Uses of Interface
org.openscience.cdk.interfaces.IAtom
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Uses of IAtom in org.openscience.cdk
Classes in org.openscience.cdk that implement IAtom Modifier and Type Class Description classAtomRepresents the idea of an chemical atom.classAtomRefAn atom ref, references a CDKIAtomindirectly.classEnzymeResidueLocatorAtom that represents part of an residue in an enzyme, like Arg255.classFragmentAtomClass to represent an IPseudoAtom which embeds an IAtomContainer.classPseudoAtomRepresents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.Fields in org.openscience.cdk declared as IAtom Modifier and Type Field Description protected IAtomLonePair. atomThe atom with which this lone pair is associated.protected IAtomSingleElectron. atomThe atom with which this single electron is associated.protected IAtom[]Association. atomsThe atoms which take part in the association.protected IAtom[]AtomContainerLegacy. atomsInternal array of atoms.protected IAtom[]Bond. atomsA list of atoms participating in this bond.Methods in org.openscience.cdk that return IAtom Modifier and Type Method Description IAtomAtom. clone()Clones this atom object and its content.IAtomAtomRef. clone()Returns a deep clone of this IChemObject.IAtomAtomRef. deref()Dereference the atom pointer once providing access to the base atom.static IAtomAtomRef. deref(IAtom atom)Utility method to dereference an atom.IAtomAtomContainer. getAtom(int idx)Get the atom at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getAtomCount().IAtomAtomContainerLegacy. getAtom(int idx)Get the atom at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getAtomCount().IAtomBond. getAtom(int position)Returns an Atom from this bond.IAtomBondRef. getAtom(int position)Returns an Atom from this bond.IAtomLonePair. getAtom()Returns the associated Atom.IAtomSingleElectron. getAtom()Returns the associated Atom.IAtomAssociation. getAtomAt(int position)Returns an Atom from this Association.IAtom[]Association. getAtoms()Returns the array of atoms making up this Association.IAtomBond. getBegin()Access the begin (or first) atom of the bond.IAtomBondRef. getBegin()Access the begin (or first) atom of the bond.IAtomBond. getConnectedAtom(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.IAtomBondRef. getConnectedAtom(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.IAtom[]Bond. getConnectedAtoms(IAtom atom)Returns all the atoms in the bond connected to the given atom.IAtom[]BondRef. getConnectedAtoms(IAtom atom)Returns all the atoms in the bond connected to the given atom.IAtomAminoAcid. getCTerminus()Retrieves the C-terminus atom.IAtomBond. getEnd()Access the end (or second) atom of the bond.IAtomBondRef. getEnd()Access the end (or second) atom of the bond.IAtomAtomContainer. getFirstAtom()Returns the atom at position 0 in the container.IAtomAtomContainerLegacy. getFirstAtom()Returns the atom at position 0 in the container.IAtomAtomContainer. getLastAtom()Returns the atom at the last position in the container.IAtomAtomContainerLegacy. getLastAtom()Returns the atom at the last position in the container.IAtomAminoAcid. getNTerminus()Retrieves the N-terminus atom.IAtomBond. getOther(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correctIBond.getConnectedAtoms(IAtom)should be used.IAtomBondRef. getOther(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correctIBond.getConnectedAtoms(IAtom)should be used.IAtomAtomContainer. newAtom(int element, int numImplH)IAtomAtomContainer. newAtom(IAtom atom)IAtomDefaultChemObjectBuilder. newAtom()Create a new atom using the default constructor.Methods in org.openscience.cdk that return types with arguments of type IAtom Modifier and Type Method Description Iterable<IAtom>AtomContainer. atoms()Returns an Iterable for looping over all atoms in this container.Iterable<IAtom>AtomContainerLegacy. atoms()Returns an Iterable for looping over all atoms in this container.Iterable<IAtom>Bond. atoms()Returns the Iterator to atoms making up this bond.Iterable<IAtom>BondRef. atoms()Returns the Iterable to atoms making up this bond.List<IAtom>AtomContainer. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>AtomContainerLegacy. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.Methods in org.openscience.cdk with parameters of type IAtom Modifier and Type Method Description voidAtomContainer. addAtom(IAtom atom)Adds an atom to this container.voidAtomContainerLegacy. addAtom(IAtom atom)Adds an atom to this container.voidBioPolymer. addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)Adds the atom to a specified Strand and a specified Monomer.voidBioPolymer. addAtom(IAtom oAtom, IStrand oStrand)Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.voidPolymer. addAtom(IAtom oAtom, IMonomer oMonomer)Adds the atom oAtom to a specified Monomer.voidStrand. addAtom(IAtom oAtom)Adds the atom oAtom without specifying a Monomer or a Strand.voidStrand. addAtom(IAtom oAtom, IMonomer oMonomer)Adds the atom oAtom to a specific Monomer.voidAminoAcid. addCTerminus(IAtom atom)Add an Atom and makes it the C-terminus atom.voidAminoAcid. addNTerminus(IAtom atom)Add an Atom and makes it the N-terminus atom.booleanAssociation. contains(IAtom atom)Returns true if the given atom participates in this Association.booleanAtomContainer. contains(IAtom atom)True, if the AtomContainer contains the given atom object.booleanAtomContainerLegacy. contains(IAtom atom)True, if the AtomContainer contains the given atom object.booleanBond. contains(IAtom atom)Returns true if the given atom participates in this bond.booleanBondRef. contains(IAtom atom)Returns true if the given atom participates in this bond.booleanLonePair. contains(IAtom atom)Returns true if the given atom participates in this lone pair.booleanRingSet. contains(IAtom atom)True, if at least one of the rings in the ringset contains the given atom.booleanSingleElectron. contains(IAtom atom)Returns true if the given atom participates in this SingleElectron.static IAtomAtomRef. deref(IAtom atom)Utility method to dereference an atom.intAtomContainer. getAtomNumber(IAtom atom)Returns the position of a given atom in the atoms array.intAtomContainerLegacy. getAtomNumber(IAtom atom)Returns the position of a given atom in the atoms array.IBondAtom. getBond(IAtom atom)Returns the bond connecting 'this' atom to the provided atom.IBondAtomContainer. getBond(IAtom beg, IAtom end)Returns the bond that connects the two given atoms.IBondAtomContainerLegacy. getBond(IAtom atom1, IAtom atom2)Returns the bond that connects the two given atoms.IBondAtomRef. getBond(IAtom atom)Returns the bond connecting 'this' atom to the provided atom.intAtomContainer. getBondNumber(IAtom beg, IAtom end)Returns the position of the bond between two given atoms in the electronContainers array.intAtomContainerLegacy. getBondNumber(IAtom atom1, IAtom atom2)Returns the position of the bond between two given atoms in the electronContainers array.doubleAtomContainer. getBondOrderSum(IAtom atom)Returns the sum of the bond orders for a given Atom.doubleAtomContainerLegacy. getBondOrderSum(IAtom atom)Returns the sum of the bond orders for a given Atom.IAtomBond. getConnectedAtom(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.IAtomBondRef. getConnectedAtom(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.IAtom[]Bond. getConnectedAtoms(IAtom atom)Returns all the atoms in the bond connected to the given atom.IAtom[]BondRef. getConnectedAtoms(IAtom atom)Returns all the atoms in the bond connected to the given atom.intAtomContainer. getConnectedAtomsCount(IAtom atom)Returns the number of connected atoms (explicit degree) to the specified atom.intAtomContainerLegacy. getConnectedAtomsCount(IAtom atom)Returns the number of connected atoms (explicit degree) to the specified atom.List<IAtom>AtomContainer. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>AtomContainerLegacy. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.intAtomContainer. getConnectedBondsCount(IAtom atom)Returns the number of connected bonds (explicit degree) to the specified atom.intAtomContainerLegacy. getConnectedBondsCount(IAtom atom)Returns the number of connected bonds (explicit degree) to the specified atom.List<IBond>AtomContainer. getConnectedBondsList(IAtom atom)Returns the bonds connected connected to the specified atom.List<IBond>AtomContainerLegacy. getConnectedBondsList(IAtom atom)Returns the bonds connected connected to the specified atom.List<IElectronContainer>AtomContainer. getConnectedElectronContainersList(IAtom atom)Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.List<IElectronContainer>AtomContainerLegacy. getConnectedElectronContainersList(IAtom atom)Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.intAtomContainer. getConnectedLonePairsCount(IAtom atom)Returns the number of lone pairs connected to the specified atom.intAtomContainerLegacy. getConnectedLonePairsCount(IAtom atom)Returns the number of lone pairs connected to the specified atom.List<ILonePair>AtomContainer. getConnectedLonePairsList(IAtom atom)Returns the lone pairs connected connected to the specified atom.List<ILonePair>AtomContainerLegacy. getConnectedLonePairsList(IAtom atom)Returns the lone pairs connected connected to the specified atom.intAtomContainer. getConnectedSingleElectronsCount(IAtom atom)Returns the number of single electrons connected to the specified atom.intAtomContainerLegacy. getConnectedSingleElectronsCount(IAtom atom)Returns the number of single electrons connected to the specified atom.List<ISingleElectron>AtomContainer. getConnectedSingleElectronsList(IAtom atom)Returns the single electrons connected connected to the specified atom.List<ISingleElectron>AtomContainerLegacy. getConnectedSingleElectronsList(IAtom atom)Returns the single electrons connected connected to the specified atom.IBond.OrderAtomContainer. getMaximumBondOrder(IAtom atom)Returns the maximum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderAtomContainerLegacy. getMaximumBondOrder(IAtom atom)Returns the maximum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderAtomContainer. getMinimumBondOrder(IAtom atom)Returns the minimum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderAtomContainerLegacy. getMinimumBondOrder(IAtom atom)Returns the minimum bond order that this atom currently has in the context of this AtomContainer.IBondRing. getNextBond(IBond bond, IAtom atom)Returns the next bond in order, relative to a given bond and atom.IAtomBond. getOther(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correctIBond.getConnectedAtoms(IAtom)should be used.IAtomBondRef. getOther(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correctIBond.getConnectedAtoms(IAtom)should be used.IRingSetRingSet. getRings(IAtom atom)Returns a vector of all rings that this atom is part of.intAtomContainer. indexOf(IAtom atom)Access the storage index of an atom.intAtomContainerLegacy. indexOf(IAtom atom)Access the storage index of an atom.IAtomAtomContainer. newAtom(IAtom atom)IBondAtomContainer. newBond(IAtom beg, IAtom end, IBond.Order order)voidAtomContainer. removeAtom(IAtom atom)Safely remove an atom from the container.voidAtomContainerLegacy. removeAtom(IAtom atom)Safely remove an atom from the container.voidAtomContainer. removeAtomAndConnectedElectronContainers(IAtom atom)Safely remove an atom from the container.voidAtomContainerLegacy. removeAtomAndConnectedElectronContainers(IAtom atom)Deprecated.voidAtomContainer. removeAtomOnly(IAtom atom)Unsafely remove atom.voidAtomContainerLegacy. removeAtomOnly(IAtom atom)Unsafely remove atom.IBondAtomContainer. removeBond(IAtom beg, IAtom end)Removes the bond that connects the two given atoms.IBondAtomContainerLegacy. removeBond(IAtom atom1, IAtom atom2)Removes the bond that connects the two given atoms.voidAtomContainer. setAtom(int idx, IAtom atom)Set the atom atidx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().voidAtomContainerLegacy. setAtom(int idx, IAtom atom)Set the atom atidx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().voidBond. setAtom(IAtom atom, int position)Sets an Atom in this bond.voidBondRef. setAtom(IAtom atom, int position)Sets an Atom in this bond.voidLonePair. setAtom(IAtom atom)Sets the associated Atom.voidSingleElectron. setAtom(IAtom atom)Sets the associated Atom.voidAssociation. setAtomAt(IAtom atom, int position)Sets an Atom in this Association.voidAssociation. setAtoms(IAtom[] atoms)Sets the array of atoms making up this Association.voidAtomContainer. setAtoms(IAtom[] newatoms)Sets the array of atoms of this AtomContainer.voidAtomContainerLegacy. setAtoms(IAtom[] newAtoms)Sets the array of atoms of this AtomContainer.voidBond. setAtoms(IAtom[] atoms)Sets the array of atoms making up this bond.voidBondRef. setAtoms(IAtom[] atoms)Sets the array of atoms making up this bond.Constructors in org.openscience.cdk with parameters of type IAtom Constructor Description Association(IAtom atom1, IAtom atom2)Constructs an association between two Atom's.Atom(IAtom org)Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance, mass number, maximum bond order, bond order sum, van der Waals and covalent radii, formal charge, hybridization, electron valency, formal neighbour count and atom type name from the given IAtomType.AtomRef(IAtom atom)Create a pointer for the provided atom.Bond(IAtom[] atoms)Constructs a multi-center bond, with undefined order and no stereo information.Bond(IAtom[] atoms, IBond.Order order)Constructs a multi-center bond, with a specified order and no stereo information.Bond(IAtom atom1, IAtom atom2)Constructs a bond with a single bond order..Bond(IAtom atom1, IAtom atom2, IBond.Order order)Constructs a bond with a given order.Bond(IAtom atom1, IAtom atom2, IBond.Order order, IBond.Stereo stereo)Constructs a bond with a given order and stereo orientation from an array of atoms.EnzymeResidueLocator(IAtom atom)Constructs an EnzymeResidueLocator from an existing Atom.LonePair(IAtom atom)Constructs an lone pair on an Atom.SingleElectron(IAtom atom)Constructs an single electron orbital on an Atom. -
Uses of IAtom in org.openscience.cdk.atomtype
Methods in org.openscience.cdk.atomtype with parameters of type IAtom Modifier and Type Method Description IAtomTypeCDKAtomTypeMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)Method that assigns an atom type to a given atom belonging to an atom container.IAtomTypeEStateAtomTypeMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)IAtomTypeIAtomTypeMatcher. findMatchingAtomType(IAtomContainer container, IAtom atom)Method that assigns an atom type to a given atom belonging to an atom container.IAtomTypeMM2AtomTypeMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atomInterface)Deprecated.Assign the mm2 atom type to a given atom.IAtomTypeMMFF94AtomTypeMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atomInterface)Deprecated.Assign the mmff94 atom type to a given atom.IAtomTypeStructGenMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.IAtomTypeSybylAtomTypeMatcher. findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)Sybyl atom type perception for a single atom.static booleanEStateAtomTypeMatcher. inSameAromaticRing(IAtomContainer m, IAtom atom1, IAtom atom2, IRingSet rs)List<IAtomType>IAtomTypeGuesser. possibleAtomTypes(IAtomContainer container, IAtom atom)Method that returns an iterator with a suitable list of atom types given the provided atom.List<IAtomType>StructGenAtomTypeGuesser. possibleAtomTypes(IAtomContainer atomContainer, IAtom atom)Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state. -
Uses of IAtom in org.openscience.cdk.charges
Methods in org.openscience.cdk.charges with parameters of type IAtom Modifier and Type Method Description doublePolarizability. calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom, boolean addExplicitH, int[][] distanceMatrix)calculate effective atom polarizability.doublePolarizability. calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom, int influenceSphereCutOff, boolean addExplicitH)calculate effective atom polarizability.doublePiElectronegativity. calculatePiElectronegativity(IAtomContainer ac, IAtom atom)calculate the electronegativity of orbitals pi.doublePiElectronegativity. calculatePiElectronegativity(IAtomContainer ac, IAtom atom, int maxIterations, int maxResonStruc)calculate the electronegativity of orbitals pi.doubleStabilizationCharges. calculatePositive(IAtomContainer atomContainer, IAtom atom)calculate the stabilization of orbitals when they contain deficiency of charge.doubleElectronegativity. calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom)calculate the electronegativity of orbitals sigma.doubleElectronegativity. calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom, int maxIterations, int maxResonStruc)calculate the electronegativity of orbitals sigma.doublePolarizability. getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer, IAtom atom)Gets the polarizabilitiyFactorForAtom. -
Uses of IAtom in org.openscience.cdk.config
Methods in org.openscience.cdk.config that return IAtom Modifier and Type Method Description IAtomAtomTypeFactory. configure(IAtom atom)Configures an atom.IAtomIsotopeFactory. configure(IAtom atom)Configures an atom.IAtomIsotopeFactory. configure(IAtom atom, IIsotope isotope)Configures an atom to have all the data of the given isotope.Methods in org.openscience.cdk.config with parameters of type IAtom Modifier and Type Method Description IAtomAtomTypeFactory. configure(IAtom atom)Configures an atom.IAtomIsotopeFactory. configure(IAtom atom)Configures an atom.IAtomIsotopeFactory. configure(IAtom atom, IIsotope isotope)Configures an atom to have all the data of the given isotope.static booleanElements. isMetal(IAtom atom)Utility method to determine if an atom is a metal.static booleanElements. isMetalloid(IAtom atom)Utility method to determine if an atom is a metalloid (B, Si, Ge, As, Sb, Te, or At). -
Uses of IAtom in org.openscience.cdk.debug
Classes in org.openscience.cdk.debug that implement IAtom Modifier and Type Class Description classDebugAtomDebugging data class.classDebugFragmentAtomClass to represent an IPseudoAtom which embeds an IAtomContainer.classDebugPDBAtomDebugging data class.classDebugPseudoAtomDebugging data class.Methods in org.openscience.cdk.debug that return IAtom Modifier and Type Method Description IAtomDebugAtom. clone()Clones this atom object and its content.IAtomDebugAminoAcid. getAtom(int idx)Get the atom at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getAtomCount().IAtomDebugAtomContainer. getAtom(int idx)Get the atom at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getAtomCount().IAtomDebugBioPolymer. getAtom(int idx)Get the atom at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getAtomCount().IAtomDebugBond. getAtom(int position)Returns an Atom from this bond.IAtomDebugCrystal. getAtom(int idx)Get the atom at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getAtomCount().IAtomDebugLonePair. getAtom()Returns the associated Atom.IAtomDebugMonomer. getAtom(int idx)Get the atom at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getAtomCount().IAtomDebugPolymer. getAtom(int idx)Get the atom at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getAtomCount().IAtomDebugRing. getAtom(int idx)Get the atom at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getAtomCount().IAtomDebugSingleElectron. getAtom()Returns the associated Atom.IAtomDebugStrand. getAtom(int idx)Get the atom at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getAtomCount().IAtomDebugBond. getBegin()Access the begin (or first) atom of the bond.IAtomDebugAminoAcid. getCTerminus()Retrieves the C-terminus atom.IAtomDebugBond. getEnd()Access the end (or second) atom of the bond.IAtomDebugAminoAcid. getFirstAtom()Returns the atom at position 0 in the container.IAtomDebugAtomContainer. getFirstAtom()Returns the atom at position 0 in the container.IAtomDebugBioPolymer. getFirstAtom()Returns the atom at position 0 in the container.IAtomDebugCrystal. getFirstAtom()Returns the atom at position 0 in the container.IAtomDebugMonomer. getFirstAtom()Returns the atom at position 0 in the container.IAtomDebugPolymer. getFirstAtom()Returns the atom at position 0 in the container.IAtomDebugRing. getFirstAtom()Returns the atom at position 0 in the container.IAtomDebugStrand. getFirstAtom()Returns the atom at position 0 in the container.IAtomDebugAminoAcid. getLastAtom()Returns the atom at the last position in the container.IAtomDebugAtomContainer. getLastAtom()Returns the atom at the last position in the container.IAtomDebugBioPolymer. getLastAtom()Returns the atom at the last position in the container.IAtomDebugCrystal. getLastAtom()Returns the atom at the last position in the container.IAtomDebugMonomer. getLastAtom()Returns the atom at the last position in the container.IAtomDebugPolymer. getLastAtom()Returns the atom at the last position in the container.IAtomDebugRing. getLastAtom()Returns the atom at the last position in the container.IAtomDebugStrand. getLastAtom()Returns the atom at the last position in the container.IAtomDebugAminoAcid. getNTerminus()Retrieves the N-terminus atom.IAtomDebugBond. getOther(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correctIBond.getConnectedAtoms(IAtom)should be used.IAtomDebugChemObjectBuilder. newAtom()Create a new atom using the default constructor.Methods in org.openscience.cdk.debug that return types with arguments of type IAtom Modifier and Type Method Description Iterable<IAtom>DebugAminoAcid. atoms()Returns an Iterable for looping over all atoms in this container.Iterable<IAtom>DebugAtomContainer. atoms()Returns an Iterable for looping over all atoms in this container.Iterable<IAtom>DebugBioPolymer. atoms()Returns an Iterable for looping over all atoms in this container.Iterable<IAtom>DebugBond. atoms()Returns the Iterator to atoms making up this bond.Iterable<IAtom>DebugCrystal. atoms()Returns an Iterable for looping over all atoms in this container.Iterable<IAtom>DebugMonomer. atoms()Returns an Iterable for looping over all atoms in this container.Iterable<IAtom>DebugPolymer. atoms()Returns an Iterable for looping over all atoms in this container.Iterable<IAtom>DebugRing. atoms()Returns an Iterable for looping over all atoms in this container.Iterable<IAtom>DebugStrand. atoms()Returns an Iterable for looping over all atoms in this container.List<IAtom>DebugAminoAcid. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>DebugAtomContainer. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>DebugBioPolymer. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>DebugCrystal. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>DebugMonomer. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>DebugPolymer. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>DebugRing. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>DebugStrand. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.Methods in org.openscience.cdk.debug with parameters of type IAtom Modifier and Type Method Description voidDebugAminoAcid. addAtom(IAtom atom)Adds an atom to this container.voidDebugAtomContainer. addAtom(IAtom atom)Adds an atom to this container.voidDebugBioPolymer. addAtom(IAtom atom)Adds an atom to this container.voidDebugBioPolymer. addAtom(IAtom oAtom, IMonomer oMonomer)Adds the atom oAtom to a specified Monomer.voidDebugBioPolymer. addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)Adds the atom to a specified Strand and a specified Monomer.voidDebugBioPolymer. addAtom(IAtom oAtom, IStrand oStrand)Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.voidDebugCrystal. addAtom(IAtom atom)Adds an atom to this container.voidDebugMonomer. addAtom(IAtom atom)Adds an atom to this container.voidDebugPolymer. addAtom(IAtom atom)Adds an atom to this container.voidDebugPolymer. addAtom(IAtom oAtom, IMonomer oMonomer)Adds the atom oAtom to a specified Monomer.voidDebugRing. addAtom(IAtom atom)Adds an atom to this container.voidDebugStrand. addAtom(IAtom atom)Adds the atom oAtom without specifying a Monomer or a Strand.voidDebugStrand. addAtom(IAtom oAtom, IMonomer oMonomer)Adds the atom oAtom to a specific Monomer.voidDebugAminoAcid. addCTerminus(IAtom atom)Add an Atom and makes it the C-terminus atom.voidDebugAminoAcid. addNTerminus(IAtom atom)Add an Atom and makes it the N-terminus atom.booleanDebugAminoAcid. contains(IAtom atom)True, if the AtomContainer contains the given atom object.booleanDebugAtomContainer. contains(IAtom atom)True, if the AtomContainer contains the given atom object.booleanDebugBioPolymer. contains(IAtom atom)True, if the AtomContainer contains the given atom object.booleanDebugBond. contains(IAtom atom)Returns true if the given atom participates in this bond.booleanDebugCrystal. contains(IAtom atom)True, if the AtomContainer contains the given atom object.booleanDebugLonePair. contains(IAtom atom)Returns true if the given atom participates in this lone pair.booleanDebugMonomer. contains(IAtom atom)True, if the AtomContainer contains the given atom object.booleanDebugPolymer. contains(IAtom atom)True, if the AtomContainer contains the given atom object.booleanDebugRing. contains(IAtom atom)True, if the AtomContainer contains the given atom object.booleanDebugRingSet. contains(IAtom atom)True, if at least one of the rings in the ringset contains the given atom.booleanDebugSingleElectron. contains(IAtom atom)Returns true if the given atom participates in this SingleElectron.booleanDebugStrand. contains(IAtom atom)True, if the AtomContainer contains the given atom object.intDebugAminoAcid. getAtomNumber(IAtom atom)Returns the position of a given atom in the atoms array.intDebugBioPolymer. getAtomNumber(IAtom atom)Returns the position of a given atom in the atoms array.intDebugCrystal. getAtomNumber(IAtom atom)Returns the position of a given atom in the atoms array.intDebugMonomer. getAtomNumber(IAtom atom)Returns the position of a given atom in the atoms array.intDebugPolymer. getAtomNumber(IAtom atom)Returns the position of a given atom in the atoms array.intDebugRing. getAtomNumber(IAtom atom)Returns the position of a given atom in the atoms array.intDebugStrand. getAtomNumber(IAtom atom)Returns the position of a given atom in the atoms array.IBondDebugAminoAcid. getBond(IAtom atom1, IAtom atom2)Returns the bond that connects the two given atoms.IBondDebugAtomContainer. getBond(IAtom atom1, IAtom atom2)Returns the bond that connects the two given atoms.IBondDebugBioPolymer. getBond(IAtom atom1, IAtom atom2)Returns the bond that connects the two given atoms.IBondDebugCrystal. getBond(IAtom atom1, IAtom atom2)Returns the bond that connects the two given atoms.IBondDebugMonomer. getBond(IAtom atom1, IAtom atom2)Returns the bond that connects the two given atoms.IBondDebugPolymer. getBond(IAtom atom1, IAtom atom2)Returns the bond that connects the two given atoms.IBondDebugRing. getBond(IAtom atom1, IAtom atom2)Returns the bond that connects the two given atoms.IBondDebugStrand. getBond(IAtom atom1, IAtom atom2)Returns the bond that connects the two given atoms.intDebugAminoAcid. getBondNumber(IAtom atom1, IAtom atom2)Returns the position of the bond between two given atoms in the electronContainers array.intDebugBioPolymer. getBondNumber(IAtom atom1, IAtom atom2)Returns the position of the bond between two given atoms in the electronContainers array.intDebugCrystal. getBondNumber(IAtom atom1, IAtom atom2)Returns the position of the bond between two given atoms in the electronContainers array.intDebugMonomer. getBondNumber(IAtom atom1, IAtom atom2)Returns the position of the bond between two given atoms in the electronContainers array.intDebugPolymer. getBondNumber(IAtom atom1, IAtom atom2)Returns the position of the bond between two given atoms in the electronContainers array.intDebugRing. getBondNumber(IAtom atom1, IAtom atom2)Returns the position of the bond between two given atoms in the electronContainers array.intDebugStrand. getBondNumber(IAtom atom1, IAtom atom2)Returns the position of the bond between two given atoms in the electronContainers array.doubleDebugAminoAcid. getBondOrderSum(IAtom atom)Returns the sum of the bond orders for a given Atom.doubleDebugAtomContainer. getBondOrderSum(IAtom atom)Returns the sum of the bond orders for a given Atom.doubleDebugBioPolymer. getBondOrderSum(IAtom atom)Returns the sum of the bond orders for a given Atom.doubleDebugCrystal. getBondOrderSum(IAtom atom)Returns the sum of the bond orders for a given Atom.doubleDebugMonomer. getBondOrderSum(IAtom atom)Returns the sum of the bond orders for a given Atom.doubleDebugPolymer. getBondOrderSum(IAtom atom)Returns the sum of the bond orders for a given Atom.doubleDebugRing. getBondOrderSum(IAtom atom)Returns the sum of the bond orders for a given Atom.doubleDebugStrand. getBondOrderSum(IAtom atom)Returns the sum of the bond orders for a given Atom.intDebugAminoAcid. getConnectedAtomsCount(IAtom atom)Returns the number of connected atoms (explicit degree) to the specified atom.intDebugAtomContainer. getConnectedAtomsCount(IAtom atom)Returns the number of connected atoms (explicit degree) to the specified atom.intDebugBioPolymer. getConnectedAtomsCount(IAtom atom)Returns the number of connected atoms (explicit degree) to the specified atom.intDebugCrystal. getConnectedAtomsCount(IAtom atom)Returns the number of connected atoms (explicit degree) to the specified atom.intDebugMonomer. getConnectedAtomsCount(IAtom atom)Returns the number of connected atoms (explicit degree) to the specified atom.intDebugPolymer. getConnectedAtomsCount(IAtom atom)Returns the number of connected atoms (explicit degree) to the specified atom.intDebugRing. getConnectedAtomsCount(IAtom atom)Returns the number of connected atoms (explicit degree) to the specified atom.intDebugStrand. getConnectedAtomsCount(IAtom atom)Returns the number of connected atoms (explicit degree) to the specified atom.List<IAtom>DebugAminoAcid. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>DebugAtomContainer. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>DebugBioPolymer. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>DebugCrystal. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>DebugMonomer. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>DebugPolymer. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>DebugRing. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>DebugStrand. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.intDebugAminoAcid. getConnectedBondsCount(IAtom atom)Returns the number of connected bonds (explicit degree) to the specified atom.intDebugAtomContainer. getConnectedBondsCount(IAtom atom)Returns the number of connected bonds (explicit degree) to the specified atom.intDebugBioPolymer. getConnectedBondsCount(IAtom atom)Returns the number of connected bonds (explicit degree) to the specified atom.intDebugCrystal. getConnectedBondsCount(IAtom atom)Returns the number of connected bonds (explicit degree) to the specified atom.intDebugMonomer. getConnectedBondsCount(IAtom atom)Returns the number of connected bonds (explicit degree) to the specified atom.intDebugPolymer. getConnectedBondsCount(IAtom atom)Returns the number of connected bonds (explicit degree) to the specified atom.intDebugRing. getConnectedBondsCount(IAtom atom)Returns the number of connected bonds (explicit degree) to the specified atom.intDebugStrand. getConnectedBondsCount(IAtom atom)Returns the number of connected bonds (explicit degree) to the specified atom.List<IBond>DebugAminoAcid. getConnectedBondsList(IAtom atom)Returns the bonds connected connected to the specified atom.List<IBond>DebugAtomContainer. getConnectedBondsList(IAtom atom)Returns the bonds connected connected to the specified atom.List<IBond>DebugBioPolymer. getConnectedBondsList(IAtom atom)Returns the bonds connected connected to the specified atom.List<IBond>DebugCrystal. getConnectedBondsList(IAtom atom)Returns the bonds connected connected to the specified atom.List<IBond>DebugMonomer. getConnectedBondsList(IAtom atom)Returns the bonds connected connected to the specified atom.List<IBond>DebugPolymer. getConnectedBondsList(IAtom atom)Returns the bonds connected connected to the specified atom.List<IBond>DebugRing. getConnectedBondsList(IAtom atom)Returns the bonds connected connected to the specified atom.List<IBond>DebugStrand. getConnectedBondsList(IAtom atom)Returns the bonds connected connected to the specified atom.List<IElectronContainer>DebugAminoAcid. getConnectedElectronContainersList(IAtom atom)Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.List<IElectronContainer>DebugAtomContainer. getConnectedElectronContainersList(IAtom atom)Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.List<IElectronContainer>DebugBioPolymer. getConnectedElectronContainersList(IAtom atom)Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.List<IElectronContainer>DebugCrystal. getConnectedElectronContainersList(IAtom atom)Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.List<IElectronContainer>DebugMonomer. getConnectedElectronContainersList(IAtom atom)Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.List<IElectronContainer>DebugPolymer. getConnectedElectronContainersList(IAtom atom)Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.List<IElectronContainer>DebugRing. getConnectedElectronContainersList(IAtom atom)Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.List<IElectronContainer>DebugStrand. getConnectedElectronContainersList(IAtom atom)Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.intDebugAminoAcid. getConnectedLonePairsCount(IAtom atom)Returns the number of lone pairs connected to the specified atom.intDebugAtomContainer. getConnectedLonePairsCount(IAtom atom)Returns the number of lone pairs connected to the specified atom.intDebugBioPolymer. getConnectedLonePairsCount(IAtom atom)Returns the number of lone pairs connected to the specified atom.intDebugCrystal. getConnectedLonePairsCount(IAtom atom)Returns the number of lone pairs connected to the specified atom.intDebugMonomer. getConnectedLonePairsCount(IAtom atom)Returns the number of lone pairs connected to the specified atom.intDebugPolymer. getConnectedLonePairsCount(IAtom atom)Returns the number of lone pairs connected to the specified atom.intDebugRing. getConnectedLonePairsCount(IAtom atom)Returns the number of lone pairs connected to the specified atom.intDebugStrand. getConnectedLonePairsCount(IAtom atom)Returns the number of lone pairs connected to the specified atom.List<ILonePair>DebugAminoAcid. getConnectedLonePairsList(IAtom atom)Returns the lone pairs connected connected to the specified atom.List<ILonePair>DebugAtomContainer. getConnectedLonePairsList(IAtom atom)Returns the lone pairs connected connected to the specified atom.List<ILonePair>DebugBioPolymer. getConnectedLonePairsList(IAtom atom)Returns the lone pairs connected connected to the specified atom.List<ILonePair>DebugCrystal. getConnectedLonePairsList(IAtom atom)Returns the lone pairs connected connected to the specified atom.List<ILonePair>DebugMonomer. getConnectedLonePairsList(IAtom atom)Returns the lone pairs connected connected to the specified atom.List<ILonePair>DebugPolymer. getConnectedLonePairsList(IAtom atom)Returns the lone pairs connected connected to the specified atom.List<ILonePair>DebugRing. getConnectedLonePairsList(IAtom atom)Returns the lone pairs connected connected to the specified atom.List<ILonePair>DebugStrand. getConnectedLonePairsList(IAtom atom)Returns the lone pairs connected connected to the specified atom.intDebugAminoAcid. getConnectedSingleElectronsCount(IAtom atom)Returns the number of single electrons connected to the specified atom.intDebugAtomContainer. getConnectedSingleElectronsCount(IAtom atom)Returns the number of single electrons connected to the specified atom.intDebugBioPolymer. getConnectedSingleElectronsCount(IAtom atom)Returns the number of single electrons connected to the specified atom.intDebugCrystal. getConnectedSingleElectronsCount(IAtom atom)Returns the number of single electrons connected to the specified atom.intDebugMonomer. getConnectedSingleElectronsCount(IAtom atom)Returns the number of single electrons connected to the specified atom.intDebugPolymer. getConnectedSingleElectronsCount(IAtom atom)Returns the number of single electrons connected to the specified atom.intDebugRing. getConnectedSingleElectronsCount(IAtom atom)Returns the number of single electrons connected to the specified atom.intDebugStrand. getConnectedSingleElectronsCount(IAtom atom)Returns the number of single electrons connected to the specified atom.List<ISingleElectron>DebugAminoAcid. getConnectedSingleElectronsList(IAtom atom)Returns the single electrons connected connected to the specified atom.List<ISingleElectron>DebugAtomContainer. getConnectedSingleElectronsList(IAtom atom)Returns the single electrons connected connected to the specified atom.List<ISingleElectron>DebugBioPolymer. getConnectedSingleElectronsList(IAtom atom)Returns the single electrons connected connected to the specified atom.List<ISingleElectron>DebugCrystal. getConnectedSingleElectronsList(IAtom atom)Returns the single electrons connected connected to the specified atom.List<ISingleElectron>DebugMonomer. getConnectedSingleElectronsList(IAtom atom)Returns the single electrons connected connected to the specified atom.List<ISingleElectron>DebugPolymer. getConnectedSingleElectronsList(IAtom atom)Returns the single electrons connected connected to the specified atom.List<ISingleElectron>DebugRing. getConnectedSingleElectronsList(IAtom atom)Returns the single electrons connected connected to the specified atom.List<ISingleElectron>DebugStrand. getConnectedSingleElectronsList(IAtom atom)Returns the single electrons connected connected to the specified atom.IBond.OrderDebugAminoAcid. getMaximumBondOrder(IAtom atom)Returns the maximum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugAtomContainer. getMaximumBondOrder(IAtom atom)Returns the maximum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugBioPolymer. getMaximumBondOrder(IAtom atom)Returns the maximum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugCrystal. getMaximumBondOrder(IAtom atom)Returns the maximum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugMonomer. getMaximumBondOrder(IAtom atom)Returns the maximum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugPolymer. getMaximumBondOrder(IAtom atom)Returns the maximum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugRing. getMaximumBondOrder(IAtom atom)Returns the maximum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugStrand. getMaximumBondOrder(IAtom atom)Returns the maximum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugAminoAcid. getMinimumBondOrder(IAtom atom)Returns the minimum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugAtomContainer. getMinimumBondOrder(IAtom atom)Returns the minimum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugBioPolymer. getMinimumBondOrder(IAtom atom)Returns the minimum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugCrystal. getMinimumBondOrder(IAtom atom)Returns the minimum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugMonomer. getMinimumBondOrder(IAtom atom)Returns the minimum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugPolymer. getMinimumBondOrder(IAtom atom)Returns the minimum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugRing. getMinimumBondOrder(IAtom atom)Returns the minimum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderDebugStrand. getMinimumBondOrder(IAtom atom)Returns the minimum bond order that this atom currently has in the context of this AtomContainer.IBondDebugRing. getNextBond(IBond bond, IAtom atom)Returns the next bond in order, relative to a given bond and atom.IAtomDebugBond. getOther(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correctIBond.getConnectedAtoms(IAtom)should be used.IRingSetDebugRingSet. getRings(IAtom atom)Returns a vector of all rings that this atom is part of.intDebugAtomContainer. indexOf(IAtom atom)Access the storage index of an atom.voidDebugAminoAcid. removeAtom(IAtom atom)Safely remove an atom from the container.voidDebugAtomContainer. removeAtom(IAtom atom)Safely remove an atom from the container.voidDebugBioPolymer. removeAtom(IAtom atom)Safely remove an atom from the container.voidDebugCrystal. removeAtom(IAtom atom)Safely remove an atom from the container.voidDebugMonomer. removeAtom(IAtom atom)Safely remove an atom from the container.voidDebugPolymer. removeAtom(IAtom atom)Safely remove an atom from the container.voidDebugRing. removeAtom(IAtom atom)Safely remove an atom from the container.voidDebugStrand. removeAtom(IAtom atom)Safely remove an atom from the container.voidDebugAminoAcid. removeAtomOnly(IAtom atom)Unsafely remove atom.voidDebugAtomContainer. removeAtomOnly(IAtom atom)Unsafely remove atom.voidDebugBioPolymer. removeAtomOnly(IAtom atom)Unsafely remove atom.voidDebugCrystal. removeAtomOnly(IAtom atom)Unsafely remove atom.voidDebugMonomer. removeAtomOnly(IAtom atom)Unsafely remove atom.voidDebugPolymer. removeAtomOnly(IAtom atom)Unsafely remove atom.voidDebugRing. removeAtomOnly(IAtom atom)Unsafely remove atom.voidDebugStrand. removeAtomOnly(IAtom atom)Unsafely remove atom.IBondDebugAminoAcid. removeBond(IAtom atom1, IAtom atom2)Removes the bond that connects the two given atoms.IBondDebugAtomContainer. removeBond(IAtom atom1, IAtom atom2)Removes the bond that connects the two given atoms.IBondDebugBioPolymer. removeBond(IAtom atom1, IAtom atom2)Removes the bond that connects the two given atoms.IBondDebugCrystal. removeBond(IAtom atom1, IAtom atom2)Removes the bond that connects the two given atoms.IBondDebugMonomer. removeBond(IAtom atom1, IAtom atom2)Removes the bond that connects the two given atoms.IBondDebugPolymer. removeBond(IAtom atom1, IAtom atom2)Removes the bond that connects the two given atoms.IBondDebugRing. removeBond(IAtom atom1, IAtom atom2)Removes the bond that connects the two given atoms.IBondDebugStrand. removeBond(IAtom atom1, IAtom atom2)Removes the bond that connects the two given atoms.voidDebugAminoAcid. setAtom(int number, IAtom atom)Set the atom atidx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().voidDebugAtomContainer. setAtom(int number, IAtom atom)Set the atom atidx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().voidDebugBioPolymer. setAtom(int number, IAtom atom)Set the atom atidx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().voidDebugBond. setAtom(IAtom atom, int position)Sets an Atom in this bond.voidDebugCrystal. setAtom(int number, IAtom atom)Set the atom atidx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().voidDebugLonePair. setAtom(IAtom atom)Sets the associated Atom.voidDebugMonomer. setAtom(int number, IAtom atom)Set the atom atidx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().voidDebugPolymer. setAtom(int number, IAtom atom)Set the atom atidx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().voidDebugRing. setAtom(int number, IAtom atom)Set the atom atidx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().voidDebugSingleElectron. setAtom(IAtom atom)Sets the associated Atom.voidDebugStrand. setAtom(int number, IAtom atom)Set the atom atidx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().voidDebugAminoAcid. setAtoms(IAtom[] atoms)Sets the array of atoms of this AtomContainer.voidDebugAtomContainer. setAtoms(IAtom[] atoms)Sets the array of atoms of this AtomContainer.voidDebugBioPolymer. setAtoms(IAtom[] atoms)Sets the array of atoms of this AtomContainer.voidDebugBond. setAtoms(IAtom[] atoms)Sets the array of atoms making up this bond.voidDebugCrystal. setAtoms(IAtom[] atoms)Sets the array of atoms of this AtomContainer.voidDebugMonomer. setAtoms(IAtom[] atoms)Sets the array of atoms of this AtomContainer.voidDebugPolymer. setAtoms(IAtom[] atoms)Sets the array of atoms of this AtomContainer.voidDebugRing. setAtoms(IAtom[] atoms)Sets the array of atoms of this AtomContainer.voidDebugStrand. setAtoms(IAtom[] atoms)Sets the array of atoms of this AtomContainer.Constructors in org.openscience.cdk.debug with parameters of type IAtom Constructor Description DebugBond(IAtom[] atoms)DebugBond(IAtom[] atoms, IBond.Order order)DebugBond(IAtom atom1, IAtom atom2)DebugBond(IAtom atom1, IAtom atom2, IBond.Order order)DebugBond(IAtom atom1, IAtom atom2, IBond.Order order, IBond.Stereo stereo)DebugLonePair(IAtom atom)DebugSingleElectron(IAtom atom) -
Uses of IAtom in org.openscience.cdk.depict
Method parameters in org.openscience.cdk.depict with type arguments of type IAtom Modifier and Type Method Description intAbbreviations. apply(IAtomContainer mol, Map<IAtom,Integer> atomSets)Generates and assigns abbreviations to a molecule.List<Sgroup>Abbreviations. generate(IAtomContainer mol, Map<IAtom,Integer> atomSets)Find all enabled abbreviations in the provided molecule. -
Uses of IAtom in org.openscience.cdk.fingerprint
Methods in org.openscience.cdk.fingerprint that return types with arguments of type IAtom Modifier and Type Method Description Collection<IAtom>SimpleAtomCanonicalizer. canonicalizeAtoms(IAtomContainer container)Methods in org.openscience.cdk.fingerprint with parameters of type IAtom Modifier and Type Method Description intSimpleAtomComparator. compare(IAtom o1, IAtom o2) -
Uses of IAtom in org.openscience.cdk.fragment
Methods in org.openscience.cdk.fragment with parameters of type IAtom Modifier and Type Method Description protected static IAtomContainerFragmentUtils. makeAtomContainer(IAtom atom, List<IBond> parts, IAtom excludedAtom)protected static List<IBond>FragmentUtils. traverse(IAtomContainer atomContainer, IAtom atom, List<IBond> bondList) -
Uses of IAtom in org.openscience.cdk.geometry
Methods in org.openscience.cdk.geometry that return IAtom Modifier and Type Method Description static IAtomGeometryTools. getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon)Deprecated.Returns the atom of the given molecule that is closest to the given coordinates.static IAtomGeometryTools. getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon, IAtom toignore)Deprecated.Returns the atom of the given molecule that is closest to the given coordinates and is not the atom.static IAtomGeometryTools. getClosestAtom(int xPosition, int yPosition, IAtomContainer atomCon)Deprecated.Returns the atom of the given molecule that is closest to the given coordinates.static IAtomGeometryTools. getClosestAtom(IAtomContainer atomCon, IAtom atom)Deprecated.Returns the atom of the given molecule that is closest to the given atom (excluding itself).static IAtomGeometryUtil. getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon)Returns the atom of the given molecule that is closest to the given coordinates.static IAtomGeometryUtil. getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon, IAtom toignore)Returns the atom of the given molecule that is closest to the given coordinates and is not the atom.static IAtomGeometryUtil. getClosestAtom(int xPosition, int yPosition, IAtomContainer atomCon)Returns the atom of the given molecule that is closest to the given coordinates.static IAtomGeometryUtil. getClosestAtom(IAtomContainer atomCon, IAtom atom)Returns the atom of the given molecule that is closest to the given atom (excluding itself).Methods in org.openscience.cdk.geometry that return types with arguments of type IAtom Modifier and Type Method Description static List<IAtom>GeometryTools. findClosestInSpace(IAtomContainer container, IAtom startAtom, int max)Deprecated.Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.static List<IAtom>GeometryUtil. findClosestInSpace(IAtomContainer container, IAtom startAtom, int max)Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.static Comparator<IAtom>GeometryUtil. polarAtomComparator(javax.vecmath.Point2d central)Sort the atoms using polar/radial coords around a central point in 2D.static Comparator<IAtom>GeometryUtil. polarAtomComparator(IAtom central)Sort the atoms using polar/radial coords around a central atom in 2D.Methods in org.openscience.cdk.geometry with parameters of type IAtom Modifier and Type Method Description doubleIRDFWeightFunction. calculate(IAtom atom, IAtom atom2)Calculates the weight for the interaction between the two atoms.double[]RDFCalculator. calculate(IAtomContainer container, IAtom atom)Calculates a RDF forAtomatom in the environment of the atoms in theAtomContainer.static javax.vecmath.Point3d[]AtomTools. calculate3DCoordinatesForLigands(IAtomContainer atomContainer, IAtom refAtom, int nwanted, double length, double angle)Adds 3D coordinates for singly-bonded ligands of a reference atom (A).static booleanBondTools. closeEnoughToBond(IAtom atom1, IAtom atom2, double distanceFudgeFactor)Returns true if the two atoms are within the distance fudge factor of each other.static List<IAtom>GeometryTools. findClosestInSpace(IAtomContainer container, IAtom startAtom, int max)Deprecated.Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.static List<IAtom>GeometryUtil. findClosestInSpace(IAtomContainer container, IAtom startAtom, int max)Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.static intGeometryTools. getBestAlignmentForLabel(IAtomContainer container, IAtom atom)Deprecated.Determines the best alignment for the label of an atom in 2D space.static intGeometryUtil. getBestAlignmentForLabel(IAtomContainer container, IAtom atom)Determines the best alignment for the label of an atom in 2D space.static intGeometryTools. getBestAlignmentForLabelXY(IAtomContainer container, IAtom atom)Deprecated.Determines the best alignment for the label of an atom in 2D space.static intGeometryUtil. getBestAlignmentForLabelXY(IAtomContainer container, IAtom atom)Determines the best alignment for the label of an atom in 2D space.static IAtomGeometryTools. getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon, IAtom toignore)Deprecated.Returns the atom of the given molecule that is closest to the given coordinates and is not the atom.static IAtomGeometryTools. getClosestAtom(IAtomContainer atomCon, IAtom atom)Deprecated.Returns the atom of the given molecule that is closest to the given atom (excluding itself).static IAtomGeometryUtil. getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon, IAtom toignore)Returns the atom of the given molecule that is closest to the given coordinates and is not the atom.static IAtomGeometryUtil. getClosestAtom(IAtomContainer atomCon, IAtom atom)Returns the atom of the given molecule that is closest to the given atom (excluding itself).static doubleBondTools. giveAngle(IAtom from, IAtom to1, IAtom to2)Calls giveAngleBothMethods with bool = true.static doubleBondTools. giveAngleBothMethods(IAtom from, IAtom to1, IAtom to2, boolean bool)Gives the angle between two lines starting at atom from and going to to1 and to2.static doubleBondTools. giveAngleFromMiddle(IAtom from, IAtom to1, IAtom to2)Calls giveAngleBothMethods with bool = false.static booleanGeometryTools. has2DCoordinates(IAtom atom)Deprecated.Determines if this Atom contains 2D coordinates.static booleanGeometryUtil. has2DCoordinates(IAtom atom)Determines if this Atom contains 2D coordinates.static booleanBondTools. isCisTrans(IAtom firstOuterAtom, IAtom firstInnerAtom, IAtom secondInnerAtom, IAtom secondOuterAtom, IAtomContainer ac)Says if two atoms are in cis or trans position around a double bond.static booleanBondTools. isLeft(IAtom whereIs, IAtom viewFrom, IAtom viewTo)Says if an atom is on the left side of a another atom seen from a certain atom or not.static booleanBondTools. isSquarePlanar(IAtomContainer container, IAtom atom)Says if an atom as a center of a square planar chirality.static booleanBondTools. isStereo(IAtomContainer container, IAtom stereoAtom)Says if an atom as a center of any valid stereo configuration or not.static intBondTools. isTetrahedral(IAtomContainer container, IAtom atom, boolean strict)Says if an atom as a center of a tetrahedral chirality.static intBondTools. isTrigonalBipyramidalOrOctahedral(IAtomContainer container, IAtom atom)Says if an atom as a center of a trigonal-bipyramidal or actahedral chirality.static Comparator<IAtom>GeometryUtil. polarAtomComparator(IAtom central)Sort the atoms using polar/radial coords around a central atom in 2D.static Comparator<IBond>GeometryUtil. polarBondComparator(IAtom central)Sort the bonds using polar/radial coords around a central atom in 2D.static javax.vecmath.Point3dAtomTools. rescaleBondLength(IAtom atom1, IAtom atom2, javax.vecmath.Point3d point2)Rescales Point2 so that length 1-2 is sum of covalent radii.static voidGeometryTools. rotate(IAtom atom, javax.vecmath.Point3d p1, javax.vecmath.Point3d p2, double angle)Deprecated.Rotates a 3D point about a specified line segment by a specified angle.static voidGeometryUtil. rotate(IAtom atom, javax.vecmath.Point3d p1, javax.vecmath.Point3d p2, double angle)Rotates a 3D point about a specified line segment by a specified angle.static voidGeometryTools. sortBy2DDistance(IAtom[] atoms, javax.vecmath.Point2d point)Deprecated.Sorts a Vector of atoms such that the 2D distances of the atom locations from a given point are smallest for the first atoms in the vector.static voidGeometryUtil. sortBy2DDistance(IAtom[] atoms, javax.vecmath.Point2d point)Sorts a Vector of atoms such that the 2D distances of the atom locations from a given point are smallest for the first atoms in the vector.static booleanBondTools. stereosAreOpposite(IAtomContainer container, IAtom atom)Says if of four atoms connected two one atom the up and down bonds are opposite or not, i.Method parameters in org.openscience.cdk.geometry with type arguments of type IAtom Modifier and Type Method Description static javax.vecmath.Point2dGeometryTools. get2DCenter(Iterable<IAtom> atoms)Deprecated.Calculates the center of the given atoms and returns it as a Point2d.static javax.vecmath.Point2dGeometryTools. get2DCenter(Iterator<IAtom> atoms)Deprecated.Calculates the center of the given atoms and returns it as a Point2d.static javax.vecmath.Point2dGeometryUtil. get2DCenter(Iterable<IAtom> atoms)Calculates the center of the given atoms and returns it as a Point2d.static javax.vecmath.Point2dGeometryUtil. get2DCenter(Iterator<IAtom> atoms)Calculates the center of the given atoms and returns it as a Point2d.static double[]GeometryUtil. getMinMax(Iterable<IAtom> atoms)Returns the minimum and maximum X and Y coordinates of the atoms.static voidProjector. project2D(IAtomContainer container, HashMap<IAtom,javax.vecmath.Point2d> renderingCoordinates)static voidGeometryUtil. reflect(Collection<IAtom> atoms, javax.vecmath.Point2d beg, javax.vecmath.Point2d end)Reflect a collection of atoms in the line formed by the two specified points (beg,end).static voidGeometryUtil. reflect(Collection<IAtom> atoms, IBond bond)Reflect a collection of atoms in the line formed by the specified bond. -
Uses of IAtom in org.openscience.cdk.geometry.alignment
Constructors in org.openscience.cdk.geometry.alignment with parameters of type IAtom Constructor Description KabschAlignment(IAtom[] al1, IAtom[] al2)Sets up variables for the alignment algorithm.KabschAlignment(IAtom[] al1, IAtom[] al2, double[] wts)Sets up variables for the alignment algorithm. -
Uses of IAtom in org.openscience.cdk.geometry.cip
Methods in org.openscience.cdk.geometry.cip that return IAtom Modifier and Type Method Description IAtomILigand. getCentralAtom()IAtomLigand. getCentralAtom()IAtomILigand. getLigandAtom()IAtomLigand. getLigandAtom()Methods in org.openscience.cdk.geometry.cip with parameters of type IAtom Modifier and Type Method Description booleanILigand. isVisited(IAtom atom)Returns a true if the atom has been visited before.booleanLigand. isVisited(IAtom atom)Returns a true if the atom has been visited before.booleanVisitedAtoms. isVisited(IAtom atom)Returns true if the given atom already has been visited.voidVisitedAtoms. visited(IAtom atom)Marks the given atom as visited.Constructors in org.openscience.cdk.geometry.cip with parameters of type IAtom Constructor Description ImplicitHydrogenLigand(IAtomContainer container, VisitedAtoms visitedAtoms, IAtom centralAtom)Ligand(IAtomContainer container, VisitedAtoms visitedAtoms, IAtom centralAtom, IAtom ligandAtom) -
Uses of IAtom in org.openscience.cdk.geometry.surface
Methods in org.openscience.cdk.geometry.surface that return types with arguments of type IAtom Modifier and Type Method Description Map<IAtom,List<javax.vecmath.Point3d>>NumericalSurface. getAtomSurfaceMap()Get the map from atom to surface points.Constructors in org.openscience.cdk.geometry.surface with parameters of type IAtom Constructor Description NeighborList(IAtom[] atoms, double radius) -
Uses of IAtom in org.openscience.cdk.graph
Methods in org.openscience.cdk.graph that return IAtom Modifier and Type Method Description IAtom[]ShortestPaths. atomsTo(int end)Reconstruct a shortest path to the provided end vertex.IAtom[]ShortestPaths. atomsTo(IAtom end)Reconstruct a shortest path to the provided end atom.static IAtom[]PathTools. findClosestByBond(IAtomContainer atomContainer, IAtom atom, int max)Returns the atoms which are closest to an atom in an AtomContainer by bonds.Methods in org.openscience.cdk.graph that return types with arguments of type IAtom Modifier and Type Method Description static List<List<IAtom>>PathTools. getAllPaths(IAtomContainer atomContainer, IAtom start, IAtom end)Get a list of all the paths between two atoms.static List<List<IAtom>>PathTools. getLimitedPathsOfLengthUpto(IAtomContainer atomContainer, IAtom start, int length, int limit)Get all the paths starting from an atom of length 0 up to the specified length.static List<List<IAtom>>PathTools. getPathsOfLength(IAtomContainer atomContainer, IAtom start, int length)Get the paths starting from an atom of specified length.static List<List<IAtom>>PathTools. getPathsOfLengthUpto(IAtomContainer atomContainer, IAtom start, int length)Get all the paths starting from an atom of length 0 upto the specified length.static List<IAtom>PathTools. getShortestPath(IAtomContainer atomContainer, IAtom start, IAtom end)Deprecated.This implementation recalculates all shortest paths from the start atom for each method call and does not indicate if there are equally short paths from the start to the end.Methods in org.openscience.cdk.graph with parameters of type IAtom Modifier and Type Method Description IAtom[]ShortestPaths. atomsTo(IAtom end)Reconstruct a shortest path to the provided end atom.static intPathTools. breadthFirstTargetSearch(IAtomContainer atomContainer, List<IAtom> sphere, IAtom target, int pathLength, int cutOff)Performs a breadthFirstTargetSearch in an AtomContainer starting with a particular sphere, which usually consists of one start atom.static booleanPathTools. depthFirstTargetSearch(IAtomContainer molecule, IAtom root, IAtom target, IAtomContainer path)Recursively performs a depth first search in a molecular graphs contained in the AtomContainer molecule, starting at the root atom and returning when it hits the target atom.intShortestPaths. distanceTo(IAtom end)Access the distance to the provided end atom.static IAtom[]PathTools. findClosestByBond(IAtomContainer atomContainer, IAtom atom, int max)Returns the atoms which are closest to an atom in an AtomContainer by bonds.ShortestPathsAllPairsShortestPaths. from(IAtom start)Access the shortest paths object for provided start atom.static List<List<IAtom>>PathTools. getAllPaths(IAtomContainer atomContainer, IAtom start, IAtom end)Get a list of all the paths between two atoms.static List<List<IAtom>>PathTools. getLimitedPathsOfLengthUpto(IAtomContainer atomContainer, IAtom start, int length, int limit)Get all the paths starting from an atom of length 0 up to the specified length.IAtomContainerSpanningTree. getPath(IAtomContainer spt, IAtom atom1, IAtom atom2)Find a path connected a1 and a2 in the tree.static List<List<IAtom>>PathTools. getPathsOfLength(IAtomContainer atomContainer, IAtom start, int length)Get the paths starting from an atom of specified length.static List<List<IAtom>>PathTools. getPathsOfLengthUpto(IAtomContainer atomContainer, IAtom start, int length)Get all the paths starting from an atom of length 0 upto the specified length.static List<IAtom>PathTools. getShortestPath(IAtomContainer atomContainer, IAtom start, IAtom end)Deprecated.This implementation recalculates all shortest paths from the start atom for each method call and does not indicate if there are equally short paths from the start to the end.intShortestPaths. nPathsTo(IAtom end)Access the number of possible paths to the end atom.int[][]ShortestPaths. pathsTo(IAtom end)Reconstruct all shortest paths to the provided end vertex.int[]ShortestPaths. pathTo(IAtom end)Reconstruct a shortest path to the provided end atom.static intCycles. smallRingSize(IAtom atom)Determine the smallest ring size an atom belongs to.static intCycles. smallRingSize(IAtom atom, int max)Determine the smallest ring size an atom belongs to.Method parameters in org.openscience.cdk.graph with type arguments of type IAtom Modifier and Type Method Description static voidPathTools. breadthFirstSearch(IAtomContainer atomContainer, List<IAtom> sphere, IAtomContainer molecule)Performs a breadthFirstSearch in an AtomContainer starting with a particular sphere, which usually consists of one start atom.static voidPathTools. breadthFirstSearch(IAtomContainer atomContainer, List<IAtom> sphere, IAtomContainer molecule, int max)Performs a breadthFirstSearch in an AtomContainer starting with a particular sphere, which usually consists of one start atom.static intPathTools. breadthFirstTargetSearch(IAtomContainer atomContainer, List<IAtom> sphere, IAtom target, int pathLength, int cutOff)Performs a breadthFirstTargetSearch in an AtomContainer starting with a particular sphere, which usually consists of one start atom.Constructors in org.openscience.cdk.graph with parameters of type IAtom Constructor Description ShortestPaths(IAtomContainer container, IAtom start)Create a new shortest paths tool for a single start atom. -
Uses of IAtom in org.openscience.cdk.graph.invariant
Methods in org.openscience.cdk.graph.invariant with parameters of type IAtom Modifier and Type Method Description static doubleHuLuIndexTool. getSqrtRadii(IAtom atom)Method parameters in org.openscience.cdk.graph.invariant with type arguments of type IAtom Modifier and Type Method Description static long[]Canon. label(IAtomContainer container, int[][] g, Comparator<IAtom> cmp)Compute the canonical labels for the provided structure. -
Uses of IAtom in org.openscience.cdk.hash
Methods in org.openscience.cdk.hash with parameters of type IAtom Modifier and Type Method Description intAtomEncoder. encode(IAtom atom, IAtomContainer container)Encode an invariant attribute of the given atom. -
Uses of IAtom in org.openscience.cdk.interfaces
Subinterfaces of IAtom in org.openscience.cdk.interfaces Modifier and Type Interface Description interfaceIFragmentAtomClass to represent an IPseudoAtom which embeds an IAtomContainer.interfaceIPDBAtomA PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.interfaceIPseudoAtomRepresents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.Methods in org.openscience.cdk.interfaces that return IAtom Modifier and Type Method Description IAtomIAtom. clone()Returns a deep clone of this IChemObject.IAtomIAtomContainer. getAtom(int idx)Get the atom at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getAtomCount().IAtomIBond. getAtom(int position)Returns an Atom from this bond.IAtomILonePair. getAtom()Returns the associated Atom.IAtomISingleElectron. getAtom()Returns the associated Atom.IAtomIBond. getBegin()Access the begin (or first) atom of the bond.IAtomITetrahedralChirality. getChiralAtom()Atom that is the chirality center.IAtomIBond. getConnectedAtom(IAtom atom)Deprecated.use the methodIBond.getOther(IAtom)default IAtomIBond. getConnectedAtom(IBond other)Get the connected atom between two bonds.IAtom[]IBond. getConnectedAtoms(IAtom atom)Returns all the atoms in the bond connected to the given atom.IAtomIAminoAcid. getCTerminus()Retrieves the C-terminus atom.IAtomIBond. getEnd()Access the end (or second) atom of the bond.IAtomIAtomContainer. getFirstAtom()Deprecated.IAtomIAtomContainer. getLastAtom()Deprecated.IAtom[]ITetrahedralChirality. getLigands()Returns an array of ligand atoms around the chiral atom.IAtomIAminoAcid. getNTerminus()Retrieves the N-terminus atom.IAtomIBond. getOther(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correctIBond.getConnectedAtoms(IAtom)should be used.default IAtomIAtomContainer. newAtom()Create a new carbon atom in this container, it will have the implicit hydrogen count initialized to 0.default IAtomIAtomContainer. newAtom(int element)Create a new atom in this container of the specified element, it will have the implicit hydrogen count initialized to 0.default IAtomIAtomContainer. newAtom(int element, int numImplH)Create a new atom in this container of the specified element and implicit hydrogen count.default IAtomIAtomContainer. newAtom(IAtom atom)Create a new atom in the container based on properties of the provided atom.IAtomIChemObjectBuilder. newAtom()Create a new atom using the default constructor.Methods in org.openscience.cdk.interfaces that return types with arguments of type IAtom Modifier and Type Method Description Iterable<IAtom>IAtomContainer. atoms()Returns an Iterable for looping over all atoms in this container.Iterable<IAtom>IBond. atoms()Returns the Iterable to atoms making up this bond.List<IAtom>IAtomContainer. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.default Iterable<IAtom>IAtom. neighbors()Iterable over the atoms connected to this atom (the neighbors).Methods in org.openscience.cdk.interfaces with parameters of type IAtom Modifier and Type Method Description voidIAtomContainer. addAtom(IAtom atom)Adds an atom to this container.voidIBioPolymer. addAtom(IAtom oAtom)Adds the atom oAtom without specifying a Monomer or a Strand.voidIBioPolymer. addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)Adds the atom to a specified Strand and a specified Monomer.voidIBioPolymer. addAtom(IAtom oAtom, IStrand oStrand)Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.voidICrystal. addAtom(IAtom atom)Adds the atom to the crystal.voidIPolymer. addAtom(IAtom oAtom)Adds the atom oAtom without specifying a Monomer.voidIPolymer. addAtom(IAtom oAtom, IMonomer oMonomer)Adds the atom oAtom to a specified Monomer.voidIStrand. addAtom(IAtom oAtom)Adds the atom oAtom without specifying a Monomer or a Strand.voidIStrand. addAtom(IAtom oAtom, IMonomer oMonomer)Adds the atom oAtom to a specific Monomer.voidIAminoAcid. addCTerminus(IAtom atom)Add an Atom and makes it the C-terminus atom.voidIAminoAcid. addNTerminus(IAtom atom)Add an Atom and makes it the N-terminus atom.booleanIAtomContainer. contains(IAtom atom)True, if the AtomContainer contains the given atom object.default booleanIBond. contains(IAtom atom)Returns true if the given atom participates in this bond.booleanILonePair. contains(IAtom atom)Returns true if the given atom participates in this lone pair.booleanIRingSet. contains(IAtom atom)True, if at least one of the rings in the ringset contains the given atom.booleanISingleElectron. contains(IAtom atom)Returns true if the given atom participates in this SingleElectron.booleanIStereoElement. contains(IAtom atom)Does the stereo element contain the provided atom.intIAtomContainer. getAtomNumber(IAtom atom)Deprecated.IBondIAtom. getBond(IAtom atom)Returns the bond connecting 'this' atom to the provided atom.IBondIAtomContainer. getBond(IAtom atom1, IAtom atom2)Returns the bond that connects the two given atoms.intIAtomContainer. getBondNumber(IAtom atom1, IAtom atom2)Deprecated.doubleIAtomContainer. getBondOrderSum(IAtom atom)Returns the sum of the bond orders for a given Atom.IAtomIBond. getConnectedAtom(IAtom atom)Deprecated.use the methodIBond.getOther(IAtom)IAtom[]IBond. getConnectedAtoms(IAtom atom)Returns all the atoms in the bond connected to the given atom.intIAtomContainer. getConnectedAtomsCount(IAtom atom)Deprecated.List<IAtom>IAtomContainer. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.intIAtomContainer. getConnectedBondsCount(IAtom atom)Returns the number of connected bonds (explicit degree) to the specified atom.List<IBond>IAtomContainer. getConnectedBondsList(IAtom atom)Returns the bonds connected connected to the specified atom.List<IElectronContainer>IAtomContainer. getConnectedElectronContainersList(IAtom atom)Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.intIAtomContainer. getConnectedLonePairsCount(IAtom atom)Returns the number of lone pairs connected to the specified atom.List<ILonePair>IAtomContainer. getConnectedLonePairsList(IAtom atom)Returns the lone pairs connected connected to the specified atom.intIAtomContainer. getConnectedSingleElectronsCount(IAtom atom)Returns the number of single electrons connected to the specified atom.List<ISingleElectron>IAtomContainer. getConnectedSingleElectronsList(IAtom atom)Returns the single electrons connected connected to the specified atom.IBond.OrderIAtomContainer. getMaximumBondOrder(IAtom atom)Returns the maximum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderIAtomContainer. getMinimumBondOrder(IAtom atom)Returns the minimum bond order that this atom currently has in the context of this AtomContainer.IBondIRing. getNextBond(IBond bond, IAtom atom)Returns the next bond in order, relative to a given bond and atom.IAtomIBond. getOther(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correctIBond.getConnectedAtoms(IAtom)should be used.IRingSetIRingSet. getRings(IAtom atom)Returns a vector of all rings that this atom is part of.intIAtomContainer. indexOf(IAtom atom)Access the storage index of an atom.default IAtomIAtomContainer. newAtom(IAtom atom)Create a new atom in the container based on properties of the provided atom.default IBondIAtomContainer. newBond(IAtom beg, IAtom end)Create a new single bond between two atoms.default IBondIAtomContainer. newBond(IAtom beg, IAtom end, IBond.Order order)Create a new bond between two atoms.voidIAtomContainer. removeAtom(IAtom atom)Safely remove an atom from the container.voidIAtomContainer. removeAtomAndConnectedElectronContainers(IAtom atom)Deprecated.Method has be renamedIAtomContainer.removeAtom(IAtom).voidIAtomContainer. removeAtomOnly(IAtom atom)Unsafely remove atom.IBondIAtomContainer. removeBond(IAtom atom1, IAtom atom2)Removes the bond that connects the two given atoms.voidIAtomContainer. setAtom(int idx, IAtom atom)Set the atom atidx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().voidIBond. setAtom(IAtom atom, int position)Sets an Atom in this bond.voidILonePair. setAtom(IAtom atom)Sets the associated Atom.voidISingleElectron. setAtom(IAtom atom)Sets the associated Atom.voidIAtomContainer. setAtoms(IAtom[] atoms)Sets the array of atoms of this AtomContainer.voidIBond. setAtoms(IAtom[] atoms)Sets the array of atoms making up this bond.Method parameters in org.openscience.cdk.interfaces with type arguments of type IAtom Modifier and Type Method Description IDoubleBondStereochemistryIDoubleBondStereochemistry. map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.IDoubleBondStereochemistryIDoubleBondStereochemistry. map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.IStereoElementIStereoElement. map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.IStereoElementIStereoElement. map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.ITetrahedralChiralityITetrahedralChirality. map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.ITetrahedralChiralityITetrahedralChirality. map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping. -
Uses of IAtom in org.openscience.cdk.io.cml
Fields in org.openscience.cdk.io.cml declared as IAtom Modifier and Type Field Description protected IAtomCMLCoreModule. currentAtomFields in org.openscience.cdk.io.cml with type parameters of type IAtom Modifier and Type Field Description protected Map<String,IAtom>CMLCoreModule. atomEnumeration -
Uses of IAtom in org.openscience.cdk.isomorphism
Methods in org.openscience.cdk.isomorphism that return types with arguments of type IAtom Modifier and Type Method Description Iterable<Map<IAtom,IAtom>>Mappings. toAtomMap()Convert the permutations to a atom-atom map.Iterable<Map<IAtom,IAtom>>Mappings. toAtomMap()Convert the permutations to a atom-atom map.Methods in org.openscience.cdk.isomorphism with parameters of type IAtom Modifier and Type Method Description abstract booleanAtomMatcher. matches(IAtom atom1, IAtom atom2)Are the semantics ofatom1compatible withatom2.booleanDfPattern. matchesRoot(IAtom root)Test whether the pattern matches at the provided atom. -
Uses of IAtom in org.openscience.cdk.isomorphism.matchers
Subinterfaces of IAtom in org.openscience.cdk.isomorphism.matchers Modifier and Type Interface Description interfaceIQueryAtomDefines the ability to be matched againstIAtom's.Classes in org.openscience.cdk.isomorphism.matchers that implement IAtom Modifier and Type Class Description classInverseSymbolSetQueryAtomDeprecated.classQueryAtomclassSymbolAndChargeQueryAtomDeprecated.classSymbolChargeIDQueryAtomclassSymbolQueryAtomDeprecated.classSymbolSetQueryAtomDeprecated.Usenew Expr(Element, 6).and(new Expr(Element, 8))etcFields in org.openscience.cdk.isomorphism.matchers declared as IAtom Modifier and Type Field Description protected IAtom[]QueryAtomContainer. atomsInternal array of atoms.protected IAtom[]QueryBond. atomsA list of atoms participating in this query bond.Methods in org.openscience.cdk.isomorphism.matchers that return IAtom Modifier and Type Method Description IAtomQueryAtom. clone()IAtomSymbolAndChargeQueryAtom. clone()Deprecated.IAtomSymbolChargeIDQueryAtom. clone()IAtomSymbolQueryAtom. clone()Deprecated.IAtomSymbolSetQueryAtom. clone()Deprecated.IAtomQueryAtomContainer. getAtom(int idx)Get the atom at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getAtomCount().IAtomQueryBond. getAtom(int position)Returns an Atom from this query bond.IAtomQueryBond. getBegin()Access the begin (or first) atom of the bond.IAtomQueryBond. getConnectedAtom(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.IAtom[]QueryBond. getConnectedAtoms(IAtom atom)Returns all the atoms in the bond connected to the given atom.IAtomQueryBond. getEnd()Access the end (or second) atom of the bond.IAtomQueryAtomContainer. getFirstAtom()Returns the atom at position 0 in the container.IAtomIRGroup. getFirstAttachmentPoint()Get the first attachment point of the RGroup.IAtomRGroup. getFirstAttachmentPoint()IAtomQueryAtomContainer. getLastAtom()Returns the atom at the last position in the container.IAtomQueryBond. getOther(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correctIBond.getConnectedAtoms(IAtom)should be used.IAtomIRGroup. getSecondAttachmentPoint()Get the optional second attachment point of the RGroup.IAtomRGroup. getSecondAttachmentPoint()Methods in org.openscience.cdk.isomorphism.matchers that return types with arguments of type IAtom Modifier and Type Method Description Iterable<IAtom>QueryAtomContainer. atoms()Returns an Iterable for looping over all atoms in this container.Iterable<IAtom>QueryBond. atoms()Returns the Iterator to atoms making up this query bond.List<IAtom>RGroupQuery. getAllRgroupQueryAtoms()Returns all R# type atoms (pseudo atoms) found in the root structure.List<IAtom>QueryAtomContainer. getConnectedAtomsList(IAtom atom)Returns an ArrayList of all atoms connected to the given atom.List<IAtom>RGroupQuery. getRgroupQueryAtoms(Integer rgroupNumber)Returns all R# type atoms (pseudo atoms) found in the root structure for a certain provided RGgroup number.Map<IAtom,Map<Integer,IBond>>IRGroupQuery. getRootAttachmentPoints()Getter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.Map<IAtom,Map<Integer,IBond>>RGroupQuery. getRootAttachmentPoints()Methods in org.openscience.cdk.isomorphism.matchers with parameters of type IAtom Modifier and Type Method Description voidQueryAtomContainer. addAtom(IAtom atom)Adds an atom to this container.booleanQueryAtomContainer. contains(IAtom atom)True, if the AtomContainer contains the given atom object.booleanQueryBond. contains(IAtom atom)Returns true if the given atom participates in this query bond.intQueryAtomContainer. getAtomNumber(IAtom atom)Returns the position of a given atom in the atoms array.IBondQueryAtom. getBond(IAtom atom)Returns the bond connecting 'this' atom to the provided atom.IBondQueryAtomContainer. getBond(IAtom atom1, IAtom atom2)Returns the bond that connects the two given atoms.intQueryAtomContainer. getBondNumber(IAtom atom1, IAtom atom2)Returns the position of the bond between two given atoms in the electronContainers array.doubleQueryAtomContainer. getBondOrderSum(IAtom atom)Deprecated.Replaced byAtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)IAtomQueryBond. getConnectedAtom(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.IAtom[]QueryBond. getConnectedAtoms(IAtom atom)Returns all the atoms in the bond connected to the given atom.intQueryAtomContainer. getConnectedAtomsCount(IAtom atom)Returns the number of atoms connected to the given atom.List<IAtom>QueryAtomContainer. getConnectedAtomsList(IAtom atom)Returns an ArrayList of all atoms connected to the given atom.intQueryAtomContainer. getConnectedBondsCount(IAtom atom)Returns the number of Bonds for a given Atom.List<IBond>QueryAtomContainer. getConnectedBondsList(IAtom atom)Returns an ArrayList of all Bonds connected to the given atom.List<IElectronContainer>QueryAtomContainer. getConnectedElectronContainersList(IAtom atom)Returns an ArrayList of all electronContainers connected to the given atom.intQueryAtomContainer. getConnectedLonePairsCount(IAtom atom)Returns the number of LonePairs for a given Atom.List<ILonePair>QueryAtomContainer. getConnectedLonePairsList(IAtom atom)Returns the array of lone pairs connected to an atom.intQueryAtomContainer. getConnectedSingleElectronsCount(IAtom atom)Returns the sum of the SingleElectron for a given Atom.List<ISingleElectron>QueryAtomContainer. getConnectedSingleElectronsList(IAtom atom)Returns an array of all SingleElectron connected to the given atom.IBond.OrderQueryAtomContainer. getMaximumBondOrder(IAtom atom)Returns the maximum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderQueryAtomContainer. getMinimumBondOrder(IAtom atom)Returns the minimum bond order that this atom currently has in the context of this AtomContainer.IAtomQueryBond. getOther(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correctIBond.getConnectedAtoms(IAtom)should be used.intQueryAtomContainer. indexOf(IAtom atom)booleanExpr. matches(IAtom atom)Test whether this expression matches an atom instance.booleanExpr. matches(IAtom atom, int stereo)booleanInverseSymbolSetQueryAtom. matches(IAtom atom)Deprecated.The matches implementation of the QueryAtom interface.booleanIQueryAtom. matches(IAtom atom)Returns true of the givenatommatches this IQueryAtom.booleanQueryAtom. matches(IAtom atom)Returns true of the givenatommatches this IQueryAtom.booleanQueryChemObject. matches(IAtom atom)booleanSymbolAndChargeQueryAtom. matches(IAtom atom)Deprecated.booleanSymbolChargeIDQueryAtom. matches(IAtom atom)booleanSymbolQueryAtom. matches(IAtom atom)Deprecated.booleanSymbolSetQueryAtom. matches(IAtom atom)Deprecated.The matches implementation of the QueryAtom interface.voidQueryAtomContainer. removeAtom(IAtom atom)Removes the given atom and all connected electronContainers from the AtomContainer.voidQueryAtomContainer. removeAtomAndConnectedElectronContainers(IAtom atom)Deprecated.voidQueryAtomContainer. removeAtomOnly(IAtom atom)Removes the given atom from the AtomContainer.IBondQueryAtomContainer. removeBond(IAtom atom1, IAtom atom2)Removes the bond that connects the two given atoms.voidQueryAtomContainer. setAtom(int idx, IAtom atom)Set the atom atidx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().voidQueryBond. setAtom(IAtom atom, int position)Sets an atom in this query bond.voidOrderQueryBond. setAtomAt(IAtom atom, int position)Deprecated.voidOrderQueryBondOrderOnly. setAtomAt(IAtom atom, int position)Deprecated.voidOrderQueryBond. setAtoms(IAtom[] atoms)Deprecated.voidOrderQueryBondOrderOnly. setAtoms(IAtom[] atoms)Deprecated.voidQueryAtomContainer. setAtoms(IAtom[] atoms)Sets the array of atoms of this AtomContainer.voidQueryBond. setAtoms(IAtom[] atoms)Sets the array of atoms making up this query bond.voidRGroup. setFirstAttachmentPoint(IAtom firstAttachmentPoint)voidRGroup. setSecondAttachmentPoint(IAtom secondAttachmentPoint)Method parameters in org.openscience.cdk.isomorphism.matchers with type arguments of type IAtom Modifier and Type Method Description voidIRGroupQuery. setRootAttachmentPoints(Map<IAtom,Map<Integer,IBond>> rootAttachmentPoints)Setter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.voidRGroupQuery. setRootAttachmentPoints(Map<IAtom,Map<Integer,IBond>> rootAttachmentPoints)Constructors in org.openscience.cdk.isomorphism.matchers with parameters of type IAtom Constructor Description QueryBond(IAtom[] atoms, IBond.Order order, IChemObjectBuilder builder)Constructs a multi-center query bond, with a specified order and no stereo information.QueryBond(IAtom[] atoms, IChemObjectBuilder builder)Constructs a multi-center query bond, with undefined order and no stereo information.QueryBond(IAtom atom1, IAtom atom2, IBond.Order order, IBond.Stereo stereo, IChemObjectBuilder builder)Constructs a query bond with a given order and stereo orientation from an array of atoms.QueryBond(IAtom atom1, IAtom atom2, IBond.Order order, IChemObjectBuilder builder)Constructs a query bond with a given order.QueryBond(IAtom atom1, IAtom atom2, IChemObjectBuilder builder)Constructs a query bond with a single query bond order..QueryBond(IAtom beg, IAtom end, Expr expr)Constructs a query bond from an expression.QueryBond(IAtom beg, IAtom end, Expr.Type type)Constructs a query bond from an expression type.QueryBond(IAtom beg, IAtom end, Expr.Type type, int val)Constructs a query bond from an expression type and value.SymbolAndChargeQueryAtom(IAtom atom)Deprecated.SymbolChargeIDQueryAtom(IAtom atom)SymbolQueryAtom(IAtom atom)Deprecated. -
Uses of IAtom in org.openscience.cdk.isomorphism.matchers.smarts
Classes in org.openscience.cdk.isomorphism.matchers.smarts that implement IAtom Modifier and Type Class Description classAliphaticAtomDeprecated.classAliphaticSymbolAtomDeprecated.classAnyAtomDeprecated.classAromaticAtomDeprecated.classAromaticSymbolAtomDeprecated.classAtomicNumberAtomDeprecated.classChiralityAtomDeprecated.classExplicitConnectionAtomDeprecated.classFormalChargeAtomDeprecated.classHybridizationNumberAtomDeprecated.classHydrogenAtomDeprecated.classImplicitHCountAtomDeprecated.classLogicalOperatorAtomDeprecated.classMassAtomDeprecated.classNonCHHeavyAtomDeprecated.classPeriodicGroupNumberAtomDeprecated.classReactionRoleQueryAtomDeprecated.classRecursiveSmartsAtomDeprecated.classRingIdentifierAtomDeprecated.classRingMembershipAtomDeprecated.classSmallestRingAtomDeprecated.classSMARTSAtomDeprecated.classTotalConnectionAtomDeprecated.classTotalHCountAtomDeprecated.classTotalRingConnectionAtomDeprecated.classTotalValencyAtomDeprecated.Methods in org.openscience.cdk.isomorphism.matchers.smarts with parameters of type IAtom Modifier and Type Method Description booleanChiralityAtom. chiralityMatches(IAtom target, int tParity, int permParity)Deprecated.Check if the atom-based chirality of the target matches.booleanSMARTSAtom. chiralityMatches(IAtom target, int tParity, int permParity)Deprecated.Check if the atom-based chirality of the target matches.StereoBond.DirectionStereoBond. direction(IAtom atom)Deprecated.booleanAliphaticAtom. matches(IAtom atom)Deprecated.booleanAliphaticSymbolAtom. matches(IAtom atom)Deprecated.booleanAnyAtom. matches(IAtom atom)Deprecated.booleanAromaticAtom. matches(IAtom atom)Deprecated.booleanAromaticSymbolAtom. matches(IAtom atom)Deprecated.booleanAtomicNumberAtom. matches(IAtom atom)Deprecated.booleanChiralityAtom. matches(IAtom atom)Deprecated.booleanExplicitConnectionAtom. matches(IAtom atom)Deprecated.Returns true of the givenatommatches this IQueryAtom.booleanFormalChargeAtom. matches(IAtom atom)Deprecated.booleanHybridizationNumberAtom. matches(IAtom atom)Deprecated.booleanHydrogenAtom. matches(IAtom atom)Deprecated.booleanImplicitHCountAtom. matches(IAtom atom)Deprecated.booleanLogicalOperatorAtom. matches(IAtom atom)Deprecated.booleanMassAtom. matches(IAtom atom)Deprecated.booleanNonCHHeavyAtom. matches(IAtom atom)Deprecated.booleanPeriodicGroupNumberAtom. matches(IAtom atom)Deprecated.booleanReactionRoleQueryAtom. matches(IAtom atom)Deprecated.booleanRecursiveSmartsAtom. matches(IAtom atom)Deprecated.booleanRingIdentifierAtom. matches(IAtom atom)Deprecated.booleanRingMembershipAtom. matches(IAtom atom)Deprecated.Returns true of the givenatommatches this IQueryAtom.booleanSmallestRingAtom. matches(IAtom atom)Deprecated.Returns true of the givenatommatches this IQueryAtom.booleanSMARTSAtom. matches(IAtom atom)Deprecated.booleanTotalConnectionAtom. matches(IAtom atom)Deprecated.Returns true of the givenatommatches this IQueryAtom.booleanTotalHCountAtom. matches(IAtom atom)Deprecated.Check if the total hydrogen count of theatomis equal to the query.booleanTotalRingConnectionAtom. matches(IAtom atom)Deprecated.Returns true of the givenatommatches this IQueryAtom.booleanTotalValencyAtom. matches(IAtom atom)Deprecated.Returns true of the givenatommatches this IQueryAtom.voidLogicalOperatorBond. setAtoms(IAtom[] atoms)Deprecated. -
Uses of IAtom in org.openscience.cdk.layout
Methods in org.openscience.cdk.layout that return IAtom Modifier and Type Method Description IAtomStructureDiagramGenerator. getOtherBondAtom(IAtom atom, IBond bond)Returns the other atom of the bond.Methods in org.openscience.cdk.layout with parameters of type IAtom Modifier and Type Method Description voidAtomPlacer. distributePartners(IAtom atom, IAtomContainer placedNeighbours, javax.vecmath.Point2d sharedAtomsCenter, IAtomContainer unplacedNeighbours, double bondLength)Distribute the bonded atoms (neighbours) of an atom such that they fill the remaining space around an atom in a geometrically nice way.static IAtomContainerAtomPlacer. getLongestUnplacedChain(IAtomContainer molecule, IAtom startAtom)Search a molecule for the longest unplaced, aliphatic chain in it.javax.vecmath.Vector2dAtomPlacer. getNextBondVector(IAtom atom, IAtom previousAtom, javax.vecmath.Point2d distanceMeasure, boolean trans)Returns the next bond vector needed for drawing an extended linear chain of atoms.IAtomStructureDiagramGenerator. getOtherBondAtom(IAtom atom, IBond bond)Returns the other atom of the bond.voidRingPlacer. partitionNonRingPartners(IAtom atom, IRing ring, IAtomContainer ringAtoms, IAtomContainer nonRingAtoms)Partition the bonding partners of a given atom into ring atoms and non-ring atomsvoidAtomPlacer. partitionPartners(IAtom atom, IAtomContainer unplacedPartners, IAtomContainer placedPartners)Partition the bonding partners of a given atom into placed (coordinates assinged) and not placed.voidHydrogenPlacer. placeHydrogens2D(IAtomContainer container, IAtom atom)Place hydrogens connected to the given atom using the average bond length in the container.voidHydrogenPlacer. placeHydrogens2D(IAtomContainer container, IAtom atom, double bondLength)Place hydrogens connected to the provided atom atom using the specified bondLength.static booleanAtomPlacer. shouldBeLinear(IAtom atom, IAtomContainer molecule)Deprecated.Method parameters in org.openscience.cdk.layout with type arguments of type IAtom Modifier and Type Method Description static voidAtomPlacer. breadthFirstSearch(IAtomContainer ac, List<IAtom> sphere, IAtomContainer[] pathes)Performs a breadthFirstSearch in an AtomContainer starting with a particular sphere, which usually consists of one start atom, and searches for the longest aliphatic chain which is yet unplaced.static StringAtomPlacer. listNumbers(IAtomContainer mol, List<IAtom> ac)Returns a string with the numbers of all atoms in a Vector relative to a given molecule.voidAtomPlacer. populatePolygonCorners(List<IAtom> atoms, javax.vecmath.Point2d center, double thetaBeg, double thetaStep, double radius)Populates the corners of a polygon with atoms.voidStructureDiagramGenerator. setMolecule(IAtomContainer mol, boolean clone, Set<IAtom> afix, Set<IBond> bfix)Assigns a molecule to be laid out. -
Uses of IAtom in org.openscience.cdk.libio.cml
Methods in org.openscience.cdk.libio.cml with parameters of type IAtom Modifier and Type Method Description org.xmlcml.cml.element.CMLAtomConvertor. cdkAtomToCMLAtom(IAtom cdkAtom)org.xmlcml.cml.element.CMLAtomConvertor. cdkAtomToCMLAtom(IAtomContainer container, IAtom cdkAtom)voidICMLCustomizer. customize(IAtom atom, Object nodeToAdd)Customized the nodeToAdd for the given Atom.voidMDMoleculeCustomizer. customize(IAtom atom, Object nodeToAdd)Customize Atom.voidPDBAtomCustomizer. customize(IAtom atom, Object nodeToAdd)voidQSARCustomizer. customize(IAtom atom, Object nodeToAdd) -
Uses of IAtom in org.openscience.cdk.libio.md
Methods in org.openscience.cdk.libio.md that return IAtom Modifier and Type Method Description IAtomChargeGroup. getSwitchingAtom()Methods in org.openscience.cdk.libio.md with parameters of type IAtom Modifier and Type Method Description voidChargeGroup. setSwitchingAtom(IAtom switchingAtom) -
Uses of IAtom in org.openscience.cdk.math.qm
Methods in org.openscience.cdk.math.qm with parameters of type IAtom Modifier and Type Method Description protected voidGaussiansBasis. setBasis(int[] nx, int[] ny, int[] nz, double[] alpha, Vector[] r, IAtom[] atoms)Set up basis with gauss funktions f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2).Constructors in org.openscience.cdk.math.qm with parameters of type IAtom Constructor Description GaussiansBasis(int[] nx, int[] ny, int[] nz, double[] alpha, Vector[] r, IAtom[] atoms)Set up basis with gauss funktions f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2).SimpleBasisSet(IAtom[] atoms)Create a base set -
Uses of IAtom in org.openscience.cdk.modeling.builder3d
Methods in org.openscience.cdk.modeling.builder3d that return IAtom Modifier and Type Method Description IAtomForceFieldConfigurator. configureAtom(IAtom atom, String hoseCode, boolean _boolean)IAtomForceFieldConfigurator. configureMM2BasedAtom(IAtom atom, String hoseCode, boolean hetRing)Configures an atom to a mm2 based atom typeIAtomForceFieldConfigurator. configureMMFF94BasedAtom(IAtom atom, String hoseCode, boolean isInHetRing)Configures an atom to a mmff94 based atom typeIAtomAtomPlacer3D. getFarthestAtom(javax.vecmath.Point3d refAtomPoint, IAtomContainer ac)Gets the farthestAtom attribute of the AtomPlacer3D object.IAtomAtomPlacer3D. getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer molecule)Gets the nextPlacedHeavyAtomWithAliphaticPlacedNeigbor from an atom container or molecule.IAtomAtomPlacer3D. getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer molecule)Gets the nextPlacedHeavyAtomWithUnplacedRingNeighbour attribute of the AtomPlacer3D object.IAtomAtomPlacer3D. getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer molecule)Gets the nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour from an atom container or molecule.IAtomAtomPlacer3D. getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom)Returns a placed atom connected to a given atom.IAtomAtomPlacer3D. getPlacedHeavyAtom(IAtomContainer molecule, IAtom atomA, IAtom atomB)Gets the first placed Heavy Atom around atomA which is not atomB.IAtomAtomTetrahedralLigandPlacer3D. getPlacedHeavyAtomInAtomContainer(IAtom atomA, IAtom atomB, IAtomContainer ac)Returns a placed neighbouring atom of a central atom atomA, which is not atomB.IAtomAtomPlacer3D. getUnplacedRingHeavyAtom(IAtomContainer molecule, IAtom atom)Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object.Methods in org.openscience.cdk.modeling.builder3d with parameters of type IAtom Modifier and Type Method Description IAtomForceFieldConfigurator. configureAtom(IAtom atom, String hoseCode, boolean _boolean)IAtomForceFieldConfigurator. configureMM2BasedAtom(IAtom atom, String hoseCode, boolean hetRing)Configures an atom to a mm2 based atom typeIAtomForceFieldConfigurator. configureMMFF94BasedAtom(IAtom atom, String hoseCode, boolean isInHetRing)Configures an atom to a mmff94 based atom typejavax.vecmath.Point3d[]AtomTetrahedralLigandPlacer3D. get3DCoordinatesForLigands(IAtom refAtom, IAtomContainer noCoords, IAtomContainer withCoords, IAtom atomC, int nwanted, double length, double angle)Adds 3D coordinates for singly-bonded ligands of a reference atom (A).javax.vecmath.Point3d[]AtomTetrahedralLigandPlacer3D. get3DCoordinatesForSP2Ligands(IAtom refAtom, IAtomContainer noCoords, IAtomContainer withCoords, IAtom atomC, double length, double angle)Main method for the calculation of the ligand coordinates for sp2 atoms.javax.vecmath.Point3d[]AtomTetrahedralLigandPlacer3D. get3DCoordinatesForSP3Ligands(IAtom refAtom, IAtomContainer noCoords, IAtomContainer withCoords, IAtom atomC, int nwanted, double length, double angle)Main method for the calculation of the ligand coordinates for sp3 atoms.javax.vecmath.Point3dAtomTetrahedralLigandPlacer3D. get3DCoordinatesForSPLigands(IAtom refAtom, IAtomContainer withCoords, double length, double angle)IAtomContainerAtomTetrahedralLigandPlacer3D. getPlacedAtomsInAtomContainer(IAtom atom, IAtomContainer ac)Gets all placed neighbouring atoms of a atom.IAtomAtomPlacer3D. getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom)Returns a placed atom connected to a given atom.IAtomAtomPlacer3D. getPlacedHeavyAtom(IAtomContainer molecule, IAtom atomA, IAtom atomB)Gets the first placed Heavy Atom around atomA which is not atomB.IAtomAtomTetrahedralLigandPlacer3D. getPlacedHeavyAtomInAtomContainer(IAtom atomA, IAtom atomB, IAtomContainer ac)Returns a placed neighbouring atom of a central atom atomA, which is not atomB.IAtomContainerAtomPlacer3D. getPlacedHeavyAtoms(IAtomContainer molecule, IAtom atom)Gets the placed Heavy Atoms connected to an atom.IAtomAtomPlacer3D. getUnplacedRingHeavyAtom(IAtomContainer molecule, IAtom atom)Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object.IAtomContainerAtomTetrahedralLigandPlacer3D. getUnsetAtomsInAtomContainer(IAtom atom, IAtomContainer ac)Gets the unsetAtomsInAtomContainer attribute of the AtomTetrahedralLigandPlacer3D object.booleanAtomTetrahedralLigandPlacer3D. hasUnsetNeighbour(IAtom atom, IAtomContainer ac)javax.vecmath.Point3dAtomTetrahedralLigandPlacer3D. rescaleBondLength(IAtom atom1, IAtom atom2, javax.vecmath.Point3d point2)Rescales Point2 so that length 1-2 is sum of covalent radii. -
Uses of IAtom in org.openscience.cdk.normalize
Methods in org.openscience.cdk.normalize with parameters of type IAtom Modifier and Type Method Description static intSMSDNormalizer. getExplicitHydrogenCount(IAtomContainer atomContainer, IAtom atom)Deprecated.Returns The number of explicit hydrogens for a given IAtom.static intSMSDNormalizer. getHydrogenCount(IAtomContainer atomContainer, IAtom atom)Deprecated.The summed implicit + explicit hydrogens of the given IAtom.static intSMSDNormalizer. getImplicitHydrogenCount(IAtomContainer atomContainer, IAtom atom)Deprecated.Returns The number of Implicit Hydrogen Count for a given IAtom. -
Uses of IAtom in org.openscience.cdk.pharmacophore
Classes in org.openscience.cdk.pharmacophore that implement IAtom Modifier and Type Class Description classPharmacophoreAtomA representation of a pharmacophore group.classPharmacophoreQueryAtomRepresents a query pharmacophore group.Methods in org.openscience.cdk.pharmacophore with parameters of type IAtom Modifier and Type Method Description static PharmacophoreAtomPharmacophoreAtom. get(IAtom atom)booleanPharmacophoreQueryAtom. matches(IAtom atom)Checks whether this query atom matches a target atom. -
Uses of IAtom in org.openscience.cdk.protein.data
Classes in org.openscience.cdk.protein.data that implement IAtom Modifier and Type Class Description classPDBAtomRepresents the idea of an atom as used in PDB files.Methods in org.openscience.cdk.protein.data with parameters of type IAtom Modifier and Type Method Description voidPDBStrand. addAtom(IAtom oAtom, IMonomer oMonomer)Adds the atom oAtom to a specified Monomer. -
Uses of IAtom in org.openscience.cdk.qsar
Methods in org.openscience.cdk.qsar with parameters of type IAtom Modifier and Type Method Description voidAbstractAtomicDescriptor. cacheDescriptorValue(IAtom atom, IAtomContainer container, IDescriptorResult value)Caches a DescriptorValue for a given IAtom.DescriptorValueIAtomicDescriptor. calculate(IAtom atom, IAtomContainer container)Calculates the descriptor value for the given IAtom.DescriptorValueIAtomPairDescriptor. calculate(IAtom atom, IAtom atom2, IAtomContainer container)Calculates the descriptor value for the given IAtom.IDescriptorResultAbstractAtomicDescriptor. getCachedDescriptorValue(IAtom atom)Returns the cached DescriptorValue for the given IAtom.static intAtomValenceTool. getValence(IAtom atom) -
Uses of IAtom in org.openscience.cdk.qsar.descriptors.atomic
Methods in org.openscience.cdk.qsar.descriptors.atomic with parameters of type IAtom Modifier and Type Method Description DescriptorValueAtomDegreeDescriptor. calculate(IAtom atom, IAtomContainer container)This method calculates the number of not-H substituents of an atom.DescriptorValueAtomHybridizationDescriptor. calculate(IAtom atom, IAtomContainer container)This method calculates the hybridization of an atom.DescriptorValueAtomHybridizationVSEPRDescriptor. calculate(IAtom atom, IAtomContainer container)This method calculates the hybridization of an atom.DescriptorValueAtomValenceDescriptor. calculate(IAtom atom, IAtomContainer container)This method calculates the valence of an atom.DescriptorValueBondsToAtomDescriptor. calculate(IAtom atom, IAtomContainer container)This method calculate the number of bonds on the shortest path between two atoms.DescriptorValueCovalentRadiusDescriptor. calculate(IAtom atom, IAtomContainer container)This method calculates the Covalent radius of an atom.DescriptorValueDistanceToAtomDescriptor. calculate(IAtom atom, IAtomContainer container)This method calculate the 3D distance between two atoms.DescriptorValueEffectiveAtomPolarizabilityDescriptor. calculate(IAtom atom, IAtomContainer ac)The method calculates the Effective Atom Polarizability of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValueInductiveAtomicHardnessDescriptor. calculate(IAtom atom, IAtomContainer ac)It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.DescriptorValueInductiveAtomicSoftnessDescriptor. calculate(IAtom atom, IAtomContainer ac)It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.DescriptorValueIPAtomicHOSEDescriptor. calculate(IAtom atom, IAtomContainer container)This method calculates the ionization potential of an atom.DescriptorValueIPAtomicLearningDescriptor. calculate(IAtom atom, IAtomContainer container)Deprecated.This method calculates the ionization potential of an atom.DescriptorValueIsProtonInAromaticSystemDescriptor. calculate(IAtom atom, IAtomContainer atomContainer)The method is a proton descriptor that evaluate if a proton is bonded to an aromatic system or if there is distance of 2 bonds.DescriptorValueIsProtonInConjugatedPiSystemDescriptor. calculate(IAtom atom, IAtomContainer atomContainer)The method is a proton descriptor that evaluates if a proton is joined to a conjugated system.DescriptorValuePartialPiChargeDescriptor. calculate(IAtom atom, IAtomContainer ac)The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValuePartialSigmaChargeDescriptor. calculate(IAtom atom, IAtomContainer ac)The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValuePartialTChargeMMFF94Descriptor. calculate(IAtom atom, IAtomContainer org)The method returns partial charges assigned to an heavy atom through MMFF94 method.DescriptorValuePartialTChargePEOEDescriptor. calculate(IAtom atom, IAtomContainer ac)The method returns partial total charges assigned to an heavy atom through PEOE method.DescriptorValuePeriodicTablePositionDescriptor. calculate(IAtom atom, IAtomContainer container)This method calculates the period of an atom.DescriptorValuePiElectronegativityDescriptor. calculate(IAtom atom, IAtomContainer atomContainer)The method calculates the pi electronegativity of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValueProtonAffinityHOSEDescriptor. calculate(IAtom atom, IAtomContainer container)This method calculates the protonation affinity of an atom.DescriptorValueProtonTotalPartialChargeDescriptor. calculate(IAtom atom, IAtomContainer ac)The method returns partial charges assigned to an heavy atom and its protons through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValueRDFProtonDescriptor_G3R. calculate(IAtom atom, IAtomContainer varAtomContainerSet)DescriptorValueRDFProtonDescriptor_G3R. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)DescriptorValueRDFProtonDescriptor_GDR. calculate(IAtom atom, IAtomContainer varAtomContainerSet)DescriptorValueRDFProtonDescriptor_GDR. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)DescriptorValueRDFProtonDescriptor_GHR_topol. calculate(IAtom atom, IAtomContainer varAtomContainerSet)DescriptorValueRDFProtonDescriptor_GHR_topol. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)DescriptorValueRDFProtonDescriptor_GHR. calculate(IAtom atom, IAtomContainer varAtomContainerSet)DescriptorValueRDFProtonDescriptor_GHR. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)DescriptorValueRDFProtonDescriptor_GSR. calculate(IAtom atom, IAtomContainer varAtomContainerSet)DescriptorValueRDFProtonDescriptor_GSR. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)DescriptorValueSigmaElectronegativityDescriptor. calculate(IAtom atom, IAtomContainer ac)The method calculates the sigma electronegativity of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValueStabilizationPlusChargeDescriptor. calculate(IAtom atom, IAtomContainer container)The method calculates the stabilization of charge of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValueVdWRadiusDescriptor. calculate(IAtom atom, IAtomContainer container)This method calculate the Van der Waals radius of an atom. -
Uses of IAtom in org.openscience.cdk.qsar.descriptors.atompair
Methods in org.openscience.cdk.qsar.descriptors.atompair with parameters of type IAtom Modifier and Type Method Description DescriptorValuePiContactDetectionDescriptor. calculate(IAtom first, IAtom second, IAtomContainer atomContainer)The method returns if two atoms have pi-contact. -
Uses of IAtom in org.openscience.cdk.qsar.descriptors.molecular
Methods in org.openscience.cdk.qsar.descriptors.molecular with parameters of type IAtom Modifier and Type Method Description protected booleanJPlogPDescriptor.JPlogPCalculator. boundTo(IAtom atom, String symbol)protected booleanJPlogPDescriptor.JPlogPCalculator. carbonylConjugated(IAtom atom)protected booleanJPlogPDescriptor.JPlogPCalculator. checkAlphaCarbonyl(IAtom atom, String symbol)Should be called from the carbonyl oxygenprotected booleanJPlogPDescriptor.JPlogPCalculator. doubleBondHetero(IAtom atom)protected booleanJPlogPDescriptor.JPlogPCalculator. electronWithdrawing(IAtom atom)protected intJPlogPDescriptor.JPlogPCalculator. getCarbonSpecial(IAtom atom)Determines and returns the SS (subsection) portion of the atomtype integer for a Carbon Atomprotected intJPlogPDescriptor.JPlogPCalculator. getDefaultSpecial(IAtom atom)Determines and returns the SS (subsection) portion of the atomtype integer for a "Default" ie not C,N,O,H,F Atomprotected intJPlogPDescriptor.JPlogPCalculator. getFluorineSpecial(IAtom atom)Determines and returns the SS (subsection) portion of the atomtype integer for a Fluorine Atomprotected intJPlogPDescriptor.JPlogPCalculator. getHydrogenSpecial(IAtom atom)Determines and returns the SS (subsection) portion of the atomtype integer for a Hydrogen Atomprotected intJPlogPDescriptor.JPlogPCalculator. getNitrogenSpecial(IAtom atom)Determines and returns the SS (subsection) portion of the atomtype integer for a Nitrogen Atomprotected doubleJPlogPDescriptor.JPlogPCalculator. getNumMoreElectronegativethanCarbon(IAtom atom)protected intJPlogPDescriptor.JPlogPCalculator. getOxygenSpecial(IAtom atom)Determines and returns the SS (subsection) portion of the atomtype integer for an Oxygen Atomprotected int[]JPlogPDescriptor.JPlogPCalculator. getPolarBondArray(IAtom atom)protected booleanJPlogPDescriptor.JPlogPCalculator. isPolar(IAtom atom)protected booleanJPlogPDescriptor.JPlogPCalculator. nextToAromatic(IAtom atom)protected intJPlogPDescriptor.JPlogPCalculator. nonHNeighbours(IAtom atom)Method parameters in org.openscience.cdk.qsar.descriptors.molecular with type arguments of type IAtom Modifier and Type Method Description static booleanWeightedPathDescriptor. unique(List<IAtom> path) -
Uses of IAtom in org.openscience.cdk.reaction
Method parameters in org.openscience.cdk.reaction with type arguments of type IAtom Modifier and Type Method Description IReactionIReactionMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)Initiates the process for the given mechanism. -
Uses of IAtom in org.openscience.cdk.reaction.mechanism
Method parameters in org.openscience.cdk.reaction.mechanism with type arguments of type IAtom Modifier and Type Method Description IReactionAdductionLPMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)Initiates the process for the given mechanism.IReactionAdductionPBMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)Initiates the process for the given mechanism.IReactionHeterolyticCleavageMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)Initiates the process for the given mechanism.IReactionHomolyticCleavageMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)Initiates the process for the given mechanism.IReactionRadicalSiteIonizationMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)Initiates the process for the given mechanism.IReactionRadicalSiteRearrangementMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)Initiates the process for the given mechanism.IReactionRearrangementChargeMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)Initiates the process for the given mechanism.IReactionRemovingSEofBMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)Initiates the process for the given mechanism.IReactionRemovingSEofNBMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)Initiates the process for the given mechanism.IReactionSharingElectronMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)Initiates the process for the given mechanism.IReactionTautomerizationMechanism. initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)Initiates the process for the given mechanism. -
Uses of IAtom in org.openscience.cdk.renderer
Methods in org.openscience.cdk.renderer that return IAtom Modifier and Type Method Description IAtomRendererModel. getHighlightedAtom()Returns the atom currently highlighted.Methods in org.openscience.cdk.renderer that return types with arguments of type IAtom Modifier and Type Method Description Map<IAtom,IAtom>RendererModel. getMerge()This is the central facility for handling "merges" of atoms.Map<IAtom,IAtom>RendererModel. getMerge()This is the central facility for handling "merges" of atoms.Map<IAtom,String>RendererModel. getToolTipTextMap()Gets the toolTipTextMap.Methods in org.openscience.cdk.renderer with parameters of type IAtom Modifier and Type Method Description StringRendererModel. getToolTipText(IAtom atom)Gets the toolTipText for atom certain atom.voidRendererModel. setHighlightedAtom(IAtom highlightedAtom)Sets the atom currently highlighted.abstract booleanSymbolVisibility. visible(IAtom atom, List<IBond> neighbors, RendererModel model)Determine if an atom with the specified bonds is visible.Method parameters in org.openscience.cdk.renderer with type arguments of type IAtom Modifier and Type Method Description voidRendererModel. setToolTipTextMap(Map<IAtom,String> map)Sets the toolTipTextMap. -
Uses of IAtom in org.openscience.cdk.renderer.color
Methods in org.openscience.cdk.renderer.color with parameters of type IAtom Modifier and Type Method Description ColorCDK2DAtomColors. getAtomColor(IAtom atom)Returns the color for a certain atom type.ColorCDK2DAtomColors. getAtomColor(IAtom atom, Color defaultColor)Returns the color for a certain atom type, and uses the given default color if it fails to identify the atom type.ColorCDKAtomColors. getAtomColor(IAtom atom)Deprecated.Returns the CDK scheme color for the given atom's element.ColorCDKAtomColors. getAtomColor(IAtom atom, Color defaultColor)Deprecated.Returns the CDK scheme color for the given atom's element, or defaults to the given color if no color is defined.ColorCPKAtomColors. getAtomColor(IAtom atom)Deprecated.Returns the font color for atom given atom.ColorCPKAtomColors. getAtomColor(IAtom atom, Color defaultColor)Deprecated.Returns the font color for atom given atom.ColorIAtomColorer. getAtomColor(IAtom atom)Returns the color for a certain atom type.default ColorIAtomColorer. getAtomColor(IAtom atom, Color defaultColor)Returns the color for a certain atom type, and uses the given default color if it fails to identify the atom type.ColorJmolColors. getAtomColor(IAtom atom)ColorJmolColors. getAtomColor(IAtom atom, Color defaultColor)ColorPartialAtomicChargeColors. getAtomColor(IAtom atom)Returns the a color reflecting the given atom's partial charge.ColorPartialAtomicChargeColors. getAtomColor(IAtom atom, Color defaultColor)Returns the a color reflecting the given atom's partial charge, or defaults to the given color if no color is defined.ColorRasmolColors. getAtomColor(IAtom atom)Returns the Rasmol color for the given atom's element.ColorRasmolColors. getAtomColor(IAtom atom, Color defaultColor)Returns the Rasmol color for the given atom's element, or defaults to the given color if no color is defined.ColorUniColor. getAtomColor(IAtom atom)Returns the color for a certain atom type.ColorUniColor. getAtomColor(IAtom atom, Color defaultColor)Returns the color for a certain atom type, and uses the given default color if it fails to identify the atom type. -
Uses of IAtom in org.openscience.cdk.renderer.elements
Methods in org.openscience.cdk.renderer.elements with parameters of type IAtom Modifier and Type Method Description static MarkedElementMarkedElement. markupAtom(IRenderingElement elem, IAtom atom)Markup a atom with the class 'atom' and optionally the ids/classes from it's properties. -
Uses of IAtom in org.openscience.cdk.renderer.generators
Methods in org.openscience.cdk.renderer.generators with parameters of type IAtom Modifier and Type Method Description protected booleanBasicAtomGenerator. canDraw(IAtom atom, IAtomContainer container, RendererModel model)Checks an atom to see if it should be drawn.IRenderingElementBasicAtomGenerator. generate(IAtomContainer atomContainer, IAtom atom, RendererModel model)Generate the rendering element(s) for a particular atom.IRenderingElementExtendedAtomGenerator. generate(IAtomContainer container, IAtom atom, RendererModel model)Generate the rendering element(s) for a particular atom.IRenderingElementBasicAtomGenerator. generateCompactElement(IAtom atom, RendererModel model)Generate a compact element for an atom, such as a circle or a square, rather than text element.AtomSymbolElementBasicAtomGenerator. generateElement(IAtom atom, int alignment, RendererModel model)Generate an atom symbol element.protected ColorBasicAtomGenerator. getAtomColor(IAtom atom, RendererModel model)Returns the drawing color of the given atom.protected booleanBasicAtomGenerator. hasCoordinates(IAtom atom)Checks an atom to see if it has 2D coordinates.protected booleanBasicAtomGenerator. invisibleCarbon(IAtom atom, IAtomContainer atomContainer, RendererModel model)Checks an atom to see if it is an 'invisible carbon' - that is, it is: a) a carbon atom and b) this carbon should not be shown.protected booleanBasicAtomGenerator. invisibleHydrogen(IAtom atom, RendererModel model)Checks an atom to see if it is an 'invisible hydrogen' - that is, it is a) an (explicit) hydrogen, and b) explicit hydrogens are set to off.protected booleanBasicAtomGenerator. isHydrogen(IAtom atom)Determines if the atom is a hydrogen.booleanAtomMassGenerator. showCarbon(IAtom atom, IAtomContainer container, RendererModel model)Returns true if the mass number of this element is set and not equal the mass number of the most abundant isotope of this element.protected booleanBasicAtomGenerator. showCarbon(IAtom carbonAtom, IAtomContainer container, RendererModel model)Checks a carbon atom to see if it should be shown. -
Uses of IAtom in org.openscience.cdk.renderer.generators.standard
Methods in org.openscience.cdk.renderer.generators.standard with parameters of type IAtom Modifier and Type Method Description booleanSelectionVisibility. visible(IAtom atom, List<IBond> neighbors, RendererModel model)Determine if an atom with the specified bonds is visible. -
Uses of IAtom in org.openscience.cdk.ringsearch
Methods in org.openscience.cdk.ringsearch with parameters of type IAtom Modifier and Type Method Description booleanRingSearch. cyclic(IAtom atom)Determine whether the provided atom belongs to a ring (is cyclic). -
Uses of IAtom in org.openscience.cdk.sgroup
Methods in org.openscience.cdk.sgroup that return types with arguments of type IAtom Modifier and Type Method Description Set<IAtom>Sgroup. getAtoms()Access the atoms of this substructure group.Methods in org.openscience.cdk.sgroup with parameters of type IAtom Modifier and Type Method Description voidSgroup. addAtom(IAtom atom)Add an atom to this Sgroup.voidSgroup. removeAtom(IAtom atom)Remove an atom from this Sgroup. -
Uses of IAtom in org.openscience.cdk.signature
Constructors in org.openscience.cdk.signature with parameters of type IAtom Constructor Description AtomSignature(IAtom atom, int height, IAtomContainer molecule)Create an atom signature for the atomatomand with a maximum height ofheight.AtomSignature(IAtom atom, int height, signature.AbstractVertexSignature.InvariantType invariantType, IAtomContainer molecule)Create an atom signature for the atomatom, with maximum height ofheight, and using a particular invariant type.AtomSignature(IAtom atom, IAtomContainer molecule)Create an atom signature for the atomatom. -
Uses of IAtom in org.openscience.cdk.silent
Classes in org.openscience.cdk.silent that implement IAtom Modifier and Type Class Description classAtomRepresents the idea of an chemical atom.classFragmentAtomClass to represent an IPseudoAtom which embeds an IAtomContainer.classPDBAtomRepresents the idea of an atom as used in PDB files.classPseudoAtomRepresents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.Fields in org.openscience.cdk.silent declared as IAtom Modifier and Type Field Description protected IAtomLonePair. atomThe atom with which this lone pair is associated.protected IAtomSingleElectron. atomThe atom with which this single electron is associated.protected IAtom[]AtomContainerLegacy. atomsInternal array of atoms.protected IAtom[]Bond. atomsA list of atoms participating in this bond.Methods in org.openscience.cdk.silent that return IAtom Modifier and Type Method Description IAtomAtom. clone()Clones this atom object and its content.IAtomAtomContainer. getAtom(int idx)Get the atom at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getAtomCount().IAtomAtomContainerLegacy. getAtom(int idx)Get the atom at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getAtomCount().IAtomBond. getAtom(int position)Returns an Atom from this bond.IAtomLonePair. getAtom()Returns the associated Atom.IAtomSingleElectron. getAtom()Returns the associated Atom.IAtomBond. getBegin()Access the begin (or first) atom of the bond.IAtomBond. getConnectedAtom(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.IAtom[]Bond. getConnectedAtoms(IAtom atom)Returns all the atoms in the bond connected to the given atom.IAtomAminoAcid. getCTerminus()Retrieves the C-terminus atom.IAtomBond. getEnd()Access the end (or second) atom of the bond.IAtomAtomContainer. getFirstAtom()Returns the atom at position 0 in the container.IAtomAtomContainerLegacy. getFirstAtom()Returns the atom at position 0 in the container.IAtomAtomContainer. getLastAtom()Returns the atom at the last position in the container.IAtomAtomContainerLegacy. getLastAtom()Returns the atom at the last position in the container.IAtomAminoAcid. getNTerminus()Retrieves the N-terminus atom.IAtomBond. getOther(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correctIBond.getConnectedAtoms(IAtom)should be used.IAtomAtomContainer. newAtom(int element, int numImplH)IAtomAtomContainer. newAtom(IAtom atom)IAtomSilentChemObjectBuilder. newAtom()Create a new atom using the default constructor.Methods in org.openscience.cdk.silent that return types with arguments of type IAtom Modifier and Type Method Description Iterable<IAtom>AtomContainer. atoms()Returns an Iterable for looping over all atoms in this container.Iterable<IAtom>AtomContainerLegacy. atoms()Returns an Iterable for looping over all atoms in this container.Iterable<IAtom>Bond. atoms()Returns the Iterator to atoms making up this bond.List<IAtom>AtomContainer. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>AtomContainerLegacy. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.Methods in org.openscience.cdk.silent with parameters of type IAtom Modifier and Type Method Description voidAtomContainer. addAtom(IAtom atom)Adds an atom to this container.voidAtomContainerLegacy. addAtom(IAtom atom)Adds an atom to this container.voidBioPolymer. addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)Adds the atom to a specified Strand and a specified Monomer.voidBioPolymer. addAtom(IAtom oAtom, IStrand oStrand)Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.voidPolymer. addAtom(IAtom oAtom, IMonomer oMonomer)Adds the atom oAtom to a specified Monomer.voidStrand. addAtom(IAtom oAtom)Adds the atom oAtom without specifying a Monomer or a Strand.voidStrand. addAtom(IAtom oAtom, IMonomer oMonomer)Adds the atom oAtom to a specific Monomer.voidAminoAcid. addCTerminus(IAtom atom)Add an Atom and makes it the C-terminus atom.voidAminoAcid. addNTerminus(IAtom atom)Add an Atom and makes it the N-terminus atom.booleanAtomContainer. contains(IAtom atom)True, if the AtomContainer contains the given atom object.booleanAtomContainerLegacy. contains(IAtom atom)True, if the AtomContainer contains the given atom object.booleanBond. contains(IAtom atom)Returns true if the given atom participates in this bond.booleanLonePair. contains(IAtom atom)Returns true if the given atom participates in this lone pair.booleanRingSet. contains(IAtom atom)True, if at least one of the rings in the ringset contains the given atom.booleanSingleElectron. contains(IAtom atom)Returns true if the given atom participates in this SingleElectron.intAtomContainer. getAtomNumber(IAtom atom)Returns the position of a given atom in the atoms array.intAtomContainerLegacy. getAtomNumber(IAtom atom)Returns the position of a given atom in the atoms array.IBondAtom. getBond(IAtom atom)Returns the bond connecting 'this' atom to the provided atom.IBondAtomContainer. getBond(IAtom beg, IAtom end)Returns the bond that connects the two given atoms.IBondAtomContainerLegacy. getBond(IAtom atom1, IAtom atom2)Returns the bond that connects the two given atoms.intAtomContainer. getBondNumber(IAtom beg, IAtom end)Returns the position of the bond between two given atoms in the electronContainers array.intAtomContainerLegacy. getBondNumber(IAtom atom1, IAtom atom2)Returns the position of the bond between two given atoms in the electronContainers array.doubleAtomContainer. getBondOrderSum(IAtom atom)Returns the sum of the bond orders for a given Atom.doubleAtomContainerLegacy. getBondOrderSum(IAtom atom)Returns the sum of the bond orders for a given Atom.IAtomBond. getConnectedAtom(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.IAtom[]Bond. getConnectedAtoms(IAtom atom)Returns all the atoms in the bond connected to the given atom.intAtomContainer. getConnectedAtomsCount(IAtom atom)Returns the number of connected atoms (explicit degree) to the specified atom.intAtomContainerLegacy. getConnectedAtomsCount(IAtom atom)Returns the number of connected atoms (explicit degree) to the specified atom.List<IAtom>AtomContainer. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.List<IAtom>AtomContainerLegacy. getConnectedAtomsList(IAtom atom)Returns the atoms connected connected to the specified atom by a bond.intAtomContainer. getConnectedBondsCount(IAtom atom)Returns the number of connected bonds (explicit degree) to the specified atom.intAtomContainerLegacy. getConnectedBondsCount(IAtom atom)Returns the number of connected bonds (explicit degree) to the specified atom.List<IBond>AtomContainer. getConnectedBondsList(IAtom atom)Returns the bonds connected connected to the specified atom.List<IBond>AtomContainerLegacy. getConnectedBondsList(IAtom atom)Returns the bonds connected connected to the specified atom.List<IElectronContainer>AtomContainer. getConnectedElectronContainersList(IAtom atom)Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.List<IElectronContainer>AtomContainerLegacy. getConnectedElectronContainersList(IAtom atom)Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.intAtomContainer. getConnectedLonePairsCount(IAtom atom)Returns the number of lone pairs connected to the specified atom.intAtomContainerLegacy. getConnectedLonePairsCount(IAtom atom)Returns the number of lone pairs connected to the specified atom.List<ILonePair>AtomContainer. getConnectedLonePairsList(IAtom atom)Returns the lone pairs connected connected to the specified atom.List<ILonePair>AtomContainerLegacy. getConnectedLonePairsList(IAtom atom)Returns the lone pairs connected connected to the specified atom.intAtomContainer. getConnectedSingleElectronsCount(IAtom atom)Returns the number of single electrons connected to the specified atom.intAtomContainerLegacy. getConnectedSingleElectronsCount(IAtom atom)Returns the number of single electrons connected to the specified atom.List<ISingleElectron>AtomContainer. getConnectedSingleElectronsList(IAtom atom)Returns the single electrons connected connected to the specified atom.List<ISingleElectron>AtomContainerLegacy. getConnectedSingleElectronsList(IAtom atom)Returns the single electrons connected connected to the specified atom.IBond.OrderAtomContainer. getMaximumBondOrder(IAtom atom)Returns the maximum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderAtomContainerLegacy. getMaximumBondOrder(IAtom atom)Returns the maximum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderAtomContainer. getMinimumBondOrder(IAtom atom)Returns the minimum bond order that this atom currently has in the context of this AtomContainer.IBond.OrderAtomContainerLegacy. getMinimumBondOrder(IAtom atom)Returns the minimum bond order that this atom currently has in the context of this AtomContainer.IBondRing. getNextBond(IBond bond, IAtom atom)Returns the next bond in order, relative to a given bond and atom.IAtomBond. getOther(IAtom atom)Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correctIBond.getConnectedAtoms(IAtom)should be used.IRingSetRingSet. getRings(IAtom atom)Returns a vector of all rings that this atom is part of.intAtomContainer. indexOf(IAtom atom)Access the storage index of an atom.intAtomContainerLegacy. indexOf(IAtom atom)Access the storage index of an atom.IAtomAtomContainer. newAtom(IAtom atom)IBondAtomContainer. newBond(IAtom beg, IAtom end, IBond.Order order)voidAtomContainer. removeAtom(IAtom atom)Safely remove an atom from the container.voidAtomContainerLegacy. removeAtom(IAtom atom)Safely remove an atom from the container.voidAtomContainer. removeAtomAndConnectedElectronContainers(IAtom atom)Safely remove an atom from the container.voidAtomContainerLegacy. removeAtomAndConnectedElectronContainers(IAtom atom)Deprecated.voidAtomContainer. removeAtomOnly(IAtom atom)Unsafely remove atom.voidAtomContainerLegacy. removeAtomOnly(IAtom atom)Unsafely remove atom.IBondAtomContainer. removeBond(IAtom beg, IAtom end)Removes the bond that connects the two given atoms.IBondAtomContainerLegacy. removeBond(IAtom atom1, IAtom atom2)Removes the bond that connects the two given atoms.voidAtomContainer. setAtom(int idx, IAtom atom)Set the atom atidx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().voidAtomContainerLegacy. setAtom(int idx, IAtom atom)Set the atom atidx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().voidBond. setAtom(IAtom atom, int position)Sets an Atom in this bond.voidLonePair. setAtom(IAtom atom)Sets the associated Atom.voidSingleElectron. setAtom(IAtom atom)Sets the associated Atom.voidAtomContainer. setAtoms(IAtom[] newatoms)Sets the array of atoms of this AtomContainer.voidAtomContainerLegacy. setAtoms(IAtom[] newAtoms)Sets the array of atoms of this AtomContainer.voidBond. setAtoms(IAtom[] atoms)Sets the array of atoms making up this bond.Constructors in org.openscience.cdk.silent with parameters of type IAtom Constructor Description Atom(IAtom org)Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance, mass number, maximum bond order, bond order sum, van der Waals and covalent radii, formal charge, hybridization, electron valency, formal neighbour count and atom type name from the given IAtomType.Bond(IAtom[] atoms)Constructs a multi-center bond, with undefined order and no stereo information.Bond(IAtom[] atoms, IBond.Order order)Constructs a multi-center bond, with a specified order and no stereo information.Bond(IAtom atom1, IAtom atom2)Constructs a bond with a single bond order..Bond(IAtom atom1, IAtom atom2, IBond.Order order)Constructs a bond with a given order.Bond(IAtom beg, IAtom end, IBond.Order order, IBond.Stereo stereo)Constructs a bond with a given order and stereo orientation from an array of atoms.LonePair(IAtom atom)Constructs an lone pair on an Atom.SingleElectron(IAtom atom)Constructs an single electron orbital on an Atom. -
Uses of IAtom in org.openscience.cdk.smiles
Methods in org.openscience.cdk.smiles that return IAtom Modifier and Type Method Description IAtomInvPair. getAtom()Methods in org.openscience.cdk.smiles that return types with arguments of type IAtom Modifier and Type Method Description static Comparator<IAtom>SmilesGenerator. createComparator(IAtomContainer mol, int flavor)Methods in org.openscience.cdk.smiles with parameters of type IAtom Modifier and Type Method Description voidInvPair. setAtom(IAtom newAtom)Constructors in org.openscience.cdk.smiles with parameters of type IAtom Constructor Description InvPair(long current, IAtom atom) -
Uses of IAtom in org.openscience.cdk.smsd
Methods in org.openscience.cdk.smsd that return types with arguments of type IAtom Modifier and Type Method Description List<Map<IAtom,IAtom>>Isomorphism. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e.List<Map<IAtom,IAtom>>Isomorphism. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e.Map<IAtom,IAtom>Isomorphism. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.Map<IAtom,IAtom>Isomorphism. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.Method parameters in org.openscience.cdk.smsd with type arguments of type IAtom Modifier and Type Method Description static Map<IBond,IBond>Isomorphism. makeBondMapOfAtomMap(IAtomContainer ac1, IAtomContainer ac2, Map<IAtom,IAtom> mapping)Deprecated.Returns bond map between source and target molecules based on the atomsstatic Map<IBond,IBond>Isomorphism. makeBondMapOfAtomMap(IAtomContainer ac1, IAtomContainer ac2, Map<IAtom,IAtom> mapping)Deprecated.Returns bond map between source and target molecules based on the atomsstatic List<Map<IBond,IBond>>Isomorphism. makeBondMapsOfAtomMaps(IAtomContainer ac1, IAtomContainer ac2, List<Map<IAtom,IAtom>> mappings)Deprecated.Returns bond maps between source and target molecules based on the atomsstatic List<Map<IBond,IBond>>Isomorphism. makeBondMapsOfAtomMaps(IAtomContainer ac1, IAtomContainer ac2, List<Map<IAtom,IAtom>> mappings)Deprecated.Returns bond maps between source and target molecules based on the atoms -
Uses of IAtom in org.openscience.cdk.smsd.algorithm.matchers
Methods in org.openscience.cdk.smsd.algorithm.matchers with parameters of type IAtom Modifier and Type Method Description booleanAtomMatcher. matches(IAtomContainer container, IAtom atom)Deprecated.booleanDefaultMCSPlusAtomMatcher. matches(IAtomContainer targetContainer, IAtom targetAtom)Deprecated.booleanDefaultRGraphAtomMatcher. matches(IAtomContainer targetContainer, IAtom targetAtom)Deprecated.booleanDefaultVFAtomMatcher. matches(TargetProperties targetContainer, IAtom targetAtom)Deprecated.booleanVFAtomMatcher. matches(TargetProperties container, IAtom atom)Deprecated.Constructors in org.openscience.cdk.smsd.algorithm.matchers with parameters of type IAtom Constructor Description DefaultMCSPlusAtomMatcher(IAtomContainer queryContainer, IAtom atom, boolean shouldMatchBonds)Deprecated.ConstructorDefaultMCSPlusAtomMatcher(IAtomContainer queryContainer, IAtom template, int blockedPositions, boolean shouldMatchBonds)Deprecated.ConstructorDefaultRGraphAtomMatcher(IAtomContainer queryContainer, IAtom atom, boolean shouldMatchBonds)Deprecated.ConstructorDefaultRGraphAtomMatcher(IAtomContainer queryContainer, IAtom template, int blockedPositions, boolean shouldMatchBonds)Deprecated.ConstructorDefaultVFAtomMatcher(IAtomContainer queryContainer, IAtom atom, boolean shouldMatchBonds)Deprecated.ConstructorDefaultVFAtomMatcher(IAtomContainer queryContainer, IAtom template, int blockedPositions, boolean shouldMatchBonds)Deprecated.Constructor -
Uses of IAtom in org.openscience.cdk.smsd.algorithm.mcsplus
Methods in org.openscience.cdk.smsd.algorithm.mcsplus that return types with arguments of type IAtom Modifier and Type Method Description List<Map<IAtom,IAtom>>MCSPlusHandler. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.List<Map<IAtom,IAtom>>MCSPlusHandler. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.Map<IAtom,IAtom>MCSPlusHandler. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.Map<IAtom,IAtom>MCSPlusHandler. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped. -
Uses of IAtom in org.openscience.cdk.smsd.algorithm.rgraph
Methods in org.openscience.cdk.smsd.algorithm.rgraph that return types with arguments of type IAtom Modifier and Type Method Description List<Map<IAtom,IAtom>>CDKMCSHandler. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.List<Map<IAtom,IAtom>>CDKMCSHandler. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.List<Map<IAtom,IAtom>>CDKSubGraphHandler. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.List<Map<IAtom,IAtom>>CDKSubGraphHandler. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.Map<IAtom,IAtom>CDKMCSHandler. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.Map<IAtom,IAtom>CDKMCSHandler. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.Map<IAtom,IAtom>CDKSubGraphHandler. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.Map<IAtom,IAtom>CDKSubGraphHandler. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped. -
Uses of IAtom in org.openscience.cdk.smsd.algorithm.single
Methods in org.openscience.cdk.smsd.algorithm.single that return types with arguments of type IAtom Modifier and Type Method Description List<Map<IAtom,IAtom>>SingleMappingHandler. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.List<Map<IAtom,IAtom>>SingleMappingHandler. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.Map<IAtom,IAtom>SingleMappingHandler. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.Map<IAtom,IAtom>SingleMappingHandler. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.protected List<Map<IAtom,IAtom>>SingleMapping. getOverLaps(IAtomContainer source, IAtomContainer target, boolean removeHydrogen)Deprecated.Returns single mapping solutions.protected List<Map<IAtom,IAtom>>SingleMapping. getOverLaps(IAtomContainer source, IAtomContainer target, boolean removeHydrogen)Deprecated.Returns single mapping solutions.protected List<Map<IAtom,IAtom>>SingleMapping. getOverLaps(IQueryAtomContainer source, IAtomContainer target, boolean removeHydrogen)Deprecated.Returns single mapping solutions.protected List<Map<IAtom,IAtom>>SingleMapping. getOverLaps(IQueryAtomContainer source, IAtomContainer target, boolean removeHydrogen)Deprecated.Returns single mapping solutions. -
Uses of IAtom in org.openscience.cdk.smsd.algorithm.vflib
Methods in org.openscience.cdk.smsd.algorithm.vflib that return types with arguments of type IAtom Modifier and Type Method Description List<Map<IAtom,IAtom>>VFlibMCSHandler. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.List<Map<IAtom,IAtom>>VFlibMCSHandler. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.List<Map<IAtom,IAtom>>VFlibSubStructureHandler. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.List<Map<IAtom,IAtom>>VFlibSubStructureHandler. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.List<Map<IAtom,IAtom>>VFlibTurboHandler. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.List<Map<IAtom,IAtom>>VFlibTurboHandler. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.Map<IAtom,IAtom>VFlibMCSHandler. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.Map<IAtom,IAtom>VFlibMCSHandler. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.Map<IAtom,IAtom>VFlibSubStructureHandler. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.Map<IAtom,IAtom>VFlibSubStructureHandler. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.Map<IAtom,IAtom>VFlibTurboHandler. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.Map<IAtom,IAtom>VFlibTurboHandler. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped. -
Uses of IAtom in org.openscience.cdk.smsd.algorithm.vflib.builder
Methods in org.openscience.cdk.smsd.algorithm.vflib.builder that return IAtom Modifier and Type Method Description IAtomTargetProperties. getAtom(int j)Deprecated.IAtomVFQueryBuilder. getAtom(INode node)Deprecated.Returns an atom associated with this node.Methods in org.openscience.cdk.smsd.algorithm.vflib.builder that return types with arguments of type IAtom Modifier and Type Method Description List<IAtom>TargetProperties. getNeighbors(IAtom atom)Deprecated.Methods in org.openscience.cdk.smsd.algorithm.vflib.builder with parameters of type IAtom Modifier and Type Method Description INodeVFQueryBuilder. addNode(VFAtomMatcher matcher, IAtom atom)Deprecated.Add and return a node for a query atomIntegerTargetProperties. countNeighbors(IAtom atom)Deprecated.IBondTargetProperties. getBond(IAtom atom1, IAtom atom2)Deprecated.List<IAtom>TargetProperties. getNeighbors(IAtom atom)Deprecated.INodeVFQueryBuilder. getNode(IAtom atom)Deprecated.Return a node for a given atom else return null -
Uses of IAtom in org.openscience.cdk.smsd.algorithm.vflib.interfaces
Methods in org.openscience.cdk.smsd.algorithm.vflib.interfaces that return IAtom Modifier and Type Method Description IAtomIQuery. getAtom(INode node)Deprecated.Returns an atom associated with this node.Methods in org.openscience.cdk.smsd.algorithm.vflib.interfaces that return types with arguments of type IAtom Modifier and Type Method Description Map<INode,IAtom>IMapper. getFirstMap(IAtomContainer target)Deprecated.Returns first solution map.Map<INode,IAtom>IMapper. getFirstMap(TargetProperties target)Deprecated.Returns first solution map.Map<INode,IAtom>IState. getMap()Deprecated.Returns the current mapping of query atoms onto target atoms.List<Map<INode,IAtom>>IMapper. getMaps(IAtomContainer target)Deprecated.Returns all solution map.List<Map<INode,IAtom>>IMapper. getMaps(TargetProperties target)Deprecated.Returns all solution map. -
Uses of IAtom in org.openscience.cdk.smsd.algorithm.vflib.map
Methods in org.openscience.cdk.smsd.algorithm.vflib.map that return IAtom Modifier and Type Method Description IAtomMatch. getTargetAtom()Deprecated.Return Target AtomMethods in org.openscience.cdk.smsd.algorithm.vflib.map that return types with arguments of type IAtom Modifier and Type Method Description Map<INode,IAtom>VFMapper. getFirstMap(IAtomContainer target)Deprecated.Returns first solution map.Map<INode,IAtom>VFMapper. getFirstMap(TargetProperties targetMolecule)Deprecated.Returns first solution map.Map<INode,IAtom>VFMCSMapper. getFirstMap(IAtomContainer target)Deprecated.Returns first solution map.Map<INode,IAtom>VFMCSMapper. getFirstMap(TargetProperties targetMolecule)Deprecated.Returns first solution map.Map<INode,IAtom>VFState. getMap()Deprecated.Returns the current mapping of query atoms onto target atoms.List<Map<INode,IAtom>>VFMapper. getMaps(IAtomContainer target)Deprecated.Returns all solution map.List<Map<INode,IAtom>>VFMapper. getMaps(TargetProperties targetMolecule)Deprecated.Returns all solution map.List<Map<INode,IAtom>>VFMCSMapper. getMaps(IAtomContainer target)Deprecated.Returns all solution map.List<Map<INode,IAtom>>VFMCSMapper. getMaps(TargetProperties targetMolecule)Deprecated.Returns all solution map.Constructors in org.openscience.cdk.smsd.algorithm.vflib.map with parameters of type IAtom Constructor Description Match(INode query, IAtom target)Deprecated.Constructor -
Uses of IAtom in org.openscience.cdk.smsd.interfaces
Methods in org.openscience.cdk.smsd.interfaces that return types with arguments of type IAtom Modifier and Type Method Description abstract List<Map<IAtom,IAtom>>AbstractMCS. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e.abstract List<Map<IAtom,IAtom>>AbstractMCS. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e.List<Map<IAtom,IAtom>>IMCSBase. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.List<Map<IAtom,IAtom>>IMCSBase. getAllAtomMapping()Deprecated.Returns all plausible mappings between query and target molecules.abstract Map<IAtom,IAtom>AbstractMCS. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.abstract Map<IAtom,IAtom>AbstractMCS. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.Map<IAtom,IAtom>IMCSBase. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped.Map<IAtom,IAtom>IMCSBase. getFirstAtomMapping()Deprecated.Returns one of the best matches with atoms mapped. -
Uses of IAtom in org.openscience.cdk.smsd.ring
Methods in org.openscience.cdk.smsd.ring that return IAtom Modifier and Type Method Description IAtomPathEdge. getSource()Deprecated.IAtomPathEdge. getTarget()Deprecated.Methods in org.openscience.cdk.smsd.ring that return types with arguments of type IAtom Modifier and Type Method Description Collection<List<IAtom>>HanserRingFinder. findRings(IAtomContainer molecule)Deprecated.Returns a collection of rings.Collection<List<IAtom>>RingFinder. findRings(IAtomContainer molecule)Deprecated.Returns Collection of atoms in Rings based on Hanser Ring Finding methodList<IAtom>PathEdge. getAtoms()Deprecated.Methods in org.openscience.cdk.smsd.ring with parameters of type IAtom Modifier and Type Method Description List<PathEdge>PathGraph. remove(IAtom atom)Deprecated.Method parameters in org.openscience.cdk.smsd.ring with type arguments of type IAtom Modifier and Type Method Description voidRingFilter. filterAtoms(int atomLimit, Collection<List<IAtom>> rings, Collection<IAtom> atoms)Deprecated.voidRingFilter. filterAtoms(IAtomContainer molecule, Collection<IAtom> atoms)Deprecated.Constructor parameters in org.openscience.cdk.smsd.ring with type arguments of type IAtom Constructor Description PathEdge(List<IAtom> atoms)Deprecated. -
Uses of IAtom in org.openscience.cdk.smsd.tools
Methods in org.openscience.cdk.smsd.tools with parameters of type IAtom Modifier and Type Method Description intBondEnergies. getEnergies(IAtom sourceAtom, IAtom targetAtom, IBond.Order bondOrder)Deprecated.Returns bond energy for a bond type, given atoms and bond typestatic intExtAtomContainerManipulator. getExplicitHydrogenCount(IAtomContainer atomContainer, IAtom atom)Deprecated.Returns The number of explicit hydrogens for a given IAtom.static intExtAtomContainerManipulator. getHydrogenCount(IAtomContainer atomContainer, IAtom atom)Deprecated.The summed implicit + explicit hydrogens of the given IAtom.static intExtAtomContainerManipulator. getImplicitHydrogenCount(IAtom atom)Deprecated.Returns The number of Implicit Hydrogen Count for a given IAtom. -
Uses of IAtom in org.openscience.cdk.stereo
Methods in org.openscience.cdk.stereo that return IAtom Modifier and Type Method Description static IAtom[]ExtendedCisTrans. findTerminalAtoms(IAtomContainer container, IBond focus)Helper method to locate two terminal atoms in a container for this extended Cis/Trans element.IAtom[]ExtendedTetrahedral. findTerminalAtoms(IAtomContainer container)Helper method to locate two terminal atoms in a container for this extended tetrahedral element.static IAtom[]ExtendedTetrahedral. findTerminalAtoms(IAtomContainer container, IAtom focus)Helper method to locate two terminal atoms in a container for a given focus.IAtomExtendedTetrahedral. focus()The central atom in the cumulated system.IAtomTetrahedralChirality. getChiralAtom()IAtom[]TetrahedralChirality. getLigands()IAtom[]ExtendedTetrahedral. peripherals()The neighbouring peripherals atoms, these are attached to the terminal atoms in the cumulated system.Methods in org.openscience.cdk.stereo that return types with arguments of type IAtom Modifier and Type Method Description protected IStereoElement<IBond,IAtom>Atropisomeric. create(IBond focus, List<IAtom> carriers, int cfg)protected IStereoElement<IAtom,IAtom>ExtendedTetrahedral. create(IAtom focus, List<IAtom> carriers, int cfg)protected IStereoElement<IAtom,IAtom>ExtendedTetrahedral. create(IAtom focus, List<IAtom> carriers, int cfg)protected IStereoElement<IAtom,IAtom>TetrahedralChirality. create(IAtom focus, List<IAtom> carriers, int config)protected IStereoElement<IAtom,IAtom>TetrahedralChirality. create(IAtom focus, List<IAtom> carriers, int config)Methods in org.openscience.cdk.stereo with parameters of type IAtom Modifier and Type Method Description protected IStereoElement<IAtom,IAtom>ExtendedTetrahedral. create(IAtom focus, List<IAtom> carriers, int cfg)protected OctahedralOctahedral. create(IAtom focus, List<IAtom> carriers, int cfg)protected SquarePlanarSquarePlanar. create(IAtom focus, List<IAtom> carriers, int cfg)protected IStereoElement<IAtom,IAtom>TetrahedralChirality. create(IAtom focus, List<IAtom> carriers, int config)protected TrigonalBipyramidalTrigonalBipyramidal. create(IAtom focus, List<IAtom> carriers, int cfg)static IBondExtendedCisTrans. findCentralBond(IAtomContainer mol, IAtom atom)Locate the central double-bond in a chain of cumulated double bonds.static IAtom[]ExtendedTetrahedral. findTerminalAtoms(IAtomContainer container, IAtom focus)Helper method to locate two terminal atoms in a container for a given focus.static StereoTool.TetrahedralSignStereoTool. getHandedness(IAtom baseAtomA, IAtom baseAtomB, IAtom baseAtomC, IAtom apexAtom)Gets the tetrahedral handedness of four atoms - three of which form the 'base' of the tetrahedron, and the other the apex.static intExtendedTetrahedral. getLength(IAtomContainer container, IAtom focus)static StereoTool.SquarePlanarShapeStereoTool. getSquarePlanarShape(IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD)Given four atoms (assumed to be in the same plane), returns the arrangement of those atoms in that plane.static ITetrahedralChirality.StereoStereoTool. getStereo(IAtom atom1, IAtom atom2, IAtom atom3, IAtom atom4)Take four atoms, and return Stereo.CLOCKWISE or Stereo.ANTI_CLOCKWISE.static booleanStereoTool. isOctahedral(IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD, IAtom atomE, IAtom atomF, IAtom atomG)Checks these 7 atoms to see if they are at the points of an octahedron.static booleanStereoTool. isSquarePlanar(IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD)Checks these four atoms for square planarity.static booleanStereoTool. isTrigonalBipyramidal(IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD, IAtom atomE, IAtom atomF)Checks these 6 atoms to see if they form a trigonal-bipyramidal shape.Method parameters in org.openscience.cdk.stereo with type arguments of type IAtom Modifier and Type Method Description protected IStereoElement<IBond,IAtom>Atropisomeric. create(IBond focus, List<IAtom> carriers, int cfg)protected IStereoElement<IAtom,IAtom>ExtendedTetrahedral. create(IAtom focus, List<IAtom> carriers, int cfg)protected OctahedralOctahedral. create(IAtom focus, List<IAtom> carriers, int cfg)protected SquarePlanarSquarePlanar. create(IAtom focus, List<IAtom> carriers, int cfg)protected IStereoElement<IAtom,IAtom>TetrahedralChirality. create(IAtom focus, List<IAtom> carriers, int config)protected TrigonalBipyramidalTrigonalBipyramidal. create(IAtom focus, List<IAtom> carriers, int cfg)IDoubleBondStereochemistryDoubleBondStereochemistry. map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)IDoubleBondStereochemistryDoubleBondStereochemistry. map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)ITetrahedralChiralityTetrahedralChirality. map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)ITetrahedralChiralityTetrahedralChirality. map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)static intOctahedral. reorder(List<IAtom> current, List<IAtom> required)static intTrigonalBipyramidal. reorder(List<IAtom> current, List<IAtom> required)Constructors in org.openscience.cdk.stereo with parameters of type IAtom Constructor Description Atropisomeric(IBond focus, IAtom[] carriers, int value)Define a new atropisomer using the focus bond and the carrier atoms.ExtendedTetrahedral(IAtom focus, IAtom[] peripherals, int config)ExtendedTetrahedral(IAtom focus, IAtom[] peripherals, ITetrahedralChirality.Stereo winding)Create an extended tetrahedral stereo element for the provided 'focus' and 'peripherals' in the given 'winding'.Octahedral(IAtom focus, IAtom[] carriers, int order)Create a new octahedral configuration.SquarePlanar(IAtom focus, IAtom[] carriers, int order)Create a square-planar configuration around a provided focus atom.TetrahedralChirality(IAtom chiralAtom, IAtom[] ligands, int config)TetrahedralChirality(IAtom chiralAtom, IAtom[] ligands, ITetrahedralChirality.Stereo stereo)TrigonalBipyramidal(IAtom focus, IAtom[] carriers, int order)Create a new trigonal bipyramidal configuration. -
Uses of IAtom in org.openscience.cdk.tools
Methods in org.openscience.cdk.tools that return types with arguments of type IAtom Modifier and Type Method Description List<IAtom>HOSECodeGenerator. getNodesInSphere(int sphereNumber)List<IAtom>[]HOSECodeGenerator. getSpheres(IAtomContainer ac, IAtom root, int noOfSpheres, boolean ringsize)This method is intended to be used to get the atoms around an atom in spheres.Methods in org.openscience.cdk.tools with parameters of type IAtom Modifier and Type Method Description voidCDKHydrogenAdder. addImplicitHydrogens(IAtomContainer container, IAtom atom)Sets the implicit hydrogen count for the indicated IAtom in the given IAtomContainer.intSaturationChecker. calculateNumberOfImplicitHydrogens(IAtom atom)intSaturationChecker. calculateNumberOfImplicitHydrogens(IAtom atom, double bondOrderSum, double singleElectronSum, List<IBond> connectedBonds, boolean throwExceptionForUnknowAtom)Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds.intSaturationChecker. calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container)Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds.intSaturationChecker. calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container, boolean throwExceptionForUnknowAtom)intSmilesValencyChecker. calculateNumberOfImplicitHydrogens(IAtom atom, double bondOrderSum, IBond.Order maxBondOrder, int neighbourCount)Calculates the number of hydrogens that can be added to the given atom to fullfil the atom's valency.intSmilesValencyChecker. calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container)booleanSaturationChecker. couldMatchAtomType(IAtomContainer atomContainer, IAtom atom, IAtomType atomType)Determines if the atom can be of type AtomType.booleanSmilesValencyChecker. couldMatchAtomType(IAtomContainer container, IAtom atom, IAtomType type)Determines if the atom can be of type AtomType.booleanSmilesValencyChecker. couldMatchAtomType(IAtom atom, double bondOrderSum, IBond.Order maxBondOrder, IAtomType type)Determines if the atom can be of type AtomType.IAtomContainerStructureResonanceGenerator. getContainer(IAtomContainer molecule, IAtom atom)Get the container which the atom is found on resonance from aIAtomContainer.doubleSaturationChecker. getCurrentMaxBondOrder(IAtom atom, IAtomContainer ac)Returns the currently maximum formable bond order for this atom.StringHOSECodeGenerator. getHOSECode(IAtomContainer ac, IAtom root, int noOfSpheres)StringHOSECodeGenerator. getHOSECode(IAtomContainer ac, IAtom root, int noOfSpheres, boolean ringsize)doubleAtomTypeAwareSaturationChecker. getMaxNoOfBonds(IAtom atom)This method calculates the number of bonds that anIAtomcan have.static double[]IonizationPotentialTool. getQSARs(IAtomContainer container, IAtom atom)Deprecated.Get the results of 7 qsar descriptors been applied.List<IAtom>[]HOSECodeGenerator. getSpheres(IAtomContainer ac, IAtom root, int noOfSpheres, boolean ringsize)This method is intended to be used to get the atoms around an atom in spheres.booleanSaturationChecker. hasPerfectConfiguration(IAtom atom, IAtomContainer ac)booleanSaturationChecker. isOverSaturated(IAtom atom, IAtomContainer ac)Checks if the current atom has exceeded its bond order sum value.booleanAtomTypeAwareSaturationChecker. isSaturated(IAtom atom, IAtomContainer container)booleanCDKValencyChecker. isSaturated(IAtom atom, IAtomContainer container)booleanIValencyChecker. isSaturated(IAtom atom, IAtomContainer container)booleanLonePairElectronChecker. isSaturated(IAtom atom, IAtomContainer ac)Checks if an Atom is saturated their lone pair electrons by comparing it with known AtomTypes.booleanSaturationChecker. isSaturated(IAtom atom, IAtomContainer ac)Checks whether an Atom is saturated by comparing it with known AtomTypes.booleanSmilesValencyChecker. isSaturated(IAtom atom, IAtomContainer container)Checks whether an Atom is saturated by comparing it with known AtomTypes.static doubleIonizationPotentialTool. predictIP(IAtomContainer container, IAtom atom)Deprecated.Method which is predict the Ionization Potential from given atom.voidLonePairElectronChecker. saturate(IAtom atom, IAtomContainer ac)Saturates an IAtom by adding the appropriate number lone pairs. -
Uses of IAtom in org.openscience.cdk.tools.manipulator
Methods in org.openscience.cdk.tools.manipulator that return IAtom Modifier and Type Method Description static IAtom[]AtomContainerManipulator. getAtomArray(List<IAtom> list)Constructs an array of Atom objects from a List of Atom objects.static IAtom[]AtomContainerManipulator. getAtomArray(IAtomContainer container)Constructs an array of Atom objects from an AtomContainer.static IAtom[]BondManipulator. getAtomArray(IBond container)Constructs an array of Atom objects from Bond.static IAtomAtomContainerManipulator. getAtomById(IAtomContainer ac, String id)Returns an atom in an atomcontainer identified by idMethods in org.openscience.cdk.tools.manipulator that return types with arguments of type IAtom Modifier and Type Method Description static List<IAtom>AtomContainerManipulator. getHeavyAtoms(IAtomContainer container)Returns a set of nodes excluding all the hydrogens.Methods in org.openscience.cdk.tools.manipulator with parameters of type IAtom Modifier and Type Method Description static voidAtomTypeManipulator. configure(IAtom atom, IAtomType atomType)Method that assign properties to an atom given a particular atomType.static voidAtomTypeManipulator. configureUnsetProperties(IAtom atom, IAtomType atomType)Method that assign properties to an atom given a particular atomType.static intAtomContainerManipulator. countExplicitHydrogens(IAtomContainer atomContainer, IAtom atom)Count explicit hydrogens.static intAtomContainerManipulator. countHydrogens(IAtomContainer atomContainer, IAtom atom)static doubleAtomContainerManipulator. getBondOrderSum(IAtomContainer container, IAtom atom)Returns the sum of the bond order equivalents for a given IAtom.static IAtomContainerAtomContainerSetManipulator. getRelevantAtomContainer(IAtomContainerSet containerSet, IAtom atom)static IAtomContainerChemModelManipulator. getRelevantAtomContainer(IChemModel chemModel, IAtom atom)This badly named methods tries to determine which AtomContainer in the ChemModel is best suited to contain added Atom's and Bond's.static IAtomContainerMoleculeSetManipulator. getRelevantAtomContainer(IAtomContainerSet moleculeSet, IAtom atom)static IAtomContainerReactionManipulator. getRelevantAtomContainer(IReaction reaction, IAtom atom)static IAtomContainerReactionSetManipulator. getRelevantAtomContainer(IReactionSet set, IAtom atom)static IReactionChemModelManipulator. getRelevantReaction(IChemModel chemModel, IAtom atom)Retrieves the first IReaction containing a given IAtom from an IChemModel.static IReactionReactionSetManipulator. getRelevantReaction(IReactionSet set, IAtom atom)static booleanRingSetManipulator. isSameRing(IRingSet ringSet, IAtom atom1, IAtom atom2)Checks ifatom1andatom2share membership in the same ring or ring system.static voidAtomContainerSetManipulator. removeAtomAndConnectedElectronContainers(IAtomContainerSet set, IAtom atom)static voidChemModelManipulator. removeAtomAndConnectedElectronContainers(IChemModel chemModel, IAtom atom)Remove an Atom and the connected ElectronContainers from all AtomContainers inside an IChemModel.static voidMoleculeSetManipulator. removeAtomAndConnectedElectronContainers(IAtomContainerSet set, IAtom atom)static voidReactionManipulator. removeAtomAndConnectedElectronContainers(IReaction reaction, IAtom atom)Removes the providedatomand its connected electron containers from the reaction.static voidReactionSetManipulator. removeAtomAndConnectedElectronContainers(IReactionSet set, IAtom atom)static booleanAtomContainerManipulator. replaceAtomByAtom(IAtomContainer container, IAtom oldAtom, IAtom newAtom)Substitute one atom in a container for another adjusting bonds, single electrons, lone pairs, and stereochemistry as required.Method parameters in org.openscience.cdk.tools.manipulator with type arguments of type IAtom Modifier and Type Method Description static voidAtomContainerManipulator. copy(IAtomContainer dest, IAtomContainer source, Collection<IAtom> atoms)Copy atoms in the collection from a 'source' molecule to the provideddestination.static voidAtomContainerManipulator. copy(IAtomContainer dest, IAtomContainer source, Predicate<IAtom> atomFilter)Copy selected atoms from a 'source' molecule to the provideddestination.static voidAtomContainerManipulator. copy(IAtomContainer dest, IAtomContainer source, Predicate<IAtom> atomFilter, Predicate<IBond> bondFilter)Copy selected atoms/bonds from a 'source' molecule to the provideddestination.static IAtomContainerAtomContainerManipulator. extractSubstructure(IAtomContainer source, Collection<IAtom> atoms)Extract a substructure from a 'source' molecule to the provideddestination based on the collection of atoms.static IAtom[]AtomContainerManipulator. getAtomArray(List<IAtom> list)Constructs an array of Atom objects from a List of Atom objects. -
Uses of IAtom in org.openscience.cdk.validate
Methods in org.openscience.cdk.validate with parameters of type IAtom Modifier and Type Method Description ValidationReportAbstractValidator. validateAtom(IAtom subject)ValidationReportBasicValidator. validateAtom(IAtom subject)ValidationReportIValidator. validateAtom(IAtom subject)ValidationReportValidatorEngine. validateAtom(IAtom subject)
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