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void org::openscience::cdk::tools::LoggingTool::debug ( Object  object  )  [inline]

Shows DEBUG output for the Object. If the object is an instanceof Throwable it will output the trace. Otherwise it will use the toString() method.

Parameters:
object Object to apply toString() too and output

Definition at line 230 of file LoggingTool.java.

Referenced by org::openscience::cdk::templates::AminoAcids::aaBondInfo(), org::openscience::cdk::applications::jchempaint::action::ZoomAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::WebLinkAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ValidateAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::UndoAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ShowChemObjectDumpAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::SaveAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::RedoAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::PerceiveAtomTypesAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::OpenAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ModifyGeneralSettingsAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ModifyDisplaySettingsAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::InsertSmilesAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::FlipAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ExportCompChemAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ExportAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ElementAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::EditDictRefsAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::EditChemObjectPropsAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::EditAtomContainerPropsAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::EditAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::DictionaryAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::CreateSmilesAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::CreateReactionAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::CreateInChIAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::CopyPasteAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ConvertToRadicalAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ConvertToPseudoAtomAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ConvertToAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::CleanupAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ChemAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ChangeIsotopeAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::ChangeAtomSymbolAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::AdjustBondOrdersAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::AddHydrogenAction::actionPerformed(), org::openscience::cdk::debug::DebugStrand::add(), org::openscience::cdk::debug::DebugRingSet::add(), org::openscience::cdk::debug::DebugRing::add(), org::openscience::cdk::debug::DebugPolymer::add(), org::openscience::cdk::debug::DebugMonomer::add(), org::openscience::cdk::debug::DebugMoleculeSet::add(), org::openscience::cdk::debug::DebugMolecule::add(), org::openscience::cdk::debug::DebugCrystal::add(), org::openscience::cdk::debug::DebugBioPolymer::add(), org::openscience::cdk::debug::DebugAtomContainerSet::add(), org::openscience::cdk::debug::DebugAtomContainer::add(), org::openscience::cdk::debug::DebugAminoAcid::add(), org::openscience::cdk::debug::DebugReaction::addAgent(), org::openscience::cdk::debug::DebugStrand::addAtom(), org::openscience::cdk::debug::DebugRing::addAtom(), org::openscience::cdk::debug::DebugPolymer::addAtom(), org::openscience::cdk::debug::DebugMonomer::addAtom(), org::openscience::cdk::debug::DebugMolecule::addAtom(), org::openscience::cdk::debug::DebugCrystal::addAtom(), org::openscience::cdk::debug::DebugBioPolymer::addAtom(), org::openscience::cdk::debug::DebugAtomContainer::addAtom(), org::openscience::cdk::debug::DebugAminoAcid::addAtom(), org::openscience::cdk::debug::DebugMoleculeSet::addAtomContainer(), org::openscience::cdk::debug::DebugAtomContainerSet::addAtomContainer(), org::openscience::cdk::debug::DebugStrand::addAtomParity(), org::openscience::cdk::debug::DebugRing::addAtomParity(), org::openscience::cdk::debug::DebugPolymer::addAtomParity(), org::openscience::cdk::debug::DebugMonomer::addAtomParity(), org::openscience::cdk::debug::DebugMolecule::addAtomParity(), org::openscience::cdk::debug::DebugCrystal::addAtomParity(), org::openscience::cdk::debug::DebugBioPolymer::addAtomParity(), org::openscience::cdk::debug::DebugAtomContainer::addAtomParity(), org::openscience::cdk::debug::DebugAminoAcid::addAtomParity(), org::openscience::cdk::debug::DebugStrand::addBond(), org::openscience::cdk::debug::DebugRing::addBond(), org::openscience::cdk::debug::DebugPolymer::addBond(), org::openscience::cdk::debug::DebugMonomer::addBond(), org::openscience::cdk::debug::DebugMolecule::addBond(), org::openscience::cdk::debug::DebugCrystal::addBond(), org::openscience::cdk::debug::DebugBioPolymer::addBond(), org::openscience::cdk::debug::DebugAtomContainer::addBond(), org::openscience::cdk::debug::DebugAminoAcid::addBond(), org::openscience::cdk::debug::DebugChemSequence::addChemModel(), org::openscience::cdk::debug::DebugChemFile::addChemSequence(), org::openscience::cdk::debug::DebugAminoAcid::addCTerminus(), org::openscience::cdk::debug::DebugStrand::addElectronContainer(), org::openscience::cdk::debug::DebugRing::addElectronContainer(), org::openscience::cdk::debug::DebugPolymer::addElectronContainer(), org::openscience::cdk::debug::DebugMonomer::addElectronContainer(), org::openscience::cdk::debug::DebugMolecule::addElectronContainer(), org::openscience::cdk::debug::DebugCrystal::addElectronContainer(), org::openscience::cdk::debug::DebugBioPolymer::addElectronContainer(), org::openscience::cdk::debug::DebugAtomContainer::addElectronContainer(), org::openscience::cdk::debug::DebugAminoAcid::addElectronContainer(), org::openscience::cdk::tools::HydrogenAdder::addExplicitHydrogensToSatisfyValency(), org::openscience::cdk::tools::HydrogenAdder::addHydrogensToSatisfyValency(), org::openscience::cdk::applications::jchempaint::action::AddHydrogenAction::addHydrogenToAllAtoms(), org::openscience::cdk::applications::jchempaint::action::AddHydrogenAction::addHydrogenToAllMolecules(), org::openscience::cdk::applications::jchempaint::action::AddHydrogenAction::addHydrogenToOneAtom(), org::openscience::cdk::debug::DebugStrand::addListener(), org::openscience::cdk::debug::DebugSingleElectron::addListener(), org::openscience::cdk::debug::DebugRing::addListener(), org::openscience::cdk::debug::DebugReactionSet::addListener(), org::openscience::cdk::debug::DebugReaction::addListener(), org::openscience::cdk::debug::DebugPseudoAtom::addListener(), org::openscience::cdk::debug::DebugPolymer::addListener(), org::openscience::cdk::debug::DebugMonomer::addListener(), org::openscience::cdk::debug::DebugMoleculeSet::addListener(), org::openscience::cdk::debug::DebugMolecule::addListener(), org::openscience::cdk::debug::DebugMapping::addListener(), org::openscience::cdk::debug::DebugLonePair::addListener(), org::openscience::cdk::debug::DebugIsotope::addListener(), org::openscience::cdk::debug::DebugElement::addListener(), org::openscience::cdk::debug::DebugElectronContainer::addListener(), org::openscience::cdk::debug::DebugCrystal::addListener(), org::openscience::cdk::debug::DebugChemSequence::addListener(), org::openscience::cdk::debug::DebugChemObject::addListener(), org::openscience::cdk::debug::DebugChemModel::addListener(), org::openscience::cdk::debug::DebugChemFile::addListener(), org::openscience::cdk::debug::DebugBond::addListener(), org::openscience::cdk::debug::DebugBioPolymer::addListener(), org::openscience::cdk::debug::DebugAtomType::addListener(), org::openscience::cdk::debug::DebugAtomParity::addListener(), org::openscience::cdk::debug::DebugAtomContainerSet::addListener(), org::openscience::cdk::debug::DebugAtomContainer::addListener(), org::openscience::cdk::debug::DebugAtom::addListener(), org::openscience::cdk::debug::DebugAminoAcid::addListener(), org::openscience::cdk::debug::DebugStrand::addLonePair(), org::openscience::cdk::debug::DebugRing::addLonePair(), org::openscience::cdk::debug::DebugPolymer::addLonePair(), org::openscience::cdk::debug::DebugMonomer::addLonePair(), org::openscience::cdk::debug::DebugMolecule::addLonePair(), org::openscience::cdk::debug::DebugCrystal::addLonePair(), org::openscience::cdk::debug::DebugBioPolymer::addLonePair(), org::openscience::cdk::debug::DebugAtomContainer::addLonePair(), org::openscience::cdk::debug::DebugAminoAcid::addLonePair(), org::openscience::cdk::debug::DebugMoleculeSet::addMolecule(), org::openscience::cdk::debug::DebugAminoAcid::addNTerminus(), org::openscience::cdk::debug::DebugReaction::addProduct(), org::openscience::cdk::debug::DebugReaction::addReactant(), org::openscience::cdk::debug::DebugReactionSet::addReaction(), org::openscience::cdk::debug::DebugStrand::addSingleElectron(), org::openscience::cdk::debug::DebugRing::addSingleElectron(), org::openscience::cdk::debug::DebugPolymer::addSingleElectron(), org::openscience::cdk::debug::DebugMonomer::addSingleElectron(), org::openscience::cdk::debug::DebugMolecule::addSingleElectron(), org::openscience::cdk::debug::DebugCrystal::addSingleElectron(), org::openscience::cdk::debug::DebugBioPolymer::addSingleElectron(), org::openscience::cdk::debug::DebugAtomContainer::addSingleElectron(), org::openscience::cdk::debug::DebugAminoAcid::addSingleElectron(), org::openscience::cdk::debug::DebugPDBPolymer::addStructure(), org::openscience::cdk::layout::StructureDiagramGenerator::allPlaced(), org::openscience::cdk::tools::LonePairElectronChecker::allSaturated(), org::openscience::cdk::structgen::deterministic::GENMDeterministicGenerator::analyseMolecularFormula(), org::openscience::cdk::layout::OverlapResolver::areIntersected(), org::openscience::cdk::tools::AtomTypeTools::assignAtomTypePropertiesToAtom(), org::openscience::cdk::debug::DebugMoleculeSet::atomContainers(), org::openscience::cdk::debug::DebugAtomContainerSet::atomContainers(), org::openscience::cdk::debug::DebugStrand::atoms(), org::openscience::cdk::debug::DebugRing::atoms(), org::openscience::cdk::debug::DebugPolymer::atoms(), org::openscience::cdk::debug::DebugMonomer::atoms(), org::openscience::cdk::debug::DebugMolecule::atoms(), org::openscience::cdk::debug::DebugCrystal::atoms(), org::openscience::cdk::debug::DebugBond::atoms(), org::openscience::cdk::debug::DebugBioPolymer::atoms(), org::openscience::cdk::debug::DebugAtomContainer::atoms(), org::openscience::cdk::debug::DebugAminoAcid::atoms(), org::openscience::cdk::debug::DebugStrand::bonds(), org::openscience::cdk::debug::DebugRing::bonds(), org::openscience::cdk::debug::DebugPolymer::bonds(), org::openscience::cdk::debug::DebugMonomer::bonds(), org::openscience::cdk::debug::DebugMolecule::bonds(), org::openscience::cdk::debug::DebugCrystal::bonds(), org::openscience::cdk::debug::DebugBioPolymer::bonds(), org::openscience::cdk::debug::DebugAtomContainer::bonds(), org::openscience::cdk::debug::DebugAminoAcid::bonds(), org::openscience::cdk::layout::AtomPlacer::breadthFirstSearch(), org::openscience::cdk::modeling::forcefield::LineSearch::brentsMethod(), org::openscience::cdk::qsar::model::R2::LinearRegressionModel::build(), org::openscience::cdk::qsar::descriptors::molecular::WHIMDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::ValenceCarbonConnectivityOrderZeroDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::ValenceCarbonConnectivityOrderOneDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::TaeAminoAcidDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::MomentOfInertiaDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::MDEDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::LengthOverBreadthDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::GravitationalIndexDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::CPSADescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::BPolDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::BCUTDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::APolDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::VdWRadiusDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::InductiveAtomicSoftnessDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::InductiveAtomicHardnessDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::CovalentRadiusDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::AtomHybridizationVSEPRDescriptor::calculate(), org::openscience::cdk::geometry::RDFCalculator::calculate(), org::openscience::cdk::charges::Polarizability::calculateBondPolarizability(), org::openscience::cdk::math::qm::ClosedShellJob::calculateD(), org::openscience::cdk::charges::Polarizability::calculateGHEffectiveAtomPolarizability(), org::openscience::cdk::charges::Polarizability::calculateKJMeanMolecularPolarizability(), org::openscience::cdk::tools::ValencyHybridChecker::calculateNumberOfImplicitHydrogens(), org::openscience::cdk::tools::ValencyChecker::calculateNumberOfImplicitHydrogens(), org::openscience::cdk::tools::SmilesValencyChecker::calculateNumberOfImplicitHydrogens(), org::openscience::cdk::tools::SaturationChecker::calculateNumberOfImplicitHydrogens(), org::openscience::cdk::io::inchi::INChIHandler::characters(), org::openscience::cdk::io::cml::CMLHandler::characters(), org::openscience::cdk::ringsearch::FiguerasSSSRFinder::checkEdges(), org::openscience::cdk::debug::DebugChemSequence::chemModels(), org::openscience::cdk::debug::DebugChemFile::chemSequences(), org::openscience::cdk::PeriodicTableElement::clone(), org::openscience::cdk::debug::DebugStrand::clone(), org::openscience::cdk::debug::DebugSingleElectron::clone(), org::openscience::cdk::debug::DebugRing::clone(), org::openscience::cdk::debug::DebugReactionSet::clone(), org::openscience::cdk::debug::DebugReaction::clone(), org::openscience::cdk::debug::DebugPseudoAtom::clone(), org::openscience::cdk::debug::DebugPolymer::clone(), org::openscience::cdk::debug::DebugMonomer::clone(), org::openscience::cdk::debug::DebugMoleculeSet::clone(), org::openscience::cdk::debug::DebugMolecule::clone(), org::openscience::cdk::debug::DebugMapping::clone(), org::openscience::cdk::debug::DebugLonePair::clone(), org::openscience::cdk::debug::DebugIsotope::clone(), org::openscience::cdk::debug::DebugElement::clone(), org::openscience::cdk::debug::DebugElectronContainer::clone(), org::openscience::cdk::debug::DebugCrystal::clone(), org::openscience::cdk::debug::DebugChemSequence::clone(), org::openscience::cdk::debug::DebugChemObject::clone(), org::openscience::cdk::debug::DebugChemModel::clone(), org::openscience::cdk::debug::DebugChemFile::clone(), org::openscience::cdk::debug::DebugBond::clone(), org::openscience::cdk::debug::DebugBioPolymer::clone(), org::openscience::cdk::debug::DebugAtomType::clone(), org::openscience::cdk::debug::DebugAtomParity::clone(), org::openscience::cdk::debug::DebugAtomContainerSet::clone(), org::openscience::cdk::debug::DebugAtomContainer::clone(), org::openscience::cdk::debug::DebugAtom::clone(), org::openscience::cdk::debug::DebugAminoAcid::clone(), org::openscience::cdk::debug::DebugBond::compare(), org::openscience::cdk::config::AtomTypeFactory::configure(), configureLog4j(), org::openscience::cdk::debug::DebugStrand::contains(), org::openscience::cdk::debug::DebugSingleElectron::contains(), org::openscience::cdk::debug::DebugRingSet::contains(), org::openscience::cdk::debug::DebugRing::contains(), org::openscience::cdk::debug::DebugPolymer::contains(), org::openscience::cdk::debug::DebugMonomer::contains(), org::openscience::cdk::debug::DebugMolecule::contains(), org::openscience::cdk::debug::DebugLonePair::contains(), org::openscience::cdk::debug::DebugCrystal::contains(), org::openscience::cdk::debug::DebugBond::contains(), org::openscience::cdk::debug::DebugBioPolymer::contains(), org::openscience::cdk::debug::DebugAtomContainer::contains(), org::openscience::cdk::debug::DebugAminoAcid::contains(), org::openscience::cdk::applications::FileConvertor::convert(), org::openscience::cdk::tools::ValencyHybridChecker::couldMatchAtomType(), org::openscience::cdk::tools::ValencyChecker::couldMatchAtomType(), org::openscience::cdk::tools::SmilesValencyChecker::couldMatchAtomType(), org::openscience::cdk::tools::SaturationChecker::couldMatchAtomType(), org::openscience::cdk::templates::AminoAcids::createAAs(), org::openscience::cdk::applications::jchempaint::JChemPaintMenuBar::createMenu(), org::openscience::cdk::applications::jchempaint::JChemPaintPopupMenu::createMenuItem(), org::openscience::cdk::applications::jchempaint::JChemPaintMenuBar::createMenuItem(), org::openscience::cdk::tools::ProteinBuilderTool::createProtein(), org::openscience::cdk::io::ReaderFactory::createReader(), org::openscience::cdk::applications::jchempaint::ToolBarMaker::createToolbarButton(), org::openscience::cdk::io::WriterFactory::createWriter(), org::openscience::cdk::modeling::forcefield::LineSearch::dbrentsMethod(), org::openscience::cdk::qsar::DescriptorEngine::DescriptorEngine(), org::openscience::cdk::aromaticity::HueckelAromaticityDetector::detectAromaticity(), org::openscience::cdk::ringsearch::AllRingsFinder::detectRings(), org::openscience::cdk::layout::OverlapResolver::displace(), org::openscience::cdk::graph::invariant::HuLuIndexTool::displayArray(), org::openscience::cdk::graph::invariant::HuLuIndexTool::displayMatrix(), org::openscience::cdk::layout::AtomPlacer::distributePartners(), org::openscience::cdk::ringsearch::AllRingsFinder::doSearch(), org::openscience::cdk::controller::AbstractController2D::drawProposedBond(), dumpClasspath(), dumpSystemProperties(), org::openscience::cdk::debug::DebugStrand::electronContainers(), org::openscience::cdk::debug::DebugRing::electronContainers(), org::openscience::cdk::debug::DebugPolymer::electronContainers(), org::openscience::cdk::debug::DebugMonomer::electronContainers(), org::openscience::cdk::debug::DebugMolecule::electronContainers(), org::openscience::cdk::debug::DebugCrystal::electronContainers(), org::openscience::cdk::debug::DebugBioPolymer::electronContainers(), org::openscience::cdk::debug::DebugAtomContainer::electronContainers(), org::openscience::cdk::debug::DebugAminoAcid::electronContainers(), org::openscience::cdk::config::ElementPTFactory::ElementPTFactory(), org::openscience::cdk::io::iterator::event::EventCMLHandler::endDocument(), org::openscience::cdk::io::iterator::event::EventCMLHandler::endObject(), org::openscience::cdk::tools::StructureResonanceGenerator::existAC(), org::openscience::cdk::tools::HOSECodeGenerator::fillUpSphereDelimiters(), org::openscience::cdk::atomtype::ValencyMatcher::findMatchingAtomType(), org::openscience::cdk::atomtype::StructGenMatcher::findMatchingAtomType(), org::openscience::cdk::atomtype::MMFF94AtomTypeMatcher::findMatchingAtomType(), org::openscience::cdk::atomtype::MM2AtomTypeMatcher::findMatchingAtomType(), org::openscience::cdk::atomtype::HybridizationStateATMatcher::findMatchingAtomType(), org::openscience::cdk::atomtype::HybridizationMatcher::findMatchingAtomType(), org::openscience::cdk::ringsearch::FiguerasSSSRFinder::findSSSR(), org::openscience::cdk::structgen::SingleStructureRandomGenerator::generate(), org::openscience::cdk::structgen::deterministic::GENMDeterministicGenerator::generate(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::generate3DCoordinates(), org::openscience::cdk::structgen::deterministic::GENMDeterministicGenerator::generateBasicFragments(), org::openscience::cdk::structgen::deterministic::GENMDeterministicGenerator::generateBasicUnits(), org::openscience::cdk::layout::StructureDiagramGenerator::generateCoordinates(), org::openscience::cdk::structgen::deterministic::GENMDeterministicGenerator::GENMDeterministicGenerator(), org::openscience::cdk::debug::DebugBond::get2DCenter(), org::openscience::cdk::debug::DebugBond::get3DCenter(), org::openscience::cdk::debug::DebugCrystal::getA(), org::openscience::cdk::applications::jchempaint::action::JCPAction::getAction(), org::openscience::cdk::debug::DebugReaction::getAgents(), org::openscience::cdk::config::AtomTypeFactory::getAllAtomTypes(), org::openscience::cdk::tools::StructureResonanceGenerator::getAllStructures(), org::openscience::cdk::debug::DebugPDBAtom::getAltLoc(), org::openscience::cdk::debug::DebugStrand::getAtom(), org::openscience::cdk::debug::DebugSingleElectron::getAtom(), org::openscience::cdk::debug::DebugRing::getAtom(), org::openscience::cdk::debug::DebugPolymer::getAtom(), org::openscience::cdk::debug::DebugMonomer::getAtom(), org::openscience::cdk::debug::DebugMolecule::getAtom(), org::openscience::cdk::debug::DebugLonePair::getAtom(), org::openscience::cdk::debug::DebugCrystal::getAtom(), org::openscience::cdk::debug::DebugBond::getAtom(), org::openscience::cdk::debug::DebugBioPolymer::getAtom(), org::openscience::cdk::debug::DebugAtomParity::getAtom(), org::openscience::cdk::debug::DebugAtomContainer::getAtom(), org::openscience::cdk::debug::DebugAminoAcid::getAtom(), org::openscience::cdk::debug::DebugMoleculeSet::getAtomContainer(), org::openscience::cdk::debug::DebugAtomContainerSet::getAtomContainer(), org::openscience::cdk::debug::DebugMoleculeSet::getAtomContainerCount(), org::openscience::cdk::debug::DebugAtomContainerSet::getAtomContainerCount(), org::openscience::cdk::debug::DebugStrand::getAtomCount(), org::openscience::cdk::debug::DebugRing::getAtomCount(), org::openscience::cdk::debug::DebugPolymer::getAtomCount(), org::openscience::cdk::debug::DebugMonomer::getAtomCount(), org::openscience::cdk::debug::DebugMolecule::getAtomCount(), org::openscience::cdk::debug::DebugCrystal::getAtomCount(), org::openscience::cdk::debug::DebugBond::getAtomCount(), org::openscience::cdk::debug::DebugBioPolymer::getAtomCount(), org::openscience::cdk::debug::DebugAtomContainer::getAtomCount(), org::openscience::cdk::debug::DebugAminoAcid::getAtomCount(), org::openscience::cdk::charges::InductivePartialCharges::getAtomicChargeIncrement(), org::openscience::cdk::debug::DebugPseudoAtom::getAtomicNumber(), org::openscience::cdk::debug::DebugIsotope::getAtomicNumber(), org::openscience::cdk::debug::DebugElement::getAtomicNumber(), org::openscience::cdk::debug::DebugAtomType::getAtomicNumber(), org::openscience::cdk::debug::DebugAtom::getAtomicNumber(), org::openscience::cdk::charges::InductivePartialCharges::getAtomicSoftnessCore(), org::openscience::cdk::debug::DebugStrand::getAtomNumber(), org::openscience::cdk::debug::DebugRing::getAtomNumber(), org::openscience::cdk::debug::DebugPolymer::getAtomNumber(), org::openscience::cdk::debug::DebugMonomer::getAtomNumber(), org::openscience::cdk::debug::DebugMolecule::getAtomNumber(), org::openscience::cdk::debug::DebugCrystal::getAtomNumber(), org::openscience::cdk::debug::DebugBioPolymer::getAtomNumber(), org::openscience::cdk::debug::DebugAtomContainer::getAtomNumber(), org::openscience::cdk::debug::DebugAminoAcid::getAtomNumber(), org::openscience::cdk::layout::OverlapResolver::getAtomOverlapScore(), org::openscience::cdk::debug::DebugStrand::getAtomParity(), org::openscience::cdk::debug::DebugRing::getAtomParity(), org::openscience::cdk::debug::DebugPolymer::getAtomParity(), org::openscience::cdk::debug::DebugMonomer::getAtomParity(), org::openscience::cdk::debug::DebugMolecule::getAtomParity(), org::openscience::cdk::debug::DebugCrystal::getAtomParity(), org::openscience::cdk::debug::DebugBioPolymer::getAtomParity(), org::openscience::cdk::debug::DebugAtomContainer::getAtomParity(), org::openscience::cdk::debug::DebugAminoAcid::getAtomParity(), org::openscience::cdk::tools::ValencyChecker::getAtomTypeFactory(), org::openscience::cdk::tools::SaturationChecker::getAtomTypeFactory(), org::openscience::cdk::tools::LonePairElectronChecker::getAtomTypeFactory(), org::openscience::cdk::debug::DebugPseudoAtom::getAtomTypeName(), org::openscience::cdk::debug::DebugAtomType::getAtomTypeName(), org::openscience::cdk::debug::DebugAtom::getAtomTypeName(), org::openscience::cdk::config::AtomTypeFactory::getAtomTypes(), org::openscience::cdk::debug::DebugCrystal::getB(), org::openscience::cdk::debug::DebugStrand::getBond(), org::openscience::cdk::debug::DebugRing::getBond(), org::openscience::cdk::debug::DebugPolymer::getBond(), org::openscience::cdk::debug::DebugMonomer::getBond(), org::openscience::cdk::debug::DebugMolecule::getBond(), org::openscience::cdk::debug::DebugCrystal::getBond(), org::openscience::cdk::debug::DebugBioPolymer::getBond(), org::openscience::cdk::debug::DebugAtomContainer::getBond(), org::openscience::cdk::debug::DebugAminoAcid::getBond(), org::openscience::cdk::debug::DebugStrand::getBondCount(), org::openscience::cdk::debug::DebugRing::getBondCount(), org::openscience::cdk::debug::DebugPolymer::getBondCount(), org::openscience::cdk::debug::DebugMonomer::getBondCount(), org::openscience::cdk::debug::DebugMolecule::getBondCount(), org::openscience::cdk::debug::DebugCrystal::getBondCount(), org::openscience::cdk::debug::DebugBioPolymer::getBondCount(), org::openscience::cdk::debug::DebugAtomContainer::getBondCount(), org::openscience::cdk::debug::DebugAminoAcid::getBondCount(), org::openscience::cdk::debug::DebugStrand::getBondNumber(), org::openscience::cdk::debug::DebugRing::getBondNumber(), org::openscience::cdk::debug::DebugPolymer::getBondNumber(), org::openscience::cdk::debug::DebugMonomer::getBondNumber(), org::openscience::cdk::debug::DebugMolecule::getBondNumber(), org::openscience::cdk::debug::DebugCrystal::getBondNumber(), org::openscience::cdk::debug::DebugBioPolymer::getBondNumber(), org::openscience::cdk::debug::DebugAtomContainer::getBondNumber(), org::openscience::cdk::debug::DebugAminoAcid::getBondNumber(), org::openscience::cdk::debug::DebugStrand::getBondOrderSum(), org::openscience::cdk::debug::DebugRing::getBondOrderSum(), org::openscience::cdk::debug::DebugPseudoAtom::getBondOrderSum(), org::openscience::cdk::debug::DebugPolymer::getBondOrderSum(), org::openscience::cdk::debug::DebugMonomer::getBondOrderSum(), org::openscience::cdk::debug::DebugMolecule::getBondOrderSum(), org::openscience::cdk::debug::DebugCrystal::getBondOrderSum(), org::openscience::cdk::debug::DebugBioPolymer::getBondOrderSum(), org::openscience::cdk::debug::DebugAtomType::getBondOrderSum(), org::openscience::cdk::debug::DebugAtomContainer::getBondOrderSum(), org::openscience::cdk::debug::DebugAtom::getBondOrderSum(), org::openscience::cdk::debug::DebugAminoAcid::getBondOrderSum(), org::openscience::cdk::debug::DebugCrystal::getC(), org::openscience::cdk::debug::DebugPDBMonomer::getChainID(), org::openscience::cdk::debug::DebugPDBAtom::getChainID(), org::openscience::cdk::debug::DebugPseudoAtom::getCharge(), org::openscience::cdk::debug::DebugAtom::getCharge(), org::openscience::cdk::debug::DebugChemSequence::getChemModel(), org::openscience::cdk::debug::DebugChemSequence::getChemModelCount(), org::openscience::cdk::debug::DebugMapping::getChemObject(), org::openscience::cdk::debug::DebugChemFile::getChemSequence(), org::openscience::cdk::debug::DebugChemFile::getChemSequenceCount(), org::openscience::cdk::io::cml::CMLResolver::getCMLType(), org::openscience::cdk::debug::DebugBond::getConnectedAtom(), org::openscience::cdk::debug::DebugStrand::getConnectedAtomsCount(), org::openscience::cdk::debug::DebugRing::getConnectedAtomsCount(), org::openscience::cdk::debug::DebugPolymer::getConnectedAtomsCount(), org::openscience::cdk::debug::DebugMonomer::getConnectedAtomsCount(), org::openscience::cdk::debug::DebugMolecule::getConnectedAtomsCount(), org::openscience::cdk::debug::DebugCrystal::getConnectedAtomsCount(), org::openscience::cdk::debug::DebugBioPolymer::getConnectedAtomsCount(), org::openscience::cdk::debug::DebugAtomContainer::getConnectedAtomsCount(), org::openscience::cdk::debug::DebugAminoAcid::getConnectedAtomsCount(), org::openscience::cdk::debug::DebugStrand::getConnectedAtomsList(), org::openscience::cdk::debug::DebugRing::getConnectedAtomsList(), org::openscience::cdk::debug::DebugPolymer::getConnectedAtomsList(), org::openscience::cdk::debug::DebugMonomer::getConnectedAtomsList(), org::openscience::cdk::debug::DebugMolecule::getConnectedAtomsList(), org::openscience::cdk::debug::DebugCrystal::getConnectedAtomsList(), org::openscience::cdk::debug::DebugBioPolymer::getConnectedAtomsList(), org::openscience::cdk::debug::DebugAtomContainer::getConnectedAtomsList(), org::openscience::cdk::debug::DebugAminoAcid::getConnectedAtomsList(), org::openscience::cdk::debug::DebugStrand::getConnectedBondsCount(), org::openscience::cdk::debug::DebugRing::getConnectedBondsCount(), org::openscience::cdk::debug::DebugPolymer::getConnectedBondsCount(), org::openscience::cdk::debug::DebugMonomer::getConnectedBondsCount(), org::openscience::cdk::debug::DebugMolecule::getConnectedBondsCount(), org::openscience::cdk::debug::DebugCrystal::getConnectedBondsCount(), org::openscience::cdk::debug::DebugBioPolymer::getConnectedBondsCount(), org::openscience::cdk::debug::DebugAtomContainer::getConnectedBondsCount(), org::openscience::cdk::debug::DebugAminoAcid::getConnectedBondsCount(), org::openscience::cdk::debug::DebugStrand::getConnectedBondsList(), org::openscience::cdk::debug::DebugRing::getConnectedBondsList(), org::openscience::cdk::debug::DebugPolymer::getConnectedBondsList(), org::openscience::cdk::debug::DebugMonomer::getConnectedBondsList(), org::openscience::cdk::debug::DebugMolecule::getConnectedBondsList(), org::openscience::cdk::debug::DebugCrystal::getConnectedBondsList(), org::openscience::cdk::debug::DebugBioPolymer::getConnectedBondsList(), org::openscience::cdk::debug::DebugAtomContainer::getConnectedBondsList(), org::openscience::cdk::debug::DebugAminoAcid::getConnectedBondsList(), org::openscience::cdk::debug::DebugStrand::getConnectedElectronContainersList(), org::openscience::cdk::debug::DebugRing::getConnectedElectronContainersList(), org::openscience::cdk::debug::DebugPolymer::getConnectedElectronContainersList(), org::openscience::cdk::debug::DebugMonomer::getConnectedElectronContainersList(), org::openscience::cdk::debug::DebugMolecule::getConnectedElectronContainersList(), org::openscience::cdk::debug::DebugCrystal::getConnectedElectronContainersList(), org::openscience::cdk::debug::DebugBioPolymer::getConnectedElectronContainersList(), org::openscience::cdk::debug::DebugAtomContainer::getConnectedElectronContainersList(), org::openscience::cdk::debug::DebugAminoAcid::getConnectedElectronContainersList(), org::openscience::cdk::debug::DebugStrand::getConnectedLonePairsCount(), org::openscience::cdk::debug::DebugRing::getConnectedLonePairsCount(), org::openscience::cdk::debug::DebugPolymer::getConnectedLonePairsCount(), org::openscience::cdk::debug::DebugMonomer::getConnectedLonePairsCount(), org::openscience::cdk::debug::DebugMolecule::getConnectedLonePairsCount(), org::openscience::cdk::debug::DebugCrystal::getConnectedLonePairsCount(), org::openscience::cdk::debug::DebugBioPolymer::getConnectedLonePairsCount(), org::openscience::cdk::debug::DebugAtomContainer::getConnectedLonePairsCount(), org::openscience::cdk::debug::DebugAminoAcid::getConnectedLonePairsCount(), org::openscience::cdk::debug::DebugStrand::getConnectedLonePairsList(), org::openscience::cdk::debug::DebugRing::getConnectedLonePairsList(), org::openscience::cdk::debug::DebugPolymer::getConnectedLonePairsList(), org::openscience::cdk::debug::DebugMonomer::getConnectedLonePairsList(), org::openscience::cdk::debug::DebugMolecule::getConnectedLonePairsList(), org::openscience::cdk::debug::DebugCrystal::getConnectedLonePairsList(), org::openscience::cdk::debug::DebugBioPolymer::getConnectedLonePairsList(), org::openscience::cdk::debug::DebugAtomContainer::getConnectedLonePairsList(), org::openscience::cdk::debug::DebugAminoAcid::getConnectedLonePairsList(), org::openscience::cdk::debug::DebugRingSet::getConnectedRings(), org::openscience::cdk::debug::DebugStrand::getConnectedSingleElectronsCount(), org::openscience::cdk::debug::DebugRing::getConnectedSingleElectronsCount(), org::openscience::cdk::debug::DebugPolymer::getConnectedSingleElectronsCount(), org::openscience::cdk::debug::DebugMonomer::getConnectedSingleElectronsCount(), org::openscience::cdk::debug::DebugMolecule::getConnectedSingleElectronsCount(), org::openscience::cdk::debug::DebugCrystal::getConnectedSingleElectronsCount(), org::openscience::cdk::debug::DebugBioPolymer::getConnectedSingleElectronsCount(), org::openscience::cdk::debug::DebugAtomContainer::getConnectedSingleElectronsCount(), org::openscience::cdk::debug::DebugAminoAcid::getConnectedSingleElectronsCount(), org::openscience::cdk::debug::DebugStrand::getConnectedSingleElectronsList(), org::openscience::cdk::debug::DebugRing::getConnectedSingleElectronsList(), org::openscience::cdk::debug::DebugPolymer::getConnectedSingleElectronsList(), org::openscience::cdk::debug::DebugMonomer::getConnectedSingleElectronsList(), org::openscience::cdk::debug::DebugMolecule::getConnectedSingleElectronsList(), org::openscience::cdk::debug::DebugCrystal::getConnectedSingleElectronsList(), org::openscience::cdk::debug::DebugBioPolymer::getConnectedSingleElectronsList(), org::openscience::cdk::debug::DebugAtomContainer::getConnectedSingleElectronsList(), org::openscience::cdk::debug::DebugAminoAcid::getConnectedSingleElectronsList(), org::openscience::cdk::controller::AbstractController2D::getContainedAtoms(), org::openscience::cdk::debug::DebugPseudoAtom::getCovalentRadius(), org::openscience::cdk::debug::DebugAtomType::getCovalentRadius(), org::openscience::cdk::debug::DebugAtom::getCovalentRadius(), org::openscience::cdk::debug::DebugChemModel::getCrystal(), org::openscience::cdk::debug::DebugAminoAcid::getCTerminus(), org::openscience::cdk::qsar::DescriptorEngine::getDescriptorClassNameByInterface(), org::openscience::cdk::qsar::DescriptorEngine::getDescriptorClassNameByPackage(), org::openscience::cdk::applications::jchempaint::JChemPaintEditorPanel::getDictionaryDatabase(), org::openscience::cdk::qsar::DescriptorEngine::getDictionaryType(), org::openscience::cdk::debug::DebugReaction::getDirection(), org::openscience::cdk::graph::invariant::HuLuIndexTool::getEAIDNumber(), org::openscience::cdk::debug::DebugStrand::getElectronContainer(), org::openscience::cdk::debug::DebugRing::getElectronContainer(), org::openscience::cdk::debug::DebugPolymer::getElectronContainer(), org::openscience::cdk::debug::DebugMonomer::getElectronContainer(), org::openscience::cdk::debug::DebugMolecule::getElectronContainer(), org::openscience::cdk::debug::DebugCrystal::getElectronContainer(), org::openscience::cdk::debug::DebugBioPolymer::getElectronContainer(), org::openscience::cdk::debug::DebugAtomContainer::getElectronContainer(), org::openscience::cdk::debug::DebugAminoAcid::getElectronContainer(), org::openscience::cdk::debug::DebugStrand::getElectronContainerCount(), org::openscience::cdk::debug::DebugRing::getElectronContainerCount(), org::openscience::cdk::debug::DebugPolymer::getElectronContainerCount(), org::openscience::cdk::debug::DebugMonomer::getElectronContainerCount(), org::openscience::cdk::debug::DebugMolecule::getElectronContainerCount(), org::openscience::cdk::debug::DebugCrystal::getElectronContainerCount(), org::openscience::cdk::debug::DebugBioPolymer::getElectronContainerCount(), org::openscience::cdk::debug::DebugAtomContainer::getElectronContainerCount(), org::openscience::cdk::debug::DebugAminoAcid::getElectronContainerCount(), org::openscience::cdk::debug::DebugSingleElectron::getElectronCount(), org::openscience::cdk::debug::DebugLonePair::getElectronCount(), org::openscience::cdk::debug::DebugElectronContainer::getElectronCount(), org::openscience::cdk::debug::DebugBond::getElectronCount(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::getElectrostaticPotentialN(), org::openscience::cdk::config::ElementPTFactory::getElement(), org::openscience::cdk::debug::DebugPDBStructure::getEndChainID(), org::openscience::cdk::debug::DebugPDBStructure::getEndInsertionCode(), org::openscience::cdk::debug::DebugPDBStructure::getEndSequenceNumber(), org::openscience::cdk::debug::DebugPseudoAtom::getExactMass(), org::openscience::cdk::debug::DebugIsotope::getExactMass(), org::openscience::cdk::debug::DebugAtomType::getExactMass(), org::openscience::cdk::debug::DebugAtom::getExactMass(), org::openscience::cdk::fingerprint::Fingerprinter::getFingerprint(), org::openscience::cdk::debug::DebugStrand::getFirstAtom(), org::openscience::cdk::debug::DebugRing::getFirstAtom(), org::openscience::cdk::debug::DebugPolymer::getFirstAtom(), org::openscience::cdk::debug::DebugMonomer::getFirstAtom(), org::openscience::cdk::debug::DebugMolecule::getFirstAtom(), org::openscience::cdk::debug::DebugCrystal::getFirstAtom(), org::openscience::cdk::debug::DebugBioPolymer::getFirstAtom(), org::openscience::cdk::debug::DebugAtomContainer::getFirstAtom(), org::openscience::cdk::debug::DebugAminoAcid::getFirstAtom(), org::openscience::cdk::debug::DebugStrand::getFlag(), org::openscience::cdk::debug::DebugSingleElectron::getFlag(), org::openscience::cdk::debug::DebugRing::getFlag(), org::openscience::cdk::debug::DebugReactionSet::getFlag(), org::openscience::cdk::debug::DebugReaction::getFlag(), org::openscience::cdk::debug::DebugPseudoAtom::getFlag(), org::openscience::cdk::debug::DebugPolymer::getFlag(), org::openscience::cdk::debug::DebugMonomer::getFlag(), org::openscience::cdk::debug::DebugMoleculeSet::getFlag(), org::openscience::cdk::debug::DebugMolecule::getFlag(), org::openscience::cdk::debug::DebugMapping::getFlag(), org::openscience::cdk::debug::DebugLonePair::getFlag(), org::openscience::cdk::debug::DebugIsotope::getFlag(), org::openscience::cdk::debug::DebugElement::getFlag(), org::openscience::cdk::debug::DebugElectronContainer::getFlag(), org::openscience::cdk::debug::DebugCrystal::getFlag(), org::openscience::cdk::debug::DebugChemSequence::getFlag(), org::openscience::cdk::debug::DebugChemObject::getFlag(), org::openscience::cdk::debug::DebugChemModel::getFlag(), org::openscience::cdk::debug::DebugChemFile::getFlag(), org::openscience::cdk::debug::DebugBond::getFlag(), org::openscience::cdk::debug::DebugBioPolymer::getFlag(), org::openscience::cdk::debug::DebugAtomType::getFlag(), org::openscience::cdk::debug::DebugAtomParity::getFlag(), org::openscience::cdk::debug::DebugAtomContainerSet::getFlag(), org::openscience::cdk::debug::DebugAtomContainer::getFlag(), org::openscience::cdk::debug::DebugAtom::getFlag(), org::openscience::cdk::debug::DebugAminoAcid::getFlag(), org::openscience::cdk::debug::DebugStrand::getFlags(), org::openscience::cdk::debug::DebugSingleElectron::getFlags(), org::openscience::cdk::debug::DebugRing::getFlags(), org::openscience::cdk::debug::DebugReactionSet::getFlags(), org::openscience::cdk::debug::DebugReaction::getFlags(), org::openscience::cdk::debug::DebugPseudoAtom::getFlags(), org::openscience::cdk::debug::DebugPolymer::getFlags(), org::openscience::cdk::debug::DebugMonomer::getFlags(), org::openscience::cdk::debug::DebugMoleculeSet::getFlags(), org::openscience::cdk::debug::DebugMolecule::getFlags(), org::openscience::cdk::debug::DebugMapping::getFlags(), org::openscience::cdk::debug::DebugLonePair::getFlags(), org::openscience::cdk::debug::DebugIsotope::getFlags(), org::openscience::cdk::debug::DebugElement::getFlags(), org::openscience::cdk::debug::DebugElectronContainer::getFlags(), org::openscience::cdk::debug::DebugCrystal::getFlags(), org::openscience::cdk::debug::DebugChemSequence::getFlags(), org::openscience::cdk::debug::DebugChemObject::getFlags(), org::openscience::cdk::debug::DebugChemModel::getFlags(), org::openscience::cdk::debug::DebugChemFile::getFlags(), org::openscience::cdk::debug::DebugBond::getFlags(), org::openscience::cdk::debug::DebugBioPolymer::getFlags(), org::openscience::cdk::debug::DebugAtomType::getFlags(), org::openscience::cdk::debug::DebugAtomParity::getFlags(), org::openscience::cdk::debug::DebugAtomContainerSet::getFlags(), org::openscience::cdk::debug::DebugAtomContainer::getFlags(), org::openscience::cdk::debug::DebugAtom::getFlags(), org::openscience::cdk::debug::DebugAminoAcid::getFlags(), org::openscience::cdk::debug::DebugPseudoAtom::getFormalCharge(), org::openscience::cdk::debug::DebugAtomType::getFormalCharge(), org::openscience::cdk::debug::DebugAtom::getFormalCharge(), org::openscience::cdk::debug::DebugPseudoAtom::getFormalNeighbourCount(), org::openscience::cdk::debug::DebugAtomType::getFormalNeighbourCount(), org::openscience::cdk::debug::DebugAtom::getFormalNeighbourCount(), org::openscience::cdk::debug::DebugPseudoAtom::getFractionalPoint3d(), org::openscience::cdk::debug::DebugAtom::getFractionalPoint3d(), org::openscience::cdk::controller::AbstractController2D::getHighlighted(), org::openscience::cdk::tools::HOSECodeGenerator::getHOSECode(), org::openscience::cdk::debug::DebugPseudoAtom::getHybridization(), org::openscience::cdk::debug::DebugAtomType::getHybridization(), org::openscience::cdk::debug::DebugAtom::getHybridization(), org::openscience::cdk::debug::DebugPseudoAtom::getHydrogenCount(), org::openscience::cdk::debug::DebugAtom::getHydrogenCount(), org::openscience::cdk::debug::DebugPDBMonomer::getICode(), org::openscience::cdk::debug::DebugPDBAtom::getICode(), org::openscience::cdk::debug::DebugStrand::getID(), org::openscience::cdk::debug::DebugSingleElectron::getID(), org::openscience::cdk::debug::DebugRing::getID(), org::openscience::cdk::debug::DebugReactionSet::getID(), org::openscience::cdk::debug::DebugReaction::getID(), org::openscience::cdk::debug::DebugPseudoAtom::getID(), org::openscience::cdk::debug::DebugPolymer::getID(), org::openscience::cdk::debug::DebugMonomer::getID(), org::openscience::cdk::debug::DebugMoleculeSet::getID(), org::openscience::cdk::debug::DebugMolecule::getID(), org::openscience::cdk::debug::DebugMapping::getID(), org::openscience::cdk::debug::DebugLonePair::getID(), org::openscience::cdk::debug::DebugIsotope::getID(), org::openscience::cdk::debug::DebugElement::getID(), org::openscience::cdk::debug::DebugElectronContainer::getID(), org::openscience::cdk::debug::DebugCrystal::getID(), org::openscience::cdk::debug::DebugChemSequence::getID(), org::openscience::cdk::debug::DebugChemObject::getID(), org::openscience::cdk::debug::DebugChemModel::getID(), org::openscience::cdk::debug::DebugChemFile::getID(), org::openscience::cdk::debug::DebugBond::getID(), org::openscience::cdk::debug::DebugBioPolymer::getID(), org::openscience::cdk::debug::DebugAtomType::getID(), org::openscience::cdk::debug::DebugAtomParity::getID(), org::openscience::cdk::debug::DebugAtomContainerSet::getID(), org::openscience::cdk::debug::DebugAtomContainer::getID(), org::openscience::cdk::debug::DebugAtom::getID(), org::openscience::cdk::debug::DebugAminoAcid::getID(), org::openscience::cdk::layout::AtomPlacer::getInitialLongestChain(), org::openscience::cdk::config::IsotopeFactory::getIsotopes(), org::openscience::cdk::applications::jchempaint::JCPPropertyHandler::getJChemPaintDir(), org::openscience::cdk::debug::DebugPseudoAtom::getLabel(), org::openscience::cdk::debug::DebugStrand::getLastAtom(), org::openscience::cdk::debug::DebugRing::getLastAtom(), org::openscience::cdk::debug::DebugPolymer::getLastAtom(), org::openscience::cdk::debug::DebugMonomer::getLastAtom(), org::openscience::cdk::debug::DebugMolecule::getLastAtom(), org::openscience::cdk::debug::DebugCrystal::getLastAtom(), org::openscience::cdk::debug::DebugBioPolymer::getLastAtom(), org::openscience::cdk::debug::DebugAtomContainer::getLastAtom(), org::openscience::cdk::debug::DebugAminoAcid::getLastAtom(), org::openscience::cdk::debug::DebugStrand::getListenerCount(), org::openscience::cdk::debug::DebugSingleElectron::getListenerCount(), org::openscience::cdk::debug::DebugRing::getListenerCount(), org::openscience::cdk::debug::DebugReactionSet::getListenerCount(), org::openscience::cdk::debug::DebugReaction::getListenerCount(), org::openscience::cdk::debug::DebugPseudoAtom::getListenerCount(), org::openscience::cdk::debug::DebugPolymer::getListenerCount(), org::openscience::cdk::debug::DebugMonomer::getListenerCount(), org::openscience::cdk::debug::DebugMoleculeSet::getListenerCount(), org::openscience::cdk::debug::DebugMolecule::getListenerCount(), org::openscience::cdk::debug::DebugMapping::getListenerCount(), org::openscience::cdk::debug::DebugLonePair::getListenerCount(), org::openscience::cdk::debug::DebugIsotope::getListenerCount(), org::openscience::cdk::debug::DebugElement::getListenerCount(), org::openscience::cdk::debug::DebugElectronContainer::getListenerCount(), org::openscience::cdk::debug::DebugCrystal::getListenerCount(), org::openscience::cdk::debug::DebugChemSequence::getListenerCount(), org::openscience::cdk::debug::DebugChemObject::getListenerCount(), org::openscience::cdk::debug::DebugChemModel::getListenerCount(), org::openscience::cdk::debug::DebugChemFile::getListenerCount(), org::openscience::cdk::debug::DebugBond::getListenerCount(), org::openscience::cdk::debug::DebugBioPolymer::getListenerCount(), org::openscience::cdk::debug::DebugAtomType::getListenerCount(), org::openscience::cdk::debug::DebugAtomParity::getListenerCount(), org::openscience::cdk::debug::DebugAtomContainerSet::getListenerCount(), org::openscience::cdk::debug::DebugAtomContainer::getListenerCount(), org::openscience::cdk::debug::DebugAtom::getListenerCount(), org::openscience::cdk::debug::DebugAminoAcid::getListenerCount(), org::openscience::cdk::debug::DebugStrand::getLonePair(), org::openscience::cdk::debug::DebugRing::getLonePair(), org::openscience::cdk::debug::DebugPolymer::getLonePair(), org::openscience::cdk::debug::DebugMonomer::getLonePair(), org::openscience::cdk::debug::DebugMolecule::getLonePair(), org::openscience::cdk::debug::DebugCrystal::getLonePair(), org::openscience::cdk::debug::DebugBioPolymer::getLonePair(), org::openscience::cdk::debug::DebugAtomContainer::getLonePair(), org::openscience::cdk::debug::DebugAminoAcid::getLonePair(), org::openscience::cdk::debug::DebugStrand::getLonePairCount(), org::openscience::cdk::debug::DebugRing::getLonePairCount(), org::openscience::cdk::debug::DebugPolymer::getLonePairCount(), org::openscience::cdk::debug::DebugMonomer::getLonePairCount(), org::openscience::cdk::debug::DebugMolecule::getLonePairCount(), org::openscience::cdk::debug::DebugCrystal::getLonePairCount(), org::openscience::cdk::debug::DebugBioPolymer::getLonePairCount(), org::openscience::cdk::debug::DebugAtomContainer::getLonePairCount(), org::openscience::cdk::debug::DebugAminoAcid::getLonePairCount(), org::openscience::cdk::debug::DebugStrand::getLonePairNumber(), org::openscience::cdk::debug::DebugRing::getLonePairNumber(), org::openscience::cdk::debug::DebugPolymer::getLonePairNumber(), org::openscience::cdk::debug::DebugMonomer::getLonePairNumber(), org::openscience::cdk::debug::DebugMolecule::getLonePairNumber(), org::openscience::cdk::debug::DebugCrystal::getLonePairNumber(), org::openscience::cdk::debug::DebugBioPolymer::getLonePairNumber(), org::openscience::cdk::debug::DebugAtomContainer::getLonePairNumber(), org::openscience::cdk::debug::DebugAminoAcid::getLonePairNumber(), org::openscience::cdk::layout::AtomPlacer::getLongestUnplacedChain(), org::openscience::cdk::config::IsotopeFactory::getMajorIsotope(), org::openscience::cdk::layout::TemplateHandler::getMappedSubstructures(), org::openscience::cdk::debug::DebugPseudoAtom::getMassNumber(), org::openscience::cdk::debug::DebugIsotope::getMassNumber(), org::openscience::cdk::debug::DebugAtomType::getMassNumber(), org::openscience::cdk::debug::DebugAtom::getMassNumber(), org::openscience::cdk::debug::DebugPseudoAtom::getMaxBondOrder(), org::openscience::cdk::debug::DebugAtomType::getMaxBondOrder(), org::openscience::cdk::debug::DebugAtom::getMaxBondOrder(), org::openscience::cdk::debug::DebugStrand::getMaximumBondOrder(), org::openscience::cdk::debug::DebugRing::getMaximumBondOrder(), org::openscience::cdk::debug::DebugPolymer::getMaximumBondOrder(), org::openscience::cdk::debug::DebugMonomer::getMaximumBondOrder(), org::openscience::cdk::debug::DebugMolecule::getMaximumBondOrder(), org::openscience::cdk::debug::DebugCrystal::getMaximumBondOrder(), org::openscience::cdk::debug::DebugBioPolymer::getMaximumBondOrder(), org::openscience::cdk::debug::DebugAtomContainer::getMaximumBondOrder(), org::openscience::cdk::debug::DebugAminoAcid::getMaximumBondOrder(), org::openscience::cdk::debug::DebugStrand::getMinimumBondOrder(), org::openscience::cdk::debug::DebugRing::getMinimumBondOrder(), org::openscience::cdk::debug::DebugPolymer::getMinimumBondOrder(), org::openscience::cdk::debug::DebugMonomer::getMinimumBondOrder(), org::openscience::cdk::debug::DebugMolecule::getMinimumBondOrder(), org::openscience::cdk::debug::DebugCrystal::getMinimumBondOrder(), org::openscience::cdk::debug::DebugBioPolymer::getMinimumBondOrder(), org::openscience::cdk::debug::DebugAtomContainer::getMinimumBondOrder(), org::openscience::cdk::debug::DebugAminoAcid::getMinimumBondOrder(), org::openscience::cdk::debug::DebugMoleculeSet::getMolecule(), org::openscience::cdk::debug::DebugMoleculeSet::getMoleculeCount(), org::openscience::cdk::debug::DebugChemModel::getMoleculeSet(), org::openscience::cdk::debug::DebugStrand::getMonomer(), org::openscience::cdk::debug::DebugPolymer::getMonomer(), org::openscience::cdk::debug::DebugBioPolymer::getMonomer(), org::openscience::cdk::debug::DebugStrand::getMonomerCount(), org::openscience::cdk::debug::DebugPolymer::getMonomerCount(), org::openscience::cdk::debug::DebugBioPolymer::getMonomerCount(), org::openscience::cdk::debug::DebugMonomer::getMonomerName(), org::openscience::cdk::debug::DebugAminoAcid::getMonomerName(), org::openscience::cdk::debug::DebugStrand::getMonomerNames(), org::openscience::cdk::debug::DebugPolymer::getMonomerNames(), org::openscience::cdk::debug::DebugBioPolymer::getMonomerNames(), org::openscience::cdk::debug::DebugStrand::getMonomers(), org::openscience::cdk::debug::DebugMonomer::getMonomerType(), org::openscience::cdk::debug::DebugAminoAcid::getMonomerType(), org::openscience::cdk::debug::DebugMoleculeSet::getMultiplier(), org::openscience::cdk::debug::DebugAtomContainerSet::getMultiplier(), org::openscience::cdk::debug::DebugMoleculeSet::getMultipliers(), org::openscience::cdk::debug::DebugAtomContainerSet::getMultipliers(), org::openscience::cdk::tools::GenerateFragments::getMurckoFrameworksAsSmileArray(), org::openscience::cdk::debug::DebugPDBAtom::getName(), org::openscience::cdk::debug::DebugPseudoAtom::getNaturalAbundance(), org::openscience::cdk::debug::DebugIsotope::getNaturalAbundance(), org::openscience::cdk::debug::DebugAtomType::getNaturalAbundance(), org::openscience::cdk::debug::DebugAtom::getNaturalAbundance(), org::openscience::cdk::debug::DebugRing::getNextBond(), org::openscience::cdk::layout::AtomPlacer::getNextBondVector(), org::openscience::cdk::debug::DebugAminoAcid::getNTerminus(), org::openscience::cdk::debug::DebugPDBAtom::getOccupancy(), org::openscience::cdk::debug::DebugBond::getOrder(), org::openscience::cdk::debug::DebugAtomParity::getParity(), org::openscience::cdk::charges::InductivePartialCharges::getPaulingElectronegativities(), org::openscience::cdk::debug::DebugPseudoAtom::getPoint2d(), org::openscience::cdk::debug::DebugAtom::getPoint2d(), org::openscience::cdk::debug::DebugPseudoAtom::getPoint3d(), org::openscience::cdk::debug::DebugAtom::getPoint3d(), org::openscience::cdk::charges::Polarizability::getPolarizabilitiyFactorForAtom(), org::openscience::cdk::controller::PopupController2D::getPopupMenu(), org::openscience::cdk::debug::DebugReaction::getProductCoefficient(), org::openscience::cdk::debug::DebugReaction::getProductCoefficients(), org::openscience::cdk::debug::DebugReaction::getProductCount(), org::openscience::cdk::debug::DebugReaction::getProducts(), org::openscience::cdk::debug::DebugStrand::getProperties(), org::openscience::cdk::debug::DebugSingleElectron::getProperties(), org::openscience::cdk::debug::DebugRing::getProperties(), org::openscience::cdk::debug::DebugReactionSet::getProperties(), org::openscience::cdk::debug::DebugReaction::getProperties(), org::openscience::cdk::debug::DebugPseudoAtom::getProperties(), org::openscience::cdk::debug::DebugPolymer::getProperties(), org::openscience::cdk::debug::DebugMonomer::getProperties(), org::openscience::cdk::debug::DebugMoleculeSet::getProperties(), org::openscience::cdk::debug::DebugMolecule::getProperties(), org::openscience::cdk::debug::DebugMapping::getProperties(), org::openscience::cdk::debug::DebugLonePair::getProperties(), org::openscience::cdk::debug::DebugIsotope::getProperties(), org::openscience::cdk::debug::DebugElement::getProperties(), org::openscience::cdk::debug::DebugElectronContainer::getProperties(), org::openscience::cdk::debug::DebugCrystal::getProperties(), org::openscience::cdk::debug::DebugChemSequence::getProperties(), org::openscience::cdk::debug::DebugChemObject::getProperties(), org::openscience::cdk::debug::DebugChemModel::getProperties(), org::openscience::cdk::debug::DebugChemFile::getProperties(), org::openscience::cdk::debug::DebugBond::getProperties(), org::openscience::cdk::debug::DebugBioPolymer::getProperties(), org::openscience::cdk::debug::DebugAtomType::getProperties(), org::openscience::cdk::debug::DebugAtomParity::getProperties(), org::openscience::cdk::debug::DebugAtomContainerSet::getProperties(), org::openscience::cdk::debug::DebugAtomContainer::getProperties(), org::openscience::cdk::debug::DebugAtom::getProperties(), org::openscience::cdk::debug::DebugAminoAcid::getProperties(), org::openscience::cdk::debug::DebugStrand::getProperty(), org::openscience::cdk::debug::DebugSingleElectron::getProperty(), org::openscience::cdk::debug::DebugRing::getProperty(), org::openscience::cdk::debug::DebugReactionSet::getProperty(), org::openscience::cdk::debug::DebugReaction::getProperty(), org::openscience::cdk::debug::DebugPseudoAtom::getProperty(), org::openscience::cdk::debug::DebugPolymer::getProperty(), org::openscience::cdk::debug::DebugMonomer::getProperty(), org::openscience::cdk::debug::DebugMoleculeSet::getProperty(), org::openscience::cdk::debug::DebugMolecule::getProperty(), org::openscience::cdk::debug::DebugMapping::getProperty(), org::openscience::cdk::debug::DebugLonePair::getProperty(), org::openscience::cdk::debug::DebugIsotope::getProperty(), org::openscience::cdk::debug::DebugElement::getProperty(), org::openscience::cdk::debug::DebugElectronContainer::getProperty(), org::openscience::cdk::debug::DebugCrystal::getProperty(), org::openscience::cdk::debug::DebugChemSequence::getProperty(), org::openscience::cdk::debug::DebugChemObject::getProperty(), org::openscience::cdk::debug::DebugChemModel::getProperty(), org::openscience::cdk::debug::DebugChemFile::getProperty(), org::openscience::cdk::debug::DebugBond::getProperty(), org::openscience::cdk::debug::DebugBioPolymer::getProperty(), org::openscience::cdk::debug::DebugAtomType::getProperty(), org::openscience::cdk::debug::DebugAtomParity::getProperty(), org::openscience::cdk::debug::DebugAtomContainerSet::getProperty(), org::openscience::cdk::debug::DebugAtomContainer::getProperty(), org::openscience::cdk::debug::DebugAtom::getProperty(), org::openscience::cdk::debug::DebugAminoAcid::getProperty(), org::openscience::cdk::debug::DebugReaction::getReactantCoefficient(), org::openscience::cdk::debug::DebugReaction::getReactantCoefficients(), org::openscience::cdk::debug::DebugReaction::getReactantCount(), org::openscience::cdk::debug::DebugReaction::getReactants(), org::openscience::cdk::debug::DebugReactionSet::getReaction(), org::openscience::cdk::debug::DebugReactionSet::getReactionCount(), org::openscience::cdk::debug::DebugChemModel::getReactionSet(), org::openscience::cdk::debug::DebugPDBAtom::getRecord(), org::openscience::cdk::debug::DebugPDBAtom::getResName(), org::openscience::cdk::applications::jchempaint::JCPPropertyHandler::getResource(), org::openscience::cdk::applications::jchempaint::JCPPropertyHandler::getResources(), org::openscience::cdk::applications::jchempaint::JCPPropertyHandler::getResourceString(), org::openscience::cdk::debug::DebugPDBAtom::getResSeq(), org::openscience::cdk::ringsearch::FiguerasSSSRFinder::getRing(), org::openscience::cdk::smiles::SmilesParser::getRingNumber(), org::openscience::cdk::debug::DebugRingSet::getRings(), org::openscience::cdk::debug::DebugChemModel::getRingSet(), org::openscience::cdk::debug::DebugRing::getRingSize(), org::openscience::cdk::renderer::AbstractRenderer2D::getScreenCoordinates(), org::openscience::cdk::debug::DebugPDBAtom::getSegID(), org::openscience::cdk::debug::DebugPDBAtom::getSerial(), org::openscience::cdk::debug::DebugStrand::getSingleElectron(), org::openscience::cdk::debug::DebugRing::getSingleElectron(), org::openscience::cdk::debug::DebugPolymer::getSingleElectron(), org::openscience::cdk::debug::DebugMonomer::getSingleElectron(), org::openscience::cdk::debug::DebugMolecule::getSingleElectron(), org::openscience::cdk::debug::DebugCrystal::getSingleElectron(), org::openscience::cdk::debug::DebugBioPolymer::getSingleElectron(), org::openscience::cdk::debug::DebugAtomContainer::getSingleElectron(), org::openscience::cdk::debug::DebugAminoAcid::getSingleElectron(), org::openscience::cdk::debug::DebugStrand::getSingleElectronCount(), org::openscience::cdk::debug::DebugRing::getSingleElectronCount(), org::openscience::cdk::debug::DebugPolymer::getSingleElectronCount(), org::openscience::cdk::debug::DebugMonomer::getSingleElectronCount(), org::openscience::cdk::debug::DebugMolecule::getSingleElectronCount(), org::openscience::cdk::debug::DebugCrystal::getSingleElectronCount(), org::openscience::cdk::debug::DebugBioPolymer::getSingleElectronCount(), org::openscience::cdk::debug::DebugAtomContainer::getSingleElectronCount(), org::openscience::cdk::debug::DebugAminoAcid::getSingleElectronCount(), org::openscience::cdk::debug::DebugStrand::getSingleElectronNumber(), org::openscience::cdk::debug::DebugRing::getSingleElectronNumber(), org::openscience::cdk::debug::DebugPolymer::getSingleElectronNumber(), org::openscience::cdk::debug::DebugMonomer::getSingleElectronNumber(), org::openscience::cdk::debug::DebugMolecule::getSingleElectronNumber(), org::openscience::cdk::debug::DebugCrystal::getSingleElectronNumber(), org::openscience::cdk::debug::DebugBioPolymer::getSingleElectronNumber(), org::openscience::cdk::debug::DebugAtomContainer::getSingleElectronNumber(), org::openscience::cdk::debug::DebugAminoAcid::getSingleElectronNumber(), org::openscience::cdk::applications::jchempaint::action::JCPAction::getSource(), org::openscience::cdk::debug::DebugCrystal::getSpaceGroup(), org::openscience::cdk::tools::HOSECodeGenerator::getSpheres(), org::openscience::cdk::debug::DebugPDBStructure::getStartChainID(), org::openscience::cdk::debug::DebugPDBStructure::getStartInsertionCode(), org::openscience::cdk::debug::DebugPDBStructure::getStartSequenceNumber(), org::openscience::cdk::debug::DebugBond::getStereo(), org::openscience::cdk::debug::DebugPseudoAtom::getStereoParity(), org::openscience::cdk::debug::DebugAtom::getStereoParity(), org::openscience::cdk::debug::DebugBioPolymer::getStrand(), org::openscience::cdk::debug::DebugBioPolymer::getStrandCount(), org::openscience::cdk::debug::DebugStrand::getStrandName(), org::openscience::cdk::debug::DebugBioPolymer::getStrandNames(), org::openscience::cdk::debug::DebugBioPolymer::getStrands(), org::openscience::cdk::debug::DebugStrand::getStrandType(), org::openscience::cdk::debug::DebugPDBPolymer::getStructures(), org::openscience::cdk::debug::DebugPDBStructure::getStructureType(), org::openscience::cdk::debug::DebugAtomParity::getSurroundingAtoms(), org::openscience::cdk::debug::DebugPseudoAtom::getSymbol(), org::openscience::cdk::debug::DebugIsotope::getSymbol(), org::openscience::cdk::debug::DebugElement::getSymbol(), org::openscience::cdk::debug::DebugAtomType::getSymbol(), org::openscience::cdk::debug::DebugAtom::getSymbol(), org::openscience::cdk::smiles::SmilesParser::getSymbolForOrganicSubsetElement(), org::openscience::cdk::debug::DebugPDBAtom::getTempFactor(), org::openscience::cdk::applications::swing::ChemObjectTree::getTree(), org::openscience::cdk::applications::jchempaint::JCPPropertyHandler::getUserHome(), org::openscience::cdk::applications::jchempaint::JCPPropertyHandler::getUserPropsFile(), org::openscience::cdk::debug::DebugPseudoAtom::getValency(), org::openscience::cdk::debug::DebugAtomType::getValency(), org::openscience::cdk::debug::DebugAtom::getValency(), org::openscience::cdk::debug::DebugPseudoAtom::getVanderwaalsRadius(), org::openscience::cdk::debug::DebugAtomType::getVanderwaalsRadius(), org::openscience::cdk::debug::DebugAtom::getVanderwaalsRadius(), org::openscience::cdk::debug::DebugCrystal::getZ(), org::openscience::cdk::protein::ProteinPocketFinder::gridToPmesh(), org::openscience::cdk::io::ReaderFactory::guessFormat(), org::openscience::cdk::layout::StructureDiagramGenerator::handleAliphatics(), org::openscience::cdk::smiles::SmilesParser::handleRing(), org::openscience::cdk::io::iterator::IteratingMDLReader::hasNext(), org::openscience::cdk::io::HINWriter::HINWriter(), org::openscience::cdk::tools::HydrogenAdder::HydrogenAdder(), org::openscience::cdk::io::INChIReader::init(), org::openscience::cdk::reaction::type::RearrangementRadical3Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementRadical2Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementRadical1Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementCation3Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementCation2Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementCation1Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementAnion3Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementAnion2Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementAnion1Reaction::initiate(), org::openscience::cdk::reaction::type::RadicalSiteInitiationReaction::initiate(), org::openscience::cdk::reaction::type::RadicalSiteInitiationHReaction::initiate(), org::openscience::cdk::reaction::type::HyperconjugationReaction::initiate(), org::openscience::cdk::reaction::type::HydrogenRearrangementGammaReaction::initiate(), org::openscience::cdk::reaction::type::HydrogenRearrangementDeltaReaction::initiate(), org::openscience::cdk::reaction::type::ElectronImpactPDBReaction::initiate(), org::openscience::cdk::reaction::type::ElectronImpactNBEReaction::initiate(), org::openscience::cdk::reaction::type::DisplacementChargeFromDonorReaction::initiate(), org::openscience::cdk::reaction::type::DisplacementChargeFromAcceptorReaction::initiate(), org::openscience::cdk::reaction::type::CleavageBondReaction::initiate(), org::openscience::cdk::reaction::type::CleavageBondMultiReaction::initiate(), org::openscience::cdk::reaction::type::CarbonylEliminationReaction::initiate(), org::openscience::cdk::reaction::type::BreakingBondReaction::initiate(), org::openscience::cdk::ringsearch::AllRingsFinder::initPathGraph(), org::openscience::cdk::debug::DebugBond::isConnectedTo(), org::openscience::cdk::config::IsotopeFactory::IsotopeFactory(), org::openscience::cdk::tools::SaturationChecker::isOverSaturated(), org::openscience::cdk::tools::ValencyHybridChecker::isSaturated(), org::openscience::cdk::tools::ValencyChecker::isSaturated(), org::openscience::cdk::tools::SmilesValencyChecker::isSaturated(), org::openscience::cdk::tools::SaturationChecker::isSaturated(), org::openscience::cdk::tools::LonePairElectronChecker::isSaturated(), org::openscience::cdk::tools::ValencyHybridChecker::isUnsaturated(), org::openscience::cdk::tools::ValencyChecker::isUnsaturated(), org::openscience::cdk::tools::SmilesValencyChecker::isUnsaturated(), org::openscience::cdk::applications::jchempaint::application::JChemPaint::JChemPaint(), org::openscience::cdk::applications::jchempaint::JChemPaintEditorPanel::JChemPaintEditorPanel(), org::openscience::cdk::controller::AbstractController2D::keyPressed(), org::openscience::cdk::controller::AbstractController2D::keyReleased(), org::openscience::cdk::controller::AbstractController2D::keyTyped(), org::openscience::cdk::layout::StructureDiagramGenerator::layoutNextRingSystem(), org::openscience::cdk::layout::StructureDiagramGenerator::layoutRingSet(), org::openscience::cdk::fingerprint::FingerprinterTool::listDifferences(), org::openscience::cdk::applications::plugin::PluginClassLoader::loadClass(), org::openscience::cdk::applications::plugin::CDKPluginManager::loadPlugins(), org::openscience::cdk::modeling::builder3d::TemplateHandler3D::loadTemplates(), org::openscience::cdk::layout::TemplateHandler::loadTemplates(), LoggingTool(), org::openscience::cdk::debug::DebugStrand::lonePairs(), org::openscience::cdk::debug::DebugRing::lonePairs(), org::openscience::cdk::debug::DebugPolymer::lonePairs(), org::openscience::cdk::debug::DebugMonomer::lonePairs(), org::openscience::cdk::debug::DebugMolecule::lonePairs(), org::openscience::cdk::debug::DebugCrystal::lonePairs(), org::openscience::cdk::debug::DebugBioPolymer::lonePairs(), org::openscience::cdk::debug::DebugAtomContainer::lonePairs(), org::openscience::cdk::debug::DebugAminoAcid::lonePairs(), org::openscience::cdk::applications::Validator::main(), org::openscience::cdk::applications::swing::MoleculeViewer2DPanel::main(), org::openscience::cdk::applications::swing::MoleculeViewer2D::main(), org::openscience::cdk::applications::FileFormatGuesser::main(), org::openscience::cdk::applications::File2Text::main(), org::openscience::cdk::layout::TemplateHandler::mapTemplateExact(), org::openscience::cdk::layout::TemplateHandler::mapTemplates(), org::openscience::cdk::debug::DebugMoleculeSet::molecules(), org::openscience::cdk::controller::AbstractController2D::mouseDragged(), org::openscience::cdk::controller::PopupController2D::mousePressed(), org::openscience::cdk::controller::AbstractController2D::mousePressed(), org::openscience::cdk::controller::AbstractController2D::mouseReleased(), org::openscience::cdk::structgen::RandomGenerator::mutate(), org::openscience::cdk::tools::SaturationChecker::newSaturate(), org::openscience::cdk::debug::DebugStrand::notifyChanged(), org::openscience::cdk::debug::DebugSingleElectron::notifyChanged(), org::openscience::cdk::debug::DebugRing::notifyChanged(), org::openscience::cdk::debug::DebugReactionSet::notifyChanged(), org::openscience::cdk::debug::DebugReaction::notifyChanged(), org::openscience::cdk::debug::DebugPseudoAtom::notifyChanged(), org::openscience::cdk::debug::DebugPolymer::notifyChanged(), org::openscience::cdk::debug::DebugMonomer::notifyChanged(), org::openscience::cdk::debug::DebugMoleculeSet::notifyChanged(), org::openscience::cdk::debug::DebugMolecule::notifyChanged(), org::openscience::cdk::debug::DebugMapping::notifyChanged(), org::openscience::cdk::debug::DebugLonePair::notifyChanged(), org::openscience::cdk::debug::DebugIsotope::notifyChanged(), org::openscience::cdk::debug::DebugElement::notifyChanged(), org::openscience::cdk::debug::DebugElectronContainer::notifyChanged(), org::openscience::cdk::debug::DebugCrystal::notifyChanged(), org::openscience::cdk::debug::DebugChemSequence::notifyChanged(), org::openscience::cdk::debug::DebugChemObject::notifyChanged(), org::openscience::cdk::debug::DebugChemModel::notifyChanged(), org::openscience::cdk::debug::DebugChemFile::notifyChanged(), org::openscience::cdk::debug::DebugBond::notifyChanged(), org::openscience::cdk::debug::DebugBioPolymer::notifyChanged(), org::openscience::cdk::debug::DebugAtomType::notifyChanged(), org::openscience::cdk::debug::DebugAtomParity::notifyChanged(), org::openscience::cdk::debug::DebugAtomContainerSet::notifyChanged(), org::openscience::cdk::debug::DebugAtomContainer::notifyChanged(), org::openscience::cdk::debug::DebugAtom::notifyChanged(), org::openscience::cdk::debug::DebugAminoAcid::notifyChanged(), org::openscience::cdk::renderer::AbstractRenderer2D::paintAtomSymbol(), org::openscience::cdk::renderer::AbstractRenderer2D::paintBonds(), org::openscience::cdk::renderer::Renderer2D::paintChemModel(), org::openscience::cdk::applications::swing::ChemObjectTree::paintChemObject(), org::openscience::cdk::renderer::AbstractRenderer2D::paintPseudoAtomLabel(), org::openscience::cdk::renderer::Renderer2D::paintReaction(), org::openscience::cdk::io::Gaussian98Reader::parseLevelOfTheory(), org::openscience::cdk::smiles::SmilesParser::parseSmiles(), org::openscience::cdk::smiles::SmilesParser::parseString(), org::openscience::cdk::applications::swing::PeriodicTablePanel::PeriodicTablePanel(), org::openscience::cdk::layout::RingPlacer::placeBridgedRing(), org::openscience::cdk::layout::RingPlacer::placeConnectedRings(), org::openscience::cdk::layout::StructureDiagramGenerator::placeFirstBond(), org::openscience::cdk::layout::RingPlacer::placeFusedRing(), org::openscience::cdk::layout::AtomPlacer::placeLinearChain(), org::openscience::cdk::layout::RingPlacer::placeRing(), org::openscience::cdk::layout::RingPlacer::placeRingSubstituents(), org::openscience::cdk::layout::RingPlacer::placeSpiroRing(), org::openscience::cdk::applications::jchempaint::UndoStack::pop(), org::openscience::cdk::layout::AtomPlacer::populatePolygonCorners(), org::openscience::cdk::atomtype::StructGenAtomTypeGuesser::possbibleAtomTypes(), org::openscience::cdk::graph::invariant::EquivalentClassPartitioner::prepareNode(), org::openscience::cdk::ringsearch::FiguerasSSSRFinder::prepareRing(), org::openscience::cdk::qsar::DescriptorEngine::process(), org::openscience::cdk::io::iterator::event::EventCMLReader::process(), org::openscience::cdk::applications::demo::EventCMLDemo::process(), org::openscience::cdk::io::inchi::INChIContentProcessorTool::processConnections(), org::openscience::cdk::io::inchi::INChIContentProcessorTool::processFormula(), org::openscience::cdk::structgen::RandomGenerator::proposeStructure(), org::openscience::cdk::protein::ProteinPocketFinder::proteinGridToPmesh(), org::openscience::cdk::protein::ProteinPocketFinder::pspGridToPmesh(), org::openscience::cdk::applications::jchempaint::UndoStack::push(), org::openscience::cdk::debug::DebugReactionSet::reactions(), org::openscience::cdk::io::VASPReader::read(), org::openscience::cdk::io::PDBReader::read(), org::openscience::cdk::io::MACiEReader::read(), org::openscience::cdk::io::MDLV3000Reader::readAtomBlock(), org::openscience::cdk::config::CDKBasedAtomTypeConfigurator::readAtomTypes(), org::openscience::cdk::config::atomtypes::AtomTypeReader::readAtomTypes(), org::openscience::cdk::protein::ProteinPocketFinder::readBioPolymer(), org::openscience::cdk::io::MDLV3000Reader::readBondBlock(), org::openscience::cdk::io::XYZReader::readChemFile(), org::openscience::cdk::io::PMPReader::readChemFile(), org::openscience::cdk::io::PDBReader::readChemFile(), org::openscience::cdk::io::MDLV2000Reader::readChemFile(), org::openscience::cdk::io::MDLReader::readChemFile(), org::openscience::cdk::io::INChIReader::readChemFile(), org::openscience::cdk::io::Gaussian98Reader::readChemFile(), org::openscience::cdk::io::CIFReader::readChemFile(), org::openscience::cdk::config::AtomTypeFactory::readConfiguration(), org::openscience::cdk::dict::DictionaryDatabase::readDictionary(), org::openscience::cdk::config::elements::ElementPTReader::readElements(), org::openscience::cdk::config::isotopes::IsotopeReader::readIsotopes(), org::openscience::cdk::io::Mol2Reader::readMolecule(), org::openscience::cdk::io::MDLV2000Reader::readMolecule(), org::openscience::cdk::io::MDLReader::readMolecule(), org::openscience::cdk::internet::WWMMatrixReader::readMolecule(), org::openscience::cdk::internet::DADMLReader::readMolecule(), org::openscience::cdk::io::SMILESReader::readMoleculeSet(), org::openscience::cdk::io::Gaussian98Reader::readNMRData(), org::openscience::cdk::io::Gaussian98Reader::readPartialCharges(), org::openscience::cdk::io::Gaussian03Reader::readPartialCharges(), org::openscience::cdk::io::MDLRXNV2000Reader::readReaction(), org::openscience::cdk::io::MDLRXNReader::readReaction(), org::openscience::cdk::io::MACiEReader::readReactions(), org::openscience::cdk::io::MDLV3000Reader::readSGroup(), org::openscience::cdk::applications::jchempaint::UndoStack::redoShift(), org::openscience::cdk::debug::DebugMapping::relatedChemObjects(), org::openscience::cdk::ringsearch::AllRingsFinder::remove(), org::openscience::cdk::debug::DebugStrand::remove(), org::openscience::cdk::debug::DebugRing::remove(), org::openscience::cdk::debug::DebugPolymer::remove(), org::openscience::cdk::debug::DebugMonomer::remove(), org::openscience::cdk::debug::DebugMolecule::remove(), org::openscience::cdk::debug::DebugCrystal::remove(), org::openscience::cdk::debug::DebugBioPolymer::remove(), org::openscience::cdk::debug::DebugAtomContainer::remove(), org::openscience::cdk::debug::DebugAminoAcid::remove(), org::openscience::cdk::debug::DebugMoleculeSet::removeAllAtomContainers(), org::openscience::cdk::debug::DebugAtomContainerSet::removeAllAtomContainers(), org::openscience::cdk::debug::DebugStrand::removeAllBonds(), org::openscience::cdk::debug::DebugRing::removeAllBonds(), org::openscience::cdk::debug::DebugPolymer::removeAllBonds(), org::openscience::cdk::debug::DebugMonomer::removeAllBonds(), org::openscience::cdk::debug::DebugMolecule::removeAllBonds(), org::openscience::cdk::debug::DebugCrystal::removeAllBonds(), org::openscience::cdk::debug::DebugBioPolymer::removeAllBonds(), org::openscience::cdk::debug::DebugAtomContainer::removeAllBonds(), org::openscience::cdk::debug::DebugAminoAcid::removeAllBonds(), org::openscience::cdk::debug::DebugStrand::removeAllElectronContainers(), org::openscience::cdk::debug::DebugRing::removeAllElectronContainers(), org::openscience::cdk::debug::DebugPolymer::removeAllElectronContainers(), org::openscience::cdk::debug::DebugMonomer::removeAllElectronContainers(), org::openscience::cdk::debug::DebugMolecule::removeAllElectronContainers(), org::openscience::cdk::debug::DebugCrystal::removeAllElectronContainers(), org::openscience::cdk::debug::DebugBioPolymer::removeAllElectronContainers(), org::openscience::cdk::debug::DebugAtomContainer::removeAllElectronContainers(), org::openscience::cdk::debug::DebugAminoAcid::removeAllElectronContainers(), org::openscience::cdk::debug::DebugStrand::removeAllElements(), org::openscience::cdk::debug::DebugRing::removeAllElements(), org::openscience::cdk::debug::DebugPolymer::removeAllElements(), org::openscience::cdk::debug::DebugMonomer::removeAllElements(), org::openscience::cdk::debug::DebugMolecule::removeAllElements(), org::openscience::cdk::debug::DebugCrystal::removeAllElements(), org::openscience::cdk::debug::DebugBioPolymer::removeAllElements(), org::openscience::cdk::debug::DebugAtomContainer::removeAllElements(), org::openscience::cdk::debug::DebugAminoAcid::removeAllElements(), org::openscience::cdk::debug::DebugReactionSet::removeAllReactions(), org::openscience::cdk::debug::DebugStrand::removeAtom(), org::openscience::cdk::debug::DebugRing::removeAtom(), org::openscience::cdk::debug::DebugPolymer::removeAtom(), org::openscience::cdk::debug::DebugMonomer::removeAtom(), org::openscience::cdk::debug::DebugMolecule::removeAtom(), org::openscience::cdk::debug::DebugCrystal::removeAtom(), org::openscience::cdk::debug::DebugBioPolymer::removeAtom(), org::openscience::cdk::debug::DebugAtomContainer::removeAtom(), org::openscience::cdk::debug::DebugAminoAcid::removeAtom(), org::openscience::cdk::debug::DebugStrand::removeAtomAndConnectedElectronContainers(), org::openscience::cdk::debug::DebugRing::removeAtomAndConnectedElectronContainers(), org::openscience::cdk::debug::DebugPolymer::removeAtomAndConnectedElectronContainers(), org::openscience::cdk::debug::DebugMonomer::removeAtomAndConnectedElectronContainers(), org::openscience::cdk::debug::DebugMolecule::removeAtomAndConnectedElectronContainers(), org::openscience::cdk::debug::DebugCrystal::removeAtomAndConnectedElectronContainers(), org::openscience::cdk::debug::DebugBioPolymer::removeAtomAndConnectedElectronContainers(), org::openscience::cdk::debug::DebugAtomContainer::removeAtomAndConnectedElectronContainers(), org::openscience::cdk::debug::DebugAminoAcid::removeAtomAndConnectedElectronContainers(), org::openscience::cdk::debug::DebugMoleculeSet::removeAtomContainer(), org::openscience::cdk::debug::DebugAtomContainerSet::removeAtomContainer(), org::openscience::cdk::debug::DebugStrand::removeBond(), org::openscience::cdk::debug::DebugRing::removeBond(), org::openscience::cdk::debug::DebugPolymer::removeBond(), org::openscience::cdk::debug::DebugMonomer::removeBond(), org::openscience::cdk::debug::DebugMolecule::removeBond(), org::openscience::cdk::debug::DebugCrystal::removeBond(), org::openscience::cdk::debug::DebugBioPolymer::removeBond(), org::openscience::cdk::debug::DebugAtomContainer::removeBond(), org::openscience::cdk::debug::DebugAminoAcid::removeBond(), org::openscience::cdk::debug::DebugChemSequence::removeChemModel(), org::openscience::cdk::debug::DebugChemFile::removeChemSequence(), org::openscience::cdk::debug::DebugStrand::removeElectronContainer(), org::openscience::cdk::debug::DebugRing::removeElectronContainer(), org::openscience::cdk::debug::DebugPolymer::removeElectronContainer(), org::openscience::cdk::debug::DebugMonomer::removeElectronContainer(), org::openscience::cdk::debug::DebugMolecule::removeElectronContainer(), org::openscience::cdk::debug::DebugCrystal::removeElectronContainer(), org::openscience::cdk::debug::DebugBioPolymer::removeElectronContainer(), org::openscience::cdk::debug::DebugAtomContainer::removeElectronContainer(), org::openscience::cdk::debug::DebugAminoAcid::removeElectronContainer(), org::openscience::cdk::debug::DebugStrand::removeListener(), org::openscience::cdk::debug::DebugSingleElectron::removeListener(), org::openscience::cdk::debug::DebugRing::removeListener(), org::openscience::cdk::debug::DebugReactionSet::removeListener(), org::openscience::cdk::debug::DebugReaction::removeListener(), org::openscience::cdk::debug::DebugPseudoAtom::removeListener(), org::openscience::cdk::debug::DebugPolymer::removeListener(), org::openscience::cdk::debug::DebugMonomer::removeListener(), org::openscience::cdk::debug::DebugMoleculeSet::removeListener(), org::openscience::cdk::debug::DebugMolecule::removeListener(), org::openscience::cdk::debug::DebugMapping::removeListener(), org::openscience::cdk::debug::DebugLonePair::removeListener(), org::openscience::cdk::debug::DebugIsotope::removeListener(), org::openscience::cdk::debug::DebugElement::removeListener(), org::openscience::cdk::debug::DebugElectronContainer::removeListener(), org::openscience::cdk::debug::DebugCrystal::removeListener(), org::openscience::cdk::debug::DebugChemSequence::removeListener(), org::openscience::cdk::debug::DebugChemObject::removeListener(), org::openscience::cdk::debug::DebugChemModel::removeListener(), org::openscience::cdk::debug::DebugChemFile::removeListener(), org::openscience::cdk::debug::DebugBond::removeListener(), org::openscience::cdk::debug::DebugBioPolymer::removeListener(), org::openscience::cdk::debug::DebugAtomType::removeListener(), org::openscience::cdk::debug::DebugAtomParity::removeListener(), org::openscience::cdk::debug::DebugAtomContainerSet::removeListener(), org::openscience::cdk::debug::DebugAtomContainer::removeListener(), org::openscience::cdk::debug::DebugAtom::removeListener(), org::openscience::cdk::debug::DebugAminoAcid::removeListener(), org::openscience::cdk::debug::DebugStrand::removeLonePair(), org::openscience::cdk::debug::DebugRing::removeLonePair(), org::openscience::cdk::debug::DebugPolymer::removeLonePair(), org::openscience::cdk::debug::DebugMonomer::removeLonePair(), org::openscience::cdk::debug::DebugMolecule::removeLonePair(), org::openscience::cdk::debug::DebugCrystal::removeLonePair(), org::openscience::cdk::debug::DebugBioPolymer::removeLonePair(), org::openscience::cdk::debug::DebugAtomContainer::removeLonePair(), org::openscience::cdk::debug::DebugAminoAcid::removeLonePair(), org::openscience::cdk::debug::DebugStrand::removeMonomer(), org::openscience::cdk::debug::DebugPolymer::removeMonomer(), org::openscience::cdk::debug::DebugBioPolymer::removeMonomer(), org::openscience::cdk::debug::DebugStrand::removeProperty(), org::openscience::cdk::debug::DebugSingleElectron::removeProperty(), org::openscience::cdk::debug::DebugRing::removeProperty(), org::openscience::cdk::debug::DebugReactionSet::removeProperty(), org::openscience::cdk::debug::DebugReaction::removeProperty(), org::openscience::cdk::debug::DebugPseudoAtom::removeProperty(), org::openscience::cdk::debug::DebugPolymer::removeProperty(), org::openscience::cdk::debug::DebugMonomer::removeProperty(), org::openscience::cdk::debug::DebugMoleculeSet::removeProperty(), org::openscience::cdk::debug::DebugMolecule::removeProperty(), org::openscience::cdk::debug::DebugMapping::removeProperty(), org::openscience::cdk::debug::DebugLonePair::removeProperty(), org::openscience::cdk::debug::DebugIsotope::removeProperty(), org::openscience::cdk::debug::DebugElement::removeProperty(), org::openscience::cdk::debug::DebugElectronContainer::removeProperty(), org::openscience::cdk::debug::DebugCrystal::removeProperty(), org::openscience::cdk::debug::DebugChemSequence::removeProperty(), org::openscience::cdk::debug::DebugChemObject::removeProperty(), org::openscience::cdk::debug::DebugChemModel::removeProperty(), org::openscience::cdk::debug::DebugChemFile::removeProperty(), org::openscience::cdk::debug::DebugBond::removeProperty(), org::openscience::cdk::debug::DebugBioPolymer::removeProperty(), org::openscience::cdk::debug::DebugAtomType::removeProperty(), org::openscience::cdk::debug::DebugAtomParity::removeProperty(), org::openscience::cdk::debug::DebugAtomContainerSet::removeProperty(), org::openscience::cdk::debug::DebugAtomContainer::removeProperty(), org::openscience::cdk::debug::DebugAtom::removeProperty(), org::openscience::cdk::debug::DebugAminoAcid::removeProperty(), org::openscience::cdk::debug::DebugStrand::removeSingleElectron(), org::openscience::cdk::debug::DebugRing::removeSingleElectron(), org::openscience::cdk::debug::DebugPolymer::removeSingleElectron(), org::openscience::cdk::debug::DebugMonomer::removeSingleElectron(), org::openscience::cdk::debug::DebugMolecule::removeSingleElectron(), org::openscience::cdk::debug::DebugCrystal::removeSingleElectron(), org::openscience::cdk::debug::DebugBioPolymer::removeSingleElectron(), org::openscience::cdk::debug::DebugAtomContainer::removeSingleElectron(), org::openscience::cdk::debug::DebugAminoAcid::removeSingleElectron(), org::openscience::cdk::debug::DebugBioPolymer::removeStrand(), org::openscience::cdk::debug::DebugMoleculeSet::replaceAtomContainer(), org::openscience::cdk::debug::DebugAtomContainerSet::replaceAtomContainer(), org::openscience::cdk::layout::StructureDiagramGenerator::resetUnplacedRings(), org::openscience::cdk::io::cml::CMLResolver::resolveEntity(), org::openscience::cdk::internet::DADMLReader::resolveLinks(), org::openscience::cdk::layout::OverlapResolver::resolveOverlap(), org::openscience::cdk::tools::AtomTypeTools::ringSystemClassifier(), org::openscience::cdk::qsar::model::R2::RModel::RModel(), org::openscience::cdk::structgen::VicinitySampler::sample(), org::openscience::cdk::tools::ValencyHybridChecker::saturate(), org::openscience::cdk::tools::ValencyChecker::saturate(), org::openscience::cdk::tools::SmilesValencyChecker::saturate(), org::openscience::cdk::tools::SaturationChecker::saturate(), org::openscience::cdk::tools::ValencyHybridChecker::saturateByIncreasingBondOrder(), org::openscience::cdk::tools::ValencyChecker::saturateByIncreasingBondOrder(), org::openscience::cdk::tools::SmilesValencyChecker::saturateByIncreasingBondOrder(), org::openscience::cdk::controller::AbstractController2D::selectNearestChemObjectIfNoneSelected(), org::openscience::cdk::debug::DebugCrystal::setA(), org::openscience::cdk::debug::DebugPDBAtom::setAltLoc(), org::openscience::cdk::debug::DebugStrand::setAtom(), org::openscience::cdk::debug::DebugSingleElectron::setAtom(), org::openscience::cdk::debug::DebugRing::setAtom(), org::openscience::cdk::debug::DebugPolymer::setAtom(), org::openscience::cdk::debug::DebugMonomer::setAtom(), org::openscience::cdk::debug::DebugMolecule::setAtom(), org::openscience::cdk::debug::DebugLonePair::setAtom(), org::openscience::cdk::debug::DebugCrystal::setAtom(), org::openscience::cdk::debug::DebugBond::setAtom(), org::openscience::cdk::debug::DebugBioPolymer::setAtom(), org::openscience::cdk::debug::DebugAtomContainer::setAtom(), org::openscience::cdk::debug::DebugAminoAcid::setAtom(), org::openscience::cdk::debug::DebugPseudoAtom::setAtomicNumber(), org::openscience::cdk::debug::DebugIsotope::setAtomicNumber(), org::openscience::cdk::debug::DebugElement::setAtomicNumber(), org::openscience::cdk::debug::DebugAtomType::setAtomicNumber(), org::openscience::cdk::debug::DebugAtom::setAtomicNumber(), org::openscience::cdk::debug::DebugStrand::setAtoms(), org::openscience::cdk::debug::DebugRing::setAtoms(), org::openscience::cdk::debug::DebugPolymer::setAtoms(), org::openscience::cdk::debug::DebugMonomer::setAtoms(), org::openscience::cdk::debug::DebugMolecule::setAtoms(), org::openscience::cdk::debug::DebugCrystal::setAtoms(), org::openscience::cdk::debug::DebugBond::setAtoms(), org::openscience::cdk::debug::DebugBioPolymer::setAtoms(), org::openscience::cdk::debug::DebugAtomContainer::setAtoms(), org::openscience::cdk::debug::DebugAminoAcid::setAtoms(), org::openscience::cdk::debug::DebugPseudoAtom::setAtomTypeName(), org::openscience::cdk::debug::DebugAtomType::setAtomTypeName(), org::openscience::cdk::debug::DebugAtom::setAtomTypeName(), org::openscience::cdk::debug::DebugCrystal::setB(), org::openscience::cdk::debug::DebugPseudoAtom::setBondOrderSum(), org::openscience::cdk::debug::DebugAtomType::setBondOrderSum(), org::openscience::cdk::debug::DebugAtom::setBondOrderSum(), org::openscience::cdk::debug::DebugCrystal::setC(), org::openscience::cdk::debug::DebugPDBMonomer::setChainID(), org::openscience::cdk::debug::DebugPDBAtom::setChainID(), org::openscience::cdk::debug::DebugPseudoAtom::setCharge(), org::openscience::cdk::debug::DebugAtom::setCharge(), org::openscience::cdk::applications::swing::DictRefEditorTableModel::setChemObject(), org::openscience::cdk::debug::DebugPseudoAtom::setCovalentRadius(), org::openscience::cdk::debug::DebugAtomType::setCovalentRadius(), org::openscience::cdk::debug::DebugAtom::setCovalentRadius(), org::openscience::cdk::debug::DebugChemModel::setCrystal(), org::openscience::cdk::debug::DebugReaction::setDirection(), org::openscience::cdk::debug::DebugSingleElectron::setElectronCount(), org::openscience::cdk::debug::DebugLonePair::setElectronCount(), org::openscience::cdk::debug::DebugElectronContainer::setElectronCount(), org::openscience::cdk::debug::DebugBond::setElectronCount(), org::openscience::cdk::debug::DebugPDBStructure::setEndChainID(), org::openscience::cdk::debug::DebugPDBStructure::setEndInsertionCode(), org::openscience::cdk::debug::DebugPDBStructure::setEndSequenceNumber(), org::openscience::cdk::debug::DebugPseudoAtom::setExactMass(), org::openscience::cdk::debug::DebugIsotope::setExactMass(), org::openscience::cdk::debug::DebugAtomType::setExactMass(), org::openscience::cdk::debug::DebugAtom::setExactMass(), org::openscience::cdk::debug::DebugStrand::setFlag(), org::openscience::cdk::debug::DebugSingleElectron::setFlag(), org::openscience::cdk::debug::DebugRing::setFlag(), org::openscience::cdk::debug::DebugReactionSet::setFlag(), org::openscience::cdk::debug::DebugReaction::setFlag(), org::openscience::cdk::debug::DebugPseudoAtom::setFlag(), org::openscience::cdk::debug::DebugPolymer::setFlag(), org::openscience::cdk::debug::DebugMonomer::setFlag(), org::openscience::cdk::debug::DebugMoleculeSet::setFlag(), org::openscience::cdk::debug::DebugMolecule::setFlag(), org::openscience::cdk::debug::DebugMapping::setFlag(), org::openscience::cdk::debug::DebugLonePair::setFlag(), org::openscience::cdk::debug::DebugIsotope::setFlag(), org::openscience::cdk::debug::DebugElement::setFlag(), org::openscience::cdk::debug::DebugElectronContainer::setFlag(), org::openscience::cdk::debug::DebugCrystal::setFlag(), org::openscience::cdk::debug::DebugChemSequence::setFlag(), org::openscience::cdk::debug::DebugChemObject::setFlag(), org::openscience::cdk::debug::DebugChemModel::setFlag(), org::openscience::cdk::debug::DebugChemFile::setFlag(), org::openscience::cdk::debug::DebugBond::setFlag(), org::openscience::cdk::debug::DebugBioPolymer::setFlag(), org::openscience::cdk::debug::DebugAtomType::setFlag(), org::openscience::cdk::debug::DebugAtomParity::setFlag(), org::openscience::cdk::debug::DebugAtomContainerSet::setFlag(), org::openscience::cdk::debug::DebugAtomContainer::setFlag(), org::openscience::cdk::debug::DebugAtom::setFlag(), org::openscience::cdk::debug::DebugAminoAcid::setFlag(), org::openscience::cdk::debug::DebugStrand::setFlags(), org::openscience::cdk::debug::DebugSingleElectron::setFlags(), org::openscience::cdk::debug::DebugRing::setFlags(), org::openscience::cdk::debug::DebugReactionSet::setFlags(), org::openscience::cdk::debug::DebugReaction::setFlags(), org::openscience::cdk::debug::DebugPseudoAtom::setFlags(), org::openscience::cdk::debug::DebugPolymer::setFlags(), org::openscience::cdk::debug::DebugMonomer::setFlags(), org::openscience::cdk::debug::DebugMoleculeSet::setFlags(), org::openscience::cdk::debug::DebugMolecule::setFlags(), org::openscience::cdk::debug::DebugMapping::setFlags(), org::openscience::cdk::debug::DebugLonePair::setFlags(), org::openscience::cdk::debug::DebugIsotope::setFlags(), org::openscience::cdk::debug::DebugElement::setFlags(), org::openscience::cdk::debug::DebugElectronContainer::setFlags(), org::openscience::cdk::debug::DebugCrystal::setFlags(), org::openscience::cdk::debug::DebugChemSequence::setFlags(), org::openscience::cdk::debug::DebugChemObject::setFlags(), org::openscience::cdk::debug::DebugChemModel::setFlags(), org::openscience::cdk::debug::DebugChemFile::setFlags(), org::openscience::cdk::debug::DebugBond::setFlags(), org::openscience::cdk::debug::DebugBioPolymer::setFlags(), org::openscience::cdk::debug::DebugAtomType::setFlags(), org::openscience::cdk::debug::DebugAtomParity::setFlags(), org::openscience::cdk::debug::DebugAtomContainerSet::setFlags(), org::openscience::cdk::debug::DebugAtomContainer::setFlags(), org::openscience::cdk::debug::DebugAtom::setFlags(), org::openscience::cdk::debug::DebugAminoAcid::setFlags(), org::openscience::cdk::modeling::forcefield::ConjugateGradientMethod::setFletcherReeves_uk(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::setForceField(), org::openscience::cdk::debug::DebugPseudoAtom::setFormalCharge(), org::openscience::cdk::debug::DebugAtomType::setFormalCharge(), org::openscience::cdk::debug::DebugAtom::setFormalCharge(), org::openscience::cdk::debug::DebugPseudoAtom::setFormalNeighbourCount(), org::openscience::cdk::debug::DebugAtomType::setFormalNeighbourCount(), org::openscience::cdk::debug::DebugAtom::setFormalNeighbourCount(), org::openscience::cdk::debug::DebugPseudoAtom::setFractionalPoint3d(), org::openscience::cdk::debug::DebugAtom::setFractionalPoint3d(), org::openscience::cdk::modeling::forcefield::StretchBendInteractions::setGradientMMFF94SumEBA(), org::openscience::cdk::modeling::forcefield::StretchBendInteractions::setHessianMMFF94SumEBA(), org::openscience::cdk::debug::DebugPseudoAtom::setHybridization(), org::openscience::cdk::debug::DebugAtomType::setHybridization(), org::openscience::cdk::debug::DebugAtom::setHybridization(), org::openscience::cdk::debug::DebugPseudoAtom::setHydrogenCount(), org::openscience::cdk::debug::DebugAtom::setHydrogenCount(), org::openscience::cdk::debug::DebugPDBMonomer::setICode(), org::openscience::cdk::debug::DebugPDBAtom::setICode(), org::openscience::cdk::debug::DebugStrand::setID(), org::openscience::cdk::debug::DebugSingleElectron::setID(), org::openscience::cdk::debug::DebugRing::setID(), org::openscience::cdk::debug::DebugReactionSet::setID(), org::openscience::cdk::debug::DebugReaction::setID(), org::openscience::cdk::debug::DebugPseudoAtom::setID(), org::openscience::cdk::debug::DebugPolymer::setID(), org::openscience::cdk::debug::DebugMonomer::setID(), org::openscience::cdk::debug::DebugMoleculeSet::setID(), org::openscience::cdk::debug::DebugMolecule::setID(), org::openscience::cdk::debug::DebugMapping::setID(), org::openscience::cdk::debug::DebugLonePair::setID(), org::openscience::cdk::debug::DebugIsotope::setID(), org::openscience::cdk::debug::DebugElement::setID(), org::openscience::cdk::debug::DebugElectronContainer::setID(), org::openscience::cdk::debug::DebugCrystal::setID(), org::openscience::cdk::debug::DebugChemSequence::setID(), org::openscience::cdk::debug::DebugChemObject::setID(), org::openscience::cdk::debug::DebugChemModel::setID(), org::openscience::cdk::debug::DebugChemFile::setID(), org::openscience::cdk::debug::DebugBond::setID(), org::openscience::cdk::debug::DebugBioPolymer::setID(), org::openscience::cdk::debug::DebugAtomType::setID(), org::openscience::cdk::debug::DebugAtomParity::setID(), org::openscience::cdk::debug::DebugAtomContainerSet::setID(), org::openscience::cdk::debug::DebugAtomContainer::setID(), org::openscience::cdk::debug::DebugAtom::setID(), org::openscience::cdk::debug::DebugAminoAcid::setID(), org::openscience::cdk::debug::DebugPseudoAtom::setLabel(), org::openscience::cdk::debug::DebugPseudoAtom::setMassNumber(), org::openscience::cdk::debug::DebugIsotope::setMassNumber(), org::openscience::cdk::debug::DebugAtomType::setMassNumber(), org::openscience::cdk::debug::DebugAtom::setMassNumber(), org::openscience::cdk::debug::DebugPseudoAtom::setMaxBondOrder(), org::openscience::cdk::debug::DebugAtomType::setMaxBondOrder(), org::openscience::cdk::debug::DebugAtom::setMaxBondOrder(), org::openscience::cdk::layout::StructureDiagramGenerator::setMolecule(), org::openscience::cdk::debug::DebugMoleculeSet::setMolecules(), org::openscience::cdk::debug::DebugChemModel::setMoleculeSet(), org::openscience::cdk::debug::DebugMonomer::setMonomerName(), org::openscience::cdk::debug::DebugAminoAcid::setMonomerName(), org::openscience::cdk::debug::DebugMonomer::setMonomerType(), org::openscience::cdk::debug::DebugAminoAcid::setMonomerType(), org::openscience::cdk::debug::DebugMoleculeSet::setMultiplier(), org::openscience::cdk::debug::DebugAtomContainerSet::setMultiplier(), org::openscience::cdk::debug::DebugMoleculeSet::setMultipliers(), org::openscience::cdk::debug::DebugAtomContainerSet::setMultipliers(), org::openscience::cdk::debug::DebugPDBAtom::setName(), org::openscience::cdk::debug::DebugPseudoAtom::setNaturalAbundance(), org::openscience::cdk::debug::DebugIsotope::setNaturalAbundance(), org::openscience::cdk::debug::DebugAtomType::setNaturalAbundance(), org::openscience::cdk::debug::DebugAtom::setNaturalAbundance(), org::openscience::cdk::debug::DebugChemObject::setNotification(), org::openscience::cdk::io::iterator::event::EventCMLHandler::setObjectProperty(), org::openscience::cdk::debug::DebugPDBAtom::setOccupancy(), org::openscience::cdk::debug::DebugBond::setOrder(), org::openscience::cdk::debug::DebugPseudoAtom::setPoint2d(), org::openscience::cdk::debug::DebugAtom::setPoint2d(), org::openscience::cdk::debug::DebugPseudoAtom::setPoint3d(), org::openscience::cdk::debug::DebugAtom::setPoint3d(), org::openscience::cdk::debug::DebugReaction::setProductCoefficient(), org::openscience::cdk::debug::DebugReaction::setProductCoefficients(), org::openscience::cdk::debug::DebugReaction::setProducts(), org::openscience::cdk::debug::DebugStrand::setProperties(), org::openscience::cdk::debug::DebugSingleElectron::setProperties(), org::openscience::cdk::debug::DebugRing::setProperties(), org::openscience::cdk::debug::DebugReactionSet::setProperties(), org::openscience::cdk::debug::DebugReaction::setProperties(), org::openscience::cdk::debug::DebugPseudoAtom::setProperties(), org::openscience::cdk::debug::DebugPolymer::setProperties(), org::openscience::cdk::debug::DebugMonomer::setProperties(), org::openscience::cdk::debug::DebugMoleculeSet::setProperties(), org::openscience::cdk::debug::DebugMolecule::setProperties(), org::openscience::cdk::debug::DebugMapping::setProperties(), org::openscience::cdk::debug::DebugLonePair::setProperties(), org::openscience::cdk::debug::DebugIsotope::setProperties(), org::openscience::cdk::debug::DebugElement::setProperties(), org::openscience::cdk::debug::DebugElectronContainer::setProperties(), org::openscience::cdk::debug::DebugCrystal::setProperties(), org::openscience::cdk::debug::DebugChemSequence::setProperties(), org::openscience::cdk::debug::DebugChemObject::setProperties(), org::openscience::cdk::debug::DebugChemModel::setProperties(), org::openscience::cdk::debug::DebugChemFile::setProperties(), org::openscience::cdk::debug::DebugBond::setProperties(), org::openscience::cdk::debug::DebugBioPolymer::setProperties(), org::openscience::cdk::debug::DebugAtomType::setProperties(), org::openscience::cdk::debug::DebugAtomParity::setProperties(), org::openscience::cdk::debug::DebugAtomContainerSet::setProperties(), org::openscience::cdk::debug::DebugAtomContainer::setProperties(), org::openscience::cdk::debug::DebugAtom::setProperties(), org::openscience::cdk::debug::DebugAminoAcid::setProperties(), org::openscience::cdk::debug::DebugStrand::setProperty(), org::openscience::cdk::debug::DebugSingleElectron::setProperty(), org::openscience::cdk::debug::DebugRing::setProperty(), org::openscience::cdk::debug::DebugReactionSet::setProperty(), org::openscience::cdk::debug::DebugReaction::setProperty(), org::openscience::cdk::debug::DebugPseudoAtom::setProperty(), org::openscience::cdk::debug::DebugPolymer::setProperty(), org::openscience::cdk::debug::DebugMonomer::setProperty(), org::openscience::cdk::debug::DebugMoleculeSet::setProperty(), org::openscience::cdk::debug::DebugMolecule::setProperty(), org::openscience::cdk::debug::DebugMapping::setProperty(), org::openscience::cdk::debug::DebugLonePair::setProperty(), org::openscience::cdk::debug::DebugIsotope::setProperty(), org::openscience::cdk::debug::DebugElement::setProperty(), org::openscience::cdk::debug::DebugElectronContainer::setProperty(), org::openscience::cdk::debug::DebugCrystal::setProperty(), org::openscience::cdk::debug::DebugChemSequence::setProperty(), org::openscience::cdk::debug::DebugChemObject::setProperty(), org::openscience::cdk::debug::DebugChemModel::setProperty(), org::openscience::cdk::debug::DebugChemFile::setProperty(), org::openscience::cdk::debug::DebugBond::setProperty(), org::openscience::cdk::debug::DebugBioPolymer::setProperty(), org::openscience::cdk::debug::DebugAtomType::setProperty(), org::openscience::cdk::debug::DebugAtomParity::setProperty(), org::openscience::cdk::debug::DebugAtomContainerSet::setProperty(), org::openscience::cdk::debug::DebugAtomContainer::setProperty(), org::openscience::cdk::debug::DebugAtom::setProperty(), org::openscience::cdk::debug::DebugAminoAcid::setProperty(), org::openscience::cdk::internet::DADMLReader::setQuery(), org::openscience::cdk::debug::DebugReaction::setReactantCoefficient(), org::openscience::cdk::debug::DebugReaction::setReactantCoefficients(), org::openscience::cdk::debug::DebugReaction::setReactants(), org::openscience::cdk::debug::DebugChemModel::setReactionSet(), org::openscience::cdk::debug::DebugPDBAtom::setRecord(), org::openscience::cdk::debug::DebugPDBAtom::setResName(), org::openscience::cdk::debug::DebugPDBAtom::setResSeq(), org::openscience::cdk::debug::DebugChemModel::setRingSet(), org::openscience::cdk::debug::DebugPDBAtom::setSegID(), org::openscience::cdk::debug::DebugPDBAtom::setSerial(), org::openscience::cdk::applications::jchempaint::JChemPaintEditorPanel::setShowToolBar(), org::openscience::cdk::debug::DebugCrystal::setSpaceGroup(), org::openscience::cdk::debug::DebugPDBStructure::setStartChainID(), org::openscience::cdk::debug::DebugPDBStructure::setStartInsertionCode(), org::openscience::cdk::debug::DebugPDBStructure::setStartSequenceNumber(), org::openscience::cdk::debug::DebugBond::setStereo(), org::openscience::cdk::debug::DebugPseudoAtom::setStereoParity(), org::openscience::cdk::debug::DebugAtom::setStereoParity(), org::openscience::cdk::debug::DebugStrand::setStrandName(), org::openscience::cdk::debug::DebugStrand::setStrandType(), org::openscience::cdk::debug::DebugPDBStructure::setStructureType(), org::openscience::cdk::debug::DebugPseudoAtom::setSymbol(), org::openscience::cdk::debug::DebugIsotope::setSymbol(), org::openscience::cdk::debug::DebugElement::setSymbol(), org::openscience::cdk::debug::DebugAtomType::setSymbol(), org::openscience::cdk::debug::DebugAtom::setSymbol(), org::openscience::cdk::debug::DebugPDBAtom::setTempFactor(), org::openscience::cdk::debug::DebugPseudoAtom::setValency(), org::openscience::cdk::debug::DebugAtomType::setValency(), org::openscience::cdk::debug::DebugAtom::setValency(), org::openscience::cdk::debug::DebugPseudoAtom::setVanderwaalsRadius(), org::openscience::cdk::debug::DebugAtomType::setVanderwaalsRadius(), org::openscience::cdk::debug::DebugAtom::setVanderwaalsRadius(), org::openscience::cdk::debug::DebugCrystal::setZ(), org::openscience::cdk::applications::jchempaint::JChemPaintPanel::showChemFile(), org::openscience::cdk::debug::DebugStrand::singleElectrons(), org::openscience::cdk::debug::DebugRing::singleElectrons(), org::openscience::cdk::debug::DebugPolymer::singleElectrons(), org::openscience::cdk::debug::DebugMonomer::singleElectrons(), org::openscience::cdk::debug::DebugMolecule::singleElectrons(), org::openscience::cdk::debug::DebugCrystal::singleElectrons(), org::openscience::cdk::debug::DebugBioPolymer::singleElectrons(), org::openscience::cdk::debug::DebugAtomContainer::singleElectrons(), org::openscience::cdk::debug::DebugAminoAcid::singleElectrons(), org::openscience::cdk::smiles::SmilesParser::SmilesParser(), org::openscience::cdk::io::inchi::INChIHandler::startElement(), org::openscience::cdk::io::iterator::event::EventCMLHandler::startObject(), org::openscience::cdk::debug::DebugStrand::stateChanged(), org::openscience::cdk::debug::DebugRing::stateChanged(), org::openscience::cdk::debug::DebugPolymer::stateChanged(), org::openscience::cdk::debug::DebugMonomer::stateChanged(), org::openscience::cdk::debug::DebugCrystal::stateChanged(), org::openscience::cdk::debug::DebugBioPolymer::stateChanged(), org::openscience::cdk::debug::DebugAminoAcid::stateChanged(), org::openscience::cdk::applications::plugin::CDKPluginManager::stateChanged(), org::openscience::cdk::qsar::model::R2::LinearRegressionModel::summary(), org::openscience::cdk::qsar::model::R2::CNNRegressionModel::summary(), org::openscience::cdk::io::SVGWriter::SVGWriter(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::translateAllPositive(), org::openscience::cdk::geometry::GeometryTools::translateAllPositive(), org::openscience::cdk::applications::jchempaint::UndoStack::undoShift(), org::openscience::cdk::controller::AbstractController2D::updateAtom(), org::openscience::cdk::io::MDLWriter::write(), org::openscience::cdk::io::CMLWriter::write(), org::openscience::cdk::io::CDKSourceCodeWriter::write(), org::openscience::cdk::io::XYZWriter::writeMolecule(), org::openscience::cdk::io::SMILESWriter::writeMolecule(), org::openscience::cdk::io::Mol2Writer::writeMolecule(), org::openscience::cdk::io::MDLRXNWriter::writeMoleculeSet(), org::openscience::cdk::protein::ProteinPocketFinder::writePocketsToPMesh(), and org::openscience::cdk::io::MDLRXNWriter::writeReaction().

                                     {
        if (doDebug) {
            if (object instanceof Throwable) {
                debugThrowable((Throwable)object);
            } else {
                debugString("" + object);
            }
        }
    }


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