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IAtom org::openscience::cdk::interfaces::IAtomContainer::getAtom ( int  number ) [inherited]

Get the atom at position number in [0,..].

Parameters:
numberThe position of the atom to be retrieved.
Returns:
The atom number
See also:
setAtom

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, and org::openscience::cdk::debug::DebugStrand.

Referenced by org::openscience::cdk::AtomContainer::add(), org::openscience::cdk::modeling::builder3d::AtomTetrahedralLigandPlacer3D::add3DCoordinatesForSinglyBondedLigands(), org::openscience::cdk::tools::GenerateFragments::addFragmentBonds(), org::openscience::cdk::tools::GenerateFragments::addFragments(), org::openscience::cdk::tools::GenerateFragments::addPathFragments(), org::openscience::cdk::modeling::builder3d::AtomPlacer3D::allHeavyAtomsPlaced(), org::openscience::cdk::layout::AtomPlacer::allPlaced(), org::openscience::cdk::modeling::forcefield::ForceFieldTools::assignCoordinatesToMolecule(), org::openscience::cdk::charges::GasteigerMarsiliPartialCharges::assignGasteigerMarsiliSigmaPartialCharges(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::assignGasteigerPiPartialCharges(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::assignPiFactors(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::assignrPiMarsilliFactors(), org::openscience::cdk::AtomContainer::AtomContainer(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::WeightedPathDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::MomentOfInertiaDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::LongestAliphaticChainDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::LargestChainDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::KappaShapeIndicesDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::HBondDonorCountDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::HBondAcceptorCountDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::CPSADescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::BCUTDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::AromaticAtomsCountDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::ALOGPDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atompair::PiContactDetectionDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::StabilizationPlusChargeDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::SigmaElectronegativityDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::ProtonTotalPartialChargeDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::PiElectronegativityDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::PartialSigmaChargeDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::IsProtonInConjugatedPiSystemDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::IsProtonInAromaticSystemDescriptor::calculate(), org::openscience::cdk::charges::PiElectronegativity::calculatePiElectronegativity(), org::openscience::cdk::charges::StabilizationCharges::calculatePositive(), org::openscience::cdk::charges::Electronegativity::calculateSigmaElectronegativity(), org::openscience::cdk::layout::AtomPlacer::calculateWeights(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::checkAllRingAtomsHasCoordinates(), org::openscience::cdk::layout::RingPlacer::checkAndMarkPlaced(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::cleanFlagReactiveCenter(), org::openscience::cdk::AtomContainer::clone(), org::openscience::cdk::isomorphism::matchers::QueryAtomContainerCreator::createAnyAtomAnyBondContainer(), org::openscience::cdk::isomorphism::matchers::QueryAtomContainerCreator::createAnyAtomContainer(), org::openscience::cdk::isomorphism::matchers::QueryAtomContainerCreator::createAnyAtomForPseudoAtomQueryContainer(), org::openscience::cdk::isomorphism::matchers::QueryAtomContainerCreator::createBasicQueryContainer(), org::openscience::cdk::tools::HOSECodeGenerator::createCode(), org::openscience::cdk::smiles::SmilesGenerator::createSMILESWithoutCheckForMultipleMolecules(), org::openscience::cdk::isomorphism::matchers::QueryAtomContainerCreator::createSymbolAndBondOrderQueryContainer(), org::openscience::cdk::isomorphism::matchers::QueryAtomContainerCreator::createSymbolAndChargeQueryContainer(), org::openscience::cdk::layout::AtomPlacer::distributePartners(), org::openscience::cdk::structgen::stochastic::operator::CrossoverMachine::doCrossover(), org::openscience::cdk::io::iterator::event::EventCMLHandler::endObject(), org::openscience::cdk::qsar::descriptors::molecular::ChiIndexUtils::evalSimpleIndex(), org::openscience::cdk::tools::StructureResonanceGenerator::existAC(), org::openscience::cdk::graph::PathTools::findClosestByBond(), org::openscience::cdk::modeling::builder3d::AtomPlacer3D::findHeavyAtomsInChain(), org::openscience::cdk::layout::StructureDiagramGenerator::fixMol(), org::openscience::cdk::layout::StructureDiagramGenerator::fixRest(), org::openscience::cdk::structgen::SingleStructureRandomGenerator::generate(), org::openscience::cdk::layout::StructureDiagramGenerator::generateCoordinates(), org::openscience::cdk::layout::StructureDiagramGenerator::generateExperimentalCoordinates(), org::openscience::cdk::tools::GenerateFragments::generateMurckoFragments(), org::openscience::cdk::ConformerContainer::get(), org::openscience::cdk::modeling::builder3d::AtomTetrahedralLigandPlacer3D::get3DCoordinatesForSP2Ligands(), org::openscience::cdk::modeling::builder3d::AtomTetrahedralLigandPlacer3D::get3DCoordinatesForSP3Ligands(), org::openscience::cdk::modeling::builder3d::AtomPlacer3D::getAllPlacedAtoms(), org::openscience::cdk::geometry::GeometryTools::getAngleRMSD(), org::openscience::cdk::structgen::stochastic::PartialFilledStructureMerger::getAnotherUnsaturatedNode(), org::openscience::cdk::structgen::SingleStructureRandomGenerator::getAnotherUnsaturatedNode(), org::openscience::cdk::layout::OverlapResolver::getAtomOverlapScore(), org::openscience::cdk::geometry::GeometryTools::getBondLengthRMSD(), org::openscience::cdk::layout::RingPlacer::getBridgeAtoms(), org::openscience::cdk::geometry::GeometryTools::getClosestAtom(), org::openscience::cdk::RingSet::getConnectedRings(), org::openscience::cdk::modeling::forcefield::ForceFieldTools::getCoordinates3xNVector(), org::openscience::cdk::tools::manipulator::MolecularFormulaManipulator::getDBE(), org::openscience::cdk::layout::AtomPlacer::getDegreeSum(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::getElectrostaticPotentialN(), org::openscience::cdk::modeling::builder3d::AtomPlacer3D::getFarthestAtom(), org::openscience::cdk::geometry::GeometryTools::getHeavyAtomRMSD(), org::openscience::cdk::tools::HOSECodeGenerator::getHOSECode(), org::openscience::cdk::layout::AtomPlacer::getInitialLongestChain(), org::openscience::cdk::layout::AtomPlacer::getLongestUnplacedChain(), org::openscience::cdk::geometry::GeometryTools::getMinMax(), org::openscience::cdk::tools::manipulator::RingSetManipulator::getMostComplexRing(), org::openscience::cdk::layout::AtomPlacer::getPlacedAtoms(), org::openscience::cdk::modeling::forcefield::ForceFieldTools::getPoint3dCoordinates(), org::openscience::cdk::tools::IonizationPotentialTool::getQSARs(), org::openscience::cdk::tools::HOSECodeGenerator::getSpheres(), org::openscience::cdk::layout::AtomPlacer::getWeightNumbers(), org::openscience::cdk::layout::StructureDiagramGenerator::handleAliphatics(), org::openscience::cdk::ConformerContainer::indexOf(), org::openscience::cdk::reaction::mechanism::TautomerizationMechanism::initiate(), org::openscience::cdk::reaction::mechanism::SharingElectronMechanism::initiate(), 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org::openscience::cdk::layout::AtomPlacer::placeLinearChain(), org::openscience::cdk::layout::RingPlacer::placeRingSubstituents(), org::openscience::cdk::layout::RingPlacer::placeSpiroRing(), org::openscience::cdk::io::inchi::INChIContentProcessorTool::processConnections(), org::openscience::cdk::structgen::RandomGenerator::proposeStructure(), org::openscience::cdk::io::MDLV3000Reader::readBondBlock(), org::openscience::cdk::io::HINReader::readChemFile(), 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::MDLV3000Reader::readSGroup(), org::openscience::cdk::smiles::DeduceBondSystemTool::removeExtraRings(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::removeHydrogens(), org::openscience::cdk::layout::StructureDiagramGenerator::resetUnplacedRings(), org::openscience::cdk::tools::AtomTypeTools::ringSystemClassifier(), org::openscience::cdk::geometry::GeometryTools::rotate(), org::openscience::cdk::geometry::alignment::KabschAlignment::rotateAtomContainer(), org::openscience::cdk::structgen::VicinitySampler::sample(), org::openscience::cdk::geometry::GeometryTools::scaleMolecule(), org::openscience::cdk::ringsearch::AllRingsFinder::selectAtom(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::setAtomsToPlace(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::setAtomsToUnPlaced(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::setAtomsToUnVisited(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::setFlags(), org::openscience::cdk::layout::StructureDiagramGenerator::setMolecule(), org::openscience::cdk::ConformerContainer::toArray(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::translateStructure(), org::openscience::cdk::io::CrystClustWriter::writeCrystal(), and org::openscience::cdk::modeling::builder3d::AtomPlacer3D::zmatrixChainToCartesian().


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