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Viewing changes to src/org/openscience/cdk/structgen/RandomGenerator.java

Committer: Bazaar Package Importer
Author(s): Paul Cager
Date: 2008-04-09 21:17:53 UTC
Revision ID: james.westby@ubuntu.com-20080409211753-46lmjw5z8mx5pd8d

Tags: upstream-1.0.2

Import upstream version 1.0.2

files added:

README

build.props

build.xml

changelog.txt

doc/javadoc

doc/lgpl.license

doc/refs

doc/refs/cheminf.bibx

javadoc.xml

src/META-INF

src/META-INF/applet-core.files

src/META-INF/applet-editor-opts.files

src/META-INF/applet-editor.files

src/META-INF/applet-viewer-opts.files

src/META-INF/applications.cdkdepends

src/META-INF/applications.datafiles

src/META-INF/applications.libdepends

src/META-INF/builder3d.cdkdepends

src/META-INF/builder3d.datafiles

src/META-INF/builder3d.libdepends

src/META-INF/builder3dtools.cdkdepends

src/META-INF/builder3dtools.libdepends

src/META-INF/charges.cdkdepends

src/META-INF/charges.libdepends

src/META-INF/control.cdkdepends

src/META-INF/control.libdepends

src/META-INF/core.cdkdepends

src/META-INF/core.datafiles

src/META-INF/core.libdepends

src/META-INF/data.cdkdepends

src/META-INF/data.libdepends

src/META-INF/datadebug.cdkdepends

src/META-INF/datadebug.libdepends

src/META-INF/experimental.cdkdepends

src/META-INF/experimental.libdepends

src/META-INF/extra.cdkdepends

src/META-INF/extra.datafiles

src/META-INF/extra.extrafiles

src/META-INF/extra.libdepends

src/META-INF/forcefield.cdkdepends

src/META-INF/forcefield.datafiles

src/META-INF/forcefield.libdepends

src/META-INF/inchi.cdkdepends

src/META-INF/inchi.libdepends

src/META-INF/interfaces.libdepends

src/META-INF/io-jmol.cdkdepends

src/META-INF/io-jmol.libdepends

src/META-INF/io.buildfiles

src/META-INF/io.cdkdepends

src/META-INF/io.datafiles

src/META-INF/io.libdepends

src/META-INF/jchempaint.applet.cdkdepends

src/META-INF/jchempaint.applet.datafiles

src/META-INF/jchempaint.applet.libdepends

src/META-INF/jchempaint.application.cdkdepends

src/META-INF/jchempaint.application.datafiles

src/META-INF/jchempaint.application.libdepends

src/META-INF/jchempaint.cdkdepends

src/META-INF/jchempaint.datafiles

src/META-INF/jchempaint.libdepends

src/META-INF/libio-cml.buildfiles

src/META-INF/libio-cml.cdkdepends

src/META-INF/libio-cml.datafiles

src/META-INF/libio-cml.libdepends

src/META-INF/libio-openbabel.cdkdepends

src/META-INF/libiomd.cdkdepends

src/META-INF/libiomd.libdepends

src/META-INF/nonotify.cdkdepends

src/META-INF/nonotify.libdepends

src/META-INF/pdb-cml.cdkdepends

src/META-INF/pdb-cml.libdepends

src/META-INF/pdb.cdkdepends

src/META-INF/pdb.extrafiles

src/META-INF/pdb.libdepends

src/META-INF/qsar-cml.cdkdepends

src/META-INF/qsar-cml.libdepends

src/META-INF/qsar-pdb.cdkdepends

src/META-INF/qsar-pdb.libdepends

src/META-INF/qsar.buildfiles

src/META-INF/qsar.cdkdepends

src/META-INF/qsar.datafiles

src/META-INF/qsar.libdepends

src/META-INF/reaction.cdkdepends

src/META-INF/reaction.datafiles

src/META-INF/reaction.libdepends

src/META-INF/render.cdkdepends

src/META-INF/render.libdepends

src/META-INF/sdg.cdkdepends

src/META-INF/sdg.libdepends

src/META-INF/smiles.cdkdepends

src/META-INF/smiles.libdepends

src/META-INF/standard.cdkdepends

src/META-INF/standard.libdepends

src/META-INF/structgen.cdkdepends

src/META-INF/structgen.libdepends

src/META-INF/svg.cdkdepends

src/META-INF/svg.libdepends

src/META-INF/test-builder3d.cdkdepends

src/META-INF/test-builder3d.devellibdepends

src/META-INF/test-builder3d.extrafiles

src/META-INF/test-builder3d.libdepends

src/META-INF/test-core.cdkdepends

src/META-INF/test-core.devellibdepends

src/META-INF/test-core.libdepends

src/META-INF/test-data.cdkdepends

src/META-INF/test-data.devellibdepends

src/META-INF/test-data.libdepends

src/META-INF/test-datadebug.cdkdepends

src/META-INF/test-datadebug.devellibdepends

src/META-INF/test-datadebug.libdepends

src/META-INF/test-experimental.cdkdepends

src/META-INF/test-experimental.devellibdepends

src/META-INF/test-experimental.extrafiles

src/META-INF/test-experimental.libdepends

src/META-INF/test-extra.cdkdepends

src/META-INF/test-extra.devellibdepends

src/META-INF/test-extra.extrafiles

src/META-INF/test-extra.libdepends

src/META-INF/test-forcefield.cdkdepends

src/META-INF/test-forcefield.devellibdepends

src/META-INF/test-forcefield.extrafiles

src/META-INF/test-forcefield.libdepends

src/META-INF/test-inchi.cdkdepends

src/META-INF/test-inchi.devellibdepends

src/META-INF/test-inchi.libdepends

src/META-INF/test-io.cdkdepends

src/META-INF/test-io.devellibdepends

src/META-INF/test-io.extrafiles

src/META-INF/test-io.libdepends

src/META-INF/test-libiomd.cdkdepends

src/META-INF/test-libiomd.devellibdepends

src/META-INF/test-libiomd.libdepends

src/META-INF/test-nonotify.cdkdepends

src/META-INF/test-nonotify.devellibdepends

src/META-INF/test-nonotify.libdepends

src/META-INF/test-osjvmts.cdkdepends

src/META-INF/test-osjvmts.devellibdepends

src/META-INF/test-osjvmts.libdepends

src/META-INF/test-pdb.cdkdepends

src/META-INF/test-pdb.devellibdepends

src/META-INF/test-pdb.extrafiles

src/META-INF/test-pdb.libdepends

src/META-INF/test-qsar.cdkdepends

src/META-INF/test-qsar.devellibdepends

src/META-INF/test-qsar.extrafiles

src/META-INF/test-qsar.libdepends

src/META-INF/test-qsarAtomic.cdkdepends

src/META-INF/test-qsarAtomic.devellibdepends

src/META-INF/test-qsarAtomic.extrafiles

src/META-INF/test-qsarAtomic.libdepends

src/META-INF/test-qsarBond.cdkdepends

src/META-INF/test-qsarBond.devellibdepends

src/META-INF/test-qsarBond.extrafiles

src/META-INF/test-qsarBond.libdepends

src/META-INF/test-qsarMolecular.cdkdepends

src/META-INF/test-qsarMolecular.devellibdepends

src/META-INF/test-qsarMolecular.extrafiles

src/META-INF/test-qsarMolecular.libdepends

src/META-INF/test-reaction.cdkdepends

src/META-INF/test-reaction.devellibdepends

src/META-INF/test-reaction.extrafiles

src/META-INF/test-reaction.libdepends

src/META-INF/test-smiles.cdkdepends

src/META-INF/test-smiles.devellibdepends

src/META-INF/test-smiles.extrafiles

src/META-INF/test-smiles.libdepends

src/META-INF/test-standard.cdkdepends

src/META-INF/test-standard.devellibdepends

src/META-INF/test-standard.extrafiles

src/META-INF/test-standard.libdepends

src/META-INF/test-structgen.cdkdepends

src/META-INF/test-structgen.devellibdepends

src/META-INF/test-structgen.libdepends

src/META-INF/test-valencycheck.cdkdepends

src/META-INF/test-valencycheck.devellibdepends

src/META-INF/test-valencycheck.extrafiles

src/META-INF/test-valencycheck.libdepends

src/META-INF/test.devellibdepends

src/META-INF/test.libdepends

src/META-INF/valencycheck.cdkdepends

src/META-INF/valencycheck.libdepends

src/cdk-apps.manifest

src/net

src/net/sf

src/net/sf/cdk

src/net/sf/cdk/tools

src/net/sf/cdk/tools/MakeJavafilesFiles.java

src/net/sf/cdk/tools/MakeRequiresfilesFiles.java

src/net/sf/cdk/tools/bibtex

src/net/sf/cdk/tools/bibtex/BibTeXMLEntry.java

src/net/sf/cdk/tools/bibtex/BibTeXMLFile.java

src/net/sf/cdk/tools/doclets

src/net/sf/cdk/tools/doclets/CDKBugTaglet.java

src/net/sf/cdk/tools/doclets/CDKCiteTaglet.java

src/net/sf/cdk/tools/doclets/CDKDictRefTaglet.java

src/net/sf/cdk/tools/doclets/CDKModuleTaglet.java

src/org

src/org/openscience

src/org/openscience/cdk

src/org/openscience/cdk/AminoAcid.java

src/org/openscience/cdk/Association.java

src/org/openscience/cdk/Atom.java

src/org/openscience/cdk/AtomContainer.java

src/org/openscience/cdk/AtomContainerSet.java

src/org/openscience/cdk/AtomParity.java

src/org/openscience/cdk/AtomType.java

src/org/openscience/cdk/BioPolymer.java

src/org/openscience/cdk/Bond.java

src/org/openscience/cdk/CDKConstants.java

src/org/openscience/cdk/ChemFile.java

src/org/openscience/cdk/ChemModel.java

src/org/openscience/cdk/ChemObject.java

src/org/openscience/cdk/ChemSequence.java

src/org/openscience/cdk/Crystal.java

src/org/openscience/cdk/DefaultChemObjectBuilder.java

src/org/openscience/cdk/ElectronContainer.java

src/org/openscience/cdk/Element.java

src/org/openscience/cdk/EnzymeResidueLocator.java

src/org/openscience/cdk/Fragment.java

src/org/openscience/cdk/FragmentAtom.java

src/org/openscience/cdk/IImplementationSpecification.java

src/org/openscience/cdk/Isotope.java

src/org/openscience/cdk/LonePair.java

src/org/openscience/cdk/Mapping.java

src/org/openscience/cdk/Molecule.java

src/org/openscience/cdk/MoleculeSet.java

src/org/openscience/cdk/Monomer.java

src/org/openscience/cdk/PeriodicTableElement.java

src/org/openscience/cdk/PhysicalConstants.java

src/org/openscience/cdk/Polymer.java

src/org/openscience/cdk/PseudoAtom.java

src/org/openscience/cdk/Reaction.java

src/org/openscience/cdk/ReactionSet.java

src/org/openscience/cdk/Ring.java

src/org/openscience/cdk/RingSet.java

src/org/openscience/cdk/SingleElectron.java

src/org/openscience/cdk/Strand.java

src/org/openscience/cdk/Vibration.java

src/org/openscience/cdk/applications

src/org/openscience/cdk/applications/APIVersionTester.java

src/org/openscience/cdk/applications/DescriptorCalculator.java

src/org/openscience/cdk/applications/DistLargeInfo.java

src/org/openscience/cdk/applications/File2Text.java

src/org/openscience/cdk/applications/FileConvertor.java

src/org/openscience/cdk/applications/FileFormatGuesser.java

src/org/openscience/cdk/applications/FingerPrinter.java

src/org/openscience/cdk/applications/SDFSubstructureFinder.java

src/org/openscience/cdk/applications/TanimotoCoefficient.java

src/org/openscience/cdk/applications/Validator.java

src/org/openscience/cdk/applications/demo

src/org/openscience/cdk/applications/demo/EventCMLDemo.java

src/org/openscience/cdk/applications/demo/SmilesViewerforDeterministicGenerator.java

src/org/openscience/cdk/applications/jchempaint

src/org/openscience/cdk/applications/jchempaint/DevelStatusBar.java

src/org/openscience/cdk/applications/jchempaint/DrawingPanel.java

src/org/openscience/cdk/applications/jchempaint/InsertTextPanel.java

src/org/openscience/cdk/applications/jchempaint/JCPConstants.java

src/org/openscience/cdk/applications/jchempaint/JCPLocalizationHandler.java

src/org/openscience/cdk/applications/jchempaint/JCPPropertyHandler.java

src/org/openscience/cdk/applications/jchempaint/JChemPaintEditorPanel.java

src/org/openscience/cdk/applications/jchempaint/JChemPaintMenuBar.java

src/org/openscience/cdk/applications/jchempaint/JChemPaintModel.java

src/org/openscience/cdk/applications/jchempaint/JChemPaintPanel.java

src/org/openscience/cdk/applications/jchempaint/JChemPaintPopupMenu.java

src/org/openscience/cdk/applications/jchempaint/JChemPaintViewerOnlyPanel.java

src/org/openscience/cdk/applications/jchempaint/StatusBar.java

src/org/openscience/cdk/applications/jchempaint/StringHelper.java

src/org/openscience/cdk/applications/jchempaint/ToolBarMaker.java

src/org/openscience/cdk/applications/jchempaint/UndoStack.java

src/org/openscience/cdk/applications/jchempaint/action

src/org/openscience/cdk/applications/jchempaint/action/AboutAction.java

src/org/openscience/cdk/applications/jchempaint/action/AddHydrogenAction.java

src/org/openscience/cdk/applications/jchempaint/action/AdjustBondOrdersAction.java

src/org/openscience/cdk/applications/jchempaint/action/ChangeAtomSymbolAction.java

src/org/openscience/cdk/applications/jchempaint/action/ChangeIsotopeAction.java

src/org/openscience/cdk/applications/jchempaint/action/ChemAction.java

src/org/openscience/cdk/applications/jchempaint/action/CleanupAction.java

src/org/openscience/cdk/applications/jchempaint/action/CloseAction.java

src/org/openscience/cdk/applications/jchempaint/action/ConvertToAction.java

src/org/openscience/cdk/applications/jchempaint/action/ConvertToPseudoAtomAction.java

src/org/openscience/cdk/applications/jchempaint/action/ConvertToRadicalAction.java

src/org/openscience/cdk/applications/jchempaint/action/CopyPasteAction.java

src/org/openscience/cdk/applications/jchempaint/action/CreateInChIAction.java

src/org/openscience/cdk/applications/jchempaint/action/CreateReactionAction.java

src/org/openscience/cdk/applications/jchempaint/action/CreateSmilesAction.java

src/org/openscience/cdk/applications/jchempaint/action/DictionaryAction.java

src/org/openscience/cdk/applications/jchempaint/action/EditAction.java

src/org/openscience/cdk/applications/jchempaint/action/EditAtomContainerPropsAction.java

src/org/openscience/cdk/applications/jchempaint/action/EditChemObjectPropsAction.java

src/org/openscience/cdk/applications/jchempaint/action/EditDictRefsAction.java

src/org/openscience/cdk/applications/jchempaint/action/ElementAction.java

src/org/openscience/cdk/applications/jchempaint/action/ExitAction.java

src/org/openscience/cdk/applications/jchempaint/action/ExportAction.java

src/org/openscience/cdk/applications/jchempaint/action/ExportCompChemAction.java

src/org/openscience/cdk/applications/jchempaint/action/FlipAction.java

src/org/openscience/cdk/applications/jchempaint/action/HelpAction.java

src/org/openscience/cdk/applications/jchempaint/action/InsertSmilesAction.java

src/org/openscience/cdk/applications/jchempaint/action/InsertStructureAction.java

src/org/openscience/cdk/applications/jchempaint/action/JCPAction.java

src/org/openscience/cdk/applications/jchempaint/action/LicenseAction.java

src/org/openscience/cdk/applications/jchempaint/action/MenuBarAction.java

src/org/openscience/cdk/applications/jchempaint/action/ModelPropsAction.java

src/org/openscience/cdk/applications/jchempaint/action/ModifyDisplaySettingsAction.java

src/org/openscience/cdk/applications/jchempaint/action/ModifyGeneralSettingsAction.java

src/org/openscience/cdk/applications/jchempaint/action/NewAction.java

src/org/openscience/cdk/applications/jchempaint/action/OpenAction.java

src/org/openscience/cdk/applications/jchempaint/action/PerceiveAtomTypesAction.java

src/org/openscience/cdk/applications/jchempaint/action/PreferencesAction.java

src/org/openscience/cdk/applications/jchempaint/action/PrintAction.java

src/org/openscience/cdk/applications/jchempaint/action/RedoAction.java

src/org/openscience/cdk/applications/jchempaint/action/SaveAction.java

src/org/openscience/cdk/applications/jchempaint/action/SaveAsAction.java

src/org/openscience/cdk/applications/jchempaint/action/SetColorSchemeAction.java

src/org/openscience/cdk/applications/jchempaint/action/ShowChemObjectDumpAction.java

src/org/openscience/cdk/applications/jchempaint/action/ShowChemObjectProperty.java

src/org/openscience/cdk/applications/jchempaint/action/ShowDictionariesAction.java

src/org/openscience/cdk/applications/jchempaint/action/StatusBarAction.java

src/org/openscience/cdk/applications/jchempaint/action/ToolBarAction.java

src/org/openscience/cdk/applications/jchempaint/action/UndoAction.java

src/org/openscience/cdk/applications/jchempaint/action/ValidateAction.java

src/org/openscience/cdk/applications/jchempaint/action/WebLinkAction.java

src/org/openscience/cdk/applications/jchempaint/action/ZoomAction.java

src/org/openscience/cdk/applications/jchempaint/applet

src/org/openscience/cdk/applications/jchempaint/applet/AppletCanvas.java

src/org/openscience/cdk/applications/jchempaint/applet/JChemPaintAbstractApplet.java

src/org/openscience/cdk/applications/jchempaint/applet/JChemPaintEditorApplet.java

src/org/openscience/cdk/applications/jchempaint/applet/JChemPaintViewerOnlyApplet.java

src/org/openscience/cdk/applications/jchempaint/application

src/org/openscience/cdk/applications/jchempaint/application/JChemPaint.java

src/org/openscience/cdk/applications/jchempaint/dialogs

src/org/openscience/cdk/applications/jchempaint/dialogs/AboutDialog.java

src/org/openscience/cdk/applications/jchempaint/dialogs/ChemObjectPropertyDialog.java

src/org/openscience/cdk/applications/jchempaint/dialogs/CreateCoordinatesForFileDialog.java

src/org/openscience/cdk/applications/jchempaint/dialogs/DictionaryDialog.java

src/org/openscience/cdk/applications/jchempaint/dialogs/EditDictRefs.java

src/org/openscience/cdk/applications/jchempaint/dialogs/GeneralFieldEditor.java

src/org/openscience/cdk/applications/jchempaint/dialogs/GeneralSettingsEditor.java

src/org/openscience/cdk/applications/jchempaint/dialogs/HelpDialog.java

src/org/openscience/cdk/applications/jchempaint/dialogs/InfoDialog.java

src/org/openscience/cdk/applications/jchempaint/dialogs/JChemPaintModelPropsEditor.java

src/org/openscience/cdk/applications/jchempaint/dialogs/LicenseDialog.java

src/org/openscience/cdk/applications/jchempaint/dialogs/ModifyGeneralSettingsDialog.java

src/org/openscience/cdk/applications/jchempaint/dialogs/ModifyRenderOptionsDialog.java

src/org/openscience/cdk/applications/jchempaint/dialogs/PTDialog.java

src/org/openscience/cdk/applications/jchempaint/dialogs/TextViewDialog.java

src/org/openscience/cdk/applications/jchempaint/dialogs/ValidateFrame.java

src/org/openscience/cdk/applications/jchempaint/dialogs/WebDialog.java

src/org/openscience/cdk/applications/jchempaint/dnd

src/org/openscience/cdk/applications/jchempaint/dnd/JCPTransferHandler.java

src/org/openscience/cdk/applications/jchempaint/io

src/org/openscience/cdk/applications/jchempaint/io/IJCPFileFilter.java

src/org/openscience/cdk/applications/jchempaint/io/JCPCompChemInputSaveFileFilter.java

src/org/openscience/cdk/applications/jchempaint/io/JCPExportFileFilter.java

src/org/openscience/cdk/applications/jchempaint/io/JCPFileFilter.java

src/org/openscience/cdk/applications/jchempaint/io/JCPFileView.java

src/org/openscience/cdk/applications/jchempaint/io/JCPSaveFileFilter.java

src/org/openscience/cdk/applications/plugin

src/org/openscience/cdk/applications/plugin/CDKPluginManager.java

src/org/openscience/cdk/applications/plugin/ICDKEditBus.java

src/org/openscience/cdk/applications/plugin/ICDKPlugin.java

src/org/openscience/cdk/applications/plugin/PluginClassLoader.java

src/org/openscience/cdk/applications/swing

src/org/openscience/cdk/applications/swing/AtomicTable.java

src/org/openscience/cdk/applications/swing/ChemObjectPropertyEditorTableModel.java

src/org/openscience/cdk/applications/swing/ChemObjectTree.java

src/org/openscience/cdk/applications/swing/ChemObjectTreeNode.java

src/org/openscience/cdk/applications/swing/DictRefEditorTableModel.java

src/org/openscience/cdk/applications/swing/FieldTablePanel.java

src/org/openscience/cdk/applications/swing/GraphRenderer.java

src/org/openscience/cdk/applications/swing/JExternalFrame.java

src/org/openscience/cdk/applications/swing/ListeningTableModel.java

src/org/openscience/cdk/applications/swing/MoleculeListPanel.java

src/org/openscience/cdk/applications/swing/MoleculeListViewer.java

src/org/openscience/cdk/applications/swing/MoleculeViewer2D.java

src/org/openscience/cdk/applications/swing/MoleculeViewer2DPanel.java

src/org/openscience/cdk/applications/swing/MoleculesTable.java

src/org/openscience/cdk/applications/swing/PeriodicTablePanel.java

src/org/openscience/cdk/applications/swing/SortedTableModel.java

src/org/openscience/cdk/applications/swing/editor

src/org/openscience/cdk/applications/swing/editor/AtomContainerEditor.java

src/org/openscience/cdk/applications/swing/editor/AtomEditor.java

src/org/openscience/cdk/applications/swing/editor/BondEditor.java

src/org/openscience/cdk/applications/swing/editor/ChemObjectEditor.java

src/org/openscience/cdk/applications/swing/editor/Controller2DModelEditor.java

src/org/openscience/cdk/applications/swing/editor/PseudoAtomEditor.java

src/org/openscience/cdk/applications/swing/editor/ReactionEditor.java

src/org/openscience/cdk/applications/swing/editor/Renderer2DModelEditor.java

src/org/openscience/cdk/applications/undoredo

src/org/openscience/cdk/applications/undoredo/AddAtomsAndBondsEdit.java

src/org/openscience/cdk/applications/undoredo/AddFuncGroupEdit.java

src/org/openscience/cdk/applications/undoredo/AddHydrogenEdit.java

src/org/openscience/cdk/applications/undoredo/AdjustBondOrdersEdit.java

src/org/openscience/cdk/applications/undoredo/BondChangeEdit.java

src/org/openscience/cdk/applications/undoredo/ChangeAtomSymbolEdit.java

src/org/openscience/cdk/applications/undoredo/ChangeChargeEdit.java

src/org/openscience/cdk/applications/undoredo/ChangeCoordsEdit.java

src/org/openscience/cdk/applications/undoredo/ChangeIsotopeEdit.java

src/org/openscience/cdk/applications/undoredo/CleanUpEdit.java

src/org/openscience/cdk/applications/undoredo/ClearAllEdit.java

src/org/openscience/cdk/applications/undoredo/ConvertToPseudoAtomEdit.java

src/org/openscience/cdk/applications/undoredo/ConvertToRadicalEdit.java

src/org/openscience/cdk/applications/undoredo/FlipEdit.java

src/org/openscience/cdk/applications/undoredo/IUndoRedoHandler.java

src/org/openscience/cdk/applications/undoredo/JCPUndoRedoHandler.java

src/org/openscience/cdk/applications/undoredo/MergeMoleculesEdit.java

src/org/openscience/cdk/applications/undoredo/MoveAtomEdit.java

src/org/openscience/cdk/applications/undoredo/RemoveAtomsAndBondsEdit.java

src/org/openscience/cdk/applications/undoredo/UndoAdapter.java

src/org/openscience/cdk/aromaticity

src/org/openscience/cdk/aromaticity/AromaticityCalculator.java

src/org/openscience/cdk/aromaticity/HueckelAromaticityDetector.java

src/org/openscience/cdk/atomtype

src/org/openscience/cdk/atomtype/EStateAtomTypeMatcher.java

src/org/openscience/cdk/atomtype/HybridizationMatcher.java

src/org/openscience/cdk/atomtype/HybridizationStateATMatcher.java

src/org/openscience/cdk/atomtype/IAtomTypeGuesser.java

src/org/openscience/cdk/atomtype/IAtomTypeMatcher.java

src/org/openscience/cdk/atomtype/MM2AtomTypeMatcher.java

src/org/openscience/cdk/atomtype/MMFF94AtomTypeMatcher.java

src/org/openscience/cdk/atomtype/StructGenAtomTypeGuesser.java

src/org/openscience/cdk/atomtype/StructGenMatcher.java

src/org/openscience/cdk/atomtype/ValencyMatcher.java

src/org/openscience/cdk/charges

src/org/openscience/cdk/charges/AtomTypeCharges.java

src/org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java

src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java

src/org/openscience/cdk/charges/InductivePartialCharges.java

src/org/openscience/cdk/charges/MMFF94PartialCharges.java

src/org/openscience/cdk/charges/Polarizability.java

src/org/openscience/cdk/config

src/org/openscience/cdk/config/AtomTypeFactory.java

src/org/openscience/cdk/config/CDKBasedAtomTypeConfigurator.java

src/org/openscience/cdk/config/ElementPTFactory.java

src/org/openscience/cdk/config/Elements.java

src/org/openscience/cdk/config/IAtomTypeConfigurator.java

src/org/openscience/cdk/config/IsotopeFactory.java

src/org/openscience/cdk/config/Symbols.java

src/org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java

src/org/openscience/cdk/config/atomtypes

src/org/openscience/cdk/config/atomtypes/AtomTypeHandler.java

src/org/openscience/cdk/config/atomtypes/AtomTypeReader.java

src/org/openscience/cdk/config/data

src/org/openscience/cdk/config/data/chemicalElements.xml

src/org/openscience/cdk/config/data/hybridization_atomtypes.xml

src/org/openscience/cdk/config/data/isotopes.xml

src/org/openscience/cdk/config/data/jmol_atomtypes.txt

src/org/openscience/cdk/config/data/log4j.properties

src/org/openscience/cdk/config/data/mm2_atomtypes.xml

src/org/openscience/cdk/config/data/mmff94_atomtypes.xml

src/org/openscience/cdk/config/data/mol2_atomtypes.xml

src/org/openscience/cdk/config/data/pdb_atomtypes.xml

src/org/openscience/cdk/config/data/structgen_atomtypes.xml

src/org/openscience/cdk/config/data/valency2_atomtypes.xml

src/org/openscience/cdk/config/data/valency_atomtypes.xml

src/org/openscience/cdk/config/data/whim_weights.txt

src/org/openscience/cdk/config/elements

src/org/openscience/cdk/config/elements/ElementPTHandler.java

src/org/openscience/cdk/config/elements/ElementPTReader.java

src/org/openscience/cdk/config/isotopes

src/org/openscience/cdk/config/isotopes/IsotopeHandler.java

src/org/openscience/cdk/config/isotopes/IsotopeReader.java

src/org/openscience/cdk/controller

src/org/openscience/cdk/controller/AbstractController2D.java

src/org/openscience/cdk/controller/CDKPopupMenu.java

src/org/openscience/cdk/controller/Controller2D.java

src/org/openscience/cdk/controller/Controller2DModel.java

src/org/openscience/cdk/controller/PopupController2D.java

src/org/openscience/cdk/controller/SimpleController2D.java

src/org/openscience/cdk/database

src/org/openscience/cdk/database/XindiceReader.java

src/org/openscience/cdk/debug

src/org/openscience/cdk/debug/DebugAminoAcid.java

src/org/openscience/cdk/debug/DebugAtom.java

src/org/openscience/cdk/debug/DebugAtomContainer.java

src/org/openscience/cdk/debug/DebugAtomContainerSet.java

src/org/openscience/cdk/debug/DebugAtomParity.java

src/org/openscience/cdk/debug/DebugAtomType.java

src/org/openscience/cdk/debug/DebugBioPolymer.java

src/org/openscience/cdk/debug/DebugBond.java

src/org/openscience/cdk/debug/DebugChemFile.java

src/org/openscience/cdk/debug/DebugChemModel.java

src/org/openscience/cdk/debug/DebugChemObject.java

src/org/openscience/cdk/debug/DebugChemObjectBuilder.java

src/org/openscience/cdk/debug/DebugChemSequence.java

src/org/openscience/cdk/debug/DebugCrystal.java

src/org/openscience/cdk/debug/DebugElectronContainer.java

src/org/openscience/cdk/debug/DebugElement.java

src/org/openscience/cdk/debug/DebugIsotope.java

src/org/openscience/cdk/debug/DebugLonePair.java

src/org/openscience/cdk/debug/DebugMapping.java

src/org/openscience/cdk/debug/DebugMolecule.java

src/org/openscience/cdk/debug/DebugMoleculeSet.java

src/org/openscience/cdk/debug/DebugMonomer.java

src/org/openscience/cdk/debug/DebugPDBAtom.java

src/org/openscience/cdk/debug/DebugPDBMonomer.java

src/org/openscience/cdk/debug/DebugPDBPolymer.java

src/org/openscience/cdk/debug/DebugPDBStructure.java

src/org/openscience/cdk/debug/DebugPolymer.java

src/org/openscience/cdk/debug/DebugPseudoAtom.java

src/org/openscience/cdk/debug/DebugReaction.java

src/org/openscience/cdk/debug/DebugReactionSet.java

src/org/openscience/cdk/debug/DebugRing.java

src/org/openscience/cdk/debug/DebugRingSet.java

src/org/openscience/cdk/debug/DebugSingleElectron.java

src/org/openscience/cdk/debug/DebugStrand.java

src/org/openscience/cdk/dict

src/org/openscience/cdk/dict/CDKDictionaryReferences.java

src/org/openscience/cdk/dict/DictRef.java

src/org/openscience/cdk/dict/Dictionary.java

src/org/openscience/cdk/dict/DictionaryDatabase.java

src/org/openscience/cdk/dict/DictionaryHandler.java

src/org/openscience/cdk/dict/Entry.java

src/org/openscience/cdk/dict/OWLFile.java

src/org/openscience/cdk/dict/data

src/org/openscience/cdk/dict/data/chemical.xml

src/org/openscience/cdk/dict/data/elements.xml

src/org/openscience/cdk/event

src/org/openscience/cdk/event/ChemObjectChangeEvent.java

src/org/openscience/cdk/event/ICDKChangeListener.java

src/org/openscience/cdk/event/ICDKSelectionChangeListener.java

src/org/openscience/cdk/exception

src/org/openscience/cdk/exception/CDKException.java

src/org/openscience/cdk/exception/IncorrectUseOfCDKCoreClassError.java

src/org/openscience/cdk/exception/InvalidSmilesException.java

src/org/openscience/cdk/exception/NoSuchAtomException.java

src/org/openscience/cdk/exception/NoSuchAtomTypeException.java

src/org/openscience/cdk/exception/UnsupportedChemObjectException.java

src/org/openscience/cdk/fingerprint

src/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java

src/org/openscience/cdk/fingerprint/Fingerprinter.java

src/org/openscience/cdk/fingerprint/FingerprinterTool.java

src/org/openscience/cdk/fingerprint/GraphOnlyFingerprinter.java

src/org/openscience/cdk/fingerprint/IFingerprinter.java

src/org/openscience/cdk/fingerprint/StandardSubstructureSets.java

src/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java

src/org/openscience/cdk/geometry

src/org/openscience/cdk/geometry/AtomTools.java

src/org/openscience/cdk/geometry/BondTools.java

src/org/openscience/cdk/geometry/CrystalGeometryTools.java

src/org/openscience/cdk/geometry/GeometryTools.java

src/org/openscience/cdk/geometry/GeometryToolsInternalCoordinates.java

src/org/openscience/cdk/geometry/IRDFWeightFunction.java

src/org/openscience/cdk/geometry/Projector.java

src/org/openscience/cdk/geometry/RDFCalculator.java

src/org/openscience/cdk/geometry/ZMatrixTools.java

src/org/openscience/cdk/geometry/alignment

src/org/openscience/cdk/geometry/alignment/KabschAlignment.java

src/org/openscience/cdk/geometry/surface

src/org/openscience/cdk/geometry/surface/NeighborList.java

src/org/openscience/cdk/geometry/surface/NumericalSurface.java

src/org/openscience/cdk/geometry/surface/Tessellate.java

src/org/openscience/cdk/geometry/surface/Triangle.java

src/org/openscience/cdk/graph

src/org/openscience/cdk/graph/AtomContainerAtomPermutor.java

src/org/openscience/cdk/graph/AtomContainerBondPermutor.java

src/org/openscience/cdk/graph/AtomContainerPermutor.java

src/org/openscience/cdk/graph/BFSShortestPath.java

src/org/openscience/cdk/graph/BiconnectivityInspector.java

src/org/openscience/cdk/graph/ConnectivityChecker.java

src/org/openscience/cdk/graph/MinimalPathIterator.java

src/org/openscience/cdk/graph/MoleculeGraphs.java

src/org/openscience/cdk/graph/PathTools.java

src/org/openscience/cdk/graph/SpanningTree.java

src/org/openscience/cdk/graph/invariant

src/org/openscience/cdk/graph/invariant/CanonicalLabeler.java

src/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java

src/org/openscience/cdk/graph/invariant/EquivalentClassPartitioner.java

src/org/openscience/cdk/graph/invariant/GIMatrix.java

src/org/openscience/cdk/graph/invariant/HuLuIndexTool.java

src/org/openscience/cdk/graph/invariant/MorganNumbersTools.java

src/org/openscience/cdk/graph/invariant/exception

src/org/openscience/cdk/graph/invariant/exception/BadMatrixFormatException.java

src/org/openscience/cdk/graph/invariant/exception/IndexOutOfBoundsException.java

src/org/openscience/cdk/graph/invariant/exception/MatrixNotInvertibleException.java

src/org/openscience/cdk/graph/matrix

src/org/openscience/cdk/graph/matrix/AdjacencyMatrix.java

src/org/openscience/cdk/graph/matrix/ConnectionMatrix.java

src/org/openscience/cdk/graph/matrix/IGraphMatrix.java

src/org/openscience/cdk/graph/matrix/TopologicalMatrix.java

src/org/openscience/cdk/graph/rebond

src/org/openscience/cdk/graph/rebond/Bspt.java

src/org/openscience/cdk/graph/rebond/Point.java

src/org/openscience/cdk/graph/rebond/RebondTool.java

src/org/openscience/cdk/inchi

src/org/openscience/cdk/inchi/InChIGenerator.java

src/org/openscience/cdk/inchi/InChIGeneratorFactory.java

src/org/openscience/cdk/inchi/InChIToStructure.java

src/org/openscience/cdk/index

src/org/openscience/cdk/index/CASNumber.java

src/org/openscience/cdk/interfaces

src/org/openscience/cdk/interfaces/IAminoAcid.java

src/org/openscience/cdk/interfaces/IAtom.java

src/org/openscience/cdk/interfaces/IAtomContainer.java

src/org/openscience/cdk/interfaces/IAtomContainerSet.java

src/org/openscience/cdk/interfaces/IAtomParity.java

src/org/openscience/cdk/interfaces/IAtomType.java

src/org/openscience/cdk/interfaces/IBioPolymer.java

src/org/openscience/cdk/interfaces/IBond.java

src/org/openscience/cdk/interfaces/IChemFile.java

src/org/openscience/cdk/interfaces/IChemModel.java

src/org/openscience/cdk/interfaces/IChemObject.java

src/org/openscience/cdk/interfaces/IChemObjectBuilder.java

src/org/openscience/cdk/interfaces/IChemObjectChangeEvent.java

src/org/openscience/cdk/interfaces/IChemObjectListener.java

src/org/openscience/cdk/interfaces/IChemSequence.java

src/org/openscience/cdk/interfaces/ICrystal.java

src/org/openscience/cdk/interfaces/IElectronContainer.java

src/org/openscience/cdk/interfaces/IElement.java

src/org/openscience/cdk/interfaces/IIsotope.java

src/org/openscience/cdk/interfaces/ILonePair.java

src/org/openscience/cdk/interfaces/IMapping.java

src/org/openscience/cdk/interfaces/IMolecule.java

src/org/openscience/cdk/interfaces/IMoleculeSet.java

src/org/openscience/cdk/interfaces/IMonomer.java

src/org/openscience/cdk/interfaces/IPDBAtom.java

src/org/openscience/cdk/interfaces/IPDBMonomer.java

src/org/openscience/cdk/interfaces/IPDBPolymer.java

src/org/openscience/cdk/interfaces/IPDBStructure.java

src/org/openscience/cdk/interfaces/IPolymer.java

src/org/openscience/cdk/interfaces/IPseudoAtom.java

src/org/openscience/cdk/interfaces/IReaction.java

src/org/openscience/cdk/interfaces/IReactionSet.java

src/org/openscience/cdk/interfaces/IRing.java

src/org/openscience/cdk/interfaces/IRingSet.java

src/org/openscience/cdk/interfaces/ISingleElectron.java

src/org/openscience/cdk/interfaces/IStrand.java

src/org/openscience/cdk/internet

src/org/openscience/cdk/internet/DADMLReader.java

src/org/openscience/cdk/internet/DADMLResult.java

src/org/openscience/cdk/internet/WWMMatrixReader.java

src/org/openscience/cdk/io

src/org/openscience/cdk/io/CDKSourceCodeWriter.java

src/org/openscience/cdk/io/CIFReader.java

src/org/openscience/cdk/io/CMLReader.java

src/org/openscience/cdk/io/CMLWriter.java

src/org/openscience/cdk/io/CTXReader.java

src/org/openscience/cdk/io/CrystClustReader.java

src/org/openscience/cdk/io/CrystClustWriter.java

src/org/openscience/cdk/io/DefaultChemObjectReader.java

src/org/openscience/cdk/io/DefaultChemObjectWriter.java

src/org/openscience/cdk/io/GamessReader.java

src/org/openscience/cdk/io/Gaussian03Reader.java

src/org/openscience/cdk/io/Gaussian98Reader.java

src/org/openscience/cdk/io/GhemicalMMReader.java

src/org/openscience/cdk/io/HINReader.java

src/org/openscience/cdk/io/HINWriter.java

src/org/openscience/cdk/io/IChemObjectIO.java

src/org/openscience/cdk/io/IChemObjectReader.java

src/org/openscience/cdk/io/IChemObjectWriter.java

src/org/openscience/cdk/io/INChIPlainTextReader.java

src/org/openscience/cdk/io/INChIReader.java

src/org/openscience/cdk/io/MACiEReader.java

src/org/openscience/cdk/io/MDLRXNReader.java

src/org/openscience/cdk/io/MDLRXNV2000Reader.java

src/org/openscience/cdk/io/MDLRXNV3000Reader.java

src/org/openscience/cdk/io/MDLRXNWriter.java

src/org/openscience/cdk/io/MDLReader.java

src/org/openscience/cdk/io/MDLV2000Reader.java

src/org/openscience/cdk/io/MDLV3000Reader.java

src/org/openscience/cdk/io/MDLWriter.java

src/org/openscience/cdk/io/Mol2Reader.java

src/org/openscience/cdk/io/Mol2Writer.java

src/org/openscience/cdk/io/PCCompoundASNReader.java

src/org/openscience/cdk/io/PDBReader.java

src/org/openscience/cdk/io/PDBWriter.java

src/org/openscience/cdk/io/PMPReader.java

src/org/openscience/cdk/io/ReaderEvent.java

src/org/openscience/cdk/io/ReaderFactory.java

src/org/openscience/cdk/io/RssWriter.java

src/org/openscience/cdk/io/SMILESReader.java

src/org/openscience/cdk/io/SMILESWriter.java

src/org/openscience/cdk/io/SVGWriter.java

src/org/openscience/cdk/io/ShelXReader.java

src/org/openscience/cdk/io/ShelXWriter.java

src/org/openscience/cdk/io/VASPReader.java

src/org/openscience/cdk/io/WriterFactory.java

src/org/openscience/cdk/io/XYZReader.java

src/org/openscience/cdk/io/XYZWriter.java

src/org/openscience/cdk/io/ZMatrixReader.java

src/org/openscience/cdk/io/cml

src/org/openscience/cdk/io/cml/CDKConvention.java

src/org/openscience/cdk/io/cml/CMLCoreModule.java

src/org/openscience/cdk/io/cml/CMLErrorHandler.java

src/org/openscience/cdk/io/cml/CMLHandler.java

src/org/openscience/cdk/io/cml/CMLReactionModule.java

src/org/openscience/cdk/io/cml/CMLResolver.java

src/org/openscience/cdk/io/cml/CMLStack.java

src/org/openscience/cdk/io/cml/ICMLConvention.java

src/org/openscience/cdk/io/cml/ICMLModule.java

src/org/openscience/cdk/io/cml/JMOLANIMATIONConvention.java

src/org/openscience/cdk/io/cml/MDLMolConvention.java

src/org/openscience/cdk/io/cml/MDMoleculeConvention.java

src/org/openscience/cdk/io/cml/PDBConvention.java

src/org/openscience/cdk/io/cml/PMPConvention.java

src/org/openscience/cdk/io/cml/QSARConvention.java

src/org/openscience/cdk/io/cml/data

src/org/openscience/cdk/io/cml/data/cml1_0.dtd

src/org/openscience/cdk/io/cml/data/cml1_0_1.dtd

src/org/openscience/cdk/io/cml/data/cml1_0_1.xsd

src/org/openscience/cdk/io/cml/data/cml23.xsd

src/org/openscience/cdk/io/cml/data/cmlAll.xsd

src/org/openscience/cdk/io/cml/data/cmlCore.xsd

src/org/openscience/cdk/io/formats

src/org/openscience/cdk/io/formats/ABINITFormat.java

src/org/openscience/cdk/io/formats/ADFFormat.java

src/org/openscience/cdk/io/formats/Aces2Format.java

src/org/openscience/cdk/io/formats/AlchemyFormat.java

src/org/openscience/cdk/io/formats/BGFFormat.java

src/org/openscience/cdk/io/formats/BSFormat.java

src/org/openscience/cdk/io/formats/CACheFormat.java

src/org/openscience/cdk/io/formats/CDKSourceCodeFormat.java

src/org/openscience/cdk/io/formats/CIFFormat.java

src/org/openscience/cdk/io/formats/CMLFormat.java

src/org/openscience/cdk/io/formats/CMLRSSFormat.java

src/org/openscience/cdk/io/formats/CRK2DFormat.java

src/org/openscience/cdk/io/formats/CRK3DFormat.java

src/org/openscience/cdk/io/formats/CTXFormat.java

src/org/openscience/cdk/io/formats/CacaoCartesianFormat.java

src/org/openscience/cdk/io/formats/CacaoInternalFormat.java

src/org/openscience/cdk/io/formats/Chem3D_Cartesian_1Format.java

src/org/openscience/cdk/io/formats/Chem3D_Cartesian_2Format.java

src/org/openscience/cdk/io/formats/ChemDrawFormat.java

src/org/openscience/cdk/io/formats/ChemtoolFormat.java

src/org/openscience/cdk/io/formats/CrystClustFormat.java

src/org/openscience/cdk/io/formats/DMol3Format.java

src/org/openscience/cdk/io/formats/DOCK5Format.java

src/org/openscience/cdk/io/formats/DaltonFormat.java

src/org/openscience/cdk/io/formats/FenskeHall_ZMatrixFormat.java

src/org/openscience/cdk/io/formats/FingerprintFormat.java

src/org/openscience/cdk/io/formats/GROMOS96Format.java

src/org/openscience/cdk/io/formats/GamessFormat.java

src/org/openscience/cdk/io/formats/Gaussian03Format.java

src/org/openscience/cdk/io/formats/Gaussian90Format.java

src/org/openscience/cdk/io/formats/Gaussian92Format.java

src/org/openscience/cdk/io/formats/Gaussian94Format.java

src/org/openscience/cdk/io/formats/Gaussian95Format.java

src/org/openscience/cdk/io/formats/Gaussian98Format.java

src/org/openscience/cdk/io/formats/GaussianInputFormat.java

src/org/openscience/cdk/io/formats/GhemicalMMFormat.java

src/org/openscience/cdk/io/formats/GhemicalSPMFormat.java

src/org/openscience/cdk/io/formats/HINFormat.java

src/org/openscience/cdk/io/formats/IChemFormat.java

src/org/openscience/cdk/io/formats/IChemFormatMatcher.java

src/org/openscience/cdk/io/formats/INChIFormat.java

src/org/openscience/cdk/io/formats/INChIPlainTextFormat.java

src/org/openscience/cdk/io/formats/IResourceFormat.java

src/org/openscience/cdk/io/formats/JMEFormat.java

src/org/openscience/cdk/io/formats/JaguarFormat.java

src/org/openscience/cdk/io/formats/MACiEFormat.java

src/org/openscience/cdk/io/formats/MDLFormat.java

src/org/openscience/cdk/io/formats/MDLRXNFormat.java

src/org/openscience/cdk/io/formats/MDLRXNV3000Format.java

src/org/openscience/cdk/io/formats/MDLV2000Format.java

src/org/openscience/cdk/io/formats/MDLV3000Format.java

src/org/openscience/cdk/io/formats/MMODFormat.java

src/org/openscience/cdk/io/formats/MOPAC2002Format.java

src/org/openscience/cdk/io/formats/MOPAC7Format.java

src/org/openscience/cdk/io/formats/MOPAC93Format.java

src/org/openscience/cdk/io/formats/MOPAC97Format.java

src/org/openscience/cdk/io/formats/MPQCFormat.java

src/org/openscience/cdk/io/formats/MacroModelFormat.java

src/org/openscience/cdk/io/formats/Mol2Format.java

src/org/openscience/cdk/io/formats/NWChemFormat.java

src/org/openscience/cdk/io/formats/PCModelFormat.java

src/org/openscience/cdk/io/formats/PDBFormat.java

src/org/openscience/cdk/io/formats/PDBMLFormat.java

src/org/openscience/cdk/io/formats/PMPFormat.java

src/org/openscience/cdk/io/formats/POVRayFormat.java

src/org/openscience/cdk/io/formats/PQSChemFormat.java

src/org/openscience/cdk/io/formats/PubChemASNFormat.java

src/org/openscience/cdk/io/formats/PubChemFormat.java

src/org/openscience/cdk/io/formats/QChemFormat.java

src/org/openscience/cdk/io/formats/RawCopyFormat.java

src/org/openscience/cdk/io/formats/SDFFormat.java

src/org/openscience/cdk/io/formats/SMARTSFormat.java

src/org/openscience/cdk/io/formats/SMILESFIXFormat.java

src/org/openscience/cdk/io/formats/SMILESFormat.java

src/org/openscience/cdk/io/formats/SVGFormat.java

src/org/openscience/cdk/io/formats/ShelXFormat.java

src/org/openscience/cdk/io/formats/SpartanFormat.java

src/org/openscience/cdk/io/formats/SybylDescriptorFormat.java

src/org/openscience/cdk/io/formats/TinkerMM2Format.java

src/org/openscience/cdk/io/formats/TinkerXYZFormat.java

src/org/openscience/cdk/io/formats/TurboMoleFormat.java

src/org/openscience/cdk/io/formats/UniChemXYZFormat.java

src/org/openscience/cdk/io/formats/VASPFormat.java

src/org/openscience/cdk/io/formats/ViewmolFormat.java

src/org/openscience/cdk/io/formats/XEDFormat.java

src/org/openscience/cdk/io/formats/XYZFormat.java

src/org/openscience/cdk/io/formats/YasaraFormat.java

src/org/openscience/cdk/io/formats/ZMatrixFormat.java

src/org/openscience/cdk/io/formats/ZindoFormat.java

src/org/openscience/cdk/io/inchi

src/org/openscience/cdk/io/inchi/INChIContentProcessorTool.java

src/org/openscience/cdk/io/inchi/INChIHandler.java

src/org/openscience/cdk/io/iterator

src/org/openscience/cdk/io/iterator/DefaultIteratingChemObjectReader.java

src/org/openscience/cdk/io/iterator/IIteratingChemObjectReader.java

src/org/openscience/cdk/io/iterator/IteratingMDLReader.java

src/org/openscience/cdk/io/iterator/IteratingSMILESReader.java

src/org/openscience/cdk/io/iterator/event

src/org/openscience/cdk/io/iterator/event/DefaultEventChemObjectReader.java

src/org/openscience/cdk/io/iterator/event/EventCMLHandler.java

src/org/openscience/cdk/io/iterator/event/EventCMLReader.java

src/org/openscience/cdk/io/iterator/event/IEventChemObjectReader.java

src/org/openscience/cdk/io/listener

src/org/openscience/cdk/io/listener/IChemObjectIOListener.java

src/org/openscience/cdk/io/listener/IReaderListener.java

src/org/openscience/cdk/io/listener/IWriterListener.java

src/org/openscience/cdk/io/listener/PropertiesListener.java

src/org/openscience/cdk/io/listener/SwingGUIListener.java

src/org/openscience/cdk/io/listener/TextGUIListener.java

src/org/openscience/cdk/io/program

src/org/openscience/cdk/io/program/GaussianInputWriter.java

src/org/openscience/cdk/io/setting

src/org/openscience/cdk/io/setting/BooleanIOSetting.java

src/org/openscience/cdk/io/setting/IOSetting.java

src/org/openscience/cdk/io/setting/IntegerIOSetting.java

src/org/openscience/cdk/io/setting/OptionIOSetting.java

src/org/openscience/cdk/io/setting/StringIOSetting.java

src/org/openscience/cdk/isomorphism

src/org/openscience/cdk/isomorphism/IsomorphismTester.java

src/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java

src/org/openscience/cdk/isomorphism/matchers

src/org/openscience/cdk/isomorphism/matchers/IQueryAtom.java

src/org/openscience/cdk/isomorphism/matchers/IQueryAtomContainer.java

src/org/openscience/cdk/isomorphism/matchers/IQueryBond.java

src/org/openscience/cdk/isomorphism/matchers/InverseSymbolSetQueryAtom.java

src/org/openscience/cdk/isomorphism/matchers/OrderQueryBond.java

src/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java

src/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreator.java

src/org/openscience/cdk/isomorphism/matchers/SymbolAndChargeQueryAtom.java

src/org/openscience/cdk/isomorphism/matchers/SymbolChargeIDQueryAtom.java

src/org/openscience/cdk/isomorphism/matchers/SymbolQueryAtom.java

src/org/openscience/cdk/isomorphism/matchers/SymbolSetQueryAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts

src/org/openscience/cdk/isomorphism/matchers/smarts/AliphaticAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/AliphaticSymbolAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java

src/org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java

src/org/openscience/cdk/isomorphism/matchers/smarts/AromaticSymbolAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/AtomicNumberAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/BracketAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/ChiralityAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/ColumnAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/ConnectionCountAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/DegreeAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/ExplicitConnectionAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/FormalChargeAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/HydrogenAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/ImplicitHCountAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/LogicalOperatorAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/LogicalOperatorBond.java

src/org/openscience/cdk/isomorphism/matchers/smarts/MassAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/OperatorContainer.java

src/org/openscience/cdk/isomorphism/matchers/smarts/OrderQueryBond.java

src/org/openscience/cdk/isomorphism/matchers/smarts/RecurseAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/RecursiveSmartsAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/RingAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/RingBond.java

src/org/openscience/cdk/isomorphism/matchers/smarts/RingIdentifierAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/RingMembershipAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.java

src/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSOperatorAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/SmallestRingAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/StereoBond.java

src/org/openscience/cdk/isomorphism/matchers/smarts/TotalConnectionAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/TotalHCountAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/TotalRingConnectionAtom.java

src/org/openscience/cdk/isomorphism/matchers/smarts/TotalValencyAtom.java

src/org/openscience/cdk/isomorphism/mcss

src/org/openscience/cdk/isomorphism/mcss/RGraph.java

src/org/openscience/cdk/isomorphism/mcss/RMap.java

src/org/openscience/cdk/isomorphism/mcss/RNode.java

src/org/openscience/cdk/iupac

src/org/openscience/cdk/iupac/parser

src/org/openscience/cdk/iupac/parser/AttachedGroup.java

src/org/openscience/cdk/iupac/parser/MoleculeBuilder.java

src/org/openscience/cdk/iupac/parser/NomParser.java

src/org/openscience/cdk/iupac/parser/NomParser.jj

src/org/openscience/cdk/iupac/parser/NomParserConstants.java

src/org/openscience/cdk/iupac/parser/NomParserTokenManager.java

src/org/openscience/cdk/iupac/parser/ParseException.java

src/org/openscience/cdk/iupac/parser/SimpleCharStream.java

src/org/openscience/cdk/iupac/parser/Token.java

src/org/openscience/cdk/iupac/parser/TokenMgrError.java

src/org/openscience/cdk/layout

src/org/openscience/cdk/layout/AtomPlacer.java

src/org/openscience/cdk/layout/HydrogenPlacer.java

src/org/openscience/cdk/layout/OverlapResolver.java

src/org/openscience/cdk/layout/RingPlacer.java

src/org/openscience/cdk/layout/StructureDiagramGenerator.java

src/org/openscience/cdk/layout/TemplateHandler.java

src/org/openscience/cdk/libio

src/org/openscience/cdk/libio/biojava

src/org/openscience/cdk/libio/biojava/Convertor.java

src/org/openscience/cdk/libio/cml

src/org/openscience/cdk/libio/cml/Convertor.java

src/org/openscience/cdk/libio/cml/ICMLCustomizer.java

src/org/openscience/cdk/libio/cml/MDMoleculeCustomizer.java

src/org/openscience/cdk/libio/cml/PDBAtomCustomizer.java

src/org/openscience/cdk/libio/cml/QSARCustomizer.java

src/org/openscience/cdk/libio/md

src/org/openscience/cdk/libio/md/ChargeGroup.java

src/org/openscience/cdk/libio/md/MDMolecule.java

src/org/openscience/cdk/libio/md/Residue.java

src/org/openscience/cdk/libio/openbabel

src/org/openscience/cdk/libio/openbabel/OpenBabelConvert.java

src/org/openscience/cdk/math

src/org/openscience/cdk/math/Complex.java

src/org/openscience/cdk/math/FortranFormat.java

src/org/openscience/cdk/math/IFunction.java

src/org/openscience/cdk/math/IMatrix.java

src/org/openscience/cdk/math/IVector.java

src/org/openscience/cdk/math/MathTools.java

src/org/openscience/cdk/math/Matrix.java

src/org/openscience/cdk/math/Primes.java

src/org/openscience/cdk/math/Quaternion.java

src/org/openscience/cdk/math/RandomNumbersTool.java

src/org/openscience/cdk/math/Vector.java

src/org/openscience/cdk/math/qm

src/org/openscience/cdk/math/qm/AngularMomentum.java

src/org/openscience/cdk/math/qm/ClosedShellJob.java

src/org/openscience/cdk/math/qm/FourierGridBasis.java

src/org/openscience/cdk/math/qm/GaussiansBasis.java

src/org/openscience/cdk/math/qm/IBasis.java

src/org/openscience/cdk/math/qm/OneElectronJob.java

src/org/openscience/cdk/math/qm/Orbitals.java

src/org/openscience/cdk/math/qm/SimpleBasisSet.java

src/org/openscience/cdk/modeling

src/org/openscience/cdk/modeling/builder3d

src/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java

src/org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3D.java

src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java

src/org/openscience/cdk/modeling/builder3d/MM2BasedAtomTypePattern.java

src/org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java

src/org/openscience/cdk/modeling/builder3d/MMFF94BasedAtomTypePattern.java

src/org/openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java

src/org/openscience/cdk/modeling/builder3d/MMFF94ParametersCall.java

src/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java

src/org/openscience/cdk/modeling/builder3d/TemplateExtractor.java

src/org/openscience/cdk/modeling/builder3d/TemplateHandler3D.java

src/org/openscience/cdk/modeling/builder3d/data

src/org/openscience/cdk/modeling/builder3d/data/ringTemplateFingerprints.txt.gz

src/org/openscience/cdk/modeling/builder3d/data/ringTemplateStructures.sdf.gz

src/org/openscience/cdk/modeling/forcefield

src/org/openscience/cdk/modeling/forcefield/AngleBending.java

src/org/openscience/cdk/modeling/forcefield/BondStretching.java

src/org/openscience/cdk/modeling/forcefield/ConjugateGradientMethod.java

src/org/openscience/cdk/modeling/forcefield/ElectrostaticInteractions.java

src/org/openscience/cdk/modeling/forcefield/ForceField.java

src/org/openscience/cdk/modeling/forcefield/ForceFieldTools.java

src/org/openscience/cdk/modeling/forcefield/GeometricMinimizer.java

src/org/openscience/cdk/modeling/forcefield/IPotentialFunction.java

src/org/openscience/cdk/modeling/forcefield/LineSearch.java

src/org/openscience/cdk/modeling/forcefield/LineSearchForTheWolfeConditions.java

src/org/openscience/cdk/modeling/forcefield/MMFF94EnergyFunction.java

src/org/openscience/cdk/modeling/forcefield/NewtonRaphsonMethod.java

src/org/openscience/cdk/modeling/forcefield/SmoothingFunctions.java

src/org/openscience/cdk/modeling/forcefield/SteepestDescentsMethod.java

src/org/openscience/cdk/modeling/forcefield/StretchBendInteractions.java

src/org/openscience/cdk/modeling/forcefield/Torsions.java

src/org/openscience/cdk/modeling/forcefield/VanDerWaalsInteractions.java

src/org/openscience/cdk/modeling/forcefield/data

src/org/openscience/cdk/modeling/forcefield/data/mm2.prm

src/org/openscience/cdk/modeling/forcefield/data/mmff94.prm

src/org/openscience/cdk/modeling/forcefield/data/mmffvdw.prm

src/org/openscience/cdk/nonotify

src/org/openscience/cdk/nonotify/NNAminoAcid.java

src/org/openscience/cdk/nonotify/NNAtom.java

src/org/openscience/cdk/nonotify/NNAtomContainer.java

src/org/openscience/cdk/nonotify/NNAtomContainerSet.java

src/org/openscience/cdk/nonotify/NNAtomParity.java

src/org/openscience/cdk/nonotify/NNAtomType.java

src/org/openscience/cdk/nonotify/NNBioPolymer.java

src/org/openscience/cdk/nonotify/NNBond.java

src/org/openscience/cdk/nonotify/NNChemFile.java

src/org/openscience/cdk/nonotify/NNChemModel.java

src/org/openscience/cdk/nonotify/NNChemObject.java

src/org/openscience/cdk/nonotify/NNChemSequence.java

src/org/openscience/cdk/nonotify/NNCrystal.java

src/org/openscience/cdk/nonotify/NNElectronContainer.java

src/org/openscience/cdk/nonotify/NNElement.java

src/org/openscience/cdk/nonotify/NNIsotope.java

src/org/openscience/cdk/nonotify/NNLonePair.java

src/org/openscience/cdk/nonotify/NNMapping.java

src/org/openscience/cdk/nonotify/NNMolecule.java

src/org/openscience/cdk/nonotify/NNMoleculeSet.java

src/org/openscience/cdk/nonotify/NNMonomer.java

src/org/openscience/cdk/nonotify/NNPDBAtom.java

src/org/openscience/cdk/nonotify/NNPDBMonomer.java

src/org/openscience/cdk/nonotify/NNPDBPolymer.java

src/org/openscience/cdk/nonotify/NNPDBStructure.java

src/org/openscience/cdk/nonotify/NNPolymer.java

src/org/openscience/cdk/nonotify/NNPseudoAtom.java

src/org/openscience/cdk/nonotify/NNReaction.java

src/org/openscience/cdk/nonotify/NNReactionSet.java

src/org/openscience/cdk/nonotify/NNRing.java

src/org/openscience/cdk/nonotify/NNRingSet.java

src/org/openscience/cdk/nonotify/NNSingleElectron.java

src/org/openscience/cdk/nonotify/NNStrand.java

src/org/openscience/cdk/nonotify/NoNotificationChemObjectBuilder.java

src/org/openscience/cdk/protein

src/org/openscience/cdk/protein/ProteinPocketFinder.java

src/org/openscience/cdk/protein/data

src/org/openscience/cdk/protein/data/PDBAtom.java

src/org/openscience/cdk/protein/data/PDBMonomer.java

src/org/openscience/cdk/protein/data/PDBPolymer.java

src/org/openscience/cdk/protein/data/PDBStrand.java

src/org/openscience/cdk/protein/data/PDBStructure.java

src/org/openscience/cdk/qsar

src/org/openscience/cdk/qsar/AbstractAtomicDescriptor.java

src/org/openscience/cdk/qsar/AbstractBondDescriptor.java

src/org/openscience/cdk/qsar/ChiIndexUtils.java

src/org/openscience/cdk/qsar/DescriptorEngine.java

src/org/openscience/cdk/qsar/DescriptorException.java

src/org/openscience/cdk/qsar/DescriptorSpecification.java

src/org/openscience/cdk/qsar/DescriptorValue.java

src/org/openscience/cdk/qsar/IAtomPairDescriptor.java

src/org/openscience/cdk/qsar/IAtomicDescriptor.java

src/org/openscience/cdk/qsar/IBondDescriptor.java

src/org/openscience/cdk/qsar/IDescriptor.java

src/org/openscience/cdk/qsar/IMolecularDescriptor.java

src/org/openscience/cdk/qsar/descriptors

src/org/openscience/cdk/qsar/descriptors/atomic

src/org/openscience/cdk/qsar/descriptors/atomic/AtomDegreeDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/AtomValenceDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/BondsToAtomDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/CovalentRadiusDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/DistanceToAtomDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/EffectiveAtomPolarizabilityDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicHardnessDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicSoftnessDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94Descriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargePEOEDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/PeriodicTablePositionDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/PiElectronegativityDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/ProtonTotalPartialChargeDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java

src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java

src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java

src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java

src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java

src/org/openscience/cdk/qsar/descriptors/atomic/SigmaElectronegativityDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atomic/VdWRadiusDescriptor.java

src/org/openscience/cdk/qsar/descriptors/atompair

src/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java

src/org/openscience/cdk/qsar/descriptors/bond

src/org/openscience/cdk/qsar/descriptors/bond/BondPartialPiChargeDescriptor.java

src/org/openscience/cdk/qsar/descriptors/bond/BondPartialSigmaChargeDescriptor.java

src/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptor.java

src/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptor.java

src/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptor.java

src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular

src/org/openscience/cdk/qsar/descriptors/molecular/ALOGP.java

src/org/openscience/cdk/qsar/descriptors/molecular/APolDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/AminoAcidCountDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/AromaticAtomsCountDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/AromaticBondsCountDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/AtomCountDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorCharge.java

src/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorMass.java

src/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorPolarizability.java

src/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/BPolDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/BondCountDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/CPSADescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/CarbonConnectivityOrderOneDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/CarbonConnectivityOrderZeroDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/ChiChainDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/ChiClusterDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/ChiPathClusterDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/ChiPathDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/EccentricConnectivityIndexDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/FragmentComplexityDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/GravitationalIndexDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/HBondDonorCountDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/IPMolecularDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/KappaShapeIndicesDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/LengthOverBreadthDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/LongestAliphaticChainDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/MDEDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/PetitjeanNumberDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/PetitjeanShapeIndexDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/RuleOfFiveDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/TPSADescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/TaeAminoAcidDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/VAdjMaDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/ValenceCarbonConnectivityOrderOneDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/ValenceCarbonConnectivityOrderZeroDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/WHIMDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/WeightDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/WeightedPathDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/WienerNumbersDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java

src/org/openscience/cdk/qsar/descriptors/molecular/ZagrebIndexDescriptor.java

src/org/openscience/cdk/qsar/model

src/org/openscience/cdk/qsar/model/IModel.java

src/org/openscience/cdk/qsar/model/QSARModelException.java

src/org/openscience/cdk/qsar/model/R

src/org/openscience/cdk/qsar/model/R/CNNClassificationModel.java

src/org/openscience/cdk/qsar/model/R/CNNClassificationModelFit.java

src/org/openscience/cdk/qsar/model/R/CNNClassificationModelPredict.java

src/org/openscience/cdk/qsar/model/R/CNNRegressionModel.java

src/org/openscience/cdk/qsar/model/R/CNNRegressionModelFit.java

src/org/openscience/cdk/qsar/model/R/CNNRegressionModelPredict.java

src/org/openscience/cdk/qsar/model/R/CNNRegressionModelSummary.java

src/org/openscience/cdk/qsar/model/R/LinearRegressionModel.java

src/org/openscience/cdk/qsar/model/R/LinearRegressionModelFit.java

src/org/openscience/cdk/qsar/model/R/LinearRegressionModelPredict.java

src/org/openscience/cdk/qsar/model/R/LinearRegressionModelSummary.java

src/org/openscience/cdk/qsar/model/R/PLSRegressionModel.java

src/org/openscience/cdk/qsar/model/R/PLSRegressionModelFit.java

src/org/openscience/cdk/qsar/model/R/PLSRegressionModelPredict.java

src/org/openscience/cdk/qsar/model/R/RModel.java

src/org/openscience/cdk/qsar/model/R2

src/org/openscience/cdk/qsar/model/R2/CNNRegressionModel.java

src/org/openscience/cdk/qsar/model/R2/LinearRegressionModel.java

src/org/openscience/cdk/qsar/model/R2/RModel.java

src/org/openscience/cdk/qsar/model/data

src/org/openscience/cdk/qsar/model/data/cdkSJava.R

src/org/openscience/cdk/qsar/model/data/cnn_3.R

src/org/openscience/cdk/qsar/model/data/cnn_4.R

src/org/openscience/cdk/qsar/model/data/helper.R

src/org/openscience/cdk/qsar/model/data/init_1.R

src/org/openscience/cdk/qsar/model/data/lm_2.R

src/org/openscience/cdk/qsar/model/data/pls_5.R

src/org/openscience/cdk/qsar/model/data/register_999.R

src/org/openscience/cdk/qsar/model/weka

src/org/openscience/cdk/qsar/model/weka/IWekaModel.java

src/org/openscience/cdk/qsar/result

src/org/openscience/cdk/qsar/result/BooleanResult.java

src/org/openscience/cdk/qsar/result/DoubleArrayResult.java

src/org/openscience/cdk/qsar/result/DoubleResult.java

src/org/openscience/cdk/qsar/result/IDescriptorResult.java

src/org/openscience/cdk/qsar/result/IntegerArrayResult.java

src/org/openscience/cdk/qsar/result/IntegerResult.java

src/org/openscience/cdk/reaction

src/org/openscience/cdk/reaction/IReactionProcess.java

src/org/openscience/cdk/reaction/ReactionSpecification.java

src/org/openscience/cdk/reaction/type

src/org/openscience/cdk/reaction/type/BreakingBondReaction.java

src/org/openscience/cdk/reaction/type/CarbonylEliminationReaction.java

src/org/openscience/cdk/reaction/type/CleavageBondMultiReaction.java

src/org/openscience/cdk/reaction/type/CleavageBondReaction.java

src/org/openscience/cdk/reaction/type/DisplacementChargeFromAcceptorReaction.java

src/org/openscience/cdk/reaction/type/DisplacementChargeFromDonorReaction.java

src/org/openscience/cdk/reaction/type/ElectronImpactNBEReaction.java

src/org/openscience/cdk/reaction/type/ElectronImpactPDBReaction.java

src/org/openscience/cdk/reaction/type/HydrogenRearrangementDeltaReaction.java

src/org/openscience/cdk/reaction/type/HydrogenRearrangementGammaReaction.java

src/org/openscience/cdk/reaction/type/HyperconjugationReaction.java

src/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReaction.java

src/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java

src/org/openscience/cdk/reaction/type/RearrangementAnion1Reaction.java

src/org/openscience/cdk/reaction/type/RearrangementAnion2Reaction.java

src/org/openscience/cdk/reaction/type/RearrangementAnion3Reaction.java

src/org/openscience/cdk/reaction/type/RearrangementCation1Reaction.java

src/org/openscience/cdk/reaction/type/RearrangementCation2Reaction.java

src/org/openscience/cdk/reaction/type/RearrangementCation3Reaction.java

src/org/openscience/cdk/reaction/type/RearrangementRadical1Reaction.java

src/org/openscience/cdk/reaction/type/RearrangementRadical2Reaction.java

src/org/openscience/cdk/reaction/type/RearrangementRadical3Reaction.java

src/org/openscience/cdk/renderer

src/org/openscience/cdk/renderer/AbstractRenderer2D.java

src/org/openscience/cdk/renderer/AlphaRenderer2D.java

src/org/openscience/cdk/renderer/Arrow.java

src/org/openscience/cdk/renderer/ArrowRenderer2D.java

src/org/openscience/cdk/renderer/GraphRendererModel.java

src/org/openscience/cdk/renderer/IRenderer2D.java

src/org/openscience/cdk/renderer/ISimpleRenderer2D.java

src/org/openscience/cdk/renderer/Renderer2D.java

src/org/openscience/cdk/renderer/Renderer2DModel.java

src/org/openscience/cdk/renderer/SimpleRenderer2D.java

src/org/openscience/cdk/renderer/color

src/org/openscience/cdk/renderer/color/CDK2DAtomColors.java

src/org/openscience/cdk/renderer/color/CDKAtomColors.java

src/org/openscience/cdk/renderer/color/CPKAtomColors.java

src/org/openscience/cdk/renderer/color/IAtomColorer.java

src/org/openscience/cdk/renderer/color/PartialAtomicChargeColors.java

src/org/openscience/cdk/ringsearch

src/org/openscience/cdk/ringsearch/AllRingsFinder.java

src/org/openscience/cdk/ringsearch/FiguerasSSSRFinder.java

src/org/openscience/cdk/ringsearch/Path.java

src/org/openscience/cdk/ringsearch/Queue.java

src/org/openscience/cdk/ringsearch/RingPartitioner.java

src/org/openscience/cdk/ringsearch/SSSRFinder.java

src/org/openscience/cdk/ringsearch/cyclebasis

src/org/openscience/cdk/ringsearch/cyclebasis/CycleBasis.java

src/org/openscience/cdk/ringsearch/cyclebasis/SimpleCycle.java

src/org/openscience/cdk/ringsearch/cyclebasis/SimpleCycleBasis.java

src/org/openscience/cdk/similarity

src/org/openscience/cdk/similarity/DistanceMoment.java

src/org/openscience/cdk/similarity/Tanimoto.java

src/org/openscience/cdk/smiles

src/org/openscience/cdk/smiles/DeduceBondSystemTool.java

src/org/openscience/cdk/smiles/InterruptableSmilesParser.java

src/org/openscience/cdk/smiles/InvPair.java

src/org/openscience/cdk/smiles/SmilesGenerator.java

src/org/openscience/cdk/smiles/SmilesParser.java

src/org/openscience/cdk/structgen

src/org/openscience/cdk/structgen/IStructureGenerationListener.java

src/org/openscience/cdk/structgen/RandomGenerator.java

src/org/openscience/cdk/structgen/SingleStructureRandomGenerator.java

src/org/openscience/cdk/structgen/VicinitySampler.java

src/org/openscience/cdk/structgen/deterministic

src/org/openscience/cdk/structgen/deterministic/EquivalentClassesDeterministicGenerator.java

src/org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.java

src/org/openscience/cdk/structgen/deterministic/Graph.java

src/org/openscience/cdk/structgen/stochastic

src/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMerger.java

src/org/openscience/cdk/structgen/stochastic/operator

src/org/openscience/cdk/structgen/stochastic/operator/ChemGraph.java

src/org/openscience/cdk/structgen/stochastic/operator/CrossoverMachine.java

src/org/openscience/cdk/templates

src/org/openscience/cdk/templates/AminoAcids.java

src/org/openscience/cdk/templates/MoleculeFactory.java

src/org/openscience/cdk/templates/saturatedhydrocarbons

src/org/openscience/cdk/templates/saturatedhydrocarbons/IsoAlkanes.java

src/org/openscience/cdk/tools

src/org/openscience/cdk/tools/AtomTypeTools.java

src/org/openscience/cdk/tools/AtomicProperties.java

src/org/openscience/cdk/tools/BremserOneSphereHOSECodePredictor.java

src/org/openscience/cdk/tools/CDKUtilities.java

src/org/openscience/cdk/tools/DataFeatures.java

src/org/openscience/cdk/tools/DataFeaturesTool.java

src/org/openscience/cdk/tools/DeAromatizationTool.java

src/org/openscience/cdk/tools/ElementComparator.java

src/org/openscience/cdk/tools/FixedSizeStack.java

src/org/openscience/cdk/tools/FormatStringBuffer.java

src/org/openscience/cdk/tools/GenerateFragments.java

src/org/openscience/cdk/tools/GridGenerator.java

src/org/openscience/cdk/tools/HOSECodeAnalyser.java

src/org/openscience/cdk/tools/HOSECodeGenerator.java

src/org/openscience/cdk/tools/HydrogenAdder.java

src/org/openscience/cdk/tools/IDCreator.java

src/org/openscience/cdk/tools/IDeduceBondOrderTool.java

src/org/openscience/cdk/tools/IValencyChecker.java

src/org/openscience/cdk/tools/IsotopeGenerator.java

src/org/openscience/cdk/tools/LoggingTool.java

src/org/openscience/cdk/tools/LonePairElectronChecker.java

src/org/openscience/cdk/tools/MFAnalyser.java

src/org/openscience/cdk/tools/Normalizer.java

src/org/openscience/cdk/tools/ProteinBuilderTool.java

src/org/openscience/cdk/tools/SaturationChecker.java

src/org/openscience/cdk/tools/SmilesValencyChecker.java

src/org/openscience/cdk/tools/StructureResonanceGenerator.java

src/org/openscience/cdk/tools/SwissArmyKnife.java

src/org/openscience/cdk/tools/ValencyChecker.java

src/org/openscience/cdk/tools/ValencyHybridChecker.java

src/org/openscience/cdk/tools/features

src/org/openscience/cdk/tools/features/MoleculeFeaturesTool.java

src/org/openscience/cdk/tools/manipulator

src/org/openscience/cdk/tools/manipulator/AminoAcidManipulator.java

src/org/openscience/cdk/tools/manipulator/AtomContainerComparator.java

src/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java

src/org/openscience/cdk/tools/manipulator/AtomContainerSetManipulator.java

src/org/openscience/cdk/tools/manipulator/AtomTypeManipulator.java

src/org/openscience/cdk/tools/manipulator/BondManipulator.java

src/org/openscience/cdk/tools/manipulator/ChemFileManipulator.java

src/org/openscience/cdk/tools/manipulator/ChemModelManipulator.java

src/org/openscience/cdk/tools/manipulator/ChemSequenceManipulator.java

src/org/openscience/cdk/tools/manipulator/MoleculeSetManipulator.java

src/org/openscience/cdk/tools/manipulator/ReactionManipulator.java

src/org/openscience/cdk/tools/manipulator/ReactionSetManipulator.java

src/org/openscience/cdk/tools/manipulator/RingSetManipulator.java

src/org/openscience/cdk/tools/manipulator/RingSizeComparator.java

src/org/openscience/cdk/validate

src/org/openscience/cdk/validate/AbstractValidator.java

src/org/openscience/cdk/validate/BasicValidator.java

src/org/openscience/cdk/validate/CDKValidator.java

src/org/openscience/cdk/validate/DictionaryValidator.java

src/org/openscience/cdk/validate/Geometry3DValidator.java

src/org/openscience/cdk/validate/IValidator.java

src/org/openscience/cdk/validate/PDBValidator.java

src/org/openscience/cdk/validate/ProblemMarker.java

src/org/openscience/cdk/validate/ValencyValidator.java

src/org/openscience/cdk/validate/ValidationReport.java

src/org/openscience/cdk/validate/ValidationTest.java

src/org/openscience/cdk/validate/ValidatorEngine.java

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src/org/openscience/cdk/structgen/RandomGenerator.java

/* $Revision: 7717 $ $Author: kaihartmann $ $Date: 2007-01-14 18:07:55 +0100 (Sun, 14 Jan 2007) $

* Contact: cdk-devel@lists.sourceforge.net

* This program is free software; you can redistribute it and/or

* modify it under the terms of the GNU Lesser General Public License

* as published by the Free Software Foundation; either version 2.1

* of the License, or (at your option) any later version.

* All we ask is that proper credit is given for our work, which includes

* - but is not limited to - adding the above copyright notice to the beginning

* of your source code files, and to any copyright notice that you may distribute

* with programs based on this work.

* 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 Lesser General Public License for more details.

* You should have received a copy of the GNU Lesser General Public License

* along with this program; if not, write to the Free Software

* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.

package org.openscience.cdk.structgen;

import org.openscience.cdk.graph.ConnectivityChecker;

import org.openscience.cdk.interfaces.IAtomContainer;

import org.openscience.cdk.interfaces.IMolecule;

import org.openscience.cdk.math.MathTools;

import org.openscience.cdk.tools.LoggingTool;

/**

* RandomGenerator is a generator of Constitutional Isomers. It needs to be

* provided with a starting constitution and it makes random moves in

* constitutional space from there.

* This generator was first suggested by J.-L. Faulon {@cdk.cite FAU96}.

* <p>Unlike the VicinitySampler, this methods does not sample

* the full Faulon vicinity.

* @see org.openscience.cdk.structgen.VicinitySampler

* @cdk.keyword structure generator

public class RandomGenerator {

LoggingTool logger = new LoggingTool(RandomGenerator.class);

private IMolecule proposedStructure = null;

private IMolecule molecule = null;

private IMolecule trial = null;

/**

* Constructs a RandomGenerator with a given starting structure.

* @param molecule The starting structure

public RandomGenerator(IMolecule molecule)

{

setMolecule(molecule);

}

/**

* Proposes a structure which can be accepted or rejected by an external

* entity. If rejected, the structure is not used as a starting point

* for the next random move in structure space.

* @return A proposed molecule

public IMolecule proposeStructure()

{

logger.debug("RandomGenerator->proposeStructure() Start");

{

try {

trial = (IMolecule)molecule.clone();

} catch (CloneNotSupportedException e) {

logger.error("Could not clone IAtomContainer!" + e.getMessage());

trial = null;

}

mutate(trial);

if(logger.isDebugEnabled()) {

String s = "BondCounts: ";

for (int f = 0; f < trial.getAtomCount(); f++) {

s += trial.getConnectedBondsCount(trial.getAtom(f)) + " ";

}

logger.debug(s);

s = "BondOrderSums: ";

for (int f = 0; f < trial.getAtomCount(); f++) {

s += trial.getBondOrderSum(trial.getAtom(f)) + " ";

}

logger.debug(s);

}

while(trial == null || !ConnectivityChecker.isConnected(trial));

proposedStructure = trial;

100

return proposedStructure;

101

}

102

103

/**

104

* Tell the RandomGenerator to accept the last structure that had been proposed.

105

106

public void acceptStructure()

107

{

108

if (proposedStructure != null)

109

{

110

molecule = proposedStructure;

111

}

112

}

113

114

115

/**

116

* Randomly chooses four atoms and alters the bonding

117

* pattern between them according to rules described

118

* in "Faulon, JCICS 1996, 36, 731".

119

120

public void mutate(IAtomContainer ac)

121

{

122

logger.debug("RandomGenerator->mutate() Start");

123

int nrOfAtoms = ac.getAtomCount();

124

int x1 = 0, x2 = 0, y1 = 0, y2 = 0;

125

double a11 = 0, a12 = 0, a22 = 0, a21 = 0;

126

double b11 = 0, lowerborder = 0, upperborder = 0;

127

128

org.openscience.cdk.interfaces.IAtom ax1 = null, ax2 = null, ay1 = null, ay2 = null;

129

org.openscience.cdk.interfaces.IBond b1 = null, b2 = null, b3 = null, b4 = null;

130

int[] choices = new int[3];

131

int choiceCounter = 0;

132

/* We need at least two non-zero bonds in order to be successful */

133

int nonZeroBondsCounter = 0;

134

135

{

136

137

{

138

nonZeroBondsCounter = 0;

139

/* Randomly choose four distinct atoms */

140

141

{

142

// this yields numbers between 0 and (nrOfAtoms - 1)

143

x1 = (int)(Math.random() * nrOfAtoms);

144

x2 = (int)(Math.random() * nrOfAtoms);

145

y1 = (int)(Math.random() * nrOfAtoms);

146

y2 = (int)(Math.random() * nrOfAtoms);

147

logger.debug("RandomGenerator->mutate(): x1, x2, y1, y2: " + x1 + ", " + x2 + ", " + y1 + ", " + y2);

148

}

149

while (!(x1 != x2 && x1 != y1 && x1 != y2 && x2 != y1 && x2 != y2 && y1 != y2));

150

ax1 = ac.getAtom(x1);

151

ay1 = ac.getAtom(y1);

152

ax2 = ac.getAtom(x2);

153

ay2 = ac.getAtom(y2);

154

/* Get four bonds for these four atoms */

155

156

b1 = ac.getBond(ax1, ay1);

157

if (b1 != null)

158

{

159

a11 = b1.getOrder();

160

nonZeroBondsCounter ++;

161

}

162

else

163

{

164

a11 = 0;

165

}

166

167

b2 = ac.getBond(ax1, ay2);

168

if (b2 != null)

169

{

170

a12 = b2.getOrder();

171

nonZeroBondsCounter ++;

172

}

173

else

174

{

175

a12 = 0;

176

}

177

178

b3 = ac.getBond(ax2, ay1);

179

if (b3 != null)

180

{

181

a21 = b3.getOrder();

182

nonZeroBondsCounter ++;

183

}

184

else

185

{

186

a21 = 0;

187

}

188

189

b4 = ac.getBond(ax2, ay2);

190

if (b4 != null)

191

{

192

a22 = b4.getOrder();

193

nonZeroBondsCounter ++;

194

}

195

else

196

{

197

a22 = 0;

198

}

199

logger.debug("RandomGenerator->mutate()->The old bond orders: a11, a12, a21, a22: " + + a11 + ", " + a12 + ", " + a21 + ", " + a22);

200

}while(nonZeroBondsCounter < 2);

201

202

203

/* Compute the range for b11 (see Faulons formulae for details) */

204

double[] cmax = {0, a11 - a22, a11 + a12 - 3, a11 + a21 - 3};

205

double[] cmin = {3, a11 + a12, a11 + a21, a11 - a22 + 3};

206

lowerborder = MathTools.max(cmax);

207

upperborder = MathTools.min(cmin);

208

/* Randomly choose b11 != a11 in the range max > r > min */

209

logger.debug("*** New Try ***");

210

logger.debug("a11 = ", a11);

211

logger.debug("upperborder = ", upperborder);

212

logger.debug("lowerborder = ", lowerborder);

213

choiceCounter = 0;

214

for (double f = lowerborder; f <= upperborder; f++)

215

{

216

if (f != a11)

217

{

218

choices[choiceCounter] = (int)f;

219

choiceCounter ++;

220

}

221

}

222

if (choiceCounter > 0)

223

{

224

b11 = choices[(int)(Math.random() * choiceCounter)];

225

}

226

227

logger.debug("b11 = " + b11);

228

}

229

while (!(b11 != a11 && (b11 >= lowerborder && b11 <= upperborder)));

230

231

double b12 = a11 + a12 - b11;

232

double b21 = a11 + a21 - b11;

233

double b22 = a22 - a11 + b11;

234

235

236

if (b11 > 0)

237

{

238

if (b1 == null)

239

{

240

b1 = ac.getBuilder().newBond(ax1, ay1, b11);

241

ac.addBond(b1);

242

}

243

else

244

{

245

b1.setOrder(b11);

246

}

247

}

248

else if (b1 != null)

249

{

250

ac.removeBond(b1);

251

}

252

253

if (b12 > 0)

254

{

255

if (b2 == null)

256

{

257

b2 = ac.getBuilder().newBond(ax1, ay2, b12);

258

ac.addBond(b2);

259

}

260

else

261

{

262

b2.setOrder(b12);

263

}

264

}

265

else if (b2 != null)

266

{

267

ac.removeBond(b2);

268

}

269

270

if (b21 > 0)

271

{

272

if (b3 == null)

273

{

274

b3 = ac.getBuilder().newBond(ax2, ay1, b21);

275

ac.addBond(b3);

276

}

277

else

278

{

279

b3.setOrder(b21);

280

}

281

}

282

else if (b3 != null)

283

{

284

ac.removeBond(b3);

285

}

286

287

if (b22 > 0)

288

{

289

if (b4 == null)

290

{

291

b4 = ac.getBuilder().newBond(ax2, ay2, b22);

292

ac.addBond(b4);

293

}

294

else

295

{

296

b4.setOrder(b22);

297

}

298

}

299

else if (b4 != null)

300

{

301

ac.removeBond(b4);

302

}

303

304

logger.debug("a11 a12 a21 a22: " + a11 + " " + a12 + " " + a21 + " " + a22);

305

logger.debug("b11 b12 b21 b22: " + b11 + " " + b12 + " " + b21 + " " + b22);

306

}

307

308

309

/**

310

* Assigns a starting structure to this generator.

311

312

* @param molecule a starting structure for this generator

313

314

public void setMolecule(IMolecule molecule)

315

{

316

this.molecule = molecule;

317

}

318

319

320

/**

321

* Returns the molecule which reflects the current state of this

322

* stochastic structure generator.

323

324

* @return The molecule

325

326

public IMolecule getMolecule()

327

{

328

return this.molecule;

329

}

330

331

}

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