[cdk] 56/62: Update upstream source from tag 'upstream/1.2.10'
Emmanuel Bourg
ebourg-guest at moszumanska.debian.org
Fri Mar 30 21:56:42 BST 2018
This is an automated email from the git hooks/post-receive script.
ebourg-guest pushed a commit to branch master
in repository cdk.
commit 7b039c1a48167f31aeb8fd9f7abb0826b6c28948
Merge: 64a9f25 fd02a76
Author: Emmanuel Bourg <ebourg at apache.org>
Date: Fri Mar 30 21:54:28 2018 +0200
Update upstream source from tag 'upstream/1.2.10'
Update to upstream version '1.2.10'
with Debian dir 7dc71d5cb7944acfbe2b98c7469529fdc87f7711
README | 119 +
build.props | 3 +
build.xml | 1183 ++
changelog.20060714.txt | 157 +
changelog.xml | 249 +
changelog.xsd | 97 +
doc/lgpl.license | 459 +
doc/refs/bibtexml.xsd | 1000 ++
doc/refs/build.xml | 49 +
doc/refs/cdknews.bibx | 280 +
doc/refs/cheminf.bibx | 971 ++
javadoc.xml | 140 +
src/META-INF/applet-core.files | 262 +
src/META-INF/applet-editor-opts.files | 314 +
src/META-INF/applet-editor.files | 328 +
src/META-INF/applet-viewer-opts.files | 1 +
src/META-INF/atomtype.cdkdepends | 4 +
src/META-INF/atomtype.datafiles | 6 +
src/META-INF/atomtype.libdepends | 1 +
src/META-INF/builder3d.cdkdepends | 13 +
src/META-INF/builder3d.datafiles | 2 +
src/META-INF/builder3d.libdepends | 3 +
src/META-INF/builder3dtools.cdkdepends | 13 +
src/META-INF/builder3dtools.libdepends | 2 +
src/META-INF/charges.cdkdepends | 9 +
src/META-INF/charges.libdepends | 3 +
src/META-INF/control.cdkdepends | 8 +
src/META-INF/control.libdepends | 2 +
src/META-INF/core.cdkdepends | 2 +
src/META-INF/core.datafiles | 6 +
src/META-INF/core.libdepends | 1 +
src/META-INF/data.cdkdepends | 3 +
src/META-INF/data.libdepends | 1 +
src/META-INF/datadebug.cdkdepends | 4 +
src/META-INF/datadebug.libdepends | 1 +
src/META-INF/dict.cdkdepends | 3 +
src/META-INF/dict.libdepends | 1 +
src/META-INF/diff.cdkdepends | 3 +
src/META-INF/diff.libdepends | 1 +
src/META-INF/extra.cdkdepends | 11 +
src/META-INF/extra.datafiles | 7 +
src/META-INF/extra.libdepends | 3 +
src/META-INF/fingerprint.cdkdepends | 9 +
src/META-INF/fingerprint.datafiles | 1 +
src/META-INF/fingerprint.libdepends | 1 +
src/META-INF/forcefield.cdkdepends | 10 +
src/META-INF/forcefield.datafiles | 2 +
src/META-INF/forcefield.libdepends | 3 +
src/META-INF/formula.cdkdepends | 4 +
src/META-INF/formula.libdepends | 2 +
src/META-INF/inchi.cdkdepends | 6 +
src/META-INF/inchi.libdepends | 4 +
src/META-INF/interfaces.libdepends | 1 +
src/META-INF/io.cdkdepends | 6 +
src/META-INF/io.datafiles | 1 +
src/META-INF/io.libdepends | 2 +
src/META-INF/ioformats.buildfiles | 1 +
src/META-INF/ioformats.cdkdepends | 1 +
src/META-INF/ionpot.cdkdepends | 10 +
src/META-INF/isomorphism.cdkdepends | 4 +
src/META-INF/isomorphism.libdepends | 3 +
src/META-INF/libiocml.buildfiles | 1 +
src/META-INF/libiocml.cdkdepends | 8 +
src/META-INF/libiocml.libdepends | 4 +
src/META-INF/libiomd.cdkdepends | 7 +
src/META-INF/libiomd.libdepends | 2 +
src/META-INF/nonotify.cdkdepends | 4 +
src/META-INF/nonotify.libdepends | 1 +
src/META-INF/pcore.cdkdepends | 9 +
src/META-INF/pcore.libdepends | 2 +
src/META-INF/pdb.cdkdepends | 7 +
src/META-INF/pdb.datafiles | 1 +
src/META-INF/pdb.libdepends | 2 +
src/META-INF/pdbcml.cdkdepends | 7 +
src/META-INF/pdbcml.libdepends | 2 +
src/META-INF/qm.cdkdepends | 3 +
src/META-INF/qm.libdepends | 1 +
src/META-INF/qsar.buildfiles | 1 +
src/META-INF/qsar.cdkdepends | 8 +
src/META-INF/qsar.datafiles | 4 +
src/META-INF/qsar.extrafiles | 1 +
src/META-INF/qsar.libdepends | 6 +
src/META-INF/qsaratomic.cdkdepends | 13 +
src/META-INF/qsaratomic.datafiles | 1 +
src/META-INF/qsaratomic.libdepends | 6 +
src/META-INF/qsarbond.cdkdepends | 11 +
src/META-INF/qsarbond.libdepends | 6 +
src/META-INF/qsarcml.cdkdepends | 7 +
src/META-INF/qsarcml.libdepends | 2 +
src/META-INF/qsarionpot.cdkdepends | 19 +
src/META-INF/qsarmolecular.cdkdepends | 15 +
src/META-INF/qsarmolecular.datafiles | 4 +
src/META-INF/qsarmolecular.extrafiles | 1 +
src/META-INF/qsarmolecular.libdepends | 6 +
src/META-INF/qsarprotein.cdkdepends | 11 +
src/META-INF/qsarprotein.libdepends | 6 +
src/META-INF/reaction.buildfiles | 2 +
src/META-INF/reaction.cdkdepends | 9 +
src/META-INF/reaction.libdepends | 5 +
src/META-INF/render.cdkdepends | 4 +
src/META-INF/render.libdepends | 2 +
src/META-INF/sdg.cdkdepends | 6 +
src/META-INF/sdg.datafiles | 2 +
src/META-INF/sdg.libdepends | 2 +
src/META-INF/smarts.autogenerated | 8 +
src/META-INF/smarts.cdkdepends | 9 +
src/META-INF/smarts.libdepends | 1 +
src/META-INF/smiles.cdkdepends | 8 +
src/META-INF/smiles.libdepends | 1 +
src/META-INF/standard.cdkdepends | 3 +
src/META-INF/standard.libdepends | 3 +
src/META-INF/structgen.cdkdepends | 6 +
src/META-INF/test-atomtype.cdkdepends | 14 +
src/META-INF/test-atomtype.devellibdepends | 2 +
src/META-INF/test-atomtype.libdepends | 3 +
src/META-INF/test-builder3d.cdkdepends | 23 +
src/META-INF/test-builder3d.devellibdepends | 2 +
src/META-INF/test-builder3d.libdepends | 4 +
src/META-INF/test-charges.cdkdepends | 16 +
src/META-INF/test-charges.devellibdepends | 2 +
src/META-INF/test-charges.libdepends | 3 +
src/META-INF/test-core.cdkdepends | 14 +
src/META-INF/test-core.devellibdepends | 2 +
src/META-INF/test-core.libdepends | 3 +
src/META-INF/test-data.cdkdepends | 8 +
src/META-INF/test-data.devellibdepends | 2 +
src/META-INF/test-data.libdepends | 2 +
src/META-INF/test-datadebug.cdkdepends | 8 +
src/META-INF/test-datadebug.devellibdepends | 2 +
src/META-INF/test-datadebug.libdepends | 2 +
src/META-INF/test-dict.cdkdepends | 3 +
src/META-INF/test-dict.devellibdepends | 2 +
src/META-INF/test-diff.cdkdepends | 6 +
src/META-INF/test-diff.devellibdepends | 1 +
src/META-INF/test-diff.libdepends | 2 +
src/META-INF/test-extra.cdkdepends | 27 +
src/META-INF/test-extra.devellibdepends | 2 +
src/META-INF/test-extra.libdepends | 7 +
src/META-INF/test-fingerprint.cdkdepends | 17 +
src/META-INF/test-fingerprint.devellibdepends | 1 +
src/META-INF/test-fingerprint.libdepends | 3 +
src/META-INF/test-forcefield.cdkdepends | 16 +
src/META-INF/test-forcefield.devellibdepends | 2 +
src/META-INF/test-forcefield.libdepends | 4 +
src/META-INF/test-formula.cdkdepends | 11 +
src/META-INF/test-formula.devellibdepends | 2 +
src/META-INF/test-formula.libdepends | 5 +
src/META-INF/test-inchi.cdkdepends | 10 +
src/META-INF/test-inchi.devellibdepends | 2 +
src/META-INF/test-inchi.libdepends | 5 +
src/META-INF/test-interfaces.cdkdepends | 5 +
src/META-INF/test-interfaces.devellibdepends | 2 +
src/META-INF/test-interfaces.libdepends | 2 +
src/META-INF/test-io.cdkdepends | 21 +
src/META-INF/test-io.devellibdepends | 2 +
src/META-INF/test-io.libdepends | 6 +
src/META-INF/test-ioformats.cdkdepends | 12 +
src/META-INF/test-ioformats.devellibdepends | 2 +
src/META-INF/test-ioformats.libdepends | 6 +
src/META-INF/test-ionpot.cdkdepends | 15 +
src/META-INF/test-ionpot.devellibdepends | 2 +
src/META-INF/test-ionpot.libdepends | 5 +
src/META-INF/test-isomorphism.cdkdepends | 6 +
src/META-INF/test-isomorphism.devellibdepends | 2 +
src/META-INF/test-isomorphism.libdepends | 3 +
src/META-INF/test-libiocml.cdkdepends | 20 +
src/META-INF/test-libiocml.devellibdepends | 2 +
src/META-INF/test-libiocml.libdepends | 5 +
src/META-INF/test-libiomd.cdkdepends | 11 +
src/META-INF/test-libiomd.devellibdepends | 2 +
src/META-INF/test-libiomd.libdepends | 4 +
src/META-INF/test-nonotify.cdkdepends | 8 +
src/META-INF/test-nonotify.devellibdepends | 2 +
src/META-INF/test-nonotify.libdepends | 2 +
src/META-INF/test-pcore.cdkdepends | 15 +
src/META-INF/test-pcore.devellibdepends | 2 +
src/META-INF/test-pcore.libdepends | 4 +
src/META-INF/test-pdb.cdkdepends | 13 +
src/META-INF/test-pdb.devellibdepends | 2 +
src/META-INF/test-pdb.libdepends | 4 +
src/META-INF/test-qm.cdkdepends | 8 +
src/META-INF/test-qm.devellibdepends | 2 +
src/META-INF/test-qm.libdepends | 1 +
src/META-INF/test-qsar.cdkdepends | 19 +
src/META-INF/test-qsar.devellibdepends | 2 +
src/META-INF/test-qsar.libdepends | 7 +
src/META-INF/test-qsaratomic.cdkdepends | 25 +
src/META-INF/test-qsaratomic.devellibdepends | 2 +
src/META-INF/test-qsaratomic.libdepends | 7 +
src/META-INF/test-qsarbond.cdkdepends | 25 +
src/META-INF/test-qsarbond.devellibdepends | 2 +
src/META-INF/test-qsarbond.libdepends | 7 +
src/META-INF/test-qsarionpot.cdkdepends | 31 +
src/META-INF/test-qsarionpot.devellibdepends | 2 +
src/META-INF/test-qsarionpot.libdepends | 7 +
src/META-INF/test-qsarmolecular.cdkdepends | 29 +
src/META-INF/test-qsarmolecular.devellibdepends | 2 +
src/META-INF/test-qsarmolecular.libdepends | 7 +
src/META-INF/test-qsarprotein.cdkdepends | 23 +
src/META-INF/test-qsarprotein.devellibdepends | 2 +
src/META-INF/test-qsarprotein.libdepends | 7 +
src/META-INF/test-reaction.cdkdepends | 15 +
src/META-INF/test-reaction.devellibdepends | 2 +
src/META-INF/test-reaction.libdepends | 5 +
src/META-INF/test-render.cdkdepends | 7 +
src/META-INF/test-render.devellibdepends | 2 +
src/META-INF/test-render.libdepends | 2 +
src/META-INF/test-sdg.cdkdepends | 13 +
src/META-INF/test-sdg.devellibdepends | 2 +
src/META-INF/test-sdg.libdepends | 3 +
src/META-INF/test-smarts.cdkdepends | 14 +
src/META-INF/test-smarts.devellibdepends | 2 +
src/META-INF/test-smarts.libdepends | 3 +
src/META-INF/test-smiles.cdkdepends | 18 +
src/META-INF/test-smiles.devellibdepends | 2 +
src/META-INF/test-smiles.libdepends | 5 +
src/META-INF/test-standard.cdkdepends | 14 +
src/META-INF/test-standard.devellibdepends | 2 +
src/META-INF/test-standard.libdepends | 5 +
src/META-INF/test-structgen.cdkdepends | 14 +
src/META-INF/test-structgen.devellibdepends | 2 +
src/META-INF/test-structgen.libdepends | 3 +
src/META-INF/test-valencycheck.cdkdepends | 13 +
src/META-INF/test-valencycheck.devellibdepends | 2 +
src/META-INF/test-valencycheck.libdepends | 3 +
src/META-INF/test.cdkdepends | 6 +
src/META-INF/test.devellibdepends | 2 +
src/META-INF/test.libdepends | 2 +
src/META-INF/valencycheck.cdkdepends | 4 +
src/META-INF/valencycheck.libdepends | 1 +
src/main/net/sf/cdk/tools/MakeJavafilesFiles.java | 302 +
.../net/sf/cdk/tools/bibtex/BibTeXMLEntry.java | 106 +
src/main/net/sf/cdk/tools/bibtex/BibTeXMLFile.java | 75 +
.../tools/copyright/CheckCopyrightStatements.java | 177 +
.../sf/cdk/tools/coverage/CheckModuleCoverage.java | 145 +
.../net/sf/cdk/tools/doclets/CDKBugTaglet.java | 100 +
.../net/sf/cdk/tools/doclets/CDKCiteTaglet.java | 158 +
.../net/sf/cdk/tools/doclets/CDKDictRefTaglet.java | 134 +
.../net/sf/cdk/tools/doclets/CDKGitTaglet.java | 127 +
.../net/sf/cdk/tools/doclets/CDKInChITaglet.java | 99 +
.../net/sf/cdk/tools/doclets/CDKModuleTaglet.java | 88 +
.../cdk/tools/doclets/CDKThreadNonSafeTaglet.java | 89 +
.../sf/cdk/tools/doclets/CDKThreadSafeTaglet.java | 90 +
src/main/org/openscience/cdk/AminoAcid.java | 167 +
src/main/org/openscience/cdk/Association.java | 194 +
src/main/org/openscience/cdk/Atom.java | 421 +
src/main/org/openscience/cdk/AtomContainer.java | 1737 ++
src/main/org/openscience/cdk/AtomContainerSet.java | 388 +
src/main/org/openscience/cdk/AtomParity.java | 159 +
src/main/org/openscience/cdk/AtomType.java | 409 +
src/main/org/openscience/cdk/BioPolymer.java | 282 +
src/main/org/openscience/cdk/Bond.java | 499 +
src/main/org/openscience/cdk/CDKConstants.java | 326 +
src/main/org/openscience/cdk/ChemFile.java | 248 +
src/main/org/openscience/cdk/ChemModel.java | 260 +
src/main/org/openscience/cdk/ChemObject.java | 462 +
src/main/org/openscience/cdk/ChemSequence.java | 233 +
.../org/openscience/cdk/ConformerContainer.java | 477 +
src/main/org/openscience/cdk/Crystal.java | 259 +
.../openscience/cdk/DefaultChemObjectBuilder.java | 366 +
.../org/openscience/cdk/ElectronContainer.java | 106 +
src/main/org/openscience/cdk/Element.java | 205 +
.../org/openscience/cdk/EnzymeResidueLocator.java | 74 +
src/main/org/openscience/cdk/FragmentAtom.java | 95 +
.../cdk/IImplementationSpecification.java | 68 +
src/main/org/openscience/cdk/Isotope.java | 301 +
src/main/org/openscience/cdk/LonePair.java | 153 +
src/main/org/openscience/cdk/Mapping.java | 136 +
src/main/org/openscience/cdk/Molecule.java | 109 +
src/main/org/openscience/cdk/MoleculeSet.java | 195 +
src/main/org/openscience/cdk/Monomer.java | 134 +
.../org/openscience/cdk/PeriodicTableElement.java | 400 +
.../org/openscience/cdk/PhysicalConstants.java | 50 +
src/main/org/openscience/cdk/Polymer.java | 213 +
src/main/org/openscience/cdk/PseudoAtom.java | 176 +
src/main/org/openscience/cdk/Reaction.java | 476 +
src/main/org/openscience/cdk/ReactionScheme.java | 131 +
src/main/org/openscience/cdk/ReactionSet.java | 251 +
src/main/org/openscience/cdk/Ring.java | 163 +
src/main/org/openscience/cdk/RingSet.java | 213 +
src/main/org/openscience/cdk/SingleElectron.java | 160 +
src/main/org/openscience/cdk/Strand.java | 258 +
src/main/org/openscience/cdk/Vibration.java | 113 +
.../org/openscience/cdk/annotations/TestClass.java | 43 +
.../openscience/cdk/annotations/TestMethod.java | 41 +
.../cdk/aromaticity/AromaticityCalculator.java | 126 +
.../aromaticity/CDKHueckelAromaticityDetector.java | 227 +
.../cdk/atomtype/CDKAtomTypeMatcher.java | 1609 ++
.../cdk/atomtype/EStateAtomTypeMatcher.java | 201 +
.../openscience/cdk/atomtype/IAtomTypeGuesser.java | 54 +
.../openscience/cdk/atomtype/IAtomTypeMatcher.java | 64 +
.../cdk/atomtype/MM2AtomTypeMatcher.java | 309 +
.../cdk/atomtype/MMFF94AtomTypeMatcher.java | 345 +
.../cdk/atomtype/StructGenAtomTypeGuesser.java | 101 +
.../openscience/cdk/atomtype/StructGenMatcher.java | 108 +
.../cdk/atomtype/SybylAtomTypeMatcher.java | 129 +
.../cdk/atomtype/mapper/AtomTypeMapper.java | 99 +
.../openscience/cdk/charges/AtomTypeCharges.java | 151 +
.../openscience/cdk/charges/Electronegativity.java | 168 +
.../charges/GasteigerMarsiliPartialCharges.java | 366 +
.../cdk/charges/GasteigerPEPEPartialCharges.java | 877 +
.../openscience/cdk/charges/IChargeCalculator.java | 33 +
.../cdk/charges/IElectronicPropertyCalculator.java | 38 +
.../cdk/charges/InductivePartialCharges.java | 404 +
.../cdk/charges/MMFF94PartialCharges.java | 141 +
.../cdk/charges/PiElectronegativity.java | 182 +
.../openscience/cdk/charges/Polarizability.java | 325 +
.../cdk/charges/StabilizationCharges.java | 153 +
.../openscience/cdk/config/AtomTypeFactory.java | 412 +
.../cdk/config/CDKBasedAtomTypeConfigurator.java | 104 +
.../openscience/cdk/config/ElementPTFactory.java | 311 +
src/main/org/openscience/cdk/config/Elements.java | 161 +
.../cdk/config/IAtomTypeConfigurator.java | 59 +
.../org/openscience/cdk/config/IsotopeFactory.java | 360 +
.../cdk/config/OWLBasedAtomTypeConfigurator.java | 77 +
src/main/org/openscience/cdk/config/Symbols.java | 186 +
.../cdk/config/TXTBasedAtomTypeConfigurator.java | 148 +
.../cdk/config/atomtypes/AtomTypeHandler.java | 268 +
.../cdk/config/atomtypes/AtomTypeReader.java | 149 +
.../cdk/config/atomtypes/OWLAtomTypeHandler.java | 156 +
.../atomtypes/OWLAtomTypeMappingHandler.java | 109 +
.../config/atomtypes/OWLAtomTypeMappingReader.java | 130 +
.../cdk/config/atomtypes/OWLAtomTypeReader.java | 132 +
.../cdk/config/data/chemicalElements.xml | 1478 ++
.../cdk/config/data/conversion_table.xml | 18 +
.../cdk/config/data/electroneg-pauling.txt | 100 +
src/main/org/openscience/cdk/config/data/html.xsl | 60 +
.../org/openscience/cdk/config/data/isotopes.xml | 16631 +++++++++++++++++++
.../openscience/cdk/config/data/jmol_atomtypes.txt | 229 +
.../openscience/cdk/config/data/log4j.properties | 10 +
.../openscience/cdk/config/data/mm2_atomtypes.xml | 886 +
.../cdk/config/data/mmff94_atomtypes.xml | 1236 ++
.../openscience/cdk/config/data/mol2_atomtypes.xml | 191 +
.../openscience/cdk/config/data/pdb_atomtypes.xml | 424 +
.../openscience/cdk/config/data/radii-covalent.txt | 76 +
.../org/openscience/cdk/config/data/radii-vdw.txt | 116 +
.../cdk/config/data/structgen_atomtypes.xml | 143 +
.../openscience/cdk/config/data/whim_weights.txt | 39 +
.../cdk/config/elements/ElementPTHandler.java | 207 +
.../cdk/config/elements/ElementPTReader.java | 151 +
.../cdk/config/fragments/EStateFragments.java | 133 +
.../cdk/config/isotopes/IsotopeHandler.java | 184 +
.../cdk/config/isotopes/IsotopeReader.java | 159 +
.../openscience/cdk/controller/CDKPopupMenu.java | 63 +
.../cdk/controller/IMouseEventRelay.java | 78 +
.../cdk/controller/IViewEventRelay.java | 35 +
.../cdk/controller/SwingEventRelay.java | 43 +
.../cdk/controller/SwingMouseEventRelay.java | 94 +
.../openscience/cdk/controller/UndoAdapter.java | 62 +
.../openscience/cdk/debug/DebugAdductFormula.java | 129 +
.../org/openscience/cdk/debug/DebugAminoAcid.java | 571 +
src/main/org/openscience/cdk/debug/DebugAtom.java | 382 +
.../openscience/cdk/debug/DebugAtomContainer.java | 547 +
.../cdk/debug/DebugAtomContainerSet.java | 222 +
.../org/openscience/cdk/debug/DebugAtomParity.java | 61 +
.../org/openscience/cdk/debug/DebugAtomType.java | 292 +
.../org/openscience/cdk/debug/DebugBioPolymer.java | 609 +
src/main/org/openscience/cdk/debug/DebugBond.java | 254 +
.../org/openscience/cdk/debug/DebugChemFile.java | 171 +
.../org/openscience/cdk/debug/DebugChemModel.java | 185 +
.../org/openscience/cdk/debug/DebugChemObject.java | 159 +
.../cdk/debug/DebugChemObjectBuilder.java | 366 +
.../openscience/cdk/debug/DebugChemSequence.java | 167 +
.../org/openscience/cdk/debug/DebugCrystal.java | 603 +
.../cdk/debug/DebugElectronContainer.java | 151 +
.../org/openscience/cdk/debug/DebugElement.java | 181 +
.../openscience/cdk/debug/DebugFragmentAtom.java | 397 +
.../org/openscience/cdk/debug/DebugIsotope.java | 220 +
.../org/openscience/cdk/debug/DebugLonePair.java | 177 +
.../org/openscience/cdk/debug/DebugMapping.java | 156 +
.../cdk/debug/DebugMolecularFormula.java | 122 +
.../cdk/debug/DebugMolecularFormulaSet.java | 100 +
.../org/openscience/cdk/debug/DebugMolecule.java | 548 +
.../openscience/cdk/debug/DebugMoleculeSet.java | 254 +
.../org/openscience/cdk/debug/DebugMonomer.java | 561 +
.../org/openscience/cdk/debug/DebugPDBAtom.java | 188 +
.../org/openscience/cdk/debug/DebugPDBMonomer.java | 61 +
.../org/openscience/cdk/debug/DebugPDBPolymer.java | 55 +
.../openscience/cdk/debug/DebugPDBStructure.java | 111 +
.../org/openscience/cdk/debug/DebugPolymer.java | 568 +
.../org/openscience/cdk/debug/DebugPseudoAtom.java | 394 +
.../org/openscience/cdk/debug/DebugReaction.java | 257 +
.../openscience/cdk/debug/DebugReactionScheme.java | 160 +
.../openscience/cdk/debug/DebugReactionSet.java | 172 +
src/main/org/openscience/cdk/debug/DebugRing.java | 581 +
.../org/openscience/cdk/debug/DebugRingSet.java | 73 +
.../openscience/cdk/debug/DebugSingleElectron.java | 175 +
.../org/openscience/cdk/debug/DebugStrand.java | 593 +
.../cdk/dict/CDKDictionaryReferences.java | 132 +
src/main/org/openscience/cdk/dict/DictRef.java | 68 +
src/main/org/openscience/cdk/dict/Dictionary.java | 135 +
.../openscience/cdk/dict/DictionaryDatabase.java | 197 +
.../openscience/cdk/dict/DictionaryHandler.java | 116 +
src/main/org/openscience/cdk/dict/Entry.java | 140 +
src/main/org/openscience/cdk/dict/EntryReact.java | 186 +
src/main/org/openscience/cdk/dict/OWLFile.java | 137 +
src/main/org/openscience/cdk/dict/OWLReact.java | 217 +
.../cdk/dict/data/atom-type-mappings.owl | 51 +
.../org/openscience/cdk/dict/data/atom-types.owl | 96 +
.../openscience/cdk/dict/data/cdk-atom-types.owl | 1471 ++
.../cdk/dict/data/cdk-sybyl-mappings.owl | 466 +
.../org/openscience/cdk/dict/data/chemical.xml | 290 +
.../cdk/dict/data/descriptor-algorithms.owl | 2685 +++
.../org/openscience/cdk/dict/data/elements.owl | 523 +
.../cdk/dict/data/reaction-processes.owl | 970 ++
.../openscience/cdk/dict/data/sybyl-atom-types.owl | 438 +
.../cdk/event/ChemObjectChangeEvent.java | 54 +
.../openscience/cdk/event/ICDKChangeListener.java | 48 +
.../cdk/event/ICDKSelectionChangeListener.java | 48 +
.../openscience/cdk/exception/CDKException.java | 66 +
.../exception/IncorrectUseOfCDKCoreClassError.java | 45 +
.../cdk/exception/InvalidSmilesException.java | 49 +
.../cdk/exception/NoSuchAtomException.java | 55 +
.../cdk/exception/NoSuchAtomTypeException.java | 55 +
.../exception/UnsupportedChemObjectException.java | 46 +
.../cdk/fingerprint/EStateFingerprinter.java | 90 +
.../cdk/fingerprint/ExtendedFingerprinter.java | 151 +
.../openscience/cdk/fingerprint/Fingerprinter.java | 302 +
.../cdk/fingerprint/FingerprinterTool.java | 103 +
.../cdk/fingerprint/GraphOnlyFingerprinter.java | 89 +
.../cdk/fingerprint/IFingerprinter.java | 59 +
.../cdk/fingerprint/MACCSFingerprinter.java | 188 +
.../cdk/fingerprint/StandardSubstructureSets.java | 52 +
.../cdk/fingerprint/SubstructureFingerprinter.java | 427 +
.../org/openscience/cdk/formula/AdductFormula.java | 359 +
.../openscience/cdk/formula/IsotopeContainer.java | 125 +
.../openscience/cdk/formula/IsotopePattern.java | 132 +
.../cdk/formula/IsotopePatternGenerator.java | 283 +
.../cdk/formula/IsotopePatternManipulator.java | 151 +
.../cdk/formula/IsotopePatternSimilarity.java | 132 +
.../openscience/cdk/formula/MassToFormulaTool.java | 645 +
.../openscience/cdk/formula/MolecularFormula.java | 403 +
.../cdk/formula/MolecularFormulaChecker.java | 137 +
.../cdk/formula/MolecularFormulaRange.java | 235 +
.../cdk/formula/MolecularFormulaSet.java | 218 +
.../openscience/cdk/formula/rules/ChargeRule.java | 122 +
.../openscience/cdk/formula/rules/ElementRule.java | 163 +
.../org/openscience/cdk/formula/rules/IRule.java | 70 +
.../cdk/formula/rules/IsotopePatternRule.java | 150 +
.../cdk/formula/rules/MMElementRule.java | 342 +
.../cdk/formula/rules/NitrogenRule.java | 154 +
.../openscience/cdk/formula/rules/RDBERule.java | 375 +
.../cdk/formula/rules/ToleranceRangeRule.java | 136 +
.../org/openscience/cdk/geometry/AtomTools.java | 464 +
.../org/openscience/cdk/geometry/BondTools.java | 619 +
.../cdk/geometry/CrystalGeometryTools.java | 222 +
.../openscience/cdk/geometry/GeometryTools.java | 1422 ++
.../cdk/geometry/IRDFWeightFunction.java | 56 +
.../org/openscience/cdk/geometry/Projector.java | 76 +
.../openscience/cdk/geometry/RDFCalculator.java | 175 +
.../org/openscience/cdk/geometry/ZMatrixTools.java | 109 +
.../cdk/geometry/alignment/KabschAlignment.java | 504 +
.../cdk/geometry/surface/NeighborList.java | 143 +
.../cdk/geometry/surface/NumericalSurface.java | 323 +
.../cdk/geometry/surface/Tessellate.java | 202 +
.../openscience/cdk/geometry/surface/Triangle.java | 44 +
.../cdk/graph/AtomContainerAtomPermutor.java | 93 +
.../cdk/graph/AtomContainerBondPermutor.java | 94 +
.../cdk/graph/AtomContainerPermutor.java | 127 +
.../org/openscience/cdk/graph/BFSShortestPath.java | 109 +
.../cdk/graph/BiconnectivityInspector.java | 273 +
.../openscience/cdk/graph/ConnectivityChecker.java | 133 +
.../openscience/cdk/graph/MinimalPathIterator.java | 317 +
.../org/openscience/cdk/graph/MoleculeGraphs.java | 105 +
src/main/org/openscience/cdk/graph/PathTools.java | 622 +
.../org/openscience/cdk/graph/SpanningTree.java | 339 +
.../cdk/graph/invariant/CanonicalLabeler.java | 261 +
.../invariant/ConjugatedPiSystemsDetector.java | 185 +
.../invariant/EquivalentClassPartitioner.java | 498 +
.../openscience/cdk/graph/invariant/GIMatrix.java | 730 +
.../cdk/graph/invariant/HuLuIndexTool.java | 291 +
.../cdk/graph/invariant/MorganNumbersTools.java | 90 +
.../exception/BadMatrixFormatException.java | 32 +
.../exception/IndexOutOfBoundsException.java | 32 +
.../exception/MatrixNotInvertibleException.java | 32 +
.../cdk/graph/matrix/AdjacencyMatrix.java | 72 +
.../cdk/graph/matrix/ConnectionMatrix.java | 74 +
.../openscience/cdk/graph/matrix/IGraphMatrix.java | 39 +
.../cdk/graph/matrix/TopologicalMatrix.java | 33 +
.../org/openscience/cdk/graph/rebond/Bspt.java | 476 +
.../org/openscience/cdk/graph/rebond/Point.java | 58 +
.../openscience/cdk/graph/rebond/RebondTool.java | 163 +
.../org/openscience/cdk/inchi/InChIGenerator.java | 419 +
.../cdk/inchi/InChIGeneratorFactory.java | 145 +
.../openscience/cdk/inchi/InChIToStructure.java | 299 +
src/main/org/openscience/cdk/index/CASNumber.java | 110 +
.../openscience/cdk/interfaces/IAdductFormula.java | 108 +
.../org/openscience/cdk/interfaces/IAminoAcid.java | 76 +
src/main/org/openscience/cdk/interfaces/IAtom.java | 150 +
.../openscience/cdk/interfaces/IAtomContainer.java | 638 +
.../cdk/interfaces/IAtomContainerSet.java | 168 +
.../openscience/cdk/interfaces/IAtomParity.java | 72 +
.../org/openscience/cdk/interfaces/IAtomType.java | 181 +
.../openscience/cdk/interfaces/IBioPolymer.java | 140 +
src/main/org/openscience/cdk/interfaces/IBond.java | 185 +
.../org/openscience/cdk/interfaces/IChemFile.java | 78 +
.../org/openscience/cdk/interfaces/IChemModel.java | 101 +
.../openscience/cdk/interfaces/IChemObject.java | 222 +
.../cdk/interfaces/IChemObjectBuilder.java | 629 +
.../cdk/interfaces/IChemObjectChangeEvent.java | 46 +
.../cdk/interfaces/IChemObjectListener.java | 47 +
.../openscience/cdk/interfaces/IChemSequence.java | 80 +
.../org/openscience/cdk/interfaces/ICrystal.java | 139 +
.../cdk/interfaces/IElectronContainer.java | 54 +
.../org/openscience/cdk/interfaces/IElement.java | 83 +
.../openscience/cdk/interfaces/IFragmentAtom.java | 62 +
.../org/openscience/cdk/interfaces/IIsotope.java | 98 +
.../org/openscience/cdk/interfaces/ILonePair.java | 65 +
.../org/openscience/cdk/interfaces/IMapping.java | 53 +
.../cdk/interfaces/IMolecularFormula.java | 208 +
.../cdk/interfaces/IMolecularFormulaSet.java | 124 +
.../org/openscience/cdk/interfaces/IMolecule.java | 37 +
.../openscience/cdk/interfaces/IMoleculeSet.java | 85 +
.../org/openscience/cdk/interfaces/IMonomer.java | 75 +
.../org/openscience/cdk/interfaces/IPDBAtom.java | 198 +
.../openscience/cdk/interfaces/IPDBMonomer.java | 83 +
.../openscience/cdk/interfaces/IPDBPolymer.java | 79 +
.../openscience/cdk/interfaces/IPDBStructure.java | 130 +
.../org/openscience/cdk/interfaces/IPolymer.java | 92 +
.../openscience/cdk/interfaces/IPseudoAtom.java | 65 +
.../org/openscience/cdk/interfaces/IReaction.java | 287 +
.../cdk/interfaces/IReactionScheme.java | 78 +
.../openscience/cdk/interfaces/IReactionSet.java | 86 +
src/main/org/openscience/cdk/interfaces/IRing.java | 65 +
.../org/openscience/cdk/interfaces/IRingSet.java | 89 +
.../cdk/interfaces/ISingleElectron.java | 72 +
.../org/openscience/cdk/interfaces/IStrand.java | 128 +
.../openscience/cdk/io/CDKSourceCodeWriter.java | 285 +
src/main/org/openscience/cdk/io/CIFReader.java | 447 +
src/main/org/openscience/cdk/io/CMLReader.java | 252 +
src/main/org/openscience/cdk/io/CMLWriter.java | 355 +
src/main/org/openscience/cdk/io/CTXReader.java | 218 +
.../org/openscience/cdk/io/CrystClustReader.java | 233 +
.../org/openscience/cdk/io/CrystClustWriter.java | 233 +
.../cdk/io/DefaultChemObjectReader.java | 92 +
.../cdk/io/DefaultChemObjectWriter.java | 62 +
src/main/org/openscience/cdk/io/FormatFactory.java | 254 +
src/main/org/openscience/cdk/io/GamessReader.java | 446 +
.../org/openscience/cdk/io/Gaussian03Reader.java | 446 +
.../org/openscience/cdk/io/Gaussian98Reader.java | 573 +
.../org/openscience/cdk/io/GhemicalMMReader.java | 281 +
src/main/org/openscience/cdk/io/HINReader.java | 292 +
src/main/org/openscience/cdk/io/HINWriter.java | 224 +
src/main/org/openscience/cdk/io/IChemObjectIO.java | 95 +
.../org/openscience/cdk/io/IChemObjectReader.java | 70 +
.../org/openscience/cdk/io/IChemObjectWriter.java | 72 +
.../openscience/cdk/io/INChIPlainTextReader.java | 202 +
src/main/org/openscience/cdk/io/INChIReader.java | 222 +
.../cdk/io/ISimpleChemObjectReader.java | 67 +
src/main/org/openscience/cdk/io/MDLRXNReader.java | 431 +
.../org/openscience/cdk/io/MDLRXNV2000Reader.java | 323 +
.../org/openscience/cdk/io/MDLRXNV3000Reader.java | 307 +
src/main/org/openscience/cdk/io/MDLRXNWriter.java | 329 +
src/main/org/openscience/cdk/io/MDLReader.java | 585 +
.../org/openscience/cdk/io/MDLV2000Reader.java | 778 +
.../org/openscience/cdk/io/MDLV3000Reader.java | 607 +
src/main/org/openscience/cdk/io/MDLWriter.java | 445 +
src/main/org/openscience/cdk/io/Mol2Reader.java | 348 +
src/main/org/openscience/cdk/io/Mol2Writer.java | 281 +
.../openscience/cdk/io/PCCompoundASNReader.java | 473 +
.../openscience/cdk/io/PCCompoundXMLReader.java | 157 +
.../openscience/cdk/io/PCSubstanceXMLReader.java | 157 +
src/main/org/openscience/cdk/io/PDBReader.java | 685 +
src/main/org/openscience/cdk/io/PDBWriter.java | 251 +
src/main/org/openscience/cdk/io/PMPReader.java | 497 +
src/main/org/openscience/cdk/io/ReaderEvent.java | 52 +
src/main/org/openscience/cdk/io/ReaderFactory.java | 196 +
src/main/org/openscience/cdk/io/RssWriter.java | 389 +
src/main/org/openscience/cdk/io/SDFWriter.java | 260 +
src/main/org/openscience/cdk/io/SMILESReader.java | 203 +
src/main/org/openscience/cdk/io/SMILESWriter.java | 185 +
src/main/org/openscience/cdk/io/ShelXReader.java | 372 +
src/main/org/openscience/cdk/io/ShelXWriter.java | 236 +
src/main/org/openscience/cdk/io/VASPReader.java | 361 +
src/main/org/openscience/cdk/io/WriterFactory.java | 176 +
src/main/org/openscience/cdk/io/XYZReader.java | 222 +
src/main/org/openscience/cdk/io/XYZWriter.java | 189 +
src/main/org/openscience/cdk/io/ZMatrixReader.java | 245 +
.../org/openscience/cdk/io/cml/CDKConvention.java | 91 +
.../org/openscience/cdk/io/cml/CMLCoreModule.java | 1577 ++
.../openscience/cdk/io/cml/CMLErrorHandler.java | 109 +
.../org/openscience/cdk/io/cml/CMLHandler.java | 164 +
.../openscience/cdk/io/cml/CMLReactionModule.java | 179 +
.../org/openscience/cdk/io/cml/CMLResolver.java | 111 +
src/main/org/openscience/cdk/io/cml/CMLStack.java | 121 +
.../openscience/cdk/io/cml/CustomSerializer.java | 70 +
.../org/openscience/cdk/io/cml/ICMLConvention.java | 40 +
.../org/openscience/cdk/io/cml/ICMLModule.java | 52 +
.../cdk/io/cml/JMOLANIMATIONConvention.java | 119 +
.../openscience/cdk/io/cml/MDLMolConvention.java | 75 +
.../cdk/io/cml/MDMoleculeConvention.java | 241 +
.../org/openscience/cdk/io/cml/PDBConvention.java | 619 +
.../org/openscience/cdk/io/cml/PMPConvention.java | 120 +
.../org/openscience/cdk/io/cml/QSARConvention.java | 166 +
.../org/openscience/cdk/io/cml/data/cml1_0.dtd | 428 +
.../org/openscience/cdk/io/cml/data/cml1_0_1.dtd | 485 +
.../org/openscience/cdk/io/cml/data/cml1_0_1.xsd | 571 +
src/main/org/openscience/cdk/io/cml/data/cml23.xsd | 9777 +++++++++++
.../org/openscience/cdk/io/cml/data/cml25b1.xsd | 10615 ++++++++++++
.../org/openscience/cdk/io/cml/data/cmlAll.xsd | 7497 +++++++++
.../org/openscience/cdk/io/cml/data/cmlCore.xsd | 5451 ++++++
.../openscience/cdk/io/formats/ABINITFormat.java | 93 +
.../org/openscience/cdk/io/formats/ADFFormat.java | 93 +
.../openscience/cdk/io/formats/Aces2Format.java | 92 +
.../openscience/cdk/io/formats/AlchemyFormat.java | 87 +
.../org/openscience/cdk/io/formats/BGFFormat.java | 87 +
.../org/openscience/cdk/io/formats/BSFormat.java | 89 +
.../openscience/cdk/io/formats/CACheFormat.java | 92 +
.../cdk/io/formats/CDKSourceCodeFormat.java | 88 +
.../org/openscience/cdk/io/formats/CIFFormat.java | 96 +
.../org/openscience/cdk/io/formats/CMLFormat.java | 110 +
.../openscience/cdk/io/formats/CMLRSSFormat.java | 87 +
.../openscience/cdk/io/formats/CRK2DFormat.java | 89 +
.../openscience/cdk/io/formats/CRK3DFormat.java | 89 +
.../org/openscience/cdk/io/formats/CTXFormat.java | 96 +
.../cdk/io/formats/CacaoCartesianFormat.java | 89 +
.../cdk/io/formats/CacaoInternalFormat.java | 89 +
.../cdk/io/formats/Chem3D_Cartesian_1Format.java | 88 +
.../cdk/io/formats/Chem3D_Cartesian_2Format.java | 88 +
.../openscience/cdk/io/formats/ChemDrawFormat.java | 88 +
.../openscience/cdk/io/formats/ChemtoolFormat.java | 89 +
.../cdk/io/formats/CrystClustFormat.java | 98 +
.../openscience/cdk/io/formats/DMol3Format.java | 88 +
.../openscience/cdk/io/formats/DOCK5Format.java | 89 +
.../openscience/cdk/io/formats/DaltonFormat.java | 94 +
.../cdk/io/formats/FenskeHall_ZMatrixFormat.java | 88 +
.../cdk/io/formats/FingerprintFormat.java | 88 +
.../openscience/cdk/io/formats/GROMOS96Format.java | 89 +
.../openscience/cdk/io/formats/GamessFormat.java | 97 +
.../cdk/io/formats/Gaussian03Format.java | 96 +
.../cdk/io/formats/Gaussian90Format.java | 93 +
.../cdk/io/formats/Gaussian92Format.java | 93 +
.../cdk/io/formats/Gaussian94Format.java | 93 +
.../cdk/io/formats/Gaussian95Format.java | 93 +
.../cdk/io/formats/Gaussian98Format.java | 95 +
.../cdk/io/formats/GaussianInputFormat.java | 89 +
.../cdk/io/formats/GhemicalMMFormat.java | 96 +
.../cdk/io/formats/GhemicalSPMFormat.java | 94 +
.../org/openscience/cdk/io/formats/HINFormat.java | 110 +
.../openscience/cdk/io/formats/IChemFormat.java | 73 +
.../cdk/io/formats/IChemFormatMatcher.java | 55 +
.../openscience/cdk/io/formats/INChIFormat.java | 96 +
.../cdk/io/formats/INChIPlainTextFormat.java | 94 +
.../cdk/io/formats/IResourceFormat.java | 72 +
.../org/openscience/cdk/io/formats/JMEFormat.java | 85 +
.../openscience/cdk/io/formats/JaguarFormat.java | 96 +
.../org/openscience/cdk/io/formats/MDLFormat.java | 123 +
.../openscience/cdk/io/formats/MDLRXNFormat.java | 96 +
.../cdk/io/formats/MDLRXNV3000Format.java | 119 +
.../openscience/cdk/io/formats/MDLV2000Format.java | 101 +
.../openscience/cdk/io/formats/MDLV3000Format.java | 96 +
.../org/openscience/cdk/io/formats/MMODFormat.java | 89 +
.../cdk/io/formats/MOPAC2002Format.java | 92 +
.../openscience/cdk/io/formats/MOPAC7Format.java | 93 +
.../openscience/cdk/io/formats/MOPAC93Format.java | 92 +
.../openscience/cdk/io/formats/MOPAC97Format.java | 92 +
.../org/openscience/cdk/io/formats/MPQCFormat.java | 89 +
.../cdk/io/formats/MacroModelFormat.java | 88 +
.../org/openscience/cdk/io/formats/Mol2Format.java | 101 +
.../openscience/cdk/io/formats/NWChemFormat.java | 95 +
.../openscience/cdk/io/formats/PCModelFormat.java | 89 +
.../org/openscience/cdk/io/formats/PDBFormat.java | 102 +
.../openscience/cdk/io/formats/PDBMLFormat.java | 92 +
.../org/openscience/cdk/io/formats/PMPFormat.java | 94 +
.../openscience/cdk/io/formats/POVRayFormat.java | 72 +
.../openscience/cdk/io/formats/PQSChemFormat.java | 89 +
.../cdk/io/formats/PubChemASNFormat.java | 91 +
.../cdk/io/formats/PubChemCompoundXMLFormat.java | 92 +
.../cdk/io/formats/PubChemCompoundsXMLFormat.java | 91 +
.../openscience/cdk/io/formats/PubChemFormat.java | 91 +
.../cdk/io/formats/PubChemSubstanceXMLFormat.java | 92 +
.../cdk/io/formats/PubChemSubstancesASNFormat.java | 91 +
.../cdk/io/formats/PubChemSubstancesXMLFormat.java | 91 +
.../openscience/cdk/io/formats/QChemFormat.java | 94 +
.../openscience/cdk/io/formats/RawCopyFormat.java | 91 +
.../org/openscience/cdk/io/formats/SDFFormat.java | 101 +
.../openscience/cdk/io/formats/SMARTSFormat.java | 89 +
.../cdk/io/formats/SMILESFIXFormat.java | 88 +
.../openscience/cdk/io/formats/SMILESFormat.java | 92 +
.../org/openscience/cdk/io/formats/SVGFormat.java | 67 +
.../openscience/cdk/io/formats/ShelXFormat.java | 101 +
.../openscience/cdk/io/formats/SpartanFormat.java | 93 +
.../cdk/io/formats/SybylDescriptorFormat.java | 91 +
.../cdk/io/formats/TinkerMM2Format.java | 89 +
.../cdk/io/formats/TinkerXYZFormat.java | 89 +
.../cdk/io/formats/TurboMoleFormat.java | 89 +
.../cdk/io/formats/UniChemXYZFormat.java | 87 +
.../org/openscience/cdk/io/formats/VASPFormat.java | 94 +
.../openscience/cdk/io/formats/ViewmolFormat.java | 88 +
.../org/openscience/cdk/io/formats/XEDFormat.java | 90 +
.../org/openscience/cdk/io/formats/XYZFormat.java | 91 +
.../openscience/cdk/io/formats/YasaraFormat.java | 89 +
.../openscience/cdk/io/formats/ZMatrixFormat.java | 94 +
.../openscience/cdk/io/formats/ZindoFormat.java | 89 +
.../cdk/io/inchi/INChIContentProcessorTool.java | 165 +
.../org/openscience/cdk/io/inchi/INChIHandler.java | 167 +
.../iterator/DefaultIteratingChemObjectReader.java | 86 +
.../io/iterator/IIteratingChemObjectReader.java | 51 +
.../io/iterator/IteratingMDLConformerReader.java | 117 +
.../cdk/io/iterator/IteratingMDLReader.java | 309 +
.../io/iterator/IteratingPCCompoundASNReader.java | 229 +
.../io/iterator/IteratingPCCompoundXMLReader.java | 181 +
.../iterator/IteratingPCSubstancesXMLReader.java | 180 +
.../cdk/io/iterator/IteratingSMILESReader.java | 226 +
.../event/DefaultEventChemObjectReader.java | 106 +
.../cdk/io/iterator/event/EventCMLHandler.java | 304 +
.../cdk/io/iterator/event/EventCMLReader.java | 195 +
.../io/iterator/event/IEventChemObjectReader.java | 51 +
.../cdk/io/listener/IChemObjectIOListener.java | 51 +
.../cdk/io/listener/IReaderListener.java | 48 +
.../cdk/io/listener/IWriterListener.java | 37 +
.../cdk/io/listener/PropertiesListener.java | 101 +
.../cdk/io/listener/SwingGUIListener.java | 132 +
.../cdk/io/listener/TextGUIListener.java | 184 +
.../cdk/io/program/GaussianInputWriter.java | 307 +
.../cdk/io/pubchemxml/PubChemXMLHelper.java | 430 +
.../DefaultRandomAccessChemObjectReader.java | 75 +
.../io/random/IRandomAccessChemObjectReader.java | 41 +
.../cdk/io/random/RandomAccessReader.java | 483 +
.../cdk/io/random/RandomAccessSDFReader.java | 130 +
.../cdk/io/setting/BooleanIOSetting.java | 66 +
.../org/openscience/cdk/io/setting/IOSetting.java | 108 +
.../cdk/io/setting/IntegerIOSetting.java | 59 +
.../cdk/io/setting/OptionIOSetting.java | 91 +
.../cdk/io/setting/StringIOSetting.java | 52 +
.../cdk/isomorphism/AtomMappingTools.java | 100 +
.../cdk/isomorphism/IsomorphismTester.java | 172 +
.../isomorphism/UniversalIsomorphismTester.java | 1083 ++
.../cdk/isomorphism/matchers/IQueryAtom.java | 43 +
.../isomorphism/matchers/IQueryAtomContainer.java | 36 +
.../cdk/isomorphism/matchers/IQueryBond.java | 47 +
.../matchers/InverseSymbolSetQueryAtom.java | 122 +
.../cdk/isomorphism/matchers/OrderQueryBond.java | 72 +
.../matchers/OrderQueryBondOrderOnly.java | 72 +
.../isomorphism/matchers/QueryAtomContainer.java | 88 +
.../matchers/QueryAtomContainerCreator.java | 262 +
.../matchers/SymbolAndChargeQueryAtom.java | 59 +
.../matchers/SymbolChargeIDQueryAtom.java | 60 +
.../cdk/isomorphism/matchers/SymbolQueryAtom.java | 70 +
.../isomorphism/matchers/SymbolSetQueryAtom.java | 121 +
.../isomorphism/matchers/smarts/AliphaticAtom.java | 63 +
.../matchers/smarts/AliphaticSymbolAtom.java | 64 +
.../cdk/isomorphism/matchers/smarts/AnyAtom.java | 63 +
.../matchers/smarts/AnyOrderQueryBond.java | 68 +
.../isomorphism/matchers/smarts/AromaticAtom.java | 62 +
.../matchers/smarts/AromaticOrSingleQueryBond.java | 72 +
.../matchers/smarts/AromaticQueryBond.java | 73 +
.../matchers/smarts/AromaticSymbolAtom.java | 53 +
.../matchers/smarts/AtomicNumberAtom.java | 61 +
.../isomorphism/matchers/smarts/ChiralityAtom.java | 88 +
.../matchers/smarts/ConnectionCountAtom.java | 77 +
.../isomorphism/matchers/smarts/DegreeAtom.java | 60 +
.../matchers/smarts/ExplicitConnectionAtom.java | 81 +
.../matchers/smarts/FormalChargeAtom.java | 67 +
.../matchers/smarts/HybridizationNumberAtom.java | 95 +
.../isomorphism/matchers/smarts/HydrogenAtom.java | 98 +
.../matchers/smarts/ImplicitHCountAtom.java | 77 +
.../matchers/smarts/LogicalOperatorAtom.java | 121 +
.../matchers/smarts/LogicalOperatorBond.java | 100 +
.../cdk/isomorphism/matchers/smarts/MassAtom.java | 63 +
.../matchers/smarts/NonCHHeavyAtom.java | 62 +
.../matchers/smarts/OrderQueryBond.java | 79 +
.../matchers/smarts/PeriodicGroupNumberAtom.java | 73 +
.../matchers/smarts/RecursiveSmartsAtom.java | 199 +
.../cdk/isomorphism/matchers/smarts/RingAtom.java | 81 +
.../cdk/isomorphism/matchers/smarts/RingBond.java | 49 +
.../matchers/smarts/RingIdentifierAtom.java | 60 +
.../matchers/smarts/RingMembershipAtom.java | 56 +
.../isomorphism/matchers/smarts/SMARTSAtom.java | 45 +
.../isomorphism/matchers/smarts/SMARTSBond.java | 52 +
.../matchers/smarts/SmallestRingAtom.java | 61 +
.../isomorphism/matchers/smarts/StereoBond.java | 47 +
.../matchers/smarts/TotalConnectionAtom.java | 69 +
.../matchers/smarts/TotalHCountAtom.java | 62 +
.../matchers/smarts/TotalRingConnectionAtom.java | 82 +
.../matchers/smarts/TotalValencyAtom.java | 57 +
.../openscience/cdk/isomorphism/mcss/RGraph.java | 622 +
.../org/openscience/cdk/isomorphism/mcss/RMap.java | 110 +
.../openscience/cdk/isomorphism/mcss/RNode.java | 150 +
.../cdk/iupac/parser/AttachedGroup.java | 129 +
.../cdk/iupac/parser/MoleculeBuilder.java | 562 +
.../openscience/cdk/iupac/parser/NomParser.java | 1878 +++
.../org/openscience/cdk/iupac/parser/NomParser.jj | 816 +
.../cdk/iupac/parser/NomParserConstants.java | 318 +
.../cdk/iupac/parser/NomParserTokenManager.java | 1180 ++
.../cdk/iupac/parser/ParseException.java | 210 +
.../cdk/iupac/parser/SimpleCharStream.java | 419 +
.../org/openscience/cdk/iupac/parser/Token.java | 99 +
.../cdk/iupac/parser/TokenMgrError.java | 151 +
.../org/openscience/cdk/layout/AtomPlacer.java | 946 ++
.../org/openscience/cdk/layout/HydrogenPlacer.java | 118 +
.../openscience/cdk/layout/OverlapResolver.java | 330 +
.../org/openscience/cdk/layout/RingPlacer.java | 711 +
.../cdk/layout/StructureDiagramGenerator.java | 1112 ++
.../openscience/cdk/layout/TemplateHandler.java | 345 +
.../cdk/layout/templates/adamantane.cml | 32 +
.../openscience/cdk/layout/templates/cubane.cml | 30 +
.../cdk/layout/templates/diamantane.cml | 42 +
.../org/openscience/cdk/layout/templates/ring1.cml | 35 +
.../openscience/cdk/layout/templates/sterane.cml | 44 +
.../cdk/layout/templates/templates.list | 5 +
.../org/openscience/cdk/libio/cml/Convertor.java | 803 +
.../openscience/cdk/libio/cml/ICMLCustomizer.java | 75 +
.../cdk/libio/cml/MDMoleculeCustomizer.java | 167 +
.../cdk/libio/cml/PDBAtomCustomizer.java | 158 +
.../openscience/cdk/libio/cml/QSARCustomizer.java | 206 +
.../org/openscience/cdk/libio/md/ChargeGroup.java | 90 +
.../org/openscience/cdk/libio/md/MDMolecule.java | 108 +
src/main/org/openscience/cdk/libio/md/Residue.java | 87 +
src/main/org/openscience/cdk/math/Complex.java | 141 +
.../org/openscience/cdk/math/FortranFormat.java | 110 +
src/main/org/openscience/cdk/math/IFunction.java | 47 +
src/main/org/openscience/cdk/math/IMatrix.java | 493 +
src/main/org/openscience/cdk/math/IVector.java | 232 +
src/main/org/openscience/cdk/math/MathTools.java | 111 +
src/main/org/openscience/cdk/math/Matrix.java | 613 +
src/main/org/openscience/cdk/math/Primes.java | 241 +
src/main/org/openscience/cdk/math/Quaternion.java | 252 +
.../openscience/cdk/math/RandomNumbersTool.java | 273 +
src/main/org/openscience/cdk/math/Vector.java | 223 +
.../openscience/cdk/math/qm/AngularMomentum.java | 141 +
.../openscience/cdk/math/qm/ClosedShellJob.java | 375 +
.../openscience/cdk/math/qm/FourierGridBasis.java | 212 +
.../openscience/cdk/math/qm/GaussiansBasis.java | 716 +
src/main/org/openscience/cdk/math/qm/IBasis.java | 124 +
.../openscience/cdk/math/qm/OneElectronJob.java | 192 +
src/main/org/openscience/cdk/math/qm/Orbitals.java | 178 +
.../openscience/cdk/math/qm/SimpleBasisSet.java | 152 +
.../cdk/modeling/builder3d/AtomPlacer3D.java | 586 +
.../builder3d/AtomTetrahedralLigandPlacer3D.java | 917 +
.../modeling/builder3d/ForceFieldConfigurator.java | 765 +
.../builder3d/MM2BasedAtomTypePattern.java | 220 +
.../builder3d/MM2BasedParameterSetReader.java | 899 +
.../builder3d/MMFF94BasedAtomTypePattern.java | 265 +
.../builder3d/MMFF94BasedParameterSetReader.java | 570 +
.../modeling/builder3d/MMFF94ParametersCall.java | 167 +
.../cdk/modeling/builder3d/ModelBuilder3D.java | 627 +
.../cdk/modeling/builder3d/TemplateExtractor.java | 564 +
.../cdk/modeling/builder3d/TemplateHandler3D.java | 277 +
.../builder3d/data/ringTemplateFingerprints.txt.gz | Bin 0 -> 4679 bytes
.../builder3d/data/ringTemplateStructures.sdf.gz | Bin 0 -> 2254746 bytes
.../cdk/modeling/forcefield/AngleBending.java | 1140 ++
.../cdk/modeling/forcefield/BondStretching.java | 531 +
.../forcefield/ConjugateGradientMethod.java | 160 +
.../forcefield/ElectrostaticInteractions.java | 544 +
.../cdk/modeling/forcefield/ForceField.java | 109 +
.../cdk/modeling/forcefield/ForceFieldTools.java | 370 +
.../modeling/forcefield/GeometricMinimizer.java | 653 +
.../modeling/forcefield/IPotentialFunction.java | 93 +
.../cdk/modeling/forcefield/LineSearch.java | 719 +
.../LineSearchForTheWolfeConditions.java | 615 +
.../modeling/forcefield/MMFF94EnergyFunction.java | 307 +
.../modeling/forcefield/NewtonRaphsonMethod.java | 137 +
.../modeling/forcefield/SmoothingFunctions.java | 84 +
.../forcefield/SteepestDescentsMethod.java | 71 +
.../forcefield/StretchBendInteractions.java | 552 +
.../cdk/modeling/forcefield/Torsions.java | 509 +
.../forcefield/VanDerWaalsInteractions.java | 821 +
.../cdk/modeling/forcefield/data/mm2.prm | 2048 +++
.../cdk/modeling/forcefield/data/mmff94.prm | 4467 +++++
.../cdk/modeling/forcefield/data/mmffvdw.prm | 106 +
.../openscience/cdk/nonotify/NNAdductFormula.java | 54 +
.../org/openscience/cdk/nonotify/NNAminoAcid.java | 55 +
src/main/org/openscience/cdk/nonotify/NNAtom.java | 80 +
.../openscience/cdk/nonotify/NNAtomContainer.java | 61 +
.../cdk/nonotify/NNAtomContainerSet.java | 52 +
.../org/openscience/cdk/nonotify/NNAtomParity.java | 57 +
.../org/openscience/cdk/nonotify/NNAtomType.java | 67 +
.../org/openscience/cdk/nonotify/NNBioPolymer.java | 54 +
src/main/org/openscience/cdk/nonotify/NNBond.java | 78 +
.../org/openscience/cdk/nonotify/NNChemFile.java | 52 +
.../org/openscience/cdk/nonotify/NNChemModel.java | 52 +
.../org/openscience/cdk/nonotify/NNChemObject.java | 67 +
.../openscience/cdk/nonotify/NNChemSequence.java | 51 +
.../org/openscience/cdk/nonotify/NNCrystal.java | 56 +
.../cdk/nonotify/NNElectronContainer.java | 54 +
.../org/openscience/cdk/nonotify/NNElement.java | 70 +
.../openscience/cdk/nonotify/NNFragmentAtom.java | 57 +
.../org/openscience/cdk/nonotify/NNIsotope.java | 77 +
.../org/openscience/cdk/nonotify/NNLonePair.java | 59 +
.../org/openscience/cdk/nonotify/NNMapping.java | 54 +
.../cdk/nonotify/NNMolecularFormula.java | 44 +
.../cdk/nonotify/NNMolecularFormulaSet.java | 49 +
.../org/openscience/cdk/nonotify/NNMolecule.java | 63 +
.../openscience/cdk/nonotify/NNMoleculeSet.java | 50 +
.../org/openscience/cdk/nonotify/NNMonomer.java | 53 +
.../org/openscience/cdk/nonotify/NNPDBAtom.java | 72 +
.../org/openscience/cdk/nonotify/NNPDBMonomer.java | 54 +
.../org/openscience/cdk/nonotify/NNPDBPolymer.java | 54 +
.../openscience/cdk/nonotify/NNPDBStructure.java | 54 +
.../org/openscience/cdk/nonotify/NNPolymer.java | 54 +
.../org/openscience/cdk/nonotify/NNPseudoAtom.java | 86 +
.../org/openscience/cdk/nonotify/NNReaction.java | 55 +
.../openscience/cdk/nonotify/NNReactionScheme.java | 50 +
.../openscience/cdk/nonotify/NNReactionSet.java | 50 +
src/main/org/openscience/cdk/nonotify/NNRing.java | 66 +
.../org/openscience/cdk/nonotify/NNRingSet.java | 50 +
.../openscience/cdk/nonotify/NNSingleElectron.java | 58 +
.../org/openscience/cdk/nonotify/NNStrand.java | 54 +
.../nonotify/NoNotificationChemObjectBuilder.java | 373 +
.../cdk/pharmacophore/PharmacophoreAngleBond.java | 78 +
.../cdk/pharmacophore/PharmacophoreAtom.java | 167 +
.../cdk/pharmacophore/PharmacophoreBond.java | 66 +
.../cdk/pharmacophore/PharmacophoreMatcher.java | 606 +
.../pharmacophore/PharmacophoreQueryAngleBond.java | 132 +
.../cdk/pharmacophore/PharmacophoreQueryAtom.java | 94 +
.../cdk/pharmacophore/PharmacophoreQueryBond.java | 129 +
.../cdk/pharmacophore/PharmacophoreUtils.java | 437 +
.../cdk/protein/ProteinPocketFinder.java | 1117 ++
.../org/openscience/cdk/protein/data/PDBAtom.java | 346 +
.../openscience/cdk/protein/data/PDBMonomer.java | 112 +
.../openscience/cdk/protein/data/PDBPolymer.java | 130 +
.../openscience/cdk/protein/data/PDBStrand.java | 96 +
.../openscience/cdk/protein/data/PDBStructure.java | 164 +
.../cdk/qsar/AbstractAtomicDescriptor.java | 88 +
.../cdk/qsar/AbstractBondDescriptor.java | 89 +
.../org/openscience/cdk/qsar/AtomValenceTool.java | 92 +
.../org/openscience/cdk/qsar/DescriptorEngine.java | 738 +
.../openscience/cdk/qsar/DescriptorException.java | 60 +
.../cdk/qsar/DescriptorSpecification.java | 92 +
.../org/openscience/cdk/qsar/DescriptorValue.java | 165 +
.../openscience/cdk/qsar/IAtomPairDescriptor.java | 48 +
.../openscience/cdk/qsar/IAtomicDescriptor.java | 46 +
.../org/openscience/cdk/qsar/IBondDescriptor.java | 46 +
src/main/org/openscience/cdk/qsar/IDescriptor.java | 171 +
.../openscience/cdk/qsar/IMolecularDescriptor.java | 63 +
.../descriptors/atomic/AtomDegreeDescriptor.java | 143 +
.../atomic/AtomHybridizationDescriptor.java | 158 +
.../atomic/AtomHybridizationVSEPRDescriptor.java | 207 +
.../descriptors/atomic/AtomValenceDescriptor.java | 131 +
.../descriptors/atomic/BondsToAtomDescriptor.java | 181 +
.../atomic/CovalentRadiusDescriptor.java | 194 +
.../atomic/DistanceToAtomDescriptor.java | 194 +
.../EffectiveAtomPolarizabilityDescriptor.java | 183 +
.../descriptors/atomic/IPAtomicHOSEDescriptor.java | 382 +
.../atomic/IPAtomicLearningDescriptor.java | 179 +
.../atomic/InductiveAtomicHardnessDescriptor.java | 265 +
.../atomic/InductiveAtomicSoftnessDescriptor.java | 263 +
.../atomic/IsProtonInAromaticSystemDescriptor.java | 218 +
.../IsProtonInConjugatedPiSystemDescriptor.java | 216 +
.../atomic/PartialPiChargeDescriptor.java | 258 +
.../atomic/PartialSigmaChargeDescriptor.java | 199 +
.../atomic/PartialTChargeMMFF94Descriptor.java | 185 +
.../atomic/PartialTChargePEOEDescriptor.java | 265 +
.../atomic/PeriodicTablePositionDescriptor.java | 201 +
.../atomic/PiElectronegativityDescriptor.java | 226 +
.../atomic/ProtonAffinityHOSEDescriptor.java | 364 +
.../atomic/ProtonTotalPartialChargeDescriptor.java | 200 +
.../atomic/RDFProtonDescriptor_G3R.java | 744 +
.../atomic/RDFProtonDescriptor_GDR.java | 605 +
.../atomic/RDFProtonDescriptor_GHR.java | 568 +
.../atomic/RDFProtonDescriptor_GHR_topol.java | 600 +
.../atomic/RDFProtonDescriptor_GSR.java | 600 +
.../atomic/SigmaElectronegativityDescriptor.java | 199 +
.../atomic/StabilizationPlusChargeDescriptor.java | 183 +
.../descriptors/atomic/VdWRadiusDescriptor.java | 167 +
.../atompair/PiContactDetectionDescriptor.java | 245 +
.../bond/AtomicNumberDifferenceDescriptor.java | 128 +
.../bond/BondPartialPiChargeDescriptor.java | 253 +
.../bond/BondPartialSigmaChargeDescriptor.java | 194 +
.../bond/BondPartialTChargeDescriptor.java | 269 +
.../bond/BondSigmaElectronegativityDescriptor.java | 193 +
.../descriptors/bond/IPBondLearningDescriptor.java | 188 +
.../descriptors/molecular/ALOGPDescriptor.java | 2105 +++
.../qsar/descriptors/molecular/APolDescriptor.java | 233 +
.../molecular/AminoAcidCountDescriptor.java | 218 +
.../molecular/AromaticAtomsCountDescriptor.java | 237 +
.../molecular/AromaticBondsCountDescriptor.java | 241 +
.../descriptors/molecular/AtomCountDescriptor.java | 244 +
.../molecular/AutocorrelationDescriptorCharge.java | 166 +
.../molecular/AutocorrelationDescriptorMass.java | 168 +
.../AutocorrelationDescriptorPolarizability.java | 202 +
.../qsar/descriptors/molecular/BCUTDescriptor.java | 498 +
.../qsar/descriptors/molecular/BPolDescriptor.java | 233 +
.../descriptors/molecular/BondCountDescriptor.java | 226 +
.../qsar/descriptors/molecular/CPSADescriptor.java | 419 +
.../molecular/CarbonTypesDescriptor.java | 237 +
.../descriptors/molecular/ChiChainDescriptor.java | 324 +
.../molecular/ChiClusterDescriptor.java | 263 +
.../qsar/descriptors/molecular/ChiIndexUtils.java | 300 +
.../molecular/ChiPathClusterDescriptor.java | 251 +
.../descriptors/molecular/ChiPathDescriptor.java | 316 +
.../EccentricConnectivityIndexDescriptor.java | 184 +
.../molecular/FragmentComplexityDescriptor.java | 189 +
.../molecular/GravitationalIndexDescriptor.java | 337 +
.../molecular/HBondAcceptorCountDescriptor.java | 246 +
.../molecular/HBondDonorCountDescriptor.java | 224 +
.../molecular/IPMolecularLearningDescriptor.java | 271 +
.../molecular/KappaShapeIndicesDescriptor.java | 293 +
.../molecular/KierHallSmartsDescriptor.java | 465 +
.../molecular/LargestChainDescriptor.java | 345 +
.../molecular/LargestPiSystemDescriptor.java | 319 +
.../molecular/LengthOverBreadthDescriptor.java | 306 +
.../molecular/LongestAliphaticChainDescriptor.java | 354 +
.../qsar/descriptors/molecular/MDEDescriptor.java | 401 +
.../molecular/MomentOfInertiaDescriptor.java | 293 +
.../molecular/PetitjeanNumberDescriptor.java | 186 +
.../molecular/PetitjeanShapeIndexDescriptor.java | 218 +
.../molecular/RotatableBondsCountDescriptor.java | 243 +
.../molecular/RuleOfFiveDescriptor.java | 253 +
.../qsar/descriptors/molecular/TPSADescriptor.java | 393 +
.../descriptors/molecular/VAdjMaDescriptor.java | 179 +
.../qsar/descriptors/molecular/WHIMDescriptor.java | 564 +
.../descriptors/molecular/WeightDescriptor.java | 251 +
.../molecular/WeightedPathDescriptor.java | 286 +
.../molecular/WienerNumbersDescriptor.java | 240 +
.../descriptors/molecular/XLogPDescriptor.java | 1628 ++
.../molecular/ZagrebIndexDescriptor.java | 174 +
.../protein/TaeAminoAcidDescriptor.java | 333 +
.../org/openscience/cdk/qsar/model/IModel.java | 51 +
.../cdk/qsar/model/QSARModelException.java | 45 +
.../cdk/qsar/model/R/CNNClassificationModel.java | 577 +
.../qsar/model/R/CNNClassificationModelFit.java | 256 +
.../model/R/CNNClassificationModelPredict.java | 148 +
.../cdk/qsar/model/R/CNNRegressionModel.java | 583 +
.../cdk/qsar/model/R/CNNRegressionModelFit.java | 251 +
.../qsar/model/R/CNNRegressionModelPredict.java | 108 +
.../qsar/model/R/CNNRegressionModelSummary.java | 172 +
.../cdk/qsar/model/R/LinearRegressionModel.java | 552 +
.../cdk/qsar/model/R/LinearRegressionModelFit.java | 178 +
.../qsar/model/R/LinearRegressionModelPredict.java | 222 +
.../qsar/model/R/LinearRegressionModelSummary.java | 192 +
.../cdk/qsar/model/R/PLSRegressionModel.java | 585 +
.../cdk/qsar/model/R/PLSRegressionModelFit.java | 211 +
.../qsar/model/R/PLSRegressionModelPredict.java | 83 +
.../org/openscience/cdk/qsar/model/R/RModel.java | 342 +
.../cdk/qsar/model/R2/CNNRegressionModel.java | 677 +
.../cdk/qsar/model/R2/LinearRegressionModel.java | 569 +
.../org/openscience/cdk/qsar/model/R2/RModel.java | 592 +
.../org/openscience/cdk/qsar/model/data/cdkSJava.R | 451 +
.../org/openscience/cdk/qsar/model/data/cnn_3.R | 83 +
.../org/openscience/cdk/qsar/model/data/cnn_4.R | 80 +
.../org/openscience/cdk/qsar/model/data/helper.R | 141 +
.../org/openscience/cdk/qsar/model/data/init_1.R | 42 +
.../org/openscience/cdk/qsar/model/data/lm_2.R | 59 +
.../org/openscience/cdk/qsar/model/data/pls_5.R | 84 +
.../openscience/cdk/qsar/model/data/register_999.R | 31 +
.../openscience/cdk/qsar/result/BooleanResult.java | 54 +
.../cdk/qsar/result/BooleanResultType.java | 45 +
.../cdk/qsar/result/DoubleArrayResult.java | 82 +
.../cdk/qsar/result/DoubleArrayResultType.java | 51 +
.../openscience/cdk/qsar/result/DoubleResult.java | 58 +
.../cdk/qsar/result/DoubleResultType.java | 45 +
.../cdk/qsar/result/IDescriptorResult.java | 50 +
.../cdk/qsar/result/IntegerArrayResult.java | 83 +
.../cdk/qsar/result/IntegerArrayResultType.java | 51 +
.../openscience/cdk/qsar/result/IntegerResult.java | 61 +
.../cdk/qsar/result/IntegerResultType.java | 45 +
.../cdk/reaction/IReactionMechanism.java | 58 +
.../openscience/cdk/reaction/IReactionProcess.java | 103 +
.../openscience/cdk/reaction/ReactionChain.java | 111 +
.../openscience/cdk/reaction/ReactionEngine.java | 181 +
.../cdk/reaction/ReactionSpecification.java | 93 +
.../reaction/mechanism/AdductionLPMechanism.java | 126 +
.../reaction/mechanism/AdductionPBMechanism.java | 136 +
.../mechanism/HeterolyticCleavageMechanism.java | 138 +
.../mechanism/HomolyticCleavageMechanism.java | 134 +
.../mechanism/RadicalSiteIonizationMechanism.java | 143 +
.../RadicalSiteRearrangementMechanism.java | 135 +
.../mechanism/RearrangementChargeMechanism.java | 177 +
.../reaction/mechanism/RemovingSEofBMechanism.java | 136 +
.../mechanism/RemovingSEofNBMechanism.java | 114 +
.../mechanism/SharingElectronMechanism.java | 129 +
.../mechanism/TautomerizationMechanism.java | 141 +
.../reaction/type/AdductionProtonLPReaction.java | 196 +
.../reaction/type/AdductionProtonPBReaction.java | 226 +
.../reaction/type/AdductionSodiumLPReaction.java | 198 +
.../reaction/type/CarbonylEliminationReaction.java | 234 +
.../reaction/type/ElectronImpactNBEReaction.java | 177 +
.../reaction/type/ElectronImpactPDBReaction.java | 199 +
.../reaction/type/ElectronImpactSDBReaction.java | 197 +
.../type/HeterolyticCleavagePBReaction.java | 210 +
.../type/HeterolyticCleavageSBReaction.java | 211 +
.../reaction/type/HomolyticCleavageReaction.java | 194 +
.../reaction/type/HyperconjugationReaction.java | 248 +
.../reaction/type/PiBondingMovementReaction.java | 240 +
.../type/RadicalChargeSiteInitiationHReaction.java | 243 +
.../type/RadicalChargeSiteInitiationReaction.java | 247 +
.../reaction/type/RadicalSiteHrAlphaReaction.java | 241 +
.../reaction/type/RadicalSiteHrBetaReaction.java | 242 +
.../reaction/type/RadicalSiteHrDeltaReaction.java | 243 +
.../reaction/type/RadicalSiteHrGammaReaction.java | 243 +
.../type/RadicalSiteInitiationHReaction.java | 243 +
.../type/RadicalSiteInitiationReaction.java | 247 +
.../reaction/type/RadicalSiteRrAlphaReaction.java | 255 +
.../reaction/type/RadicalSiteRrBetaReaction.java | 254 +
.../reaction/type/RadicalSiteRrDeltaReaction.java | 254 +
.../reaction/type/RadicalSiteRrGammaReaction.java | 255 +
.../reaction/type/RearrangementAnionReaction.java | 247 +
.../reaction/type/RearrangementCationReaction.java | 253 +
.../type/RearrangementLonePairReaction.java | 251 +
.../type/RearrangementRadicalReaction.java | 259 +
.../cdk/reaction/type/SharingAnionReaction.java | 210 +
.../cdk/reaction/type/SharingChargeDBReaction.java | 212 +
.../cdk/reaction/type/SharingChargeSBReaction.java | 213 +
.../cdk/reaction/type/SharingLonePairReaction.java | 210 +
.../cdk/reaction/type/TautomerizationReaction.java | 273 +
.../reaction/type/parameters/IParameterReact.java | 62 +
.../reaction/type/parameters/ParameterReact.java | 79 +
.../type/parameters/SetReactionCenter.java | 36 +
.../cdk/renderer/GraphRendererModel.java | 236 +
.../org/openscience/cdk/renderer/JCPAction2D.java | 357 +
.../cdk/renderer/color/CDK2DAtomColors.java | 85 +
.../cdk/renderer/color/CDKAtomColors.java | 67 +
.../cdk/renderer/color/CPKAtomColors.java | 173 +
.../cdk/renderer/color/IAtomColorer.java | 50 +
.../renderer/color/PartialAtomicChargeColors.java | 69 +
.../openscience/cdk/ringsearch/AllRingsFinder.java | 412 +
.../cdk/ringsearch/FiguerasSSSRFinder.java | 459 +
src/main/org/openscience/cdk/ringsearch/Path.java | 155 +
src/main/org/openscience/cdk/ringsearch/Queue.java | 77 +
.../cdk/ringsearch/RingPartitioner.java | 150 +
.../org/openscience/cdk/ringsearch/SSSRFinder.java | 213 +
.../cdk/ringsearch/cyclebasis/CycleBasis.java | 269 +
.../cdk/ringsearch/cyclebasis/SimpleCycle.java | 144 +
.../ringsearch/cyclebasis/SimpleCycleBasis.java | 1051 ++
.../openscience/cdk/similarity/DistanceMoment.java | 226 +
.../org/openscience/cdk/similarity/Tanimoto.java | 119 +
.../cdk/smiles/DeduceBondSystemTool.java | 819 +
src/main/org/openscience/cdk/smiles/InvPair.java | 179 +
.../openscience/cdk/smiles/SmilesGenerator.java | 1907 +++
.../org/openscience/cdk/smiles/SmilesParser.java | 850 +
.../cdk/smiles/smarts/SMARTSQueryTool.java | 544 +
.../cdk/smiles/smarts/parser/ASTAliphatic.java | 57 +
.../cdk/smiles/smarts/parser/ASTAnyAtom.java | 57 +
.../cdk/smiles/smarts/parser/ASTAromatic.java | 57 +
.../cdk/smiles/smarts/parser/ASTAtom.java | 60 +
.../cdk/smiles/smarts/parser/ASTAtomicMass.java | 67 +
.../cdk/smiles/smarts/parser/ASTAtomicNumber.java | 71 +
.../cdk/smiles/smarts/parser/ASTCharge.java | 91 +
.../cdk/smiles/smarts/parser/ASTChirality.java | 86 +
.../cdk/smiles/smarts/parser/ASTElement.java | 73 +
.../cdk/smiles/smarts/parser/ASTExplicitAtom.java | 74 +
.../smarts/parser/ASTExplicitConnectivity.java | 71 +
.../smarts/parser/ASTExplicitHighAndBond.java | 53 +
.../parser/ASTExplicitHighAndExpression.java | 53 +
.../cdk/smiles/smarts/parser/ASTGroup.java | 57 +
.../smarts/parser/ASTHybrdizationNumber.java | 44 +
.../smiles/smarts/parser/ASTImplicitHCount.java | 71 +
.../smarts/parser/ASTImplicitHighAndBond.java | 53 +
.../parser/ASTImplicitHighAndExpression.java | 54 +
.../cdk/smiles/smarts/parser/ASTLowAndBond.java | 53 +
.../smiles/smarts/parser/ASTLowAndExpression.java | 65 +
.../smiles/smarts/parser/ASTNonCHHeavyAtom.java | 32 +
.../cdk/smiles/smarts/parser/ASTNotBond.java | 66 +
.../cdk/smiles/smarts/parser/ASTNotExpression.java | 66 +
.../cdk/smiles/smarts/parser/ASTOrBond.java | 53 +
.../cdk/smiles/smarts/parser/ASTOrExpression.java | 53 +
.../smarts/parser/ASTPeriodicGroupNumber.java | 58 +
.../smarts/parser/ASTPrimitiveAtomExpression.java | 52 +
.../cdk/smiles/smarts/parser/ASTReaction.java | 52 +
.../parser/ASTRecursiveSmartsExpression.java | 52 +
.../smiles/smarts/parser/ASTRingConnectivity.java | 72 +
.../smiles/smarts/parser/ASTRingIdentifier.java | 73 +
.../smiles/smarts/parser/ASTRingMembership.java | 71 +
.../cdk/smiles/smarts/parser/ASTSimpleBond.java | 71 +
.../smiles/smarts/parser/ASTSmallestRingSize.java | 71 +
.../cdk/smiles/smarts/parser/ASTSmarts.java | 53 +
.../cdk/smiles/smarts/parser/ASTStart.java | 58 +
.../smiles/smarts/parser/ASTTotalConnectivity.java | 71 +
.../cdk/smiles/smarts/parser/ASTTotalHCount.java | 71 +
.../cdk/smiles/smarts/parser/ASTValence.java | 71 +
.../smiles/smarts/parser/JJTSMARTSParserState.java | 128 +
.../openscience/cdk/smiles/smarts/parser/Node.java | 69 +
.../cdk/smiles/smarts/parser/ParseException.java | 220 +
.../cdk/smiles/smarts/parser/SMARTSParser.java | 3072 ++++
.../cdk/smiles/smarts/parser/SMARTSParser.jj | 1577 ++
.../cdk/smiles/smarts/parser/SMARTSParser.jjt | 762 +
.../smarts/parser/SMARTSParserConstants.java | 351 +
.../smarts/parser/SMARTSParserTokenManager.java | 894 +
.../smarts/parser/SMARTSParserTreeConstants.java | 94 +
.../smiles/smarts/parser/SMARTSParserVisitor.java | 51 +
.../cdk/smiles/smarts/parser/SimpleCharStream.java | 429 +
.../cdk/smiles/smarts/parser/SimpleNode.java | 183 +
.../cdk/smiles/smarts/parser/Token.java | 109 +
.../cdk/smiles/smarts/parser/TokenMgrError.java | 161 +
.../smarts/parser/visitor/Smarts2MQLVisitor.java | 323 +
.../smarts/parser/visitor/SmartsDumpVisitor.java | 339 +
.../smarts/parser/visitor/SmartsQueryVisitor.java | 649 +
.../structgen/IStructureGenerationListener.java | 37 +
.../openscience/cdk/structgen/RandomGenerator.java | 343 +
.../structgen/SingleStructureRandomGenerator.java | 195 +
.../openscience/cdk/structgen/VicinitySampler.java | 287 +
.../stochastic/PartialFilledStructureMerger.java | 178 +
.../structgen/stochastic/operator/ChemGraph.java | 162 +
.../stochastic/operator/CrossoverMachine.java | 202 +
.../org/openscience/cdk/templates/AminoAcids.java | 243 +
.../openscience/cdk/templates/MoleculeFactory.java | 1379 ++
.../saturatedhydrocarbons/IsoAlkanes.java | 83 +
.../org/openscience/cdk/tools/AtomTypeTools.java | 182 +
.../openscience/cdk/tools/AtomicProperties.java | 119 +
.../tools/BremserOneSphereHOSECodePredictor.java | 778 +
.../openscience/cdk/tools/CDKHydrogenAdder.java | 142 +
.../org/openscience/cdk/tools/CDKUtilities.java | 308 +
.../openscience/cdk/tools/CDKValencyChecker.java | 103 +
.../org/openscience/cdk/tools/DataFeatures.java | 97 +
.../openscience/cdk/tools/DataFeaturesTool.java | 73 +
.../openscience/cdk/tools/DeAromatizationTool.java | 151 +
.../openscience/cdk/tools/ElementComparator.java | 83 +
.../org/openscience/cdk/tools/FixedSizeStack.java | 83 +
.../openscience/cdk/tools/FormatStringBuffer.java | 531 +
.../openscience/cdk/tools/GenerateFragments.java | 561 +
.../org/openscience/cdk/tools/GridGenerator.java | 466 +
.../openscience/cdk/tools/HOSECodeAnalyser.java | 87 +
.../openscience/cdk/tools/HOSECodeGenerator.java | 866 +
src/main/org/openscience/cdk/tools/IDCreator.java | 353 +
.../cdk/tools/IDeduceBondOrderTool.java | 45 +
.../org/openscience/cdk/tools/IValencyChecker.java | 51 +
.../cdk/tools/IonizationPotentialTool.java | 508 +
.../org/openscience/cdk/tools/LoggingTool.java | 810 +
.../cdk/tools/LonePairElectronChecker.java | 129 +
src/main/org/openscience/cdk/tools/Normalizer.java | 122 +
.../org/openscience/cdk/tools/PeriodicTable.java | 234 +
.../openscience/cdk/tools/ProteinBuilderTool.java | 156 +
.../openscience/cdk/tools/SaturationChecker.java | 715 +
.../cdk/tools/SmilesValencyChecker.java | 392 +
.../cdk/tools/StructureResonanceGenerator.java | 464 +
.../org/openscience/cdk/tools/SwissArmyKnife.java | 116 +
.../cdk/tools/diff/AtomContainerDiff.java | 91 +
.../org/openscience/cdk/tools/diff/AtomDiff.java | 74 +
.../openscience/cdk/tools/diff/AtomTypeDiff.java | 77 +
.../org/openscience/cdk/tools/diff/BondDiff.java | 74 +
.../openscience/cdk/tools/diff/ChemObjectDiff.java | 68 +
.../cdk/tools/diff/ElectronContainerDiff.java | 67 +
.../openscience/cdk/tools/diff/ElementDiff.java | 69 +
.../openscience/cdk/tools/diff/IsotopeDiff.java | 69 +
.../openscience/cdk/tools/diff/LonePairDiff.java | 66 +
.../cdk/tools/diff/SingleElectronDiff.java | 66 +
.../cdk/tools/diff/tree/AbstractDifference.java | 36 +
.../tools/diff/tree/AbstractDifferenceList.java | 73 +
.../diff/tree/AtomTypeHybridizationDifference.java | 61 +
.../cdk/tools/diff/tree/BondOrderDifference.java | 61 +
.../tools/diff/tree/BooleanArrayDifference.java | 92 +
.../cdk/tools/diff/tree/BooleanDifference.java | 60 +
.../cdk/tools/diff/tree/ChemObjectDifference.java | 62 +
.../cdk/tools/diff/tree/DoubleDifference.java | 68 +
.../cdk/tools/diff/tree/IDifference.java | 31 +
.../cdk/tools/diff/tree/IDifferenceList.java | 42 +
.../cdk/tools/diff/tree/IntegerDifference.java | 66 +
.../cdk/tools/diff/tree/Point2dDifference.java | 82 +
.../cdk/tools/diff/tree/Point3dDifference.java | 87 +
.../cdk/tools/diff/tree/StringDifference.java | 66 +
.../cdk/tools/features/MoleculeFeaturesTool.java | 74 +
.../tools/manipulator/AminoAcidManipulator.java | 96 +
.../tools/manipulator/AtomContainerComparator.java | 172 +
.../manipulator/AtomContainerManipulator.java | 823 +
.../manipulator/AtomContainerSetManipulator.java | 261 +
.../cdk/tools/manipulator/AtomTypeManipulator.java | 131 +
.../cdk/tools/manipulator/BondManipulator.java | 331 +
.../cdk/tools/manipulator/ChemFileManipulator.java | 159 +
.../tools/manipulator/ChemModelManipulator.java | 380 +
.../tools/manipulator/ChemSequenceManipulator.java | 122 +
.../manipulator/MolecularFormulaManipulator.java | 1099 ++
.../MolecularFormulaRangeManipulator.java | 128 +
.../MolecularFormulaSetManipulator.java | 251 +
.../tools/manipulator/MoleculeSetManipulator.java | 135 +
.../cdk/tools/manipulator/ReactionManipulator.java | 291 +
.../manipulator/ReactionSchemeManipulator.java | 345 +
.../tools/manipulator/ReactionSetManipulator.java | 299 +
.../cdk/tools/manipulator/RingManipulator.java | 64 +
.../cdk/tools/manipulator/RingSetManipulator.java | 302 +
.../cdk/tools/manipulator/RingSizeComparator.java | 81 +
.../cdk/validate/AbstractValidator.java | 122 +
.../openscience/cdk/validate/BasicValidator.java | 403 +
.../org/openscience/cdk/validate/CDKValidator.java | 82 +
.../cdk/validate/DictionaryValidator.java | 120 +
.../cdk/validate/Geometry3DValidator.java | 59 +
.../org/openscience/cdk/validate/IValidator.java | 70 +
.../openscience/cdk/validate/ProblemMarker.java | 72 +
.../openscience/cdk/validate/ValidationReport.java | 148 +
.../openscience/cdk/validate/ValidationTest.java | 73 +
.../openscience/cdk/validate/ValidatorEngine.java | 327 +
1272 files changed, 294846 insertions(+)
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