Mercurial > repos > marcel > caddsuite_mac10_6
changeset 10:eda78e0f5df6 draft default tip
Deleted selected files
author | marcel |
---|---|
date | Sun, 30 Nov 2014 03:46:08 -0500 |
parents | 488032d372e1 |
children | |
files | CADDSuite-1.6/.DS_Store CADDSuite-1.6/._.DS_Store CADDSuite-1.6/._changelog.txt CADDSuite-1.6/AntitargetRescorer CADDSuite-1.6/AutoModel CADDSuite-1.6/BindingDBCleaner CADDSuite-1.6/CADDSuite-description.txt CADDSuite-1.6/CombiLibGenerator CADDSuite-1.6/ConstraintsFinder CADDSuite-1.6/Converter CADDSuite-1.6/DBExporter CADDSuite-1.6/DBImporter CADDSuite-1.6/DockResultMerger CADDSuite-1.6/EvenSplit CADDSuite-1.6/FeatureSelector CADDSuite-1.6/GalaxyConfigGenerator CADDSuite-1.6/GridBuilder CADDSuite-1.6/IMGDock CADDSuite-1.6/InputPartitioner CADDSuite-1.6/InputReader CADDSuite-1.6/InteractionConstraintDefiner CADDSuite-1.6/LigCheck CADDSuite-1.6/Ligand3DGenerator CADDSuite-1.6/LigandFileSplitter CADDSuite-1.6/ModelCreator CADDSuite-1.6/MolCombine CADDSuite-1.6/MolDepict CADDSuite-1.6/MolFilter CADDSuite-1.6/MolPredictor CADDSuite-1.6/PDBCutter CADDSuite-1.6/PDBDownload CADDSuite-1.6/PocketCutter CADDSuite-1.6/PocketDetector CADDSuite-1.6/Predictor CADDSuite-1.6/PropertyModifier CADDSuite-1.6/PropertyPlotter CADDSuite-1.6/ProteinCheck CADDSuite-1.6/ProteinProtonator CADDSuite-1.6/README CADDSuite-1.6/RMSDCalculator CADDSuite-1.6/ScoreAnalyzer CADDSuite-1.6/SimilarityAnalyzer CADDSuite-1.6/SimpleRescorer CADDSuite-1.6/SpatialConstraintDefiner CADDSuite-1.6/SurfaceMatcher CADDSuite-1.6/TaGRes CADDSuite-1.6/TaGRes-train CADDSuite-1.6/Validator CADDSuite-1.6/VendorFinder CADDSuite-1.6/WaterFinder CADDSuite-1.6/bin/._gnuplot CADDSuite-1.6/bin/AntitargetRescorer.bin CADDSuite-1.6/bin/AutoModel.bin CADDSuite-1.6/bin/BindingDBCleaner.bin CADDSuite-1.6/bin/CombiLibGenerator.bin CADDSuite-1.6/bin/ConstraintsFinder.bin CADDSuite-1.6/bin/Converter.bin CADDSuite-1.6/bin/DBExporter.bin CADDSuite-1.6/bin/DBImporter.bin CADDSuite-1.6/bin/DockResultMerger.bin CADDSuite-1.6/bin/EvenSplit.bin CADDSuite-1.6/bin/FeatureSelector.bin CADDSuite-1.6/bin/GalaxyConfigGenerator.bin CADDSuite-1.6/bin/GridBuilder.bin CADDSuite-1.6/bin/IMGDock.bin CADDSuite-1.6/bin/InputPartitioner.bin CADDSuite-1.6/bin/InputReader.bin CADDSuite-1.6/bin/InteractionConstraintDefiner.bin CADDSuite-1.6/bin/LigCheck.bin CADDSuite-1.6/bin/Ligand3DGenerator.bin CADDSuite-1.6/bin/LigandFileSplitter.bin CADDSuite-1.6/bin/ModelCreator.bin CADDSuite-1.6/bin/MolCombine.bin CADDSuite-1.6/bin/MolDepict.bin CADDSuite-1.6/bin/MolFilter.bin CADDSuite-1.6/bin/MolPredictor.bin CADDSuite-1.6/bin/PDBCutter.bin CADDSuite-1.6/bin/PDBDownload.bin CADDSuite-1.6/bin/PocketCutter.bin CADDSuite-1.6/bin/PocketDetector.bin CADDSuite-1.6/bin/Predictor.bin CADDSuite-1.6/bin/PropertyModifier.bin CADDSuite-1.6/bin/PropertyPlotter.bin CADDSuite-1.6/bin/ProteinCheck.bin CADDSuite-1.6/bin/ProteinProtonator.bin CADDSuite-1.6/bin/RMSDCalculator.bin CADDSuite-1.6/bin/ScoreAnalyzer.bin CADDSuite-1.6/bin/SimilarityAnalyzer.bin CADDSuite-1.6/bin/SimpleRescorer.bin CADDSuite-1.6/bin/SpatialConstraintDefiner.bin CADDSuite-1.6/bin/SurfaceMatcher.bin CADDSuite-1.6/bin/TaGRes-train.bin CADDSuite-1.6/bin/TaGRes.bin CADDSuite-1.6/bin/Validator.bin CADDSuite-1.6/bin/VendorFinder.bin CADDSuite-1.6/bin/WaterFinder.bin CADDSuite-1.6/bin/convert CADDSuite-1.6/bin/gnuplot CADDSuite-1.6/changelog.txt CADDSuite-1.6/data/Amber/amber96-docking.ini CADDSuite-1.6/data/OpenBabel/._CMakeLists.txt CADDSuite-1.6/data/OpenBabel/._MACCS.txt CADDSuite-1.6/data/OpenBabel/._SMARTS_InteLigand.txt CADDSuite-1.6/data/OpenBabel/._UFF.prm CADDSuite-1.6/data/OpenBabel/._aromatic.h CADDSuite-1.6/data/OpenBabel/._aromatic.txt CADDSuite-1.6/data/OpenBabel/._atomtyp.h CADDSuite-1.6/data/OpenBabel/._atomtyp.txt CADDSuite-1.6/data/OpenBabel/._babel_povray3.inc CADDSuite-1.6/data/OpenBabel/._bin2hex.pl CADDSuite-1.6/data/OpenBabel/._bondtyp.h CADDSuite-1.6/data/OpenBabel/._bondtyp.txt CADDSuite-1.6/data/OpenBabel/._element.h CADDSuite-1.6/data/OpenBabel/._element.txt CADDSuite-1.6/data/OpenBabel/._fragments.txt CADDSuite-1.6/data/OpenBabel/._gaff.dat CADDSuite-1.6/data/OpenBabel/._gaff.prm CADDSuite-1.6/data/OpenBabel/._genheaders.sh CADDSuite-1.6/data/OpenBabel/._ghemical.prm CADDSuite-1.6/data/OpenBabel/._isotope-small.txt CADDSuite-1.6/data/OpenBabel/._isotope.h CADDSuite-1.6/data/OpenBabel/._isotope.txt CADDSuite-1.6/data/OpenBabel/._logp.txt CADDSuite-1.6/data/OpenBabel/._mm2.prm CADDSuite-1.6/data/OpenBabel/._mmff94.ff CADDSuite-1.6/data/OpenBabel/._mmff94s.ff CADDSuite-1.6/data/OpenBabel/._mmffang.par CADDSuite-1.6/data/OpenBabel/._mmffbndk.par CADDSuite-1.6/data/OpenBabel/._mmffbond.par CADDSuite-1.6/data/OpenBabel/._mmffchg.par CADDSuite-1.6/data/OpenBabel/._mmffdef.par CADDSuite-1.6/data/OpenBabel/._mmffdfsb.par CADDSuite-1.6/data/OpenBabel/._mmffoop.par CADDSuite-1.6/data/OpenBabel/._mmffpbci.par CADDSuite-1.6/data/OpenBabel/._mmffprop.par CADDSuite-1.6/data/OpenBabel/._mmffs_oop.par CADDSuite-1.6/data/OpenBabel/._mmffs_tor.par CADDSuite-1.6/data/OpenBabel/._mmffstbn.par CADDSuite-1.6/data/OpenBabel/._mmfftor.par CADDSuite-1.6/data/OpenBabel/._mmffvdw.par CADDSuite-1.6/data/OpenBabel/._mr.txt CADDSuite-1.6/data/OpenBabel/._patterns.txt CADDSuite-1.6/data/OpenBabel/._phmodel.txt CADDSuite-1.6/data/OpenBabel/._phmodeldata.h CADDSuite-1.6/data/OpenBabel/._plugindefines.txt CADDSuite-1.6/data/OpenBabel/._psa.txt CADDSuite-1.6/data/OpenBabel/._qeq.txt CADDSuite-1.6/data/OpenBabel/._resdata.h CADDSuite-1.6/data/OpenBabel/._resdata.txt CADDSuite-1.6/data/OpenBabel/._ringtyp.txt CADDSuite-1.6/data/OpenBabel/._space-groups.txt CADDSuite-1.6/data/OpenBabel/._space-groups.xsl CADDSuite-1.6/data/OpenBabel/._superatom.txt CADDSuite-1.6/data/OpenBabel/._svgformat.script CADDSuite-1.6/data/OpenBabel/._templates.sdf CADDSuite-1.6/data/OpenBabel/._torlib.h CADDSuite-1.6/data/OpenBabel/._torlib.txt CADDSuite-1.6/data/OpenBabel/._types.h CADDSuite-1.6/data/OpenBabel/._types.txt CADDSuite-1.6/data/OpenBabel/CMakeLists.txt CADDSuite-1.6/data/OpenBabel/MACCS.txt CADDSuite-1.6/data/OpenBabel/Makefile CADDSuite-1.6/data/OpenBabel/SMARTS_InteLigand.txt CADDSuite-1.6/data/OpenBabel/UFF.prm CADDSuite-1.6/data/OpenBabel/aromatic.h CADDSuite-1.6/data/OpenBabel/aromatic.txt CADDSuite-1.6/data/OpenBabel/atomtyp.h CADDSuite-1.6/data/OpenBabel/atomtyp.txt CADDSuite-1.6/data/OpenBabel/babel_povray3.inc CADDSuite-1.6/data/OpenBabel/bin2hex.pl CADDSuite-1.6/data/OpenBabel/bondtyp.h CADDSuite-1.6/data/OpenBabel/bondtyp.txt CADDSuite-1.6/data/OpenBabel/cmake_install.cmake CADDSuite-1.6/data/OpenBabel/element.h CADDSuite-1.6/data/OpenBabel/element.txt CADDSuite-1.6/data/OpenBabel/fragments.txt CADDSuite-1.6/data/OpenBabel/gaff.dat CADDSuite-1.6/data/OpenBabel/gaff.prm CADDSuite-1.6/data/OpenBabel/genheaders.sh CADDSuite-1.6/data/OpenBabel/ghemical.prm CADDSuite-1.6/data/OpenBabel/isotope-small.txt CADDSuite-1.6/data/OpenBabel/isotope.h CADDSuite-1.6/data/OpenBabel/isotope.txt CADDSuite-1.6/data/OpenBabel/logp.txt CADDSuite-1.6/data/OpenBabel/mm2.prm CADDSuite-1.6/data/OpenBabel/mmff94.ff CADDSuite-1.6/data/OpenBabel/mmff94s.ff CADDSuite-1.6/data/OpenBabel/mmffang.par CADDSuite-1.6/data/OpenBabel/mmffbndk.par CADDSuite-1.6/data/OpenBabel/mmffbond.par CADDSuite-1.6/data/OpenBabel/mmffchg.par CADDSuite-1.6/data/OpenBabel/mmffdef.par CADDSuite-1.6/data/OpenBabel/mmffdfsb.par CADDSuite-1.6/data/OpenBabel/mmffoop.par CADDSuite-1.6/data/OpenBabel/mmffpbci.par CADDSuite-1.6/data/OpenBabel/mmffprop.par CADDSuite-1.6/data/OpenBabel/mmffs_oop.par CADDSuite-1.6/data/OpenBabel/mmffs_tor.par CADDSuite-1.6/data/OpenBabel/mmffstbn.par CADDSuite-1.6/data/OpenBabel/mmfftor.par CADDSuite-1.6/data/OpenBabel/mmffvdw.par CADDSuite-1.6/data/OpenBabel/mr.txt CADDSuite-1.6/data/OpenBabel/patterns.txt CADDSuite-1.6/data/OpenBabel/phmodel.txt CADDSuite-1.6/data/OpenBabel/phmodeldata.h CADDSuite-1.6/data/OpenBabel/plugindefines.txt CADDSuite-1.6/data/OpenBabel/psa.txt CADDSuite-1.6/data/OpenBabel/qeq.txt CADDSuite-1.6/data/OpenBabel/resdata.h CADDSuite-1.6/data/OpenBabel/resdata.txt CADDSuite-1.6/data/OpenBabel/ringtyp.txt CADDSuite-1.6/data/OpenBabel/space-groups.txt CADDSuite-1.6/data/OpenBabel/space-groups.xsl CADDSuite-1.6/data/OpenBabel/superatom.txt CADDSuite-1.6/data/OpenBabel/svgformat.script CADDSuite-1.6/data/OpenBabel/templates.sdf CADDSuite-1.6/data/OpenBabel/torlib.h CADDSuite-1.6/data/OpenBabel/torlib.txt CADDSuite-1.6/data/OpenBabel/types.h CADDSuite-1.6/data/OpenBabel/types.txt CADDSuite-1.6/data/QSAR/atomic_electron_affinities.data CADDSuite-1.6/data/QSAR/atomic_ionization_potentials.data CADDSuite-1.6/data/QSAR/atomic_polarizabilities.data CADDSuite-1.6/data/QSAR/dragon_descriptors.txt CADDSuite-1.6/data/XRAY/spacegroups.dat CADDSuite-1.6/data/atomtyping/AMBERTypes.dat CADDSuite-1.6/data/atomtyping/GAFFTypes.dat CADDSuite-1.6/data/atomtyping/SYBYLTypes.dat CADDSuite-1.6/data/bond_lengths/BondOrder.xml CADDSuite-1.6/data/bond_lengths/BondOrderGAFF.xml CADDSuite-1.6/data/bond_lengths/bond_lengths.db CADDSuite-1.6/data/bond_lengths/bond_lengths_mmff94.ini CADDSuite-1.6/data/fragments/A.db CADDSuite-1.6/data/fragments/ACE.db CADDSuite-1.6/data/fragments/ALA.db CADDSuite-1.6/data/fragments/ARG.db CADDSuite-1.6/data/fragments/ASN.db CADDSuite-1.6/data/fragments/ASP.db CADDSuite-1.6/data/fragments/Benzene-Skeleton.db CADDSuite-1.6/data/fragments/C.db CADDSuite-1.6/data/fragments/CA.db CADDSuite-1.6/data/fragments/CYS.db CADDSuite-1.6/data/fragments/Editing-Fragments.db CADDSuite-1.6/data/fragments/Fragments.db CADDSuite-1.6/data/fragments/G.db CADDSuite-1.6/data/fragments/GLN.db CADDSuite-1.6/data/fragments/GLU.db CADDSuite-1.6/data/fragments/GLY.db CADDSuite-1.6/data/fragments/HIS.db CADDSuite-1.6/data/fragments/HOH.db CADDSuite-1.6/data/fragments/ILE.db CADDSuite-1.6/data/fragments/Indole-Skeleton.db CADDSuite-1.6/data/fragments/LEU.db CADDSuite-1.6/data/fragments/LYS.db CADDSuite-1.6/data/fragments/MET.db CADDSuite-1.6/data/fragments/MG.db CADDSuite-1.6/data/fragments/MSE.db CADDSuite-1.6/data/fragments/NME.db CADDSuite-1.6/data/fragments/Names.Amber.db CADDSuite-1.6/data/fragments/Names.CHARMM.db CADDSuite-1.6/data/fragments/Names.DNA.db CADDSuite-1.6/data/fragments/Names.Discover.db CADDSuite-1.6/data/fragments/Names.Star.db CADDSuite-1.6/data/fragments/Names.XPLOR.db CADDSuite-1.6/data/fragments/PCA.db CADDSuite-1.6/data/fragments/PHE.db CADDSuite-1.6/data/fragments/PRO.db CADDSuite-1.6/data/fragments/Pyrrole-Skeleton.db CADDSuite-1.6/data/fragments/SER.db CADDSuite-1.6/data/fragments/T.db CADDSuite-1.6/data/fragments/THR.db CADDSuite-1.6/data/fragments/TRP.db CADDSuite-1.6/data/fragments/TYR.db CADDSuite-1.6/data/fragments/U.db CADDSuite-1.6/data/fragments/VAL.db CADDSuite-1.6/data/fragments/ZN.db CADDSuite-1.6/data/fragments/functionalGroups.smarts CADDSuite-1.6/data/gnuplot/FreeSans.ttf CADDSuite-1.6/data/gnuplot/prologue.ps CADDSuite-1.6/galaxyconfigs/confFiles.py CADDSuite-1.6/galaxyconfigs/countResidues.sh CADDSuite-1.6/galaxyconfigs/datatypes_conf.xml CADDSuite-1.6/galaxyconfigs/molFiles.py CADDSuite-1.6/galaxyconfigs/tool_conf.xml CADDSuite-1.6/galaxyconfigs/tools/AntitargetRescorer.xml CADDSuite-1.6/galaxyconfigs/tools/AutoModel.xml CADDSuite-1.6/galaxyconfigs/tools/BindingDBCleaner.xml CADDSuite-1.6/galaxyconfigs/tools/CombiLibGenerator.xml CADDSuite-1.6/galaxyconfigs/tools/ConstraintsFinder.xml CADDSuite-1.6/galaxyconfigs/tools/Converter.xml CADDSuite-1.6/galaxyconfigs/tools/DBExporter.xml CADDSuite-1.6/galaxyconfigs/tools/DBImporter.xml CADDSuite-1.6/galaxyconfigs/tools/DockResultMerger.xml CADDSuite-1.6/galaxyconfigs/tools/EvenSplit.xml CADDSuite-1.6/galaxyconfigs/tools/FeatureSelector.xml CADDSuite-1.6/galaxyconfigs/tools/GalaxyConfigGenerator.xml CADDSuite-1.6/galaxyconfigs/tools/GridBuilder.xml CADDSuite-1.6/galaxyconfigs/tools/IMGDock.xml CADDSuite-1.6/galaxyconfigs/tools/InputPartitioner.xml CADDSuite-1.6/galaxyconfigs/tools/InputReader.xml CADDSuite-1.6/galaxyconfigs/tools/InteractionConstraintDefiner.xml CADDSuite-1.6/galaxyconfigs/tools/LigCheck.xml CADDSuite-1.6/galaxyconfigs/tools/Ligand3DGenerator.xml CADDSuite-1.6/galaxyconfigs/tools/LigandFileSplitter.xml CADDSuite-1.6/galaxyconfigs/tools/ModelCreator.xml CADDSuite-1.6/galaxyconfigs/tools/MolCombine.xml CADDSuite-1.6/galaxyconfigs/tools/MolDepict.xml CADDSuite-1.6/galaxyconfigs/tools/MolFilter.xml CADDSuite-1.6/galaxyconfigs/tools/MolPredictor.xml CADDSuite-1.6/galaxyconfigs/tools/PDBCutter.xml CADDSuite-1.6/galaxyconfigs/tools/PDBDownload.xml CADDSuite-1.6/galaxyconfigs/tools/PocketCutter.xml CADDSuite-1.6/galaxyconfigs/tools/PocketDetector.xml CADDSuite-1.6/galaxyconfigs/tools/Predictor.xml CADDSuite-1.6/galaxyconfigs/tools/PropertyModifier.xml CADDSuite-1.6/galaxyconfigs/tools/PropertyPlotter.xml CADDSuite-1.6/galaxyconfigs/tools/ProteinCheck.xml CADDSuite-1.6/galaxyconfigs/tools/ProteinProtonator.xml CADDSuite-1.6/galaxyconfigs/tools/RMSDCalculator.xml CADDSuite-1.6/galaxyconfigs/tools/ScoreAnalyzer.xml CADDSuite-1.6/galaxyconfigs/tools/SimilarityAnalyzer.xml CADDSuite-1.6/galaxyconfigs/tools/SimpleRescorer.xml CADDSuite-1.6/galaxyconfigs/tools/SpatialConstraintDefiner.xml CADDSuite-1.6/galaxyconfigs/tools/SurfaceMatcher.xml CADDSuite-1.6/galaxyconfigs/tools/TaGRes-train.xml CADDSuite-1.6/galaxyconfigs/tools/TaGRes.xml CADDSuite-1.6/galaxyconfigs/tools/Validator.xml CADDSuite-1.6/galaxyconfigs/tools/VendorFinder.xml CADDSuite-1.6/galaxyconfigs/tools/WaterFinder.xml CADDSuite-1.6/galaxyconfigs/tools/upload.xml CADDSuite-1.6/install.sh CADDSuite-1.6/lib/.DS_Store CADDSuite-1.6/lib/._.DS_Store CADDSuite-1.6/lib/._libQtCore.dylib CADDSuite-1.6/lib/._libQtNetwork.dylib CADDSuite-1.6/lib/._libQtSql.dylib CADDSuite-1.6/lib/._libQtXml.dylib CADDSuite-1.6/lib/._libboost_iostreams.dylib CADDSuite-1.6/lib/._libboost_regex.dylib CADDSuite-1.6/lib/._libboost_system.dylib CADDSuite-1.6/lib/._libboost_thread.dylib CADDSuite-1.6/lib/._libgsl.dylib CADDSuite-1.6/lib/._libgslcblas.dylib CADDSuite-1.6/lib/._libmysqlclient.18.dylib CADDSuite-1.6/lib/libBALL.1.4.dylib CADDSuite-1.6/lib/libMagickCore.5.dylib CADDSuite-1.6/lib/libMagickWand.5.dylib CADDSuite-1.6/lib/libQtCore.dylib CADDSuite-1.6/lib/libQtNetwork.dylib CADDSuite-1.6/lib/libQtSql.dylib CADDSuite-1.6/lib/libQtXml.dylib CADDSuite-1.6/lib/libboost_iostreams.dylib CADDSuite-1.6/lib/libboost_regex.dylib CADDSuite-1.6/lib/libboost_system.dylib CADDSuite-1.6/lib/libboost_thread.dylib CADDSuite-1.6/lib/libgsl.dylib CADDSuite-1.6/lib/libgslcblas.dylib CADDSuite-1.6/lib/libmysqlclient.18.dylib CADDSuite-1.6/lib/libopenbabel.4.dylib CADDSuite-1.6/lib/openbabel/APIInterface.so CADDSuite-1.6/lib/openbabel/CSRformat.so CADDSuite-1.6/lib/openbabel/MCDLformat.so CADDSuite-1.6/lib/openbabel/MNAformat.so CADDSuite-1.6/lib/openbabel/PQSformat.so CADDSuite-1.6/lib/openbabel/abinitformat.so CADDSuite-1.6/lib/openbabel/acrformat.so CADDSuite-1.6/lib/openbabel/adfformat.so CADDSuite-1.6/lib/openbabel/alchemyformat.so CADDSuite-1.6/lib/openbabel/amberformat.so CADDSuite-1.6/lib/openbabel/balstformat.so CADDSuite-1.6/lib/openbabel/bgfformat.so CADDSuite-1.6/lib/openbabel/boxformat.so CADDSuite-1.6/lib/openbabel/cacaoformat.so CADDSuite-1.6/lib/openbabel/cacheformat.so CADDSuite-1.6/lib/openbabel/carformat.so CADDSuite-1.6/lib/openbabel/castepformat.so CADDSuite-1.6/lib/openbabel/cccformat.so CADDSuite-1.6/lib/openbabel/cdxmlformat.so CADDSuite-1.6/lib/openbabel/chem3dformat.so CADDSuite-1.6/lib/openbabel/chemdrawcdx.so CADDSuite-1.6/lib/openbabel/chemdrawct.so CADDSuite-1.6/lib/openbabel/chemkinformat.so CADDSuite-1.6/lib/openbabel/chemtoolformat.so CADDSuite-1.6/lib/openbabel/cifformat.so CADDSuite-1.6/lib/openbabel/cmlformat.so CADDSuite-1.6/lib/openbabel/cmlreactformat.so CADDSuite-1.6/lib/openbabel/copyformat.so CADDSuite-1.6/lib/openbabel/crkformat.so CADDSuite-1.6/lib/openbabel/cssrformat.so CADDSuite-1.6/lib/openbabel/dlpolyformat.so CADDSuite-1.6/lib/openbabel/dmolformat.so CADDSuite-1.6/lib/openbabel/fastaformat.so CADDSuite-1.6/lib/openbabel/fastsearchformat.so CADDSuite-1.6/lib/openbabel/fchkformat.so CADDSuite-1.6/lib/openbabel/featformat.so CADDSuite-1.6/lib/openbabel/fhformat.so CADDSuite-1.6/lib/openbabel/fhiaimsformat.so CADDSuite-1.6/lib/openbabel/fingerprintformat.so CADDSuite-1.6/lib/openbabel/freefracformat.so CADDSuite-1.6/lib/openbabel/gamessformat.so CADDSuite-1.6/lib/openbabel/gamessukformat.so CADDSuite-1.6/lib/openbabel/gausscubeformat.so CADDSuite-1.6/lib/openbabel/gaussformat.so CADDSuite-1.6/lib/openbabel/gausszmatformat.so CADDSuite-1.6/lib/openbabel/ghemicalformat.so CADDSuite-1.6/lib/openbabel/groformat.so CADDSuite-1.6/lib/openbabel/gromos96format.so CADDSuite-1.6/lib/openbabel/gulpformat.so CADDSuite-1.6/lib/openbabel/hinformat.so CADDSuite-1.6/lib/openbabel/inchiformat.so CADDSuite-1.6/lib/openbabel/jaguarformat.so CADDSuite-1.6/lib/openbabel/mdlformat.so CADDSuite-1.6/lib/openbabel/mmcifformat.so CADDSuite-1.6/lib/openbabel/mmodformat.so CADDSuite-1.6/lib/openbabel/mol2format.so CADDSuite-1.6/lib/openbabel/moldenformat.so CADDSuite-1.6/lib/openbabel/molproformat.so CADDSuite-1.6/lib/openbabel/molreport.so CADDSuite-1.6/lib/openbabel/mopacformat.so CADDSuite-1.6/lib/openbabel/mpdformat.so CADDSuite-1.6/lib/openbabel/mpqcformat.so CADDSuite-1.6/lib/openbabel/msiformat.so CADDSuite-1.6/lib/openbabel/msmsformat.so CADDSuite-1.6/lib/openbabel/nulformat.so CADDSuite-1.6/lib/openbabel/nwchemformat.so CADDSuite-1.6/lib/openbabel/opendxformat.so CADDSuite-1.6/lib/openbabel/outformat.so CADDSuite-1.6/lib/openbabel/pcmodelformat.so CADDSuite-1.6/lib/openbabel/pdbformat.so CADDSuite-1.6/lib/openbabel/pdbqtformat.so CADDSuite-1.6/lib/openbabel/plugin_charges.so CADDSuite-1.6/lib/openbabel/plugin_descriptors.so CADDSuite-1.6/lib/openbabel/plugin_fingerprints.so CADDSuite-1.6/lib/openbabel/plugin_forcefields.so CADDSuite-1.6/lib/openbabel/plugin_ops.so CADDSuite-1.6/lib/openbabel/pngformat.so CADDSuite-1.6/lib/openbabel/povrayformat.so CADDSuite-1.6/lib/openbabel/pqrformat.so CADDSuite-1.6/lib/openbabel/pubchem.so CADDSuite-1.6/lib/openbabel/pwscfformat.so CADDSuite-1.6/lib/openbabel/qchemformat.so CADDSuite-1.6/lib/openbabel/reportformat.so CADDSuite-1.6/lib/openbabel/rsmiformat.so CADDSuite-1.6/lib/openbabel/rxnformat.so CADDSuite-1.6/lib/openbabel/shelxformat.so CADDSuite-1.6/lib/openbabel/smilesformat.so CADDSuite-1.6/lib/openbabel/svgformat.so CADDSuite-1.6/lib/openbabel/textformat.so CADDSuite-1.6/lib/openbabel/thermoformat.so CADDSuite-1.6/lib/openbabel/tinkerformat.so CADDSuite-1.6/lib/openbabel/titleformat.so CADDSuite-1.6/lib/openbabel/turbomoleformat.so CADDSuite-1.6/lib/openbabel/unichemformat.so CADDSuite-1.6/lib/openbabel/vaspformat.so CADDSuite-1.6/lib/openbabel/viewmolformat.so CADDSuite-1.6/lib/openbabel/xedformat.so CADDSuite-1.6/lib/openbabel/xmlformat.so CADDSuite-1.6/lib/openbabel/xsfformat.so CADDSuite-1.6/lib/openbabel/xyzformat.so CADDSuite-1.6/lib/openbabel/yasaraformat.so CADDSuite-1.6/lib/openbabel/zindoformat.so CADDSuite-1.6/license.txt CADDSuite-1.6/setPathes.sh CADDSuite-1.6/suite_config.xml |
diffstat | 464 files changed, 0 insertions(+), 90551 deletions(-) [+] |
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line diff
--- a/CADDSuite-1.6/AntitargetRescorer Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/AntitargetRescorer.bin "$@"
--- a/CADDSuite-1.6/AutoModel Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/AutoModel.bin "$@"
--- a/CADDSuite-1.6/BindingDBCleaner Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/BindingDBCleaner.bin "$@"
--- a/CADDSuite-1.6/CADDSuite-description.txt Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -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 - -Off-target search: - - PocketCutter: cut binding pocket surface - - SurfaceMatcher: match two protein surfaces onto each other - -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').
--- a/CADDSuite-1.6/CombiLibGenerator Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/CombiLibGenerator.bin "$@"
--- a/CADDSuite-1.6/ConstraintsFinder Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/ConstraintsFinder.bin "$@"
--- a/CADDSuite-1.6/Converter Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/Converter.bin "$@"
--- a/CADDSuite-1.6/DBExporter Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/DBExporter.bin "$@"
--- a/CADDSuite-1.6/DBImporter Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/DBImporter.bin "$@"
--- a/CADDSuite-1.6/DockResultMerger Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/DockResultMerger.bin "$@"
--- a/CADDSuite-1.6/EvenSplit Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/EvenSplit.bin "$@"
--- a/CADDSuite-1.6/FeatureSelector Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/FeatureSelector.bin "$@"
--- a/CADDSuite-1.6/GalaxyConfigGenerator Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/GalaxyConfigGenerator.bin "$@"
--- a/CADDSuite-1.6/GridBuilder Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/GridBuilder.bin "$@"
--- a/CADDSuite-1.6/IMGDock Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/IMGDock.bin "$@"
--- a/CADDSuite-1.6/InputPartitioner Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/InputPartitioner.bin "$@"
--- a/CADDSuite-1.6/InputReader Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/InputReader.bin "$@"
--- a/CADDSuite-1.6/InteractionConstraintDefiner Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/InteractionConstraintDefiner.bin "$@"
--- a/CADDSuite-1.6/LigCheck Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/LigCheck.bin "$@"
--- a/CADDSuite-1.6/Ligand3DGenerator Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/Ligand3DGenerator.bin "$@"
--- a/CADDSuite-1.6/LigandFileSplitter Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/LigandFileSplitter.bin "$@"
--- a/CADDSuite-1.6/ModelCreator Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/ModelCreator.bin "$@"
--- a/CADDSuite-1.6/MolCombine Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/MolCombine.bin "$@"
--- a/CADDSuite-1.6/MolDepict Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/MolDepict.bin "$@"
--- a/CADDSuite-1.6/MolFilter Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/MolFilter.bin "$@"
--- a/CADDSuite-1.6/MolPredictor Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/MolPredictor.bin "$@"
--- a/CADDSuite-1.6/PDBCutter Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/PDBCutter.bin "$@"
--- a/CADDSuite-1.6/PDBDownload Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/PDBDownload.bin "$@"
--- a/CADDSuite-1.6/PocketCutter Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/PocketCutter.bin "$@"
--- a/CADDSuite-1.6/PocketDetector Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/PocketDetector.bin "$@"
--- a/CADDSuite-1.6/Predictor Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/Predictor.bin "$@"
--- a/CADDSuite-1.6/PropertyModifier Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/PropertyModifier.bin "$@"
--- a/CADDSuite-1.6/PropertyPlotter Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/PropertyPlotter.bin "$@"
--- a/CADDSuite-1.6/ProteinCheck Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/ProteinCheck.bin "$@"
--- a/CADDSuite-1.6/ProteinProtonator Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/ProteinProtonator.bin "$@"
--- a/CADDSuite-1.6/README Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ ------------------------------------------------------------------------ - 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. - -
--- a/CADDSuite-1.6/RMSDCalculator Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/RMSDCalculator.bin "$@"
--- a/CADDSuite-1.6/ScoreAnalyzer Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/ScoreAnalyzer.bin "$@"
--- a/CADDSuite-1.6/SimilarityAnalyzer Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/SimilarityAnalyzer.bin "$@"
--- a/CADDSuite-1.6/SimpleRescorer Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/SimpleRescorer.bin "$@"
--- a/CADDSuite-1.6/SpatialConstraintDefiner Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/SpatialConstraintDefiner.bin "$@"
--- a/CADDSuite-1.6/SurfaceMatcher Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/SurfaceMatcher.bin "$@"
--- a/CADDSuite-1.6/TaGRes Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/TaGRes.bin "$@"
--- a/CADDSuite-1.6/TaGRes-train Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/TaGRes-train.bin "$@"
--- a/CADDSuite-1.6/Validator Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/Validator.bin "$@"
--- a/CADDSuite-1.6/VendorFinder Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/VendorFinder.bin "$@"
--- a/CADDSuite-1.6/WaterFinder Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#!/bin/bash - export BASE_DIR=`dirname "$0"` - . "$BASE_DIR"/setPathes.sh - "$BASE_DIR"/bin/WaterFinder.bin "$@"
--- a/CADDSuite-1.6/changelog.txt Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,104 +0,0 @@ -Version 1.6, 12-15-2012: - - Enhanced SurfaceMatcher; included correlation contributions for matching interior of binding pockets onto each other. - - Enhanced calculation of topological similarities. - -Version 1.5, 07-18-2012: - - Changed scoring function to include greatly improved solvation term !!! - - Added SurfaceMatcher. It finds the best superposition of two binding pocket surfaces using FFT !! - - Added PocketCutter, which allows to cut receptor atoms contributing to the SES of the binding pocket of a receptor. This output can then be used with SurfaceMatcher. - - Added k-mean clustering to MolDB - - For DBExporter and similarity search, allow to set threshold for max. desired molecules per query mol - - Allow to filter compound library by vendor name using DBExporter - - Allow to restrict similarity search to molecules with molecular weigth similar to the one of query molecule - - Added diversity criteria to DB similarity search and to MolFilter - - Optional automatic detection of ref. ligand (using largest heterosystem) added to PDBCutter - - PDBCutter can now also download ligand sdf with correct topology from PDB server instead just writing a pdb with unkown bond orders - - Adapted default penalty value set by SpatialConstraintDefiner and PocketDetector - -Version 1.1, 01-10-2012: - - Eradicated use of external tool 'tar'. ScoreGridSets are now compressed using boost's gzip support. Multiple ScoreGridSets are automatically. concatenated and saved as one gzipped file - - Added default atom type for grid calculation - - Fixed default state of galaxy check-boxes - - Some small fixes for g++ 4.6 - - Changed some default output formats of many tools to mol2.gz. This will only have an effect if _no_ valid file extension is specified. - - Gave some more tools the ability to delete their input file after sucessful execution - - The last two points together allow to reduce required disk space for common docking pipeline by about 95%. - -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 automatic QSAR model creation 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
--- a/CADDSuite-1.6/data/Amber/amber96-docking.ini Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1666 +0,0 @@ -; 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
--- a/CADDSuite-1.6/data/OpenBabel/CMakeLists.txt Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -# 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)
--- a/CADDSuite-1.6/data/OpenBabel/MACCS.txt Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,199 +0,0 @@ -#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
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--- a/CADDSuite-1.6/data/OpenBabel/SMARTS_InteLigand.txt Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,983 +0,0 @@ -# -# 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
--- a/CADDSuite-1.6/data/OpenBabel/UFF.prm Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,277 +0,0 @@ -# -# 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
--- a/CADDSuite-1.6/data/OpenBabel/aromatic.h Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ -/*************************************************************** -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 -
--- a/CADDSuite-1.6/data/OpenBabel/aromatic.txt Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,59 +0,0 @@ -############################################################################## -# # -# 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
--- a/CADDSuite-1.6/data/OpenBabel/atomtyp.h Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,316 +0,0 @@ -/*************************************************************** -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, - 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--- a/CADDSuite-1.6/data/OpenBabel/atomtyp.txt Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,259 +0,0 @@ -############################################################################## -# # -# 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 ########################## -
--- a/CADDSuite-1.6/data/OpenBabel/babel_povray3.inc Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1229 +0,0 @@ -//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 - }
--- a/CADDSuite-1.6/data/OpenBabel/bin2hex.pl Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,144 +0,0 @@ -#!/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; -
--- a/CADDSuite-1.6/data/OpenBabel/bondtyp.h Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,132 +0,0 @@ -/*************************************************************** -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, - 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--- a/CADDSuite-1.6/data/OpenBabel/bondtyp.txt Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -############################################################################## -# # -# 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
--- a/CADDSuite-1.6/data/OpenBabel/cmake_install.cmake Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,78 +0,0 @@ -# Install script for directory: /Volumes/Work/CADDSuite-git/contrib/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 - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/aromatic.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/atomtyp.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/babel_povray3.inc" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/bondtyp.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/element.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/fragments.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/gaff.dat" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/gaff.prm" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/ghemical.prm" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/isotope-small.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/isotope.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/logp.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/MACCS.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmff94.ff" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmff94s.ff" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmffang.par" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmffbndk.par" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmffbond.par" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmffchg.par" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmffdef.par" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmffdfsb.par" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmffoop.par" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmffpbci.par" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmffprop.par" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmffstbn.par" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmfftor.par" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmffvdw.par" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmffs_oop.par" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mmffs_tor.par" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/mr.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/patterns.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/phmodel.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/plugindefines.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/psa.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/qeq.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/resdata.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/ringtyp.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/SMARTS_InteLigand.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/space-groups.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/superatom.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/svgformat.script" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/torlib.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/types.txt" - "/Volumes/Work/CADDSuite-git/contrib/openbabel-2.3.1/data/UFF.prm" - ) -ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified") -
--- a/CADDSuite-1.6/data/OpenBabel/element.h Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,616 +0,0 @@ -/*************************************************************** -This file is part of the Open Babel project. -This is copyright under the GNU General Public License (GPL) -For more information, see <http://openbabel.org/> - -This file contains a binary representation of data tables - used by Open Babel. It is used as a fallback if the textual - data table is not found at runtime. It is not a normal header. -***************************************************************/ - - -#ifndef OB_ELEMENT_H -#define OB_ELEMENT_H - -namespace OpenBabel -{ -static const char ElementData[] = { - 0x30,0x09,0x58,0x78,0x09,0x30,0x2E,0x30,0x30,0x09,0x30,0x2E,0x30,0x30,0x09, - 0x30,0x2E,0x30,0x30,0x09,0x30,0x2E,0x30,0x30,0x09,0x30,0x09,0x30,0x09,0x30, - 0x2E,0x30,0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x2E,0x30,0x37,0x09,0x30,0x2E, - 0x35,0x30,0x09,0x30,0x2E,0x37,0x30,0x09,0x44,0x75,0x6D,0x6D,0x79,0x0A,0x31, - 0x09,0x48,0x09,0x32,0x2E,0x32,0x30,0x09,0x30,0x2E,0x33,0x31,0x09,0x30,0x2E, - 0x33,0x31,0x09,0x31,0x2E,0x31,0x30,0x09,0x31,0x09,0x31,0x2E,0x30,0x30,0x37, - 0x39,0x34,0x09,0x32,0x2E,0x32,0x30,0x09,0x31,0x33,0x2E,0x35,0x39,0x38,0x34, - 0x09,0x30,0x2E,0x37,0x35,0x34,0x32,0x30,0x33,0x37,0x35,0x09,0x30,0x2E,0x37, - 0x35,0x09,0x30,0x2E,0x37,0x35,0x09,0x30,0x2E,0x37,0x35,0x09,0x48,0x79,0x64, - 0x72,0x6F,0x67,0x65,0x6E,0x0A,0x32,0x09,0x48,0x65,0x09,0x30,0x2E,0x30,0x30, - 0x09,0x30,0x2E,0x32,0x38,0x09,0x30,0x2E,0x32,0x38,0x09,0x31,0x2E,0x34,0x30, - 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0x30,0x2E,0x39,0x39,0x09,0x30,0x2E,0x30,0x30,0x09,0x30,0x2E,0x30,0x38,0x09, - 0x55,0x6E,0x75,0x6E,0x68,0x65,0x78,0x69,0x75,0x6D,0x0A,0x31,0x31,0x37,0x09, - 0x55,0x75,0x68,0x09,0x30,0x2E,0x30,0x30,0x09,0x31,0x2E,0x36,0x30,0x09,0x31, - 0x2E,0x36,0x30,0x09,0x32,0x2E,0x30,0x30,0x09,0x36,0x09,0x32,0x39,0x34,0x09, - 0x30,0x2E,0x30,0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x2E,0x39,0x39,0x09,0x30, - 0x2E,0x30,0x30,0x09,0x30,0x2E,0x30,0x37,0x09,0x55,0x6E,0x75,0x6E,0x73,0x65, - 0x70,0x74,0x69,0x75,0x6D,0x0A,0x31,0x31,0x38,0x09,0x55,0x75,0x68,0x09,0x30, - 0x2E,0x30,0x30,0x09,0x31,0x2E,0x36,0x30,0x09,0x31,0x2E,0x36,0x30,0x09,0x32, - 0x2E,0x30,0x30,0x09,0x36,0x09,0x32,0x39,0x34,0x09,0x30,0x2E,0x30,0x30,0x09, - 0x30,0x09,0x30,0x09,0x30,0x2E,0x39,0x39,0x09,0x30,0x2E,0x30,0x30,0x09,0x30, - 0x2E,0x30,0x36,0x09,0x55,0x6E,0x75,0x6E,0x6F,0x63,0x74,0x69,0x75,0x6D,0x0A, -0x00}; - -} // namespace OpenBabel -#endif // OB_ELEMENT_H -
--- a/CADDSuite-1.6/data/OpenBabel/element.txt Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,153 +0,0 @@ -############################################################################## -# # -# Open Babel file: element.txt # -# # -# Some portions Copyright (c) 2001-2009 Geoffrey R. Hutchison # -# Part of the Open Babel package, under the GNU General Public License (GPL)# -# # -# Created from the Blue Obelisk Cheminformatics Data Repository # -# Direct Source: http://www.blueobelisk.org/ # -# http://www.blueobelisk.org/repos/blueobelisk/elements.xml # -# (includes furhter bibliographic citation information) # -# # -# Allred and Rochow Electronegativity from: # -# http://www.hull.ac.uk/chemistry/electroneg.php?type=Allred-Rochow # -# # -# Columns represent: (used by data.cpp:OBElementTable and OBElement) # -# - atomic number (used as an index to the vector as well) # -# - elemental symbol # -# - Allred and Rochow electronegativity 0.0 if unknown # -# - covalent radii (in Angstrom) 1.6 if unknown # -# from http://dx.doi.org/10.1039/b801115j # -# - "bond order" radii -- ignored, but included for compatibility # -# - van der Waals radii (in Angstrom) 2.0 if unknown # -# from http://dx.doi.org/10.1021/jp8111556 # -# - maximum bond valence 6 if unknown # -# - IUPAC recommended atomic masses (in amu) # -# - Pauling electronegativity 0.0 if unknown # -# - ionization potential (in eV) 0.0 if unknown # -# - electron affinity (in eV) 0.0 if unknown # -# - RGB values (defaults for visualization) # -# - element name (in English) # -# # -############################################################################## -#Num Symb ARENeg RCov RBO RVdW MaxBnd Mass ElNeg. Ionization ElAffinity Red Green Blue Name -0 Xx 0.00 0.00 0.00 0.00 0 0 0.00 0 0 0.07 0.50 0.70 Dummy -1 H 2.20 0.31 0.31 1.10 1 1.00794 2.20 13.5984 0.75420375 0.75 0.75 0.75 Hydrogen -2 He 0.00 0.28 0.28 1.40 0 4.002602 0.00 24.5874 0 0.85 1.00 1.00 Helium -3 Li 0.97 1.28 1.28 1.81 1 6.941 0.98 5.3917 0.618049 0.80 0.50 1.00 Lithium -4 Be 1.47 0.96 0.96 1.53 2 9.012182 1.57 9.3227 0 0.76 1.00 0.00 Beryllium -5 B 2.01 0.84 0.84 1.92 4 10.811 2.04 8.298 0.279723 1.00 0.71 0.71 Boron -6 C 2.50 0.76 0.76 1.70 4 12.0107 2.55 11.2603 1.262118 0.40 0.40 0.40 Carbon -7 N 3.07 0.71 0.71 1.55 4 14.0067 3.04 14.5341 -0.07 0.05 0.05 1.00 Nitrogen -8 O 3.50 0.66 0.66 1.52 2 15.9994 3.44 13.6181 1.461112 1.00 0.05 0.05 Oxygen -9 F 4.10 0.57 0.57 1.47 1 18.9984032 3.98 17.4228 3.4011887 0.50 0.70 1.00 Fluorine -10 Ne 0.00 0.58 0.58 1.54 0 20.1797 0.00 21.5645 0 0.70 0.89 0.96 Neon -11 Na 1.01 1.66 1.66 2.27 1 22.98977 0.93 5.1391 0.547926 0.67 0.36 0.95 Sodium -12 Mg 1.23 1.41 1.41 1.73 2 24.3050 1.31 7.6462 0 0.54 1.00 0.00 Magnesium -13 Al 1.47 1.21 1.21 1.84 6 26.981538 1.61 5.9858 0.43283 0.75 0.65 0.65 Aluminium -14 Si 1.74 1.11 1.11 2.10 6 28.0855 1.90 8.1517 1.389521 0.50 0.60 0.60 Silicon -15 P 2.06 1.07 1.07 1.80 6 30.973761 2.19 10.4867 0.7465 1.00 0.50 0.00 Phosphorus -16 S 2.44 1.05 1.05 1.80 6 32.065 2.58 10.36 2.0771029 0.70 0.70 0.00 Sulfur -17 Cl 2.83 1.02 1.02 1.75 1 35.453 3.16 12.9676 3.612724 0.12 0.94 0.12 Chlorine -18 Ar 0.00 1.06 1.06 1.88 0 39.948 0.00 15.7596 0 0.50 0.82 0.89 Argon -19 K 0.91 2.03 2.03 2.75 1 39.0983 0.82 4.3407 0.501459 0.56 0.25 0.83 Potassium -20 Ca 1.04 1.76 1.76 2.31 2 40.078 1.00 6.1132 0.02455 0.24 1.00 0.00 Calcium -21 Sc 1.20 1.70 1.70 2.30 6 44.95591 1.36 6.5615 0.188 0.90 0.90 0.90 Scandium -22 Ti 1.32 1.60 1.60 2.15 6 47.867 1.54 6.8281 0.084 0.75 0.76 0.78 Titanium -23 V 1.45 1.53 1.53 2.05 6 50.9415 1.63 6.7462 0.525 0.65 0.65 0.67 Vanadium -24 Cr 1.56 1.39 1.39 2.05 6 51.9961 1.66 6.7665 0.67584 0.54 0.60 0.78 Chromium -25 Mn 1.60 1.39 1.39 2.05 8 54.938049 1.55 7.434 0 0.61 0.48 0.78 Manganese -26 Fe 1.64 1.32 1.32 2.05 6 55.845 1.83 7.9024 0.151 0.88 0.40 0.20 Iron -27 Co 1.70 1.26 1.26 2.00 6 58.9332 1.88 7.881 0.6633 0.94 0.56 0.63 Cobalt -28 Ni 1.75 1.24 1.24 2.00 6 58.6934 1.91 7.6398 1.15716 0.31 0.82 0.31 Nickel -29 Cu 1.75 1.32 1.32 2.00 6 63.546 1.90 7.7264 1.23578 0.78 0.50 0.20 Copper -30 Zn 1.66 1.22 1.22 2.10 6 65.38 1.65 9.3942 0 0.49 0.50 0.69 Zinc -31 Ga 1.82 1.22 1.22 1.87 3 69.723 1.81 5.9993 0.41 0.76 0.56 0.56 Gallium -32 Ge 2.02 1.20 1.20 2.11 4 72.64 2.01 7.8994 1.232712 0.40 0.56 0.56 Germanium -33 As 2.20 1.19 1.19 1.85 3 74.92160 2.18 9.7886 0.814 0.74 0.50 0.89 Arsenic -34 Se 2.48 1.20 1.20 1.90 2 78.96 2.55 9.7524 2.02067 1.00 0.63 0.00 Selenium -35 Br 2.74 1.20 1.20 1.83 1 79.904 2.96 11.8138 3.363588 0.65 0.16 0.16 Bromine -36 Kr 0.00 1.16 1.16 2.02 0 83.798 3.00 13.9996 0 0.36 0.72 0.82 Krypton -37 Rb 0.89 2.20 2.20 3.03 1 85.4678 0.82 4.1771 0.485916 0.44 0.18 0.69 Rubidium -38 Sr 0.99 1.95 1.95 2.49 2 87.62 0.95 5.6949 0.05206 0.00 1.00 0.00 Strontium -39 Y 1.11 1.90 1.90 2.40 6 88.90585 1.22 6.2173 0.307 0.58 1.00 1.00 Yttrium -40 Zr 1.22 1.75 1.75 2.30 6 91.224 1.33 6.6339 0.426 0.58 0.88 0.88 Zirconium -41 Nb 1.23 1.64 1.64 2.15 6 92.90638 1.60 6.7589 0.893 0.45 0.76 0.79 Niobium -42 Mo 1.30 1.54 1.54 2.10 6 95.96 2.16 7.0924 0.7472 0.33 0.71 0.71 Molybdenum -43 Tc 1.36 1.47 1.47 2.05 6 98 1.90 7.28 0.55 0.23 0.62 0.62 Technetium -44 Ru 1.42 1.46 1.46 2.05 6 101.07 2.20 7.3605 1.04638 0.14 0.56 0.56 Ruthenium -45 Rh 1.45 1.42 1.42 2.00 6 102.90550 2.28 7.4589 1.14289 0.04 0.49 0.55 Rhodium -46 Pd 1.35 1.39 1.39 2.05 6 106.42 2.20 8.3369 0.56214 0.00 0.41 0.52 Palladium -47 Ag 1.42 1.45 1.45 2.10 6 107.8682 1.93 7.5762 1.30447 0.88 0.88 1.00 Silver -48 Cd 1.46 1.44 1.44 2.20 6 112.411 1.69 8.9938 0 1.00 0.85 0.56 Cadmium -49 In 1.49 1.42 1.42 2.20 3 114.818 1.78 5.7864 0.404 0.65 0.46 0.45 Indium -50 Sn 1.72 1.39 1.39 1.93 4 118.701 1.96 7.3439 1.112066 0.40 0.50 0.50 Tin -51 Sb 1.82 1.39 1.39 2.17 3 121.760 2.05 8.6084 1.047401 0.62 0.39 0.71 Antimony -52 Te 2.01 1.38 1.38 2.06 2 127.60 2.10 9.0096 1.970875 0.83 0.48 0.00 Tellurium -53 I 2.21 1.39 1.39 1.98 1 126.90447 2.66 10.4513 3.059038 0.58 0.00 0.58 Iodine -54 Xe 0.00 1.40 1.40 2.16 0 131.293 2.60 12.1298 0 0.26 0.62 0.69 Xenon -55 Cs 0.86 2.44 2.44 3.43 1 132.90545 0.79 3.8939 0.471626 0.34 0.09 0.56 Caesium -56 Ba 0.97 2.15 2.15 2.68 2 137.327 0.89 5.2117 0.14462 0.00 0.79 0.00 Barium -57 La 1.08 2.07 2.07 2.50 12 138.9055 1.10 5.5769 0.47 0.44 0.83 1.00 Lanthanum -58 Ce 0.00 2.04 2.04 2.48 6 140.116 1.12 5.5387 0.5 1.00 1.00 0.78 Cerium -59 Pr 0.00 2.03 2.03 2.47 6 140.90765 1.13 5.473 0.5 0.85 1.00 0.78 Praseodymium -60 Nd 0.00 2.01 2.01 2.45 6 144.24 1.14 5.525 0.5 0.78 1.00 0.78 Neodymium -61 Pm 0.00 1.99 1.99 2.43 6 145 0.00 5.582 0.5 0.64 1.00 0.78 Promethium -62 Sm 0.00 1.98 1.98 2.42 6 150.36 1.17 5.6437 0.5 0.56 1.00 0.78 Samarium -63 Eu 0.00 1.98 1.98 2.40 6 151.964 0.00 5.6704 0.5 0.38 1.00 0.78 Europium -64 Gd 0.00 1.96 1.96 2.38 6 157.25 1.20 6.1498 0.5 0.27 1.00 0.78 Gadolinium -65 Tb 0.00 1.94 1.94 2.37 6 158.92534 0.00 5.8638 0.5 0.19 1.00 0.78 Terbium -66 Dy 0.00 1.92 1.92 2.35 6 162.500 1.22 5.9389 0.5 0.12 1.00 0.78 Dysprosium -67 Ho 0.00 1.92 1.92 2.33 6 164.93032 1.23 6.0215 0.5 0.00 1.00 0.61 Holmium -68 Er 0.00 1.89 1.89 2.32 6 167.259 1.24 6.1077 0.5 0.00 0.90 0.46 Erbium -69 Tm 0.00 1.90 1.90 2.30 6 168.93421 1.25 6.1843 0.5 0.00 0.83 0.32 Thulium -70 Yb 0.00 1.87 1.87 2.28 6 173.054 0.00 6.2542 0.5 0.00 0.75 0.22 Ytterbium -71 Lu 0.00 1.87 1.87 2.27 6 174.9668 1.27 5.4259 0.5 0.00 0.67 0.14 Lutetium -72 Hf 1.23 1.75 1.75 2.25 6 178.49 1.30 6.8251 0 0.30 0.76 1.00 Hafnium -73 Ta 1.33 1.70 1.70 2.20 6 180.9479 1.50 7.5496 0.322 0.30 0.65 1.00 Tantalum -74 W 1.40 1.62 1.62 2.10 6 183.84 2.36 7.864 0.815 0.13 0.58 0.84 Tungsten -75 Re 1.46 1.51 1.51 2.05 6 186.207 1.90 7.8335 0.15 0.15 0.49 0.67 Rhenium -76 Os 1.52 1.44 1.44 2.00 6 190.23 2.20 8.4382 1.0778 0.15 0.40 0.59 Osmium -77 Ir 1.55 1.41 1.41 2.00 6 192.217 2.20 8.967 1.56436 0.09 0.33 0.53 Iridium -78 Pt 1.44 1.36 1.36 2.05 6 195.078 2.28 8.9588 2.1251 0.96 0.93 0.82 Platinum -79 Au 1.42 1.36 1.36 2.10 6 196.96655 2.54 9.2255 2.30861 0.80 0.82 0.12 Gold -80 Hg 1.44 1.32 1.32 2.05 6 200.59 2.00 10.4375 0 0.71 0.71 0.76 Mercury -81 Tl 1.44 1.45 1.45 1.96 3 204.3833 1.62 6.1082 0.377 0.65 0.33 0.30 Thallium -82 Pb 1.55 1.46 1.46 2.02 4 207.2 2.33 7.4167 0.364 0.34 0.35 0.38 Lead -83 Bi 1.67 1.48 1.48 2.07 3 208.98040 2.02 7.2855 0.942363 0.62 0.31 0.71 Bismuth -84 Po 1.76 1.40 1.40 1.97 2 209 2.00 8.414 1.9 0.67 0.36 0.00 Polonium -85 At 1.90 1.50 1.50 2.02 1 210 2.20 0 2.8 0.46 0.31 0.27 Astatine -86 Rn 0.00 1.50 1.50 2.20 0 222 0.00 10.7485 0 0.26 0.51 0.59 Radon -87 Fr 0.00 2.60 2.60 3.48 1 223 0.70 4.0727 0 0.26 0.00 0.40 Francium -88 Ra 0.00 2.21 2.21 2.83 2 226 0.90 5.2784 0 0.00 0.49 0.00 Radium -89 Ac 0.00 2.15 2.15 2.00 6 227 1.10 5.17 0 0.44 0.67 0.98 Actinium -90 Th 0.00 2.06 2.06 2.40 6 232.0381 1.30 6.3067 0 0.00 0.73 1.00 Thorium -91 Pa 0.00 2.00 2.00 2.00 6 231.03588 1.50 5.89 0 0.00 0.63 1.00 Protactinium -92 U 0.00 1.96 1.96 2.30 6 238.02891 1.38 6.1941 0 0.00 0.56 1.00 Uranium -93 Np 0.00 1.90 1.90 2.00 6 237 1.36 6.2657 0 0.00 0.50 1.00 Neptunium -94 Pu 0.00 1.87 1.87 2.00 6 244 1.28 6.026 0 0.00 0.42 1.00 Plutonium -95 Am 0.00 1.80 1.80 2.00 6 243 1.30 5.9738 0 0.33 0.36 0.95 Americium -96 Cm 0.00 1.69 1.69 2.00 6 247 1.30 5.9914 0 0.47 0.36 0.89 Curium -97 Bk 0.00 1.60 1.60 2.00 6 247 1.30 6.1979 0 0.54 0.31 0.89 Berkelium -98 Cf 0.00 1.60 1.60 2.00 6 251 1.30 6.2817 0 0.63 0.21 0.83 Californium -99 Es 0.00 1.60 1.60 2.00 6 252 1.30 6.42 0 0.70 0.12 0.83 Einsteinium -100 Fm 0.00 1.60 1.60 2.00 6 257 1.30 6.5 0 0.70 0.12 0.73 Fermium -101 Md 0.00 1.60 1.60 2.00 6 258 1.30 6.58 0 0.70 0.05 0.65 Mendelevium -102 No 0.00 1.60 1.60 2.00 6 259 1.30 6.65 0 0.74 0.05 0.53 Nobelium -103 Lr 0.00 1.60 1.60 2.00 6 262 0.00 4.9 0 0.78 0.00 0.40 Lawrencium -104 Rf 0.00 1.60 1.60 2.00 6 267 0.00 6 0 0.80 0.00 0.35 Rutherfordium -105 Db 0.00 1.60 1.60 2.00 6 268 0.00 0 0 0.82 0.00 0.31 Dubnium -106 Sg 0.00 1.60 1.60 2.00 6 271 0.00 0 0 0.85 0.00 0.27 Seaborgium -107 Bh 0.00 1.60 1.60 2.00 6 272 0.00 0 0 0.88 0.00 0.22 Bohrium -108 Hs 0.00 1.60 1.60 2.00 6 270 0.00 0 0 0.90 0.00 0.18 Hassium -109 Mt 0.00 1.60 1.60 2.00 6 268 0.00 0 0 0.92 0.00 0.15 Meitnerium -110 Ds 0.00 1.60 1.60 2.00 6 281 0.00 0 0 0.93 0.00 0.14 Darmstadtium -111 Rg 0.00 1.60 1.60 2.00 6 280 0.00 0 0 0.94 0.00 0.13 Roentgenium -112 Cn 0.00 1.60 1.60 2.00 6 285 0.00 0 0 0.95 0.00 0.12 Copernicium -113 Uut 0.00 1.60 1.60 2.00 6 284 0.00 0 0 0.96 0.00 0.11 Ununtrium -114 Uuq 0.00 1.60 1.60 2.00 6 289 0.00 0 0 0.97 0.00 0.10 Ununquadium -115 Uup 0.00 1.60 1.60 2.00 6 288 0.00 0 0 0.98 0.00 0.09 Ununpentium -116 Uuh 0.00 1.60 1.60 2.00 6 293 0.00 0 0 0.99 0.00 0.08 Ununhexium -117 Uuh 0.00 1.60 1.60 2.00 6 294 0.00 0 0 0.99 0.00 0.07 Ununseptium -118 Uuh 0.00 1.60 1.60 2.00 6 294 0.00 0 0 0.99 0.00 0.06 Ununoctium
--- a/CADDSuite-1.6/data/OpenBabel/fragments.txt Sat Dec 15 13:16:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33785 +0,0 @@ -# -# Open Babel file: fragments.txt -# -# Copyright (c) 2007-2008 by Geoffrey R Hutchison -# Part of the Open Babel package, under the GNU General Public License (GPL) -# -# Fragments for OBBuilder coordinate generation -# These consist of a generic SMARTS pattern -# followed by the 3D coordinates of all heavy atoms -# -# Fragments are ordered by length of SMARTS pattern -# (i.e., most complicated will match first) -# -# This file contains ~1000 of the most common ring fragments -# from analysis over the NCI database and ZINC -# -# NCI: http://cactus.nci.nih.gov/ncidb2/download.html -# ZINC: http://zinc.docking.org/ -# -A1AA[A@@]2(AA1)A[A@H]1[A@H](A[A@@H]3[A@@H]1AA[A@H]1[A@@H]3AA[A@H]3AAAA[A@H]13)A2 - -6.211 -1.460 -0.030 - -5.943 -0.593 1.206 - -5.091 0.648 0.864 - -3.994 0.300 -0.169 - -4.538 -0.250 -1.367 - -5.898 -0.674 -1.321 - -3.111 1.535 -0.461 - -1.792 1.261 0.318 - -2.126 0.038 1.158 - -0.839 -0.820 1.272 - 0.215 0.187 0.788 - -0.505 0.862 -0.397 - 0.361 2.038 -0.842 - 1.787 1.544 -1.206 - 2.492 0.838 -0.023 - 1.643 -0.352 0.504 - 1.731 -1.601 -0.389 - 3.140 -1.884 -0.874 - 4.220 -1.079 -0.124 - 5.652 -1.521 -0.524 - 6.711 -0.431 -0.189 - 6.283 0.453 0.974 - 4.934 1.171 0.717 - 3.983 0.435 -0.283 - -3.106 -0.636 0.409 -A1A=A2AA3AA[A@@]45[A@@H]3A[A@@H]2[A@H]2[A@@H](A1)AAA(a1aaaaa51)[A@H]42 - -3.888 0.914 0.115 - -3.459 -0.469 0.519 - -2.450 -1.056 -0.087 - -1.962 -2.361 0.428 - -0.673 -2.830 -0.062 - 0.191 -3.047 1.144 - 0.602 -1.615 1.554 - 0.598 -0.812 0.219 - 0.084 -1.793 -0.806 - -0.800 -1.233 -1.901 - -1.848 -0.330 -1.263 - -1.065 0.868 -0.767 - -1.865 2.101 -0.431 - -2.873 1.838 0.542 - -0.974 3.251 0.020 - 0.403 2.844 0.453 - 0.828 1.570 0.379 - 2.076 1.022 0.182 - 3.313 1.677 0.144 - 4.435 0.913 -0.126 - 4.355 -0.449 -0.358 - 3.133 -1.117 -0.307 - 2.013 -0.363 -0.016 - -0.183 0.472 0.416 -A1AA[A@@H]2[A@H](A1)AA[A@H]1[A@@H]2AA[A@@H]2[A@H]1AA[A@@H]1AAA[A@@H]21 - 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