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List org::openscience::cdk::interfaces::IAtomContainer::getConnectedAtomsList ( IAtom  atom  )  [inherited]

Returns an ArrayList of all atoms connected to the given atom.

Parameters:
atom The atom the bond partners are searched of.
Returns:
The ArrayList with the connected atoms

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::charges::MMFF94PartialCharges::assignMMFF94PartialCharges(), org::openscience::cdk::tools::HOSECodeGenerator::breadthFirstSearch(), org::openscience::cdk::qsar::descriptors::molecular::TPSADescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::HBondDonorCountDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::molecular::HBondAcceptorCountDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::IsProtonInAromaticSystemDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::IPAtomicDescriptor::calculateCarbonylDescriptor(), org::openscience::cdk::graph::invariant::ConjugatedPiSystemsDetector::checkAtom(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::countExplicitHydrogens(), org::openscience::cdk::graph::invariant::CanonicalLabeler::createInvarLabel(), org::openscience::cdk::qsar::ChiIndexUtils::deltavPhosphorous(), org::openscience::cdk::qsar::ChiIndexUtils::deltavSulphur(), org::openscience::cdk::atomtype::EStateAtomTypeMatcher::findMatchingAtomType(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::getAngleRMSD(), org::openscience::cdk::structgen::stochastic::PartialFilledStructureMerger::getAnotherUnsaturatedNode(), org::openscience::cdk::structgen::SingleStructureRandomGenerator::getAnotherUnsaturatedNode(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getAromaticCarbonsCount(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getAromaticNitrogensCount(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getAtomTypeXCount(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::getBestAlignmentForLabel(), org::openscience::cdk::geometry::GeometryTools::getBestAlignmentForLabel(), org::openscience::cdk::geometry::GeometryToolsInternalCoordinates::getBondLengthRMSD(), org::openscience::cdk::layout::RingPlacer::getBridgeAtoms(), org::openscience::cdk::smiles::SmilesGenerator::getCanNeigh(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getCarbonsCount(), org::openscience::cdk::controller::AbstractController2D::getConnectedAtomsCenter(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getDoubleBondedCarbonsCount(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getDoubleBondedNitrogenCount(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getDoubleBondedOxygenCount(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getDoubleBondedSulfurCount(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::getElectrostaticPotentialN(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getHalogenCount(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getHydrogenCount(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getIfCarbonIsHydrophobic(), org::openscience::cdk::graph::invariant::MorganNumbersTools::getLongMorganNumbers(), org::openscience::cdk::graph::invariant::MorganNumbersTools::getMorganNumbers(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getOxygenCount(), org::openscience::cdk::graph::PathTools::getPathsOfLength(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getPiSystemsCount(), org::openscience::cdk::modeling::builder3d::AtomTetrahedralLigandPlacer3D::getPlacedHeavyAtomInAtomContainer(), org::openscience::cdk::tools::GenerateFragments::getPossibleLinkerSubstituents(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getPresenceOfCarbonil(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getPresenceOfHydroxy(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getPresenceOfNitro(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getPresenceOfSulfat(), org::openscience::cdk::graph::PathTools::getShortestPath(), org::openscience::cdk::modeling::builder3d::AtomTetrahedralLigandPlacer3D::getUnsetAtomsInAtomContainer(), org::openscience::cdk::layout::AtomPlacer::getWeightNumbers(), org::openscience::cdk::reaction::type::HyperconjugationReaction::initiate(), org::openscience::cdk::reaction::type::CarbonylEliminationReaction::initiate(), org::openscience::cdk::smiles::SmilesGenerator::isEndOfDoubleBond(), org::openscience::cdk::geometry::BondTools::isEndOfDoubleBond(), org::openscience::cdk::geometry::BondTools::isSquarePlanar(), org::openscience::cdk::smiles::SmilesGenerator::isStartOfDoubleBond(), org::openscience::cdk::geometry::BondTools::isStartOfDoubleBond(), org::openscience::cdk::geometry::BondTools::isStereo(), org::openscience::cdk::geometry::BondTools::isTetrahedral(), org::openscience::cdk::geometry::BondTools::isTrigonalBipyramidalOrOctahedral(), org::openscience::cdk::smiles::SmilesGenerator::isValidDoubleBondConfiguration(), org::openscience::cdk::geometry::BondTools::isValidDoubleBondConfiguration(), org::openscience::cdk::isomorphism::matchers::smarts::HydrogenAtom::matches(), org::openscience::cdk::tools::HOSECodeGenerator::nextSphere(), org::openscience::cdk::smiles::SmilesGenerator::parseChain(), org::openscience::cdk::layout::RingPlacer::partitionNonRingPartners(), org::openscience::cdk::layout::AtomPlacer::partitionPartners(), org::openscience::cdk::graph::invariant::CanonicalLabeler::primeProduct(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::removeHydrogens(), org::openscience::cdk::geometry::BondTools::stereosAreOpposite(), and org::openscience::cdk::tools::GenerateFragments::zeroAtomLinker().


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