Logo Search packages:      
Sourcecode: cdk version File versions  Download package

IChemObjectBuilder org::openscience::cdk::interfaces::IChemObject::getBuilder (  ) [inherited]

Returns a ChemObjectBuilder for the data classes that extend this class.

Returns:
The IChemObjectBuilder matching this IChemObject

Implemented in org::openscience::cdk::ChemObject, org::openscience::cdk::debug::DebugAminoAcid, org::openscience::cdk::debug::DebugAtom, org::openscience::cdk::debug::DebugAtomContainer, org::openscience::cdk::debug::DebugAtomContainerSet, org::openscience::cdk::debug::DebugAtomType, org::openscience::cdk::debug::DebugBioPolymer, org::openscience::cdk::debug::DebugBond, org::openscience::cdk::debug::DebugChemFile, org::openscience::cdk::debug::DebugChemModel, org::openscience::cdk::debug::DebugChemObject, org::openscience::cdk::debug::DebugChemSequence, org::openscience::cdk::debug::DebugCrystal, org::openscience::cdk::debug::DebugElectronContainer, org::openscience::cdk::debug::DebugElement, org::openscience::cdk::debug::DebugFragmentAtom, org::openscience::cdk::debug::DebugIsotope, org::openscience::cdk::debug::DebugLonePair, org::openscience::cdk::debug::DebugMapping, org::openscience::cdk::debug::DebugMolecule, org::openscience::cdk::debug::DebugMoleculeSet, org::openscience::cdk::debug::DebugMonomer, org::openscience::cdk::debug::DebugPolymer, org::openscience::cdk::debug::DebugPseudoAtom, org::openscience::cdk::debug::DebugReaction, org::openscience::cdk::debug::DebugReactionScheme, org::openscience::cdk::debug::DebugReactionSet, org::openscience::cdk::debug::DebugRing, org::openscience::cdk::debug::DebugSingleElectron, org::openscience::cdk::debug::DebugStrand, org::openscience::cdk::nonotify::NNAminoAcid, org::openscience::cdk::nonotify::NNAtom, org::openscience::cdk::nonotify::NNAtomContainer, org::openscience::cdk::nonotify::NNAtomContainerSet, org::openscience::cdk::nonotify::NNAtomType, org::openscience::cdk::nonotify::NNBioPolymer, org::openscience::cdk::nonotify::NNBond, org::openscience::cdk::nonotify::NNChemFile, org::openscience::cdk::nonotify::NNChemModel, org::openscience::cdk::nonotify::NNChemObject, org::openscience::cdk::nonotify::NNChemSequence, org::openscience::cdk::nonotify::NNCrystal, org::openscience::cdk::nonotify::NNElectronContainer, org::openscience::cdk::nonotify::NNElement, org::openscience::cdk::nonotify::NNFragmentAtom, org::openscience::cdk::nonotify::NNIsotope, org::openscience::cdk::nonotify::NNLonePair, org::openscience::cdk::nonotify::NNMapping, org::openscience::cdk::nonotify::NNMolecule, org::openscience::cdk::nonotify::NNMoleculeSet, org::openscience::cdk::nonotify::NNMonomer, org::openscience::cdk::nonotify::NNPDBAtom, org::openscience::cdk::nonotify::NNPDBMonomer, org::openscience::cdk::nonotify::NNPDBPolymer, org::openscience::cdk::nonotify::NNPDBStructure, org::openscience::cdk::nonotify::NNPolymer, org::openscience::cdk::nonotify::NNPseudoAtom, org::openscience::cdk::nonotify::NNReaction, org::openscience::cdk::nonotify::NNReactionScheme, org::openscience::cdk::nonotify::NNReactionSet, org::openscience::cdk::nonotify::NNRing, org::openscience::cdk::nonotify::NNRingSet, org::openscience::cdk::nonotify::NNSingleElectron, and org::openscience::cdk::nonotify::NNStrand.

Referenced by org::openscience::cdk::tools::manipulator::AminoAcidManipulator::addAcidicOxygen(), org::openscience::cdk::tools::GenerateFragments::addPathFragments(), org::openscience::cdk::qsar::descriptors::molecular::AminoAcidCountDescriptor::AminoAcidCountDescriptor(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::assignGasteigerPiPartialCharges(), org::openscience::cdk::graph::rebond::RebondTool::bondAtom(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::BCUTDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::ALOGPDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::bond::BondPartialSigmaChargeDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::PartialSigmaChargeDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::IsProtonInAromaticSystemDescriptor::calculate(), org::openscience::cdk::tools::SaturationChecker::calculateNumberOfImplicitHydrogens(), org::openscience::cdk::charges::PiElectronegativity::calculatePiElectronegativity(), org::openscience::cdk::charges::Electronegativity::calculateSigmaElectronegativity(), org::openscience::cdk::config::ElementPTFactory::configureE(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::convertImplicitToExplicitHydrogens(), org::openscience::cdk::ringsearch::RingPartitioner::convertToAtomContainer(), org::openscience::cdk::tools::manipulator::ChemModelManipulator::createNewMolecule(), org::openscience::cdk::tools::manipulator::ReactionSchemeManipulator::createReactionScheme(), org::openscience::cdk::graph::invariant::ConjugatedPiSystemsDetector::detect(), org::openscience::cdk::ringsearch::AllRingsFinder::detectRings(), org::openscience::cdk::structgen::stochastic::operator::CrossoverMachine::doCrossover(), org::openscience::cdk::tools::manipulator::ReactionSchemeManipulator::extractPrecursorReaction(), org::openscience::cdk::tools::manipulator::ReactionSchemeManipulator::extractSubsequentReaction(), org::openscience::cdk::tools::manipulator::ReactionSchemeManipulator::extractTopReactions(), org::openscience::cdk::ringsearch::AllRingsFinder::findAllRings(), org::openscience::cdk::ringsearch::AllRingsFinder::findAllRingsInIsolatedRingSystem(), org::openscience::cdk::graph::PathTools::findClosestByBond(), org::openscience::cdk::atomtype::EStateAtomTypeMatcher::findMatchingAtomType(), org::openscience::cdk::structgen::SingleStructureRandomGenerator::generate(), org::openscience::cdk::layout::StructureDiagramGenerator::generateExperimentalCoordinates(), org::openscience::cdk::inchi::InChIGenerator::generateInchiFromCDKAtomContainer(), org::openscience::cdk::smiles::SmilesGenerator::generateMassString(), org::openscience::cdk::tools::GenerateFragments::generateMurckoFragments(), org::openscience::cdk::tools::manipulator::ChemModelManipulator::getAllAtomContainers(), org::openscience::cdk::tools::manipulator::RingSetManipulator::getAllInOneContainer(), org::openscience::cdk::tools::manipulator::ReactionSetManipulator::getAllMolecules(), org::openscience::cdk::tools::manipulator::ReactionManipulator::getAllMolecules(), org::openscience::cdk::tools::manipulator::ReactionManipulator::getAllProducts(), org::openscience::cdk::tools::manipulator::ReactionManipulator::getAllReactants(), org::openscience::cdk::tools::manipulator::ReactionSchemeManipulator::getAllReactions(), org::openscience::cdk::tools::manipulator::MolecularFormulaManipulator::getAtomContainer(), org::openscience::cdk::RingSet::getConnectedRings(), org::openscience::cdk::tools::StructureResonanceGenerator::getContainers(), org::openscience::cdk::graph::SpanningTree::getCyclicFragmentsContainer(), org::openscience::cdk::tools::manipulator::MolecularFormulaManipulator::getDBE(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::getElectrostaticPotentialN(), org::openscience::cdk::tools::manipulator::MolecularFormulaManipulator::getHTML(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::getHyperconjugationInteractions(), org::openscience::cdk::layout::AtomPlacer::getInitialLongestChain(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::getIntersection(), org::openscience::cdk::layout::AtomPlacer::getLongestUnplacedChain(), org::openscience::cdk::layout::TemplateHandler::getMappedSubstructures(), org::openscience::cdk::tools::manipulator::MolecularFormulaSetManipulator::getMaxOccurrenceElements(), org::openscience::cdk::tools::manipulator::MolecularFormulaSetManipulator::getMinOccurrenceElements(), org::openscience::cdk::tools::manipulator::MolecularFormulaManipulator::getMolecularFormula(), org::openscience::cdk::tools::manipulator::ReactionSchemeManipulator::getMoleculeSet(), org::openscience::cdk::tools::manipulator::MolecularFormulaManipulator::getNaturalExactMass(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::getNaturalExactMass(), org::openscience::cdk::layout::StructureDiagramGenerator::getPlacedAtoms(), org::openscience::cdk::layout::AtomPlacer::getPlacedAtoms(), org::openscience::cdk::modeling::builder3d::AtomTetrahedralLigandPlacer3D::getPlacedAtomsInAtomContainer(), org::openscience::cdk::modeling::builder3d::AtomPlacer3D::getPlacedHeavyAtoms(), org::openscience::cdk::charges::Polarizability::getPolarizabilitiyFactorForAtom(), org::openscience::cdk::tools::manipulator::ReactionSetManipulator::getRelevantReactions(), org::openscience::cdk::tools::manipulator::ReactionSetManipulator::getRelevantReactionsAsProduct(), org::openscience::cdk::tools::manipulator::ReactionSetManipulator::getRelevantReactionsAsReactant(), org::openscience::cdk::RingSet::getRings(), org::openscience::cdk::tools::StructureResonanceGenerator::getStructures(), org::openscience::cdk::layout::StructureDiagramGenerator::getUnplacedAtoms(), org::openscience::cdk::modeling::builder3d::AtomTetrahedralLigandPlacer3D::getUnsetAtomsInAtomContainer(), org::openscience::cdk::reaction::type::TautomerizationReaction::initiate(), org::openscience::cdk::reaction::type::SharingLonePairReaction::initiate(), org::openscience::cdk::reaction::type::SharingChargeSBReaction::initiate(), org::openscience::cdk::reaction::type::SharingChargeDBReaction::initiate(), org::openscience::cdk::reaction::type::SharingAnionReaction::initiate(), org::openscience::cdk::reaction::type::RearrangementRadicalReaction::initiate(), org::openscience::cdk::reaction::type::RearrangementLonePairReaction::initiate(), org::openscience::cdk::reaction::type::RearrangementCationReaction::initiate(), org::openscience::cdk::reaction::type::RearrangementAnionReaction::initiate(), org::openscience::cdk::reaction::type::RadicalSiteInitiationReaction::initiate(), org::openscience::cdk::reaction::type::RadicalSiteInitiationHReaction::initiate(), org::openscience::cdk::reaction::type::RadicalChargeSiteInitiationReaction::initiate(), org::openscience::cdk::reaction::type::RadicalChargeSiteInitiationHReaction::initiate(), org::openscience::cdk::reaction::type::HyperconjugationReaction::initiate(), org::openscience::cdk::reaction::type::HomolyticCleavageReaction::initiate(), org::openscience::cdk::reaction::type::HeterolyticCleavageSBReaction::initiate(), org::openscience::cdk::reaction::type::HeterolyticCleavagePBReaction::initiate(), org::openscience::cdk::reaction::type::ElectronImpactSDBReaction::initiate(), org::openscience::cdk::reaction::type::ElectronImpactPDBReaction::initiate(), org::openscience::cdk::reaction::type::ElectronImpactNBEReaction::initiate(), org::openscience::cdk::reaction::type::CarbonylEliminationReaction::initiate(), org::openscience::cdk::reaction::type::AdductionSodiumLPReaction::initiate(), org::openscience::cdk::reaction::type::AdductionProtonPBReaction::initiate(), org::openscience::cdk::reaction::type::AdductionProtonLPReaction::initiate(), org::openscience::cdk::reaction::mechanism::TautomerizationMechanism::initiate(), org::openscience::cdk::reaction::mechanism::RadicalSiteRearrangementMechanism::initiate(), org::openscience::cdk::reaction::mechanism::AdductionPBMechanism::initiate(), org::openscience::cdk::reaction::mechanism::AdductionLPMechanism::initiate(), org::openscience::cdk::tools::IonizationPotentialTool::initiateIonization(), org::openscience::cdk::graph::ConnectivityChecker::isConnected(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::layoutMolecule(), org::openscience::cdk::layout::StructureDiagramGenerator::layoutNextRingSystem(), org::openscience::cdk::templates::MoleculeFactory::makeAdenine(), org::openscience::cdk::structgen::RandomGenerator::mutate(), org::openscience::cdk::tools::manipulator::ChemModelManipulator::newChemModel(), org::openscience::cdk::smiles::SmilesParser::parseSmiles(), org::openscience::cdk::graph::ConnectivityChecker::partitionIntoMolecules(), org::openscience::cdk::ringsearch::RingPartitioner::partitionRings(), org::openscience::cdk::layout::StructureDiagramGenerator::placeFirstBond(), org::openscience::cdk::layout::AtomPlacer::placeLinearChain(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::placeLinearChains3D(), org::openscience::cdk::layout::RingPlacer::placeRingSubstituents(), org::openscience::cdk::io::inchi::INChIContentProcessorTool::processConnections(), org::openscience::cdk::io::inchi::INChIContentProcessorTool::processFormula(), org::openscience::cdk::isomorphism::UniversalIsomorphismTester::project(), org::openscience::cdk::io::SMILESReader::read(), org::openscience::cdk::io::Mol2Reader::read(), org::openscience::cdk::io::MDLRXNV3000Reader::read(), org::openscience::cdk::io::MDLRXNV2000Reader::read(), org::openscience::cdk::io::GhemicalMMReader::read(), org::openscience::cdk::io::MDLV3000Reader::readAtomBlock(), org::openscience::cdk::io::MDLV3000Reader::readBondBlock(), org::openscience::cdk::io::ZMatrixReader::readChemFile(), org::openscience::cdk::io::XYZReader::readChemFile(), org::openscience::cdk::io::ShelXReader::readChemFile(), org::openscience::cdk::io::PMPReader::readChemFile(), org::openscience::cdk::io::PDBReader::readChemFile(), org::openscience::cdk::io::MDLV2000Reader::readChemFile(), org::openscience::cdk::io::MDLRXNReader::readChemFile(), org::openscience::cdk::io::MDLReader::readChemFile(), org::openscience::cdk::io::INChIPlainTextReader::readChemFile(), org::openscience::cdk::io::HINReader::readChemFile(), org::openscience::cdk::io::Gaussian98Reader::readChemFile(), org::openscience::cdk::io::GamessReader::readChemFile(), org::openscience::cdk::io::CIFReader::readChemFile(), org::openscience::cdk::io::MDLRXNReader::readChemModel(), org::openscience::cdk::io::Gaussian98Reader::readCoordinates(), org::openscience::cdk::io::Gaussian03Reader::readCoordinates(), org::openscience::cdk::io::GamessReader::readCoordinates(), org::openscience::cdk::io::Mol2Reader::readMolecule(), org::openscience::cdk::io::MDLV2000Reader::readMolecule(), org::openscience::cdk::io::MDLReader::readMolecule(), org::openscience::cdk::io::MDLV3000Reader::readSGroup(), org::openscience::cdk::smiles::DeduceBondSystemTool::recoverRingSystem(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::removeHydrogens(), org::openscience::cdk::tools::manipulator::ReactionManipulator::reverse(), org::openscience::cdk::tools::SaturationChecker::saturate(), org::openscience::cdk::tools::LonePairElectronChecker::saturate(), org::openscience::cdk::tools::SmilesValencyChecker::saturateByIncreasingBondOrder(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::searchAndPlaceBranches(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::setBranchAtom(), org::openscience::cdk::layout::StructureDiagramGenerator::setMolecule(), org::openscience::cdk::tools::manipulator::ReactionSchemeManipulator::setScheme(), org::openscience::cdk::layout::StructureDiagramGenerator::StructureDiagramGenerator(), org::openscience::cdk::formula::rules::ElementRule::validate(), org::openscience::cdk::io::SDFWriter::write(), org::openscience::cdk::io::PDBWriter::write(), org::openscience::cdk::io::MDLWriter::write(), org::openscience::cdk::io::HINWriter::write(), and org::openscience::cdk::io::MDLWriter::writeMolecule().


Generated by  Doxygen 1.6.0   Back to index