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Iterable<IAtom> org::openscience::cdk::interfaces::IAtomContainer::atoms (  ) [inherited]

Returns an Iterable for looping over all atoms in this container.

Returns:
An Iterable with the atoms in 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, and org::openscience::cdk::debug::DebugStrand.

Referenced by org::openscience::cdk::charges::MMFF94PartialCharges::assignMMFF94PartialCharges(), org::openscience::cdk::qsar::descriptors::molecular::TPSADescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::ChiPathDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::ChiPathClusterDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::ChiClusterDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::ChiChainDescriptor::calculate(), org::openscience::cdk::geometry::RDFCalculator::calculate(), org::openscience::cdk::charges::StabilizationCharges::calculatePositive(), org::openscience::cdk::BioPolymer::clone(), org::openscience::cdk::templates::AminoAcids::createAAs(), org::openscience::cdk::tools::IDCreator::createIDsForAtomContainer(), org::openscience::cdk::graph::invariant::CanonicalLabeler::createInvarLabel(), org::openscience::cdk::smiles::SmilesGenerator::createSMILES(), org::openscience::cdk::tools::StructureResonanceGenerator::existAC(), org::openscience::cdk::tools::IonizationPotentialTool::familyBond(), org::openscience::cdk::fingerprint::Fingerprinter::findPathes(), org::openscience::cdk::geometry::CrystalGeometryTools::fractionalToCartesian(), org::openscience::cdk::inchi::InChIGenerator::generateInchiFromCDKAtomContainer(), org::openscience::cdk::similarity::DistanceMoment::generateMoments(), org::openscience::cdk::geometry::GeometryTools::get2DCenter(), org::openscience::cdk::geometry::GeometryTools::get2DCentreOfMass(), org::openscience::cdk::geometry::GeometryTools::get3DCenter(), org::openscience::cdk::geometry::GeometryTools::get3DCentreOfMass(), org::openscience::cdk::FragmentAtom::getExactMass(), org::openscience::cdk::layout::TemplateHandler::getMappedSubstructures(), org::openscience::cdk::geometry::GeometryTools::has2DCoordinatesNew(), org::openscience::cdk::geometry::GeometryTools::has3DCoordinates(), org::openscience::cdk::geometry::CrystalGeometryTools::hasCrystalCoordinates(), org::openscience::cdk::layout::TemplateHandler::haveSameAtoms(), org::openscience::cdk::reaction::type::TautomerizationReaction::initiate(), org::openscience::cdk::reaction::type::SharingLonePairReaction::initiate(), org::openscience::cdk::reaction::type::SharingChargeSBReaction::initiate(), org::openscience::cdk::reaction::type::SharingChargeDBReaction::initiate(), org::openscience::cdk::reaction::type::SharingAnionReaction::initiate(), org::openscience::cdk::reaction::type::RearrangementLonePairReaction::initiate(), org::openscience::cdk::reaction::type::RearrangementCationReaction::initiate(), org::openscience::cdk::reaction::type::RearrangementAnionReaction::initiate(), org::openscience::cdk::reaction::type::HyperconjugationReaction::initiate(), org::openscience::cdk::reaction::type::ElectronImpactNBEReaction::initiate(), org::openscience::cdk::reaction::type::CarbonylEliminationReaction::initiate(), org::openscience::cdk::reaction::type::AdductionSodiumLPReaction::initiate(), org::openscience::cdk::reaction::type::AdductionProtonLPReaction::initiate(), org::openscience::cdk::aromaticity::CDKHueckelAromaticityDetector::isRingSystemSproutedWithNonRingDoubleBonds(), org::openscience::cdk::layout::StructureDiagramGenerator::layoutRingSet(), org::openscience::cdk::pharmacophore::PharmacophoreMatcher::matches(), org::openscience::cdk::smiles::SmilesParser::parseSmiles(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::removingFlagsAromaticity(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::setAtomProperties(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::setFlags(), org::openscience::cdk::io::cml::MDMoleculeConvention::startElement(), org::openscience::cdk::geometry::GeometryTools::translate2D(), org::openscience::cdk::geometry::GeometryTools::translate2DCenterTo(), org::openscience::cdk::geometry::GeometryTools::translate2DCentreOfMassTo(), org::openscience::cdk::geometry::GeometryTools::translateAllPositive(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::unregisterAtomListeners(), and org::openscience::cdk::io::HINWriter::writeMolecule().


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