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void org::openscience::cdk::interfaces::IAtomContainer::addAtom ( IAtom  atom  )  [inherited]

Adds an atom to this container.

Parameters:
atom The atom to be added to this container

Implemented in org::openscience::cdk::AtomContainer, org::openscience::cdk::debug::DebugAminoAcid, org::openscience::cdk::debug::DebugAtomContainer, org::openscience::cdk::debug::DebugBioPolymer, org::openscience::cdk::debug::DebugCrystal, org::openscience::cdk::debug::DebugMolecule, org::openscience::cdk::debug::DebugMonomer, org::openscience::cdk::debug::DebugPolymer, org::openscience::cdk::debug::DebugRing, org::openscience::cdk::debug::DebugStrand, org::openscience::cdk::interfaces::IBioPolymer, org::openscience::cdk::interfaces::ICrystal, org::openscience::cdk::interfaces::IPolymer, org::openscience::cdk::interfaces::IStrand, org::openscience::cdk::isomorphism::matchers::QueryAtomContainer, and org::openscience::cdk::Strand.

Referenced by org::openscience::cdk::applications::jchempaint::action::EditAction::actionPerformed(), org::openscience::cdk::Strand::addAtom(), org::openscience::cdk::Polymer::addAtom(), org::openscience::cdk::tools::HydrogenAdder::addExplicitHydrogensToSatisfyValency(), org::openscience::cdk::tools::GenerateFragments::addFragments(), org::openscience::cdk::tools::GenerateFragments::addPathFragments(), org::openscience::cdk::graph::PathTools::breadthFirstSearch(), org::openscience::cdk::AtomContainer::clone(), org::openscience::cdk::ringsearch::RingPartitioner::convertToAtomContainer(), org::openscience::cdk::structgen::deterministic::GENMDeterministicGenerator::convertToMol(), org::openscience::cdk::ringsearch::AllRingsFinder::detectRings(), org::openscience::cdk::io::iterator::event::EventCMLHandler::endObject(), org::openscience::cdk::inchi::InChIToStructure::generateAtomContainerFromInchi(), org::openscience::cdk::structgen::deterministic::GENMDeterministicGenerator::generateIsomers(), org::openscience::cdk::tools::GenerateFragments::generateMurckoFragments(), org::openscience::cdk::modeling::builder3d::AtomPlacer3D::getAllPlacedAtoms(), org::openscience::cdk::controller::AbstractController2D::getConnectedAtomsCenter(), org::openscience::cdk::controller::AbstractController2D::getContainedAtoms(), org::openscience::cdk::graph::SpanningTree::getCyclicFragmentsContainer(), org::openscience::cdk::controller::AbstractController2D::getHighlighted(), 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::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::tools::GenerateFragments::getPossibleLinkerSubstituents(), org::openscience::cdk::modeling::builder3d::AtomPlacer3D::getUnplacedAtoms(), org::openscience::cdk::layout::StructureDiagramGenerator::getUnplacedAtoms(), org::openscience::cdk::modeling::builder3d::AtomTetrahedralLigandPlacer3D::getUnsetAtomsInAtomContainer(), org::openscience::cdk::reaction::type::HyperconjugationReaction::initiate(), org::openscience::cdk::graph::ConnectivityChecker::isConnected(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::layoutMolecule(), org::openscience::cdk::smiles::SmilesParser::parseString(), org::openscience::cdk::graph::ConnectivityChecker::partitionIntoMolecules(), org::openscience::cdk::layout::RingPlacer::partitionNonRingPartners(), org::openscience::cdk::layout::AtomPlacer::partitionPartners(), org::openscience::cdk::layout::StructureDiagramGenerator::placeFirstBond(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::placeLinearChains3D(), org::openscience::cdk::io::inchi::INChIContentProcessorTool::processFormula(), org::openscience::cdk::isomorphism::UniversalIsomorphismTester::project(), org::openscience::cdk::io::MDLV3000Reader::readAtomBlock(), org::openscience::cdk::io::ZMatrixReader::readChemFile(), org::openscience::cdk::io::XYZReader::readChemFile(), org::openscience::cdk::io::PMPReader::readChemFile(), org::openscience::cdk::io::PDBReader::readChemFile(), org::openscience::cdk::io::HINReader::readChemFile(), org::openscience::cdk::io::Gaussian98Reader::readCoordinates(), org::openscience::cdk::io::Gaussian03Reader::readCoordinates(), org::openscience::cdk::smiles::DeduceBondSystemTool::recoverRingSystem(), org::openscience::cdk::applications::undoredo::AddHydrogenEdit::redoExplicitHydrogenAdding(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::removeHydrogens(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::searchAndPlaceBranches(), org::openscience::cdk::controller::AbstractController2D::selectNearestChemObjectIfNoneSelected(), and org::openscience::cdk::modeling::builder3d::ModelBuilder3D::setBranchAtom().


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