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Iterator org::openscience::cdk::interfaces::IAtomContainer::atoms (  )  [inherited]

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

Returns:
An Iterator 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::applications::jchempaint::action::PerceiveAtomTypesAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::CreateReactionAction::actionPerformed(), org::openscience::cdk::tools::HydrogenAdder::addExplicitHydrogensToSatisfyValency(), org::openscience::cdk::tools::HydrogenAdder::addImplicitHydrogensToSatisfyValency(), org::openscience::cdk::charges::MMFF94PartialCharges::assignMMFF94PartialCharges(), org::openscience::cdk::graph::SpanningTree::buildSpanningTree(), org::openscience::cdk::qsar::descriptors::molecular::TPSADescriptor::calculate(), org::openscience::cdk::qsar::descriptors::bond::IPBondDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::IPAtomicDescriptor::calculateCarbonylDescriptor(), org::openscience::cdk::BioPolymer::clone(), org::openscience::cdk::applications::FileConvertor::convert(), 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::geometry::CrystalGeometryTools::fractionalToCartesian(), org::openscience::cdk::inchi::InChIGenerator::generateInchiFromCDKAtomContainer(), org::openscience::cdk::similarity::DistanceMoment::generateMoments(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::get2DCenter(), org::openscience::cdk::geometry::GeometryTools::get2DCenter(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::get2DCentreOfMass(), org::openscience::cdk::geometry::GeometryTools::get2DCentreOfMass(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::get3DCenter(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::get3DCentreOfMass(), org::openscience::cdk::tools::IsotopeGenerator::getIsotopes(), org::openscience::cdk::layout::TemplateHandler::getMappedSubstructures(), org::openscience::cdk::geometry::GeometryTools::getScaleFactor(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::has2DCoordinatesNew(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::has3DCoordinates(), org::openscience::cdk::geometry::CrystalGeometryTools::hasCrystalCoordinates(), org::openscience::cdk::layout::TemplateHandler::haveSameAtoms(), org::openscience::cdk::aromaticity::AromaticityCalculator::isAromatic(), org::openscience::cdk::layout::StructureDiagramGenerator::layoutRingSet(), org::openscience::cdk::controller::AbstractController2D::makeRingAromatic(), org::openscience::cdk::controller::AbstractController2D::moveSelectedAtomsWith(), org::openscience::cdk::applications::jchempaint::JChemPaintPanel::scaleAndCenterMolecule(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::setAtomProperties(), org::openscience::cdk::io::cml::MDMoleculeConvention::startElement(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::translate2D(), org::openscience::cdk::geometry::GeometryTools::translate2D(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::translate2DCenterTo(), org::openscience::cdk::geometry::GeometryTools::translate2DCenterTo(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::translate2DCentreOfMassTo(), org::openscience::cdk::geometry::GeometryTools::translate2DCentreOfMassTo(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::translateAllPositive(), org::openscience::cdk::geometry::GeometryTools::translateAllPositive(), and org::openscience::cdk::io::HINWriter::writeMolecule().


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