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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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) |
Modifier and Type | Method and Description |
---|---|
Collection<IAtom> |
SimpleAtomCanonicalizer.canonicalizeAtoms(IAtomContainer container) |
Modifier and Type | Method and Description |
---|---|
int |
SimpleAtomComparator.compare(IAtom o1,
IAtom o2) |
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) |
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.
|
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.
|
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.
|
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).
|
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.
|
Modifier and Type | Method and Description |
---|---|
IAtom |
Ligand.getCentralAtom()
|
IAtom |
ILigand.getCentralAtom()
|
IAtom |
Ligand.getLigandAtom()
|
IAtom |
ILigand.getLigandAtom()
|
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.
|
Constructor and Description |
---|
ImplicitHydrogenLigand(IAtomContainer container,
VisitedAtoms visitedAtoms,
IAtom centralAtom) |
Ligand(IAtomContainer container,
VisitedAtoms visitedAtoms,
IAtom centralAtom,
IAtom ligandAtom) |
Modifier and Type | Method and Description |
---|---|
Map<IAtom,List<javax.vecmath.Point3d>> |
NumericalSurface.getAtomSurfaceMap()
Get the map from atom to surface points.
|
Constructor and Description |
---|
NeighborList(IAtom[] atoms,
double radius) |
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.
|
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) |
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.
|
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.
|
Constructor and Description |
---|
ShortestPaths(IAtomContainer container,
IAtom start)
Create a new shortest paths tool for a single start atom.
|
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.
|
Modifier and Type | Method and Description |
---|---|
int |
AtomEncoder.encode(IAtom atom,
IAtomContainer container)
Encode an invariant attribute of the given atom.
|
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.
|
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.
|
IAtom |
IAtomContainer.getLastAtom()
Deprecated.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
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.
|
Modifier and Type | Field and Description |
---|---|
protected IAtom |
CMLCoreModule.currentAtom |
Modifier and Type | Field and Description |
---|---|
protected Map<String,IAtom> |
CMLCoreModule.atomEnumeration |
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.
|
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.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IQueryAtom
Defines the ability to be matched against
IAtom 's. |
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 |
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.
|
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 |
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() |
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.
|
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) |
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.
|
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.
|
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.
|
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.
|
Modifier and Type | Method and Description |
---|---|
IAtom |
StructureDiagramGenerator.getOtherBondAtom(IAtom atom,
IBond bond)
Returns the other atom of the bond.
|
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.
|
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.
|
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.
|
Modifier and Type | Method and Description |
---|---|
IAtom |
ChargeGroup.getSwitchingAtom() |
Modifier and Type | Method and Description |
---|---|
void |
ChargeGroup.setSwitchingAtom(IAtom switchingAtom) |
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).
|
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
|
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.
|
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.
|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
PharmacophoreAtom
A representation of a pharmacophore group.
|
class |
PharmacophoreQueryAtom
Represents a query pharmacophore group.
|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
PDBAtom
Represents the idea of an atom as used in PDB files.
|
Modifier and Type | Method and Description |
---|---|
void |
PDBStrand.addAtom(IAtom oAtom,
IMonomer oMonomer)
Adds the atom oAtom to a specified Monomer.
|
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) |
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) |
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
PiContactDetectionDescriptor.calculate(IAtom first,
IAtom second,
IAtomContainer atomContainer)
The method returns if two atoms have pi-contact.
|
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) |
Modifier and Type | Method and Description |
---|---|
IReaction |
IReactionMechanism.initiate(IAtomContainerSet atomContainerSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
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.
|
Modifier and Type | Method and Description |
---|---|
IAtom |
RendererModel.getHighlightedAtom()
Returns the atom currently highlighted.
|
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.
|
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.
|
Modifier and Type | Method and Description |
---|---|
void |
RendererModel.setToolTipTextMap(Map<IAtom,String> map)
Sets the toolTipTextMap.
|
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.
|
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.
|
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.
|
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.
|
Modifier and Type | Method and Description |
---|---|
boolean |
RingSearch.cyclic(IAtom atom)
Determine whether the provided atom belongs to a ring (is cyclic).
|
Modifier and Type | Method and Description |
---|---|
Set<IAtom> |
Sgroup.getAtoms()
Access the atoms of this substructure group.
|
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.
|
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 . |
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.
|
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.
|
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.
|
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.
|
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.
|
Modifier and Type | Method and Description |
---|---|
IAtom |
InvPair.getAtom() |
Modifier and Type | Method and Description |
---|---|
static Comparator<IAtom> |
SmilesGenerator.createComparator(IAtomContainer mol,
int flavor) |
Modifier and Type | Method and Description |
---|---|
void |
InvPair.setAtom(IAtom newAtom) |
Constructor and Description |
---|
InvPair(long current,
IAtom atom) |
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.
|
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
|
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.
|
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
|
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.
|
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.
|
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.
|
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.
|
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.
|
Modifier and Type | Method and Description |
---|---|
List<IAtom> |
TargetProperties.getNeighbors(IAtom atom)
Deprecated.
|
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
|
Modifier and Type | Method and Description |
---|---|
IAtom |
IQuery.getAtom(INode node)
Deprecated.
Returns an atom associated with this node.
|
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.
|
Modifier and Type | Method and Description |
---|---|
IAtom |
Match.getTargetAtom()
Deprecated.
Return Target Atom
|
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.
|
Constructor and Description |
---|
Match(INode query,
IAtom target)
Deprecated.
Constructor
|
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.
|
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.
|
Modifier and Type | Method and Description |
---|---|
IAtom |
PathEdge.getSource()
Deprecated.
|
IAtom |
PathEdge.getTarget()
Deprecated.
|
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.
|
Modifier and Type | Method and Description |
---|---|
List<PathEdge> |
PathGraph.remove(IAtom atom)
Deprecated.
|
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 and Description |
---|
PathEdge(List<IAtom> atoms)
Deprecated.
|
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.
|
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.
|
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) |
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 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 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.
|
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) |
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.
|
Modifier and Type | Field and Description |
---|---|
protected List<IAtom> |
HOSECodeGenerator.sphereNodesWithAtoms |
Modifier and Type | Method and Description |
---|---|
List<IAtom> |
HOSECodeGenerator.getNodesInSphere(int sphereNumber) |
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)
|
String |
HOSECodeGenerator.getHOSECode(IAtomContainer ac,
IAtom root,
int noOfSpheres,
boolean ringsize)
|
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.
|
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
|
Modifier and Type | Method and Description |
---|---|
static List<IAtom> |
AtomContainerManipulator.getHeavyAtoms(IAtomContainer container)
Returns a set of nodes excluding all the hydrogens.
|
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.
|
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.
|
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) |
Copyright © 2021. All rights reserved.