Uses of Interface
org.openscience.cdk.interfaces.IAtom

Packages that use IAtom

Package	Description
org.openscience.cdk
org.openscience.cdk.atomtype
org.openscience.cdk.charges
org.openscience.cdk.config
org.openscience.cdk.debug
org.openscience.cdk.fingerprint
org.openscience.cdk.fragment
org.openscience.cdk.geometry
org.openscience.cdk.geometry.alignment
org.openscience.cdk.geometry.cip
org.openscience.cdk.geometry.surface
org.openscience.cdk.graph
org.openscience.cdk.graph.invariant
org.openscience.cdk.hash
org.openscience.cdk.interfaces
org.openscience.cdk.io.cml
org.openscience.cdk.isomorphism
org.openscience.cdk.isomorphism.matchers
org.openscience.cdk.isomorphism.matchers.smarts
org.openscience.cdk.layout
org.openscience.cdk.libio.cml
org.openscience.cdk.libio.md
org.openscience.cdk.math.qm
org.openscience.cdk.modeling.builder3d
org.openscience.cdk.normalize
org.openscience.cdk.pharmacophore
org.openscience.cdk.protein.data
org.openscience.cdk.qsar
org.openscience.cdk.qsar.descriptors.atomic
org.openscience.cdk.qsar.descriptors.atompair
org.openscience.cdk.qsar.descriptors.molecular
org.openscience.cdk.reaction
org.openscience.cdk.reaction.mechanism
org.openscience.cdk.renderer
org.openscience.cdk.renderer.color
org.openscience.cdk.renderer.elements
org.openscience.cdk.renderer.generators
org.openscience.cdk.renderer.generators.standard
org.openscience.cdk.ringsearch
org.openscience.cdk.sgroup
org.openscience.cdk.signature
org.openscience.cdk.silent
org.openscience.cdk.smiles
org.openscience.cdk.smsd
org.openscience.cdk.smsd.algorithm.matchers
org.openscience.cdk.smsd.algorithm.mcsplus
org.openscience.cdk.smsd.algorithm.rgraph
org.openscience.cdk.smsd.algorithm.single
org.openscience.cdk.smsd.algorithm.vflib
org.openscience.cdk.smsd.algorithm.vflib.builder
org.openscience.cdk.smsd.algorithm.vflib.interfaces
org.openscience.cdk.smsd.algorithm.vflib.map
org.openscience.cdk.smsd.filters
org.openscience.cdk.smsd.interfaces
org.openscience.cdk.smsd.ring
org.openscience.cdk.smsd.tools
org.openscience.cdk.stereo
org.openscience.cdk.tools
org.openscience.cdk.tools.manipulator
org.openscience.cdk.validate

Uses of IAtom in org.openscience.cdk

Classes in org.openscience.cdk that implement IAtom

Modifier and Type	Class and Description
class	Atom Represents the idea of an chemical atom.
class	AtomRef An atom ref, references a CDK IAtom indirectly.
class	EnzymeResidueLocator Atom that represents part of an residue in an enzyme, like Arg255.
class	FragmentAtom Class to represent an IPseudoAtom which embeds an IAtomContainer.
class	PseudoAtom Represents 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 and Description
protected IAtom	SingleElectron.atom The atom with which this single electron is associated.
protected IAtom	LonePair.atom The atom with which this lone pair is associated.
protected IAtom[]	Association.atoms The atoms which take part in the association.
protected IAtom[]	Bond.atoms A list of atoms participating in this bond.
protected IAtom[]	AtomContainer.atoms Internal array of atoms.

Methods in org.openscience.cdk that return IAtom

Modifier and Type	Method and Description
IAtom	Atom.clone() Clones this atom object and its content.
IAtom	AtomRef.clone() Returns a deep clone of this IChemObject.
IAtom	AtomRef.deref() Dereference the atom pointer once providing access to the base atom.
static IAtom	AtomRef.deref(IAtom atom) Utility method to dereference an atom.
IAtom	SingleElectron.getAtom() Returns the associated Atom.
IAtom	LonePair.getAtom() Returns the associated Atom.
IAtom	Bond.getAtom(int position) Returns an Atom from this bond.
IAtom	AtomContainer.getAtom(int idx) Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
IAtom	BondRef.getAtom(int position) Returns an Atom from this bond.
IAtom	Association.getAtomAt(int position) Returns an Atom from this Association.
IAtom[]	Association.getAtoms() Returns the array of atoms making up this Association.
IAtom	Bond.getBegin() Access the begin (or first) atom of the bond.
IAtom	BondRef.getBegin() Access the begin (or first) atom of the bond.
IAtom	Bond.getConnectedAtom(IAtom atom) Returns the other atom in the bond, the atom is connected to the given atom.
IAtom	BondRef.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.
IAtom	AminoAcid.getCTerminus() Retrieves the C-terminus atom.
IAtom	Bond.getEnd() Access the end (or second) atom of the bond.
IAtom	BondRef.getEnd() Access the end (or second) atom of the bond.
IAtom	AtomContainer.getFirstAtom() Returns the atom at position 0 in the container.
IAtom	AtomContainer.getLastAtom() Returns the atom at the last position in the container.
IAtom	AminoAcid.getNTerminus() Retrieves the N-terminus atom.
IAtom	Bond.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 correct IBond.getConnectedAtoms(IAtom) should be used.
IAtom	BondRef.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 correct IBond.getConnectedAtoms(IAtom) should be used.
IAtom	DefaultChemObjectBuilder.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 and Description
Iterable<IAtom>	Bond.atoms() Returns the Iterator to atoms making up this bond.
Iterable<IAtom>	AtomContainer.atoms() Returns an Iterable for looping over all atoms in this container.
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.

Methods in org.openscience.cdk with parameters of type IAtom

Modifier and Type	Method and Description
void	Strand.addAtom(IAtom oAtom) Adds the atom oAtom without specifying a Monomer or a Strand.
void	AtomContainer.addAtom(IAtom atom) Adds an atom to this container.
void	Strand.addAtom(IAtom oAtom, IMonomer oMonomer) Adds the atom oAtom to a specific Monomer.
void	Polymer.addAtom(IAtom oAtom, IMonomer oMonomer) Adds the atom oAtom to a specified Monomer.
void	BioPolymer.addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand) Adds the atom to a specified Strand and a specified Monomer.
void	BioPolymer.addAtom(IAtom oAtom, IStrand oStrand) Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
void	AminoAcid.addCTerminus(IAtom atom) Add an Atom and makes it the C-terminus atom.
void	AminoAcid.addNTerminus(IAtom atom) Add an Atom and makes it the N-terminus atom.
boolean	Association.contains(IAtom atom) Returns true if the given atom participates in this Association.
boolean	SingleElectron.contains(IAtom atom) Returns true if the given atom participates in this SingleElectron.
boolean	Bond.contains(IAtom atom) Returns true if the given atom participates in this bond.
boolean	LonePair.contains(IAtom atom) Returns true if the given atom participates in this lone pair.
boolean	RingSet.contains(IAtom atom) True, if at least one of the rings in the ringset contains the given atom.
boolean	AtomContainer.contains(IAtom atom) True, if the AtomContainer contains the given atom object.
boolean	BondRef.contains(IAtom atom) Returns true if the given atom participates in this bond.
static IAtom	AtomRef.deref(IAtom atom) Utility method to dereference an atom.
int	AtomContainer.getAtomNumber(IAtom atom) Returns the position of a given atom in the atoms array.
IBond	Atom.getBond(IAtom atom) Returns the bond connecting 'this' atom to the provided atom.
IBond	AtomRef.getBond(IAtom atom) Returns the bond connecting 'this' atom to the provided atom.
IBond	AtomContainer.getBond(IAtom atom1, IAtom atom2) Returns the bond that connects the two given atoms.
int	AtomContainer.getBondNumber(IAtom atom1, IAtom atom2) Returns the position of the bond between two given atoms in the electronContainers array.
double	AtomContainer.getBondOrderSum(IAtom atom) Returns the sum of the bond orders for a given Atom.
IAtom	Bond.getConnectedAtom(IAtom atom) Returns the other atom in the bond, the atom is connected to the given atom.
IAtom	BondRef.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.
int	AtomContainer.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.
int	AtomContainer.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<IElectronContainer>	AtomContainer.getConnectedElectronContainersList(IAtom atom) Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
int	AtomContainer.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.
int	AtomContainer.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.
IBond.Order	AtomContainer.getMaximumBondOrder(IAtom atom) Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	AtomContainer.getMinimumBondOrder(IAtom atom) Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
IBond	Ring.getNextBond(IBond bond, IAtom atom) Returns the next bond in order, relative to a given bond and atom.
IAtom	Bond.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 correct IBond.getConnectedAtoms(IAtom) should be used.
IAtom	BondRef.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 correct IBond.getConnectedAtoms(IAtom) should be used.
IRingSet	RingSet.getRings(IAtom atom) Returns a vector of all rings that this atom is part of.
int	AtomContainer.indexOf(IAtom atom) Access the storage index of an atom.
void	AtomContainer.removeAtom(IAtom atom) Safely remove an atom from the container.
void	AtomContainer.removeAtomAndConnectedElectronContainers(IAtom atom) Deprecated.
void	AtomContainer.removeAtomOnly(IAtom atom) Unsafely remove atom.
IBond	AtomContainer.removeBond(IAtom atom1, IAtom atom2) Removes the bond that connects the two given atoms.
void	SingleElectron.setAtom(IAtom atom) Sets the associated Atom.
void	LonePair.setAtom(IAtom atom) Sets the associated Atom.
void	Bond.setAtom(IAtom atom, int position) Sets an Atom in this bond.
void	BondRef.setAtom(IAtom atom, int position) Sets an Atom in this bond.
void	AtomContainer.setAtom(int idx, IAtom atom) Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
void	Association.setAtomAt(IAtom atom, int position) Sets an Atom in this Association.
void	Association.setAtoms(IAtom[] atoms) Sets the array of atoms making up this Association.
void	Bond.setAtoms(IAtom[] atoms) Sets the array of atoms making up this bond.
void	AtomContainer.setAtoms(IAtom[] newAtoms) Sets the array of atoms of this AtomContainer.
void	BondRef.setAtoms(IAtom[] atoms) Sets the array of atoms making up this bond.

Constructors in org.openscience.cdk with parameters of type IAtom

Constructor and Description
Association(IAtom atom1, IAtom atom2) Constructs an association between two Atom's.
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 and Description
IAtomType	MMFF94AtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer, IAtom atomInterface) Deprecated. Assign the mmff94 atom type to a given atom.
IAtomType	MM2AtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer, IAtom atomInterface) Deprecated. Assign the mm2 atom type to a given atom.
IAtomType	StructGenMatcher.findMatchingAtomType(IAtomContainer atomContainer, IAtom atom) Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.
IAtomType	IAtomTypeMatcher.findMatchingAtomType(IAtomContainer container, IAtom atom) Method that assigns an atom type to a given atom belonging to an atom container.
IAtomType	CDKAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer, IAtom atom) Method that assigns an atom type to a given atom belonging to an atom container.
IAtomType	EStateAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
IAtomType	SybylAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer, IAtom atom) Sybyl atom type perception for a single atom.
static boolean	EStateAtomTypeMatcher.inSameAromaticRing(IAtomContainer m, IAtom atom1, IAtom atom2, IRingSet rs)
List<IAtomType>	StructGenAtomTypeGuesser.possibleAtomTypes(IAtomContainer atomContainer, IAtom atom) Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.
List<IAtomType>	IAtomTypeGuesser.possibleAtomTypes(IAtomContainer container, IAtom atom) Method that returns an iterator with a suitable list of atom types given the provided atom.

Uses of IAtom in org.openscience.cdk.charges

Methods in org.openscience.cdk.charges with parameters of type IAtom

Modifier and Type	Method and Description
double	Polarizability.calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom, boolean addExplicitH, int[][] distanceMatrix) calculate effective atom polarizability.
double	Polarizability.calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom, int influenceSphereCutOff, boolean addExplicitH) calculate effective atom polarizability.
double	PiElectronegativity.calculatePiElectronegativity(IAtomContainer ac, IAtom atom) calculate the electronegativity of orbitals pi.
double	PiElectronegativity.calculatePiElectronegativity(IAtomContainer ac, IAtom atom, int maxIterations, int maxResonStruc) calculate the electronegativity of orbitals pi.
double	StabilizationCharges.calculatePositive(IAtomContainer atomContainer, IAtom atom) calculate the stabilization of orbitals when they contain deficiency of charge.
double	Electronegativity.calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom) calculate the electronegativity of orbitals sigma.
double	Electronegativity.calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom, int maxIterations, int maxResonStruc) calculate the electronegativity of orbitals sigma.
double	Polarizability.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 and Description
IAtom	AtomTypeFactory.configure(IAtom atom) Configures an atom.
IAtom	IsotopeFactory.configure(IAtom atom) Configures an atom.
IAtom	IsotopeFactory.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 and Description
IAtom	AtomTypeFactory.configure(IAtom atom) Configures an atom.
IAtom	IsotopeFactory.configure(IAtom atom) Configures an atom.
IAtom	IsotopeFactory.configure(IAtom atom, IIsotope isotope) Configures an atom to have all the data of the given isotope.
static boolean	Elements.isMetal(IAtom atom) Utility method to determine if an atom is a metal.

Uses of IAtom in org.openscience.cdk.debug

Classes in org.openscience.cdk.debug that implement IAtom

Modifier and Type	Class and Description
class	DebugAtom Debugging data class.
class	DebugFragmentAtom Class to represent an IPseudoAtom which embeds an IAtomContainer.
class	DebugPDBAtom Debugging data class.
class	DebugPseudoAtom Debugging data class.

Methods in org.openscience.cdk.debug that return IAtom

Modifier and Type	Method and Description
IAtom	DebugAtom.clone() Clones this atom object and its content.
IAtom	DebugLonePair.getAtom() Returns the associated Atom.
IAtom	DebugSingleElectron.getAtom() Returns the associated Atom.
IAtom	DebugStrand.getAtom(int idx) Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
IAtom	DebugRing.getAtom(int idx) Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
IAtom	DebugBond.getAtom(int position) Returns an Atom from this bond.
IAtom	DebugCrystal.getAtom(int idx) Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
IAtom	DebugAminoAcid.getAtom(int idx) Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
IAtom	DebugPolymer.getAtom(int idx) Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
IAtom	DebugBioPolymer.getAtom(int idx) Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
IAtom	DebugMonomer.getAtom(int idx) Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
IAtom	DebugAtomContainer.getAtom(int idx) Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
IAtom	DebugBond.getBegin() Access the begin (or first) atom of the bond.
IAtom	DebugAminoAcid.getCTerminus() Retrieves the C-terminus atom.
IAtom	DebugBond.getEnd() Access the end (or second) atom of the bond.
IAtom	DebugStrand.getFirstAtom() Returns the atom at position 0 in the container.
IAtom	DebugRing.getFirstAtom() Returns the atom at position 0 in the container.
IAtom	DebugCrystal.getFirstAtom() Returns the atom at position 0 in the container.
IAtom	DebugAminoAcid.getFirstAtom() Returns the atom at position 0 in the container.
IAtom	DebugPolymer.getFirstAtom() Returns the atom at position 0 in the container.
IAtom	DebugBioPolymer.getFirstAtom() Returns the atom at position 0 in the container.
IAtom	DebugMonomer.getFirstAtom() Returns the atom at position 0 in the container.
IAtom	DebugAtomContainer.getFirstAtom() Returns the atom at position 0 in the container.
IAtom	DebugStrand.getLastAtom() Returns the atom at the last position in the container.
IAtom	DebugRing.getLastAtom() Returns the atom at the last position in the container.
IAtom	DebugCrystal.getLastAtom() Returns the atom at the last position in the container.
IAtom	DebugAminoAcid.getLastAtom() Returns the atom at the last position in the container.
IAtom	DebugPolymer.getLastAtom() Returns the atom at the last position in the container.
IAtom	DebugBioPolymer.getLastAtom() Returns the atom at the last position in the container.
IAtom	DebugMonomer.getLastAtom() Returns the atom at the last position in the container.
IAtom	DebugAtomContainer.getLastAtom() Returns the atom at the last position in the container.
IAtom	DebugAminoAcid.getNTerminus() Retrieves the N-terminus atom.
IAtom	DebugBond.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 correct IBond.getConnectedAtoms(IAtom) should be used.
IAtom	DebugChemObjectBuilder.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 and Description
Iterable<IAtom>	DebugStrand.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>	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>	DebugAminoAcid.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>	DebugBioPolymer.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>	DebugAtomContainer.atoms() Returns an Iterable for looping over all atoms in this container.
List<IAtom>	DebugStrand.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>	DebugCrystal.getConnectedAtomsList(IAtom atom) Returns the atoms connected connected to the specified atom by a bond.
List<IAtom>	DebugAminoAcid.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>	DebugBioPolymer.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>	DebugAtomContainer.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 and Description
void	DebugStrand.addAtom(IAtom atom) Adds the atom oAtom without specifying a Monomer or a Strand.
void	DebugRing.addAtom(IAtom atom) Adds an atom to this container.
void	DebugCrystal.addAtom(IAtom atom) Adds an atom to this container.
void	DebugAminoAcid.addAtom(IAtom atom) Adds an atom to this container.
void	DebugPolymer.addAtom(IAtom atom) Adds an atom to this container.
void	DebugBioPolymer.addAtom(IAtom atom) Adds an atom to this container.
void	DebugMonomer.addAtom(IAtom atom) Adds an atom to this container.
void	DebugAtomContainer.addAtom(IAtom atom) Adds an atom to this container.
void	DebugStrand.addAtom(IAtom oAtom, IMonomer oMonomer) Adds the atom oAtom to a specific Monomer.
void	DebugPolymer.addAtom(IAtom oAtom, IMonomer oMonomer) Adds the atom oAtom to a specified Monomer.
void	DebugBioPolymer.addAtom(IAtom oAtom, IMonomer oMonomer) Adds the atom oAtom to a specified Monomer.
void	DebugBioPolymer.addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand) Adds the atom to a specified Strand and a specified Monomer.
void	DebugBioPolymer.addAtom(IAtom oAtom, IStrand oStrand) Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
void	DebugAminoAcid.addCTerminus(IAtom atom) Add an Atom and makes it the C-terminus atom.
void	DebugAminoAcid.addNTerminus(IAtom atom) Add an Atom and makes it the N-terminus atom.
boolean	DebugStrand.contains(IAtom atom) True, if the AtomContainer contains the given atom object.
boolean	DebugRing.contains(IAtom atom) True, if the AtomContainer contains the given atom object.
boolean	DebugBond.contains(IAtom atom) Returns true if the given atom participates in this bond.
boolean	DebugCrystal.contains(IAtom atom) True, if the AtomContainer contains the given atom object.
boolean	DebugAminoAcid.contains(IAtom atom) True, if the AtomContainer contains the given atom object.
boolean	DebugLonePair.contains(IAtom atom) Returns true if the given atom participates in this lone pair.
boolean	DebugPolymer.contains(IAtom atom) True, if the AtomContainer contains the given atom object.
boolean	DebugRingSet.contains(IAtom atom) True, if at least one of the rings in the ringset contains the given atom.
boolean	DebugBioPolymer.contains(IAtom atom) True, if the AtomContainer contains the given atom object.
boolean	DebugMonomer.contains(IAtom atom) True, if the AtomContainer contains the given atom object.
boolean	DebugSingleElectron.contains(IAtom atom) Returns true if the given atom participates in this SingleElectron.
boolean	DebugAtomContainer.contains(IAtom atom) True, if the AtomContainer contains the given atom object.
int	DebugStrand.getAtomNumber(IAtom atom) Returns the position of a given atom in the atoms array.
int	DebugRing.getAtomNumber(IAtom atom) Returns the position of a given atom in the atoms array.
int	DebugCrystal.getAtomNumber(IAtom atom) Returns the position of a given atom in the atoms array.
int	DebugAminoAcid.getAtomNumber(IAtom atom) Returns the position of a given atom in the atoms array.
int	DebugPolymer.getAtomNumber(IAtom atom) Returns the position of a given atom in the atoms array.
int	DebugBioPolymer.getAtomNumber(IAtom atom) Returns the position of a given atom in the atoms array.
int	DebugMonomer.getAtomNumber(IAtom atom) Returns the position of a given atom in the atoms array.
IBond	DebugStrand.getBond(IAtom atom1, IAtom atom2) Returns the bond that connects the two given atoms.
IBond	DebugRing.getBond(IAtom atom1, IAtom atom2) Returns the bond that connects the two given atoms.
IBond	DebugCrystal.getBond(IAtom atom1, IAtom atom2) Returns the bond that connects the two given atoms.
IBond	DebugAminoAcid.getBond(IAtom atom1, IAtom atom2) Returns the bond that connects the two given atoms.
IBond	DebugPolymer.getBond(IAtom atom1, IAtom atom2) Returns the bond that connects the two given atoms.
IBond	DebugBioPolymer.getBond(IAtom atom1, IAtom atom2) Returns the bond that connects the two given atoms.
IBond	DebugMonomer.getBond(IAtom atom1, IAtom atom2) Returns the bond that connects the two given atoms.
IBond	DebugAtomContainer.getBond(IAtom atom1, IAtom atom2) Returns the bond that connects the two given atoms.
int	DebugStrand.getBondNumber(IAtom atom1, IAtom atom2) Returns the position of the bond between two given atoms in the electronContainers array.
int	DebugRing.getBondNumber(IAtom atom1, IAtom atom2) Returns the position of the bond between two given atoms in the electronContainers array.
int	DebugCrystal.getBondNumber(IAtom atom1, IAtom atom2) Returns the position of the bond between two given atoms in the electronContainers array.
int	DebugAminoAcid.getBondNumber(IAtom atom1, IAtom atom2) Returns the position of the bond between two given atoms in the electronContainers array.
int	DebugPolymer.getBondNumber(IAtom atom1, IAtom atom2) Returns the position of the bond between two given atoms in the electronContainers array.
int	DebugBioPolymer.getBondNumber(IAtom atom1, IAtom atom2) Returns the position of the bond between two given atoms in the electronContainers array.
int	DebugMonomer.getBondNumber(IAtom atom1, IAtom atom2) Returns the position of the bond between two given atoms in the electronContainers array.
double	DebugStrand.getBondOrderSum(IAtom atom) Returns the sum of the bond orders for a given Atom.
double	DebugRing.getBondOrderSum(IAtom atom) Returns the sum of the bond orders for a given Atom.
double	DebugCrystal.getBondOrderSum(IAtom atom) Returns the sum of the bond orders for a given Atom.
double	DebugAminoAcid.getBondOrderSum(IAtom atom) Returns the sum of the bond orders for a given Atom.
double	DebugPolymer.getBondOrderSum(IAtom atom) Returns the sum of the bond orders for a given Atom.
double	DebugBioPolymer.getBondOrderSum(IAtom atom) Returns the sum of the bond orders for a given Atom.
double	DebugMonomer.getBondOrderSum(IAtom atom) Returns the sum of the bond orders for a given Atom.
double	DebugAtomContainer.getBondOrderSum(IAtom atom) Returns the sum of the bond orders for a given Atom.
int	DebugStrand.getConnectedAtomsCount(IAtom atom) Returns the number of connected atoms (explicit degree) to the specified atom.
int	DebugRing.getConnectedAtomsCount(IAtom atom) Returns the number of connected atoms (explicit degree) to the specified atom.
int	DebugCrystal.getConnectedAtomsCount(IAtom atom) Returns the number of connected atoms (explicit degree) to the specified atom.
int	DebugAminoAcid.getConnectedAtomsCount(IAtom atom) Returns the number of connected atoms (explicit degree) to the specified atom.
int	DebugPolymer.getConnectedAtomsCount(IAtom atom) Returns the number of connected atoms (explicit degree) to the specified atom.
int	DebugBioPolymer.getConnectedAtomsCount(IAtom atom) Returns the number of connected atoms (explicit degree) to the specified atom.
int	DebugMonomer.getConnectedAtomsCount(IAtom atom) Returns the number of connected atoms (explicit degree) to the specified atom.
int	DebugAtomContainer.getConnectedAtomsCount(IAtom atom) Returns the number of connected atoms (explicit degree) to the specified atom.
List<IAtom>	DebugStrand.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>	DebugCrystal.getConnectedAtomsList(IAtom atom) Returns the atoms connected connected to the specified atom by a bond.
List<IAtom>	DebugAminoAcid.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>	DebugBioPolymer.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>	DebugAtomContainer.getConnectedAtomsList(IAtom atom) Returns the atoms connected connected to the specified atom by a bond.
int	DebugStrand.getConnectedBondsCount(IAtom atom) Returns the number of connected bonds (explicit degree) to the specified atom.
int	DebugRing.getConnectedBondsCount(IAtom atom) Returns the number of connected bonds (explicit degree) to the specified atom.
int	DebugCrystal.getConnectedBondsCount(IAtom atom) Returns the number of connected bonds (explicit degree) to the specified atom.
int	DebugAminoAcid.getConnectedBondsCount(IAtom atom) Returns the number of connected bonds (explicit degree) to the specified atom.
int	DebugPolymer.getConnectedBondsCount(IAtom atom) Returns the number of connected bonds (explicit degree) to the specified atom.
int	DebugBioPolymer.getConnectedBondsCount(IAtom atom) Returns the number of connected bonds (explicit degree) to the specified atom.
int	DebugMonomer.getConnectedBondsCount(IAtom atom) Returns the number of connected bonds (explicit degree) to the specified atom.
int	DebugAtomContainer.getConnectedBondsCount(IAtom atom) Returns the number of connected bonds (explicit degree) to the specified atom.
List<IBond>	DebugStrand.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>	DebugCrystal.getConnectedBondsList(IAtom atom) Returns the bonds connected connected to the specified atom.
List<IBond>	DebugAminoAcid.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>	DebugBioPolymer.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>	DebugAtomContainer.getConnectedBondsList(IAtom atom) Returns the bonds 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.
List<IElectronContainer>	DebugRing.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>	DebugAminoAcid.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>	DebugBioPolymer.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>	DebugAtomContainer.getConnectedElectronContainersList(IAtom atom) Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
int	DebugStrand.getConnectedLonePairsCount(IAtom atom) Returns the number of lone pairs connected to the specified atom.
int	DebugRing.getConnectedLonePairsCount(IAtom atom) Returns the number of lone pairs connected to the specified atom.
int	DebugCrystal.getConnectedLonePairsCount(IAtom atom) Returns the number of lone pairs connected to the specified atom.
int	DebugAminoAcid.getConnectedLonePairsCount(IAtom atom) Returns the number of lone pairs connected to the specified atom.
int	DebugPolymer.getConnectedLonePairsCount(IAtom atom) Returns the number of lone pairs connected to the specified atom.
int	DebugBioPolymer.getConnectedLonePairsCount(IAtom atom) Returns the number of lone pairs connected to the specified atom.
int	DebugMonomer.getConnectedLonePairsCount(IAtom atom) Returns the number of lone pairs connected to the specified atom.
int	DebugAtomContainer.getConnectedLonePairsCount(IAtom atom) Returns the number of lone pairs connected to the specified atom.
List<ILonePair>	DebugStrand.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>	DebugCrystal.getConnectedLonePairsList(IAtom atom) Returns the lone pairs connected connected to the specified atom.
List<ILonePair>	DebugAminoAcid.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>	DebugBioPolymer.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>	DebugAtomContainer.getConnectedLonePairsList(IAtom atom) Returns the lone pairs connected connected to the specified atom.
int	DebugStrand.getConnectedSingleElectronsCount(IAtom atom) Returns the number of single electrons connected to the specified atom.
int	DebugRing.getConnectedSingleElectronsCount(IAtom atom) Returns the number of single electrons connected to the specified atom.
int	DebugCrystal.getConnectedSingleElectronsCount(IAtom atom) Returns the number of single electrons connected to the specified atom.
int	DebugAminoAcid.getConnectedSingleElectronsCount(IAtom atom) Returns the number of single electrons connected to the specified atom.
int	DebugPolymer.getConnectedSingleElectronsCount(IAtom atom) Returns the number of single electrons connected to the specified atom.
int	DebugBioPolymer.getConnectedSingleElectronsCount(IAtom atom) Returns the number of single electrons connected to the specified atom.
int	DebugMonomer.getConnectedSingleElectronsCount(IAtom atom) Returns the number of single electrons connected to the specified atom.
int	DebugAtomContainer.getConnectedSingleElectronsCount(IAtom atom) Returns the number of single electrons connected to the specified atom.
List<ISingleElectron>	DebugStrand.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>	DebugCrystal.getConnectedSingleElectronsList(IAtom atom) Returns the single electrons connected connected to the specified atom.
List<ISingleElectron>	DebugAminoAcid.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>	DebugBioPolymer.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>	DebugAtomContainer.getConnectedSingleElectronsList(IAtom atom) Returns the single electrons connected connected to the specified atom.
IBond.Order	DebugStrand.getMaximumBondOrder(IAtom atom) Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugRing.getMaximumBondOrder(IAtom atom) Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugCrystal.getMaximumBondOrder(IAtom atom) Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugAminoAcid.getMaximumBondOrder(IAtom atom) Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugPolymer.getMaximumBondOrder(IAtom atom) Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugBioPolymer.getMaximumBondOrder(IAtom atom) Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugMonomer.getMaximumBondOrder(IAtom atom) Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugAtomContainer.getMaximumBondOrder(IAtom atom) Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugStrand.getMinimumBondOrder(IAtom atom) Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugRing.getMinimumBondOrder(IAtom atom) Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugCrystal.getMinimumBondOrder(IAtom atom) Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugAminoAcid.getMinimumBondOrder(IAtom atom) Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugPolymer.getMinimumBondOrder(IAtom atom) Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugBioPolymer.getMinimumBondOrder(IAtom atom) Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugMonomer.getMinimumBondOrder(IAtom atom) Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	DebugAtomContainer.getMinimumBondOrder(IAtom atom) Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
IBond	DebugRing.getNextBond(IBond bond, IAtom atom) Returns the next bond in order, relative to a given bond and atom.
IAtom	DebugBond.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 correct IBond.getConnectedAtoms(IAtom) should be used.
IRingSet	DebugRingSet.getRings(IAtom atom) Returns a vector of all rings that this atom is part of.
int	DebugAtomContainer.indexOf(IAtom atom) Access the storage index of an atom.
void	DebugStrand.removeAtom(IAtom atom) Safely remove an atom from the container.
void	DebugRing.removeAtom(IAtom atom) Safely remove an atom from the container.
void	DebugCrystal.removeAtom(IAtom atom) Safely remove an atom from the container.
void	DebugAminoAcid.removeAtom(IAtom atom) Safely remove an atom from the container.
void	DebugPolymer.removeAtom(IAtom atom) Safely remove an atom from the container.
void	DebugBioPolymer.removeAtom(IAtom atom) Safely remove an atom from the container.
void	DebugMonomer.removeAtom(IAtom atom) Safely remove an atom from the container.
void	DebugAtomContainer.removeAtom(IAtom atom) Safely remove an atom from the container.
void	DebugStrand.removeAtomOnly(IAtom atom) Unsafely remove atom.
void	DebugRing.removeAtomOnly(IAtom atom) Unsafely remove atom.
void	DebugCrystal.removeAtomOnly(IAtom atom) Unsafely remove atom.
void	DebugAminoAcid.removeAtomOnly(IAtom atom) Unsafely remove atom.
void	DebugPolymer.removeAtomOnly(IAtom atom) Unsafely remove atom.
void	DebugBioPolymer.removeAtomOnly(IAtom atom) Unsafely remove atom.
void	DebugMonomer.removeAtomOnly(IAtom atom) Unsafely remove atom.
void	DebugAtomContainer.removeAtomOnly(IAtom atom) Unsafely remove atom.
IBond	DebugStrand.removeBond(IAtom atom1, IAtom atom2) Removes the bond that connects the two given atoms.
IBond	DebugRing.removeBond(IAtom atom1, IAtom atom2) Removes the bond that connects the two given atoms.
IBond	DebugCrystal.removeBond(IAtom atom1, IAtom atom2) Removes the bond that connects the two given atoms.
IBond	DebugAminoAcid.removeBond(IAtom atom1, IAtom atom2) Removes the bond that connects the two given atoms.
IBond	DebugPolymer.removeBond(IAtom atom1, IAtom atom2) Removes the bond that connects the two given atoms.
IBond	DebugBioPolymer.removeBond(IAtom atom1, IAtom atom2) Removes the bond that connects the two given atoms.
IBond	DebugMonomer.removeBond(IAtom atom1, IAtom atom2) Removes the bond that connects the two given atoms.
IBond	DebugAtomContainer.removeBond(IAtom atom1, IAtom atom2) Removes the bond that connects the two given atoms.
void	DebugLonePair.setAtom(IAtom atom) Sets the associated Atom.
void	DebugSingleElectron.setAtom(IAtom atom) Sets the associated Atom.
void	DebugBond.setAtom(IAtom atom, int position) Sets an Atom in this bond.
void	DebugStrand.setAtom(int number, IAtom atom) Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
void	DebugRing.setAtom(int number, IAtom atom) Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
void	DebugCrystal.setAtom(int number, IAtom atom) Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
void	DebugAminoAcid.setAtom(int number, IAtom atom) Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
void	DebugPolymer.setAtom(int number, IAtom atom) Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
void	DebugBioPolymer.setAtom(int number, IAtom atom) Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
void	DebugMonomer.setAtom(int number, IAtom atom) Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
void	DebugAtomContainer.setAtom(int number, IAtom atom) Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
void	DebugStrand.setAtoms(IAtom[] atoms) Sets the array of atoms of this AtomContainer.
void	DebugRing.setAtoms(IAtom[] atoms) Sets the array of atoms of this AtomContainer.
void	DebugBond.setAtoms(IAtom[] atoms) Sets the array of atoms making up this bond.
void	DebugCrystal.setAtoms(IAtom[] atoms) Sets the array of atoms of this AtomContainer.
void	DebugAminoAcid.setAtoms(IAtom[] atoms) Sets the array of atoms of this AtomContainer.
void	DebugPolymer.setAtoms(IAtom[] atoms) Sets the array of atoms of this AtomContainer.
void	DebugBioPolymer.setAtoms(IAtom[] atoms) Sets the array of atoms of this AtomContainer.
void	DebugMonomer.setAtoms(IAtom[] atoms) Sets the array of atoms of this AtomContainer.
void	DebugAtomContainer.setAtoms(IAtom[] atoms) Sets the array of atoms of this AtomContainer.

Constructors in org.openscience.cdk.debug with parameters of type IAtom

Constructor and 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.fingerprint

Methods in org.openscience.cdk.fingerprint that return types with arguments of type IAtom

Modifier and Type	Method and Description
Collection<IAtom>	SimpleAtomCanonicalizer.canonicalizeAtoms(IAtomContainer container)

Methods in org.openscience.cdk.fingerprint with parameters of type IAtom

Modifier and Type	Method and Description
int	SimpleAtomComparator.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 and Description
protected static IAtomContainer	FragmentUtils.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 and Description
static IAtom	GeometryTools.getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon) Deprecated. Returns the atom of the given molecule that is closest to the given coordinates.
static IAtom	GeometryUtil.getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon) Returns the atom of the given molecule that is closest to the given coordinates.
static IAtom	GeometryTools.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 IAtom	GeometryUtil.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 IAtom	GeometryTools.getClosestAtom(IAtomContainer atomCon, IAtom atom) Deprecated. Returns the atom of the given molecule that is closest to the given atom (excluding itself).
static IAtom	GeometryUtil.getClosestAtom(IAtomContainer atomCon, IAtom atom) Returns the atom of the given molecule that is closest to the given atom (excluding itself).
static IAtom	GeometryTools.getClosestAtom(int xPosition, int yPosition, IAtomContainer atomCon) Deprecated. Returns the atom of the given molecule that is closest to the given coordinates.
static IAtom	GeometryUtil.getClosestAtom(int xPosition, int yPosition, IAtomContainer atomCon) Returns the atom of the given molecule that is closest to the given coordinates.

Methods in org.openscience.cdk.geometry that return types with arguments of type IAtom

Modifier and Type	Method and 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.

Methods in org.openscience.cdk.geometry with parameters of type IAtom

Modifier and Type	Method and Description
double[]	RDFCalculator.calculate(IAtomContainer container, IAtom atom) Calculates a RDF for Atom atom in the environment of the atoms in the AtomContainer.
double	IRDFWeightFunction.calculate(IAtom atom, IAtom atom2) Calculates the weight for the interaction between the two atoms.
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 boolean	BondTools.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 int	GeometryTools.getBestAlignmentForLabel(IAtomContainer container, IAtom atom) Deprecated. Determines the best alignment for the label of an atom in 2D space.
static int	GeometryUtil.getBestAlignmentForLabel(IAtomContainer container, IAtom atom) Determines the best alignment for the label of an atom in 2D space.
static int	GeometryTools.getBestAlignmentForLabelXY(IAtomContainer container, IAtom atom) Deprecated. Determines the best alignment for the label of an atom in 2D space.
static int	GeometryUtil.getBestAlignmentForLabelXY(IAtomContainer container, IAtom atom) Determines the best alignment for the label of an atom in 2D space.
static IAtom	GeometryTools.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 IAtom	GeometryUtil.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 IAtom	GeometryTools.getClosestAtom(IAtomContainer atomCon, IAtom atom) Deprecated. Returns the atom of the given molecule that is closest to the given atom (excluding itself).
static IAtom	GeometryUtil.getClosestAtom(IAtomContainer atomCon, IAtom atom) Returns the atom of the given molecule that is closest to the given atom (excluding itself).
static double	BondTools.giveAngle(IAtom from, IAtom to1, IAtom to2) Calls giveAngleBothMethods with bool = true.
static double	BondTools.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 double	BondTools.giveAngleFromMiddle(IAtom from, IAtom to1, IAtom to2) Calls giveAngleBothMethods with bool = false.
static boolean	GeometryTools.has2DCoordinates(IAtom atom) Deprecated. Determines if this Atom contains 2D coordinates.
static boolean	GeometryUtil.has2DCoordinates(IAtom atom) Determines if this Atom contains 2D coordinates.
static boolean	BondTools.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 boolean	BondTools.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 boolean	BondTools.isSquarePlanar(IAtomContainer container, IAtom atom) Says if an atom as a center of a square planar chirality.
static boolean	BondTools.isStereo(IAtomContainer container, IAtom stereoAtom) Says if an atom as a center of any valid stereo configuration or not.
static int	BondTools.isTetrahedral(IAtomContainer container, IAtom atom, boolean strict) Says if an atom as a center of a tetrahedral chirality.
static int	BondTools.isTrigonalBipyramidalOrOctahedral(IAtomContainer container, IAtom atom) Says if an atom as a center of a trigonal-bipyramidal or actahedral chirality.
static javax.vecmath.Point3d	AtomTools.rescaleBondLength(IAtom atom1, IAtom atom2, javax.vecmath.Point3d point2) Rescales Point2 so that length 1-2 is sum of covalent radii.
static void	GeometryTools.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 void	GeometryUtil.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 void	GeometryTools.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 void	GeometryUtil.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 boolean	BondTools.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 and Description
static javax.vecmath.Point2d	GeometryTools.get2DCenter(Iterable<IAtom> atoms) Deprecated. Calculates the center of the given atoms and returns it as a Point2d.
static javax.vecmath.Point2d	GeometryUtil.get2DCenter(Iterable<IAtom> atoms) Calculates the center of the given atoms and returns it as a Point2d.
static javax.vecmath.Point2d	GeometryTools.get2DCenter(Iterator<IAtom> atoms) Deprecated. Calculates the center of the given atoms and returns it as a Point2d.
static javax.vecmath.Point2d	GeometryUtil.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 void	Projector.project2D(IAtomContainer container, HashMap<IAtom,javax.vecmath.Point2d> renderingCoordinates)
static void	GeometryUtil.reflect(Collection<IAtom> atoms, IBond bond) Reflect a collection of atoms in the line formed by the specified bond.
static void	GeometryUtil.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).

Uses of IAtom in org.openscience.cdk.geometry.alignment

Constructors in org.openscience.cdk.geometry.alignment with parameters of type IAtom

Constructor and Description
KabschAlignment(IAtom[] al1, IAtom[] al2) Sets up variables for the alignment algorithm.
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.
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 and Description
IAtom	Ligand.getCentralAtom() The central IAtom to which this ligand is connected via one IBond.
IAtom	ILigand.getCentralAtom() The central IAtom to which this ligand is connected via one IBond.
IAtom	Ligand.getLigandAtom() IAtom of the ligand that is connected to the chiral IAtom via one IBond.
IAtom	ILigand.getLigandAtom() IAtom of the ligand that is connected to the central IAtom via one IBond.

Methods in org.openscience.cdk.geometry.cip with parameters of type IAtom

Modifier and Type	Method and Description
boolean	Ligand.isVisited(IAtom atom) Returns a true if the atom has been visited before.
boolean	VisitedAtoms.isVisited(IAtom atom) Returns true if the given atom already has been visited.
boolean	ILigand.isVisited(IAtom atom) Returns a true if the atom has been visited before.
void	VisitedAtoms.visited(IAtom atom) Marks the given atom as visited.

Constructors in org.openscience.cdk.geometry.cip with parameters of type IAtom

Constructor and 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 and 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 and 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 and Description
IAtom[]	ShortestPaths.atomsTo(IAtom end) Reconstruct a shortest path to the provided end atom.
IAtom[]	ShortestPaths.atomsTo(int end) Reconstruct a shortest path to the provided end vertex.
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 and 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. Replaced by ShortestPaths.atomsTo(IAtom)

Methods in org.openscience.cdk.graph with parameters of type IAtom

Modifier and Type	Method and Description
IAtom[]	ShortestPaths.atomsTo(IAtom end) Reconstruct a shortest path to the provided end atom.
static int	PathTools.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 boolean	PathTools.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.
int	ShortestPaths.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.
ShortestPaths	AllPairsShortestPaths.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.
IAtomContainer	SpanningTree.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. Replaced by ShortestPaths.atomsTo(IAtom)
int	ShortestPaths.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.

Method parameters in org.openscience.cdk.graph with type arguments of type IAtom

Modifier and Type	Method and Description
static void	PathTools.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 void	PathTools.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 int	PathTools.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 and 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

Method parameters in org.openscience.cdk.graph.invariant with type arguments of type IAtom

Modifier and Type	Method and 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 and Description
int	AtomEncoder.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 and Description
interface	IFragmentAtom Class to represent an IPseudoAtom which embeds an IAtomContainer.
interface	IPDBAtom A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.
interface	IPseudoAtom Represents 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 and Description
IAtom	IAtom.clone() Returns a deep clone of this IChemObject.
IAtom	ILonePair.getAtom() Returns the associated Atom.
IAtom	ISingleElectron.getAtom() Returns the associated Atom.
IAtom	IBond.getAtom(int position) Returns an Atom from this bond.
IAtom	IAtomContainer.getAtom(int idx) Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
IAtom	IBond.getBegin() Access the begin (or first) atom of the bond.
IAtom	ITetrahedralChirality.getChiralAtom() Atom that is the chirality center.
IAtom	IBond.getConnectedAtom(IAtom atom) Deprecated. use the method IBond.getOther(IAtom)
IAtom[]	IBond.getConnectedAtoms(IAtom atom) Returns all the atoms in the bond connected to the given atom.
IAtom	IAminoAcid.getCTerminus() Retrieves the C-terminus atom.
IAtom	IBond.getEnd() Access the end (or second) atom of the bond.
IAtom	IAtomContainer.getFirstAtom() Deprecated. use IAtomContainer.getAtom(int)
IAtom	IAtomContainer.getLastAtom() Deprecated. use IAtomContainer.getAtom(int)
IAtom[]	ITetrahedralChirality.getLigands() Returns an array of ligand atoms around the chiral atom.
IAtom	IAminoAcid.getNTerminus() Retrieves the N-terminus atom.
IAtom	IBond.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 correct IBond.getConnectedAtoms(IAtom) should be used.
IAtom	IChemObjectBuilder.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 and Description
Iterable<IAtom>	IBond.atoms() Returns the Iterable to atoms making up this bond.
Iterable<IAtom>	IAtomContainer.atoms() Returns an Iterable for looping over all atoms in this container.
List<IAtom>	IAtomContainer.getConnectedAtomsList(IAtom atom) Returns the atoms connected connected to the specified atom by a bond.

Methods in org.openscience.cdk.interfaces with parameters of type IAtom

Modifier and Type	Method and Description
void	ICrystal.addAtom(IAtom atom) Adds the atom to the crystal.
void	IPolymer.addAtom(IAtom oAtom) Adds the atom oAtom without specifying a Monomer.
void	IBioPolymer.addAtom(IAtom oAtom) Adds the atom oAtom without specifying a Monomer or a Strand.
void	IStrand.addAtom(IAtom oAtom) Adds the atom oAtom without specifying a Monomer or a Strand.
void	IAtomContainer.addAtom(IAtom atom) Adds an atom to this container.
void	IPolymer.addAtom(IAtom oAtom, IMonomer oMonomer) Adds the atom oAtom to a specified Monomer.
void	IStrand.addAtom(IAtom oAtom, IMonomer oMonomer) Adds the atom oAtom to a specific Monomer.
void	IBioPolymer.addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand) Adds the atom to a specified Strand and a specified Monomer.
void	IBioPolymer.addAtom(IAtom oAtom, IStrand oStrand) Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
void	IAminoAcid.addCTerminus(IAtom atom) Add an Atom and makes it the C-terminus atom.
void	IAminoAcid.addNTerminus(IAtom atom) Add an Atom and makes it the N-terminus atom.
boolean	ILonePair.contains(IAtom atom) Returns true if the given atom participates in this lone pair.
boolean	IBond.contains(IAtom atom) Returns true if the given atom participates in this bond.
boolean	IStereoElement.contains(IAtom atom) Does the stereo element contain the provided atom.
boolean	IRingSet.contains(IAtom atom) True, if at least one of the rings in the ringset contains the given atom.
boolean	IAtomContainer.contains(IAtom atom) True, if the AtomContainer contains the given atom object.
boolean	ISingleElectron.contains(IAtom atom) Returns true if the given atom participates in this SingleElectron.
int	IAtomContainer.getAtomNumber(IAtom atom) Deprecated. use IAtomContainer.indexOf(IAtom)
IBond	IAtom.getBond(IAtom atom) Returns the bond connecting 'this' atom to the provided atom.
IBond	IAtomContainer.getBond(IAtom atom1, IAtom atom2) Returns the bond that connects the two given atoms.
int	IAtomContainer.getBondNumber(IAtom atom1, IAtom atom2) Deprecated. use IAtomContainer.indexOf(IBond)
double	IAtomContainer.getBondOrderSum(IAtom atom) Returns the sum of the bond orders for a given Atom.
IAtom	IBond.getConnectedAtom(IAtom atom) Deprecated. use the method IBond.getOther(IAtom)
IAtom[]	IBond.getConnectedAtoms(IAtom atom) Returns all the atoms in the bond connected to the given atom.
int	IAtomContainer.getConnectedAtomsCount(IAtom atom) Deprecated. use IAtomContainer.getConnectedBondsCount(IAtom)
List<IAtom>	IAtomContainer.getConnectedAtomsList(IAtom atom) Returns the atoms connected connected to the specified atom by a bond.
int	IAtomContainer.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.
int	IAtomContainer.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.
int	IAtomContainer.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.Order	IAtomContainer.getMaximumBondOrder(IAtom atom) Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	IAtomContainer.getMinimumBondOrder(IAtom atom) Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
IBond	IRing.getNextBond(IBond bond, IAtom atom) Returns the next bond in order, relative to a given bond and atom.
IAtom	IBond.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 correct IBond.getConnectedAtoms(IAtom) should be used.
IRingSet	IRingSet.getRings(IAtom atom) Returns a vector of all rings that this atom is part of.
int	IAtomContainer.indexOf(IAtom atom) Access the storage index of an atom.
void	IAtomContainer.removeAtom(IAtom atom) Safely remove an atom from the container.
void	IAtomContainer.removeAtomAndConnectedElectronContainers(IAtom atom) Deprecated. Method has be renamed IAtomContainer.removeAtom(IAtom).
void	IAtomContainer.removeAtomOnly(IAtom atom) Unsafely remove atom.
IBond	IAtomContainer.removeBond(IAtom atom1, IAtom atom2) Removes the bond that connects the two given atoms.
void	ILonePair.setAtom(IAtom atom) Sets the associated Atom.
void	ISingleElectron.setAtom(IAtom atom) Sets the associated Atom.
void	IBond.setAtom(IAtom atom, int position) Sets an Atom in this bond.
void	IAtomContainer.setAtom(int idx, IAtom atom) Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
void	IBond.setAtoms(IAtom[] atoms) Sets the array of atoms making up this bond.
void	IAtomContainer.setAtoms(IAtom[] atoms) Sets the array of atoms of this AtomContainer.

Method parameters in org.openscience.cdk.interfaces with type arguments of type IAtom

Modifier and Type	Method and Description
ITetrahedralChirality	ITetrahedralChirality.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.
ITetrahedralChirality	ITetrahedralChirality.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.
IStereoElement	IStereoElement.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.
IStereoElement	IStereoElement.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.
IDoubleBondStereochemistry	IDoubleBondStereochemistry.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.
IDoubleBondStereochemistry	IDoubleBondStereochemistry.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 and Description
protected IAtom	CMLCoreModule.currentAtom

Fields in org.openscience.cdk.io.cml with type parameters of type IAtom

Modifier and Type	Field and 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 and 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 and Description
abstract boolean	AtomMatcher.matches(IAtom atom1, IAtom atom2) Are the semantics of atom1 compatible with atom2.
boolean	DfPattern.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 and Description
interface	IQueryAtom Defines the ability to be matched against IAtom's.

Classes in org.openscience.cdk.isomorphism.matchers that implement IAtom

Modifier and Type	Class and Description
class	InverseSymbolSetQueryAtom Deprecated. @deprecated Use new Expr(Element, 6).and(new Expr(Element, 8)).negate() etc
class	QueryAtom
class	SymbolAndChargeQueryAtom Deprecated.
class	SymbolChargeIDQueryAtom
class	SymbolQueryAtom Deprecated.
class	SymbolSetQueryAtom Deprecated. Use new Expr(Element, 6).and(new Expr(Element, 8)) etc

Fields in org.openscience.cdk.isomorphism.matchers declared as IAtom

Modifier and Type	Field and Description
protected IAtom[]	QueryBond.atoms A list of atoms participating in this query bond.
protected IAtom[]	QueryAtomContainer.atoms Internal array of atoms.

Methods in org.openscience.cdk.isomorphism.matchers that return IAtom

Modifier and Type	Method and Description
IAtom	SymbolSetQueryAtom.clone() Deprecated.
IAtom	SymbolAndChargeQueryAtom.clone() Deprecated.
IAtom	SymbolQueryAtom.clone() Deprecated.
IAtom	QueryAtom.clone()
IAtom	SymbolChargeIDQueryAtom.clone()
IAtom	QueryBond.getAtom(int position) Returns an Atom from this query bond.
IAtom	QueryAtomContainer.getAtom(int idx) Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
IAtom	QueryBond.getBegin() Access the begin (or first) atom of the bond.
IAtom	QueryBond.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.
IAtom	QueryBond.getEnd() Access the end (or second) atom of the bond.
IAtom	QueryAtomContainer.getFirstAtom() Returns the atom at position 0 in the container.
IAtom	RGroup.getFirstAttachmentPoint()
IAtom	IRGroup.getFirstAttachmentPoint() Get the first attachment point of the RGroup.
IAtom	QueryAtomContainer.getLastAtom() Returns the atom at the last position in the container.
IAtom	QueryBond.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 correct IBond.getConnectedAtoms(IAtom) should be used.
IAtom	RGroup.getSecondAttachmentPoint()
IAtom	IRGroup.getSecondAttachmentPoint() Get the optional second attachment point of the RGroup.

Methods in org.openscience.cdk.isomorphism.matchers that return types with arguments of type IAtom

Modifier and Type	Method and Description
Iterable<IAtom>	QueryBond.atoms() Returns the Iterator to atoms making up this query bond.
Iterable<IAtom>	QueryAtomContainer.atoms() Returns an Iterable for looping over all atoms in this container.
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>>	RGroupQuery.getRootAttachmentPoints()
Map<IAtom,Map<Integer,IBond>>	IRGroupQuery.getRootAttachmentPoints() Getter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.

Methods in org.openscience.cdk.isomorphism.matchers with parameters of type IAtom

Modifier and Type	Method and Description
void	QueryAtomContainer.addAtom(IAtom atom) Adds an atom to this container.
boolean	QueryBond.contains(IAtom atom) Returns true if the given atom participates in this query bond.
boolean	QueryAtomContainer.contains(IAtom atom) True, if the AtomContainer contains the given atom object.
int	QueryAtomContainer.getAtomNumber(IAtom atom) Returns the position of a given atom in the atoms array.
IBond	QueryAtom.getBond(IAtom atom) Returns the bond connecting 'this' atom to the provided atom.
IBond	QueryAtomContainer.getBond(IAtom atom1, IAtom atom2) Returns the bond that connects the two given atoms.
int	QueryAtomContainer.getBondNumber(IAtom atom1, IAtom atom2) Returns the position of the bond between two given atoms in the electronContainers array.
double	QueryAtomContainer.getBondOrderSum(IAtom atom) Deprecated. Replaced by AtomContainerManipulator#getBondOrderSum(IAtomContainer, IAtom)
IAtom	QueryBond.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.
int	QueryAtomContainer.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.
int	QueryAtomContainer.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.
int	QueryAtomContainer.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.
int	QueryAtomContainer.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.Order	QueryAtomContainer.getMaximumBondOrder(IAtom atom) Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	QueryAtomContainer.getMinimumBondOrder(IAtom atom) Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
IAtom	QueryBond.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 correct IBond.getConnectedAtoms(IAtom) should be used.
int	QueryAtomContainer.indexOf(IAtom atom)
boolean	SymbolSetQueryAtom.matches(IAtom atom) Deprecated. The matches implementation of the QueryAtom interface.
boolean	SymbolAndChargeQueryAtom.matches(IAtom atom) Deprecated.
boolean	InverseSymbolSetQueryAtom.matches(IAtom atom) Deprecated. The matches implementation of the QueryAtom interface.
boolean	SymbolQueryAtom.matches(IAtom atom) Deprecated.
boolean	QueryAtom.matches(IAtom atom) Returns true of the given atom matches this IQueryAtom.
boolean	SymbolChargeIDQueryAtom.matches(IAtom atom)
boolean	Expr.matches(IAtom atom) Test whether this expression matches an atom instance.
boolean	QueryChemObject.matches(IAtom atom)
boolean	IQueryAtom.matches(IAtom atom) Returns true of the given atom matches this IQueryAtom.
boolean	Expr.matches(IAtom atom, int stereo)
void	QueryAtomContainer.removeAtom(IAtom atom) Removes the given atom and all connected electronContainers from the AtomContainer.
void	QueryAtomContainer.removeAtomAndConnectedElectronContainers(IAtom atom) Deprecated.
void	QueryAtomContainer.removeAtomOnly(IAtom atom) Removes the given atom from the AtomContainer.
IBond	QueryAtomContainer.removeBond(IAtom atom1, IAtom atom2) Removes the bond that connects the two given atoms.
void	QueryBond.setAtom(IAtom atom, int position) Sets an atom in this query bond.
void	QueryAtomContainer.setAtom(int idx, IAtom atom) Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
void	OrderQueryBondOrderOnly.setAtomAt(IAtom atom, int position) Deprecated.
void	OrderQueryBond.setAtomAt(IAtom atom, int position) Deprecated.
void	OrderQueryBondOrderOnly.setAtoms(IAtom[] atoms) Deprecated.
void	OrderQueryBond.setAtoms(IAtom[] atoms) Deprecated.
void	QueryBond.setAtoms(IAtom[] atoms) Sets the array of atoms making up this query bond.
void	QueryAtomContainer.setAtoms(IAtom[] atoms) Sets the array of atoms of this AtomContainer.
void	RGroup.setFirstAttachmentPoint(IAtom firstAttachmentPoint)
void	RGroup.setSecondAttachmentPoint(IAtom secondAttachmentPoint)

Method parameters in org.openscience.cdk.isomorphism.matchers with type arguments of type IAtom

Modifier and Type	Method and Description
void	RGroupQuery.setRootAttachmentPoints(Map<IAtom,Map<Integer,IBond>> rootAttachmentPoints)
void	IRGroupQuery.setRootAttachmentPoints(Map<IAtom,Map<Integer,IBond>> rootAttachmentPoints) Setter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.

Constructors in org.openscience.cdk.isomorphism.matchers with parameters of type IAtom

Constructor and 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 beg, IAtom end, Expr.Type type) Constructs an query bond from an expression type.
QueryBond(IAtom beg, IAtom end, Expr.Type type, int val) Constructs an query bond from an expression type and value.
QueryBond(IAtom beg, IAtom end, Expr expr) Constructs an query bond from an expression.
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..
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 and Description
class	AliphaticAtom Deprecated.
class	AliphaticSymbolAtom Deprecated.
class	AnyAtom Deprecated.
class	AromaticAtom Deprecated.
class	AromaticSymbolAtom Deprecated.
class	AtomicNumberAtom Deprecated.
class	ChiralityAtom Deprecated.
class	ExplicitConnectionAtom Deprecated.
class	FormalChargeAtom Deprecated.
class	HybridizationNumberAtom Deprecated.
class	HydrogenAtom Deprecated.
class	ImplicitHCountAtom Deprecated.
class	LogicalOperatorAtom Deprecated.
class	MassAtom Deprecated.
class	NonCHHeavyAtom Deprecated.
class	PeriodicGroupNumberAtom Deprecated.
class	ReactionRoleQueryAtom Deprecated.
class	RecursiveSmartsAtom Deprecated.
class	RingIdentifierAtom Deprecated.
class	RingMembershipAtom Deprecated.
class	SmallestRingAtom Deprecated.
class	SMARTSAtom Deprecated.
class	TotalConnectionAtom Deprecated.
class	TotalHCountAtom Deprecated.
class	TotalRingConnectionAtom Deprecated.
class	TotalValencyAtom Deprecated.

Methods in org.openscience.cdk.isomorphism.matchers.smarts with parameters of type IAtom

Modifier and Type	Method and Description
boolean	ChiralityAtom.chiralityMatches(IAtom target, int tParity, int permParity) Deprecated. Check if the atom-based chirality of the target matches.
boolean	SMARTSAtom.chiralityMatches(IAtom target, int tParity, int permParity) Deprecated. Check if the atom-based chirality of the target matches.
StereoBond.Direction	StereoBond.direction(IAtom atom) Deprecated.
boolean	TotalHCountAtom.matches(IAtom atom) Deprecated. Check if the total hydrogen count of the atom is equal to the query.
boolean	RecursiveSmartsAtom.matches(IAtom atom) Deprecated.
boolean	AtomicNumberAtom.matches(IAtom atom) Deprecated.
boolean	RingIdentifierAtom.matches(IAtom atom) Deprecated.
boolean	ChiralityAtom.matches(IAtom atom) Deprecated.
boolean	ExplicitConnectionAtom.matches(IAtom atom) Deprecated. Returns true of the given atom matches this IQueryAtom.
boolean	AliphaticSymbolAtom.matches(IAtom atom) Deprecated.
boolean	AromaticSymbolAtom.matches(IAtom atom) Deprecated.
boolean	ReactionRoleQueryAtom.matches(IAtom atom) Deprecated.
boolean	HybridizationNumberAtom.matches(IAtom atom) Deprecated.
boolean	SMARTSAtom.matches(IAtom atom) Deprecated.
boolean	TotalRingConnectionAtom.matches(IAtom atom) Deprecated. Returns true of the given atom matches this IQueryAtom.
boolean	TotalConnectionAtom.matches(IAtom atom) Deprecated. Returns true of the given atom matches this IQueryAtom.
boolean	SmallestRingAtom.matches(IAtom atom) Deprecated. Returns true of the given atom matches this IQueryAtom.
boolean	FormalChargeAtom.matches(IAtom atom) Deprecated.
boolean	TotalValencyAtom.matches(IAtom atom) Deprecated. Returns true of the given atom matches this IQueryAtom.
boolean	AliphaticAtom.matches(IAtom atom) Deprecated.
boolean	RingMembershipAtom.matches(IAtom atom) Deprecated. Returns true of the given atom matches this IQueryAtom.
boolean	AnyAtom.matches(IAtom atom) Deprecated.
boolean	AromaticAtom.matches(IAtom atom) Deprecated.
boolean	HydrogenAtom.matches(IAtom atom) Deprecated.
boolean	NonCHHeavyAtom.matches(IAtom atom) Deprecated.
boolean	MassAtom.matches(IAtom atom) Deprecated.
boolean	PeriodicGroupNumberAtom.matches(IAtom atom) Deprecated.
boolean	ImplicitHCountAtom.matches(IAtom atom) Deprecated.
boolean	LogicalOperatorAtom.matches(IAtom atom) Deprecated.
void	LogicalOperatorBond.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 and Description
IAtom	StructureDiagramGenerator.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 and Description
void	AtomPlacer.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 IAtomContainer	AtomPlacer.getLongestUnplacedChain(IAtomContainer molecule, IAtom startAtom) Search a molecule for the longest unplaced, aliphatic chain in it.
javax.vecmath.Vector2d	AtomPlacer.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.
IAtom	StructureDiagramGenerator.getOtherBondAtom(IAtom atom, IBond bond) Returns the other atom of the bond.
void	RingPlacer.partitionNonRingPartners(IAtom atom, IRing ring, IAtomContainer ringAtoms, IAtomContainer nonRingAtoms) Partition the bonding partners of a given atom into ring atoms and non-ring atoms
void	AtomPlacer.partitionPartners(IAtom atom, IAtomContainer unplacedPartners, IAtomContainer placedPartners) Partition the bonding partners of a given atom into placed (coordinates assinged) and not placed.
void	HydrogenPlacer.placeHydrogens2D(IAtomContainer container, IAtom atom) Place hydrogens connected to the given atom using the average bond length in the container.
void	HydrogenPlacer.placeHydrogens2D(IAtomContainer container, IAtom atom, double bondLength) Place hydrogens connected to the provided atom atom using the specified bondLength.
static boolean	AtomPlacer.shouldBeLinear(IAtom atom, IAtomContainer molecule) Deprecated.

Method parameters in org.openscience.cdk.layout with type arguments of type IAtom

Modifier and Type	Method and Description
static void	AtomPlacer.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 String	AtomPlacer.listNumbers(IAtomContainer mol, List<IAtom> ac) Returns a string with the numbers of all atoms in a Vector relative to a given molecule.
void	AtomPlacer.populatePolygonCorners(List<IAtom> atoms, javax.vecmath.Point2d center, double thetaBeg, double thetaStep, double radius) Populates the corners of a polygon with atoms.
void	StructureDiagramGenerator.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 and Description
org.xmlcml.cml.element.CMLAtom	Convertor.cdkAtomToCMLAtom(IAtom cdkAtom)
org.xmlcml.cml.element.CMLAtom	Convertor.cdkAtomToCMLAtom(IAtomContainer container, IAtom cdkAtom)
void	PDBAtomCustomizer.customize(IAtom atom, Object nodeToAdd)
void	MDMoleculeCustomizer.customize(IAtom atom, Object nodeToAdd) Customize Atom.
void	QSARCustomizer.customize(IAtom atom, Object nodeToAdd)
void	ICMLCustomizer.customize(IAtom atom, Object nodeToAdd) Customized the nodeToAdd for the given Atom.

Uses of IAtom in org.openscience.cdk.libio.md

Methods in org.openscience.cdk.libio.md that return IAtom

Modifier and Type	Method and Description
IAtom	ChargeGroup.getSwitchingAtom()

Methods in org.openscience.cdk.libio.md with parameters of type IAtom

Modifier and Type	Method and Description
void	ChargeGroup.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 and Description
protected void	GaussiansBasis.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 and 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 and Description
IAtom	ForceFieldConfigurator.configureAtom(IAtom atom, String hoseCode, boolean _boolean)
IAtom	ForceFieldConfigurator.configureMM2BasedAtom(IAtom atom, String hoseCode, boolean hetRing) Configures an atom to a mm2 based atom type
IAtom	ForceFieldConfigurator.configureMMFF94BasedAtom(IAtom atom, String hoseCode, boolean isInHetRing) Configures an atom to a mmff94 based atom type
IAtom	AtomPlacer3D.getFarthestAtom(javax.vecmath.Point3d refAtomPoint, IAtomContainer ac) Gets the farthestAtom attribute of the AtomPlacer3D object.
IAtom	AtomPlacer3D.getNextPlacedHeavyAtomWithUnplacedAliphaticNeighbour(IAtomContainer molecule) Gets the nextPlacedHeavyAtomWithAliphaticPlacedNeigbor from an atom container or molecule.
IAtom	AtomPlacer3D.getNextPlacedHeavyAtomWithUnplacedRingNeighbour(IAtomContainer molecule) Gets the nextPlacedHeavyAtomWithUnplacedRingNeighbour attribute of the AtomPlacer3D object.
IAtom	AtomPlacer3D.getNextUnplacedHeavyAtomWithAliphaticPlacedNeighbour(IAtomContainer molecule) Gets the nextUnplacedHeavyAtomWithAliphaticPlacedNeighbour from an atom container or molecule.
IAtom	AtomPlacer3D.getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom) Returns a placed atom connected to a given atom.
IAtom	AtomPlacer3D.getPlacedHeavyAtom(IAtomContainer molecule, IAtom atomA, IAtom atomB) Gets the first placed Heavy Atom around atomA which is not atomB.
IAtom	AtomTetrahedralLigandPlacer3D.getPlacedHeavyAtomInAtomContainer(IAtom atomA, IAtom atomB, IAtomContainer ac) Returns a placed neighbouring atom of a central atom atomA, which is not atomB.
IAtom	AtomPlacer3D.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 and Description
IAtom	ForceFieldConfigurator.configureAtom(IAtom atom, String hoseCode, boolean _boolean)
IAtom	ForceFieldConfigurator.configureMM2BasedAtom(IAtom atom, String hoseCode, boolean hetRing) Configures an atom to a mm2 based atom type
IAtom	ForceFieldConfigurator.configureMMFF94BasedAtom(IAtom atom, String hoseCode, boolean isInHetRing) Configures an atom to a mmff94 based atom type
javax.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.Point3d	AtomTetrahedralLigandPlacer3D.get3DCoordinatesForSPLigands(IAtom refAtom, IAtomContainer withCoords, double length, double angle)
IAtomContainer	AtomTetrahedralLigandPlacer3D.getPlacedAtomsInAtomContainer(IAtom atom, IAtomContainer ac) Gets all placed neighbouring atoms of a atom.
IAtom	AtomPlacer3D.getPlacedHeavyAtom(IAtomContainer molecule, IAtom atom) Returns a placed atom connected to a given atom.
IAtom	AtomPlacer3D.getPlacedHeavyAtom(IAtomContainer molecule, IAtom atomA, IAtom atomB) Gets the first placed Heavy Atom around atomA which is not atomB.
IAtom	AtomTetrahedralLigandPlacer3D.getPlacedHeavyAtomInAtomContainer(IAtom atomA, IAtom atomB, IAtomContainer ac) Returns a placed neighbouring atom of a central atom atomA, which is not atomB.
IAtomContainer	AtomPlacer3D.getPlacedHeavyAtoms(IAtomContainer molecule, IAtom atom) Gets the placed Heavy Atoms connected to an atom.
IAtom	AtomPlacer3D.getUnplacedRingHeavyAtom(IAtomContainer molecule, IAtom atom) Gets the unplacedRingHeavyAtom attribute of the AtomPlacer3D object.
IAtomContainer	AtomTetrahedralLigandPlacer3D.getUnsetAtomsInAtomContainer(IAtom atom, IAtomContainer ac) Gets the unsetAtomsInAtomContainer attribute of the AtomTetrahedralLigandPlacer3D object.
boolean	AtomTetrahedralLigandPlacer3D.hasUnsetNeighbour(IAtom atom, IAtomContainer ac)
javax.vecmath.Point3d	AtomTetrahedralLigandPlacer3D.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 and Description
static int	SMSDNormalizer.getExplicitHydrogenCount(IAtomContainer atomContainer, IAtom atom) Deprecated. Returns The number of explicit hydrogens for a given IAtom.
static int	SMSDNormalizer.getHydrogenCount(IAtomContainer atomContainer, IAtom atom) Deprecated. The summed implicit + explicit hydrogens of the given IAtom.
static int	SMSDNormalizer.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 and Description
class	PharmacophoreAtom A representation of a pharmacophore group.
class	PharmacophoreQueryAtom Represents a query pharmacophore group.

Methods in org.openscience.cdk.pharmacophore with parameters of type IAtom

Modifier and Type	Method and Description
static PharmacophoreAtom	PharmacophoreAtom.get(IAtom atom)
boolean	PharmacophoreQueryAtom.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 and Description
class	PDBAtom Represents 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 and Description
void	PDBStrand.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 and Description
void	AbstractAtomicDescriptor.cacheDescriptorValue(IAtom atom, IAtomContainer container, IDescriptorResult value) Caches a DescriptorValue for a given IAtom.
DescriptorValue	IAtomicDescriptor.calculate(IAtom atom, IAtomContainer container) Calculates the descriptor value for the given IAtom.
DescriptorValue	IAtomPairDescriptor.calculate(IAtom atom, IAtom atom2, IAtomContainer container) Calculates the descriptor value for the given IAtom.
IDescriptorResult	AbstractAtomicDescriptor.getCachedDescriptorValue(IAtom atom) Returns the cached DescriptorValue for the given IAtom.
static int	AtomValenceTool.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 and Description
DescriptorValue	IPAtomicLearningDescriptor.calculate(IAtom atom, IAtomContainer container) Deprecated. This method calculates the ionization potential of an atom.
DescriptorValue	PartialTChargeMMFF94Descriptor.calculate(IAtom atom, IAtomContainer org) The method returns partial charges assigned to an heavy atom through MMFF94 method.
DescriptorValue	IPAtomicHOSEDescriptor.calculate(IAtom atom, IAtomContainer container) This method calculates the ionization potential of an atom.
DescriptorValue	CovalentRadiusDescriptor.calculate(IAtom atom, IAtomContainer container) This method calculates the Covalent radius of an atom.
DescriptorValue	RDFProtonDescriptor_GDR.calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue	RDFProtonDescriptor_GHR.calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue	AtomValenceDescriptor.calculate(IAtom atom, IAtomContainer container) This method calculates the valence of an atom.
DescriptorValue	PartialSigmaChargeDescriptor.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.
DescriptorValue	EffectiveAtomPolarizabilityDescriptor.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.
DescriptorValue	AtomHybridizationDescriptor.calculate(IAtom atom, IAtomContainer container) This method calculates the hybridization of an atom.
DescriptorValue	IsProtonInConjugatedPiSystemDescriptor.calculate(IAtom atom, IAtomContainer atomContainer) The method is a proton descriptor that evaluates if a proton is joined to a conjugated system.
DescriptorValue	IsProtonInAromaticSystemDescriptor.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.
DescriptorValue	DistanceToAtomDescriptor.calculate(IAtom atom, IAtomContainer container) This method calculate the 3D distance between two atoms.
DescriptorValue	VdWRadiusDescriptor.calculate(IAtom atom, IAtomContainer container) This method calculate the Van der Waals radius of an atom.
DescriptorValue	InductiveAtomicHardnessDescriptor.calculate(IAtom atom, IAtomContainer ac) It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.
DescriptorValue	BondsToAtomDescriptor.calculate(IAtom atom, IAtomContainer container) This method calculate the number of bonds on the shortest path between two atoms.
DescriptorValue	PiElectronegativityDescriptor.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.
DescriptorValue	RDFProtonDescriptor_GSR.calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue	StabilizationPlusChargeDescriptor.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.
DescriptorValue	ProtonAffinityHOSEDescriptor.calculate(IAtom atom, IAtomContainer container) This method calculates the protonation affinity of an atom.
DescriptorValue	ProtonTotalPartialChargeDescriptor.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.
DescriptorValue	SigmaElectronegativityDescriptor.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.
DescriptorValue	RDFProtonDescriptor_GHR_topol.calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue	PeriodicTablePositionDescriptor.calculate(IAtom atom, IAtomContainer container) This method calculates the period of an atom.
DescriptorValue	AtomHybridizationVSEPRDescriptor.calculate(IAtom atom, IAtomContainer container) This method calculates the hybridization of an atom.
DescriptorValue	InductiveAtomicSoftnessDescriptor.calculate(IAtom atom, IAtomContainer ac) It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.
DescriptorValue	AtomDegreeDescriptor.calculate(IAtom atom, IAtomContainer container) This method calculates the number of not-H substituents of an atom.
DescriptorValue	RDFProtonDescriptor_G3R.calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue	PartialPiChargeDescriptor.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.
DescriptorValue	PartialTChargePEOEDescriptor.calculate(IAtom atom, IAtomContainer ac) The method returns partial total charges assigned to an heavy atom through PEOE method.
DescriptorValue	RDFProtonDescriptor_GDR.calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
DescriptorValue	RDFProtonDescriptor_GHR.calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
DescriptorValue	RDFProtonDescriptor_GSR.calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
DescriptorValue	RDFProtonDescriptor_GHR_topol.calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
DescriptorValue	RDFProtonDescriptor_G3R.calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)

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 and Description
DescriptorValue	PiContactDetectionDescriptor.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 and Description
protected boolean	JPlogPDescriptor.JPlogPCalculator.boundTo(IAtom atom, String symbol)
protected boolean	JPlogPDescriptor.JPlogPCalculator.carbonylConjugated(IAtom atom)
protected boolean	JPlogPDescriptor.JPlogPCalculator.checkAlphaCarbonyl(IAtom atom, String symbol) Should be called from the carbonyl oxygen
protected boolean	JPlogPDescriptor.JPlogPCalculator.doubleBondHetero(IAtom atom)
protected boolean	JPlogPDescriptor.JPlogPCalculator.electronWithdrawing(IAtom atom)
protected int	JPlogPDescriptor.JPlogPCalculator.getCarbonSpecial(IAtom atom) Determines and returns the SS (subsection) portion of the atomtype integer for a Carbon Atom
protected int	JPlogPDescriptor.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 Atom
protected int	JPlogPDescriptor.JPlogPCalculator.getFluorineSpecial(IAtom atom) Determines and returns the SS (subsection) portion of the atomtype integer for a Fluorine Atom
protected int	JPlogPDescriptor.JPlogPCalculator.getHydrogenSpecial(IAtom atom) Determines and returns the SS (subsection) portion of the atomtype integer for a Hydrogen Atom
protected int	JPlogPDescriptor.JPlogPCalculator.getNitrogenSpecial(IAtom atom) Determines and returns the SS (subsection) portion of the atomtype integer for a Nitrogen Atom
protected double	JPlogPDescriptor.JPlogPCalculator.getNumMoreElectronegativethanCarbon(IAtom atom)
protected int	JPlogPDescriptor.JPlogPCalculator.getOxygenSpecial(IAtom atom) Determines and returns the SS (subsection) portion of the atomtype integer for an Oxygen Atom
protected int[]	JPlogPDescriptor.JPlogPCalculator.getPolarBondArray(IAtom atom)
protected boolean	JPlogPDescriptor.JPlogPCalculator.isPolar(IAtom atom)
protected boolean	JPlogPDescriptor.JPlogPCalculator.nextToAromatic(IAtom atom)
protected int	JPlogPDescriptor.JPlogPCalculator.nonHNeighbours(IAtom atom)

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 and Description
IReaction	IReactionMechanism.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 and Description
IReaction	SharingElectronMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	TautomerizationMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	RemovingSEofNBMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	RemovingSEofBMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	RadicalSiteIonizationMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	HeterolyticCleavageMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	HomolyticCleavageMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	AdductionPBMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	RearrangementChargeMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	AdductionLPMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	RadicalSiteRearrangementMechanism.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 and Description
IAtom	RendererModel.getHighlightedAtom() Returns the atom currently highlighted.

Methods in org.openscience.cdk.renderer that return types with arguments of type IAtom

Modifier and Type	Method and 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 and Description
String	RendererModel.getToolTipText(IAtom atom) Gets the toolTipText for atom certain atom.
void	RendererModel.setHighlightedAtom(IAtom highlightedAtom) Sets the atom currently highlighted.
abstract boolean	SymbolVisibility.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 and Description
void	RendererModel.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 and Description
Color	JmolColors.getAtomColor(IAtom atom)
Color	RasmolColors.getAtomColor(IAtom atom) Returns the Rasmol color for the given atom's element.
Color	CDK2DAtomColors.getAtomColor(IAtom atom) Returns the color for a certain atom type.
Color	CDKAtomColors.getAtomColor(IAtom atom) Deprecated. Returns the CDK scheme color for the given atom's element.
Color	CPKAtomColors.getAtomColor(IAtom atom) Deprecated. Returns the font color for atom given atom.
Color	PartialAtomicChargeColors.getAtomColor(IAtom atom) Returns the a color reflecting the given atom's partial charge.
Color	IAtomColorer.getAtomColor(IAtom atom) Returns the color for a certain atom type.
Color	UniColor.getAtomColor(IAtom atom) Returns the color for a certain atom type.
Color	JmolColors.getAtomColor(IAtom atom, Color defaultColor)
Color	RasmolColors.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.
Color	CDK2DAtomColors.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.
Color	CDKAtomColors.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.
Color	CPKAtomColors.getAtomColor(IAtom atom, Color defaultColor) Deprecated. Returns the font color for atom given atom.
Color	PartialAtomicChargeColors.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.
Color	IAtomColorer.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.
Color	UniColor.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 and Description
static MarkedElement	MarkedElement.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 and Description
protected boolean	BasicAtomGenerator.canDraw(IAtom atom, IAtomContainer container, RendererModel model) Checks an atom to see if it should be drawn.
IRenderingElement	ExtendedAtomGenerator.generate(IAtomContainer container, IAtom atom, RendererModel model) Generate the rendering element(s) for a particular atom.
IRenderingElement	BasicAtomGenerator.generate(IAtomContainer atomContainer, IAtom atom, RendererModel model) Generate the rendering element(s) for a particular atom.
IRenderingElement	BasicAtomGenerator.generateCompactElement(IAtom atom, RendererModel model) Generate a compact element for an atom, such as a circle or a square, rather than text element.
AtomSymbolElement	BasicAtomGenerator.generateElement(IAtom atom, int alignment, RendererModel model) Generate an atom symbol element.
protected Color	BasicAtomGenerator.getAtomColor(IAtom atom, RendererModel model) Returns the drawing color of the given atom.
protected boolean	BasicAtomGenerator.hasCoordinates(IAtom atom) Checks an atom to see if it has 2D coordinates.
protected boolean	BasicAtomGenerator.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 boolean	BasicAtomGenerator.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 boolean	BasicAtomGenerator.isHydrogen(IAtom atom) Determines if the atom is a hydrogen.
boolean	AtomMassGenerator.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 boolean	BasicAtomGenerator.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 and Description
boolean	SelectionVisibility.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 and Description
boolean	RingSearch.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 and 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 and Description
void	Sgroup.addAtom(IAtom atom) Add an atom to this Sgroup.
void	Sgroup.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 and Description
AtomSignature(IAtom atom, IAtomContainer molecule) Create an atom signature for the atom atom.
AtomSignature(IAtom atom, int height, signature.AbstractVertexSignature.InvariantType invariantType, IAtomContainer molecule) Create an atom signature for the atom atom, with maximum height of height, and using a particular invariant type.
AtomSignature(IAtom atom, int height, IAtomContainer molecule) Create an atom signature for the atom atom and with a maximum height of height.

Uses of IAtom in org.openscience.cdk.silent

Fields in org.openscience.cdk.silent declared as IAtom

Modifier and Type	Field and Description
protected IAtom	SingleElectron.atom The atom with which this single electron is associated.
protected IAtom	LonePair.atom The atom with which this lone pair is associated.
protected IAtom[]	Bond.atoms A list of atoms participating in this bond.
protected IAtom[]	AtomContainer.atoms Internal array of atoms.

Methods in org.openscience.cdk.silent that return IAtom

Modifier and Type	Method and Description
IAtom	Atom.clone() Clones this atom object and its content.
IAtom	SingleElectron.getAtom() Returns the associated Atom.
IAtom	LonePair.getAtom() Returns the associated Atom.
IAtom	Bond.getAtom(int position) Returns an Atom from this bond.
IAtom	AtomContainer.getAtom(int idx) Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().
IAtom	Bond.getBegin() Access the begin (or first) atom of the bond.
IAtom	Bond.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	AminoAcid.getCTerminus() Retrieves the C-terminus atom.
IAtom	Bond.getEnd() Access the end (or second) atom of the bond.
IAtom	AtomContainer.getFirstAtom() Returns the atom at position 0 in the container.
IAtom	AtomContainer.getLastAtom() Returns the atom at the last position in the container.
IAtom	AminoAcid.getNTerminus() Retrieves the N-terminus atom.
IAtom	Bond.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 correct IBond.getConnectedAtoms(IAtom) should be used.
IAtom	SilentChemObjectBuilder.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 and Description
Iterable<IAtom>	Bond.atoms() Returns the Iterator to atoms making up this bond.
Iterable<IAtom>	AtomContainer.atoms() Returns an Iterable for looping over all atoms in this container.
List<IAtom>	AtomContainer.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 and Description
void	Strand.addAtom(IAtom oAtom) Adds the atom oAtom without specifying a Monomer or a Strand.
void	AtomContainer.addAtom(IAtom atom) Adds an atom to this container.
void	Strand.addAtom(IAtom oAtom, IMonomer oMonomer) Adds the atom oAtom to a specific Monomer.
void	Polymer.addAtom(IAtom oAtom, IMonomer oMonomer) Adds the atom oAtom to a specified Monomer.
void	BioPolymer.addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand) Adds the atom to a specified Strand and a specified Monomer.
void	BioPolymer.addAtom(IAtom oAtom, IStrand oStrand) Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
void	AminoAcid.addCTerminus(IAtom atom) Add an Atom and makes it the C-terminus atom.
void	AminoAcid.addNTerminus(IAtom atom) Add an Atom and makes it the N-terminus atom.
boolean	SingleElectron.contains(IAtom atom) Returns true if the given atom participates in this SingleElectron.
boolean	Bond.contains(IAtom atom) Returns true if the given atom participates in this bond.
boolean	LonePair.contains(IAtom atom) Returns true if the given atom participates in this lone pair.
boolean	RingSet.contains(IAtom atom) True, if at least one of the rings in the ringset contains the given atom.
boolean	AtomContainer.contains(IAtom atom) True, if the AtomContainer contains the given atom object.
int	AtomContainer.getAtomNumber(IAtom atom) Returns the position of a given atom in the atoms array.
IBond	Atom.getBond(IAtom atom) Returns the bond connecting 'this' atom to the provided atom.
IBond	AtomContainer.getBond(IAtom atom1, IAtom atom2) Returns the bond that connects the two given atoms.
int	AtomContainer.getBondNumber(IAtom atom1, IAtom atom2) Returns the position of the bond between two given atoms in the electronContainers array.
double	AtomContainer.getBondOrderSum(IAtom atom) Returns the sum of the bond orders for a given Atom.
IAtom	Bond.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.
int	AtomContainer.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.
int	AtomContainer.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<IElectronContainer>	AtomContainer.getConnectedElectronContainersList(IAtom atom) Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
int	AtomContainer.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.
int	AtomContainer.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.
IBond.Order	AtomContainer.getMaximumBondOrder(IAtom atom) Returns the maximum bond order that this atom currently has in the context of this AtomContainer.
IBond.Order	AtomContainer.getMinimumBondOrder(IAtom atom) Returns the minimum bond order that this atom currently has in the context of this AtomContainer.
IBond	Ring.getNextBond(IBond bond, IAtom atom) Returns the next bond in order, relative to a given bond and atom.
IAtom	Bond.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 correct IBond.getConnectedAtoms(IAtom) should be used.
IRingSet	RingSet.getRings(IAtom atom) Returns a vector of all rings that this atom is part of.
int	AtomContainer.indexOf(IAtom atom) Access the storage index of an atom.
void	AtomContainer.removeAtom(IAtom atom) Safely remove an atom from the container.
void	AtomContainer.removeAtomAndConnectedElectronContainers(IAtom atom) Deprecated.
void	AtomContainer.removeAtomOnly(IAtom atom) Unsafely remove atom.
IBond	AtomContainer.removeBond(IAtom atom1, IAtom atom2) Removes the bond that connects the two given atoms.
void	SingleElectron.setAtom(IAtom atom) Sets the associated Atom.
void	LonePair.setAtom(IAtom atom) Sets the associated Atom.
void	Bond.setAtom(IAtom atom, int position) Sets an Atom in this bond.
void	AtomContainer.setAtom(int idx, IAtom atom) Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().
void	Bond.setAtoms(IAtom[] atoms) Sets the array of atoms making up this bond.
void	AtomContainer.setAtoms(IAtom[] newAtoms) Sets the array of atoms of this AtomContainer.

Constructors in org.openscience.cdk.silent with parameters of type IAtom

Constructor and Description
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 and Description
IAtom	InvPair.getAtom()

Methods in org.openscience.cdk.smiles that return types with arguments of type IAtom

Modifier and Type	Method and 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 and Description
void	InvPair.setAtom(IAtom newAtom)

Constructors in org.openscience.cdk.smiles with parameters of type IAtom

Constructor and 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 and 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 and 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 atoms
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 atoms
static 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
static 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 and Description
boolean	DefaultMCSPlusAtomMatcher.matches(IAtomContainer targetContainer, IAtom targetAtom) Deprecated.
boolean	AtomMatcher.matches(IAtomContainer container, IAtom atom) Deprecated.
boolean	DefaultRGraphAtomMatcher.matches(IAtomContainer targetContainer, IAtom targetAtom) Deprecated.
boolean	VFAtomMatcher.matches(TargetProperties container, IAtom atom) Deprecated.
boolean	DefaultVFAtomMatcher.matches(TargetProperties targetContainer, IAtom targetAtom) Deprecated.

Constructors in org.openscience.cdk.smsd.algorithm.matchers with parameters of type IAtom

Constructor and Description
DefaultMCSPlusAtomMatcher(IAtomContainer queryContainer, IAtom atom, boolean shouldMatchBonds) Deprecated. Constructor
DefaultMCSPlusAtomMatcher(IAtomContainer queryContainer, IAtom template, int blockedPositions, boolean shouldMatchBonds) Deprecated. Constructor
DefaultRGraphAtomMatcher(IAtomContainer queryContainer, IAtom atom, boolean shouldMatchBonds) Deprecated. Constructor
DefaultRGraphAtomMatcher(IAtomContainer queryContainer, IAtom template, int blockedPositions, boolean shouldMatchBonds) Deprecated. Constructor
DefaultVFAtomMatcher(IAtomContainer queryContainer, IAtom atom, boolean shouldMatchBonds) Deprecated. Constructor
DefaultVFAtomMatcher(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 and 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 and Description
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.
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.
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.
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.

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 and 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 and Description
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.
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.
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.
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.

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 and Description
IAtom	VFQueryBuilder.getAtom(INode node) Deprecated. Returns an atom associated with this node.
IAtom	TargetProperties.getAtom(int j) Deprecated.

Methods in org.openscience.cdk.smsd.algorithm.vflib.builder that return types with arguments of type IAtom

Modifier and Type	Method and 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 and Description
INode	VFQueryBuilder.addNode(VFAtomMatcher matcher, IAtom atom) Deprecated. Add and return a node for a query atom
Integer	TargetProperties.countNeighbors(IAtom atom) Deprecated.
IBond	TargetProperties.getBond(IAtom atom1, IAtom atom2) Deprecated.
List<IAtom>	TargetProperties.getNeighbors(IAtom atom) Deprecated.
INode	VFQueryBuilder.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 and Description
IAtom	IQuery.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 and 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 and Description
IAtom	Match.getTargetAtom() Deprecated. Return Target Atom

Methods in org.openscience.cdk.smsd.algorithm.vflib.map that return types with arguments of type IAtom

Modifier and Type	Method and Description
Map<INode,IAtom>	VFMCSMapper.getFirstMap(IAtomContainer target) Deprecated. Returns first solution map.
Map<INode,IAtom>	VFMapper.getFirstMap(IAtomContainer target) Deprecated. Returns first solution map.
Map<INode,IAtom>	VFMCSMapper.getFirstMap(TargetProperties targetMolecule) Deprecated. Returns first solution map.
Map<INode,IAtom>	VFMapper.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>>	VFMCSMapper.getMaps(IAtomContainer target) Deprecated. Returns all solution map.
List<Map<INode,IAtom>>	VFMapper.getMaps(IAtomContainer target) Deprecated. Returns all solution map.
List<Map<INode,IAtom>>	VFMCSMapper.getMaps(TargetProperties targetMolecule) Deprecated. Returns all solution map.
List<Map<INode,IAtom>>	VFMapper.getMaps(TargetProperties targetMolecule) Deprecated. Returns all solution map.

Constructors in org.openscience.cdk.smsd.algorithm.vflib.map with parameters of type IAtom

Constructor and Description
Match(INode query, IAtom target) Deprecated. Constructor

Uses of IAtom in org.openscience.cdk.smsd.filters

Constructor parameters in org.openscience.cdk.smsd.filters with type arguments of type IAtom

Constructor and Description
ChemicalFilters(List<Map<Integer,Integer>> allMCS, List<Map<IAtom,IAtom>> allAtomMCS, Map<Integer,Integer> firstSolution, Map<IAtom,IAtom> firstAtomMCS, IAtomContainer sourceMol, IAtomContainer targetMol) Deprecated. This class has all the three chemical filters supported by the SMSD.
ChemicalFilters(List<Map<Integer,Integer>> allMCS, List<Map<IAtom,IAtom>> allAtomMCS, Map<Integer,Integer> firstSolution, Map<IAtom,IAtom> firstAtomMCS, IAtomContainer sourceMol, IAtomContainer targetMol) Deprecated. This class has all the three chemical filters supported by the SMSD.
ChemicalFilters(List<Map<Integer,Integer>> allMCS, List<Map<IAtom,IAtom>> allAtomMCS, Map<Integer,Integer> firstSolution, Map<IAtom,IAtom> firstAtomMCS, IAtomContainer sourceMol, IAtomContainer targetMol) Deprecated. This class has all the three chemical filters supported by the SMSD.
ChemicalFilters(List<Map<Integer,Integer>> allMCS, List<Map<IAtom,IAtom>> allAtomMCS, Map<Integer,Integer> firstSolution, Map<IAtom,IAtom> firstAtomMCS, IAtomContainer sourceMol, IAtomContainer targetMol) Deprecated. This class has all the three chemical filters supported by the SMSD.

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 and 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 and Description
IAtom	PathEdge.getSource() Deprecated.
IAtom	PathEdge.getTarget() Deprecated.

Methods in org.openscience.cdk.smsd.ring that return types with arguments of type IAtom

Modifier and Type	Method and Description
Collection<List<IAtom>>	RingFinder.findRings(IAtomContainer molecule) Deprecated. Returns Collection of atoms in Rings based on Hanser Ring Finding method
Collection<List<IAtom>>	HanserRingFinder.findRings(IAtomContainer molecule) Deprecated. Returns a collection of rings.
List<IAtom>	PathEdge.getAtoms() Deprecated.

Methods in org.openscience.cdk.smsd.ring with parameters of type IAtom

Modifier and Type	Method and 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 and Description
void	RingFilter.filterAtoms(IAtomContainer molecule, Collection<IAtom> atoms) Deprecated.
void	RingFilter.filterAtoms(int atomLimit, Collection<List<IAtom>> rings, Collection<IAtom> atoms) Deprecated.
void	RingFilter.filterAtoms(int atomLimit, Collection<List<IAtom>> rings, Collection<IAtom> atoms) Deprecated.

Constructor parameters in org.openscience.cdk.smsd.ring with type arguments of type IAtom

Constructor and 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 and Description
int	BondEnergies.getEnergies(IAtom sourceAtom, IAtom targetAtom, IBond.Order bondOrder) Deprecated. Returns bond energy for a bond type, given atoms and bond type
static int	ExtAtomContainerManipulator.getExplicitHydrogenCount(IAtomContainer atomContainer, IAtom atom) Deprecated. Returns The number of explicit hydrogens for a given IAtom.
static int	ExtAtomContainerManipulator.getHydrogenCount(IAtomContainer atomContainer, IAtom atom) Deprecated. The summed implicit + explicit hydrogens of the given IAtom.
static int	ExtAtomContainerManipulator.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 and Description
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.
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.focus() The central atom in the cumulated system.
IAtom	TetrahedralChirality.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 and Description
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)
protected IStereoElement<IBond,IAtom>	Atropisomeric.create(IBond focus, List<IAtom> carriers, int cfg)

Methods in org.openscience.cdk.stereo with parameters of type IAtom

Modifier and Type	Method and Description
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 TrigonalBipyramidal	TrigonalBipyramidal.create(IAtom focus, List<IAtom> carriers, int cfg)
protected SquarePlanar	SquarePlanar.create(IAtom focus, List<IAtom> carriers, int cfg)
protected Octahedral	Octahedral.create(IAtom focus, List<IAtom> carriers, int cfg)
static IBond	ExtendedCisTrans.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.TetrahedralSign	StereoTool.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 int	ExtendedTetrahedral.getLength(IAtomContainer container, IAtom focus)
static StereoTool.SquarePlanarShape	StereoTool.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.Stereo	StereoTool.getStereo(IAtom atom1, IAtom atom2, IAtom atom3, IAtom atom4) Take four atoms, and return Stereo.CLOCKWISE or Stereo.ANTI_CLOCKWISE.
static boolean	StereoTool.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 boolean	StereoTool.isSquarePlanar(IAtom atomA, IAtom atomB, IAtom atomC, IAtom atomD) Checks these four atoms for square planarity.
static boolean	StereoTool.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 and Description
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 TrigonalBipyramidal	TrigonalBipyramidal.create(IAtom focus, List<IAtom> carriers, int cfg)
protected SquarePlanar	SquarePlanar.create(IAtom focus, List<IAtom> carriers, int cfg)
protected Octahedral	Octahedral.create(IAtom focus, List<IAtom> carriers, int cfg)
protected IStereoElement<IBond,IAtom>	Atropisomeric.create(IBond focus, List<IAtom> carriers, int cfg)
IDoubleBondStereochemistry	DoubleBondStereochemistry.map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)
IDoubleBondStereochemistry	DoubleBondStereochemistry.map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)
ITetrahedralChirality	TetrahedralChirality.map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)
ITetrahedralChirality	TetrahedralChirality.map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)

Constructors in org.openscience.cdk.stereo with parameters of type IAtom

Constructor and 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, 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'.
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.
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.
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, int config)
TetrahedralChirality(IAtom chiralAtom, IAtom[] ligands, ITetrahedralChirality.Stereo stereo)
TetrahedralChirality(IAtom chiralAtom, IAtom[] ligands, ITetrahedralChirality.Stereo stereo)
TrigonalBipyramidal(IAtom focus, IAtom[] carriers, int order) Create a new trigonal bipyramidal configuration.
TrigonalBipyramidal(IAtom focus, IAtom[] carriers, int order) Create a new trigonal bipyramidal configuration.

Uses of IAtom in org.openscience.cdk.tools

Fields in org.openscience.cdk.tools with type parameters of type IAtom

Modifier and Type	Field and Description
protected List<IAtom>	HOSECodeGenerator.sphereNodesWithAtoms

Methods in org.openscience.cdk.tools that return types with arguments of type IAtom

Modifier and Type	Method and Description
List<IAtom>	HOSECodeGenerator.getNodesInSphere(int sphereNumber)

Methods in org.openscience.cdk.tools with parameters of type IAtom

Modifier and Type	Method and Description
void	CDKHydrogenAdder.addImplicitHydrogens(IAtomContainer container, IAtom atom) Sets the implicit hydrogen count for the indicated IAtom in the given IAtomContainer.
int	SaturationChecker.calculateNumberOfImplicitHydrogens(IAtom atom)
int	SaturationChecker.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.
int	SmilesValencyChecker.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.
int	SmilesValencyChecker.calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container)
int	SaturationChecker.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.
int	SaturationChecker.calculateNumberOfImplicitHydrogens(IAtom atom, IAtomContainer container, boolean throwExceptionForUnknowAtom)
boolean	SmilesValencyChecker.couldMatchAtomType(IAtomContainer container, IAtom atom, IAtomType type) Determines if the atom can be of type AtomType.
boolean	SaturationChecker.couldMatchAtomType(IAtomContainer atomContainer, IAtom atom, IAtomType atomType) Determines if the atom can be of type AtomType.
boolean	SmilesValencyChecker.couldMatchAtomType(IAtom atom, double bondOrderSum, IBond.Order maxBondOrder, IAtomType type) Determines if the atom can be of type AtomType.
IAtomContainer	StructureResonanceGenerator.getContainer(IAtomContainer molecule, IAtom atom) Get the container which the atom is found on resonance from a IAtomContainer.
double	SaturationChecker.getCurrentMaxBondOrder(IAtom atom, IAtomContainer ac) Returns the currently maximum formable bond order for this atom.
String	HOSECodeGenerator.getHOSECode(IAtomContainer ac, IAtom root, int noOfSpheres) Produces a HOSE code for Atom root in the IAtomContainer ac.
String	HOSECodeGenerator.getHOSECode(IAtomContainer ac, IAtom root, int noOfSpheres, boolean ringsize) Produces a HOSE code for Atom root in the IAtomContainer ac.
double	AtomTypeAwareSaturationChecker.getMaxNoOfBonds(IAtom atom) This method calculates the number of bonds that an IAtom can 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.
boolean	SaturationChecker.hasPerfectConfiguration(IAtom atom, IAtomContainer ac)
boolean	SaturationChecker.isOverSaturated(IAtom atom, IAtomContainer ac) Checks if the current atom has exceeded its bond order sum value.
boolean	IValencyChecker.isSaturated(IAtom atom, IAtomContainer container)
boolean	AtomTypeAwareSaturationChecker.isSaturated(IAtom atom, IAtomContainer container)
boolean	SmilesValencyChecker.isSaturated(IAtom atom, IAtomContainer container) Checks whether an Atom is saturated by comparing it with known AtomTypes.
boolean	SaturationChecker.isSaturated(IAtom atom, IAtomContainer ac) Checks whether an Atom is saturated by comparing it with known AtomTypes.
boolean	CDKValencyChecker.isSaturated(IAtom atom, IAtomContainer container)
boolean	LonePairElectronChecker.isSaturated(IAtom atom, IAtomContainer ac) Checks if an Atom is saturated their lone pair electrons by comparing it with known AtomTypes.
static double	IonizationPotentialTool.predictIP(IAtomContainer container, IAtom atom) Deprecated. Method which is predict the Ionization Potential from given atom.
void	LonePairElectronChecker.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 and Description
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 IAtom[]	AtomContainerManipulator.getAtomArray(List<IAtom> list) Constructs an array of Atom objects from a List of Atom objects.
static IAtom	AtomContainerManipulator.getAtomById(IAtomContainer ac, String id) Returns an atom in an atomcontainer identified by id

Methods in org.openscience.cdk.tools.manipulator that return types with arguments of type IAtom

Modifier and Type	Method and 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 and Description
static void	AtomTypeManipulator.configure(IAtom atom, IAtomType atomType) Method that assign properties to an atom given a particular atomType.
static void	AtomTypeManipulator.configureUnsetProperties(IAtom atom, IAtomType atomType) Method that assign properties to an atom given a particular atomType.
static int	AtomContainerManipulator.countExplicitHydrogens(IAtomContainer atomContainer, IAtom atom) Count explicit hydrogens.
static int	AtomContainerManipulator.countHydrogens(IAtomContainer atomContainer, IAtom atom)
static double	AtomContainerManipulator.getBondOrderSum(IAtomContainer container, IAtom atom) Returns the sum of the bond order equivalents for a given IAtom.
static IAtomContainer	MoleculeSetManipulator.getRelevantAtomContainer(IAtomContainerSet moleculeSet, IAtom atom)
static IAtomContainer	AtomContainerSetManipulator.getRelevantAtomContainer(IAtomContainerSet containerSet, IAtom atom)
static IAtomContainer	ChemModelManipulator.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 IAtomContainer	ReactionManipulator.getRelevantAtomContainer(IReaction reaction, IAtom atom)
static IAtomContainer	ReactionSetManipulator.getRelevantAtomContainer(IReactionSet set, IAtom atom)
static IReaction	ChemModelManipulator.getRelevantReaction(IChemModel chemModel, IAtom atom) Retrieves the first IReaction containing a given IAtom from an IChemModel.
static IReaction	ReactionSetManipulator.getRelevantReaction(IReactionSet set, IAtom atom)
static boolean	RingSetManipulator.isSameRing(IRingSet ringSet, IAtom atom1, IAtom atom2) Checks if atom1 and atom2 share membership in the same ring or ring system.
static void	MoleculeSetManipulator.removeAtomAndConnectedElectronContainers(IAtomContainerSet set, IAtom atom)
static void	AtomContainerSetManipulator.removeAtomAndConnectedElectronContainers(IAtomContainerSet set, IAtom atom)
static void	ChemModelManipulator.removeAtomAndConnectedElectronContainers(IChemModel chemModel, IAtom atom) Remove an Atom and the connected ElectronContainers from all AtomContainers inside an IChemModel.
static void	ReactionManipulator.removeAtomAndConnectedElectronContainers(IReaction reaction, IAtom atom)
static void	ReactionSetManipulator.removeAtomAndConnectedElectronContainers(IReactionSet set, IAtom atom)
static boolean	AtomContainerManipulator.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 and Description
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 and Description
ValidationReport	AbstractValidator.validateAtom(IAtom subject)
ValidationReport	BasicValidator.validateAtom(IAtom subject)
ValidationReport	IValidator.validateAtom(IAtom subject)
ValidationReport	ValidatorEngine.validateAtom(IAtom subject)