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

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

Parameters:
number The 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::applications::jchempaint::action::FlipAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::EditAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::DictionaryAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::CreateReactionAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::CopyPasteAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::CleanupAction::actionPerformed(), org::openscience::cdk::modeling::builder3d::AtomTetrahedralLigandPlacer3D::add3DCoordinatesForSinglyBondedLigands(), org::openscience::cdk::tools::GenerateFragments::addFragmentBonds(), org::openscience::cdk::tools::GenerateFragments::addFragments(), org::openscience::cdk::applications::jchempaint::action::AddHydrogenAction::addHydrogenToAllMolecules(), org::openscience::cdk::tools::GenerateFragments::addPathFragments(), 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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::AromaticAtomsCountDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::bond::ResonancePositiveChargeDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atompair::PiContactDetectionDescriptor::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::qsar::descriptors::atomic::IPAtomicDescriptor::calculate(), org::openscience::cdk::layout::AtomPlacer::calculateWeights(), org::openscience::cdk::graph::invariant::CanonicalLabeler::canonLabel(), org::openscience::cdk::controller::AbstractController2D::centerAtom(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::checkAllRingAtomsHasCoordinates(), org::openscience::cdk::layout::RingPlacer::checkAndMarkPlaced(), org::openscience::cdk::reaction::type::RearrangementCation3Reaction::cleanFlagReactiveCenter(), org::openscience::cdk::reaction::type::RadicalSiteInitiationHReaction::cleanFlagReactiveCenter(), org::openscience::cdk::reaction::type::BreakingBondReaction::cleanFlagReactiveCenter(), org::openscience::cdk::qsar::descriptors::bond::ResonancePositiveChargeDescriptor::cleanFlagReactiveCenter(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::cleanFlagReactiveCenter(), org::openscience::cdk::AtomContainer::clone(), org::openscience::cdk::config::IsotopeFactory::configureAtoms(), org::openscience::cdk::applications::FileConvertor::convert(), org::openscience::cdk::isomorphism::matchers::QueryAtomContainerCreator::createAnyAtomAnyBondContainer(), org::openscience::cdk::isomorphism::matchers::QueryAtomContainerCreator::createAnyAtomContainer(), org::openscience::cdk::isomorphism::matchers::QueryAtomContainerCreator::createAnyAtomForPseudoAtomQueryContainer(), org::openscience::cdk::controller::AbstractController2D::createAttachRing(), 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::createSymbolAndChargeQueryContainer(), org::openscience::cdk::aromaticity::HueckelAromaticityDetector::detectAromaticity(), org::openscience::cdk::layout::AtomPlacer::distributePartners(), 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org::openscience::cdk::smiles::DeduceBondSystemTool::removeExtraRings(), org::openscience::cdk::tools::StructureResonanceGenerator::removeFlags(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::removeHydrogens(), org::openscience::cdk::layout::StructureDiagramGenerator::resetUnplacedRings(), org::openscience::cdk::renderer::AbstractRenderer2D::ringIsAromatic(), org::openscience::cdk::tools::AtomTypeTools::ringSystemClassifier(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::rotate(), org::openscience::cdk::geometry::alignment::KabschAlignment::rotateAtomContainer(), org::openscience::cdk::structgen::VicinitySampler::sample(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::scaleMolecule(), 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::renderer::Renderer2DModel::setExternalSelectedPart(), org::openscience::cdk::tools::StructureResonanceGenerator::setID(), org::openscience::cdk::layout::StructureDiagramGenerator::setMolecule(), org::openscience::cdk::aromaticity::HueckelAromaticityDetector::setRingFlags(), org::openscience::cdk::renderer::Renderer2DModel::setSelectedPart(), org::openscience::cdk::isomorphism::matchers::smarts::SMARTSOperatorAtom::toString(), org::openscience::cdk::modeling::builder3d::ModelBuilder3D::translateStructure(), org::openscience::cdk::applications::undoredo::AddHydrogenEdit::undoExplicitHydrogenAdding(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::unregisterAtomListeners(), org::openscience::cdk::controller::AbstractController2D::updateMoleculeCoordinates(), 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