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boolean org::openscience::cdk::interfaces::IAtomContainer::contains ( IAtom  atom ) [inherited]

True, if the AtomContainer contains the given atom object.

Parameters:
atomthe atom this AtomContainer is searched for
Returns:
True, if the AtomContainer contains the given atom object

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::addFragments(), org::openscience::cdk::tools::GenerateFragments::addPathFragments(), org::openscience::cdk::qsar::descriptors::atompair::PiContactDetectionDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::IsProtonInConjugatedPiSystemDescriptor::calculate(), org::openscience::cdk::charges::StabilizationCharges::calculatePositive(), org::openscience::cdk::tools::GenerateFragments::checkPath(), org::openscience::cdk::RingSet::contains(), org::openscience::cdk::ringsearch::RingPartitioner::convertToAtomContainer(), org::openscience::cdk::graph::invariant::ConjugatedPiSystemsDetector::detect(), org::openscience::cdk::tools::IonizationPotentialTool::familyBond(), org::openscience::cdk::tools::GenerateFragments::generateMurckoFragments(), org::openscience::cdk::RingSet::getConnectedRings(), org::openscience::cdk::tools::StructureResonanceGenerator::getContainers(), org::openscience::cdk::graph::SpanningTree::getCyclicFragmentsContainer(), org::openscience::cdk::layout::TemplateHandler::getMappedSubstructures(), org::openscience::cdk::tools::GenerateFragments::getPossibleLinkerSubstituents(), org::openscience::cdk::RingSet::getRings(), org::openscience::cdk::layout::TemplateHandler::haveSameAtoms(), org::openscience::cdk::qsar::descriptors::atompair::PiContactDetectionDescriptor::isANeighboorsInAnAtomContainer(), org::openscience::cdk::tools::manipulator::RingSetManipulator::isSameRing(), org::openscience::cdk::layout::StructureDiagramGenerator::layoutRingSet(), org::openscience::cdk::layout::RingPlacer::partitionNonRingPartners(), org::openscience::cdk::layout::RingPlacer::placeBridgedRing(), org::openscience::cdk::smiles::DeduceBondSystemTool::recoverRingSystem(), org::openscience::cdk::tools::manipulator::ChemModelManipulator::removeAtomAndConnectedElectronContainers(), org::openscience::cdk::tools::manipulator::ChemModelManipulator::removeElectronContainer(), and org::openscience::cdk::charges::GasteigerPEPEPartialCharges::setAntiFlags().

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