing water hydrogens before protonating and optimizing water molecules
+	- Fixed a parameter-related regression in IMGDock that led to the accidental use of non grid-based scoring functions
+	- Display meaningful error if autmatic QSAR model is attempted with data not containing any response variables
+
+Version 1.0, 11-04-2011:
+	- Added support for advanced parameters and parameter sections
+	- Added some missing 'supported_formats' and 'tool_category' tags
+	- Fixed tar compression on Mac
+	- Fix for use of libsvm 3.1
+	- Fix for use of created release packages on MacOS 10.7
+	- Added missing flag to MolPredictor.
+
+Version 0.9.6, 08-20-2011:
+	- MolFilter: Use union of SMARTS matches instead of intersection
+	- Support for reading and writing compressed molecule files (*.gz)
+	- Added optional parameter for output log-file to DBImporter
+	- Added flag for disabling uniqueness-check to LigCheck
+	- mol2-files: disabled gaff atom-typing for speed-up
+	- drf-files: automatically add new protein-conformations
+	- Ligand3DGenerator: disable fallback-use of openbabel-UFF force field since it turned out to be unstable
+	- InputReader: made sure to always calculate correct set of features
+	- Fixed a nan problem during centering of QSAR data
+
+Version 0.9.5, 07-12-2011:
+	- Let rescoring search for correct LigCheck molecule property-tags
+	- Indicate optional parameters in galaxy interface
+	- Fixed compilation with disabled QuEasyViz
+	- Added missing gnuplot data file to release archive
+	- Set some default values for flags for use in GUIs
+	- Clarified EvenSplit docu
+
+Version 0.9.4, 06-27-2011:
+	- Fixed tool-startup script for pathes containing whitespaces
+	- New tool SpatialConstraintDefiner
+	- New tool InteractionConstraintDefiner
+	- Removed superficial pathes from startup-script
+	- Slight change in ParamFile format (i.e. the files written with -write_par)
+	- Renamed IMeedyDock to IMGDock
+
+Version 0.9.3, 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 0.9.2, 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 0.9.1, 04-12-2011:
+	- All tools now write a manual text to cout as well as to parameter xml-file (as generated by -write_par)
+
+Version 0.9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/Amber/amber96-docking.ini	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,1666 @@
+; This file contains parameter needed for nonbonded ScoringComponents.
+; The parameters were converted from parm96.dat using amber2ini and all sections for bonded parameters were removed since are not needed for docking.
+; Furthermore, lennard-jones and AtomType parameters for some metal ions were obtained from the sources indicated in the comment column and added to this file.
+
+[Options]
+key:0
+@SCEE=1.2
+; please check the settings for SCEE! AMBER91/89a requires a value of 2.0 here!
+
+
+
+
+[HydrophilicTypes]
+; ignored
+;
+C   H   HO  N   NA  NB  NC  N2  NT  N2  N3  N*  O   OH  OS  P   O2 
+
+
+[HydrogenBonds]
+ver:version key:I key:J value:A value:B
+@unit_A=kcal/mol*A^12
+@unit_B=kcal/mol*A^10
+;
+;
+;  Rev  I   J      A          B
+;  --- --- --- ---------- ----------
+   1.0  HW OW     0.0000     0.0000
+
+
+[AtomTypes]
+value:ver key:type value:mass value:comment
+@unit=g/mol
+;
+;
+;   Rev Type    mass      comment
+;   --- ---- ---------- ----------------------------------
+    1.0  BR    79.90000 "bromine"
+    1.0  C     12.01000 "sp2 C carbonyl group "
+    1.0  F     19.00000 "fluorine"
+    1.0  I    126.90000 "iodine"
+    1.0  H      1.00800 "H bonded to nitrogen atoms"
+    1.0  IM    35.45000 "assumed to be Cl-"
+    1.0  IP    22.99000 "assumed to be Na+"
+    1.0  IB   131.00000 "'big ion w/ waters' for vacuum (Na+, 6H2O)"
+    1.0  N     14.01000 "sp2 nitrogen in amide groups"
+    1.0  O     16.00000 "carbonyl group oxygen"
+    1.0  P     30.97000 "phosphate"
+    1.0  S     32.06000 "sulphur in disulfide linkage"
+    1.0  Cu    63.55000 "copper"
+    1.0  Fe    55.00000 "iron"
+    1.0  Li     6.94000 "lithium"
+    1.0  K     39.10000 "potassium"
+    1.0  Rb    85.47000 "rubidium"
+    1.0  Cs   132.91000 "cesium"
+    ant  Cl    35.450   "same as cl"
+    2.0  Ca    40.08000 "calcium"
+    1.0  Mg    24.30500 "magnesium"
+    ant  Zn    65.4     "Zn2+, taken from parm99.dat (antechamber)"
+
+
+[LennardJones]
+ver:version key:I value:R value:epsilon
+@unit_R=Angstrom
+@unit_epsilon=kcal/mol
+@format=RE
+;
+;
+;  Rev  I      R       epsilon    comment
+;  --- --- ---------- ---------- -------------------------
+   1.0 Ca   1.600000   0.100000 " calcium from parm91.dat"
+   1.0 H    0.600000   0.015700 " !Ferguson base pair geom."
+   1.0 O    1.661200   0.210000 " OPLS"
+   1.0 C    1.908000   0.086000 " OPLS"
+   1.0 N    1.824000   0.170000 " OPLS"
+   1.0 S    2.000000   0.250000 " W. Cornell CH3SH and CH3SCH3 FEP's"
+   1.0 P    2.100000   0.200000 " JCC,7,(1986),230;"
+   1.0 IM   2.470000   0.100000 " Cl- Smith & Dang, JCP 1994,100:5,3757"
+   1.0 IB   5.000000   0.100000 " solvated ion for vacuum approximation"
+   1.0 Li   1.137000   0.018300 " Li+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 IP   1.868000   0.002770 " Na+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 K    2.658000   0.000328 " K+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 Rb   2.956000   0.000170 " Rb+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 Cs   3.395000   0.000081 " Cs+ Aqvist JPC 1990,94,8021. (adapted)"
+   1.0 I    2.350000   0.400000 " JCC,7,(1986),230;"
+   1.0 F    1.750000   0.061000 " Gough et al. JCC 13,(1992),963."
+   ant Cl   2.47       0.1      " Cl- Smith & Dang, JCP 1994,100:5,3757, taken from parm99.dat (antechamber)"
+   ant Zn   1.10       0.0125   " Zn2+, Merz,PAK, JACS,113,8262,(1991), taken from parm99.dat (antechamber)"
+   ant Mg   0.7926     0.8947   " Mg2+ Aqvist JPC 1990,94,8021.(adapted), taken from parm99.dat (antechamber)"
+;   ant Cl  1.9480  0.2650  "same as cl"
+;   1.0 Mg   1.170000   0.100000 " magnesium from parm91.dat"
+
+
+[ResidueImproperTorsions]
+key:name
+;
+;
+;    res:atom
+;  -------------
+   ALA:N
+   ALA:C
+   GLY:N
+   GLY:C
+   SER:N
+   SER:C
+   THR:N
+   THR:C
+   LEU:N
+   LEU:C
+   ILE:N
+   ILE:C
+   VAL:N
+   VAL:C
+   ASN:N
+   ASN:C
+   ASN:CG
+   ASN:ND2
+   GLN:N
+   GLN:C
+   GLN:CD
+   GLN:NE2
+   ARG:N
+   ARG:C
+   ARG:CZ
+   ARG:NE
+   ARG:NH1
+   ARG:NH2
+   HIS:N
+   HIS:C
+   HIS:ND1
+   HIS:CD2
+   HIS:CE1
+   HIS:CG
+   HIS:N
+   HIS:C
+   HIS:NE2
+   HIS:CD2
+   HIS:CE1
+   HIS:CG
+   HIS:N
+   HIS:C
+   HIS:ND1
+   HIS:NE2
+   HIS:CD2
+   HIS:CE1
+   HIS:CG
+   TRP:N
+   TRP:C
+   TRP:NE1
+   TRP:CZ2
+   TRP:CH2
+   TRP:CZ3
+   TRP:CE3
+   TRP:CD1
+   TRP:CG
+   PHE:N
+   PHE:C
+   PHE:CD2
+   PHE:CE2
+   PHE:CZ
+   PHE:CE1
+   PHE:CD1
+   PHE:CG
+   TYR:N
+   TYR:C
+   TYR:CD2
+   TYR:CE2
+   TYR:CE1
+   TYR:CD1
+   TYR:CG
+   TYR:CZ
+   GLU:N
+   GLU:C
+   GLU:CD
+   ASP:N
+   ASP:C
+   ASP:CG
+   LYS:N
+   LYS:C
+   LYN:N
+   LYN:C
+   PRO:C
+   PRO:N
+   CYS:N
+   CYS:C
+   CYM:N
+   CYM:C
+   CYS-S:N
+   CYS-S:C
+   MET:N
+   MET:C
+   ACE:C
+   NME:N
+   ASH:N
+   ASH:C
+   ASH:CG
+   GLH:N
+   GLH:C
+   GLH:CD
+   ALA-N:C
+   GLY-N:C
+   SER-N:C
+   THR-N:C
+   LEU-N:C
+   ILE-N:C
+   VAL-N:C
+   ASN-N:C
+   ASN-N:CG
+   ASN-N:ND2
+   GLN-N:C
+   GLN-N:CD
+   GLN-N:NE2
+   ARG-N:C
+   ARG-N:CZ
+   ARG-N:NE
+   ARG-N:NH1
+   ARG-N:NH2
+   HIS-N:C
+   HIS-N:ND1
+   HIS-N:CD2
+   HIS-N:CE1
+   HIS-N:CG
+   HIS-N:C
+   HIS-N:NE2
+   HIS-N:CD2
+   HIS-N:CE1
+   HIS-N:CG
+   HIS-N:C
+   HIS-N:ND1
+   HIS-N:NE2
+   HIS-N:CD2
+   HIS-N:CE1
+   HIS-N:CG
+   TRP-N:C
+   TRP-N:NE1
+   TRP-N:CZ2
+   TRP-N:CH2
+   TRP-N:CZ3
+   TRP-N:CE3
+   TRP-N:CD1
+   TRP-N:CG
+   PHE-N:C
+   PHE-N:CD2
+   PHE-N:CE2
+   PHE-N:CZ
+   PHE-N:CE1
+   PHE-N:CD1
+   PHE-N:CG
+   TYR-N:C
+   TYR-N:CD2
+   TYR-N:CE2
+   TYR-N:CE1
+   TYR-N:CD1
+   TYR-N:CG
+   TYR-N:CZ
+   GLU-N:C
+   GLU-N:CD
+   ASP-N:C
+   ASP-N:CG
+   LYS-N:C
+   PRO-N:C
+   CYS-N:C
+   CYS-NS:C
+   MET-N:C
+   ALA-C:N
+   ALA-C:C
+   GLY-C:N
+   GLY-C:C
+   SER-C:N
+   SER-C:C
+   THR-C:N
+   THR-C:C
+   LEU-C:N
+   LEU-C:C
+   ILE-C:N
+   ILE-C:C
+   VAL-C:N
+   VAL-C:C
+   ASN-C:N
+   ASN-C:C
+   ASN-C:CG
+   ASN-C:ND2
+   GLN-C:N
+   GLN-C:C
+   GLN-C:CD
+   GLN-C:NE2
+   ARG-C:N
+   ARG-C:C
+   ARG-C:CZ
+   ARG-C:NE
+   ARG-C:NH1
+   ARG-C:NH2
+   HIS-C:N
+   HIS-C:C
+   HIS-C:ND1
+   HIS-C:CD2
+   HIS-C:CE1
+   HIS-C:CG
+   HIS-C:N
+   HIS-C:C
+   HIS-C:NE2
+   HIS-C:CD2
+   HIS-C:CE1
+   HIS-C:CG
+   HIS-C:N
+   HIS-C:C
+   HIS-C:ND1
+   HIS-C:NE2
+   HIS-C:CD2
+   HIS-C:CE1
+   HIS-C:CG
+   TRP-C:N
+   TRP-C:C
+   TRP-C:NE1
+   TRP-C:CZ2
+   TRP-C:CH2
+   TRP-C:CZ3
+   TRP-C:CE3
+   TRP-C:CD1
+   TRP-C:CG
+   PHE-C:N
+   PHE-C:C
+   PHE-C:CD2
+   PHE-C:CE2
+   PHE-C:CZ
+   PHE-C:CE1
+   PHE-C:CD1
+   PHE-C:CG
+   TYR-C:N
+   TYR-C:C
+   TYR-C:CD2
+   TYR-C:CE2
+   TYR-C:CE1
+   TYR-C:CD1
+   TYR-C:CG
+   TYR-C:CZ
+   GLU-C:N
+   GLU-C:C
+   GLU-C:CD
+   ASP-C:N
+   ASP-C:C
+   ASP-C:CG
+   LYS-C:N
+   LYS-C:C
+   PRO-C:C
+   PRO-C:N
+   CYS-C:N
+   CYS-C:C
+   CYS-CS:N
+   CYS-CS:C
+   MET-C:N
+   MET-C:C
+
+[ChargesAndTypeNames]
+ver:version key:name value:q value:type
+@unit_q=e0
+   1.0 ALA:N      -0.41570 N    
+   1.0 ALA:H       0.27190 H    
+   1.0 ALA:CA      0.03370 CT   
+   1.0 ALA:HA      0.08230 H1   
+   1.0 ALA:CB     -0.18250 CT   
+   1.0 ALA:1HB     0.06030 HC   
+   1.0 ALA:2HB     0.06030 HC   
+   1.0 ALA:3HB     0.06030 HC   
+   1.0 ALA:C       0.59730 C    
+   1.0 ALA:O      -0.56790 O    
+   1.0 GLY:N      -0.41570 N    
+   1.0 GLY:H       0.27190 H    
+   1.0 GLY:CA     -0.02520 CT   
+   1.0 GLY:1HA     0.06980 H1   
+   1.0 GLY:2HA     0.06980 H1   
+   1.0 GLY:C       0.59730 C    
+   1.0 GLY:O      -0.56790 O    
+   1.0 SER:N      -0.41570 N    
+   1.0 SER:H       0.27190 H    
+   1.0 SER:CA     -0.02490 CT   
+   1.0 SER:HA      0.08430 H1   
+   1.0 SER:CB      0.21170 CT   
+   1.0 SER:1HB     0.03520 H1   
+   1.0 SER:2HB     0.03520 H1   
+   1.0 SER:OG     -0.65460 OH   
+   1.0 SER:HG      0.42750 HO   
+   1.0 SER:C       0.59730 C    
+   1.0 SER:O      -0.56790 O    
+   1.0 THR:N      -0.41570 N    
+   1.0 THR:H       0.27190 H    
+   1.0 THR:CA     -0.03890 CT   
+   1.0 THR:HA      0.10070 H1   
+   1.0 THR:CB      0.36540 CT   
+   1.0 THR:HB      0.00430 H1   
+   1.0 THR:CG2    -0.24380 CT   
+   1.0 THR:1HG2    0.06420 HC   
+   1.0 THR:2HG2    0.06420 HC   
+   1.0 THR:3HG2    0.06420 HC   
+   1.0 THR:OG1    -0.67610 OH   
+   1.0 THR:HG1     0.41020 HO   
+   1.0 THR:C       0.59730 C    
+   1.0 THR:O      -0.56790 O    
+   1.0 LEU:N      -0.41570 N    
+   1.0 LEU:H       0.27190 H    
+   1.0 LEU:CA     -0.05180 CT   
+   1.0 LEU:HA      0.09220 H1   
+   1.0 LEU:CB     -0.11020 CT   
+   1.0 LEU:1HB     0.04570 HC   
+   1.0 LEU:2HB     0.04570 HC   
+   1.0 LEU:CG      0.35310 CT   
+   1.0 LEU:HG     -0.03610 HC   
+   1.0 LEU:CD1    -0.41210 CT   
+   1.0 LEU:1HD1    0.10000 HC   
+   1.0 LEU:2HD1    0.10000 HC   
+   1.0 LEU:3HD1    0.10000 HC   
+   1.0 LEU:CD2    -0.41210 CT   
+   1.0 LEU:1HD2    0.10000 HC   
+   1.0 LEU:2HD2    0.10000 HC   
+   1.0 LEU:3HD2    0.10000 HC   
+   1.0 LEU:C       0.59730 C    
+   1.0 LEU:O      -0.56790 O    
+   1.0 ILE:N      -0.41570 N    
+   1.0 ILE:H       0.27190 H    
+   1.0 ILE:CA     -0.05970 CT   
+   1.0 ILE:HA      0.08690 H1   
+   1.0 ILE:CB      0.13030 CT   
+   1.0 ILE:HB      0.01870 HC   
+   1.0 ILE:CG2    -0.32040 CT   
+   1.0 ILE:1HG2    0.08820 HC   
+   1.0 ILE:2HG2    0.08820 HC   
+   1.0 ILE:3HG2    0.08820 HC   
+   1.0 ILE:CG1    -0.04300 CT   
+   1.0 ILE:1HG1    0.02360 HC   
+   1.0 ILE:2HG1    0.02360 HC   
+   1.0 ILE:CD1    -0.06600 CT   
+   1.0 ILE:1HD1    0.01860 HC   
+   1.0 ILE:2HD1    0.01860 HC   
+   1.0 ILE:3HD1    0.01860 HC   
+   1.0 ILE:C       0.59730 C    
+   1.0 ILE:O      -0.56790 O    
+   1.0 VAL:N      -0.41570 N    
+   1.0 VAL:H       0.27190 H    
+   1.0 VAL:CA     -0.08750 CT   
+   1.0 VAL:HA      0.09690 H1   
+   1.0 VAL:CB      0.29850 CT   
+   1.0 VAL:HB     -0.02970 HC   
+   1.0 VAL:CG1    -0.31920 CT   
+   1.0 VAL:1HG1    0.07910 HC   
+   1.0 VAL:2HG1    0.07910 HC   
+   1.0 VAL:3HG1    0.07910 HC   
+   1.0 VAL:CG2    -0.31920 CT   
+   1.0 VAL:1HG2    0.07910 HC   
+   1.0 VAL:2HG2    0.07910 HC   
+   1.0 VAL:3HG2    0.07910 HC   
+   1.0 VAL:C       0.59730 C    
+   1.0 VAL:O      -0.56790 O    
+   1.0 ASN:N      -0.41570 N    
+   1.0 ASN:H       0.27190 H    
+   1.0 ASN:CA      0.01430 CT   
+   1.0 ASN:HA      0.10480 H1   
+   1.0 ASN:CB     -0.20410 CT   
+   1.0 ASN:1HB     0.07970 HC   
+   1.0 ASN:2HB     0.07970 HC   
+   1.0 ASN:CG      0.71300 C    
+   1.0 ASN:OD1    -0.59310 O    
+   1.0 ASN:ND2    -0.91910 N    
+   1.0 ASN:1HD2    0.41960 H    
+   1.0 ASN:2HD2    0.41960 H    
+   1.0 ASN:C       0.59730 C    
+   1.0 ASN:O      -0.56790 O    
+   1.0 GLN:N      -0.41570 N    
+   1.0 GLN:H       0.27190 H    
+   1.0 GLN:CA     -0.00310 CT   
+   1.0 GLN:HA      0.08500 H1   
+   1.0 GLN:CB     -0.00360 CT   
+   1.0 GLN:1HB     0.01710 HC   
+   1.0 GLN:2HB     0.01710 HC   
+   1.0 GLN:CG     -0.06450 CT   
+   1.0 GLN:1HG     0.03520 HC   
+   1.0 GLN:2HG     0.03520 HC   
+   1.0 GLN:CD      0.69510 C    
+   1.0 GLN:OE1    -0.60860 O    
+   1.0 GLN:NE2    -0.94070 N    
+   1.0 GLN:1HE2    0.42510 H    
+   1.0 GLN:2HE2    0.42510 H    
+   1.0 GLN:C       0.59730 C    
+   1.0 GLN:O      -0.56790 O    
+   1.0 ARG:N      -0.34790 N    
+   1.0 ARG:H       0.27470 H    
+   1.0 ARG:CA     -0.26370 CT   
+   1.0 ARG:HA      0.15600 H1   
+   1.0 ARG:CB     -0.00070 CT   
+   1.0 ARG:1HB     0.03270 HC   
+   1.0 ARG:2HB     0.03270 HC   
+   1.0 ARG:CG      0.03900 CT   
+   1.0 ARG:1HG     0.02850 HC   
+   1.0 ARG:2HG     0.02850 HC   
+   1.0 ARG:CD      0.04860 CT   
+   1.0 ARG:1HD     0.06870 H1   
+   1.0 ARG:2HD     0.06870 H1   
+   1.0 ARG:NE     -0.52950 N2   
+   1.0 ARG:HE      0.34560 H    
+   1.0 ARG:CZ      0.80760 CA   
+   1.0 ARG:NH1    -0.86270 N2   
+   1.0 ARG:1HH1    0.44780 H    
+   1.0 ARG:2HH1    0.44780 H    
+   1.0 ARG:NH2    -0.86270 N2   
+   1.0 ARG:1HH2    0.44780 H    
+   1.0 ARG:2HH2    0.44780 H    
+   1.0 ARG:C       0.73410 C    
+   1.0 ARG:O      -0.58940 O    
+   1.0 HIS:N      -0.34790 N    
+   1.0 HIS:H       0.27470 H    
+   1.0 HIS:CA     -0.13540 CT   
+   1.0 HIS:HA      0.12120 H1   
+   1.0 HIS:CB     -0.04140 CT   
+   1.0 HIS:1HB     0.08100 HC   
+   1.0 HIS:2HB     0.08100 HC   
+   1.0 HIS:CG     -0.00120 CC   
+   1.0 HIS:ND1    -0.15130 NA   
+   1.0 HIS:HD1     0.38660 H    
+   1.0 HIS:CE1    -0.01700 CR   
+   1.0 HIS:HE1     0.26810 H5   
+   1.0 HIS:NE2    -0.17180 NA   
+   1.0 HIS:CD2    -0.11410 CW   
+   1.0 HIS:HD2     0.23170 H4   
+   1.0 HIS:C       0.73410 C    
+   1.0 HIS:O      -0.58940 O    
+   1.0 HIS:N      -0.34790 N    
+   1.0 HIS:H       0.27470 H    
+   1.0 HIS:CA     -0.13540 CT   
+   1.0 HIS:HA      0.12120 H1   
+   1.0 HIS:CB     -0.04140 CT   
+   1.0 HIS:1HB     0.08100 HC   
+   1.0 HIS:2HB     0.08100 HC   
+   1.0 HIS:CG     -0.00120 CC   
+   1.0 HIS:ND1    -0.15130 NA   
+   1.0 HIS:CE1    -0.01700 CR   
+   1.0 HIS:HE1     0.26810 H5   
+   1.0 HIS:NE2    -0.17180 NA   
+   1.0 HIS:HE2     0.39110 H    
+   1.0 HIS:CD2    -0.11410 CW   
+   1.0 HIS:HD2     0.23170 H4   
+   1.0 HIS:C       0.73410 C    
+   1.0 HIS:O      -0.58940 O    
+   1.0 HIS:N      -0.34790 N    
+   1.0 HIS:H       0.27470 H    
+   1.0 HIS:CA     -0.13540 CT   
+   1.0 HIS:HA      0.12120 H1   
+   1.0 HIS:CB     -0.04140 CT   
+   1.0 HIS:1HB     0.08100 HC   
+   1.0 HIS:2HB     0.08100 HC   
+   1.0 HIS:CG     -0.00120 CC   
+   1.0 HIS:ND1    -0.15130 NA   
+   1.0 HIS:HD1     0.38660 H    
+   1.0 HIS:CE1    -0.01700 CR   
+   1.0 HIS:HE1     0.26810 H5   
+   1.0 HIS:NE2    -0.17180 NA   
+   1.0 HIS:HE2     0.39110 H    
+   1.0 HIS:CD2    -0.11410 CW   
+   1.0 HIS:HD2     0.23170 H4   
+   1.0 HIS:C       0.73410 C    
+   1.0 HIS:O      -0.58940 O    
+   1.0 TRP:N      -0.41570 N    
+   1.0 TRP:H       0.27190 H    
+   1.0 TRP:CA     -0.02750 CT   
+   1.0 TRP:HA      0.11230 H1   
+   1.0 TRP:CB     -0.00500 CT   
+   1.0 TRP:1HB     0.03390 HC   
+   1.0 TRP:2HB     0.03390 HC   
+   1.0 TRP:CG     -0.14150 C*   
+   1.0 TRP:CD1    -0.16380 CW   
+   1.0 TRP:HD1     0.20620 H4   
+   1.0 TRP:NE1    -0.34180 NA   
+   1.0 TRP:HE1     0.34120 H    
+   1.0 TRP:CE2     0.13800 CN   
+   1.0 TRP:CZ2    -0.26010 CA   
+   1.0 TRP:HZ2     0.15720 HA   
+   1.0 TRP:CH2    -0.11340 CA   
+   1.0 TRP:HH2     0.14170 HA   
+   1.0 TRP:CZ3    -0.19720 CA   
+   1.0 TRP:HZ3     0.14470 HA   
+   1.0 TRP:CE3    -0.23870 CA   
+   1.0 TRP:HE3     0.17000 HA   
+   1.0 TRP:CD2     0.12430 CB   
+   1.0 TRP:C       0.59730 C    
+   1.0 TRP:O      -0.56790 O    
+   1.0 PHE:N      -0.41570 N    
+   1.0 PHE:H       0.27190 H    
+   1.0 PHE:CA     -0.00240 CT   
+   1.0 PHE:HA      0.09780 H1   
+   1.0 PHE:CB     -0.03430 CT   
+   1.0 PHE:1HB     0.02950 HC   
+   1.0 PHE:2HB     0.02950 HC   
+   1.0 PHE:CG      0.01180 CA   
+   1.0 PHE:CD1    -0.12560 CA   
+   1.0 PHE:HD1     0.13300 HA   
+   1.0 PHE:CE1    -0.17040 CA   
+   1.0 PHE:HE1     0.14300 HA   
+   1.0 PHE:CZ     -0.10720 CA   
+   1.0 PHE:HZ      0.12970 HA   
+   1.0 PHE:CE2    -0.17040 CA   
+   1.0 PHE:HE2     0.14300 HA   
+   1.0 PHE:CD2    -0.12560 CA   
+   1.0 PHE:HD2     0.13300 HA   
+   1.0 PHE:C       0.59730 C    
+   1.0 PHE:O      -0.56790 O    
+   1.0 TYR:N      -0.41570 N    
+   1.0 TYR:H       0.27190 H    
+   1.0 TYR:CA     -0.00140 CT   
+   1.0 TYR:HA      0.08760 H1   
+   1.0 TYR:CB     -0.01520 CT   
+   1.0 TYR:1HB     0.02950 HC   
+   1.0 TYR:2HB     0.02950 HC   
+   1.0 TYR:CG     -0.00110 CA   
+   1.0 TYR:CD1    -0.19060 CA   
+   1.0 TYR:HD1     0.16990 HA   
+   1.0 TYR:CE1    -0.23410 CA   
+   1.0 TYR:HE1     0.16560 HA   
+   1.0 TYR:CZ      0.32260 C    
+   1.0 TYR:OH     -0.55790 OH   
+   1.0 TYR:HH      0.39920 HO   
+   1.0 TYR:CE2    -0.23410 CA   
+   1.0 TYR:HE2     0.16560 HA   
+   1.0 TYR:CD2    -0.19060 CA   
+   1.0 TYR:HD2     0.16990 HA   
+   1.0 TYR:C       0.59730 C    
+   1.0 TYR:O      -0.56790 O    
+   1.0 GLU:N      -0.51630 N    
+   1.0 GLU:H       0.29360 H    
+   1.0 GLU:CA      0.03970 CT   
+   1.0 GLU:HA      0.11050 H1   
+   1.0 GLU:CB      0.05600 CT   
+   1.0 GLU:1HB    -0.01730 HC   
+   1.0 GLU:2HB    -0.01730 HC   
+   1.0 GLU:CG      0.01360 CT   
+   1.0 GLU:1HG    -0.04250 HC   
+   1.0 GLU:2HG    -0.04250 HC   
+   1.0 GLU:CD      0.80540 C    
+   1.0 GLU:OE1    -0.81880 O2   
+   1.0 GLU:OE2    -0.81880 O2   
+   1.0 GLU:C       0.53660 C    
+   1.0 GLU:O      -0.58190 O    
+   1.0 ASP:N      -0.51630 N    
+   1.0 ASP:H       0.29360 H    
+   1.0 ASP:CA      0.03810 CT   
+   1.0 ASP:HA      0.08800 H1   
+   1.0 ASP:CB     -0.03030 CT   
+   1.0 ASP:1HB    -0.01220 HC   
+   1.0 ASP:2HB    -0.01220 HC   
+   1.0 ASP:CG      0.79940 C    
+   1.0 ASP:OD1    -0.80140 O2   
+   1.0 ASP:OD2    -0.80140 O2   
+   1.0 ASP:C       0.53660 C    
+   1.0 ASP:O      -0.58190 O    
+   1.0 LYS:N      -0.34790 N    
+   1.0 LYS:H       0.27470 H    
+   1.0 LYS:CA     -0.24000 CT   
+   1.0 LYS:HA      0.14260 H1   
+   1.0 LYS:CB     -0.00940 CT   
+   1.0 LYS:1HB     0.03620 HC   
+   1.0 LYS:2HB     0.03620 HC   
+   1.0 LYS:CG      0.01870 CT   
+   1.0 LYS:1HG     0.01030 HC   
+   1.0 LYS:2HG     0.01030 HC   
+   1.0 LYS:CD     -0.04790 CT   
+   1.0 LYS:1HD     0.06210 HC   
+   1.0 LYS:2HD     0.06210 HC   
+   1.0 LYS:CE     -0.01430 CT   
+   1.0 LYS:1HE     0.11350 HP   
+   1.0 LYS:2HE     0.11350 HP   
+   1.0 LYS:NZ     -0.38540 N3   
+   1.0 LYS:1HZ     0.34000 H    
+   1.0 LYS:2HZ     0.34000 H    
+   1.0 LYS:3HZ     0.34000 H    
+   1.0 LYS:C       0.73410 C    
+   1.0 LYS:O      -0.58940 O    
+   1.0 LYN:N      -0.41570 N    
+   1.0 LYN:H       0.27190 H    
+   1.0 LYN:CA     -0.07206 CT   
+   1.0 LYN:HA      0.09940 H1   
+   1.0 LYN:CB     -0.04845 CT   
+   1.0 LYN:HB2     0.03400 HC   
+   1.0 LYN:HB3     0.03400 HC   
+   1.0 LYN:CG      0.06612 CT   
+   1.0 LYN:HG2     0.01041 HC   
+   1.0 LYN:HG3     0.01041 HC   
+   1.0 LYN:CD     -0.03768 CT   
+   1.0 LYN:HD2     0.01155 HC   
+   1.0 LYN:HD3     0.01155 HC   
+   1.0 LYN:CE      0.32604 CT   
+   1.0 LYN:HE2    -0.03358 HP   
+   1.0 LYN:HE3    -0.03358 HP   
+   1.0 LYN:NZ     -1.03581 N3   
+   1.0 LYN:HZ2     0.38604 H    
+   1.0 LYN:HZ3     0.38604 H    
+   1.0 LYN:C       0.59730 C    
+   1.0 LYN:O      -0.56790 O    
+   1.0 PRO:N      -0.25480 N    
+   1.0 PRO:CD      0.01920 CT   
+   1.0 PRO:1HD     0.03910 H1   
+   1.0 PRO:2HD     0.03910 H1   
+   1.0 PRO:CG      0.01890 CT   
+   1.0 PRO:1HG     0.02130 HC   
+   1.0 PRO:2HG     0.02130 HC   
+   1.0 PRO:CB     -0.00700 CT   
+   1.0 PRO:1HB     0.02530 HC   
+   1.0 PRO:2HB     0.02530 HC   
+   1.0 PRO:CA     -0.02660 CT   
+   1.0 PRO:HA      0.06410 H1   
+   1.0 PRO:C       0.58960 C    
+   1.0 PRO:O      -0.57480 O    
+   1.0 CYS:N      -0.41570 N    
+   1.0 CYS:H       0.27190 H    
+   1.0 CYS:CA      0.02130 CT   
+   1.0 CYS:HA      0.11240 H1   
+   1.0 CYS:CB     -0.12310 CT   
+   1.0 CYS:1HB     0.11120 H1   
+   1.0 CYS:2HB     0.11120 H1   
+   1.0 CYS:SG     -0.31190 SH   
+   1.0 CYS:HG      0.19330 HS   
+   1.0 CYS:C       0.59730 C    
+   1.0 CYS:O      -0.56790 O    
+   1.0 CYM:N      -0.46300 N    
+   1.0 CYM:HN      0.25200 H    
+   1.0 CYM:CA      0.03500 CT   
+   1.0 CYM:HA      0.04800 H1   
+   1.0 CYM:CB     -0.73600 CT   
+   1.0 CYM:HB3     0.24400 H1   
+   1.0 CYM:HB2     0.24400 H1   
+   1.0 CYM:SG     -0.73600 SH   
+   1.0 CYM:C       0.61600 C    
+   1.0 CYM:O      -0.50400 O    
+   1.0 CYS-S:N    -0.41570 N    
+   1.0 CYS-S:H     0.27190 H    
+   1.0 CYS-S:CA    0.04290 CT   
+   1.0 CYS-S:HA    0.07660 H1   
+   1.0 CYS-S:CB   -0.07900 CT   
+   1.0 CYS-S:1HB   0.09100 H1   
+   1.0 CYS-S:2HB   0.09100 H1   
+   1.0 CYS-S:SG   -0.10810 S    
+   1.0 CYS-S:C     0.59730 C    
+   1.0 CYS-S:O    -0.56790 O    
+   1.0 MET:N      -0.41570 N    
+   1.0 MET:H       0.27190 H    
+   1.0 MET:CA     -0.02370 CT   
+   1.0 MET:HA      0.08800 H1   
+   1.0 MET:CB      0.03420 CT   
+   1.0 MET:1HB     0.02410 HC   
+   1.0 MET:2HB     0.02410 HC   
+   1.0 MET:CG      0.00180 CT   
+   1.0 MET:1HG     0.04400 H1   
+   1.0 MET:2HG     0.04400 H1   
+   1.0 MET:SD     -0.27370 S    
+   1.0 MET:CE     -0.05360 CT   
+   1.0 MET:1HE     0.06840 H1   
+   1.0 MET:2HE     0.06840 H1   
+   1.0 MET:3HE     0.06840 H1   
+   1.0 MET:C       0.59730 C    
+   1.0 MET:O      -0.56790 O    
+   1.0 ACE:1HH3    0.11230 HC   
+   1.0 ACE:CH3    -0.36620 CT   
+   1.0 ACE:2HH3    0.11230 HC   
+   1.0 ACE:3HH3    0.11230 HC   
+   1.0 ACE:C       0.59720 C    
+   1.0 ACE:O      -0.56790 O    
+   1.0 HOH:1H      0.41700 HW   
+   1.0 HOH:O      -0.83400 OW   
+   1.0 HOH:2H      0.41700 HW   
+   1.0 HOH:H1      0.41700 HW   
+   1.0 HOH:O      -0.83400 OW   
+   1.0 HOH:H2      0.41700 HW   
+   1.0 WAT:1H      0.41700 HW   
+   1.0 WAT:O      -0.83400 OW   
+   1.0 WAT:2H      0.41700 HW   
+   1.0 ASH:N      -0.41570 N    
+   1.0 ASH:H       0.27190 H    
+   1.0 ASH:CA      0.03410 CT   
+   1.0 ASH:HA      0.08640 H1   
+   1.0 ASH:CB     -0.03160 CT   
+   1.0 ASH:HB2     0.04880 HC   
+   1.0 ASH:HB3     0.04880 HC   
+   1.0 ASH:CG      0.64620 C    
+   1.0 ASH:OD1    -0.55540 O    
+   1.0 ASH:OD2    -0.63760 OH   
+   1.0 ASH:HD2     0.47470 HO   
+   1.0 ASH:C       0.59730 C    
+   1.0 ASH:O      -0.56790 O    
+   1.0 GLH:N      -0.41570 N    
+   1.0 GLH:H       0.27190 H    
+   1.0 GLH:CA      0.01450 CT   
+   1.0 GLH:HA      0.07790 H1   
+   1.0 GLH:CB     -0.00710 CT   
+   1.0 GLH:HB2     0.02560 HC   
+   1.0 GLH:HB3     0.02560 HC   
+   1.0 GLH:CG     -0.01740 CT   
+   1.0 GLH:HG2     0.04300 HC   
+   1.0 GLH:HG3     0.04300 HC   
+   1.0 GLH:CD      0.68010 C    
+   1.0 GLH:OE1    -0.58380 O    
+   1.0 GLH:OE2    -0.65110 OH   
+   1.0 GLH:HE2     0.46410 HO   
+   1.0 GLH:C       0.59730 C    
+   1.0 GLH:O      -0.56790 O    
+   1.0 CIP:NA+     1.00000 IP   
+   1.0 CIM:CL-    -1.00000 IM   
+   1.0 ALA-N:N     0.14140 N3   
+   1.0 ALA-N:1H    0.19970 H    
+   1.0 ALA-N:2H    0.19970 H    
+   1.0 ALA-N:3H    0.19970 H    
+   1.0 ALA-N:CA    0.09620 CT   
+   1.0 ALA-N:HA    0.08890 HP   
+   1.0 ALA-N:CB   -0.05970 CT   
+   1.0 ALA-N:1HB   0.03000 HC   
+   1.0 ALA-N:2HB   0.03000 HC   
+   1.0 ALA-N:3HB   0.03000 HC   
+   1.0 ALA-N:C     0.61630 C    
+   1.0 ALA-N:O    -0.57220 O    
+   1.0 GLY-N:N     0.29430 N3   
+   1.0 GLY-N:1H    0.16420 H    
+   1.0 GLY-N:2H    0.16420 H    
+   1.0 GLY-N:3H    0.16420 H    
+   1.0 GLY-N:CA   -0.01000 CT   
+   1.0 GLY-N:1HA   0.08950 HP   
+   1.0 GLY-N:2HA   0.08950 HP   
+   1.0 GLY-N:C     0.61630 C    
+   1.0 GLY-N:O    -0.57220 O    
+   1.0 SER-N:N     0.18490 N3   
+   1.0 SER-N:1H    0.18980 H    
+   1.0 SER-N:2H    0.18980 H    
+   1.0 SER-N:3H    0.18980 H    
+   1.0 SER-N:CA    0.05670 CT   
+   1.0 SER-N:HA    0.07820 HP   
+   1.0 SER-N:CB    0.25960 CT   
+   1.0 SER-N:1HB   0.02730 H1   
+   1.0 SER-N:2HB   0.02730 H1   
+   1.0 SER-N:OG   -0.67140 OH   
+   1.0 SER-N:HG    0.42390 HO   
+   1.0 SER-N:C     0.61630 C    
+   1.0 SER-N:O    -0.57220 O    
+   1.0 THR-N:N     0.18120 N3   
+   1.0 THR-N:1H    0.19340 H    
+   1.0 THR-N:2H    0.19340 H    
+   1.0 THR-N:3H    0.19340 H    
+   1.0 THR-N:CA    0.00340 CT   
+   1.0 THR-N:HA    0.10870 HP   
+   1.0 THR-N:CB    0.45140 CT   
+   1.0 THR-N:HB   -0.03230 H1   
+   1.0 THR-N:CG2  -0.25540 CT   
+   1.0 THR-N:1HG2  0.06270 HC   
+   1.0 THR-N:2HG2  0.06270 HC   
+   1.0 THR-N:3HG2  0.06270 HC   
+   1.0 THR-N:OG1  -0.67640 OH   
+   1.0 THR-N:HG1   0.40700 HO   
+   1.0 THR-N:C     0.61630 C    
+   1.0 THR-N:O    -0.57220 O    
+   1.0 LEU-N:N     0.10100 N3   
+   1.0 LEU-N:1H    0.21480 H    
+   1.0 LEU-N:2H    0.21480 H    
+   1.0 LEU-N:3H    0.21480 H    
+   1.0 LEU-N:CA    0.01040 CT   
+   1.0 LEU-N:HA    0.10530 HP   
+   1.0 LEU-N:CB   -0.02440 CT   
+   1.0 LEU-N:1HB   0.02560 HC   
+   1.0 LEU-N:2HB   0.02560 HC   
+   1.0 LEU-N:CG    0.34210 CT   
+   1.0 LEU-N:HG   -0.03800 HC   
+   1.0 LEU-N:CD1  -0.41060 CT   
+   1.0 LEU-N:1HD1  0.09800 HC   
+   1.0 LEU-N:2HD1  0.09800 HC   
+   1.0 LEU-N:3HD1  0.09800 HC   
+   1.0 LEU-N:CD2  -0.41040 CT   
+   1.0 LEU-N:1HD2  0.09800 HC   
+   1.0 LEU-N:2HD2  0.09800 HC   
+   1.0 LEU-N:3HD2  0.09800 HC   
+   1.0 LEU-N:C     0.61230 C    
+   1.0 LEU-N:O    -0.57130 O    
+   1.0 ILE-N:N     0.03110 N3   
+   1.0 ILE-N:1H    0.23290 H    
+   1.0 ILE-N:2H    0.23290 H    
+   1.0 ILE-N:3H    0.23290 H    
+   1.0 ILE-N:CA    0.02570 CT   
+   1.0 ILE-N:HA    0.10310 HP   
+   1.0 ILE-N:CB    0.18850 CT   
+   1.0 ILE-N:HB    0.02130 HC   
+   1.0 ILE-N:CG2  -0.37200 CT   
+   1.0 ILE-N:1HG2  0.09470 HC   
+   1.0 ILE-N:2HG2  0.09470 HC   
+   1.0 ILE-N:3HG2  0.09470 HC   
+   1.0 ILE-N:CG1  -0.03870 CT   
+   1.0 ILE-N:1HG1  0.02010 HC   
+   1.0 ILE-N:2HG1  0.02010 HC   
+   1.0 ILE-N:CD1  -0.09080 CT   
+   1.0 ILE-N:1HD1  0.02260 HC   
+   1.0 ILE-N:2HD1  0.02260 HC   
+   1.0 ILE-N:3HD1  0.02260 HC   
+   1.0 ILE-N:C     0.61230 C    
+   1.0 ILE-N:O    -0.57130 O    
+   1.0 VAL-N:N     0.05770 N3   
+   1.0 VAL-N:1H    0.22720 H    
+   1.0 VAL-N:2H    0.22720 H    
+   1.0 VAL-N:3H    0.22720 H    
+   1.0 VAL-N:CA   -0.00540 CT   
+   1.0 VAL-N:HA    0.10930 HP   
+   1.0 VAL-N:CB    0.31960 CT   
+   1.0 VAL-N:HB   -0.02210 HC   
+   1.0 VAL-N:CG1  -0.31290 CT   
+   1.0 VAL-N:1HG1  0.07350 HC   
+   1.0 VAL-N:2HG1  0.07350 HC   
+   1.0 VAL-N:3HG1  0.07350 HC   
+   1.0 VAL-N:CG2  -0.31290 CT   
+   1.0 VAL-N:1HG2  0.07350 HC   
+   1.0 VAL-N:2HG2  0.07350 HC   
+   1.0 VAL-N:3HG2  0.07350 HC   
+   1.0 VAL-N:C     0.61630 C    
+   1.0 VAL-N:O    -0.57220 O    
+   1.0 ASN-N:N     0.18010 N3   
+   1.0 ASN-N:1H    0.19210 H    
+   1.0 ASN-N:2H    0.19210 H    
+   1.0 ASN-N:3H    0.19210 H    
+   1.0 ASN-N:CA    0.03680 CT   
+   1.0 ASN-N:HA    0.12310 HP   
+   1.0 ASN-N:CB   -0.02830 CT   
+   1.0 ASN-N:1HB   0.05150 HC   
+   1.0 ASN-N:2HB   0.05150 HC   
+   1.0 ASN-N:CG    0.58330 C    
+   1.0 ASN-N:OD1  -0.57440 O    
+   1.0 ASN-N:ND2  -0.86340 N    
+   1.0 ASN-N:1HD2  0.40970 H    
+   1.0 ASN-N:2HD2  0.40970 H    
+   1.0 ASN-N:C     0.61630 C    
+   1.0 ASN-N:O    -0.57220 O    
+   1.0 GLN-N:N     0.14930 N3   
+   1.0 GLN-N:1H    0.19960 H    
+   1.0 GLN-N:2H    0.19960 H    
+   1.0 GLN-N:3H    0.19960 H    
+   1.0 GLN-N:CA    0.05360 CT   
+   1.0 GLN-N:HA    0.10150 HP   
+   1.0 GLN-N:CB    0.06510 CT   
+   1.0 GLN-N:1HB   0.00500 HC   
+   1.0 GLN-N:2HB   0.00500 HC   
+   1.0 GLN-N:CG   -0.09030 CT   
+   1.0 GLN-N:1HG   0.03310 HC   
+   1.0 GLN-N:2HG   0.03310 HC   
+   1.0 GLN-N:CD    0.73540 C    
+   1.0 GLN-N:OE1  -0.61330 O    
+   1.0 GLN-N:NE2  -1.00310 N    
+   1.0 GLN-N:1HE2  0.44290 H    
+   1.0 GLN-N:2HE2  0.44290 H    
+   1.0 GLN-N:C     0.61230 C    
+   1.0 GLN-N:O    -0.57130 O    
+   1.0 ARG-N:N     0.13050 N3   
+   1.0 ARG-N:1H    0.20830 H    
+   1.0 ARG-N:2H    0.20830 H    
+   1.0 ARG-N:3H    0.20830 H    
+   1.0 ARG-N:CA   -0.02230 CT   
+   1.0 ARG-N:HA    0.12420 HP   
+   1.0 ARG-N:CB    0.01180 CT   
+   1.0 ARG-N:1HB   0.02260 HC   
+   1.0 ARG-N:2HB   0.02260 HC   
+   1.0 ARG-N:CG    0.02360 CT   
+   1.0 ARG-N:1HG   0.03090 HC   
+   1.0 ARG-N:2HG   0.03090 HC   
+   1.0 ARG-N:CD    0.09350 CT   
+   1.0 ARG-N:1HD   0.05270 H1   
+   1.0 ARG-N:2HD   0.05270 H1   
+   1.0 ARG-N:NE   -0.56500 N2   
+   1.0 ARG-N:HE    0.35920 H    
+   1.0 ARG-N:CZ    0.82810 CA   
+   1.0 ARG-N:NH1  -0.86930 N2   
+   1.0 ARG-N:1HH1  0.44940 H    
+   1.0 ARG-N:2HH1  0.44940 H    
+   1.0 ARG-N:NH2  -0.86930 N2   
+   1.0 ARG-N:1HH2  0.44940 H    
+   1.0 ARG-N:2HH2  0.44940 H    
+   1.0 ARG-N:C     0.72140 C    
+   1.0 ARG-N:O    -0.60130 O    
+   1.0 HIS-N:N     0.25600 N3   
+   1.0 HIS-N:1H    0.17040 H    
+   1.0 HIS-N:2H    0.17040 H    
+   1.0 HIS-N:3H    0.17040 H    
+   1.0 HIS-N:CA    0.05810 CT   
+   1.0 HIS-N:HA    0.10470 HP   
+   1.0 HIS-N:CB    0.04840 CT   
+   1.0 HIS-N:1HB   0.05310 HC   
+   1.0 HIS-N:2HB   0.05310 HC   
+   1.0 HIS-N:CG   -0.02360 CC   
+   1.0 HIS-N:ND1  -0.15100 NA   
+   1.0 HIS-N:HD1   0.38210 H    
+   1.0 HIS-N:CE1  -0.00110 CR   
+   1.0 HIS-N:HE1   0.26450 H5   
+   1.0 HIS-N:NE2  -0.17390 NA   
+   1.0 HIS-N:CD2  -0.14330 CW   
+   1.0 HIS-N:HD2   0.24950 H4   
+   1.0 HIS-N:C     0.72140 C    
+   1.0 HIS-N:O    -0.60130 O    
+   1.0 HIS-N:N     0.25600 N3   
+   1.0 HIS-N:1H    0.17040 H    
+   1.0 HIS-N:2H    0.17040 H    
+   1.0 HIS-N:3H    0.17040 H    
+   1.0 HIS-N:CA    0.05810 CT   
+   1.0 HIS-N:HA    0.10470 HP   
+   1.0 HIS-N:CB    0.04840 CT   
+   1.0 HIS-N:1HB   0.05310 HC   
+   1.0 HIS-N:2HB   0.05310 HC   
+   1.0 HIS-N:CG   -0.02360 CC   
+   1.0 HIS-N:ND1  -0.15100 NA   
+   1.0 HIS-N:CE1  -0.00110 CR   
+   1.0 HIS-N:HE1   0.26450 H5   
+   1.0 HIS-N:NE2  -0.17390 NA   
+   1.0 HIS-N:HE2   0.39210 H    
+   1.0 HIS-N:CD2  -0.14330 CW   
+   1.0 HIS-N:HD2   0.24950 H4   
+   1.0 HIS-N:C     0.72140 C    
+   1.0 HIS-N:O    -0.60130 O    
+   1.0 HIS-N:N     0.25600 N3   
+   1.0 HIS-N:1H    0.17040 H    
+   1.0 HIS-N:2H    0.17040 H    
+   1.0 HIS-N:3H    0.17040 H    
+   1.0 HIS-N:CA    0.05810 CT   
+   1.0 HIS-N:HA    0.10470 HP   
+   1.0 HIS-N:CB    0.04840 CT   
+   1.0 HIS-N:1HB   0.05310 HC   
+   1.0 HIS-N:2HB   0.05310 HC   
+   1.0 HIS-N:CG   -0.02360 CC   
+   1.0 HIS-N:ND1  -0.15100 NA   
+   1.0 HIS-N:HD1   0.38210 H    
+   1.0 HIS-N:CE1  -0.00110 CR   
+   1.0 HIS-N:HE1   0.26450 H5   
+   1.0 HIS-N:NE2  -0.17390 NA   
+   1.0 HIS-N:HE2   0.39210 H    
+   1.0 HIS-N:CD2  -0.14330 CW   
+   1.0 HIS-N:HD2   0.24950 H4   
+   1.0 HIS-N:C     0.72140 C    
+   1.0 HIS-N:O    -0.60130 O    
+   1.0 TRP-N:N     0.19130 N3   
+   1.0 TRP-N:1H    0.18880 H    
+   1.0 TRP-N:2H    0.18880 H    
+   1.0 TRP-N:3H    0.18880 H    
+   1.0 TRP-N:CA    0.04210 CT   
+   1.0 TRP-N:HA    0.11620 HP   
+   1.0 TRP-N:CB    0.05430 CT   
+   1.0 TRP-N:1HB   0.02220 HC   
+   1.0 TRP-N:2HB   0.02220 HC   
+   1.0 TRP-N:CG   -0.16540 C*   
+   1.0 TRP-N:CD1  -0.17880 CW   
+   1.0 TRP-N:HD1   0.21950 H4   
+   1.0 TRP-N:NE1  -0.34440 NA   
+   1.0 TRP-N:HE1   0.34120 H    
+   1.0 TRP-N:CE2   0.15750 CN   
+   1.0 TRP-N:CZ2  -0.27100 CA   
+   1.0 TRP-N:HZ2   0.15890 HA   
+   1.0 TRP-N:CH2  -0.10800 CA   
+   1.0 TRP-N:HH2   0.14110 HA   
+   1.0 TRP-N:CZ3  -0.20340 CA   
+   1.0 TRP-N:HZ3   0.14580 HA   
+   1.0 TRP-N:CE3  -0.22650 CA   
+   1.0 TRP-N:HE3   0.16460 HA   
+   1.0 TRP-N:CD2   0.11320 CB   
+   1.0 TRP-N:C     0.61230 C    
+   1.0 TRP-N:O    -0.57130 O    
+   1.0 PHE-N:N     0.17370 N3   
+   1.0 PHE-N:1H    0.19210 H    
+   1.0 PHE-N:2H    0.19210 H    
+   1.0 PHE-N:3H    0.19210 H    
+   1.0 PHE-N:CA    0.07330 CT   
+   1.0 PHE-N:HA    0.10410 HP   
+   1.0 PHE-N:CB    0.03300 CT   
+   1.0 PHE-N:1HB   0.01040 HC   
+   1.0 PHE-N:2HB   0.01040 HC   
+   1.0 PHE-N:CG    0.00310 CA   
+   1.0 PHE-N:CD1  -0.13920 CA   
+   1.0 PHE-N:HD1   0.13740 HA   
+   1.0 PHE-N:CE1  -0.16020 CA   
+   1.0 PHE-N:HE1   0.14330 HA   
+   1.0 PHE-N:CZ   -0.12080 CA   
+   1.0 PHE-N:HZ    0.13290 HA   
+   1.0 PHE-N:CE2  -0.16030 CA   
+   1.0 PHE-N:HE2   0.14330 HA   
+   1.0 PHE-N:CD2  -0.13910 CA   
+   1.0 PHE-N:HD2   0.13740 HA   
+   1.0 PHE-N:C     0.61230 C    
+   1.0 PHE-N:O    -0.57130 O    
+   1.0 TYR-N:N     0.19400 N3   
+   1.0 TYR-N:1H    0.18730 H    
+   1.0 TYR-N:2H    0.18730 H    
+   1.0 TYR-N:3H    0.18730 H    
+   1.0 TYR-N:CA    0.05700 CT   
+   1.0 TYR-N:HA    0.09830 HP   
+   1.0 TYR-N:CB    0.06590 CT   
+   1.0 TYR-N:1HB   0.01020 HC   
+   1.0 TYR-N:2HB   0.01020 HC   
+   1.0 TYR-N:CG   -0.02050 CA   
+   1.0 TYR-N:CD1  -0.20020 CA   
+   1.0 TYR-N:HD1   0.17200 HA   
+   1.0 TYR-N:CE1  -0.22390 CA   
+   1.0 TYR-N:HE1   0.16500 HA   
+   1.0 TYR-N:CZ    0.31390 C    
+   1.0 TYR-N:OH   -0.55780 OH   
+   1.0 TYR-N:HH    0.40010 HO   
+   1.0 TYR-N:CE2  -0.22390 CA   
+   1.0 TYR-N:HE2   0.16500 HA   
+   1.0 TYR-N:CD2  -0.20020 CA   
+   1.0 TYR-N:HD2   0.17200 HA   
+   1.0 TYR-N:C     0.61230 C    
+   1.0 TYR-N:O    -0.57130 O    
+   1.0 GLU-N:N     0.00170 N3   
+   1.0 GLU-N:1H    0.23910 H    
+   1.0 GLU-N:2H    0.23910 H    
+   1.0 GLU-N:3H    0.23910 H    
+   1.0 GLU-N:CA    0.05880 CT   
+   1.0 GLU-N:HA    0.12020 HP   
+   1.0 GLU-N:CB    0.09090 CT   
+   1.0 GLU-N:1HB  -0.02320 HC   
+   1.0 GLU-N:2HB  -0.02320 HC   
+   1.0 GLU-N:CG   -0.02360 CT   
+   1.0 GLU-N:1HG  -0.03150 HC   
+   1.0 GLU-N:2HG  -0.03150 HC   
+   1.0 GLU-N:CD    0.80870 C    
+   1.0 GLU-N:OE1  -0.81890 O2   
+   1.0 GLU-N:OE2  -0.81890 O2   
+   1.0 GLU-N:C     0.56210 C    
+   1.0 GLU-N:O    -0.58890 O    
+   1.0 ASP-N:N     0.07820 N3   
+   1.0 ASP-N:1H    0.22000 H    
+   1.0 ASP-N:2H    0.22000 H    
+   1.0 ASP-N:3H    0.22000 H    
+   1.0 ASP-N:CA    0.02920 CT   
+   1.0 ASP-N:HA    0.11410 HP   
+   1.0 ASP-N:CB   -0.02350 CT   
+   1.0 ASP-N:1HB  -0.01690 HC   
+   1.0 ASP-N:2HB  -0.01690 HC   
+   1.0 ASP-N:CG    0.81940 C    
+   1.0 ASP-N:OD1  -0.80840 O2   
+   1.0 ASP-N:OD2  -0.80840 O2   
+   1.0 ASP-N:C     0.56210 C    
+   1.0 ASP-N:O    -0.58890 O    
+   1.0 LYS-N:N     0.09660 N3   
+   1.0 LYS-N:1H    0.21650 H    
+   1.0 LYS-N:2H    0.21650 H    
+   1.0 LYS-N:3H    0.21650 H    
+   1.0 LYS-N:CA   -0.00150 CT   
+   1.0 LYS-N:HA    0.11800 HP   
+   1.0 LYS-N:CB    0.02120 CT   
+   1.0 LYS-N:1HB   0.02830 HC   
+   1.0 LYS-N:2HB   0.02830 HC   
+   1.0 LYS-N:CG   -0.00480 CT   
+   1.0 LYS-N:1HG   0.01210 HC   
+   1.0 LYS-N:2HG   0.01210 HC   
+   1.0 LYS-N:CD   -0.06080 CT   
+   1.0 LYS-N:1HD   0.06330 HC   
+   1.0 LYS-N:2HD   0.06330 HC   
+   1.0 LYS-N:CE   -0.01810 CT   
+   1.0 LYS-N:1HE   0.11710 HP   
+   1.0 LYS-N:2HE   0.11710 HP   
+   1.0 LYS-N:NZ   -0.37640 N3   
+   1.0 LYS-N:1HZ   0.33820 H    
+   1.0 LYS-N:2HZ   0.33820 H    
+   1.0 LYS-N:3HZ   0.33820 H    
+   1.0 LYS-N:C     0.72140 C    
+   1.0 LYS-N:O    -0.60130 O    
+   1.0 PRO-N:N    -0.20200 N3
+   1.0 PRO-N:1H    0.31200 H    
+   1.0 PRO-N:2H    0.31200 H    
+   1.0 PRO-N:3H    0.31200 H    
+   1.0 PRO-N:CD   -0.01200 CT   
+   1.0 PRO-N:1HD   0.10000 HP   
+   1.0 PRO-N:2HD   0.10000 HP   
+   1.0 PRO-N:CG   -0.12100 CT   
+   1.0 PRO-N:1HG   0.10000 HC   
+   1.0 PRO-N:2HG   0.10000 HC   
+   1.0 PRO-N:CB   -0.11500 CT   
+   1.0 PRO-N:1HB   0.10000 HC   
+   1.0 PRO-N:2HB   0.10000 HC   
+   1.0 PRO-N:CA    0.10000 CT   
+   1.0 PRO-N:HA    0.10000 HP   
+   1.0 PRO-N:C     0.52600 C    
+   1.0 PRO-N:O    -0.50000 O    
+   1.0 CYS-N:N     0.13250 N3   
+   1.0 CYS-N:1H    0.20230 H    
+   1.0 CYS-N:2H    0.20230 H    
+   1.0 CYS-N:3H    0.20230 H    
+   1.0 CYS-N:CA    0.09270 CT   
+   1.0 CYS-N:HA    0.14110 HP   
+   1.0 CYS-N:CB   -0.11950 CT   
+   1.0 CYS-N:1HB   0.11880 H1   
+   1.0 CYS-N:2HB   0.11880 H1   
+   1.0 CYS-N:SG   -0.32980 SH   
+   1.0 CYS-N:HSG   0.19750 HS   
+   1.0 CYS-N:C     0.61230 C    
+   1.0 CYS-N:O    -0.57130 O    
+   1.0 CYS-NS:N    0.20690 N3   
+   1.0 CYS-NS:1H   0.18150 H    
+   1.0 CYS-NS:2H   0.18150 H    
+   1.0 CYS-NS:3H   0.18150 H    
+   1.0 CYS-NS:CA   0.10550 CT   
+   1.0 CYS-NS:HA   0.09220 HP   
+   1.0 CYS-NS:CB  -0.02770 CT   
+   1.0 CYS-NS:1HB  0.06800 H1   
+   1.0 CYS-NS:2HB  0.06800 H1   
+   1.0 CYS-NS:SG  -0.09840 S    
+   1.0 CYS-NS:C    0.61230 C    
+   1.0 CYS-NS:O   -0.57130 O    
+   1.0 MET-N:N     0.15920 N3   
+   1.0 MET-N:1H    0.19840 H    
+   1.0 MET-N:2H    0.19840 H    
+   1.0 MET-N:3H    0.19840 H    
+   1.0 MET-N:CA    0.02210 CT   
+   1.0 MET-N:HA    0.11160 HP   
+   1.0 MET-N:CB    0.08650 CT   
+   1.0 MET-N:1HB   0.01250 HC   
+   1.0 MET-N:2HB   0.01250 HC   
+   1.0 MET-N:CG    0.03340 CT   
+   1.0 MET-N:1HG   0.02920 H1   
+   1.0 MET-N:2HG   0.02920 H1   
+   1.0 MET-N:SD   -0.27740 S    
+   1.0 MET-N:CE   -0.03410 CT   
+   1.0 MET-N:1HE   0.05970 H1   
+   1.0 MET-N:2HE   0.05970 H1   
+   1.0 MET-N:3HE   0.05970 H1   
+   1.0 MET-N:C     0.61230 C    
+   1.0 MET-N:O    -0.57130 O    
+   1.0 ALA-C:N    -0.38210 N    
+   1.0 ALA-C:H     0.26810 H    
+   1.0 ALA-C:CA   -0.17470 CT   
+   1.0 ALA-C:HA    0.10670 H1   
+   1.0 ALA-C:CB   -0.20930 CT   
+   1.0 ALA-C:1HB   0.07640 HC   
+   1.0 ALA-C:2HB   0.07640 HC   
+   1.0 ALA-C:3HB   0.07640 HC   
+   1.0 ALA-C:C     0.77310 C    
+   1.0 ALA-C:O    -0.80550 O2   
+   1.0 ALA-C:OXT  -0.80550 O2   
+   1.0 GLY-C:N    -0.38210 N    
+   1.0 GLY-C:H     0.26810 H    
+   1.0 GLY-C:CA   -0.24930 CT   
+   1.0 GLY-C:1HA   0.10560 H1   
+   1.0 GLY-C:2HA   0.10560 H1   
+   1.0 GLY-C:C     0.72310 C    
+   1.0 GLY-C:O    -0.78550 O2   
+   1.0 GLY-C:OXT  -0.78550 O2   
+   1.0 SER-C:N    -0.38210 N    
+   1.0 SER-C:H     0.26810 H    
+   1.0 SER-C:CA   -0.27220 CT   
+   1.0 SER-C:HA    0.13040 H1   
+   1.0 SER-C:CB    0.11230 CT   
+   1.0 SER-C:1HB   0.08130 H1   
+   1.0 SER-C:2HB   0.08130 H1   
+   1.0 SER-C:OG   -0.65140 OH   
+   1.0 SER-C:HG    0.44740 HO   
+   1.0 SER-C:C     0.81130 C    
+   1.0 SER-C:O    -0.81320 O2   
+   1.0 SER-C:OXT  -0.81320 O2   
+   1.0 THR-C:N    -0.38210 N    
+   1.0 THR-C:H     0.26810 H    
+   1.0 THR-C:CA   -0.24200 CT   
+   1.0 THR-C:HA    0.12070 H1   
+   1.0 THR-C:CB    0.30250 CT   
+   1.0 THR-C:HB    0.00780 H1   
+   1.0 THR-C:CG2  -0.18530 CT   
+   1.0 THR-C:1HG2  0.05860 HC   
+   1.0 THR-C:2HG2  0.05860 HC   
+   1.0 THR-C:3HG2  0.05860 HC   
+   1.0 THR-C:OG1  -0.64960 OH   
+   1.0 THR-C:HG1   0.41190 HO   
+   1.0 THR-C:C     0.78100 C    
+   1.0 THR-C:O    -0.80440 O2   
+   1.0 THR-C:OXT  -0.80440 O2   
+   1.0 LEU-C:N    -0.38210 N    
+   1.0 LEU-C:H     0.26810 H    
+   1.0 LEU-C:CA   -0.28470 CT   
+   1.0 LEU-C:HA    0.13460 H1   
+   1.0 LEU-C:CB   -0.24690 CT   
+   1.0 LEU-C:1HB   0.09740 HC   
+   1.0 LEU-C:2HB   0.09740 HC   
+   1.0 LEU-C:CG    0.37060 CT   
+   1.0 LEU-C:HG   -0.03740 HC   
+   1.0 LEU-C:CD1  -0.41630 CT   
+   1.0 LEU-C:1HD1  0.10380 HC   
+   1.0 LEU-C:2HD1  0.10380 HC   
+   1.0 LEU-C:3HD1  0.10380 HC   
+   1.0 LEU-C:CD2  -0.41630 CT   
+   1.0 LEU-C:1HD2  0.10380 HC   
+   1.0 LEU-C:2HD2  0.10380 HC   
+   1.0 LEU-C:3HD2  0.10380 HC   
+   1.0 LEU-C:C     0.83260 C    
+   1.0 LEU-C:O    -0.81990 O2   
+   1.0 LEU-C:OXT  -0.81990 O2   
+   1.0 ILE-C:N    -0.38210 N    
+   1.0 ILE-C:H     0.26810 H    
+   1.0 ILE-C:CA   -0.31000 CT   
+   1.0 ILE-C:HA    0.13750 H1   
+   1.0 ILE-C:CB    0.03630 CT   
+   1.0 ILE-C:HB    0.07660 HC   
+   1.0 ILE-C:CG2  -0.34980 CT   
+   1.0 ILE-C:1HG2  0.10210 HC   
+   1.0 ILE-C:2HG2  0.10210 HC   
+   1.0 ILE-C:3HG2  0.10210 HC   
+   1.0 ILE-C:CG1  -0.03230 CT   
+   1.0 ILE-C:1HG1  0.03210 HC   
+   1.0 ILE-C:2HG1  0.03210 HC   
+   1.0 ILE-C:CD1  -0.06990 CT   
+   1.0 ILE-C:1HD1  0.01960 HC   
+   1.0 ILE-C:2HD1  0.01960 HC   
+   1.0 ILE-C:3HD1  0.01960 HC   
+   1.0 ILE-C:C     0.83430 C    
+   1.0 ILE-C:O    -0.81900 O2   
+   1.0 ILE-C:OXT  -0.81900 O2   
+   1.0 NME-C:N      -0.41570 N    
+   1.0 NME-C:H       0.27190 H    
+   1.0 NME-C:CH3    -0.14900 CT   
+   1.0 NME-C:1HH3    0.09760 H1   
+   1.0 NME-C:2HH3    0.09760 H1   
+   1.0 NME-C:3HH3    0.09760 H1   
+   1.0 VAL-C:N    -0.38210 N    
+   1.0 VAL-C:H     0.26810 H    
+   1.0 VAL-C:CA   -0.34380 CT   
+   1.0 VAL-C:HA    0.14380 H1   
+   1.0 VAL-C:CB    0.19400 CT   
+   1.0 VAL-C:HB    0.03080 HC   
+   1.0 VAL-C:CG1  -0.30640 CT   
+   1.0 VAL-C:1HG1  0.08360 HC   
+   1.0 VAL-C:2HG1  0.08360 HC   
+   1.0 VAL-C:3HG1  0.08360 HC   
+   1.0 VAL-C:CG2  -0.30640 CT   
+   1.0 VAL-C:1HG2  0.08360 HC   
+   1.0 VAL-C:2HG2  0.08360 HC   
+   1.0 VAL-C:3HG2  0.08360 HC   
+   1.0 VAL-C:C     0.83500 C    
+   1.0 VAL-C:O    -0.81730 O2   
+   1.0 VAL-C:OXT  -0.81730 O2   
+   1.0 ASN-C:N    -0.38210 N    
+   1.0 ASN-C:H     0.26810 H    
+   1.0 ASN-C:CA   -0.20800 CT   
+   1.0 ASN-C:HA    0.13580 H1   
+   1.0 ASN-C:CB   -0.22990 CT   
+   1.0 ASN-C:1HB   0.10230 HC   
+   1.0 ASN-C:2HB   0.10230 HC   
+   1.0 ASN-C:CG    0.71530 C    
+   1.0 ASN-C:OD1  -0.60100 O    
+   1.0 ASN-C:ND2  -0.90840 N    
+   1.0 ASN-C:1HD2  0.41500 H    
+   1.0 ASN-C:2HD2  0.41500 H    
+   1.0 ASN-C:C     0.80500 C    
+   1.0 ASN-C:O    -0.81470 O2   
+   1.0 ASN-C:OXT  -0.81470 O2   
+   1.0 GLN-C:N    -0.38210 N    
+   1.0 GLN-C:H     0.26810 H    
+   1.0 GLN-C:CA   -0.22480 CT   
+   1.0 GLN-C:HA    0.12320 H1   
+   1.0 GLN-C:CB   -0.06640 CT   
+   1.0 GLN-C:1HB   0.04520 HC   
+   1.0 GLN-C:2HB   0.04520 HC   
+   1.0 GLN-C:CG   -0.02100 CT   
+   1.0 GLN-C:1HG   0.02030 HC   
+   1.0 GLN-C:2HG   0.02030 HC   
+   1.0 GLN-C:CD    0.70930 C    
+   1.0 GLN-C:OE1  -0.60980 O    
+   1.0 GLN-C:NE2  -0.95740 N    
+   1.0 GLN-C:1HE2  0.43040 H    
+   1.0 GLN-C:2HE2  0.43040 H    
+   1.0 GLN-C:C     0.77750 C    
+   1.0 GLN-C:O    -0.80420 O2   
+   1.0 GLN-C:OXT  -0.80420 O2   
+   1.0 ARG-C:N    -0.34810 N    
+   1.0 ARG-C:H     0.27640 H    
+   1.0 ARG-C:CA   -0.30680 CT   
+   1.0 ARG-C:HA    0.14470 H1   
+   1.0 ARG-C:CB   -0.03740 CT   
+   1.0 ARG-C:1HB   0.03710 HC   
+   1.0 ARG-C:2HB   0.03710 HC   
+   1.0 ARG-C:CG    0.07440 CT   
+   1.0 ARG-C:1HG   0.01850 HC   
+   1.0 ARG-C:2HG   0.01850 HC   
+   1.0 ARG-C:CD    0.11140 CT   
+   1.0 ARG-C:1HD   0.04680 H1   
+   1.0 ARG-C:2HD   0.04680 H1   
+   1.0 ARG-C:NE   -0.55640 N2   
+   1.0 ARG-C:HE    0.34790 H    
+   1.0 ARG-C:CZ    0.83680 CA   
+   1.0 ARG-C:NH1  -0.87370 N2   
+   1.0 ARG-C:1HH1  0.44930 H    
+   1.0 ARG-C:2HH1  0.44930 H    
+   1.0 ARG-C:NH2  -0.87370 N2   
+   1.0 ARG-C:1HH2  0.44930 H    
+   1.0 ARG-C:2HH2  0.44930 H    
+   1.0 ARG-C:C     0.85570 C    
+   1.0 ARG-C:O    -0.82660 O2   
+   1.0 ARG-C:OXT  -0.82660 O2   
+   1.0 HIS-C:N    -0.34810 N    
+   1.0 HIS-C:H     0.27640 H    
+   1.0 HIS-C:CA   -0.14450 CT   
+   1.0 HIS-C:HA    0.11150 H1   
+   1.0 HIS-C:CB   -0.08000 CT   
+   1.0 HIS-C:1HB   0.08680 HC   
+   1.0 HIS-C:2HB   0.08680 HC   
+   1.0 HIS-C:CG    0.02980 CC   
+   1.0 HIS-C:ND1  -0.15010 NA   
+   1.0 HIS-C:HD1   0.38830 H    
+   1.0 HIS-C:CE1  -0.02510 CR   
+   1.0 HIS-C:HE1   0.26940 H5   
+   1.0 HIS-C:NE2  -0.16830 NA   
+   1.0 HIS-C:CD2  -0.12560 CW   
+   1.0 HIS-C:HD2   0.23360 H4   
+   1.0 HIS-C:C     0.80320 C    
+   1.0 HIS-C:O    -0.81770 O2   
+   1.0 HIS-C:OXT  -0.81770 O2   
+   1.0 HIS-C:N    -0.34810 N    
+   1.0 HIS-C:H     0.27640 H    
+   1.0 HIS-C:CA   -0.14450 CT   
+   1.0 HIS-C:HA    0.11150 H1   
+   1.0 HIS-C:CB   -0.08000 CT   
+   1.0 HIS-C:1HB   0.08680 HC   
+   1.0 HIS-C:2HB   0.08680 HC   
+   1.0 HIS-C:CG    0.02980 CC   
+   1.0 HIS-C:ND1  -0.15010 NA   
+   1.0 HIS-C:CE1  -0.02510 CR   
+   1.0 HIS-C:HE1   0.26940 H5   
+   1.0 HIS-C:NE2  -0.16830 NA   
+   1.0 HIS-C:HE2   0.39130 H    
+   1.0 HIS-C:CD2  -0.12560 CW   
+   1.0 HIS-C:HD2   0.23360 H4   
+   1.0 HIS-C:C     0.80320 C    
+   1.0 HIS-C:O    -0.81770 O2   
+   1.0 HIS-C:OXT  -0.81770 O2   
+   1.0 HIS-C:N    -0.34810 N    
+   1.0 HIS-C:H     0.27640 H    
+   1.0 HIS-C:CA   -0.14450 CT   
+   1.0 HIS-C:HA    0.11150 H1   
+   1.0 HIS-C:CB   -0.08000 CT   
+   1.0 HIS-C:1HB   0.08680 HC   
+   1.0 HIS-C:2HB   0.08680 HC   
+   1.0 HIS-C:CG    0.02980 CC   
+   1.0 HIS-C:ND1  -0.15010 NA   
+   1.0 HIS-C:HD1   0.38830 H    
+   1.0 HIS-C:CE1  -0.02510 CR   
+   1.0 HIS-C:HE1   0.26940 H5   
+   1.0 HIS-C:NE2  -0.16830 NA   
+   1.0 HIS-C:HE2   0.39130 H    
+   1.0 HIS-C:CD2  -0.12560 CW   
+   1.0 HIS-C:HD2   0.23360 H4   
+   1.0 HIS-C:C     0.80320 C    
+   1.0 HIS-C:O    -0.81770 O2   
+   1.0 HIS-C:OXT  -0.81770 O2   
+   1.0 TRP-C:N    -0.38210 N    
+   1.0 TRP-C:H     0.26810 H    
+   1.0 TRP-C:CA   -0.20840 CT   
+   1.0 TRP-C:HA    0.12720 H1   
+   1.0 TRP-C:CB   -0.07420 CT   
+   1.0 TRP-C:1HB   0.04970 HC   
+   1.0 TRP-C:2HB   0.04970 HC   
+   1.0 TRP-C:CG   -0.07960 C*   
+   1.0 TRP-C:CD1  -0.18080 CW   
+   1.0 TRP-C:HD1   0.20430 H4   
+   1.0 TRP-C:NE1  -0.33160 NA   
+   1.0 TRP-C:HE1   0.34130 H    
+   1.0 TRP-C:CE2   0.12220 CN   
+   1.0 TRP-C:CZ2  -0.25940 CA   
+   1.0 TRP-C:HZ2   0.15670 HA   
+   1.0 TRP-C:CH2  -0.10200 CA   
+   1.0 TRP-C:HH2   0.14010 HA   
+   1.0 TRP-C:CZ3  -0.22870 CA   
+   1.0 TRP-C:HZ3   0.15070 HA   
+   1.0 TRP-C:CE3  -0.18370 CA   
+   1.0 TRP-C:HE3   0.14910 HA   
+   1.0 TRP-C:CD2   0.10780 CB   
+   1.0 TRP-C:C     0.76580 C    
+   1.0 TRP-C:O    -0.80110 O2   
+   1.0 TRP-C:OXT  -0.80110 O2   
+   1.0 PHE-C:N    -0.38210 N    
+   1.0 PHE-C:H     0.26810 H    
+   1.0 PHE-C:CA   -0.18250 CT   
+   1.0 PHE-C:HA    0.10980 H1   
+   1.0 PHE-C:CB   -0.09590 CT   
+   1.0 PHE-C:1HB   0.04430 HC   
+   1.0 PHE-C:2HB   0.04430 HC   
+   1.0 PHE-C:CG    0.05520 CA   
+   1.0 PHE-C:CD1  -0.13000 CA   
+   1.0 PHE-C:HD1   0.14080 HA   
+   1.0 PHE-C:CE1  -0.18470 CA   
+   1.0 PHE-C:HE1   0.14610 HA   
+   1.0 PHE-C:CZ   -0.09440 CA   
+   1.0 PHE-C:HZ    0.12800 HA   
+   1.0 PHE-C:CE2  -0.18470 CA   
+   1.0 PHE-C:HE2   0.14610 HA   
+   1.0 PHE-C:CD2  -0.13000 CA   
+   1.0 PHE-C:HD2   0.14080 HA   
+   1.0 PHE-C:C     0.76600 C    
+   1.0 PHE-C:O    -0.80260 O2   
+   1.0 PHE-C:OXT  -0.80260 O2   
+   1.0 TYR-C:N    -0.38210 N    
+   1.0 TYR-C:H     0.26810 H    
+   1.0 TYR-C:CA   -0.20150 CT   
+   1.0 TYR-C:HA    0.10920 H1   
+   1.0 TYR-C:CB   -0.07520 CT   
+   1.0 TYR-C:1HB   0.04900 HC   
+   1.0 TYR-C:2HB   0.04900 HC   
+   1.0 TYR-C:CG    0.02430 CA   
+   1.0 TYR-C:CD1  -0.19220 CA   
+   1.0 TYR-C:HD1   0.17800 HA   
+   1.0 TYR-C:CE1  -0.24580 CA   
+   1.0 TYR-C:HE1   0.16730 HA   
+   1.0 TYR-C:CZ    0.33950 C    
+   1.0 TYR-C:OH   -0.56430 OH   
+   1.0 TYR-C:HH    0.40170 HO   
+   1.0 TYR-C:CE2  -0.24580 CA   
+   1.0 TYR-C:HE2   0.16730 HA   
+   1.0 TYR-C:CD2  -0.19220 CA   
+   1.0 TYR-C:HD2   0.17800 HA   
+   1.0 TYR-C:C     0.78170 C    
+   1.0 TYR-C:O    -0.80700 O2   
+   1.0 TYR-C:OXT  -0.80700 O2   
+   1.0 GLU-C:N    -0.51920 N    
+   1.0 GLU-C:H     0.30550 H    
+   1.0 GLU-C:CA   -0.20590 CT   
+   1.0 GLU-C:HA    0.13990 H1   
+   1.0 GLU-C:CB    0.00710 CT   
+   1.0 GLU-C:1HB  -0.00780 HC   
+   1.0 GLU-C:2HB  -0.00780 HC   
+   1.0 GLU-C:CG    0.06750 CT   
+   1.0 GLU-C:1HG  -0.05480 HC   
+   1.0 GLU-C:2HG  -0.05480 HC   
+   1.0 GLU-C:CD    0.81830 C    
+   1.0 GLU-C:OE1  -0.82200 O2   
+   1.0 GLU-C:OE2  -0.82200 O2   
+   1.0 GLU-C:C     0.74200 C    
+   1.0 GLU-C:O    -0.79300 O2   
+   1.0 GLU-C:OXT  -0.79300 O2   
+   1.0 ASP-C:N    -0.51920 N    
+   1.0 ASP-C:H     0.30550 H    
+   1.0 ASP-C:CA   -0.18170 CT   
+   1.0 ASP-C:HA    0.10460 H1   
+   1.0 ASP-C:CB   -0.06770 CT   
+   1.0 ASP-C:1HB  -0.02120 HC   
+   1.0 ASP-C:2HB  -0.02120 HC   
+   1.0 ASP-C:CG    0.88510 C    
+   1.0 ASP-C:OD1  -0.81620 O2   
+   1.0 ASP-C:OD2  -0.81620 O2   
+   1.0 ASP-C:C     0.72560 C    
+   1.0 ASP-C:O    -0.78870 O2   
+   1.0 ASP-C:OXT  -0.78870 O2   
+   1.0 LYS-C:N    -0.34810 N    
+   1.0 LYS-C:H     0.27640 H    
+   1.0 LYS-C:CA   -0.29030 CT   
+   1.0 LYS-C:HA    0.14380 H1   
+   1.0 LYS-C:CB   -0.05380 CT   
+   1.0 LYS-C:1HB   0.04820 HC   
+   1.0 LYS-C:2HB   0.04820 HC   
+   1.0 LYS-C:CG    0.02270 CT   
+   1.0 LYS-C:1HG   0.01340 HC   
+   1.0 LYS-C:2HG   0.01340 HC   
+   1.0 LYS-C:CD   -0.03920 CT   
+   1.0 LYS-C:1HD   0.06110 HC   
+   1.0 LYS-C:2HD   0.06110 HC   
+   1.0 LYS-C:CE   -0.01760 CT   
+   1.0 LYS-C:1HE   0.11210 HP   
+   1.0 LYS-C:2HE   0.11210 HP   
+   1.0 LYS-C:NZ   -0.37410 N3   
+   1.0 LYS-C:1HZ   0.33740 H    
+   1.0 LYS-C:2HZ   0.33740 H    
+   1.0 LYS-C:3HZ   0.33740 H    
+   1.0 LYS-C:C     0.84880 C    
+   1.0 LYS-C:O    -0.82520 O2   
+   1.0 LYS-C:OXT  -0.82520 O2   
+   1.0 PRO-C:N    -0.28020 N    
+   1.0 PRO-C:CD    0.04340 CT   
+   1.0 PRO-C:1HD   0.03310 H1   
+   1.0 PRO-C:2HD   0.03310 H1   
+   1.0 PRO-C:CG    0.04660 CT   
+   1.0 PRO-C:1HG   0.01720 HC   
+   1.0 PRO-C:2HG   0.01720 HC   
+   1.0 PRO-C:CB   -0.05430 CT   
+   1.0 PRO-C:1HB   0.03810 HC   
+   1.0 PRO-C:2HB   0.03810 HC   
+   1.0 PRO-C:CA   -0.13360 CT   
+   1.0 PRO-C:HA    0.07760 H1   
+   1.0 PRO-C:C     0.66310 C    
+   1.0 PRO-C:O    -0.76970 O2   
+   1.0 PRO-C:OXT  -0.76970 O2   
+   1.0 CYS-C:N    -0.38210 N    
+   1.0 CYS-C:H     0.26810 H    
+   1.0 CYS-C:CA   -0.16350 CT   
+   1.0 CYS-C:HA    0.13960 H1   
+   1.0 CYS-C:CB   -0.19960 CT   
+   1.0 CYS-C:1HB   0.14370 H1   
+   1.0 CYS-C:2HB   0.14370 H1   
+   1.0 CYS-C:SG   -0.31020 SH   
+   1.0 CYS-C:HSG   0.20680 HS   
+   1.0 CYS-C:C     0.74970 C    
+   1.0 CYS-C:O    -0.79810 O2   
+   1.0 CYS-C:OXT  -0.79810 O2   
+   1.0 CYS-CS:N   -0.38210 N    
+   1.0 CYS-CS:H    0.26810 H    
+   1.0 CYS-CS:CA  -0.13180 CT   
+   1.0 CYS-CS:HA   0.09380 H1   
+   1.0 CYS-CS:CB  -0.19430 CT   
+   1.0 CYS-CS:1HB  0.12280 H1   
+   1.0 CYS-CS:2HB  0.12280 H1   
+   1.0 CYS-CS:SG  -0.05290 S    
+   1.0 CYS-CS:C    0.76180 C    
+   1.0 CYS-CS:O   -0.80410 O2   
+   1.0 CYS-CS:OXT -0.80410 O2   
+   1.0 MET-C:N    -0.38210 N    
+   1.0 MET-C:H     0.26810 H    
+   1.0 MET-C:CA   -0.25970 CT   
+   1.0 MET-C:HA    0.12770 H1   
+   1.0 MET-C:CB   -0.02360 CT   
+   1.0 MET-C:1HB   0.04800 HC   
+   1.0 MET-C:2HB   0.04800 HC   
+   1.0 MET-C:CG    0.04920 CT   
+   1.0 MET-C:1HG   0.03170 H1   
+   1.0 MET-C:2HG   0.03170 H1   
+   1.0 MET-C:SD   -0.26920 S    
+   1.0 MET-C:CE   -0.03760 CT   
+   1.0 MET-C:1HE   0.06250 H1   
+   1.0 MET-C:2HE   0.06250 H1   
+   1.0 MET-C:3HE   0.06250 H1   
+   1.0 MET-C:C     0.80130 C    
+   1.0 MET-C:O    -0.81050 O2   
+   1.0 MET-C:OXT  -0.81050 O2   
+   1.0 CA:CA       2.00000 C0
+   1.0 MG:MG       2.00000 MG
+   1.0 CH4-M:C       0.00000 CT
+   1.0 CH4-M:1H      0.00000 H1
+   1.0 CH4-M:2H      0.00000 H1
+   1.0 CH4-M:3H      0.00000 H1
+   1.0 CH4-M:4H      0.00000 H1
+   1.0 PCA:N      -0.720984 N
+   1.0 PCA:H       0.374677 H
+   1.0 PCA:CA     -0.025874 CT
+   1.0 PCA:C       0.865161 C
+   1.0 PCA:O      -0.798202 O
+   1.0 PCA:CB      0.114954 CT
+   1.0 PCA:CG     -0.126748 CT
+   1.0 PCA:CD      0.770356 C
+   1.0 PCA:OE     -0.682912 O
+   1.0 PCA:HA      0.039708 H1
+   1.0 PCA:1HB     0.000266 HC
+   1.0 PCA:2HB    -0.031861 HC
+   1.0 PCA:1HG     0.034072 HC
+   1.0 PCA:2HG     0.025655 HC
+   1.0 PCA:OXT    -0.838268 O
+   1.0 PCA-N:N      -0.720984 N
+   1.0 PCA-N:H       0.374677 H
+   1.0 PCA-N:CA     -0.025874 CT
+   1.0 PCA-N:C       0.865161 C
+   1.0 PCA-N:O      -0.798202 O
+   1.0 PCA-N:CB      0.114954 CT
+   1.0 PCA-N:CG     -0.126748 CT
+   1.0 PCA-N:CD      0.770356 C
+   1.0 PCA-N:OE     -0.682912 O
+   1.0 PCA-N:HA      0.039708 H1
+   1.0 PCA-N:1HB     0.000266 HC
+   1.0 PCA-N:2HB    -0.031861 HC
+   1.0 PCA-N:1HG     0.034072 HC
+   1.0 PCA-N:2HG     0.025655 HC
+   1.0 PCA-M:N      -0.720984 N
+   1.0 PCA-M:H       0.374677 H
+   1.0 PCA-M:CA     -0.025874 CT
+   1.0 PCA-M:C       0.865161 C
+   1.0 PCA-M:O      -0.798202 O
+   1.0 PCA-M:CB      0.114954 CT
+   1.0 PCA-M:CG     -0.126748 CT
+   1.0 PCA-M:CD      0.770356 C
+   1.0 PCA-M:OE     -0.682912 O
+   1.0 PCA-M:HA      0.039708 H1
+   1.0 PCA-M:1HB     0.000266 HC
+   1.0 PCA-M:2HB    -0.031861 HC
+   1.0 PCA-M:1HG     0.034072 HC
+   1.0 PCA-M:2HG     0.025655 HC
+   1.0 PCA-M:OXT    -0.838268 O
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/CMakeLists.txt	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,54 @@
+# 2008-03-15
+
+set(to_install
+    aromatic.txt
+    atomtyp.txt
+    babel_povray3.inc
+    bondtyp.txt
+    element.txt
+    fragments.txt
+    gaff.dat
+    gaff.prm
+    ghemical.prm
+    isotope-small.txt
+    isotope.txt
+    logp.txt
+    MACCS.txt
+    mmff94.ff
+    mmff94s.ff
+    mmffang.par
+    mmffbndk.par
+    mmffbond.par
+    mmffchg.par
+    mmffdef.par
+    mmffdfsb.par
+    mmffoop.par
+    mmffpbci.par
+    mmffprop.par
+    mmffstbn.par
+    mmfftor.par
+    mmffvdw.par
+    mmffs_oop.par
+    mmffs_tor.par
+    mr.txt
+    patterns.txt
+    phmodel.txt
+    plugindefines.txt
+    psa.txt
+    qeq.txt
+    resdata.txt
+    ringtyp.txt
+    SMARTS_InteLigand.txt
+    space-groups.txt
+    superatom.txt
+    svgformat.script
+    torlib.txt
+    types.txt
+    UFF.prm
+)
+
+if(NOT MSVC)
+  install(FILES ${to_install} DESTINATION share/openbabel/${BABEL_VERSION})
+else(NOT MSVC)
+  install(FILES ${to_install} DESTINATION bin/data)
+endif(NOT MSVC)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/MACCS.txt	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,199 @@
+#Comments after SMARTS
+# Extracted from RDKit r1553 Nov 2010 rdkit/Chem/MACCSKeys.py
+#
+# Copyright (C) 2001-2008 greg Landrum and Rational Discovery LLC
+#
+#   @@ All Rights Reserved @@
+#  This file is part of the RDKit.
+#  The contents are covered by the terms of the BSD license
+#  which is included in the file license.txt, found at the root
+#  of the RDKit source tree.
+#
+# SMARTS definitions for the publically available MACCS keys
+
+# I compared the MACCS fingerprints generated here with those from two
+# other packages (not MDL, unfortunately). Of course there are
+# disagreements between the various fingerprints still, but I think
+# these definitions work pretty well. Some notes:
+
+# 1) most of the differences have to do with aromaticity
+# 2) there's a discrepancy sometimes because the current RDKit
+# definitions do not require multiple matches to be distinct. e.g. the
+# SMILES C(=O)CC(=O) can match the (hypothetical) key O=CC twice in my
+# definition. It's not clear to me what the correct behavior is.
+# 3) Some keys are not fully defined in the MDL documentation
+# 4) Two keys, 125 and 166, have to be done outside of SMARTS.
+# 5) Key 1 (ISOTOPE) isn't defined
+
+# these are SMARTS patterns corresponding to the MDL MACCS keys
+  1:('?',0), # ISOTOPE
+  #2:('[#103,#104,#105,#106,#107,#106,#109,#110,#111,#112]',0),  # ISOTOPE Not complete
+  2:('[#103,#104]',0),  # ISOTOPE Not complete
+  3:('[Ge,As,Se,Sn,Sb,Te,Tl,Pb,Bi]',0), # Group IVa,Va,VIa Periods 4-6 (Ge...)  *NOTE* spec wrong
+  4:('[Ac,Th,Pa,U,Np,Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr]',0), # actinide
+  5:('[Sc,Ti,Y,Zr,Hf]',0), # Group IIIB,IVB (Sc...)  *NOTE* spec wrong
+  6:('[La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu]',0), # Lanthanide
+  7:('[V,Cr,Mn,Nb,Mo,Tc,Ta,W,Re]',0), # Group VB,VIB,VIIB (V...) *NOTE* spec wrong
+  8:('[!#6;!#1]1~*~*~*~1',0), # QAAA@1
+  9:('[Fe,Co,Ni,Ru,Rh,Pd,Os,Ir,Pt]',0), # Group VIII (Fe...)
+  10:('[Be,Mg,Ca,Sr,Ba,Ra]',0), # Group IIa (Alkaline earth)
+  11:('*1~*~*~*~1',0), # 4M Ring
+  12:('[Cu,Zn,Ag,Cd,Au,Hg]',0), # Group IB,IIB (Cu..)
+  13:('[#8]~[#7](~[#6])~[#6]',0), # ON(C)C
+  14:('[#16]-[#16]',0), # S-S
+  15:('[#8]~[#6](~[#8])~[#8]',0), # OC(O)O
+  16:('[!#6;!#1]1~*~*~1',0), # QAA@1
+  17:('[#6]#[#6]',0), #CTC
+  18:('[B,Al,Ga,In,Tl]',0), # Group IIIA (B...) *NOTE* spec wrong
+  19:('*1~*~*~*~*~*~*~1',0), # 7M Ring
+  20:('[Si]',0), #Si
+  21:('[#6]=[#6](~[!#6;!#1])~[!#6;!#1]',0), # C=C(Q)Q
+  22:('*1~*~*~1',0), # 3M Ring
+  23:('[#7]~[#6](~[#8])~[#8]',0), # NC(O)O
+  24:('[#7]-[#8]',0), # N-O
+  25:('[#7]~[#6](~[#7])~[#7]',0), # NC(N)N
+  26:('[#6]=;@[#6](@*)@*',0), # C$=C($A)$A
+  27:('[I]',0), # I
+  28:('[!#6;!#1]~[CH2]~[!#6;!#1]',0), # QCH2Q
+  29:('[#15]',0),# P
+  30:('[#6]~[!#6;!#1](~[#6])(~[#6])~*',0), # CQ(C)(C)A
+  31:('[!#6;!#1]~[F,Cl,Br,I]',0), # QX
+  32:('[#6]~[#16]~[#7]',0), # CSN
+  33:('[#7]~[#16]',0), # NS
+  34:('[CH2]=*',0), # CH2=A
+  35:('[Li,Na,K,Rb,Cs,Fr]',0), # Group IA (Alkali Metal)
+  36:('[#16R]',0), # S Heterocycle
+  37:('[#7]~[#6](~[#8])~[#7]',0), # NC(O)N
+  38:('[#7]~[#6](~[#6])~[#7]',0), # NC(C)N
+  39:('[#8]~[#16](~[#8])~[#8]',0), # OS(O)O
+  40:('[#16]-[#8]',0), # S-O
+  41:('[#6]#[#7]',0), # CTN
+  42:('F',0), # F
+  43:('[!C;!c;!#1;!H0]~*~[!C;!c;!#1;!H0]',0), # QHAQH
+  44:('?',0), # OTHER
+  45:('[#6]=[#6]~[#7]',0), # C=CN
+  46:('Br',0), # BR
+  47:('[#16]~*~[#7]',0), # SAN
+  48:('[#8]~[!#6;!#1](~[#8])(~[#8])',0), # OQ(O)O
+  49:('[!+0]',0), # CHARGE  
+  50:('[#6]=[#6](~[#6])~[#6]',0), # C=C(C)C
+  51:('[#6]~[#16]~[#8]',0), # CSO
+  52:('[#7]~[#7]',0), # NN
+  53:('[!#6;!#1;!H0]~*~*~*~[!#6;!#1;!H0]',0), # QHAAAQH
+  54:('[!#6;!#1;!H0]~*~*~[!#6;!#1;!H0]',0), # QHAAQH
+  55:('[#8]~[#16]~[#8]',0), #OSO
+  56:('[#8]~[#7](~[#8])~[#6]',0), # ON(O)C
+  57:('[#8R]',0), # O Heterocycle
+  58:('[!#6;!#1]~[#16]~[!#6;!#1]',0), # QSQ
+  59:('[#16]!:*:*',0), # Snot%A%A
+  60:('[#16]=[#8]',0), # S=O
+  61:('*~[#16](~*)~*',0), # AS(A)A
+  62:('*@*!@*@*',0), # A$!A$A
+  63:('[#7]=[#8]',0), # N=O
+  64:('*@*!@[#16]',0), # A$A!S
+  65:('c:n',0), # C%N
+  66:('[#6]~[#6](~[#6])(~[#6])~*',0), # CC(C)(C)A
+  67:('[!#6;!#1]~[#16]',0), # QS
+  68:('[!#6;!#1;!H0]~[!#6;!#1;!H0]',0), # QHQH (&...) FIX: incomplete definition
+  69:('[!#6;!#1]~[!#6;!#1;!H0]',0), # QQH
+  70:('[!#6;!#1]~[#7]~[!#6;!#1]',0), # QNQ
+  71:('[#7]~[#8]',0), # NO
+  72:('[#8]~*~*~[#8]',0), # OAAO
+  73:('[#16]=*',0), # S=A
+  74:('[CH3]~*~[CH3]',0), # CH3ACH3
+  75:('*!@[#7]@*',0), # A!N$A
+  76:('[#6]=[#6](~*)~*',0), # C=C(A)A
+  77:('[#7]~*~[#7]',0), # NAN
+  78:('[#6]=[#7]',0), # C=N
+  79:('[#7]~*~*~[#7]',0), # NAAN
+  80:('[#7]~*~*~*~[#7]',0), # NAAAN
+  81:('[#16]~*(~*)~*',0), # SA(A)A
+  82:('*~[CH2]~[!#6;!#1;!H0]',0), # ACH2QH
+  83:('[!#6;!#1]1~*~*~*~*~1',0), # QAAAA@1
+  84:('[NH2]',0), #NH2
+  85:('[#6]~[#7](~[#6])~[#6]',0), # CN(C)C
+  86:('[C;H2,H3][!#6;!#1][C;H2,H3]',0), # CH2QCH2
+  87:('[F,Cl,Br,I]!@*@*',0), # X!A$A
+  88:('[#16]',0), # S
+  89:('[#8]~*~*~*~[#8]',0), # OAAAO
+  90:('[$([!#6;!#1;!H0]~*~*~[CH2]~*),$([!#6;!#1;!H0;R]1@[R]@[R]@[CH2;R]1),$([!#6;!#1;!H0]~[R]1@[R]@[CH2;R]1)]',0), # QHAACH2A
+  91:('[$([!#6;!#1;!H0]~*~*~*~[CH2]~*),$([!#6;!#1;!H0;R]1@[R]@[R]@[R]@[CH2;R]1),$([!#6;!#1;!H0]~[R]1@[R]@[R]@[CH2;R]1),$([!#6;!#1;!H0]~*~[R]1@[R]@[CH2;R]1)]',0), # QHAAACH2A
+  92:('[#8]~[#6](~[#7])~[#6]',0), # OC(N)C
+  93:('[!#6;!#1]~[CH3]',0), # QCH3
+  94:('[!#6;!#1]~[#7]',0), # QN
+  95:('[#7]~*~*~[#8]',0), # NAAO
+  96:('*1~*~*~*~*~1',0), # 5 M ring
+  97:('[#7]~*~*~*~[#8]',0), # NAAAO
+  98:('[!#6;!#1]1~*~*~*~*~*~1',0), # QAAAAA@1
+  99:('[#6]=[#6]',0), # C=C
+  100:('*~[CH2]~[#7]',0), # ACH2N
+  101:('[$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1)]',0), # 8M Ring or larger. This only handles up to ring sizes of 14
+  102:('[!#6;!#1]~[#8]',0), # QO
+  103:('Cl',0), # CL
+  104:('[!#6;!#1;!H0]~*~[CH2]~*',0), # QHACH2A
+  105:('*@*(@*)@*',0), # A$A($A)$A
+  106:('[!#6;!#1]~*(~[!#6;!#1])~[!#6;!#1]',0), # QA(Q)Q
+  107:('[F,Cl,Br,I]~*(~*)~*',0), # XA(A)A
+  108:('[CH3]~*~*~*~[CH2]~*',0), # CH3AAACH2A
+  109:('*~[CH2]~[#8]',0), # ACH2O
+  110:('[#7]~[#6]~[#8]',0), # NCO
+  111:('[#7]~*~[CH2]~*',0), # NACH2A
+  112:('*~*(~*)(~*)~*',0), # AA(A)(A)A
+  113:('[#8]!:*:*',0), # Onot%A%A
+  114:('[CH3]~[CH2]~*',0), # CH3CH2A
+  115:('[CH3]~*~[CH2]~*',0), # CH3ACH2A
+  116:('[$([CH3]~*~*~[CH2]~*),$([CH3]~*1~*~[CH2]1)]',0), # CH3AACH2A
+  117:('[#7]~*~[#8]',0), # NAO
+  118:('[$(*~[CH2]~[CH2]~*),$(*1~[CH2]~[CH2]1)]',1), # ACH2CH2A > 1
+  119:('[#7]=*',0), # N=A
+  120:('[!#6;R]',1), # Heterocyclic atom > 1 (&...) FIX: incomplete definition
+  121:('[#7;R]',0), # N Heterocycle
+  122:('*~[#7](~*)~*',0), # AN(A)A
+  123:('[#8]~[#6]~[#8]',0), # OCO
+  124:('[!#6;!#1]~[!#6;!#1]',0), # QQ
+  125:('?',0), # Aromatic Ring > 1
+  126:('*!@[#8]!@*',0), # A!O!A
+  127:('*@*!@[#8]',1), # A$A!O > 1 (&...) FIX: incomplete definition
+  128:('[$(*~[CH2]~*~*~*~[CH2]~*),$([R]1@[CH2;R]@[R]@[R]@[R]@[CH2;R]1),$(*~[CH2]~[R]1@[R]@[R]@[CH2;R]1),$(*~[CH2]~*~[R]1@[R]@[CH2;R]1)]',0), # ACH2AAACH2A
+  129:('[$(*~[CH2]~*~*~[CH2]~*),$([R]1@[CH2]@[R]@[R]@[CH2;R]1),$(*~[CH2]~[R]1@[R]@[CH2;R]1)]',0), # ACH2AACH2A
+  130:('[!#6;!#1]~[!#6;!#1]',1), # QQ > 1 (&...)  FIX: incomplete definition
+  131:('[!#6;!#1;!H0]',1), # QH > 1
+  132:('[#8]~*~[CH2]~*',0), # OACH2A
+  133:('*@*!@[#7]',0), # A$A!N
+  134:('[F,Cl,Br,I]',0), # X (HALOGEN)
+  135:('[#7]!:*:*',0), # Nnot%A%A
+  136:('[#8]=*',1), # O=A>1 
+  137:('[!C;!c;R]',0), # Heterocycle
+  138:('[!#6;!#1]~[CH2]~*',1), # QCH2A>1 (&...) FIX: incomplete definition
+  139:('[O;!H0]',0), # OH
+  140:('[#8]',3), # O > 3 (&...) FIX: incomplete definition
+  141:('[CH3]',2), # CH3 > 2  (&...) FIX: incomplete definition
+  142:('[#7]',1), # N > 1
+  143:('*@*!@[#8]',0), # A$A!O
+  144:('*!:*:*!:*',0), # Anot%A%Anot%A
+  145:('*1~*~*~*~*~*~1',1), # 6M ring > 1
+  146:('[#8]',2), # O > 2
+  147:('[$(*~[CH2]~[CH2]~*),$([R]1@[CH2;R]@[CH2;R]1)]',0), # ACH2CH2A
+  148:('*~[!#6;!#1](~*)~*',0), # AQ(A)A
+  149:('[C;H3,H4]',1), # CH3 > 1
+  150:('*!@*@*!@*',0), # A!A$A!A
+  151:('[#7;!H0]',0), # NH
+  152:('[#8]~[#6](~[#6])~[#6]',0), # OC(C)C
+  153:('[!#6;!#1]~[CH2]~*',0), # QCH2A
+  154:('[#6]=[#8]',0), # C=O
+  155:('*!@[CH2]!@*',0), # A!CH2!A
+  156:('[#7]~*(~*)~*',0), # NA(A)A
+  157:('[#6]-[#8]',0), # C-O
+  158:('[#6]-[#7]',0), # C-N
+  159:('[#8]',1), # O>1
+  160:('[C;H3,H4]',0), #CH3
+  161:('[#7]',0), # N
+  162:('a',0), # Aromatic
+  163:('*1~*~*~*~*~*~1',0), # 6M Ring
+  164:('[#8]',0), # O
+  165:('[R]',0), # Ring
+  166:('?',0), # Fragments  FIX: this can't be done in SMARTS
+
+# obabel -:"CNO" -oftp -xs
+# 24: N-O	68: QHQH (&...) 	69: QQH	71: NO	93: QCH3	94: QN	102: QO
+# 124: QQ	131: QH > 1	*2  139: OH	151: NH	158: C-N	160: CH3	161: N	164: O	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/Makefile	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,178 @@
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+# because they might be regenerated.
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/SMARTS_InteLigand.txt	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,983 @@
+#
+#              SMARTS Patterns for Functional Group Classification 
+#
+#              written by Christian Laggner 
+#              Copyright 2005 Inte:Ligand Software-Entwicklungs und Consulting GmbH
+#
+#              Released under the Lesser General Public License (LGPL license)
+#              see http://www.gnu.org/copyleft/lesser.html
+#              Modified from Version 221105
+#####################################################################################################
+
+# General Stuff:
+# These patters were written in an attempt to represent the classification of organic compounds 
+# from the viewpoint of an organic chemist.
+# They are often very restrictive. This may be generally a good thing, but it also takes some time
+# for filtering/indexing large compound sets. 
+# For filtering undesired groups (in druglike compounds) one will want to have more general patterns 
+# (e.g. you don't want *any* halide of *any* acid, *neither* aldehyde *nor* formyl esters and amides, ...). 
+#
+
+# Part I: Carbon 
+# ==============
+
+
+# I.1: Carbon-Carbon Bonds
+# ------------------------
+
+# I.1.1 Alkanes:
+
+Primary_carbon: [CX4H3][#6]
+
+Secondary_carbon: [CX4H2]([#6])[#6]
+
+Tertiary_carbon: [CX4H1]([#6])([#6])[#6]
+
+Quaternary_carbon: [CX4]([#6])([#6])([#6])[#6]
+
+
+# I.1.2 C-C double and Triple Bonds
+
+Alkene: [CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])] 
+# sp2 C may be substituted only by C or H - 
+# does not hit ketenes and allenes, nor enamines, enols and the like
+
+Alkyne: [CX2]#[CX2]
+# non-carbon substituents (e.g. alkynol ethers) are rather rare, thus no further discrimination
+
+Allene: [CX3]=[CX2]=[CX3]
+
+
+# I.2: One Carbon-Hetero Bond
+# ---------------------------
+
+
+# I.2.1 Alkyl Halogenides
+
+Alkylchloride: [ClX1][CX4]
+# will also hit chloromethylethers and the like, but no chloroalkenes, -alkynes or -aromats 
+# a more restrictive version can be obtained by modifying the Alcohol string.
+
+Alkylfluoride: [FX1][CX4]
+
+Alkylbromide: [BrX1][CX4]
+
+Alkyliodide: [IX1][CX4]
+
+
+# I.2.2 Alcohols and Ethers
+
+Alcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])]
+# nonspecific definition, no acetals, aminals, and the like
+
+Primary_alcohol: [OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])]
+
+Secondary_alcohol: [OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])]
+
+Tertiary_alcohol: [OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])]
+
+Dialkylether: [OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]
+# no acetals and the like; no enolethers
+
+Dialkylthioether: [SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]
+# no acetals and the like; no enolethers
+
+Alkylarylether: [OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]
+# no acetals and the like; no enolethers
+
+Diarylether: [c][OX2][c]
+
+Alkylarylthioether: [SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]
+
+Diarylthioether: [c][SX2][c]
+
+Oxonium: [O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])]
+# can't be aromatic, thus O and not #8
+
+# I.2.3 Amines
+
+Amine: [NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])]
+# hits all amines (prim/sec/tert/quart), including ammonium salts, also enamines, but not amides, imides, aminals, ...
+
+# the following amines include also the protonated forms 
+
+Primary_aliph_amine: [NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
+
+Secondary_aliph_amine: [NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
+
+Tertiary_aliph_amine: [NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
+
+Quaternary_aliph_ammonium: [NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
+
+Primary_arom_amine: [NX3H2+0,NX4H3+]c
+
+Secondary_arom_amine: [NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
+
+Tertiary_arom_amine: [NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
+
+Quaternary_arom_ammonium: [NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
+
+Secondary_mixed_amine: [NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])]
+
+Tertiary_mixed_amine: [NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])]
+
+Quaternary_mixed_ammonium: [NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])]
+
+Ammonium: [N+;!$([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])]
+# only C and H substituents allowed. Quaternary or protonated amines
+# NX4+ or Nv4+ is not recognized by Daylight's depictmatch if less than four C are present
+
+
+# I.2.4 Others
+
+Alkylthiol: [SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])]
+
+Dialkylthioether: [SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])]
+
+Alkylarylthioether: [SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])]
+
+Disulfide: [SX2D2][SX2D2]
+
+1,2-Aminoalcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])]
+# does not hit alpha-amino acids, enaminoalcohols, 1,2-aminoacetals, o-aminophenols, etc.
+
+1,2-Diol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H]
+# does not hit alpha-hydroxy acids, enolalcohols, 1,2-hydroxyacetals, 1,2-diphenols, etc.
+
+1,1-Diol: [OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H]
+
+Hydroperoxide: [OX2H][OX2]
+#does not neccessarily have to be connected to a carbon atom, includes also hydrotrioxides
+
+Peroxo: [OX2D2][OX2D2]
+
+Organolithium_compounds: [LiX1][#6,#14]
+
+Organomagnesium_compounds: [MgX2][#6,#14]
+# not restricted to Grignard compounds, also dialkyl Mg
+
+Organometallic_compounds: [!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-]
+# very general, includes all metals covalently bound to carbon 
+
+
+# I.3: Two Carbon-Hetero Bonds (Carbonyl and Derivatives)
+# ----------------------------
+
+# I.3.1 Double Bond to Hetero
+
+Aldehyde: [$([CX3H][#6]),$([CX3H2])]=[OX1]
+# hits aldehydes including formaldehyde
+
+Ketone: [#6][CX3](=[OX1])[#6]
+# does not include oxo-groups connected to a (hetero-) aromatic ring
+
+Thioaldehyde: [$([CX3H][#6]),$([CX3H2])]=[SX1]
+
+Thioketone: [#6][CX3](=[SX1])[#6]
+# does not include thioxo-groups connected to a (hetero-) aromatic ring
+
+Imine: [NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])]
+# nitrogen is not part of an amidelike strukture, nor of an aromatic ring, but can be part of an aminal or similar
+
+Immonium: [NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])]
+
+Oxime: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H]
+
+Oximether: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])]
+# ether, not ester or amide; does not hit isoxazole
+
+
+# I.3.2. Two Single Bonds to Hetero
+
+Acetal: [OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]
+# does not hit hydroxy-methylesters, ketenacetals, hemiacetals, orthoesters, etc.
+
+Hemiacetal: [OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]
+
+Aminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6] 
+# Ns are not part of an amide or similar. v3 ist to exclude nitro and similar groups
+
+Hemiaminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H]
+
+Thioacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])]
+
+Thiohemiacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H]
+
+Halogen_acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]
+# hits chloromethylenethers and other reactive alkylating agents
+
+Acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
+# includes all of the above and other combinations (S-C-N, hydrates, ...), but still no aminomethylenesters and similar
+
+Halogenmethylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]
+# also reactive alkylating agents. Acid does not have to be carboxylic acid, also S- and P-based acids allowed
+
+NOS_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
+# Same as above, but N,O or S instead of halogen. Ester/amide allowed only on one side 
+
+Hetero_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]
+# Combination of the last two patterns
+
+Cyanhydrine: [NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H]
+
+
+# I.3.3 Single Bond to Hetero, C=C Double Bond (Enols and Similar)
+
+Chloroalkene: [ClX1][CX3]=[CX3]
+
+Fluoroalkene: [FX1][CX3]=[CX3]
+
+Bromoalkene: [BrX1][CX3]=[CX3]
+
+Iodoalkene: [IX1][CX3]=[CX3]
+
+Enol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3]
+# no phenols
+
+Endiol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H]
+# no 1,2-diphenols, ketenacetals, ...
+
+Enolether: [OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3]
+# finds also endiodiethers, but not enolesters, no aromats
+
+Enolester: [OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])]
+
+
+Enamine: [NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3]
+# does not hit amines attached to aromatic rings, nor may the nitrogen be aromatic
+
+Thioenol: [SX2H][CX3;$([H1]),$(C[#6])]=[CX3]
+
+Thioenolether: [SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3]
+
+
+# I.4: Three Carbon-Hetero Bonds (Carboxyl and Derivatives)
+# ------------------------------
+
+Acylchloride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1] 
+
+Acylfluoride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1] 
+
+Acylbromide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1] 
+
+Acyliodide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1]
+
+Acylhalide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1]
+# all of the above
+
+
+# The following contains all simple carboxylic combinations of O, N, S, & Hal -
+# - acids, esters, amides, ... as well as a few extra cases (anhydride, hydrazide...)
+# Cyclic structures (including aromats) like lactones, lactames, ... got their own  
+# definitions. Structures where both heteroatoms are part of an aromatic ring  
+# (oxazoles, imidazoles, ...) were excluded.
+
+Carboxylic_acid: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])]
+# includes carboxylate anions
+
+Carboxylic_ester:  [CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
+# does not hit anhydrides or lactones
+
+Lactone: [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
+# may also be aromatic
+
+Carboxylic_anhydride: [CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1])
+# anhydride formed by two carboxylic acids, no mixed anhydrides (e.g. between carboxylic acid and sulfuric acid); may be part of a ring, even aromatic
+
+Carboxylic_acid_derivative: [$([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6]
+# includes most of the structures of I.4 and many more, also 1,3-heteroaromatics such as isoxazole
+
+Carbothioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])]
+# hits both tautomeric forms, as well as anions
+
+Carbothioic_S_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])]
+
+Carbothioic_S_lactone: [#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])]
+# may also be aromatic
+
+Carbothioic_O_ester: [CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])]
+
+Carbothioic_O_lactone: [#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])]
+
+Carbothioic_halide: [CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1]
+
+Carbodithioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])]
+
+Carbodithioic_ester: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])]
+
+Carbodithiolactone: [#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])]
+
+
+Amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+# does not hit lactames
+
+Primary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2]
+
+Secondary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])]
+
+Tertiary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])]
+
+Lactam: [#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+# cyclic amides, may also be aromatic
+
+Alkyl_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])
+# may be part of a ring, even aromatic. only C allowed at central N. May also be triacyl amide
+
+N_hetero_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])
+# everything else than H or C at central N
+
+Imide_acidic: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1])
+# can be deprotonated
+
+Thioamide: [$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+# does not hit thiolactames
+
+Thiolactam: [#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+# cyclic thioamides, may also be aromatic
+
+
+Oximester: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])]
+# may also be part of a ring / aromatic
+
+Amidine: [NX3;!$(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])]
+# only basic amidines, not as part of aromatic ring (e.g. imidazole)
+
+Hydroxamic_acid: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])]
+
+Hydroxamic_acid_ester: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])]
+# does not hit anhydrides of carboxylic acids withs hydroxamic acids
+
+
+Imidoacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
+# not cyclic 
+
+Imidoacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]  
+# the enamide-form of lactames. may be aromatic like 2-hydroxypyridine 
+
+Imidoester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]
+# esters of the above structures. no anhydrides. 
+
+Imidolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]
+# no oxazoles and similar
+
+Imidothioacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]
+# not cyclic 
+
+Imidothioacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]  
+# the enamide-form of thiolactames. may be aromatic like 2-thiopyridine 
+
+Imidothioester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]
+# thioesters of the above structures. no anhydrides. 
+
+Imidothiolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]
+# no thioxazoles and similar
+
+Amidine: [#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])]
+# only basic amidines, not substituted by carbonyl or thiocarbonyl, not as part of a ring 
+
+Imidolactam: [#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])]  
+# one of the two C~N bonds is part of a ring (may be aromatic), but not both - thus no imidazole
+
+Imidoylhalide: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]
+# not cyclic
+
+Imidoylhalide_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]
+# may also be aromatic
+ 
+# may be ring, aromatic, substituted with carbonyls, hetero, ...
+# (everything else would get too complicated)
+
+Amidrazone: [$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])]
+# hits both tautomers. as above, it may be ring, aromatic, substituted with carbonyls, hetero, ...
+
+
+Alpha_aminoacid: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-]
+# N may be alkylated, but not part of an amide (as in peptides), ionic forms are included
+# includes also non-natural aminoacids with double-bonded or two aliph./arom. substituents at alpha-C 
+# N may not be aromatic as in 1H-pyrrole-2-carboxylic acid
+
+Alpha_hydroxyacid: [OX2H][C][CX3](=[OX1])[OX2H,OX1-]
+
+Peptide_middle: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]
+# finds peptidic structures which are neither C- nor N-terminal. Both neighbours must be amino-acids/peptides
+
+Peptide_C_term: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-]
+# finds C-terminal amino acids
+
+Peptide_N_term: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]
+# finds N-terminal amino acids. As above, N may be substituted, but not part of an amide-bond.
+
+
+Carboxylic_orthoester: [#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6] 
+# hits also anhydride like struktures (e. g. HC(OMe)2-OC=O residues)
+
+Ketene: [CX3]=[CX2]=[OX1]
+
+Ketenacetal: [#7X2,#8X3,#16X2;$(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3]
+# includes aminals, silylacetals, ketenesters, etc. C=C DB is not aromatic, everything else may be
+
+Nitrile: [NX1]#[CX2]
+# includes cyanhydrines
+
+Isonitrile: [CX1-]#[NX2+]
+
+
+Vinylogous_carbonyl_or_carboxyl_derivative: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I]
+# may be part of a ring, even aromatic
+
+Vinylogous_acid: [#6X3](=[OX1])[#6X3]=,:[#6X3][$([OX2H]),$([OX1-])]
+
+Vinylogous_ester: [#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!$(C=[O,N,S])]
+
+Vinylogous_amide: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Vinylogous_halide: [#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1]
+
+
+
+# I.5: Four Carbon-Hetero Bonds (Carbonic Acid and Derivatives)
+# -----------------------------
+
+Carbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
+# may be part of a ring, even aromatic
+
+Carbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1]
+
+Carbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])]
+# unstable
+
+Carbonic_acid_derivatives: [!#6][#6X3](=[!#6])[!#6]
+
+
+Thiocarbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])]
+# may be part of a ring, even aromatic
+
+Thiocarbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1]
+
+Thiocarbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])]
+
+
+Urea:[#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])]
+# no check whether part of imide, biuret, etc. Aromatic structures are only hit if
+# both N share no double bonds, like in the dioxo-form of uracil
+
+Thiourea: [#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])]
+
+Isourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])]
+# O may be substituted. no check whether further amide-like bonds are present. Aromatic 
+# structures are only hit if single bonded N shares no additional double bond, like in
+# the 1-hydroxy-3-oxo form of uracil
+
+Isothiourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])]
+
+Guanidine: [N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+]
+# also hits guanidinium salts. v3 and v4 to avoid nitroamidines
+
+Carbaminic_acid: [NX3]C(=[OX1])[O;X2H,X1-]
+# quite unstable, unlikely to be found. Also hits salts
+
+Urethan: [#7X3][#6](=[OX1])[#8X2][#6]
+# also hits when part of a ring, no check whether the last C is part of carbonyl
+
+Biuret: [#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3]
+
+Semicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
+
+Carbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1]
+
+Semicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
+
+Carbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1]
+
+Thiosemicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
+
+Thiocarbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1]
+
+Thiosemicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
+
+Thiocarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1]
+
+
+Isocyanate: [NX2]=[CX2]=[OX1]
+
+Cyanate: [OX2][CX2]#[NX1]
+
+Isothiocyanate: [NX2]=[CX2]=[SX1]
+
+Thiocyanate: [SX2][CX2]#[NX1]
+
+Carbodiimide: [NX2]=[CX2]=[NX2]
+
+Orthocarbonic_derivatives: [CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I]
+# halogen allowed just once, to avoid mapping to -OCF3 and similar groups (much more
+# stable as for example C(OCH3)4)
+
+
+# I.6 Aromatics
+# -------------
+
+# I know that this classification is not very logical, arylamines are found under I.2 ...
+
+Phenol: [OX2H][c]
+
+1,2-Diphenol: [OX2H][c][c][OX2H]
+
+Arylchloride: [Cl][c]
+
+Arylfluoride: [F][c]
+
+Arylbromide: [Br][c]
+
+Aryliodide: [I][c]
+
+Arylthiol: [SX2H][c]
+
+Iminoarene: [c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])]
+# N may be substituted with H or C, but not carbonyl or similar
+# aromatic atom is always C, not S or P (these are not planar when substituted)
+
+Oxoarene: [c]=[OX1]
+
+Thioarene: [c]=[SX1]
+
+Hetero_N_basic_H: [nX3H1+0]
+# as in pyrole. uncharged to exclude pyridinium ions
+
+Hetero_N_basic_no_H: [nX3H0+0]
+# as in N-methylpyrole. uncharged to exclude pyridinium ions
+
+Hetero_N_nonbasic: [nX2,nX3+]
+# as in pyridine, pyridinium
+
+Hetero_O: [o]
+
+Hetero_S: [sX2]
+# X2 because Daylight's depictmatch falsely describes C1=CS(=O)C=C1 as aromatic
+# (is not planar because of lonepair at S)
+
+Heteroaromatic: [a;!c]
+
+
+# Part II: N, S, P, Si, B 
+# =======================
+
+
+# II.1 Nitrogen
+# -------------
+
+Nitrite: [NX2](=[OX1])[O;$([X2]),$([X1-])]
+# hits nitrous acid, its anion, esters, and other O-substituted derivatives 
+
+Thionitrite: [SX2][NX2]=[OX1]
+
+Nitrate: [$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])] 
+# hits nitric acid, its anion, esters, and other O-substituted derivatives 
+
+Nitro: [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]
+# hits nitro groups attached to C,N, ... but not nitrates
+
+Nitroso: [NX2](=[OX1])[!#7;!#8]
+# no nitrites, no nitrosamines
+
+Azide: [NX1]~[NX2]~[NX2,NX1]
+# hits both mesomeric forms, also anion
+
+Acylazide: [CX3](=[OX1])[NX2]~[NX2]~[NX1]
+
+Diazo: [$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])] 
+
+Diazonium: [#6][NX2+]#[NX1]
+
+Nitrosamine: [#7;!$(N*=O)][NX2]=[OX1]
+
+Nitrosamide: [NX2](=[OX1])N-*=O
+# includes nitrososulfonamides
+
+N-Oxide: [$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])] 
+# Hits both forms. Won't hit azoxy, nitro, nitroso, or nitrate.
+
+
+Hydrazine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])]
+# no hydrazides
+
+Hydrazone: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6]
+
+Hydroxylamine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])]
+# no discrimination between O-, N-, and O,N-substitution
+
+
+# II.2 Sulfur
+# -----------
+
+Sulfon: [$([SX4](=[OX1])(=[OX1])([#6])[#6]),$([SX4+2]([OX1-])([OX1-])([#6])[#6])]
+# can't be aromatic, thus S and not #16
+
+Sulfoxide: [$([SX3](=[OX1])([#6])[#6]),$([SX3+]([OX1-])([#6])[#6])]
+
+Sulfonium: [S+;!$([S]~[!#6]);!$([S]*~[#7,#8,#15,#16])]
+# can't be aromatic, thus S and not #16
+
+Sulfuric_acid: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
+# includes anions
+
+Sulfuric_monoester: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
+
+Sulfuric_diester: [SX4](=[OX1])(=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
+
+Sulfuric_monoamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
+
+Sulfuric_diamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Sulfuric_esteramide: [SX4](=[OX1])(=[OX1])([#7X3][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
+
+Sulfuric_derivative: [SX4D4](=[!#6])(=[!#6])([!#6])[!#6]
+# everything else (would not be a "true" derivative of sulfuric acid, if one of the substituents were less electronegative 
+# than sulfur, but this should be very very rare, anyway)
+
+
+
+#### sulfurous acid and derivatives missing!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+
+
+
+Sulfonic_acid: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])]
+
+Sulfonamide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Sulfonic_ester: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])]
+
+Sulfonic_halide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1]
+
+Sulfonic_derivative: [SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6]
+# includes all of the above and many more
+# for comparison: this is what "all sulfonic derivatives but not the ones above" would look like:
+# [$([SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6;!O])[!#6]),$([SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[!$([FX1,ClX1,BrX1,IX1]);!$([#6]);!$([OX2H]);!$([OX1-]);!$([OX2][#6;!$(C=[O,N,S])]);!$([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])])]
+
+
+Sulfinic_acid: [SX3;$([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])]
+
+Sulfinic_amide: [SX3;$([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Sulfinic_ester: [SX3;$([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
+
+Sulfinic_halide: [SX3;$([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1]
+
+Sulfinic_derivative: [SX3;$([H1]),$([H0][#6])](=[!#6])[!#6]
+
+Sulfenic_acid: [SX2;$([H1]),$([H0][#6])][$([OX2H]),$([OX1-])]
+
+Sulfenic_amide: [SX2;$([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Sulfenic_ester: [SX2;$([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])]
+
+Sulfenic_halide: [SX2;$([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1]
+
+Sulfenic_derivative: [SX2;$([H1]),$([H0][#6])][!#6]
+
+
+# II.3 Phosphorous
+# ----------------
+
+Phosphine: [PX3;$([H3]),$([H2][#6]),$([H1]([#6])[#6]),$([H0]([#6])([#6])[#6])]
+# similar to amine, but less restrictive: includes also amide- and aminal-analogues 
+
+Phosphine_oxide: [PX4;$([H3]=[OX1]),$([H2](=[OX1])[#6]),$([H1](=[OX1])([#6])[#6]),$([H0](=[OX1])([#6])([#6])[#6])]
+
+Phosphonium: [P+;!$([P]~[!#6]);!$([P]*~[#7,#8,#15,#16])]
+# similar to Ammonium
+
+Phosphorylen: [PX4;$([H3]=[CX3]),$([H2](=[CX3])[#6]),$([H1](=[CX3])([#6])[#6]),$([H0](=[CX3])([#6])([#6])[#6])]
+
+
+# conventions for the following acids and derivatives: 
+# acids find protonated and deprotonated acids
+# esters do not find mixed anhydrides ( ...P-O-C(=O))
+# derivatives: subtituents which go in place of the OH and =O are not H or C (may also be O, 
+# thus including acids and esters)
+
+Phosphonic_acid: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
+# includes anions
+
+Phosphonic_monoester: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphonic_diester: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphonic_monoamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphonic_diamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphonic_esteramide: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphonic_acid_derivative: [PX4;$([H1]),$([H0][#6])](=[!#6])([!#6])[!#6]
+# all of the above and much more 
+
+
+Phosphoric_acid: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
+# includes anions
+
+Phosphoric_monoester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphoric_diester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphoric_triester: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphoric_monoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphoric_diamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphoric_triamide: [PX4D4](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphoric_monoestermonoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphoric_diestermonoamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphoric_monoesterdiamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphoric_acid_derivative: [PX4D4](=[!#6])([!#6])([!#6])[!#6]
+
+
+Phosphinic_acid: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])]
+
+Phosphinic_ester: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphinic_amide: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphinic_acid_derivative: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6]
+
+
+Phosphonous_acid: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
+
+Phosphonous_monoester: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphonous_diester: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
+
+Phosphonous_monoamide: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphonous_diamide: [PX3;$([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphonous_esteramide: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphonous_derivatives: [PX3;$([D2]),$([D3][#6])]([!#6])[!#6]
+
+
+Phosphinous_acid: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])]
+
+Phosphinous_ester: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])]
+
+Phosphinous_amide: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
+
+Phosphinous_derivatives: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6]
+
+
+# II.4 Silicon
+# ------------
+
+Quart_silane: [SiX4]([#6])([#6])([#6])[#6]
+# four C-substituents. non-reactive, non-toxic, in experimental phase for drug development
+
+Non-quart_silane: [SiX4;$([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])]
+# has 1-4 hydride(s), reactive. Daylight's depictmatch does not add hydrogens automatically to 
+# the free positions at Si, thus Hs had to be added implicitly
+
+Silylmonohalide: [SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6]
+# reagents for inserting protection groups
+
+Het_trialkylsilane: [SiX4]([!#6])([#6])([#6])[#6]
+# mostly acid-labile protection groups such as trimethylsilyl-ethers 
+
+Dihet_dialkylsilane: [SiX4]([!#6])([!#6])([#6])[#6]
+
+Trihet_alkylsilane: [SiX4]([!#6])([!#6])([!#6])[#6]
+
+Silicic_acid_derivative: [SiX4]([!#6])([!#6])([!#6])[!#6]
+# four substituent which are neither C nor H
+
+
+# II.5 Boron
+# ----------
+
+Trialkylborane: [BX3]([#6])([#6])[#6] 
+# also carbonyls allowed
+
+Boric_acid_derivatives: [BX3]([!#6])([!#6])[!#6]
+# includes acids, esters, amides, ... H-substituent at B is very rare.
+
+Boronic_acid_derivative: [BX3]([!#6])([!#6])[!#6]
+# # includes acids, esters, amides, ...
+
+Borohydride: [BH1,BH2,BH3,BH4]
+# at least one H attached to B
+
+Quaternary_boron: [BX4]
+# mostly borates (negative charge), in complex with Lewis-base
+
+
+
+# Part III: Some Special Patterns
+# ===============================
+
+
+# III.1 Chains
+# ------------
+
+# some simple chains
+
+
+
+# III.2 Rings
+# -----------
+
+Aromatic: a
+
+Heterocyclic: [!#6;!R0]
+# may be aromatic or not
+
+Epoxide: [OX2r3]1[#6r3][#6r3]1
+# toxic/reactive. may be annelated to aromat, but must not be aromatic itself (oxirane-2,3-dione)
+
+NH_aziridine: [NX3H1r3]1[#6r3][#6r3]1
+# toxic/reactive according to Maybridge's garbage filter
+
+Spiro: [D4R;$(*(@*)(@*)(@*)@*)]
+# at least two different rings can be found which are sharing just one atom.
+# these two rings can be connected by a third ring, so it matches also some 
+# bridged systems, like morphine
+
+Annelated_rings: [R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]
+# two different rings sharing exactly two atoms
+
+Bridged_rings: [R;$(*(@*)(@*)@*);!$([D4R;$(*(@*)(@*)(@*)@*)]);!$([R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])])]
+# part of two or more rings, not spiro, not annelated -> finds bridgehead atoms, 
+# but only if they are not annelated at the same time - otherwise impossible (?)
+# to distinguish from non-bridgehead annelated atoms
+
+# some basic ring-patterns (just size, no other information):
+
+
+
+
+
+# III.3 Sugars and Nucleosides/Nucleotides, Steroids
+# --------------------------------------------------
+
+# because of the large variety of sugar derivatives, different patterns can be applied.
+# The choice of patterns and their combinations will depend on the contents of the database
+# e.g. natural products, nucleoside analoges with modified sugars, ... as well as on the 
+# desired restriction
+
+
+Sugar_pattern_1: [OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)]
+# 5 or 6-membered ring containing one O and at least one (r5) or two (r6) oxygen-substituents. 
+
+Sugar_pattern_2: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
+# 5 or 6-membered ring containing one O and an acetal-like bond at postion 2. 
+
+Sugar_pattern_combi: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)]
+# combination of the two above
+
+Sugar_pattern_2_reducing: [OX2;$([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)]
+# 5 or 6-membered cyclic hemi-acetal
+
+Sugar_pattern_2_alpha: [OX2;$([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
+# 5 or 6-membered cyclic hemi-acetal
+
+Sugar_pattern_2_beta: [OX2;$([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
+# 5 or 6-membered cyclic hemi-acetal
+
+##Poly_sugar_1: ([OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)].[OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)])
+# pattern1 occours more than once (in same molecule, but moieties don't have to be adjacent!)
+
+##Poly_sugar_2: ([OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)].[OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)])
+# pattern2 occours more than once (in same molecule, but moieties don't have to be adjacent!)
+
+
+# III.4 Everything else...
+# ------------------------
+
+Conjugated_double_bond: *=*[*]=,#,:[*]
+
+Conjugated_tripple_bond: *#*[*]=,#,:[*]
+
+Cis_double_bond: */[D2]=[D2]\*
+# only one single-bonded substituent on each DB-atom. no aromats. 
+# only found when character of DB is explicitely stated.
+
+Trans_double_bond: */[D2]=[D2]/*
+# analog
+
+Mixed_anhydrides: [$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))]
+# should hits all combinations of two acids
+
+Halogen_on_hetero: [FX1,ClX1,BrX1,IX1][!#6]
+
+Halogen_multi_subst: [F,Cl,Br,I;!$([X1]);!$([X0-])]
+# Halogen which is not mono-substituted nor an anion, e.g. chlorate.
+# Most of these cases should be also filtered by Halogen_on_hetero.
+
+Trifluoromethyl: [FX1][CX4;!$([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1])
+# C with three F attached, connected to anything which is not another halogen
+
+C_ONS_bond: [#6]~[#7,#8,#16]
+# probably all drug-like molecules have at least one O, N, or S connected to a C -> nice filter
+
+## Mixture: (*).(*)
+# two or more seperate parts, may also be salt
+# component-level grouping is not yet supported in Open Babel Version 2.0
+
+
+Charged: [!+0]
+
+Anion: [-1,-2,-3,-4,-5,-6,-7]
+
+Kation: [+1,+2,+3,+4,+5,+6,+7]
+
+Salt: ([-1,-2,-3,-4,-5,-6,-7]).([+1,+2,+3,+4,+5,+6,+7])
+# two or more seperate components with opposite charges
+
+##Zwitterion: ([-1,-2,-3,-4,-5,-6,-7].[+1,+2,+3,+4,+5,+6,+7])
+# both negative and positive charges somewhere within the same molecule. 
+
+1,3-Tautomerizable: [$([#7X2,OX1,SX1]=*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=*),$([#7X3,OX2,SX2;!H0]*:n)]
+# 1,3 migration of H allowed. Includes keto/enol and amide/enamide. 
+# Aromatic rings must stay aromatic - no keto form of phenol 
+
+1,5-Tautomerizable: [$([#7X2,OX1,SX1]=,:**=,:*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=**=*),$([#7X3,OX2,SX2;!H0]*=,:**:n)]
+
+Rotatable_bond: [!$(*#*)&!D1]-!@[!$(*#*)&!D1]
+# taken from http://www.daylight.com/support/contrib/smarts/content.html
+
+Michael_acceptor: [CX3]=[CX3][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])]
+# the classical case: C=C near carbonyl, nitrile, nitro, or similar
+# Oxo-heteroaromats and similar are not included.
+
+Dicarbodiazene: [CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1])
+# Michael-like acceptor, see Mitsunobu reaction
+
+# H-Bond_donor:
+
+# H-Bond_acceptor:
+
+# Pos_ionizable:
+
+# Neg_ionizable:
+
+# Unlikely_ions: 
+# O+,N-,C+,C-, ...
+
+CH-acidic: [$([CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]),$([CX4;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)]
+# C-H alpha to carbony, nitro or similar, C is not double-bonded, only C, H, S,P=O and nitro substituents allowed. 
+# pentadiene is included. acids, their salts, prim./sec. amides, and imides are excluded. 
+# hits also CH-acidic_strong
+
+CH-acidic_strong: [CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])]([$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])])[$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]
+# same as above (without pentadiene), but carbonyl or similar on two or three sides
+
+Chiral_center_specified: [$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)]
+# Hits atoms with tetrahedral chirality, if chiral center is specified in the SMILES string
+# depictmach does not find oxonium, sulfonium, or sulfoxides!
+
+# Chiral_center_unspecified: [$([*@?](~*)(~*)(*)*),$([*@?H](*)(*)*),$([*@?](~*)(*)*),$([*@?H](~*)~*)]
+# Hits atoms with tetrahedral chirality, if chiral center is not specified in the SMILES string
+# "@?" (unspecified chirality) is not yet supported in Open Babel Version 2.0 
+ 
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/UFF.prm	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,277 @@
+#
+# Open Babel file: UFF.prm
+#
+# Force field parameters for UFF, the Universal Force Field
+# Used by OBForceField and OBUFFForceField
+#
+# J. Am. Chem. Soc. (1992) 114(25) p. 10024-10035.
+# The parameters in this file are taken from the UFF implementation in RDKit
+# http://rdkit.org/
+#
+# Atom typing rules are based on UFF published atom descriptions
+# atom [SMARTS] [atomtype] [description]
+# These must be sorted according to the element and complexity
+#  of the type rule (i.e., generic rules first, more specific rules later)
+#
+# Parameters follow later
+# param Atom	r1	theta0	x1	D1	zeta	Z1	Vi	Uj	Xi	Hard	Radius
+
+#atom [#0]     Du          Dummy atom (e.g., ligand attachment point)
+atom [#1]     H_          Generic hydrogen
+atom [#1D2]   H_b         Bridging hydrogen
+atom [#2]     He4+4       Helium
+atom [#3]     Li          Lithium
+atom [#4]     Be3+2       Generic Be
+atom [#5]     B_2         Trigonal planar boron
+atom [#5D4]   B_3         Tetrahedral boron
+atom [#6]     C_3         Generic sp3 C
+atom [C^2]    C_2         sp2 non-aromatic C
+atom [C^1]    C_1         sp hybridized C
+atom [c]      C_R         aromatic C
+atom [#6H1D3r5] C_R       aromatic C (cyclopentadienyl ring)
+atom [#7]     N_3         Generic sp3 N
+atom [N^2]    N_2         sp2 non-aromatic N
+atom [N^1]    N_1         sp hybridized N
+atom [n]      N_R         aromatic N
+atom [#8]     O_3         generic, sp3 hybridized O
+atom [#8][#14] O_3_z      sp3 hybridized O for zeolites
+atom [O^2]    O_2         sp2 hybridized O
+atom [O^1]    O_1         sp hybridized O
+atom [o]      O_R         aromatic O
+atom [#9]     F_          generic F
+atom [#10]    Ne4+4
+atom [#11]    Na
+atom [#12]    Mg3+2
+atom [#13]    Al3
+atom [#14]    Si3
+#atom [#15]   P_3+q       Organometallic phosphine ligands
+atom [#15]    P_3+3       generic phosphorus
+atom [#15D5]  P_3+5       formal charge +5
+atom [#16]    S_3+2       generic S
+atom [#16+4]  S_3+4       S+4  ( SO2 )
+atom [#16+6]  S_3+6       S+6  ( SO3 / H2SO4 )
+atom [S^2]    S_2         non-aromatic sp2 S
+atom [s]      S_R         aromatic S
+atom [#17]    Cl
+atom [#18]    Ar4+4
+atom [#19]    K_
+atom [#20]    Ca6+2
+atom [#21]    Sc3+3
+atom [#22]    Ti6+4       generic Ti (6-valent)
+atom [#22D3]  Ti3+4
+atom [#23]    V_3+5
+atom [#24]    Cr6+3
+atom [#25]    Mn6+2
+atom [#26]    Fe6+2       generic Fe (6-valent)
+atom [#26D3]  Fe3+2
+atom [#27]    Co6+3
+atom [#28]    Ni4+2
+atom [#29]    Cu3+1
+atom [#30]    Zn3+2
+atom [#31]    Ga3+3
+atom [#32]    Ge3
+atom [#33]    As3+3
+atom [#34]    Se3+2
+atom [#35]    Br
+atom [#36]    Kr4+4
+atom [#37]    Rb
+atom [#38]    Sr6+2
+atom [#39]    Y_3+3
+atom [#40]    Zr3+4
+atom [#41]    Nb3+5
+atom [#42]    Mo6+6       generic Mo (6-valent)
+atom [#42D3]  Mo3+6       trivalent Mo
+atom [#43]    Tc6+5
+atom [#44]    Ru6+2
+atom [#45]    Rh6+3
+atom [#46]    Pd4+2
+atom [#47]    Ag1+1
+atom [#48]    Cd3+2
+atom [#49]    In3+3
+atom [#50]    Sn3
+atom [#51]    Sb3+3
+atom [#52]    Te3+2
+atom [#53]    I_
+atom [#54]    Xe4+4
+atom [#55]     Cs
+atom [#56]     Ba6+2
+atom [#57]     La3+3
+atom [#58]     Ce6+3
+atom [#59]     Pr6+3
+atom [#60]     Nd6+3
+atom [#61]     Pm6+3
+atom [#62]     Sm6+3
+atom [#63]     Eu6+3
+atom [#64]     Gd6+3
+atom [#65]     Tb6+3
+atom [#66]     Dy6+3
+atom [#67]     Ho6+3
+atom [#68]     Er6+3
+atom [#69]     Tm6+3
+atom [#70]     Yb6+3
+atom [#71]     Lu6+3
+atom [#72]     Hf3+4
+atom [#73]     Ta3+5
+atom [#74]     W_6+6       generic W (6-valent)
+atom [#74D3+4] W_3+4
+atom [#74D3+6] W_3+6
+atom [#75]     Re6+5       generic Re (6-valent)
+atom [#75D3]   Re3+7       trivalent Re
+atom [#76]     Os6+6
+atom [#77]     Ir6+3
+atom [#78]     Pt4+2
+atom [#79]     Au4+3
+atom [#80]     Hg1+2
+atom [#81]     Tl3+3
+atom [#82]     Pb3
+atom [#83]     Bi3+3
+atom [#84]     Po3+2
+atom [#85]     At
+atom [#86]     Rn4+4
+atom [#87]     Fr
+atom [#88]     Ra6+2
+atom [#89]     Ac6+3
+atom [#90]     Th6+4
+atom [#91]     Pa6+4
+atom [#92]     U_6+4
+atom [#93]     Np6+4
+atom [#94]     Pu6+4
+atom [#95]     Am6+4
+atom [#96]     Cm6+3
+atom [#97]     Bk6+3
+atom [#98]     Cf6+3
+atom [#99]     Es6+3
+atom [#100]    Fm6+3
+atom [#101]    Md6+3
+atom [#102]    No6+3
+atom [#103]    Lw6+3
+
+# Atom          r1	theta0	x1	D1	zeta	Z1	Vi	Uj	Xi	Hard	Radius
+param Du  0.01   180 0.4 5000 12	10.0	0 0 9.66	14.92	0.7
+param H_	0.354	180	2.886	0.044	12	0.712	0	0	4.528	6.9452	0.371
+param H_b	0.46	83.5	2.886	0.044	12	0.712	0	0	4.528	6.9452	0.371
+param He4+4	0.849	90	2.362	0.056	15.24	0.098	0	0	9.66	14.92	1.3
+param Li	1.336	180	2.451	0.025	12	1.026	0	2	3.006	2.386	1.557
+param Be3+2	1.074	109.47	2.745	0.085	12	1.565	0	2	4.877	4.443	1.24
+param B_3	0.838	109.47	4.083	0.18	12.052	1.755	0	2	5.11	4.75	0.822
+param B_2	0.828	120	4.083	0.18	12.052	1.755	0	2	5.11	4.75	0.822
+param C_3	0.757	109.47	3.851	0.105	12.73	1.912	2.119	2	5.343	5.063	0.759
+param C_R	0.729	120	3.851	0.105	12.73	1.912	0	2	5.343	5.063	0.759
+param C_2	0.732	120	3.851	0.105	12.73	1.912	0	2	5.343	5.063	0.759
+param C_1	0.706	180	3.851	0.105	12.73	1.912	0	2	5.343	5.063	0.759
+param N_3	0.7	106.7	3.66	0.069	13.407	2.544	0.45	2	6.899	5.88	0.715
+param N_R	0.699	120	3.66	0.069	13.407	2.544	0	2	6.899	5.88	0.715
+param N_2	0.685	111.2	3.66	0.069	13.407	2.544	0	2	6.899	5.88	0.715
+param N_1	0.656	180	3.66	0.069	13.407	2.544	0	2	6.899	5.88	0.715
+param O_3	0.658	104.51	3.5	0.06	14.085	2.3	0.018	2	8.741	6.682	0.669
+param O_3_z	0.528	146	3.5	0.06	14.085	2.3	0.018	2	8.741	6.682	0.669
+param O_R	0.68	110	3.5	0.06	14.085	2.3	0	2	8.741	6.682	0.669
+param O_2	0.634	120	3.5	0.06	14.085	2.3	0	2	8.741	6.682	0.669
+param O_1	0.639	180	3.5	0.06	14.085	2.3	0	2	8.741	6.682	0.669
+param F_	0.668	180	3.364	0.05	14.762	1.735	0	2	10.874	7.474	0.706
+param Ne4+4	0.92	90	3.243	0.042	15.44	0.194	0	2	11.04	10.55	1.768
+param Na	1.539	180	2.983	0.03	12	1.081	0	1.25	2.843	2.296	2.085
+param Mg3+2	1.421	109.47	3.021	0.111	12	1.787	0	1.25	3.951	3.693	1.5
+param Al3	1.244	109.47	4.499	0.505	11.278	1.792	0	1.25	4.06	3.59	1.201
+param Si3	1.117	109.47	4.295	0.402	12.175	2.323	1.225	1.25	4.168	3.487	1.176
+param P_3+3	1.101	93.8	4.147	0.305	13.072	2.863	2.4	1.25	5.463	4	1.102
+param P_3+5	1.056	109.47	4.147	0.305	13.072	2.863	2.4	1.25	5.463	4	1.102
+param P_3+q	1.056	109.47	4.147	0.305	13.072	2.863	2.4	1.25	5.463	4	1.102
+param S_3+2	1.064	92.1	4.035	0.274	13.969	2.703	0.484	1.25	6.928	4.486	1.047
+param S_3+4	1.049	103.2	4.035	0.274	13.969	2.703	0.484	1.25	6.928	4.486	1.047
+param S_3+6	1.027	109.47	4.035	0.274	13.969	2.703	0.484	1.25	6.928	4.486	1.047
+param S_R	1.077	92.2	4.035	0.274	13.969	2.703	0	1.25	6.928	4.486	1.047
+param S_2	0.854	120	4.035	0.274	13.969	2.703	0	1.25	6.928	4.486	1.047
+param Cl	1.044	180	3.947	0.227	14.866	2.348	0	1.25	8.564	4.946	0.994
+param Ar4+4	1.032	90	3.868	0.185	15.763	0.3	0	1.25	9.465	6.355	2.108
+param K_	1.953	180	3.812	0.035	12	1.165	0	0.7	2.421	1.92	2.586
+param Ca6+2	1.761	90	3.399	0.238	12	2.141	0	0.7	3.231	2.88	2
+param Sc3+3	1.513	109.47	3.295	0.019	12	2.592	0	0.7	3.395	3.08	1.75
+param Ti3+4	1.412	109.47	3.175	0.017	12	2.659	0	0.7	3.47	3.38	1.607
+param Ti6+4	1.412	90	3.175	0.017	12	2.659	0	0.7	3.47	3.38	1.607
+param V_3+5	1.402	109.47	3.144	0.016	12	2.679	0	0.7	3.65	3.41	1.47
+param Cr6+3	1.345	90	3.023	0.015	12	2.463	0	0.7	3.415	3.865	1.402
+param Mn6+2	1.382	90	2.961	0.013	12	2.43	0	0.7	3.325	4.105	1.533
+param Fe3+2	1.27	109.47	2.912	0.013	12	2.43	0	0.7	3.76	4.14	1.393
+param Fe6+2	1.335	90	2.912	0.013	12	2.43	0	0.7	3.76	4.14	1.393
+param Co6+3	1.241	90	2.872	0.014	12	2.43	0	0.7	4.105	4.175	1.406
+param Ni4+2	1.164	90	2.834	0.015	12	2.43	0	0.7	4.465	4.205	1.398
+param Cu3+1	1.302	109.47	3.495	0.005	12	1.756	0	0.7	4.2	4.22	1.434
+param Zn3+2	1.193	109.47	2.763	0.124	12	1.308	0	0.7	5.106	4.285	1.4
+param Ga3+3	1.26	109.47	4.383	0.415	11	1.821	0	0.7	3.641	3.16	1.211
+param Ge3	1.197	109.47	4.28	0.379	12	2.789	0.701	0.7	4.051	3.438	1.189
+param As3+3	1.211	92.1	4.23	0.309	13	2.864	1.5	0.7	5.188	3.809	1.204
+param Se3+2	1.19	90.6	4.205	0.291	14	2.764	0.335	0.7	6.428	4.131	1.224
+param Br	1.192	180	4.189	0.251	15	2.519	0	0.7	7.79	4.425	1.141
+param Kr4+4	1.147	90	4.141	0.22	16	0.452	0	0.7	8.505	5.715	2.27
+param Rb	2.26	180	4.114	0.04	12	1.592	0	0.2	2.331	1.846	2.77
+param Sr6+2	2.052	90	3.641	0.235	12	2.449	0	0.2	3.024	2.44	2.415
+param Y_3+3	1.698	109.47	3.345	0.072	12	3.257	0	0.2	3.83	2.81	1.998
+param Zr3+4	1.564	109.47	3.124	0.069	12	3.667	0	0.2	3.4	3.55	1.758
+param Nb3+5	1.473	109.47	3.165	0.059	12	3.618	0	0.2	3.55	3.38	1.603
+param Mo6+6	1.467	90	3.052	0.056	12	3.4	0	0.2	3.465	3.755	1.53
+param Mo3+6	1.484	109.47	3.052	0.056	12	3.4	0	0.2	3.465	3.755	1.53
+param Tc6+5	1.322	90	2.998	0.048	12	3.4	0	0.2	3.29	3.99	1.5
+param Ru6+2	1.478	90	2.963	0.056	12	3.4	0	0.2	3.575	4.015	1.5
+param Rh6+3	1.332	90	2.929	0.053	12	3.5	0	0.2	3.975	4.005	1.509
+param Pd4+2	1.338	90	2.899	0.048	12	3.21	0	0.2	4.32	4	1.544
+param Ag1+1	1.386	180	3.148	0.036	12	1.956	0	0.2	4.436	3.134	1.622
+param Cd3+2	1.403	109.47	2.848	0.228	12	1.65	0	0.2	5.034	3.957	1.6
+param In3+3	1.459	109.47	4.463	0.599	11	2.07	0	0.2	3.506	2.896	1.404
+param Sn3	1.398	109.47	4.392	0.567	12	2.961	0.199	0.2	3.987	3.124	1.354
+param Sb3+3	1.407	91.6	4.42	0.449	13	2.704	1.1	0.2	4.899	3.342	1.404
+param Te3+2	1.386	90.25	4.47	0.398	14	2.882	0.3	0.2	5.816	3.526	1.38
+param I_	1.382	180	4.5	0.339	15	2.65	0	0.2	6.822	3.762	1.333
+param Xe4+4	1.267	90	4.404	0.332	12	0.556	0	0.2	7.595	4.975	2.459
+param Cs	2.57	180	4.517	0.045	12	1.573	0	0.1	2.183	1.711	2.984
+param Ba6+2	2.277	90	3.703	0.364	12	2.727	0	0.1	2.814	2.396	2.442
+param La3+3	1.943	109.47	3.522	0.017	12	3.3	0	0.1	2.8355	2.7415	2.071
+param Ce6+3	1.841	90	3.556	0.013	12	3.3	0	0.1	2.774	2.692	1.925
+param Pr6+3	1.823	90	3.606	0.01	12	3.3	0	0.1	2.858	2.564	2.007
+param Nd6+3	1.816	90	3.575	0.01	12	3.3	0	0.1	2.8685	2.6205	2.007
+param Pm6+3	1.801	90	3.547	0.009	12	3.3	0	0.1	2.881	2.673	2
+param Sm6+3	1.78	90	3.52	0.008	12	3.3	0	0.1	2.9115	2.7195	1.978
+param Eu6+3	1.771	90	3.493	0.008	12	3.3	0	0.1	2.8785	2.7875	2.227
+param Gd6+3	1.735	90	3.368	0.009	12	3.3	0	0.1	3.1665	2.9745	1.968
+param Tb6+3	1.732	90	3.451	0.007	12	3.3	0	0.1	3.018	2.834	1.954
+param Dy6+3	1.71	90	3.428	0.007	12	3.3	0	0.1	3.0555	2.8715	1.934
+param Ho6+3	1.696	90	3.409	0.007	12	3.416	0	0.1	3.127	2.891	1.925
+param Er6+3	1.673	90	3.391	0.007	12	3.3	0	0.1	3.1865	2.9145	1.915
+param Tm6+3	1.66	90	3.374	0.006	12	3.3	0	0.1	3.2514	2.9329	2
+param Yb6+3	1.637	90	3.355	0.228	12	2.618	0	0.1	3.2889	2.965	2.158
+param Lu6+3	1.671	90	3.64	0.041	12	3.271	0	0.1	2.9629	2.4629	1.896
+param Hf3+4	1.611	109.47	3.141	0.072	12	3.921	0	0.1	3.7	3.4	1.759
+param Ta3+5	1.511	109.47	3.17	0.081	12	4.075	0	0.1	5.1	2.85	1.605
+param W_6+6	1.392	90	3.069	0.067	12	3.7	0	0.1	4.63	3.31	1.538
+param W_3+4	1.526	109.47	3.069	0.067	12	3.7	0	0.1	4.63	3.31	1.538
+param W_3+6	1.38	109.47	3.069	0.067	12	3.7	0	0.1	4.63	3.31	1.538
+param Re6+5	1.372	90	2.954	0.066	12	3.7	0	0.1	3.96	3.92	1.6
+param Re3+7	1.314	109.47	2.954	0.066	12	3.7	0	0.1	3.96	3.92	1.6
+param Os6+6	1.372	90	3.12	0.037	12	3.7	0	0.1	5.14	3.63	1.7
+param Ir6+3	1.371	90	2.84	0.073	12	3.731	0	0.1	5	4	1.866
+param Pt4+2	1.364	90	2.754	0.08	12	3.382	0	0.1	4.79	4.43	1.557
+param Au4+3	1.262	90	3.293	0.039	12	2.625	0	0.1	4.894	2.586	1.618
+param Hg1+2	1.34	180	2.705	0.385	12	1.75	0	0.1	6.27	4.16	1.6
+param Tl3+3	1.518	120	4.347	0.68	11	2.068	0	0.1	3.2	2.9	1.53
+param Pb3	1.459	109.47	4.297	0.663	12	2.846	0.1	0.1	3.9	3.53	1.444
+param Bi3+3	1.512	90	4.37	0.518	13	2.47	1	0.1	4.69	3.74	1.514
+param Po3+2	1.5	90	4.709	0.325	14	2.33	0.3	0.1	4.21	4.21	1.48
+param At	1.545	180	4.75	0.284	15	2.24	0	0.1	4.75	4.75	1.47
+param Rn4+4	1.42	90	4.765	0.248	16	0.583	0	0.1	5.37	5.37	2.2
+param Fr	2.88	180	4.9	0.05	12	1.847	0	0	2	2	2.3
+param Ra6+2	2.512	90	3.677	0.404	12	2.92	0	0	2.843	2.434	2.2
+param Ac6+3	1.983	90	3.478	0.033	12	3.9	0	0	2.835	2.835	2.108
+param Th6+4	1.721	90	3.396	0.026	12	4.202	0	0	3.175	2.905	2.018
+param Pa6+4	1.711	90	3.424	0.022	12	3.9	0	0	2.985	2.905	1.8
+param U_6+4	1.684	90	3.395	0.022	12	3.9	0	0	3.341	2.853	1.713
+param Np6+4	1.666	90	3.424	0.019	12	3.9	0	0	3.549	2.717	1.8
+param Pu6+4	1.657	90	3.424	0.016	12	3.9	0	0	3.243	2.819	1.84
+param Am6+4	1.66	90	3.381	0.014	12	3.9	0	0	2.9895	3.0035	1.942
+param Cm6+3	1.801	90	3.326	0.013	12	3.9	0	0	2.8315	3.1895	1.9
+param Bk6+3	1.761	90	3.339	0.013	12	3.9	0	0	3.1935	3.0355	1.9
+param Cf6+3	1.75	90	3.313	0.013	12	3.9	0	0	3.197	3.101	1.9
+param Es6+3	1.724	90	3.299	0.012	12	3.9	0	0	3.333	3.089	1.9
+param Fm6+3	1.712	90	3.286	0.012	12	3.9	0	0	3.4	3.1	1.9
+param Md6+3	1.689	90	3.274	0.011	12	3.9	0	0	3.47	3.11	1.9
+param No6+3	1.679	90	3.248	0.011	12	3.9	0	0	3.475	3.175	1.9
+param Lw6+3	1.698	90	3.236	0.011	12	3.9	0	0	3.5	3.2	1.9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/aromatic.h	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,43 @@
+/***************************************************************
+This file is part of the Open Babel project.
+This is copyright under the GNU General Public License (GPL)
+For more information, see <http://openbabel.org/>
+
+This file contains a binary representation of data tables
+ used by Open Babel. It is used as a fallback if the textual
+ data table is not found at runtime. It is not a normal header.
+***************************************************************/
+
+
+#ifndef OB_AROMATIC_H
+#define OB_AROMATIC_H
+
+namespace OpenBabel
+{
+static const char AromaticData[] = {
+ 0x5B,0x23,0x36,0x72,0x44,0x32,0x5D,0x09,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,
+ 0x23,0x36,0x72,0x44,0x33,0x5D,0x7E,0x21,0x40,0x5B,0x23,0x38,0x5D,0x09,0x09,
+ 0x30,0x09,0x31,0x0A,0x5B,0x23,0x36,0x72,0x44,0x32,0x2B,0x2C,0x23,0x36,0x72,
+ 0x44,0x33,0x2B,0x5D,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x36,0x72,0x5D,
+ 0x3D,0x40,0x2A,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x36,0x72,0x44,0x33,
+ 0x5D,0x3D,0x21,0x40,0x2A,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x36,0x72,
+ 0x44,0x33,0x5D,0x3D,0x21,0x40,0x5B,0x21,0x23,0x36,0x5D,0x09,0x09,0x30,0x09,
+ 0x30,0x0A,0x5B,0x23,0x36,0x72,0x44,0x33,0x2D,0x5D,0x09,0x09,0x32,0x09,0x32,
+ 0x0A,0x5B,0x23,0x37,0x72,0x44,0x32,0x5D,0x09,0x09,0x09,0x31,0x09,0x32,0x0A,
+ 0x5B,0x23,0x37,0x72,0x44,0x33,0x5D,0x20,0x31,0x20,0x32,0x0A,0x5B,0x23,0x37,
+ 0x72,0x5D,0x28,0x2D,0x40,0x2A,0x29,0x2D,0x40,0x2A,0x20,0x09,0x09,0x31,0x09,
+ 0x32,0x0A,0x5B,0x23,0x37,0x72,0x44,0x32,0x5D,0x3D,0x40,0x2A,0x09,0x09,0x31,
+ 0x09,0x31,0x0A,0x5B,0x23,0x37,0x72,0x44,0x33,0x2B,0x5D,0x09,0x09,0x31,0x09,
+ 0x31,0x0A,0x5B,0x23,0x37,0x72,0x44,0x33,0x5D,0x3D,0x4F,0x09,0x09,0x31,0x09,
+ 0x31,0x0A,0x5B,0x23,0x37,0x72,0x44,0x32,0x2D,0x5D,0x09,0x09,0x32,0x09,0x32,
+ 0x0A,0x5B,0x23,0x38,0x72,0x5D,0x09,0x09,0x09,0x32,0x09,0x32,0x0A,0x5B,0x23,
+ 0x38,0x72,0x2B,0x5D,0x09,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x31,0x36,
+ 0x72,0x44,0x32,0x5D,0x09,0x09,0x32,0x09,0x32,0x0A,0x5B,0x23,0x31,0x36,0x72,
+ 0x44,0x32,0x2B,0x5D,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x31,0x36,0x72,
+ 0x44,0x33,0x5D,0x3D,0x21,0x40,0x4F,0x09,0x09,0x32,0x09,0x32,0x0A,0x5B,0x23,
+ 0x31,0x35,0x72,0x44,0x33,0x5D,0x09,0x09,0x32,0x09,0x32,0x0A,0x5B,0x23,0x33,
+ 0x34,0x72,0x44,0x32,0x5D,0x09,0x09,0x32,0x09,0x32,0x0A,0x00};
+
+} // namespace OpenBabel
+#endif // OB_AROMATIC_H
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/aromatic.txt	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,59 @@
+##############################################################################
+#                                                                            #
+#	                Open Babel file: aromatic.txt                            # #                                                                            #
+#                                                                            #
+#  Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc.              #
+#  Some portions Copyright (c) 2001-2005 Geoffrey R. Hutchison               #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+# SMARTS patterns with minimum and maximum pi-electrons contributed to an    #
+#   aromatic system (used by typer.cpp:OBAromaticTyper)                      #
+# The LAST PATTERN MATCHED is used to assign values, so that patterns should #
+#   be ordered from more general to more specific                            #
+#                                                                            #
+##############################################################################
+
+#PATTERN		MIN	MAX
+
+#carbon patterns
+[#6rD2]			1	1
+# exo ketone or alcohol -- don't know which
+[#6rD3]~!@[#8]		0	1
+[#6rD2+,#6rD3+]		1	1
+[#6r]=@*		1	1
+[#6rD3]=!@*		1	1
+# external double bonds to hetero atoms contribute no electrons to the 
+# aromatic systems -- quinoid systems are non-aromatic, e.g. 1,4-benzoquinone
+[#6rD3]=!@[!#6]		0	0
+[#6rD3-]		2	2
+
+#nitrogen patterns
+[#7rD2]			1	2
+[#7rD3]                 1       2
+[#7r](-@*)-@*  		1	2
+[#7rD2]=@*		1	1
+[#7rD3+]		1	1
+[#7rD3]=O		1	1
+[#7rD2-]		2	2
+
+#oxygen patterns
+[#8r]			2	2
+[#8r+]			1	1
+
+#sulfur patterns
+[#16rD2]		2	2
+[#16rD2+]		1	1
+[#16rD3]=!@O		2	2
+
+#other misc patterns
+# Accounts Chem Res 1978 11 p. 153
+# phosphole, phosphabenzene (not v. aromatic)
+[#15rD3]		2	2
+# selenophene
+[#34rD2]		2	2
+# arsabenzene, etc. (*really* not v. aromatic)
+#[#33rD3]		2	2
+# tellurophene, etc. (*really* not v. aromatic)
+#[#52rD2]		2	2
+# stilbabenzene, etc. (very little aromatic character)
+#[#51rD3]		2	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/atomtyp.h	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,316 @@
+/***************************************************************
+This file is part of the Open Babel project.
+This is copyright under the GNU General Public License (GPL)
+For more information, see <http://openbabel.org/>
+
+This file contains a binary representation of data tables
+ used by Open Babel. It is used as a fallback if the textual
+ data table is not found at runtime. It is not a normal header.
+***************************************************************/
+
+
+#ifndef OB_ATOMTYP_H
+#define OB_ATOMTYP_H
+
+namespace OpenBabel
+{
+static const char AtomTypeData[] = {
+ 0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x44,0x34,0x5D,0x20,0x33,0x20,0x23,
+ 0x61,0x6E,0x79,0x20,0x34,0x2D,0x76,0x61,0x6C,0x65,0x6E,0x74,0x20,0x61,0x74,
+ 0x6F,0x6D,0x20,0x2D,0x2D,0x20,0x74,0x65,0x74,0x72,0x61,0x68,0x65,0x64,0x72,
+ 0x61,0x6C,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x44,0x35,0x5D,0x20,
+ 0x35,0x20,0x23,0x61,0x6E,0x79,0x20,0x35,0x2D,0x76,0x61,0x6C,0x65,0x6E,0x74,
+ 0x20,0x61,0x74,0x6F,0x6D,0x20,0x2D,0x2D,0x20,0x74,0x72,0x69,0x67,0x62,0x69,
+ 0x70,0x79,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x44,0x36,0x5D,0x20,
+ 0x36,0x20,0x23,0x61,0x6E,0x79,0x20,0x36,0x2D,0x76,0x61,0x6C,0x65,0x6E,0x74,
+ 0x20,0x61,0x74,0x6F,0x6D,0x20,0x2D,0x2D,0x20,0x6F,0x63,0x74,0x0A,0x49,0x4E,
+ 0x54,0x48,0x59,0x42,0x20,0x5B,0x43,0x5D,0x20,0x33,0x20,0x23,0x73,0x70,0x33,
+ 0x20,0x63,0x61,0x72,0x62,0x6F,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,
+ 0x5B,0x63,0x2C,0x24,0x28,0x43,0x3D,0x2A,0x29,0x5D,0x20,0x32,0x20,0x23,0x73,
+ 0x70,0x32,0x20,0x63,0x61,0x72,0x62,0x6F,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,
+ 0x42,0x20,0x5B,0x24,0x28,0x43,0x23,0x2A,0x29,0x2C,0x24,0x28,0x43,0x28,0x3D,
+ 0x2A,0x29,0x3D,0x2A,0x29,0x5D,0x20,0x31,0x20,0x23,0x73,0x70,0x20,0x63,0x61,
+ 0x72,0x62,0x6F,0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x4E,0x5D,
+ 0x20,0x33,0x20,0x23,0x73,0x70,0x33,0x20,0x6E,0x69,0x74,0x72,0x6F,0x67,0x65,
+ 0x6E,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x6E,0x2C,0x24,0x28,0x4E,
+ 0x3D,0x2A,0x29,0x2C,0x24,0x28,0x4E,0x5B,0x23,0x36,0x2C,0x23,0x37,0x2C,0x23,
+ 0x38,0x5D,0x3D,0x2C,0x3A,0x2C,0x23,0x2A,0x29,0x5D,0x20,0x32,0x20,0x23,0x73,
+ 0x70,0x32,0x20,0x6E,0x69,0x74,0x72,0x6F,0x67,0x65,0x6E,0x0A,0x49,0x4E,0x54,
+ 0x48,0x59,0x42,0x20,0x5B,0x4E,0x44,0x31,0x2C,0x4E,0x44,0x32,0x2C,0x4E,0x44,
+ 0x33,0x5D,0x61,0x20,0x32,0x20,0x23,0x73,0x70,0x32,0x20,0x6E,0x69,0x74,0x72,
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+ 0x20,0x4F,0x33,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x38,0x5E,
+ 0x32,0x5D,0x20,0x4F,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x24,
+ 0x28,0x4F,0x61,0x29,0x5D,0x20,0x4F,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,
+ 0x20,0x5B,0x24,0x28,0x5B,0x4F,0x44,0x32,0x5D,0x43,0x3D,0x5B,0x4F,0x2C,0x53,
+ 0x5D,0x29,0x5D,0x20,0x4F,0x33,0x20,0x23,0x65,0x73,0x74,0x65,0x72,0x20,0x6F,
+ 0x78,0x79,0x67,0x65,0x6E,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x24,
+ 0x28,0x4F,0x61,0x29,0x5D,0x20,0x4F,0x33,0x20,0x23,0x61,0x72,0x6F,0x6D,0x61,
+ 0x74,0x69,0x63,0x20,0x65,0x74,0x68,0x65,0x72,0x0A,0x45,0x58,0x54,0x54,0x59,
+ 0x50,0x20,0x5B,0x23,0x38,0x2D,0x5D,0x20,0x4F,0x2D,0x0A,0x45,0x58,0x54,0x54,
+ 0x59,0x50,0x20,0x5B,0x24,0x28,0x5B,0x23,0x38,0x44,0x31,0x5D,0x7E,0x5B,0x23,
+ 0x36,0x5E,0x32,0x5D,0x7E,0x5B,0x23,0x38,0x44,0x31,0x5D,0x29,0x5D,0x20,0x4F,
+ 0x2E,0x63,0x6F,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x31,
+ 0x35,0x5D,0x20,0x50,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x31,
+ 0x35,0x58,0x34,0x2B,0x5D,0x20,0x50,0x33,0x2B,0x0A,0x45,0x58,0x54,0x54,0x59,
+ 0x50,0x20,0x5B,0x23,0x31,0x35,0x3B,0x24,0x28,0x5B,0x23,0x31,0x35,0x44,0x34,
+ 0x5D,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x28,0x7E,0x5B,0x4F,0x44,0x31,
+ 0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5D,0x20,0x50,0x61,0x63,0x0A,
+ 0x45,0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x31,0x35,0x3B,0x24,0x28,0x5B,
+ 0x23,0x31,0x35,0x44,0x33,0x5D,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x7E,
+ 0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5D,0x20,0x50,0x61,0x63,0x0A,0x45,0x58,0x54,
+ 0x54,0x59,0x50,0x20,0x5B,0x23,0x31,0x36,0x5D,0x20,0x53,0x33,0x0A,0x45,0x58,
+ 0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x31,0x36,0x44,0x33,0x2B,0x2C,0x23,0x31,
+ 0x36,0x58,0x33,0x2B,0x5D,0x20,0x53,0x33,0x2B,0x0A,0x45,0x58,0x54,0x54,0x59,
+ 0x50,0x20,0x5B,0x23,0x31,0x36,0x3B,0x73,0x2C,0x24,0x28,0x5B,0x53,0x44,0x31,
+ 0x5D,0x3D,0x2A,0x29,0x5D,0x20,0x53,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,
+ 0x20,0x5B,0x23,0x31,0x36,0x44,0x34,0x3B,0x24,0x28,0x53,0x28,0x3D,0x4F,0x29,
+ 0x28,0x3D,0x4F,0x29,0x29,0x5D,0x20,0x53,0x6F,0x32,0x0A,0x45,0x58,0x54,0x54,
+ 0x59,0x50,0x20,0x5B,0x23,0x31,0x36,0x44,0x33,0x3B,0x24,0x28,0x53,0x28,0x3D,
+ 0x4F,0x29,0x29,0x5D,0x20,0x53,0x6F,0x78,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,
+ 0x20,0x5B,0x23,0x31,0x36,0x3B,0x24,0x28,0x5B,0x23,0x31,0x36,0x44,0x34,0x5D,
+ 0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,
+ 0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5D,0x20,0x53,0x61,0x63,0x0A,0x45,
+ 0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x31,0x36,0x3B,0x24,0x28,0x5B,0x23,
+ 0x31,0x36,0x44,0x33,0x5D,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,
+ 0x4F,0x44,0x31,0x5D,0x29,0x5D,0x20,0x53,0x61,0x63,0x0A,0x45,0x58,0x54,0x54,
+ 0x59,0x50,0x20,0x5B,0x23,0x35,0x5D,0x20,0x42,0x32,0x0A,0x45,0x58,0x54,0x54,
+ 0x59,0x50,0x20,0x5B,0x23,0x35,0x44,0x34,0x5D,0x20,0x42,0x33,0x0A,0x00};
+
+} // namespace OpenBabel
+#endif // OB_ATOMTYP_H
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/atomtyp.txt	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,259 @@
+##############################################################################
+#                                                                            #
+#                   Open Babel file: atomtyp.txt                             #
+#                                                                            #
+#                                                                            #
+#  Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc.              #
+#  Some portions Copyright (c) 2001-2008 Geoffrey R. Hutchison               #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+# SMARTS patterns for atom typing (used by typer.cpp:OBAtomTyper)            #
+#                                                                            #
+# INTHYB: used to assign the internal hybridization values for atoms         #
+# IMPVAL: used to assign the implicit valence of an atom                     #
+# EXTTYP: used to assign the external type of an atom for translation to     #
+#         package specific types (i.e. Sybyl Mol2)                           #
+#        (these should correspond to INT type names in types.txt too.)       #
+#                                                                            #
+# The LAST PATTERN MATCHED is used to assign values with the corresponding   #
+# INTHYB, IMPVAL, and EXTTYP values. Additions to this file should be placed #
+# in the EXTRA DEFINITIONS section (to separate from original patterns.)     #
+#                                                                            #
+##############################################################################
+
+INTHYB  [D4]                      3       #any 4-valent atom -- tetrahedral
+INTHYB  [D5]                      5       #any 5-valent atom -- trigbipy
+INTHYB  [D6]                      6       #any 6-valent atom -- oct
+INTHYB  [C]                       3       #sp3 carbon
+INTHYB  [c,$(C=*)]                2       #sp2 carbon
+# INTHYB  [$([#6]([#8D1])[#8D1])]   2     # Commented out after PR#3089597
+INTHYB  [$(C#*),$(C(=*)=*)]       1       #sp  carbon
+
+INTHYB  [N]                       3       #sp3 nitrogen
+INTHYB  [n,$(N=*),$(N[#6,#7,#8]=,:,#*)] 2 #sp2 nitrogen
+INTHYB  [ND1,ND2,ND3]a            2       #sp2 nitrogen
+INTHYB  [$(N#*),$([ND2](=*)=*)]   1       #sp  nitrogen
+
+INTHYB  [O]                       3       #sp3 oxygen
+INTHYB  [o,$(O=*),$(O[#6,#7,#8]=,:*)] 2   #sp2 oxygen
+INTHYB  [$([#8D1][#6][#8D1])]     2       #sp2 oxygen
+INTHYB  [$(O#*)]                  1       #sp  oxygen
+
+INTHYB  [P]                       3       #sp3 phosphorus
+INTHYB  [#15;$([PD1]=*)]          2       #sp2 phosphorus
+INTHYB  [PD5]			  5	  #sp3d phosphorus, as in PF5
+INTHYB  [Pv5]			  5	  #sp3d phosphorus, as in H3PO4
+INTHYB  [S]                       3       #sp3 sulfur
+INTHYB  [#16;s,$([SD1]=*)]        2       #sp2 sulfur
+INTHYB  [SD6]			  6	  #sp3d2 sulfur, as in SF6
+INTHYB  [B]                       2       #sp2 boron
+INTHYB  [BD4]                     3       #sp3 boron
+
+INTHYB  [Al]                      2       # typical sp2 Al (and family)
+INTHYB  [Ga]                      2
+INTHYB  [In]                      2
+INTHYB  [Tl]                      2
+INTHYB  [AlD4]                    3       # sp3 Al
+INTHYB  [Si]                      3       # sp3 Si (and family)
+INTHYB  [Pb]                      3
+INTHYB  [Ge;!D5]                  3
+INTHYB  [Sn;!D5]                  3
+INTHYB  [AsD3]                    3       # AsCl3 (AsCl5 handled by D5 above)
+INTHYB  [SbD3]                    3       #
+# SbD5, AsD5 are all trigbpy so are handled by D5 above
+INTHYB  [BiD3]                    3       # 
+INTHYB  [BiD5]                    6       # BiF5 is square-pyr, not trigbpy 
+
+INTHYB  [se]                      2       # aromatic sp2 Se
+INTHYB  [Se]                      3       # sp3 hybridization Se (and family)
+INTHYB  [Te]                      3
+INTHYB  [Po]                      3
+
+INTHYB  [Be]                      1       # Alkaline earth, like sp hybrids
+INTHYB  [Mg]                      1
+INTHYB  [Ca]                      1
+INTHYB  [Sr]                      1
+INTHYB  [Ba]                      1
+INTHYB  [Ra]                      1
+
+#INTHYB  [Pt]                      4 # normally square planar
+#INTHYB  [Pd]                      4
+#INTHYB  [Cu]                      4
+#INTHYB  [Ag]                      4
+#INTHYB  [Au]                      4
+
+#
+#IMPLICIT VALENCE RULES
+#
+#IMPVAL  [#3,#11,#19,#37,#55,#87]  1 # Alkali metals
+#IMPVAL  [#4,#12,#20,#38,#56,#88]  2 # Alkaline earth
+
+IMPVAL  [#5+]                     2
+IMPVAL  [#5-]                     4
+IMPVAL  [#5]                      3 # Generic boron
+IMPVAL [$([#6+]=*)]		          2
+IMPVAL [$([#6+]#*)]		          1 # just for InChI C2
+
+IMPVAL  [#6^3]                    4
+IMPVAL  [#6^2]                    3
+IMPVAL  [#6^1]                    2
+IMPVAL  [#6^3+]                   3
+IMPVAL  [#6^2+]                   2
+IMPVAL  [#6^1+]                   1
+
+IMPVAL  [#6^3-]                   3
+IMPVAL  [#6^2-]                   2
+IMPVAL  [#6^1-]                   1 # isocyanides, CO (valence=1, bond order=3)
+IMPVAL  [c+]                      2
+
+IMPVAL  [N^3]                     3
+IMPVAL  [N^3+]                    4
+IMPVAL  [N^2]                     3
+#IMPVAL  [N^2-,N^3-]              2
+IMPVAL  [ND1^1]                   1
+IMPVAL  [ND2^1]                   2
+IMPVAL  [$(N([OD1])*)]            3
+IMPVAL  [$(NC=O)]                 3
+#IMPVAL  [$(n(c=O)c=O)]           3 # aromatic diimide
+IMPVAL  [$(N(~[OD1])~[OD1])]      3
+IMPVAL  [$([Nr0]C=[Nr0])]         3
+IMPVAL  [$(N=*)]                  2
+#IMPVAL [$([Nr0]=C[Nr0])]         3
+IMPVAL  [$([Nr0]=C[Nr0])]         2
+IMPVAL  [$([N+r0]=C[Nr0])]        3 # patch from Steve Constable
+IMPVAL  [$([#7D1-]=*)]            1
+IMPVAL  [N^1-]                    1 # N2O [N-]=[N+]=O (valence=1, bondorder=2)
+IMPVAL  [N-]                      2
+IMPVAL  [n]                       2
+IMPVAL  [n-]                      2
+IMPVAL  [n+]                      3
+IMPVAL  [$([#7-]=*)]              1
+IMPVAL  [$([#7+]#*)]              2
+IMPVAL  [$([#7+]=*)]              3
+IMPVAL  [$([#7+](=*)=*)]          2
+
+IMPVAL [$([#8+]#*)] 1
+
+IMPVAL [#8]                       2 # Generic O
+IMPVAL [#8-]                      1
+IMPVAL [#8-2]                     0
+IMPVAL [#8+]                      3
+IMPVAL [$([#8]=*)]                1
+IMPVAL [#8^1+]                    1 # carbon monoxide
+
+IMPVAL  [#9D0]                    1
+IMPVAL  [#9D0-]                   0 #[F-]
+
+IMPVAL  [#13]                     3 # generic Al
+
+IMPVAL  [#14]                     4 # regular sp3 Si
+IMPVAL  [#14^2]                   2 # silylenes
+IMPVAL  [$([#14]=*)]              3 # e.g., Si=O
+IMPVAL  [$([#14](=*)=*)]          0 # e.g., Si(=O)=O
+IMPVAL  [$([#14+]#*)]		          1 # just for InChI Si2
+IMPVAL  [$([#14-]#*)]		          1 # just for InChI Si2
+
+IMPVAL  [#15D4]                   4
+IMPVAL  [#15D3]                   3
+IMPVAL  [#15D2]                   3
+IMPVAL  [#15D1^3]                 3
+IMPVAL  [#15D1^2]                 3
+IMPVAL  [#15D0]                   3
+IMPVAL  [$([#15]=[#6])]           2
+IMPVAL  [pD2]                     2
+IMPVAL  [$([#15]=[#8])]           4 # phosphinate (double bond = one valence)
+IMPVAL  [$([#15](=[#8])=[#8])]    3 # metaphosphate (double bond = one valence)
+IMPVAL  [$([#15+](=[#8])([#8]))]  0 # R-P+O2
+
+IMPVAL  [#16]                     2 #revised CM April 2008
+IMPVAL  [$([#16D1]=*)]            1
+IMPVAL  [$([#16D3](=O)(=O)-O)]    4 #e.g. O[S](=O)=O
+IMPVAL  [$([#16D2](=O)-O)]        3 # e.g. O[S]=O
+IMPVAL  [#16D1-]                  1
+
+IMPVAL  [#17D0]                   1
+IMPVAL  [#17D0-]                  0 #[Cl-]
+
+IMPVAL  [#31]                     3
+IMPVAL  [#32]                     4
+
+IMPVAL  [#33]                     3
+IMPVAL  [as]                      3
+
+IMPVAL  [#34]                     2
+
+IMPVAL  [#35D0]                   1
+IMPVAL  [#35D0-]                  0 #[Br-]
+
+#IMPVAL  [#49,#81]                 3 # In, Tl, like Ga
+#IMPVAL  [#50,#82]                 4 # Sn, Pb, like Ge
+#IMPVAL  [#51,#83]                 3 # Sb, Bi, like As
+
+IMPVAL  [#52]                     2
+IMPVAL  [#53D0]                   1
+IMPVAL  [#53D0-]                  0 #[I-]
+
+#
+#EXTERNAL TYPE RULES
+#
+
+# Tinker OH hydrogens for MM2
+# Fixes PR# 1839274
+EXTTYP  [#1][#8]        HO
+
+EXTTYP  [#7^3]          N3
+EXTTYP  [#7X4]          N3+
+EXTTYP  [#7^2]          Npl
+EXTTYP  [#7^1]          N1
+EXTTYP  [$(N=*)]        N2
+EXTTYP  [$([Nr0]C(=[Nr0])[Nr0])]    Ng+
+EXTTYP  [$([Nr0]=C([Nr0])[Nr0])]    Ng+
+EXTTYP  [$([ND1]=C[ND1])]     Ng+
+EXTTYP  [$([ND1]C=[ND1])]     Ng+
+EXTTYP  [$(N(O)*)]        Nox
+EXTTYP  [$(NC=[O,S])]       Nam
+EXTTYP  [$(N(~[OD1])~[OD1])]      Ntr
+EXTTYP  [n]         Nar
+
+EXTTYP  [#6^3]          C3
+EXTTYP  [#6^2]          C2
+EXTTYP  [$(C(=O)[OD1])]       Cac
+EXTTYP  [c]         Car
+EXTTYP  [#6^1]          C1
+EXTTYP  [#6+]         C+
+EXTTYP  [#6-]         C-
+
+EXTTYP  [#8^3]          O3
+EXTTYP  [#8^2]          O2
+EXTTYP  [$(Oa)]         O2
+#The following 2 lines used for correct Sybyl atom typing
+EXTTYP  [$([OD2]C=[O,S])]     O3  #ester oxygen
+EXTTYP  [$(Oa)]         O3      #aromatic ether
+EXTTYP  [#8-]         O-
+EXTTYP  [$([#8D1]~[#6^2]~[#8D1])]     O.co2
+
+EXTTYP  [#15]         P
+EXTTYP  [#15X4+]        P3+
+EXTTYP  [#15;$([#15D4](~[OD1])(~[OD1])~[OD1])]  Pac
+EXTTYP  [#15;$([#15D3](~[OD1])~[OD1])]    Pac
+
+EXTTYP  [#16]         S3
+EXTTYP  [#16D3+,#16X3+]       S3+
+EXTTYP  [#16;s,$([SD1]=*)]      S2
+EXTTYP  [#16D4;$(S(=O)(=O))]      So2
+EXTTYP  [#16D3;$(S(=O))]      Sox
+EXTTYP  [#16;$([#16D4](~[OD1])(~[OD1])~[OD1])]  Sac
+EXTTYP  [#16;$([#16D3](~[OD1])~[OD1])]    Sac
+
+EXTTYP  [#5]          B2
+EXTTYP  [#5D4]          B3
+
+######################## Add Extra Definitions Here ##########################
+
+#INTHYB  [U]                      3
+#INTHYB  [W]                      3
+#INTHYB  [Mo]			  6 # for development
+#INTHYB  [Cr]			  5 # for development
+
+############################# End Extra Definitions ##########################
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/babel_povray3.inc	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,1229 @@
+//Include for Babel
+//Copyright (c) by Steffen Reith and Oliver Weichold 1996-2002
+//  This program is free software; you can redistribute it and/or modify
+//  it under the terms of the GNU General Public License as published by
+//  the Free Software Foundation version 2 of the License.
+//EMail: streit@streit.cc
+//For chemical questions send mail to
+//weichold@sas.upenn.edu
+
+//$Id: babel_povray3.inc 3895 2010-07-22 10:36:05Z baoilleach $
+
+#include "colors.inc"
+#include "metals.inc"
+
+//Do a ball and sticks model as default (nothing defined)
+#ifndef (BAS)
+ #ifndef (SPF)
+  #ifndef (CST)
+   #declare BAS = true;
+   #declare SPF = false;
+   #declare CST = false;
+  #end
+ #end
+#end
+
+//Default: No Ball and Sticks-model (if undefined)
+#ifndef (BAS)
+ #declare BAS = false;
+#end
+
+//Default: No Spacefill-model (if undefined)
+#ifndef (SPF)
+ #declare SPF = false;
+#end
+
+//Default: No capped sticks-model (if undefined)
+#ifndef (CST)
+ #declare CST = false;
+#end
+
+//Is a model (BAS, SPF or CST) selected ?
+#if (!((BAS | SPF) | CST))
+
+ //Terminate parsing
+ #error "You have to select BAS (default), SPF or CST" 
+
+#end
+
+//Select only one model
+#if ((BAS & SPF) | ((BAS & CST) | (SPF & CST)))
+
+ //Terminate parsing
+ #error "You have to select only one model-type" 
+
+#end
+
+//Display copyright
+#render "\n\n"
+#render "\nbabel31.inc (C) 1996-2002 by\n"
+#render "Oliver Weichold (weichold@sas.upenn.edu)\n"
+#render "and Steffen Reith (streit@streit.cc)\n"
+#render "\n\n"
+
+//TRANS mode off by default (only needed for transparent textures)
+#ifndef (TRANS)
+#declare TRANS = false;
+#end 
+
+#if (TRANS)
+#include "glass.inc"
+#end
+
+//Finishs for atoms (Nonmetals, Transmetals, Halfmetals and Metals)
+#if (TRANS)
+
+ #declare TransFinish = finish {
+                                ambient 0.1
+                                diffuse 0.1
+                                specular 0.8
+                                reflection 0.1
+                                roughness 0.0003
+                                phong 1 phong_size 400
+                               }                      
+
+ //Transparent finishs
+ #declare MetalFinish      = finish {TransFinish}
+ #declare HalfMetalFinish  = finish {TransFinish}
+ #declare NonMetalFinish   = finish {TransFinish}
+ #declare TransMetalFinish = finish {TransFinish}
+ #declare Bond_0_Finish    = finish {TransFinish}
+ #declare Bond_1_Finish    = finish {TransFinish}
+ #declare Bond_2_Finish    = finish {TransFinish}
+ #declare Bond_3_Finish    = finish {TransFinish}
+ #declare Bond_4_Finish    = finish {TransFinish}
+ #declare Bond_5_Finish    = finish {TransFinish}
+
+ //Filter values for transparent finishs  
+ #declare MetalFilter       = 1.00;
+ #declare HalfMetalFilter   = 0.95;
+ #declare NonMetalFilter    = 1.00;
+ #declare TransMetalFilter  = 0.95;
+ #declare Bond_0_Filter     = 0.00;
+ #declare Bond_1_Filter     = 0.90;
+ #declare Bond_2_Filter     = 0.90;
+ #declare Bond_3_Filter     = 0.90;
+ #declare Bond_4_Filter     = 0.90;
+ #declare Bond_5_Filter     = 0.90;
+
+#else
+
+ //Solid finishs
+ #declare MetalFinish      = finish {F_MetalA}
+ #declare HalfMetalFinish  = finish {F_MetalD}
+ #declare NonMetalFinish   = finish {
+
+                            ambient 0.2
+                            diffuse 0.8
+                            brilliance 1.0 
+                            phong 1.0      
+                            phong_size 80
+                            reflection 0.25
+
+                           }
+ #declare TransMetalFinish = finish {F_MetalD}
+ #declare Bond_0_Finish    = finish {F_MetalC}
+ #declare Bond_1_Finish    = finish {F_MetalC}
+ #declare Bond_2_Finish    = finish {F_MetalC}
+ #declare Bond_3_Finish    = finish {F_MetalC}
+ #declare Bond_4_Finish    = finish {F_MetalC}
+ #declare Bond_5_Finish    = finish {F_MetalC}
+
+ //No additional filter (texture is not transparent)
+ #declare MetalFilter       = 0.0;
+ #declare HalfMetalFilter   = 0.0;
+ #declare NonMetalFilter    = 0.0;
+ #declare TransMetalFilter  = 0.0;
+ #declare Bond_0_Filter     = 0.0;
+ #declare Bond_1_Filter     = 0.0;
+ #declare Bond_2_Filter     = 0.0;
+ #declare Bond_3_Filter     = 0.0;
+ #declare Bond_4_Filter     = 0.0;
+ #declare Bond_5_Filter     = 0.0;
+
+#end
+
+//Thickness of Bonds (see Makro Bond_order)
+#if (CST)
+
+ // For capped-stick models you must use _one_ Bond_Thick ! 
+ #declare Bond_Thick_0 = 0.1;
+ #declare Bond_Thick_1 = Bond_Thick_0; 
+ #declare Bond_Thick_2 = Bond_Thick_0;
+ #declare Bond_Thick_3 = Bond_Thick_0;
+ #declare Bond_Thick_4 = Bond_Thick_0;
+ #declare Bond_Thick_5 = Bond_Thick_0;
+
+#else
+
+ #declare Bond_Thick_0 = 0.1;
+ #declare Bond_Thick_1 = 0.1;
+ #declare Bond_Thick_2 = 0.1;
+ #declare Bond_Thick_3 = 0.1;
+ #declare Bond_Thick_4 = 0.1;
+ #declare Bond_Thick_5 = 0.1;
+
+#end
+
+//Colors for Bonds (see Makro Bond_order)
+#declare Bond_0_Color = rgbf <1.00,0.725,0.275,Bond_0_Filter>; 
+#declare Bond_1_Color = rgbf <1.00,0.725,0.275,Bond_1_Filter>;
+#declare Bond_2_Color = rgbf <1.00,0.725,0.275,Bond_2_Filter>;
+#declare Bond_3_Color = rgbf <1.00,0.725,0.275,Bond_3_Filter>;
+#declare Bond_4_Color = rgbf <1.00,0.725,0.275,Bond_4_Filter>;
+#declare Bond_5_Color = rgbf <1.00,0.725,0.275,Bond_5_Filter>;
+
+#declare Bond_0_Color = rgbf <0.95,0.95,0.1,Bond_0_Filter>;
+#declare Bond_1_Color = rgbf <0.95,0.95,0.1,Bond_1_Filter>;
+#declare Bond_2_Color = rgbf <0.95,0.95,0.1,Bond_2_Filter>;
+#declare Bond_3_Color = rgbf <0.95,0.95,0.1,Bond_3_Filter>;
+#declare Bond_4_Color = rgbf <0.95,0.95,0.1,Bond_4_Filter>;
+#declare Bond_5_Color = rgbf <0.95,0.95,0.1,Bond_5_Filter>;
+
+//The bond declarations
+#declare bond_0 = cylinder {
+                            <0,0,0>
+                            <1,0,0>
+                            Bond_Thick_0
+                            texture {
+
+                             pigment {color Bond_0_Color}
+                             finish {Bond_0_Finish}
+
+                            }
+#if (TRANS)
+			    interior{ I_Glass}
+#end
+                           }
+#declare bond_1 = cylinder {
+                            <0,0,0>
+                            <1,0,0>
+                            Bond_Thick_1
+                            texture {
+
+                             pigment {color Bond_1_Color}
+                             finish {Bond_1_Finish}
+
+                            }
+#if (TRANS)
+			    interior{ I_Glass}
+#end
+                           }
+#declare bond_2 = cylinder {
+                            <0,0,0>
+                            <1,0,0>
+                            Bond_Thick_2
+                            texture {
+
+                             pigment {color Bond_2_Color}
+                             finish {Bond_2_Finish}
+
+                            }
+#if (TRANS)
+			    interior{ I_Glass}
+#end
+                           }
+#declare bond_3 = cylinder {
+                            <0,0,0>
+                            <1,0,0>
+                            Bond_Thick_3
+                            texture {
+
+                             pigment {color Bond_3_Color}
+                             finish {Bond_3_Finish}
+
+                            }
+#if (TRANS)
+			    interior{ I_Glass}
+#end
+                           }
+#declare bond_4 = cylinder {
+                            <0,0,0>
+                            <1,0,0>
+                            Bond_Thick_4
+                            texture {
+
+                             pigment {color Bond_4_Color}
+                             finish {Bond_4_Finish}
+
+                            }
+#if (TRANS)
+			    interior{ I_Glass}
+#end
+                           }
+#declare bond_5 = cylinder {
+                            <0,0,0>
+                            <1,0,0>
+                            Bond_Thick_5
+                            texture {
+
+                             pigment {color Bond_5_Color}
+                             finish {Bond_5_Finish}
+
+                            }
+#if (TRANS)
+			    interior{ I_Glass}
+#end
+                           }
+
+//Generic definition of an atom
+#if (BAS)
+#render "\n\nCalculate a ball and sticks model of :"
+#declare atom = sphere {<0,0,0>,0.6}
+#end
+#if (SPF)  
+#render "\n\nCalculate a spacefill model of :"
+#declare atom = sphere {<0,0,0>,1.66}
+#end
+#if (CST)  
+#render "\n\nCalculate a capped sticks model of :"
+#declare atom = sphere {<0,0,0>,1.0}
+#end
+
+//For Povray 3.1 only
+#version 3.1;
+
+//For capped sticks models we use Bond_Thick_0 for all atom radii
+#if (CST)
+
+ #declare Radius_C1 = Bond_Thick_0;
+ #declare Radius_C2 = Bond_Thick_0;
+ #declare Radius_C3 = Bond_Thick_0;
+ #declare Radius_H  = Bond_Thick_0;
+ #declare Radius_D =  Bond_Thick_0;
+ #declare Radius_O  = Bond_Thick_0;
+ #declare Radius_N  = Bond_Thick_0;
+ #declare Radius_S  = Bond_Thick_0;
+ #declare Radius_P  = Bond_Thick_0;
+ #declare Radius_F  = Bond_Thick_0;
+ #declare Radius_Cl = Bond_Thick_0;
+ #declare Radius_Br = Bond_Thick_0;
+ #declare Radius_I  = Bond_Thick_0;
+		      
+ #declare Radius_Si = Bond_Thick_0;
+ #declare Radius_B  = Bond_Thick_0;
+ #declare Radius_Ge = Bond_Thick_0;
+ #declare Radius_Se = Bond_Thick_0;
+
+ #declare Radius_Ca  = Bond_Thick_0;
+ #declare Radius_Ca2 = Bond_Thick_0;
+ #declare Radius_Sn  = Bond_Thick_0;
+ #declare Radius_Sn2 = Bond_Thick_0;
+ #declare Radius_Sn4 = Bond_Thick_0;
+ #declare Radius_Pb  = Bond_Thick_0;
+ #declare Radius_Pb2 = Bond_Thick_0;
+ #declare Radius_Pb4 = Bond_Thick_0;
+ #declare Radius_Te  = Bond_Thick_0;
+ #declare Radius_Te4 = Bond_Thick_0;
+ #declare Radius_Te6 = Bond_Thick_0;
+ #declare Radius_Na  = Bond_Thick_0;
+ #declare Radius_Na1 = Bond_Thick_0;
+ #declare Radius_K   = Bond_Thick_0;
+ #declare Radius_K1  = Bond_Thick_0;
+ #declare Radius_Li  = Bond_Thick_0;
+ #declare Radius_Li1 = Bond_Thick_0;
+ #declare Radius_Al  = Bond_Thick_0;
+ #declare Radius_Al3 = Bond_Thick_0;
+
+ #declare Radius_Mn  = Bond_Thick_0;
+ #declare Radius_Mn2 = Bond_Thick_0;
+ #declare Radius_Mn3 = Bond_Thick_0;
+ #declare Radius_Mn4 = Bond_Thick_0;
+ #declare Radius_W   = Bond_Thick_0;
+ #declare Radius_W4  = Bond_Thick_0;
+ #declare Radius_W6  = Bond_Thick_0;
+ #declare Radius_Fe  = Bond_Thick_0;
+ #declare Radius_Fe2 = Bond_Thick_0;
+ #declare Radius_Fe3 = Bond_Thick_0;
+ #declare Radius_Pd  = Bond_Thick_0;
+ #declare Radius_Pd2 = Bond_Thick_0;
+ #declare Radius_Pd4 = Bond_Thick_0;
+ #declare Radius_Ni  = Bond_Thick_0;
+ #declare Radius_Ni2 = Bond_Thick_0;
+ #declare Radius_Ni3 = Bond_Thick_0;
+ #declare Radius_Cu  = Bond_Thick_0;
+ #declare Radius_Cu1 = Bond_Thick_0;
+ #declare Radius_Cu2 = Bond_Thick_0;
+ #declare Radius_V   = Bond_Thick_0;
+ #declare Radius_V2  = Bond_Thick_0;
+ #declare Radius_V3  = Bond_Thick_0;
+ #declare Radius_V4  = Bond_Thick_0;
+ #declare Radius_V5  = Bond_Thick_0;
+ #declare Radius_Zn  = Bond_Thick_0;
+ #declare Radius_Zn2 = Bond_Thick_0;
+
+#else
+
+ //Atom radii in A as published in J. Emsley, The Elements, 
+ //Clarender Press, Oxford 1991
+
+ //All uncharged radii are kovalent. The values for Na and V are calculated 
+ //from the atomic radius (10% less).
+ //We use the kovalent radii for the description of metal atoms. If you want to
+ //use ion radii, just replace the radius in the atom description. 
+ //E.g., replace
+ //
+ //scale Radius_Zn
+ //
+ //by
+ //
+ //scale Radius_Zn2
+ //
+ //for creating a sphere with the ion radius of Zn2+.
+
+ #declare Radius_C1 = 0.770;
+ #declare Radius_C2 = 0.670;
+ #declare Radius_C3 = 0.600;
+
+ #declare Radius_H  = 0.370;
+ #declare Radius_D  = 0.370;
+ #declare Radius_O  = 0.660;
+ #declare Radius_N  = 0.700;
+ #declare Radius_S  = 1.040;
+ #declare Radius_P  = 1.100;
+ #declare Radius_F  = 0.580;
+ #declare Radius_Cl = 0.990; 
+ #declare Radius_Br = 1.142;
+ #declare Radius_I  = 1.330;
+
+ #declare Radius_Si = 1.170;
+ #declare Radius_B  = 0.880;
+ #declare Radius_Ge = 1.220;
+ #declare Radius_Se = 1.170;
+
+ #declare Radius_Ca  = 1.740;
+ #declare Radius_Ca2 = 1.060;
+ #declare Radius_Sn  = 1.400;
+ #declare Radius_Sn2 = 0.930;
+ #declare Radius_Sn4 = 0.740;
+ #declare Radius_Pb  = 1.540;
+ #declare Radius_Pb2 = 1.320;
+ #declare Radius_Pb4 = 0.890;
+ #declare Radius_Te  = 1.370;
+ #declare Radius_Te4 = 0.970;
+ #declare Radius_Te6 = 0.560;
+ #declare Radius_Na  = 1.380;
+ #declare Radius_Na1 = 0.980;
+ #declare Radius_K   = 2.030;
+ #declare Radius_K1  = 1.330;
+ #declare Radius_Li  = 1.230;
+ #declare Radius_Li1 = 0.780;
+ #declare Radius_Al  = 1.250;
+ #declare Radius_Al3 = 0.570;
+
+ #declare Radius_Mn  = 1.170;
+ #declare Radius_Mn2 = 0.910;
+ #declare Radius_Mn3 = 0.700;
+ #declare Radius_Mn4 = 0.520;
+ #declare Radius_W   = 1.300;
+ #declare Radius_W4  = 0.680;
+ #declare Radius_W6  = 0.620;
+ #declare Radius_Fe  = 1.165;
+ #declare Radius_Fe2 = 0.820;
+ #declare Radius_Fe3 = 0.670;
+ #declare Radius_Pd  = 1.280;
+ #declare Radius_Pd2 = 0.860;
+ #declare Radius_Pd4 = 0.640;
+ #declare Radius_Ni  = 1.150;
+ #declare Radius_Ni2 = 0.780;
+ #declare Radius_Ni3 = 0.620;
+ #declare Radius_Cu  = 1.170;
+ #declare Radius_Cu1 = 0.960;
+ #declare Radius_Cu2 = 0.720;
+ #declare Radius_V   = 1.188;
+ #declare Radius_V2  = 0.720;
+ #declare Radius_V3  = 0.650;
+ #declare Radius_V4  = 0.610;
+ #declare Radius_V5  = 0.590;
+ #declare Radius_Zn  = 1.250;
+ #declare Radius_Zn2 = 0.830;
+
+#end
+
+//Atom descriptions
+
+//Section: Nonmetals
+#declare Color_C1 = rgbf <0.00,0.00,0.00,NonMetalFilter>;
+#declare Atom_C1 = object { 
+                           
+                    atom
+                    scale Radius_C1
+                    texture {
+ 
+                     pigment {color Color_C1}
+                     finish {NonMetalFinish}
+ 
+                    }                           
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+
+                   }
+#declare Atom_C	   = Atom_C1
+#declare Atom_Cac  = Atom_C1
+#declare Atom_Cbl  = Atom_C1
+#declare Atom_Cmi  = Atom_C1
+#declare Atom_Crad = Atom_C1
+#declare Atom_Cx   = Atom_C1
+#declare Atom_Nr   = Atom_C1
+
+#declare Radius_Cac  = Radius_C1;
+#declare Radius_Cbl  = Radius_C1;
+#declare Radius_Cmi  = Radius_C1;
+#declare Radius_Crad = Radius_C1;
+#declare Radius_Cx   = Radius_C1;
+#declare Radius_Nr   = Radius_C1;
+
+#declare Color_C   = Color_C1;
+#declare Color_Cac  = Color_C1;
+#declare Color_Cbl  = Color_C1;
+#declare Color_Cmi  = Color_C1;
+#declare Color_Crad = Color_C1;
+#declare Color_Cx   = Color_C1;
+#declare Color_Nr   = Color_C1;
+
+#declare Color_C2 = rgbf <0.00,0.00,0.00,NonMetalFilter>;
+#declare Atom_C2  = object { 
+
+                     atom
+                     scale Radius_C2
+                     texture {
+ 
+                      pigment {color Color_C2}
+                      finish {NonMetalFinish}
+ 
+                     }                           
+#if (TRANS)
+	             interior{ I_Glass}
+#end
+                    }
+
+#declare Color_C3 = rgbf <0.00,0.00,0.00,NonMetalFilter>;
+#declare Atom_C3 = object { 
+
+                    atom
+                    scale Radius_C3
+                    texture {
+ 
+                     pigment {color Color_C3}
+                     finish {NonMetalFinish}
+
+                    }                           
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+#declare Atom_Car = Atom_C3
+#declare Atom_Cpl = Atom_C3
+#declare Atom_Cx  = Atom_C3
+
+#declare Radius_Car = Radius_C3;
+#declare Radius_Cpl = Radius_C3;
+#declare Radius_Cx  = Radius_C3;
+
+#declare Color_Car = Color_C3;
+#declare Color_Cpl = Color_C3;
+#declare Color_Cx  = Color_C3;
+
+#declare Color_H = rgbf <1.00,1.00,1.00,NonMetalFilter>;
+#declare Atom_H = object { 
+                   
+                   atom
+                   scale Radius_H
+                   texture {
+ 
+                    pigment {color Color_H}
+                    finish {NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+#declare Atom_HC  = Atom_H
+#declare Atom_HO  = Atom_H
+#declare Atom_HN  = Atom_H
+#declare Atom_Hpl = Atom_H
+
+#declare Radius_HC  = Radius_H;
+#declare Radius_HO  = Radius_H;
+#declare Radius_HN  = Radius_H;
+#declare Radius_Hpl = Radius_H;
+
+#declare Color_HC  = Color_H;
+#declare Color_HO  = Color_H;
+#declare Color_HN  = Color_H;
+#declare Color_Hpl = Color_H;
+
+#declare Color_D = rgbf <0.85,0.85,0.95,NonMetalFilter>;
+#declare Atom_D = object { 
+                          
+                   atom
+                   scale Radius_D
+                   texture {
+ 
+                    pigment {color Color_D}
+                    finish {NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+#declare Atom_DC = Atom_D
+
+#declare Radius_DC = Radius_D;
+
+#declare Color_DC = Color_D;
+
+#declare Color_O = rgbf <1.00,0.00,0.00,NonMetalFilter>;
+#declare Atom_O = object { 
+
+                   atom
+                   scale Radius_O
+                   texture {
+
+                    pigment {color Color_O}
+                    finish {NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+#declare Atom_O3   = Atom_O
+#declare Atom_O2   = Atom_O
+#declare Atom_Omi  = Atom_O
+#declare Atom_OCO2 = Atom_O
+#declare Atom_Oany = Atom_O
+#declare Atom_Oco2 = Atom_O
+
+#declare Radius_O3   = Radius_O;
+#declare Radius_O2   = Radius_O;
+#declare Radius_Omi  = Radius_O;
+#declare Radius_OCO2 = Radius_O;
+#declare Radius_Oany = Radius_O;
+#declare Radius_Oco2 = Radius_O;
+
+#declare Color_O3   = Color_O;
+#declare Color_O2   = Color_O;
+#declare Color_Omi  = Color_O;
+#declare Color_OCO2 = Color_O;
+#declare Color_Oany = Color_O;
+#declare Color_Oco2 = Color_O;
+
+#declare Color_N = rgbf <0.14,0.42,0.56,NonMetalFilter>;
+#declare Atom_N = object { 
+     
+                   atom
+                   scale Radius_N
+                   texture {
+                         
+                    pigment {color Color_N}
+                    finish {NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+#declare Atom_NPL3 = Atom_N
+#declare Atom_N2   = Atom_N
+#declare Atom_N4   = Atom_N
+#declare Atom_N3   = Atom_N
+#declare Atom_Npl  = Atom_N
+#declare Atom_N2pl = Atom_N
+#declare Atom_Naz  = Atom_N
+#declare Atom_N1   = Atom_N
+#declare Atom_Nox  = Atom_N
+#declare Atom_Ntr  = Atom_N
+#declare Atom_NC   = Atom_N
+#declare Atom_Nar  = Atom_N
+#declare Atom_Nam  = Atom_N
+#declare Atom_Ngpl = Atom_N
+#declare Atom_N3pl = Atom_N
+#declare Atom_Nany = Atom_N
+
+#declare Radius_NPL3 = Radius_N;
+#declare Radius_N2   = Radius_N;
+#declare Radius_N4   = Radius_N;
+#declare Radius_N3   = Radius_N;
+#declare Radius_Npl  = Radius_N;
+#declare Radius_N2pl = Radius_N;
+#declare Radius_Naz  = Radius_N;
+#declare Radius_N1   = Radius_N;
+#declare Radius_Nox  = Radius_N;
+#declare Radius_Ntr  = Radius_N;
+#declare Radius_NC   = Radius_N;
+#declare Radius_Nar  = Radius_N;
+#declare Radius_Nam  = Radius_N;
+#declare Radius_Ngpl = Radius_N;
+#declare Radius_N3pl = Radius_N;
+#declare Radius_Nany = Radius_N;
+
+#declare Color_NPL3 = Color_N;
+#declare Color_N2   = Color_N;
+#declare Color_N4   = Color_N;
+#declare Color_N3   = Color_N;
+#declare Color_Npl  = Color_N;
+#declare Color_N2pl = Color_N;
+#declare Color_Naz  = Color_N;
+#declare Color_N1   = Color_N;
+#declare Color_Nox  = Color_N;
+#declare Color_Ntr  = Color_N;
+#declare Color_NC   = Color_N;
+#declare Color_Nar  = Color_N;
+#declare Color_Nam  = Color_N;
+#declare Color_Ngpl = Color_N;
+#declare Color_N3pl = Color_N;
+#declare Color_Nany = Color_N;
+
+#declare Color_F = rgbf<1.00,1.00,0.88,NonMetalFilter>;
+#declare Atom_F = object {
+
+                   atom
+                   scale Radius_F
+                   texture {
+                   
+                    pigment {color Color_F}
+                    finish {NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+
+#declare Color_Cl = rgbf <0.20,0.80,0.20,NonMetalFilter>;
+#declare Atom_Cl = object {
+
+                    atom
+                    scale Radius_Cl
+                    texture {
+                
+                     pigment {color Color_Cl}
+                     finish {NonMetalFinish}
+ 
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Br = rgbf <0.65,0.16,0.16,NonMetalFilter>;
+#declare Atom_Br = object {
+
+                    atom
+                    scale Radius_Br
+                    texture {
+                    
+                     pigment {color Color_Br}
+                     finish {NonMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_I = rgbf<0.58,0.44,0.86,NonMetalFilter>;
+#declare Atom_I = object {
+
+                   atom
+                   scale Radius_I
+                   texture {
+                  
+                    pigment {color Color_I}
+                    finish {NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+
+#declare Color_P = rgbf <1.00,0.50,0.00,NonMetalFilter>;
+#declare Atom_P = object {
+
+                   atom
+                   scale Radius_P
+                   texture {
+                   
+                    pigment {color Color_P}
+                    finish{NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+#declare Atom_Pac  = Atom_P
+#declare Atom_P3   = Atom_P
+#declare Atom_Pox  = Atom_P
+#declare Atom_P3pl = Atom_P
+
+#declare Radius_Pac  = Radius_P;
+#declare Radius_P3   = Radius_P;
+#declare Radius_Pox  = Radius_P;
+#declare Radius_P3pl = Radius_P;
+
+#declare Color_Pac  = Color_P;
+#declare Color_P3   = Color_P;
+#declare Color_Pox  = Color_P;
+#declare Color_P3pl = Color_P;
+
+#declare Color_S = rgbf <1.00,1.00,0.00,NonMetalFilter>;
+#declare Atom_S = object {
+
+                   atom
+                   scale Radius_S
+                   texture {
+                         
+                    pigment {color Color_S}
+                    finish {NonMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+#declare Atom_S3pl = Atom_S
+#declare Atom_S3   = Atom_S
+#declare Atom_S2   = Atom_S
+#declare Atom_Sac  = Atom_S
+#declare Atom_Sox  = Atom_S
+#declare Atom_Sany = Atom_S
+#declare Atom_So   = Atom_S
+
+#declare Radius_S3pl = Radius_S;
+#declare Radius_S3   = Radius_S;
+#declare Radius_S2   = Radius_S;
+#declare Radius_Sac  = Radius_S;
+#declare Radius_Sox  = Radius_S;
+#declare Radius_Sany = Radius_S;
+#declare Radius_So   = Radius_S;
+
+#declare Color_S3pl = Color_S;
+#declare Color_S3   = Color_S;
+#declare Color_S2   = Color_S;
+#declare Color_Sac  = Color_S;
+#declare Color_Sox  = Color_S;
+#declare Color_Sany = Color_S;
+#declare Color_So   = Color_S;
+
+//A special color for halfmetals
+#declare HalfMetalColor = rgbf <0.6,0.6,0.85,HalfMetalFilter>; 
+
+//Section: HalfMetals
+#declare Color_B = rgbf <0,1.0,0,HalfMetalFilter>;
+#declare Atom_B = object {
+
+                   atom
+                   scale Radius_B
+                   texture {
+                   
+                    pigment {color Color_B}
+                    finish {HalfMetalFinish}
+                   
+                   }
+#if (TRANS)
+                   interior{ I_Glass}
+#end
+                  }
+#declare Atom_Bac = Atom_B
+#declare Atom_Box = Atom_B
+
+#declare Radius_Bac = Radius_B;
+#declare Radius_Box = Radius_B;
+
+#declare Color_Bac = Color_B;
+#declare Color_Box = Color_B;
+
+#declare Color_Si = HalfMetalColor;
+#declare Atom_Si = object {
+ 
+                    atom
+                    scale Radius_Si
+                    texture {
+
+                     pigment {color Color_Si}
+                     finish {HalfMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+
+#declare Color_Ge = HalfMetalColor;
+#declare Atom_Ge = object { 
+
+                    atom
+                    scale Radius_Ge
+                    texture {
+
+                     pigment {color Color_Ge}
+                     finish {HalfMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+#declare Color_Se = HalfMetalColor;
+#declare Atom_Se = object { 
+
+                    atom
+                    scale Radius_Se
+                    texture {
+
+                     pigment {color Color_Se}
+                     finish {HalfMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+//Metals
+#declare Color_Metal = rgbf <0.94,0.93,0.90,MetalFilter>;
+
+#declare Color_Te = rgbf <0.6,0.6,0.6,MetalFilter>;
+#declare Atom_Te = object { 
+
+                    atom
+                    scale Radius_Te
+                    texture {
+
+                     pigment {color Color_Te}
+                     finish {MetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Li = Color_Metal;
+#declare Atom_Li = object { 
+
+                    atom
+                    scale Radius_Li                          
+                    texture {
+                     
+                     pigment {color Color_Li}
+                     finish {MetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Na = Color_Metal;
+#declare Atom_Na = object { 
+
+                    atom
+                    scale Radius_Na
+                    texture {
+                      
+                     pigment {color Color_Na}
+                     finish {MetalFinish}
+   
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_K = Color_Metal;
+#declare Atom_K = object { 
+
+                   atom
+                   scale Radius_K
+                   texture {
+                           
+                    pigment {color Color_K}
+                    finish {MetalFinish}
+
+                   }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                  }
+
+#declare Color_Ca = Color_Metal;
+#declare Atom_Ca = object {
+ 
+                    atom
+                    scale Radius_Ca
+                    texture {
+                     
+                     pigment {color Color_Ca}
+                     finish {MetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Al = Color_Metal;
+#declare Atom_Al = object { 
+
+                    atom
+                    scale Radius_Al
+                    texture {
+                    
+                     pigment {color Color_Al}
+                     finish {MetalFinish}
+ 
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Sn = Color_Metal;
+#declare Atom_Sn = object { 
+
+                    atom
+                    scale Radius_Sn
+                    texture {
+                    
+                     pigment {color Color_Sn}
+                     finish {MetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Pb = Color_Metal;
+#declare Atom_Pb = object { 
+
+                    atom
+                    scale Radius_Pb
+                    texture {
+                     
+                     pigment {color Color_Pb}
+                     finish {MetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+//TransMetals
+#declare Color_TransMetal = rgbf <0.94,0.93,0.90,TransMetalFilter>;
+
+#declare Color_W = Color_TransMetal;
+#declare Atom_W = object { 
+
+                   atom
+                   scale Radius_W
+                   texture {
+
+                    pigment {color Color_W}
+                    finish {TransMetalFinish}
+
+                   }
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+
+#declare Color_Pd = Color_TransMetal;
+#declare Atom_Pd = object { 
+
+                    atom
+                    scale Radius_Pd
+                    texture {
+  
+                     pigment {color Color_Pd}
+                     finish {TransMetalFinish}
+ 
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Ni = Color_TransMetal;
+#declare Atom_Ni = object { 
+
+                    atom
+                    scale Radius_Ni
+                    texture {
+
+                     pigment {color Color_Ni}
+                     finish {TransMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Cu = rgbf <0.50,0.25,0.15,TransMetalFilter>;
+#declare Atom_Cu = object { 
+
+                    atom
+                    scale Radius_Cu
+
+                    texture {
+
+                     pigment {color Color_Cu}
+                     finish {TransMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Mn = Color_TransMetal;
+#declare Atom_Mn = object { 
+
+                    atom
+                    scale Radius_Mn
+                    texture {
+
+                     pigment {color Color_Mn}
+                     finish {TransMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+#declare Color_Fe = Color_TransMetal;
+#declare Atom_Fe = object { 
+
+                    atom
+                    scale Radius_Fe
+
+                    texture {
+
+                     pigment {color Color_Fe}
+                     finish {TransMetalFinish}
+
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   }
+
+
+#declare Color_V = Color_TransMetal;
+#declare Atom_V = object {
+                    
+                   atom
+                   scale Radius_V
+                   texture {
+                     
+                    pigment {color Color_V}
+                    finish {TransMetalFinish}
+                     
+                   } 
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }
+
+#declare Atom_V2 = object {
+                    
+                   atom
+                   scale Radius_V2
+                   texture {
+                     
+                    pigment {color Color_V}
+                    finish {TransMetalFinish}
+                     
+                   } 
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }  
+
+#declare Atom_V3 = object {
+                    
+                   atom
+                   scale Radius_V3
+                   texture {
+                     
+                    pigment {color Color_V}
+                    finish {TransMetalFinish}
+                     
+                   } 
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }  
+
+#declare Atom_V4 = object {
+                    
+                   atom
+                   scale Radius_V4
+                   texture {
+                     
+                    pigment {color Color_V}
+                    finish {TransMetalFinish}
+                     
+                   } 
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  } 
+
+#declare Atom_V5 = object {
+                    
+                   atom
+                   scale Radius_V5
+                   texture {
+                     
+                    pigment {color Color_V}
+                    finish {TransMetalFinish}
+                     
+                   } 
+#if (TRANS)
+	           interior{ I_Glass}
+#end
+                  }  
+
+
+#declare Color_Zn = Color_TransMetal;
+#declare Atom_Zn = object {
+                    
+                    atom
+                    scale Radius_Zn
+                    texture {
+                     
+                     pigment {color Color_Zn} 
+                     finish {TransMetalFinish}
+                     
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   } 
+
+#declare Atom_Zn2 = object {
+                    
+                    atom
+                    scale Radius_Zn2
+                    texture {
+                     
+                     pigment {color Color_Zn} 
+                     finish {TransMetalFinish}
+                     
+                    }
+#if (TRANS)
+	            interior{ I_Glass}
+#end
+                   } 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/bin2hex.pl	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,144 @@
+#!/usr/bin/env perl
+# bin2hex.pl
+
+########################################################################
+# Copyright (C) 2001 by OpenEye Scientific Software, Inc.
+# Some portions Copyright (c) 2002 by Geoffrey R. Hutchison
+#
+# This file is part of the Open Babel project.
+# For more information, see <http://openbabel.org/>
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation version 2 of the License.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+########################################################################
+
+
+# Autoflush STDOUT
+#STDOUT->autoflush(1);
+$| = 1;
+
+$argc = @ARGV;
+if( $argc == 2 ) {
+    $filename = @ARGV[0];
+    $arrayname = @ARGV[1];
+
+    $pos = index($filename,".");
+    if( $pos > 0 ) {
+        $guard = uc(substr($filename,0,$pos));
+    } else {
+        $guard = uc($filename);
+    }
+} elsif( $argc == 3 ) {
+    $filename = @ARGV[0];
+    $arrayname = @ARGV[1];
+    $guard = @ARGV[2];
+} else {
+    print "usage:  bin2hex.pl <binaryfile> <arrayname>\n\n";
+    exit;
+}
+
+$debug = 0;
+
+open(F,$filename) || die "Error: Unable to open binary file!\n";
+
+if( !$debug ) {
+    print "/***************************************************************\n";
+    print "This file is part of the Open Babel project.\n";
+    print "This is copyright under the GNU General Public License (GPL)\n";
+    print "For more information, see <http://openbabel.org/>\n\n";
+    print "This file contains a binary representation of data tables\n";
+    print " used by Open Babel. It is used as a fallback if the textual\n";
+    print " data table is not found at runtime. It is not a normal header.\n";
+    print "***************************************************************/\n";
+    print "\n\n";
+
+    print "#ifndef OB_" . $guard . "_H\n";
+    print "#define OB_" . $guard . "_H\n\n";
+    print "namespace OpenBabel\n{\n";
+    print "static const char " . $arrayname . "[] = {\n ";
+}
+
+binmode(F);
+
+$col = 0;
+$init = 0;
+$ignore = 0;
+$newline = 1;
+$spacerun = 0; # collapse runs of spaces
+
+while( !eof(F) ) {
+    $ch = ord(getc(F));
+    if( $ch == 13 ) { # ignore \r characters
+        $ch = 0;
+    }
+
+    if ( $spacerun ) {
+        if ( $ch == 32 ) {
+            $ch = 0;
+        } else {
+            $spacerun = 0;
+        }
+    } elsif ( $ch == 32) {
+        $spacerun = 1;
+    }
+
+    if( $ignore ) {
+        if( $ch == 10 ) { # found the \n after an '#' ignore comment
+            $ignore = 0;
+        }
+        $ch = 0;
+    } elsif( $newline ) { # just saw a \n -- do we see real text
+        if( $ch == 10 ) {
+            $ch = 0;
+        } elsif ( $ch == 35 ) { # ignore anything after a '#' until a \n
+            $ignore = 1;
+            $ch = 0;
+        } elsif( $ch == 32 ) { # space
+            $ch = 0;
+        } elsif( $ch == 9 ) { # tab
+            $ch = 0;
+        } elsif( $ch ) { # something else, so clear the blank-line boolean
+            $newline = 0;
+        }
+    } elsif( $ch == 10 ) { # set the blank-line detector
+        $newline = 1;
+    }
+
+    if( $ch ) {
+        if( $debug ) {
+            print chr($ch);
+        } else {
+            if( $init ) {
+                print ",";
+            } else {
+                $init = 1;
+            }
+            if( $col >= 15 ) {
+                print "\n ";
+                $col = 0;
+            }
+            print sprintf("0x%02X",$ch);
+            $col++;
+        }
+    }
+}
+
+if( !$debug ) {
+    if( $col >= 15 ) {
+        print ",\n0x00};\n\n";
+    } else {
+        print ",0x00};\n\n";
+    }
+    print "} // namespace OpenBabel\n";
+    print "#endif // OB_" . $guard . "_H\n\n";
+}
+
+close(F);
+exit;
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/bondtyp.h	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,132 @@
+/***************************************************************
+This file is part of the Open Babel project.
+This is copyright under the GNU General Public License (GPL)
+For more information, see <http://openbabel.org/>
+
+This file contains a binary representation of data tables
+ used by Open Babel. It is used as a fallback if the textual
+ data table is not found at runtime. It is not a normal header.
+***************************************************************/
+
+
+#ifndef OB_BONDTYP_H
+#define OB_BONDTYP_H
+
+namespace OpenBabel
+{
+static const char BondTypeData[] = {
+ 0x2A,0x31,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x32,0x29,
+ 0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x32,0x2A,0x5B,
+ 0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x33,0x29,0x5B,0x23,0x36,
+ 0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x33,0x2A,0x5B,0x23,0x36,0x5D,
+ 0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x34,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,
+ 0x36,0x5D,0x5B,0x23,0x36,0x5D,0x34,0x2A,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,
+ 0x37,0x44,0x33,0x5D,0x35,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,
+ 0x23,0x36,0x5D,0x35,0x31,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,0x32,
+ 0x20,0x31,0x20,0x31,0x20,0x33,0x20,0x31,0x20,0x33,0x20,0x34,0x20,0x32,0x20,
+ 0x34,0x20,0x35,0x20,0x31,0x20,0x35,0x20,0x32,0x20,0x31,0x20,0x35,0x20,0x36,
+ 0x20,0x32,0x20,0x36,0x20,0x37,0x20,0x31,0x20,0x37,0x20,0x38,0x20,0x32,0x20,
+ 0x37,0x20,0x39,0x20,0x31,0x20,0x39,0x20,0x31,0x30,0x20,0x32,0x20,0x31,0x30,
+ 0x20,0x31,0x31,0x20,0x31,0x20,0x31,0x31,0x20,0x38,0x20,0x31,0x20,0x31,0x31,
+ 0x20,0x31,0x32,0x20,0x32,0x20,0x31,0x32,0x20,0x31,0x33,0x20,0x31,0x20,0x31,
+ 0x33,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x33,0x20,0x31,0x35,0x20,0x32,0x20,
+ 0x31,0x35,0x20,0x31,0x36,0x20,0x31,0x20,0x31,0x36,0x20,0x31,0x37,0x20,0x32,
+ 0x20,0x31,0x37,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x37,0x20,0x31,0x38,0x20,
+ 0x31,0x20,0x31,0x38,0x20,0x31,0x39,0x20,0x32,0x20,0x31,0x39,0x20,0x32,0x30,
+ 0x20,0x31,0x20,0x31,0x39,0x20,0x32,0x31,0x20,0x31,0x20,0x32,0x31,0x20,0x32,
+ 0x32,0x20,0x32,0x20,0x32,0x32,0x20,0x32,0x33,0x20,0x31,0x20,0x32,0x33,0x20,
+ 0x32,0x30,0x20,0x32,0x0A,0x2A,0x31,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,
+ 0x44,0x33,0x5D,0x32,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,
+ 0x36,0x5D,0x32,0x2A,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x5D,0x33,0x29,
+ 0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x33,0x2A,0x5B,
+ 0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x34,0x29,0x5B,0x23,0x36,
+ 0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x34,0x2A,0x5B,0x23,0x36,0x5D,
+ 0x28,0x5B,0x23,0x37,0x5D,0x35,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,
+ 0x5B,0x23,0x36,0x5D,0x35,0x31,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,
+ 0x32,0x20,0x31,0x20,0x31,0x20,0x33,0x20,0x31,0x20,0x33,0x20,0x34,0x20,0x32,
+ 0x20,0x34,0x20,0x35,0x20,0x31,0x20,0x35,0x20,0x32,0x20,0x31,0x20,0x35,0x20,
+ 0x36,0x20,0x32,0x20,0x36,0x20,0x37,0x20,0x31,0x20,0x37,0x20,0x38,0x20,0x32,
+ 0x20,0x37,0x20,0x39,0x20,0x31,0x20,0x39,0x20,0x31,0x30,0x20,0x32,0x20,0x31,
+ 0x30,0x20,0x31,0x31,0x20,0x31,0x20,0x31,0x31,0x20,0x38,0x20,0x31,0x20,0x31,
+ 0x31,0x20,0x31,0x32,0x20,0x32,0x20,0x31,0x32,0x20,0x31,0x33,0x20,0x31,0x20,
+ 0x31,0x33,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x33,0x20,0x31,0x35,0x20,0x32,
+ 0x20,0x31,0x35,0x20,0x31,0x36,0x20,0x31,0x20,0x31,0x36,0x20,0x31,0x37,0x20,
+ 0x32,0x20,0x31,0x37,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x37,0x20,0x31,0x38,
+ 0x20,0x31,0x20,0x31,0x38,0x20,0x31,0x39,0x20,0x32,0x20,0x31,0x39,0x20,0x32,
+ 0x30,0x20,0x31,0x20,0x31,0x39,0x20,0x32,0x31,0x20,0x31,0x20,0x32,0x31,0x20,
+ 0x32,0x32,0x20,0x32,0x20,0x32,0x32,0x20,0x32,0x33,0x20,0x31,0x20,0x32,0x33,
+ 0x20,0x32,0x30,0x20,0x32,0x0A,0x2A,0x31,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,
+ 0x37,0x5D,0x32,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,
+ 0x5D,0x32,0x2A,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x5D,0x33,0x29,0x5B,
+ 0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x33,0x2A,0x5B,0x23,
+ 0x36,0x5D,0x28,0x5B,0x23,0x37,0x5D,0x34,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,
+ 0x36,0x5D,0x5B,0x23,0x36,0x5D,0x34,0x2A,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,
+ 0x37,0x5D,0x35,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,
+ 0x5D,0x35,0x31,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,0x32,0x20,0x31,
+ 0x20,0x31,0x20,0x33,0x20,0x31,0x20,0x33,0x20,0x34,0x20,0x32,0x20,0x34,0x20,
+ 0x35,0x20,0x31,0x20,0x35,0x20,0x32,0x20,0x31,0x20,0x35,0x20,0x36,0x20,0x32,
+ 0x20,0x36,0x20,0x37,0x20,0x31,0x20,0x37,0x20,0x38,0x20,0x32,0x20,0x37,0x20,
+ 0x39,0x20,0x31,0x20,0x39,0x20,0x31,0x30,0x20,0x32,0x20,0x31,0x30,0x20,0x31,
+ 0x31,0x20,0x31,0x20,0x31,0x31,0x20,0x38,0x20,0x31,0x20,0x31,0x31,0x20,0x31,
+ 0x32,0x20,0x32,0x20,0x31,0x32,0x20,0x31,0x33,0x20,0x31,0x20,0x31,0x33,0x20,
+ 0x31,0x34,0x20,0x31,0x20,0x31,0x33,0x20,0x31,0x35,0x20,0x32,0x20,0x31,0x35,
+ 0x20,0x31,0x36,0x20,0x31,0x20,0x31,0x36,0x20,0x31,0x37,0x20,0x32,0x20,0x31,
+ 0x37,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x37,0x20,0x31,0x38,0x20,0x31,0x20,
+ 0x31,0x38,0x20,0x31,0x39,0x20,0x32,0x20,0x31,0x39,0x20,0x32,0x30,0x20,0x31,
+ 0x20,0x31,0x39,0x20,0x32,0x31,0x20,0x31,0x20,0x32,0x31,0x20,0x32,0x32,0x20,
+ 0x32,0x20,0x32,0x32,0x20,0x32,0x33,0x20,0x31,0x20,0x32,0x33,0x20,0x32,0x30,
+ 0x20,0x32,0x0A,0x5B,0x23,0x37,0x44,0x32,0x5D,0x5B,0x23,0x37,0x44,0x32,0x5E,
+ 0x31,0x5D,0x5B,0x23,0x37,0x44,0x31,0x5D,0x09,0x09,0x30,0x20,0x31,0x20,0x32,
+ 0x20,0x31,0x20,0x32,0x20,0x32,0x0A,0x5B,0x23,0x38,0x44,0x31,0x5D,0x5B,0x23,
+ 0x37,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x38,0x44,0x31,0x5D,0x29,0x2A,
+ 0x09,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,0x32,0x20,0x32,0x20,0x31,
+ 0x20,0x33,0x20,0x31,0x0A,0x5B,0x23,0x31,0x36,0x44,0x34,0x5D,0x28,0x5B,0x23,
+ 0x38,0x44,0x31,0x5D,0x29,0x28,0x5B,0x23,0x38,0x44,0x31,0x5D,0x29,0x28,0x2A,
+ 0x29,0x28,0x2A,0x29,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,
+ 0x32,0x20,0x30,0x20,0x33,0x20,0x31,0x20,0x30,0x20,0x34,0x20,0x31,0x0A,0x5B,
+ 0x23,0x31,0x35,0x44,0x34,0x5D,0x28,0x5B,0x23,0x38,0x44,0x31,0x5D,0x29,0x28,
+ 0x2A,0x29,0x28,0x2A,0x29,0x28,0x2A,0x29,0x09,0x30,0x20,0x31,0x20,0x32,0x20,
+ 0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,0x20,0x30,0x20,0x34,
+ 0x20,0x31,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x38,
+ 0x44,0x31,0x5D,0x29,0x28,0x5B,0x23,0x38,0x5D,0x29,0x2A,0x09,0x09,0x30,0x20,
+ 0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,
+ 0x0A,0x5B,0x23,0x38,0x44,0x31,0x5D,0x5B,0x23,0x36,0x44,0x32,0x5E,0x31,0x5D,
+ 0x5B,0x23,0x38,0x44,0x31,0x5D,0x09,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,
+ 0x20,0x32,0x20,0x32,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,
+ 0x23,0x38,0x44,0x31,0x5D,0x29,0x28,0x5B,0x23,0x37,0x5D,0x29,0x2A,0x09,0x09,
+ 0x30,0x20,0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,
+ 0x20,0x31,0x0A,0x5B,0x23,0x33,0x34,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,
+ 0x38,0x44,0x31,0x5D,0x29,0x28,0x5B,0x23,0x38,0x5D,0x29,0x2A,0x09,0x09,0x30,
+ 0x20,0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,
+ 0x31,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x38,0x44,
+ 0x31,0x5D,0x29,0x28,0x5B,0x23,0x31,0x36,0x5D,0x29,0x2A,0x09,0x09,0x30,0x20,
+ 0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,
+ 0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x31,0x36,0x44,
+ 0x31,0x5D,0x29,0x28,0x5B,0x23,0x31,0x36,0x5D,0x29,0x2A,0x09,0x09,0x30,0x20,
+ 0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,
+ 0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x5D,0x28,0x5B,0x23,0x31,0x36,0x44,
+ 0x31,0x5D,0x29,0x28,0x5B,0x23,0x37,0x5D,0x29,0x2A,0x09,0x09,0x30,0x20,0x31,
+ 0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,0x0A,
+ 0x5B,0x23,0x36,0x5E,0x32,0x5D,0x5B,0x23,0x36,0x44,0x32,0x5E,0x31,0x5D,0x5B,
+ 0x23,0x36,0x5E,0x32,0x5D,0x09,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,
+ 0x32,0x20,0x32,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,0x5D,
+ 0x28,0x5B,0x23,0x37,0x44,0x31,0x48,0x30,0x3B,0x21,0x52,0x5D,0x29,0x28,0x5B,
+ 0x23,0x37,0x3B,0x21,0x52,0x5D,0x29,0x2A,0x09,0x30,0x20,0x31,0x20,0x32,0x20,
+ 0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,0x0A,0x5B,0x23,0x36,
+ 0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,0x5D,0x28,0x5B,0x23,0x37,0x44,0x32,0x48,
+ 0x31,0x3B,0x21,0x52,0x5D,0x29,0x28,0x5B,0x23,0x37,0x3B,0x21,0x52,0x5D,0x29,
+ 0x2A,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,
+ 0x20,0x33,0x20,0x31,0x0A,0x5B,0x23,0x36,0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,
+ 0x5D,0x28,0x5B,0x23,0x37,0x44,0x33,0x48,0x32,0x3B,0x21,0x52,0x5D,0x29,0x28,
+ 0x5B,0x23,0x37,0x3B,0x21,0x52,0x5D,0x29,0x2A,0x09,0x30,0x20,0x31,0x20,0x32,
+ 0x20,0x30,0x20,0x32,0x20,0x31,0x20,0x30,0x20,0x33,0x20,0x31,0x0A,0x5B,0x23,
+ 0x36,0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,0x5D,0x28,0x5B,0x23,0x31,0x2C,0x23,
+ 0x36,0x5D,0x29,0x28,0x5B,0x23,0x31,0x2C,0x23,0x36,0x5D,0x29,0x5B,0x23,0x37,
+ 0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,0x5D,0x28,0x5B,0x23,0x31,0x5D,0x29,0x5B,
+ 0x23,0x36,0x5D,0x09,0x30,0x20,0x31,0x20,0x31,0x20,0x30,0x20,0x32,0x20,0x31,
+ 0x20,0x30,0x20,0x33,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x31,0x20,0x33,0x20,
+ 0x35,0x20,0x31,0x0A,0x00};
+
+} // namespace OpenBabel
+#endif // OB_BONDTYP_H
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/bondtyp.txt	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,76 @@
+##############################################################################
+#                                                                            #
+#    Open Babel file: bondtyp.txt                                            #
+#                                                                            #
+#  Copyright (c) 2002-2005 by Geoffrey R Hutchison                           #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+# Used by bondtyper.cpp::OBBondTyper (and thus OBMol::PerceiveBondOrders()   #
+#                                                                            #
+# List of functional groups with double, triple (etc.) bond orders           #
+# Pattern       Atom1 Atom2 Bond Order (repeat as needed)                    #
+# * = Any atom (for setting non-multiple bonds)                              #
+#                                                                            #
+# NOTE: These are applied in order, first to last.                           #
+#     So it's generally better to have a long (specifc) SMARTS first.        #
+#     (all bonds must be single bonds to match)                              #
+#                                                                            #
+##############################################################################
+
+# Porphyrin / phthalocyanine (3 patterns for three separate bonding motifs)
+# this one has explicit bonds to all four nitrogens (e.g., metal bond or hydrogens)
+#0  1    2       3   4   5  6  7     8      9  10  11  12 13   14     15 16   17  18 19  20       21 22  23
+*1[#6]([#7D3]2)[#6][#6][#6]2*[#6]([#7D3]3)[#6][#6][#6]3*[#6]([#7D3]4)[#6][#6][#6]4*[#6]([#7D3]5)[#6][#6][#6]51	0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
+
+# this one has explicit bonds to two nitrogens (12 and 14)
+#0  1    2       3   4   5  6  7    8     9  10  11  12 13   14     15 16   17  18 19  20    21 22  23
+*1[#6]([#7D3]2)[#6][#6][#6]2*[#6]([#7]3)[#6][#6][#6]3*[#6]([#7D3]4)[#6][#6][#6]4*[#6]([#7]5)[#6][#6][#6]51	0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
+
+# and this one doesn't have any explicit bonds to the nitrogens
+#0  1    2     3   4   5  6  7    8     9  10  11  12 13   14   15  16  17 18 19   20    21 22  23
+*1[#6]([#7]2)[#6][#6][#6]2*[#6]([#7]3)[#6][#6][#6]3*[#6]([#7]4)[#6][#6][#6]4*[#6]([#7]5)[#6][#6][#6]51	0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2
+
+# Azide
+[#7D2][#7D2^1][#7D1]		0 1 2 1 2 2
+# Nitro
+[#8D1][#7D3^2]([#8D1])*		0 1 2 1 2 2 1 3 1
+# Sulphone
+[#16D4]([#8D1])([#8D1])(*)(*)	0 1 2 0 2 2 0 3 1 0 4 1
+# Phosphone
+[#15D4]([#8D1])(*)(*)(*)	0 1 2 0 2 1 0 3 1 0 4 1
+
+# Carboxylic Acid, ester, etc.
+[#6D3^2]([#8D1])([#8])*		0 1 2 0 2 1 0 3 1
+# Carbon dioxide
+[#8D1][#6D2^1][#8D1]		0 1 2 1 2 2
+# Amide C(=O)N
+[#6D3^2]([#8D1])([#7])*		0 1 2 0 2 1 0 3 1
+# Seleninic acid Se(=O)OH
+[#34D3^2]([#8D1])([#8])*		0 1 2 0 2 1 0 3 1
+# Thioacid / Thioester C(=O)S
+[#6D3^2]([#8D1])([#16])*		0 1 2 0 2 1 0 3 1
+# dithioacid / dithioester C(=S)S
+[#6D3^2]([#16D1])([#16])*		0 1 2 0 2 1 0 3 1
+# thioamide C(=S)N
+[#6D3^2]([#16D1])([#7])*		0 1 2 0 2 1 0 3 1
+
+# allene C=C=C
+# (this is problematic -- need to make sure the center carbon is sp)
+[#6^2][#6D2^1][#6^2]		0 1 2 1 2 2
+
+# guanidinium and amidine -C(=NH)NH2 without hydrogens
+[#6D3^2;!R]([#7D1H0;!R])([#7;!R])*	0 1 2 0 2 1 0 3 1
+# and also with hydrogens
+# (this can normally be figured out, but is needed to avoid matching the next SMARTS)
+[#6D3^2;!R]([#7D2H1;!R])([#7;!R])*	0 1 2 0 2 1 0 3 1
+# and also with more hydrogens than normal (protonated)
+[#6D3^2;!R]([#7D3H2;!R])([#7;!R])*	0 1 2 0 2 1 0 3 1
+
+# Schiff base, protonated
+[#6D3^2;!R]([#1,#6])([#1,#6])[#7D3^2;!R]([#1])[#6]	0 1 1 0 2 1 0 3 2 3 4 1 3 5 1
+
+### other potential functional groups that may (or may not) be useful to add
+# imidines ( N=C/N\C=N
+# sulfoxides
+# heme / porphyrin
+# phthalocyanine
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/cmake_install.cmake	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,78 @@
+# Install script for directory: /Users/marcel/Documents/openbabel-2.3.1/data
+
+# Set the install prefix
+IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+  SET(CMAKE_INSTALL_PREFIX "/usr/local")
+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 "${COMPONENT}")
+  ELSE(COMPONENT)
+    SET(CMAKE_INSTALL_COMPONENT)
+  ENDIF(COMPONENT)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT)
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/openbabel/2.3.1" TYPE FILE FILES
+    "/Users/marcel/Documents/openbabel-2.3.1/data/aromatic.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/atomtyp.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/babel_povray3.inc"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/bondtyp.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/element.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/fragments.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/gaff.dat"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/gaff.prm"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/ghemical.prm"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/isotope-small.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/isotope.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/logp.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/MACCS.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmff94.ff"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmff94s.ff"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmffang.par"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmffbndk.par"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmffbond.par"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmffchg.par"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmffdef.par"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmffdfsb.par"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmffoop.par"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmffpbci.par"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmffprop.par"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmffstbn.par"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmfftor.par"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmffvdw.par"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmffs_oop.par"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mmffs_tor.par"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/mr.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/patterns.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/phmodel.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/plugindefines.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/psa.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/qeq.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/resdata.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/ringtyp.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/SMARTS_InteLigand.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/space-groups.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/superatom.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/svgformat.script"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/torlib.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/types.txt"
+    "/Users/marcel/Documents/openbabel-2.3.1/data/UFF.prm"
+    )
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/element.h	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,616 @@
+/***************************************************************
+This file is part of the Open Babel project.
+This is copyright under the GNU General Public License (GPL)
+For more information, see <http://openbabel.org/>
+
+This file contains a binary representation of data tables
+ used by Open Babel. It is used as a fallback if the textual
+ data table is not found at runtime. It is not a normal header.
+***************************************************************/
+
+
+#ifndef OB_ELEMENT_H
+#define OB_ELEMENT_H
+
+namespace OpenBabel
+{
+static const char ElementData[] = {
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+0x00};
+
+} // namespace OpenBabel
+#endif // OB_ELEMENT_H
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CADDSuite-1.0.1/data/OpenBabel/element.txt	Tue Nov 15 10:53:16 2011 -0500
@@ -0,0 +1,153 @@
+##############################################################################
+#                                                                            #
+#	                Open Babel file: element.txt                         #
+#                                                                            #
+#  Some portions Copyright (c) 2001-2009 Geoffrey R. Hutchison               #
+#  Part of the Open Babel package, under the GNU General Public License (GPL)#
+#                                                                            #
+#  Created from the Blue Obelisk Cheminformatics Data Repository             #
+#  Direct Source: http://www.blueobelisk.org/                                #
+#       http://www.blueobelisk.org/repos/blueobelisk/elements.xml            #
+#  (includes furhter bibliographic citation information)                     #
+#                                                                            #
+#  Allred and Rochow Electronegativity from:                                 #
+#  http://www.hull.ac.uk/chemistry/electroneg.php?type=Allred-Rochow         #
+#                                                                            #
+#  Columns represent:  (used by data.cpp:OBElementTable and OBElement)       #
+#   - atomic number (used as an index to the vector as well)                 #
+#   - elemental symbol							     #
+#   - Allred and Rochow electronegativity  0.0 if unknown		     #
+#   - covalent radii (in Angstrom)         1.6 if unknown		     #
+#       from http://dx.doi.org/10.1039/b801115j                              #
+#   - "bond order" radii -- ignored, but included for compatibility          #
+#   - van der Waals radii (in Angstrom)	   2.0 if unknown		     #
+#       from http://dx.doi.org/10.1021/jp8111556                             #
+#   - maximum bond valence		   6 if unknown			     #
+#   - IUPAC recommended atomic masses (in amu)				     #
+#   - Pauling electronegativity		   0.0 if unknown		     #
+#   - ionization potential (in eV)         0.0 if unknown                    #
+#   - electron affinity (in eV)            0.0 if unknown                    #
+#   - RGB values (defaults for visualization)				     #
+#   - element name (in English)						     #
+#                                                                            #
+##############################################################################
+#Num	Symb	ARENeg	RCov	RBO	RVdW	MaxBnd	Mass	ElNeg.	Ionization	ElAffinity	Red	Green	Blue	Name
+0	Xx	0.00	0.00	0.00	0.00	0	0	0.00	0	0	0.07	0.50	0.70	Dummy
+1	H	2.20	0.31	0.31	1.10	1	1.00794	2.20	13.5984	0.75420375	0.75	0.75	0.75	Hydrogen
+2	He	0.00	0.28	0.28	1.40	0	4.002602	0.00	24.5874	0	0.85	1.00	1.00	Helium
+3	Li	0.97	1.28	1.28	1.81	1	6.941	0.98	5.3917	0.618049	0.80	0.50	1.00	Lithium
+4	Be	1.47	0.96	0.96	1.53	2	9.012182	1.57	9.3227	0	0.76	1.00	0.00	Beryllium
+5	B	2.01	0.84	0.84	1.92	4	10.811	2.04	8.298	0.279723	1.00	0.71	0.71	Boron
+6	C	2.50	0.76	0.76	1.70	4	12.0107	2.55	11.2603	1.262118	0.40	0.40	0.40	Carbon
+7	N	3.07	0.71	0.71	1.55	4	14.0067	3.04	14.5341	-0.07	0.05	0.05	1.00	Nitrogen
+8	O	3.50	0.66	0.66	1.52	2	15.9994	3.44	13.6181	1.461112	1.00	0.05	0.05	Oxygen
+9	F	4.10	0.57	0.57	1.47	1	18.9984032	3.98	17.4228	3.4011887	0.50	0.70	1.00	Fluorine
+10	Ne	0.00	0.58	0.58	1.54	0	20.1797	0.00	21.5645	0	0.70	0.89	0.96	Neon
+11	Na	1.01	1.66	1.66	2.27	1	22.98977	0.93	5.1391	0.547926	0.67	0.36	0.95	Sodium
+12	Mg	1.23	1.41	1.41	1.73	2	24.3050	1.31	7.6462	0	0.54	1.00	0.00	Magnesium
+13	Al	1.47	1.21	1.21	1.84	6	26.981538	1.61	5.9858	0.43283	0.75	0.65	0.65	Aluminium
+14	Si	1.74	1.11	1.11	2.10	6	28.0855	1.90	8.1517	1.389521	0.50	0.60	0.60	Silicon
+15	P	2.06	1.07	1.07	1.80	6	30.973761	2.19	10.4867	0.7465	1.00	0.50	0.00	Phosphorus
+16	S	2.44	1.05	1.05	1.80	6	32.065	2.58	10.36	2.0771029	0.70	0.70	0.00	Sulfur
+17	Cl	2.83	1.02	1.02	1.75	1	35.453	3.16	12.9676	3.612724	0.12	0.94	0.12	Chlorine
+18	Ar	0.00	1.06	1.06	1.88	0	39.948	0.00	15.7596	0	0.50	0.82	0.89	Argon