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int org::openscience::cdk::interfaces::IAtomContainer::getAtomNumber ( IAtom  atom ) [inherited]

Returns the position of a given atom in the atoms array. It returns -1 if the atom atom does not exist.

Parameters:
atomThe atom to be sought
Returns:
The Position of the atom in the atoms array in [0,..].

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::tools::GenerateFragments::addFragmentBonds(), org::openscience::cdk::qsar::descriptors::atompair::PiContactDetectionDescriptor::calculate(), org::openscience::cdk::charges::PiElectronegativity::calculatePiElectronegativity(), org::openscience::cdk::charges::StabilizationCharges::calculatePositive(), 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::isomorphism::matchers::QueryAtomContainerCreator::createSymbolAndBondOrderQueryContainer(), org::openscience::cdk::isomorphism::matchers::QueryAtomContainerCreator::createSymbolAndChargeQueryContainer(), org::openscience::cdk::layout::AtomPlacer::distributePartners(), org::openscience::cdk::tools::StructureResonanceGenerator::existAC(), org::openscience::cdk::modeling::builder3d::AtomPlacer3D::findHeavyAtomsInChain(), org::openscience::cdk::geometry::GeometryTools::getAngleRMSD(), org::openscience::cdk::geometry::GeometryTools::getBondLengthRMSD(), org::openscience::cdk::qsar::descriptors::molecular::ChiIndexUtils::getUniqueBondSubgraphs(), org::openscience::cdk::layout::AtomPlacer::getWeightNumbers(), org::openscience::cdk::layout::StructureDiagramGenerator::handleAliphatics(), org::openscience::cdk::reaction::mechanism::TautomerizationMechanism::initiate(), org::openscience::cdk::reaction::mechanism::SharingElectronMechanism::initiate(), org::openscience::cdk::reaction::mechanism::RemovingSEofNBMechanism::initiate(), org::openscience::cdk::reaction::mechanism::RemovingSEofBMechanism::initiate(), org::openscience::cdk::reaction::mechanism::RearrangementChargeMechanism::initiate(), org::openscience::cdk::reaction::mechanism::RadicalSiteRearrangementMechanism::initiate(), org::openscience::cdk::reaction::mechanism::RadicalSiteIonizationMechanism::initiate(), org::openscience::cdk::reaction::mechanism::HomolyticCleavageMechanism::initiate(), org::openscience::cdk::reaction::mechanism::HeterolyticCleavageMechanism::initiate(), org::openscience::cdk::reaction::mechanism::AdductionPBMechanism::initiate(), org::openscience::cdk::reaction::mechanism::AdductionLPMechanism::initiate(), org::openscience::cdk::isomorphism::matchers::smarts::RecursiveSmartsAtom::initilizeBitSets(), org::openscience::cdk::smiles::SmilesGenerator::isEndOfDoubleBond(), org::openscience::cdk::geometry::BondTools::isEndOfDoubleBond(), org::openscience::cdk::smiles::SmilesGenerator::isStartOfDoubleBond(), org::openscience::cdk::geometry::BondTools::isStartOfDoubleBond(), org::openscience::cdk::isomorphism::UniversalIsomorphismTester::makeAtomsMapOfBondsMap(), org::openscience::cdk::isomorphism::matchers::smarts::RecursiveSmartsAtom::matches(), org::openscience::cdk::layout::RingPlacer::placeBridgedRing(), org::openscience::cdk::layout::StructureDiagramGenerator::placeFirstBond(), org::openscience::cdk::layout::RingPlacer::placeFusedRing(), org::openscience::cdk::layout::RingPlacer::placeRingSubstituents(), org::openscience::cdk::layout::AtomPlacer::populatePolygonCorners(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::setFlags(), and org::openscience::cdk::io::HINWriter::writeMolecule().

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