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IBond org::openscience::cdk::interfaces::IAtomContainer::getBond ( int  number  )  [inherited]

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

Parameters:
number The position of the bond to be retrieved.
Returns:
The bond number

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::DictionaryAction::actionPerformed(), org::openscience::cdk::applications::jchempaint::action::AdjustBondOrdersAction::actionPerformed(), org::openscience::cdk::tools::GenerateFragments::addFragmentBonds(), org::openscience::cdk::tools::GenerateFragments::addFragments(), org::openscience::cdk::tools::GenerateFragments::addPathFragments(), org::openscience::cdk::AtomContainer::AtomContainer(), org::openscience::cdk::graph::rebond::RebondTool::bondAtom(), org::openscience::cdk::tools::HOSECodeGenerator::breadthFirstSearch(), org::openscience::cdk::graph::SpanningTree::buildSpanningTree(), org::openscience::cdk::qsar::descriptors::bond::ResonancePositiveChargeDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::bond::IPBondDescriptor::calculate(), org::openscience::cdk::qsar::descriptors::atomic::IPAtomicDescriptor::calculateCarbonylDescriptor(), org::openscience::cdk::reaction::type::RearrangementRadical3Reaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::RearrangementRadical2Reaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::RearrangementRadical1Reaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::RearrangementCation3Reaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::RearrangementCation2Reaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::RearrangementCation1Reaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::RearrangementAnion3Reaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::RearrangementAnion2Reaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::RearrangementAnion1Reaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::RadicalSiteInitiationReaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::RadicalSiteInitiationHReaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::ElectronImpactPDBReaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::DisplacementChargeFromDonorReaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::DisplacementChargeFromAcceptorReaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::CleavageBondReaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::CleavageBondMultiReaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::CarbonylEliminationReaction::cleanFlagBOND(), org::openscience::cdk::reaction::type::BreakingBondReaction::cleanFlagBOND(), 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::ringsearch::RingPartitioner::convertToAtomContainer(), org::openscience::cdk::tools::DeAromatizationTool::deAromatize(), org::openscience::cdk::qsar::ChiIndexUtils::deltavPhosphorous(), org::openscience::cdk::qsar::ChiIndexUtils::deltavSulphur(), org::openscience::cdk::aromaticity::HueckelAromaticityDetector::detectAromaticity(), org::openscience::cdk::ringsearch::AllRingsFinder::detectRings(), org::openscience::cdk::atomtype::EStateAtomTypeMatcher::findMatchingAtomType(), org::openscience::cdk::qsar::descriptors::molecular::XLogPDescriptor::getAtomTypeXCount(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::getBondArray(), org::openscience::cdk::layout::OverlapResolver::getBondOverlapScore(), org::openscience::cdk::graph::SpanningTree::getCyclicFragmentsContainer(), 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::getHyperconjugationInteractions(), org::openscience::cdk::graph::matrix::ConnectionMatrix::getMatrix(), org::openscience::cdk::graph::matrix::AdjacencyMatrix::getMatrix(), org::openscience::cdk::graph::MoleculeGraphs::getMoleculeGraph(), org::openscience::cdk::layout::StructureDiagramGenerator::getNextAtomWithAliphaticUnplacedNeigbors(), 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::tools::StructureResonanceGenerator::getStructures(), org::openscience::cdk::charges::GasteigerPEPEPartialCharges::getTopologicalFactors(), org::openscience::cdk::qsar::ChiIndexUtils::getUniqueBondSubgraphs(), org::openscience::cdk::graph::SpanningTree::identifyBonds(), org::openscience::cdk::reaction::type::RearrangementRadical3Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementRadical2Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementRadical1Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementCation3Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementCation2Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementCation1Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementAnion3Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementAnion2Reaction::initiate(), org::openscience::cdk::reaction::type::RearrangementAnion1Reaction::initiate(), org::openscience::cdk::reaction::type::RadicalSiteInitiationReaction::initiate(), org::openscience::cdk::reaction::type::RadicalSiteInitiationHReaction::initiate(), org::openscience::cdk::reaction::type::HyperconjugationReaction::initiate(), org::openscience::cdk::reaction::type::ElectronImpactPDBReaction::initiate(), org::openscience::cdk::reaction::type::DisplacementChargeFromDonorReaction::initiate(), org::openscience::cdk::reaction::type::DisplacementChargeFromAcceptorReaction::initiate(), org::openscience::cdk::reaction::type::CleavageBondReaction::initiate(), org::openscience::cdk::reaction::type::CleavageBondMultiReaction::initiate(), org::openscience::cdk::reaction::type::CarbonylEliminationReaction::initiate(), org::openscience::cdk::reaction::type::BreakingBondReaction::initiate(), org::openscience::cdk::isomorphism::matchers::smarts::RecursiveSmartsAtom::initilizeBitSets(), org::openscience::cdk::smiles::SmilesGenerator::isEndOfDoubleBond(), org::openscience::cdk::geometry::BondTools::isEndOfDoubleBond(), org::openscience::cdk::smiles::SmilesGenerator::isStartOfDoubleBond(), org::openscience::cdk::geometry::BondTools::isStartOfDoubleBond(), org::openscience::cdk::layout::StructureDiagramGenerator::layoutRingSet(), org::openscience::cdk::isomorphism::UniversalIsomorphismTester::makeAtomsMapOfBondsMap(), org::openscience::cdk::structgen::RandomGenerator::mutate(), org::openscience::cdk::tools::HOSECodeGenerator::nextSphere(), org::openscience::cdk::tools::Normalizer::normalize(), org::openscience::cdk::smiles::SmilesGenerator::parseAtom(), org::openscience::cdk::smiles::SmilesGenerator::parseBond(), org::openscience::cdk::smiles::SmilesGenerator::parseChain(), org::openscience::cdk::layout::RingPlacer::placeBridgedRing(), org::openscience::cdk::layout::RingPlacer::placeFusedRing(), org::openscience::cdk::layout::AtomPlacer::placeLinearChain(), org::openscience::cdk::isomorphism::UniversalIsomorphismTester::project(), org::openscience::cdk::smiles::DeduceBondSystemTool::recoverRingSystem(), org::openscience::cdk::applications::undoredo::AddHydrogenEdit::redoExplicitHydrogenAdding(), org::openscience::cdk::tools::StructureResonanceGenerator::removeFlags(), org::openscience::cdk::tools::manipulator::AtomContainerManipulator::removeHydrogens(), org::openscience::cdk::structgen::VicinitySampler::sample(), org::openscience::cdk::geometry::BondTools::stereosAreOpposite(), org::openscience::cdk::smiles::DeduceBondSystemTool::storeRingSystem(), and org::openscience::cdk::applications::undoredo::AddHydrogenEdit::undoExplicitHydrogenAdding().


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