Modifier and Type | Class and Description |
---|---|
class |
AminoAcid
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
|
class |
AtomContainer
Base class for all chemical objects that maintain a list of Atoms and
ElectronContainers.
|
class |
BioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
|
class |
Crystal
Class representing a molecular crystal.
|
class |
Molecule
Represents the concept of a chemical molecule, an object composed of
atoms connected by bonds.
|
class |
Monomer
A Monomer is an AtomContainer which stores additional monomer specific
informations for a group of Atoms.
|
class |
Polymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
|
class |
Ring
Class representing a ring structure in a molecule.
|
class |
Strand
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
AtomContainer.clone()
Clones this AtomContainer object and its content.
|
IAtomContainer |
ConformerContainer.get(int i)
Get the conformer at a specified position.
|
IAtomContainer |
AtomContainerSet.getAtomContainer(int number)
Returns the AtomContainer at position
number in the
container. |
IAtomContainer |
FragmentAtom.getFragment() |
IAtomContainer |
ConformerContainer.remove(int i)
Removes the conformer at the specified position.
|
IAtomContainer |
ConformerContainer.set(int i,
IAtomContainer atomContainer) |
Modifier and Type | Method and Description |
---|---|
Iterable<IAtomContainer> |
AtomContainerSet.atomContainers()
Get an iterator for this AtomContainerSet.
|
Iterator<IAtomContainer> |
ConformerContainer.iterator()
Gets an iterator over the conformers.
|
ListIterator<IAtomContainer> |
ConformerContainer.listIterator() |
ListIterator<IAtomContainer> |
ConformerContainer.listIterator(int i) |
Iterable<IAtomContainer> |
MoleculeSet.molecules()
Returns the array of Molecules of this container.
|
List<IAtomContainer> |
ConformerContainer.subList(int i,
int i1) |
Modifier and Type | Method and Description |
---|---|
boolean |
ConformerContainer.add(IAtomContainer atomContainer)
Add a conformer to the end of the list.
|
void |
AtomContainer.add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
ConformerContainer.add(int i,
IAtomContainer atomContainer) |
void |
MoleculeSet.addAtomContainer(IAtomContainer atomContainer)
Adds an atomContainer to this container.
|
void |
AtomContainerSet.addAtomContainer(IAtomContainer atomContainer)
Adds an atomContainer to this container.
|
void |
MoleculeSet.addAtomContainer(IAtomContainer atomContainer,
double multiplier)
Adds an atomContainer to this container with the given
multiplier.
|
void |
AtomContainerSet.addAtomContainer(IAtomContainer atomContainer,
double multiplier)
Adds an atomContainer to this container with the given
multiplier.
|
boolean |
RingSet.contains(IAtomContainer ring)
Checks for presence of a ring in this RingSet.
|
Double |
AtomContainerSet.getMultiplier(IAtomContainer container)
Returns the multiplier of the given AtomContainer.
|
void |
AtomContainer.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
AtomContainerSet.removeAtomContainer(IAtomContainer atomContainer)
Removes an AtomContainer from this container.
|
void |
AtomContainerSet.replaceAtomContainer(int position,
IAtomContainer container)
Replace the AtomContainer at a specific position (array has to be large enough).
|
IAtomContainer |
ConformerContainer.set(int i,
IAtomContainer atomContainer) |
void |
FragmentAtom.setFragment(IAtomContainer fragment) |
boolean |
AtomContainerSet.setMultiplier(IAtomContainer container,
Double multiplier)
Sets the coefficient of a AtomContainer to a given value.
|
Modifier and Type | Method and Description |
---|---|
boolean |
ConformerContainer.addAll(Collection<? extends IAtomContainer> atomContainers) |
boolean |
ConformerContainer.addAll(int i,
Collection<? extends IAtomContainer> iAtomContainers) |
void |
AtomContainerSet.sortAtomContainers(Comparator<IAtomContainer> comparator)
Sort the AtomContainers and multipliers using a provided Comparator
|
Constructor and Description |
---|
AtomContainer(IAtomContainer container)
Constructs an AtomContainer with a copy of the atoms and electronContainers
of another AtomContainer (A shallow copy, i.e., with the same objects as in
the original AtomContainer).
|
ConformerContainer(IAtomContainer atomContainer)
Create a ConformerContainer object from a single molecule object.
|
ConformerContainer(IAtomContainer[] atomContainers)
Create a ConformerContainer from an array of molecules.
|
Crystal(IAtomContainer container)
Constructs a new crystal with zero length cell axis
and adds the atoms in the AtomContainer as cell content.
|
Molecule(IAtomContainer container)
Constructs a Molecule with
a shallow copy of the atoms and bonds of an AtomContainer.
|
Ring(IAtomContainer atomContainer)
Constructs a ring from the atoms in an IAtomContainer object.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
DoubleBondAcceptingAromaticityDetector.detectAromaticity(IAtomContainer atomContainer) |
static boolean |
CDKHueckelAromaticityDetector.detectAromaticity(IAtomContainer atomContainer) |
static boolean |
AromaticityCalculator.isAromatic(IRing ring,
IAtomContainer atomContainer)
Tests the
ring in the molecule for aromaticity. |
Modifier and Type | Method and Description |
---|---|
IAtomType[] |
SybylAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer) |
IAtomType[] |
StructGenMatcher.findMatchingAtomType(IAtomContainer atomContainer) |
IAtomType[] |
MMFF94AtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer) |
IAtomType[] |
MM2AtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer) |
IAtomType[] |
IAtomTypeMatcher.findMatchingAtomType(IAtomContainer container)
Method that assigns atom types to atoms in the given atom container.
|
IAtomType[] |
EStateAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer) |
IAtomType[] |
CDKAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer) |
IAtomType |
SybylAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom)
Sybyl atom type perception for a single atom.
|
IAtomType |
StructGenMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atom)
Finds the AtomType matching the Atom's element symbol, formal charge and
hybridization state.
|
IAtomType |
MMFF94AtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atomInterface)
Assign the mmff94 atom type to a given atom.
|
IAtomType |
MM2AtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom atomInterface)
Assign the mm2 atom type to a given atom.
|
IAtomType |
IAtomTypeMatcher.findMatchingAtomType(IAtomContainer container,
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 |
CDKAtomTypeMatcher.findMatchingAtomType(IAtomContainer atomContainer,
IAtom 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 |
---|---|
IAtomContainer |
GasteigerMarsiliPartialCharges.assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac,
boolean setCharge)
Main method which assigns Gasteiger Marisili partial sigma charges
|
IAtomContainer |
GasteigerPEPEPartialCharges.assignGasteigerPiPartialCharges(IAtomContainer ac,
boolean setCharge)
Main method which assigns Gasteiger partial pi charges.
|
IAtomContainer |
InductivePartialCharges.assignInductivePartialCharges(IAtomContainer ac)
Main method, set charge as atom properties
|
IAtomContainer |
MMFF94PartialCharges.assignMMFF94PartialCharges(IAtomContainer ac)
Main method which assigns MMFF94 partial charges
|
IAtomContainer |
AtomTypeCharges.setCharges(IAtomContainer atomContainer)
Sets initial charges for atom types
+1 for cationic atom types
-1 for anionic atom types
carboxylic oxygen -0.5
phosphorylic oxygen -0.66
sulfanilic oxygen -0.5
or to formal charge (which must be determined elsewhere or set manually)
polycations are not handled by this approach
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
GasteigerMarsiliPartialCharges.assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac,
boolean setCharge)
Main method which assigns Gasteiger Marisili partial sigma charges
|
IAtomContainer |
GasteigerPEPEPartialCharges.assignGasteigerPiPartialCharges(IAtomContainer ac,
boolean setCharge)
Main method which assigns Gasteiger partial pi charges.
|
double[] |
GasteigerMarsiliPartialCharges.assignGasteigerSigmaMarsiliFactors(IAtomContainer ac)
Method which stores and assigns the factors a,b,c and CHI+
|
IAtomContainer |
InductivePartialCharges.assignInductivePartialCharges(IAtomContainer ac)
Main method, set charge as atom properties
|
IAtomContainer |
MMFF94PartialCharges.assignMMFF94PartialCharges(IAtomContainer ac)
Main method which assigns MMFF94 partial charges
|
double |
Polarizability.calculateBondPolarizability(IAtomContainer atomContainer,
IBond bond)
calculate bond polarizability
|
void |
MMFF94PartialCharges.calculateCharges(IAtomContainer container) |
void |
InductivePartialCharges.calculateCharges(IAtomContainer container) |
void |
IElectronicPropertyCalculator.calculateCharges(IAtomContainer container) |
void |
GasteigerPEPEPartialCharges.calculateCharges(IAtomContainer container) |
void |
GasteigerMarsiliPartialCharges.calculateCharges(IAtomContainer container) |
void |
AtomTypeCharges.calculateCharges(IAtomContainer container) |
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 |
Polarizability.calculateKJMeanMolecularPolarizability(IAtomContainer atomContainer)
calculates the mean molecular polarizability as described in paper of Kang and Jhorn
|
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 |
InductivePartialCharges.getAtomicSoftnessCore(IAtomContainer ac,
int atomPosition)
Gets the atomicSoftnessCore attribute of the InductivePartialCharges object
|
double[] |
InductivePartialCharges.getPaulingElectronegativities(IAtomContainer ac,
boolean modified)
Gets the paulingElectronegativities attribute of the
InductivePartialCharges object
|
double |
Polarizability.getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer,
IAtom atom)
Gets the polarizabilitiyFactorForAtom
|
IAtomContainer |
AtomTypeCharges.setCharges(IAtomContainer atomContainer)
Sets initial charges for atom types
+1 for cationic atom types
-1 for anionic atom types
carboxylic oxygen -0.5
phosphorylic oxygen -0.66
sulfanilic oxygen -0.5
or to formal charge (which must be determined elsewhere or set manually)
polycations are not handled by this approach
|
Modifier and Type | Method and Description |
---|---|
void |
IsotopeFactory.configureAtoms(IAtomContainer container)
Configures atoms in an AtomContainer to
carry all the correct data according to their element type.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugAminoAcid
Debugging data class.
|
class |
DebugAtomContainer
Debugging data class.
|
class |
DebugBioPolymer
Debugging data class.
|
class |
DebugCrystal
Debugging data class.
|
class |
DebugMolecule
Debugging data class.
|
class |
DebugMonomer
Debugging data class.
|
class |
DebugPDBMonomer
Debugging data class.
|
class |
DebugPDBPolymer
Debugging data class.
|
class |
DebugPolymer
Debugging data class.
|
class |
DebugRing
Debugging data class.
|
class |
DebugStrand
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
DebugAtomContainer.clone() |
IAtomContainer |
DebugMoleculeSet.getAtomContainer(int number) |
IAtomContainer |
DebugAtomContainerSet.getAtomContainer(int number) |
IAtomContainer |
DebugFragmentAtom.getFragment() |
Modifier and Type | Method and Description |
---|---|
Iterable<IAtomContainer> |
DebugMoleculeSet.atomContainers() |
Iterable<IAtomContainer> |
DebugAtomContainerSet.atomContainers() |
Iterable<IAtomContainer> |
DebugMoleculeSet.molecules() |
Modifier and Type | Method and Description |
---|---|
void |
DebugStrand.add(IAtomContainer atomContainer) |
void |
DebugRing.add(IAtomContainer atomContainer) |
void |
DebugPolymer.add(IAtomContainer atomContainer) |
void |
DebugMonomer.add(IAtomContainer atomContainer) |
void |
DebugMolecule.add(IAtomContainer atomContainer) |
void |
DebugCrystal.add(IAtomContainer atomContainer) |
void |
DebugBioPolymer.add(IAtomContainer atomContainer) |
void |
DebugAtomContainer.add(IAtomContainer atomContainer) |
void |
DebugAminoAcid.add(IAtomContainer atomContainer) |
void |
DebugMoleculeSet.addAtomContainer(IAtomContainer atomContainer) |
void |
DebugAtomContainerSet.addAtomContainer(IAtomContainer atomContainer) |
void |
DebugMoleculeSet.addAtomContainer(IAtomContainer atomContainer,
double multiplier) |
void |
DebugAtomContainerSet.addAtomContainer(IAtomContainer atomContainer,
double multiplier) |
Double |
DebugMoleculeSet.getMultiplier(IAtomContainer container) |
Double |
DebugAtomContainerSet.getMultiplier(IAtomContainer container) |
void |
DebugStrand.remove(IAtomContainer atomContainer) |
void |
DebugRing.remove(IAtomContainer atomContainer) |
void |
DebugPolymer.remove(IAtomContainer atomContainer) |
void |
DebugMonomer.remove(IAtomContainer atomContainer) |
void |
DebugMolecule.remove(IAtomContainer atomContainer) |
void |
DebugCrystal.remove(IAtomContainer atomContainer) |
void |
DebugBioPolymer.remove(IAtomContainer atomContainer) |
void |
DebugAtomContainer.remove(IAtomContainer atomContainer) |
void |
DebugAminoAcid.remove(IAtomContainer atomContainer) |
void |
DebugMoleculeSet.removeAtomContainer(IAtomContainer atomContainer) |
void |
DebugAtomContainerSet.removeAtomContainer(IAtomContainer atomContainer) |
void |
DebugMoleculeSet.replaceAtomContainer(int position,
IAtomContainer container) |
void |
DebugAtomContainerSet.replaceAtomContainer(int position,
IAtomContainer container) |
void |
DebugFragmentAtom.setFragment(IAtomContainer fragment) |
boolean |
DebugMoleculeSet.setMultiplier(IAtomContainer container,
Double multiplier) |
boolean |
DebugAtomContainerSet.setMultiplier(IAtomContainer container,
Double multiplier) |
Constructor and Description |
---|
DebugAtomContainer(IAtomContainer container) |
DebugCrystal(IAtomContainer container) |
DebugMolecule(IAtomContainer container) |
DebugRing(IAtomContainer container) |
Modifier and Type | Method and Description |
---|---|
BitSet |
SubstructureFingerprinter.getFingerprint(IAtomContainer atomContainer)
Calculates the substructure fingerprint for the given AtomContainer.
|
BitSet |
PubchemFingerprinter.getFingerprint(IAtomContainer atomContainer)
Calculate 881 bit Pubchem fingerprint for a molecule.
|
BitSet |
MACCSFingerprinter.getFingerprint(IAtomContainer atomContainer)
Calculates the substructure fingerprint for the given AtomContainer.
|
BitSet |
IFingerprinter.getFingerprint(IAtomContainer container)
Returns the fingerprint for the given IAtomContainer.
|
BitSet |
HybridizationFingerprinter.getFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given AtomContainer.
|
BitSet |
Fingerprinter.getFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given AtomContainer.
|
BitSet |
ExtendedFingerprinter.getFingerprint(IAtomContainer container)
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
|
BitSet |
EStateFingerprinter.getFingerprint(IAtomContainer atomContainer)
Calculates the substructure fingerprint for the given AtomContainer.
|
BitSet |
Fingerprinter.getFingerprint(IAtomContainer container,
AllRingsFinder ringFinder)
Generates a fingerprint of the default size for the given AtomContainer.
|
BitSet |
GraphOnlyFingerprinter.getFingerprint(IAtomContainer container,
int size) |
BitSet |
ExtendedFingerprinter.getFingerprint(IAtomContainer atomContainer,
IRingSet ringSet,
List<IRingSet> rslist)
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
|
Map<String,Integer> |
HybridizationFingerprinter.getRawFingerprint(IAtomContainer container) |
Modifier and Type | Method and Description |
---|---|
IAtomContainer[] |
MurckoFragmenter.getFragmentsAsContainers()
Get all frameworks and ring systems as
IAtomContainer objects. |
IAtomContainer[] |
IFragmenter.getFragmentsAsContainers()
Get fragments generated as
IAtomContainer objects. |
IAtomContainer[] |
ExhaustiveFragmenter.getFragmentsAsContainers()
Get the fragments generated as
IAtomContainer objects.. |
IAtomContainer[] |
MurckoFragmenter.getFrameworksAsContainers()
Get frameworks as
IAtomContainer as objects. |
IAtomContainer[] |
MurckoFragmenter.getRingSystemsAsContainers()
Get rings systems as
IAtomContainer objects. |
Modifier and Type | Method and Description |
---|---|
void |
MurckoFragmenter.generateFragments(IAtomContainer atomContainer)
Perform the fragmentation procedure.
|
void |
IFragmenter.generateFragments(IAtomContainer atomContainer)
Generate fragments for the input molecule.
|
void |
ExhaustiveFragmenter.generateFragments(IAtomContainer atomContainer)
Generate fragments for the input molecule.
|
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 . |
static void |
GeometryTools.center(IAtomContainer atomCon,
Dimension areaDim)
Centers the molecule in the given area
See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
|
static List<IAtom> |
GeometryTools.findClosestInSpace(IAtomContainer container,
IAtom startAtom,
int max)
Returns the atoms which are closes to an atom in an AtomContainer by
distance in 3d.
|
static javax.vecmath.Point2d |
GeometryTools.get2DCenter(IAtomContainer container)
Returns the geometric center of all the atoms in the atomContainer.
|
static javax.vecmath.Point2d |
GeometryTools.get2DCentreOfMass(IAtomContainer ac)
Calculates the center of mass for the
Atom s in the
AtomContainer for the 2D coordinates. |
static Dimension |
GeometryTools.get2DDimension(IAtomContainer atomCon)
Returns the java.awt.Dimension of a molecule
See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
|
static javax.vecmath.Point3d |
GeometryTools.get3DCenter(IAtomContainer ac)
Returns the geometric center of all the atoms in this atomContainer.
|
static javax.vecmath.Point3d |
GeometryTools.get3DCentreOfMass(IAtomContainer ac)
Calculates the center of mass for the
Atom s in the
AtomContainer for the 2D coordinates. |
static double |
GeometryTools.getAllAtomRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms,
boolean Coords3d)
Return the RMSD between the 2 aligned molecules.
|
static double |
GeometryTools.getAngleRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms)
Return the variation of each angle value between the 2 aligned molecules.
|
static int |
GeometryTools.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)
Determines the best alignment for the label of an atom in 2D space.
|
static double |
GeometryTools.getBondLengthAverage(IAtomContainer container)
An average of all 2D bond length values is produced.
|
static double |
GeometryTools.getBondLengthAverage3D(IAtomContainer container)
An average of all 3D bond length values is produced, using point3ds in atoms.
|
static double |
GeometryTools.getBondLengthRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms,
boolean Coords3d)
Return the RMSD of bonds length between the 2 aligned molecules.
|
static IAtom |
GeometryTools.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)
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)
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)
Returns the atom of the given molecule that is closest to the given
coordinates.
|
static IBond |
GeometryTools.getClosestBond(double xPosition,
double yPosition,
IAtomContainer atomCon)
Returns the bond of the given molecule that is closest to the given
coordinates.
|
static IBond |
GeometryTools.getClosestBond(int xPosition,
int yPosition,
IAtomContainer atomCon)
Returns the bond of the given molecule that is closest to the given
coordinates.
|
static double |
GeometryTools.getHeavyAtomRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms,
boolean hetAtomOnly,
boolean Coords3d)
Return the RMSD of the heavy atoms between the 2 aligned molecules.
|
static double[] |
GeometryTools.getMinMax(IAtomContainer container)
Returns the minimum and maximum X and Y coordinates of the atoms in the
AtomContainer.
|
static double |
GeometryTools.getNormalizationFactor(IAtomContainer container)
Calculates the normalization factor in order to get an average bond length
of 1.5.
|
static Rectangle2D |
GeometryTools.getRectangle2D(IAtomContainer container)
Returns the 2D rectangle spanning the space occupied by the atom
container.
|
static double |
GeometryTools.getScaleFactor(IAtomContainer container,
double bondLength)
Determines the scale factor for displaying a structure loaded from disk in
a frame.
|
static boolean |
GeometryTools.has2DCoordinates(IAtomContainer container)
Determines if this AtomContainer contains 2D coordinates.
|
static int |
GeometryTools.has2DCoordinatesNew(IAtomContainer container)
Determines if this AtomContainer contains 2D coordinates for some or all molecules.
|
static boolean |
GeometryTools.has3DCoordinates(IAtomContainer container)
Determines if this model contains 3D coordinates
|
static boolean |
CrystalGeometryTools.hasCrystalCoordinates(IAtomContainer container)
Determines if this model contains fractional (crystal) 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.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 boolean |
BondTools.isValidDoubleBondConfiguration(IAtomContainer container,
IBond bond)
Tells if a certain bond is center of a valid double bond configuration.
|
static void |
BondTools.makeUpDownBonds(IAtomContainer container) |
static Map<Integer,Integer> |
GeometryTools.mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
double searchRadius,
Map<Integer,Integer> mappedAtoms)
Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest
AtomContainer) atomcontainer.
|
static void |
Projector.project2D(IAtomContainer container) |
static void |
Projector.project2D(IAtomContainer container,
HashMap renderingCoordinates) |
static void |
GeometryTools.rotate(IAtomContainer atomCon,
javax.vecmath.Point2d center,
double angle)
Rotates a molecule around a given center by a given angle
|
static void |
GeometryTools.scaleMolecule(IAtomContainer atomCon,
Dimension areaDim,
double fillFactor)
Scales a molecule such that it fills a given percentage of a given
dimension
See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
|
static void |
GeometryTools.scaleMolecule(IAtomContainer atomCon,
double scaleFactor)
Multiplies all the coordinates of the atoms of the given molecule with the
scalefactor.
|
static Rectangle2D |
GeometryTools.shiftContainer(IAtomContainer container,
Rectangle2D bounds,
Rectangle2D last,
double gap)
Shift the container horizontally to the right to make its bounds not
overlap with the other bounds.
|
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.
|
static void |
GeometryTools.translate2D(IAtomContainer atomCon,
double transX,
double transY)
Translates the given molecule by the given Vector.
|
static void |
GeometryTools.translate2D(IAtomContainer atomCon,
javax.vecmath.Vector2d vector)
Translates a molecule from the origin to a new point denoted by a vector.
|
static void |
GeometryTools.translate2DCenterTo(IAtomContainer container,
javax.vecmath.Point2d p)
Translates the geometric 2DCenter of the given
AtomContainer container to the specified Point2d p.
|
static void |
GeometryTools.translate2DCentreOfMassTo(IAtomContainer atomCon,
javax.vecmath.Point2d p)
Translates a molecule from the origin to a new point denoted by a vector.
|
static void |
GeometryTools.translateAllPositive(IAtomContainer atomCon)
Adds an automatically calculated offset to the coordinates of all atoms
such that all coordinates are positive and the smallest x or y coordinate
is exactly zero.
|
Modifier and Type | Method and Description |
---|---|
void |
KabschAlignment.rotateAtomContainer(IAtomContainer ac)
Rotates the
IAtomContainer coordinates by the rotation matrix. |
Constructor and Description |
---|
KabschAlignment(IAtomContainer ac1,
IAtomContainer ac2)
Sets up variables for the alignment algorithm.
|
KabschAlignment(IAtomContainer ac1,
IAtomContainer ac2,
double[] wts)
Sets up variables for the alignment algorithm.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
Ligand.getAtomContainer()
IAtomContainer of which this ligand is part. |
IAtomContainer |
ILigand.getAtomContainer()
IAtomContainer of which this ligand is part. |
Modifier and Type | Method and Description |
---|---|
static org.openscience.cdk.geometry.cip.LigancyFourChirality |
CIPTool.defineLigancyFourChirality(IAtomContainer container,
int chiralAtom,
int ligand1,
int ligand2,
int ligand3,
int ligand4,
ITetrahedralChirality.Stereo stereo)
Creates a ligancy four chirality around a single chiral atom, where the involved
atoms are identified by there index in the
IAtomContainer . |
static ILigand |
CIPTool.defineLigand(IAtomContainer container,
VisitedAtoms visitedAtoms,
int chiralAtom,
int ligandAtom)
Creates a ligand attached to a single chiral atom, where the involved
atoms are identified by there index in the
IAtomContainer . |
static CIPTool.CIP_CHIRALITY |
CIPTool.getCIPChirality(IAtomContainer container,
ITetrahedralChirality stereoCenter)
Returns the R or S chirality according to the CIP rules, based on the given
chirality information.
|
Constructor and Description |
---|
ImplicitHydrogenLigand(IAtomContainer container,
VisitedAtoms visitedAtoms,
IAtom centralAtom) |
Ligand(IAtomContainer container,
VisitedAtoms visitedAtoms,
IAtom centralAtom,
IAtom ligandAtom) |
Constructor and Description |
---|
NumericalSurface(IAtomContainer atomContainer)
Constructor to initialize the surface calculation with default values.
|
NumericalSurface(IAtomContainer atomContainer,
double solvent_radius,
int tesslevel)
Constructor to initialize the surface calculation with user specified values.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
SpanningTree.getCyclicFragmentsContainer()
Returns an IAtomContainer which contains all the atoms and bonds which
are involved in ring systems.
|
IAtomContainer |
SpanningTree.getPath(IAtomContainer spt,
IAtom a1,
IAtom a2) |
IAtomContainer |
SpanningTree.getSpanningTree() |
IAtomContainer |
AtomContainerPermutor.next() |
Modifier and Type | Method and Description |
---|---|
static void |
PathTools.breadthFirstSearch(IAtomContainer atomContainer,
List<IAtom> sphere,
IMolecule 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,
IMolecule 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.
|
static boolean |
PathTools.depthFirstTargetSearch(IAtomContainer molecule,
IAtom root,
IAtom target,
IAtomContainer path)
Recursivly perfoms 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.
|
static IAtom[] |
PathTools.findClosestByBond(IAtomContainer atomContainer,
IAtom atom,
int max)
Returns the atoms which are closest to an atom in an AtomContainer by bonds.
|
static List<List<IAtom>> |
PathTools.getAllPaths(IAtomContainer atomContainer,
IAtom start,
IAtom end)
Get a list of all the paths between two atoms.
|
static int |
PathTools.getMolecularGraphDiameter(IAtomContainer atomContainer)
Returns the diameter of the molecular graph.
|
static int |
PathTools.getMolecularGraphRadius(IAtomContainer atomContainer)
Returns the radius of the molecular graph.
|
static org._3pq.jgrapht.graph.SimpleGraph |
MoleculeGraphs.getMoleculeGraph(IAtomContainer molecule)
Creates a molecule graph for use with jgrapht.
|
IAtomContainer |
SpanningTree.getPath(IAtomContainer spt,
IAtom a1,
IAtom a2) |
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)
Returns a list of atoms in the shortest path between two atoms.
|
static int |
PathTools.getVertexCountAtDistance(IAtomContainer atomContainer,
int distance)
Returns the number of vertices that are a distance 'd' apart.
|
static boolean |
ConnectivityChecker.isConnected(IAtomContainer atomContainer)
Check whether a set of atoms in an
IAtomContainer is connected. |
static IMoleculeSet |
ConnectivityChecker.partitionIntoMolecules(IAtomContainer atomContainer)
Partitions the atoms in an AtomContainer into covalently connected components.
|
void |
AtomContainerPermutor.setAtomContainer(IAtomContainer ac) |
Constructor and Description |
---|
AtomContainerAtomPermutor(IAtomContainer ac) |
AtomContainerBondPermutor(IAtomContainer ac) |
SpanningTree(IAtomContainer atomContainer) |
Modifier and Type | Method and Description |
---|---|
void |
CanonicalLabeler.canonLabel(IAtomContainer atomContainer)
Canonically label the fragment.
|
static IAtomContainerSet |
ConjugatedPiSystemsDetector.detect(IAtomContainer ac)
Detect all conjugated pi systems in an AtomContainer.
|
static long[] |
MorganNumbersTools.getMorganNumbers(IAtomContainer atomContainer)
Makes an array containing the morgan numbers of the atoms of atomContainer.
|
static String[] |
MorganNumbersTools.getMorganNumbersWithElementSymbol(IAtomContainer atomContainer)
Makes an array containing the morgan numbers+element symbol of the atoms of atomContainer.
|
static long[] |
InChINumbersTools.getNumbers(IAtomContainer atomContainer)
Makes an array containing the InChI atom numbers of the non-hydrogen
atoms in the atomContainer.
|
int[] |
EquivalentClassPartitioner.getTopoEquivClassbyHuXu(IAtomContainer atomContainer)
Get the topological equivalent class of the molecule
|
double[] |
EquivalentClassPartitioner.prepareNode(IAtomContainer atomContainer)
Prepare the node identifier.
|
Constructor and Description |
---|
EquivalentClassPartitioner(IAtomContainer atomContainer)
Constructor for the TopologicalEquivalentClass object
|
Modifier and Type | Method and Description |
---|---|
static int[][] |
TopologicalMatrix.getMatrix(IAtomContainer container)
Returns the topological matrix for the given AtomContainer.
|
static double[][] |
ConnectionMatrix.getMatrix(IAtomContainer container)
Returns the connection matrix representation of this AtomContainer.
|
static int[][] |
AdjacencyMatrix.getMatrix(IAtomContainer container)
Returns the adjacency matrix for the given AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
void |
RebondTool.rebond(IAtomContainer container)
Rebonding using a Binary Space Partition Tree.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
InChIToStructure.getAtomContainer()
Returns generated molecule.
|
Modifier and Type | Method and Description |
---|---|
InChIGenerator |
InChIGeneratorFactory.getInChIGenerator(IAtomContainer container)
Gets an Standard InChI generator for a
IAtomContainer . |
InChIGenerator |
InChIGeneratorFactory.getInChIGenerator(IAtomContainer container,
List<net.sf.jniinchi.INCHI_OPTION> options)
Gets InChI generator for CDK IAtomContainer.
|
InChIGenerator |
InChIGeneratorFactory.getInChIGenerator(IAtomContainer container,
String options)
Gets InChI generator for CDK IAtomContainer.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IAminoAcid
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
|
interface |
IBioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
|
interface |
ICrystal
Class representing a molecular crystal.
|
interface |
IMolecule
Represents a set of Molecules.
|
interface |
IMonomer
A Monomer is an AtomContainer which stores additional monomer specific
informations for a group of Atoms.
|
interface |
IPDBMonomer
Represents the idea of an protein monomer as found in PDB files.
|
interface |
IPDBPolymer
A PDBPolymer is a subclass of a BioPolymer which is supposed to store
additional informations about the BioPolymer which are connected to BioPolymers.
|
interface |
IPolymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
|
interface |
IRing
Class representing a ring structure in a molecule.
|
interface |
IStrand
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
IAtomContainer.clone() |
IAtomContainer |
IAtomContainerSet.getAtomContainer(int number)
Returns the AtomContainer at position
number in the
container. |
IAtomContainer |
IFragmentAtom.getFragment()
Returns the fully expended form of the IFragmentAtom.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IAtomContainer> |
IAtomContainerSet.atomContainers()
Get an Iterable for this AtomContainerSet.
|
Iterable<IAtomContainer> |
IMoleculeSet.molecules()
Returns the array of Molecules of this container.
|
Modifier and Type | Method and Description |
---|---|
void |
ICrystal.add(IAtomContainer container)
Adds the atoms in the AtomContainer as cell content.
|
void |
IAtomContainer.add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
IAtomContainerSet.addAtomContainer(IAtomContainer atomContainer)
Adds an atomContainer to this container.
|
void |
IAtomContainerSet.addAtomContainer(IAtomContainer atomContainer,
double multiplier)
Adds an atomContainer to this container with the given
multiplier.
|
boolean |
IRingSet.contains(IAtomContainer container)
True, if this set contains the IAtomContainer.
|
Double |
IAtomContainerSet.getMultiplier(IAtomContainer container)
Returns the multiplier of the given AtomContainer.
|
void |
IAtomContainer.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
IAtomContainerSet.removeAtomContainer(IAtomContainer atomContainer)
Removes an AtomContainer from this container.
|
void |
IAtomContainerSet.replaceAtomContainer(int position,
IAtomContainer container)
Replace the AtomContainer at a specific position (array has to be large enough).
|
void |
IFragmentAtom.setFragment(IAtomContainer fragment)
Sets the fully expended form of the IFragmentAtom.
|
boolean |
IAtomContainerSet.setMultiplier(IAtomContainer container,
Double multiplier)
Sets the coefficient of a AtomContainer to a given value.
|
Modifier and Type | Method and Description |
---|---|
void |
IAtomContainerSet.sortAtomContainers(Comparator<IAtomContainer> comparator)
Sort the AtomContainers using a provided Comparator.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
MDLV3000Reader.readConnectionTable(IChemObjectBuilder builder) |
Modifier and Type | Method and Description |
---|---|
void |
MDLV3000Reader.readAtomBlock(IAtomContainer readData)
Reads the atoms, coordinates and charges.
|
void |
MDLV3000Reader.readBondBlock(IAtomContainer readData)
Reads the bond atoms, order and stereo configuration.
|
String |
MDLV3000Reader.readHeader(IAtomContainer readData) |
void |
MDLV3000Reader.readSGroup(IAtomContainer readData)
Reads labels.
|
void |
MDLV2000Writer.writeMolecule(IAtomContainer container)
Writes a Molecule to an OutputStream in MDL sdf format.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
INChIContentProcessorTool.processFormula(IAtomContainer parsedContent,
String atomsEncoding)
Processes the content from the formula field of the INChI.
|
Modifier and Type | Method and Description |
---|---|
void |
INChIContentProcessorTool.processConnections(String bondsEncoding,
IAtomContainer container,
int source)
Processes the content from the connections field of the INChI.
|
IAtomContainer |
INChIContentProcessorTool.processFormula(IAtomContainer parsedContent,
String atomsEncoding)
Processes the content from the formula field of the INChI.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
IteratingSMILESReader.next()
Get the next molecule from the stream.
|
IAtomContainer |
IteratingPCCompoundXMLReader.next() |
IAtomContainer |
IteratingPCCompoundASNReader.next() |
IAtomContainer |
IteratingMDLReader.next()
Returns the next IMolecule.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
IEventChemObjectReader.getAtomContainer() |
IAtomContainer |
EventCMLReader.getAtomContainer() |
IAtomContainer |
EventCMLHandler.getAtomContainer() |
Modifier and Type | Method and Description |
---|---|
static IAtomContainer |
UniversalIsomorphismTester.project(List<RMap> rMapList,
IAtomContainer g,
int id)
Projects a list of
RMap on a molecule. |
Modifier and Type | Method and Description |
---|---|
static List<IAtomContainer> |
UniversalIsomorphismTester.getOverlaps(IAtomContainer g1,
IAtomContainer g2)
Returns all the maximal common substructure between twp atom containers.
|
static List<IAtomContainer> |
UniversalIsomorphismTester.projectList(List<List<RMap>> rMapsList,
IAtomContainer g,
int id)
Projects a list of RMapsList on a molecule.
|
Modifier and Type | Method and Description |
---|---|
static RGraph |
UniversalIsomorphismTester.buildRGraph(IAtomContainer g1,
IAtomContainer g2)
Builds the
RGraph ( resolution graph ), from two atomContainer
(description of the two molecules to compare)
This is the interface point between the CDK model and
the generic MCSS algorithm based on the RGRaph. |
static List<RMap> |
UniversalIsomorphismTester.checkSingleAtomCases(IAtomContainer g1,
IAtomContainer g2)
Checks for single atom cases before doing subgraph/isomorphism search.
|
static BitSet |
UniversalIsomorphismTester.getBitSet(IAtomContainer ac)
Transforms an AtomContainer into a
BitSet (which's size = number of bond
in the atomContainer, all the bit are set to true). |
static List<RMap> |
UniversalIsomorphismTester.getIsomorphAtomsMap(IAtomContainer g1,
IAtomContainer g2)
Returns the first isomorph 'atom mapping' found for g2 in g1.
|
static List<RMap> |
UniversalIsomorphismTester.getIsomorphMap(IAtomContainer g1,
IAtomContainer g2)
Returns the first isomorph mapping found or null.
|
static List<List<RMap>> |
UniversalIsomorphismTester.getIsomorphMaps(IAtomContainer g1,
IAtomContainer g2)
Returns all the isomorph 'mappings' found between two
atom containers.
|
static List<IAtomContainer> |
UniversalIsomorphismTester.getOverlaps(IAtomContainer g1,
IAtomContainer g2)
Returns all the maximal common substructure between twp atom containers.
|
static List<RMap> |
UniversalIsomorphismTester.getSubgraphAtomsMap(IAtomContainer g1,
IAtomContainer g2)
Returns the first subgraph 'atom mapping' found for g2 in g1, where g2 must be a substructure
of g1.
|
static List<List<RMap>> |
UniversalIsomorphismTester.getSubgraphAtomsMaps(IAtomContainer g1,
IAtomContainer g2)
Returns all subgraph 'atom mappings' found for g2 in g1, where g2 must be a substructure
of g1.
|
static List<RMap> |
UniversalIsomorphismTester.getSubgraphMap(IAtomContainer g1,
IAtomContainer g2)
Returns the first subgraph 'bond mapping' found for g2 in g1.
|
static List<List<RMap>> |
UniversalIsomorphismTester.getSubgraphMaps(IAtomContainer g1,
IAtomContainer g2)
Returns all the subgraph 'bond mappings' found for g2 in g1.
|
static boolean |
UniversalIsomorphismTester.isIsomorph(IAtomContainer g1,
IAtomContainer g2)
Tests if g1 and g2 are isomorph.
|
static boolean |
UniversalIsomorphismTester.isSubgraph(IAtomContainer g1,
IAtomContainer g2)
Tests if g2 a subgraph of g1.
|
static List<RMap> |
UniversalIsomorphismTester.makeAtomsMapOfBondsMap(List<RMap> l,
IAtomContainer g1,
IAtomContainer g2)
This makes a map of matching atoms out of a map of matching bonds as produced by the
get(Subgraph|Ismorphism)Map methods.
|
static List<List<RMap>> |
UniversalIsomorphismTester.makeAtomsMapsOfBondsMaps(List<List<RMap>> l,
IAtomContainer g1,
IAtomContainer g2)
This makes maps of matching atoms out of a maps of matching bonds as produced by the
get(Subgraph|Ismorphism)Maps methods.
|
static Map<Integer,Integer> |
AtomMappingTools.mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms)
Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest
AtomContainer) atomContainer.
|
static IAtomContainer |
UniversalIsomorphismTester.project(List<RMap> rMapList,
IAtomContainer g,
int id)
Projects a list of
RMap on a molecule. |
static List<IAtomContainer> |
UniversalIsomorphismTester.projectList(List<List<RMap>> rMapsList,
IAtomContainer g,
int id)
Projects a list of RMapsList on a molecule.
|
static List<List<RMap>> |
UniversalIsomorphismTester.search(IAtomContainer g1,
IAtomContainer g2,
BitSet c1,
BitSet c2,
boolean findAllStructure,
boolean findAllMap)
General
RGraph parsing method (usually not used directly)
This method is the entry point for the recursive search
adapted to the atom container input. |
Modifier and Type | Interface and Description |
---|---|
interface |
IQueryAtomContainer
General concept of a IAtomContainer aimed at doing molecular subgraph
queries using the UniversalIsomorphismTester.
|
Modifier and Type | Class and Description |
---|---|
class |
QueryAtomContainer |
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
RGroup.getGroup() |
IAtomContainer |
RGroupQuery.getRootStructure() |
IAtomContainer |
IRGroupQuery.getRootStructure()
Getter for the root structure of this R-Group.
|
Modifier and Type | Method and Description |
---|---|
List<IAtomContainer> |
RGroupQuery.getAllConfigurations() |
List<IAtomContainer> |
IRGroupQuery.getAllConfigurations()
Produces all combinations of the root structure (scaffold) with the R-groups
substituted in valid ways, using each R-group's definitions and conditions.
|
List<IAtomContainer> |
RGroupQuery.getSubstituents() |
List<IAtomContainer> |
IRGroupQuery.getSubstituents()
Return all the substituent atom containers, in other words the atom containers
defined in this RGroupQuery except for the root structure.
|
Modifier and Type | Method and Description |
---|---|
void |
QueryAtomContainer.add(IAtomContainer container) |
static QueryAtomContainer |
QueryAtomContainerCreator.createAnyAtomAnyBondContainer(IAtomContainer container,
boolean aromaticity)
Creates a QueryAtomContainer with wildcard atoms and wildcard bonds.
|
static QueryAtomContainer |
QueryAtomContainerCreator.createAnyAtomContainer(IAtomContainer container,
boolean aromaticity)
Creates a QueryAtomContainer with AnyAtoms / Aromatic Atoms and OrderQueryBonds / AromaticQueryBonds.
|
static QueryAtomContainer |
QueryAtomContainerCreator.createAnyAtomForPseudoAtomQueryContainer(IAtomContainer container)
Creates a QueryAtomContainer with SymbolQueryAtom's and
OrderQueryBond's.
|
static QueryAtomContainer |
QueryAtomContainerCreator.createBasicQueryContainer(IAtomContainer container)
Creates a QueryAtomContainer with SymbolQueryAtom's, AromaticQueryBond's and
OrderQueryBond's.
|
static QueryAtomContainer |
QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(IAtomContainer container)
Creates a QueryAtomContainer with SymbolQueryAtom's and OrderQueryBond's.
|
static QueryAtomContainer |
QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(IAtomContainer container)
Creates a QueryAtomContainer with SymbolAncChargeQueryAtom's and
OrderQueryBond's.
|
static QueryAtomContainer |
QueryAtomContainerCreator.createSymbolChargeIDQueryContainer(IAtomContainer container) |
void |
RGroup.setGroup(IAtomContainer group) |
void |
RGroupQuery.setRootStructure(IAtomContainer rootStructure) |
void |
IRGroupQuery.setRootStructure(IAtomContainer rootStructure)
Setter for the root structure of this R-Group.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
RecursiveSmartsAtom.getAtomContainer() |
IAtomContainer |
HydrogenAtom.getAtomContainer()
Returns local copy of IAtomContainer.
|
Modifier and Type | Method and Description |
---|---|
void |
RecursiveSmartsAtom.setAtomContainer(IAtomContainer atomContainer) |
void |
HydrogenAtom.setAtomContainer(IAtomContainer atomContainer)
Sets IAtomContainer.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
AtomPlacer.getInitialLongestChain(IMolecule molecule)
Search an aliphatic molecule for the longest chain.
|
IAtomContainer |
AtomPlacer.getLongestUnplacedChain(IMolecule molecule,
IAtom startAtom)
Search a molecule for the longest unplaced, aliphatic chain in it.
|
IAtomContainer |
AtomPlacer.getMolecule()
Return the molecule the AtomPlacer currently works with
|
IAtomContainer |
AtomPlacer.getPlacedAtoms(IAtomContainer ac)
Get all the placed atoms in an AtomContainer
|
IAtomContainer |
TemplateHandler.getTemplateAt(int position)
Gets the templateAt attribute of the TemplateHandler object
|
IAtomContainer |
RingPlacer.placeRingSubstituents(IRingSet rs,
double bondLength)
Positions the aliphatic substituents of a ring system
|
IAtomContainer |
TemplateHandler.removeMolecule(IAtomContainer molecule) |
Modifier and Type | Method and Description |
---|---|
void |
TemplateHandler.addMolecule(IAtomContainer molecule)
Adds a Molecule to the list of templates use by this TemplateHandler.
|
boolean |
AtomPlacer.allPlaced(IAtomContainer ac)
True is all the atoms in the given AtomContainer have been placed
|
void |
AtomPlacer.breadthFirstSearch(IAtomContainer ac,
Vector 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.
|
void |
AtomPlacer.breadthFirstSearch(IAtomContainer ac,
Vector 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.
|
double |
OverlapResolver.displace(IAtomContainer ac,
Vector overlappingAtoms,
Vector overlappingBonds)
Makes a small displacement to some atoms or rings in the given
atomcontainer.
|
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.
|
double |
OverlapResolver.getAtomOverlapScore(IAtomContainer ac,
Vector overlappingAtoms)
Calculates a score based on the overlap of atoms.
|
double |
OverlapResolver.getBondOverlapScore(IAtomContainer ac,
Vector overlappingBonds)
Calculates a score based on the intersection of bonds.
|
IAtomContainerSet |
TemplateHandler.getMappedSubstructures(IAtomContainer molecule)
Checks if one of the loaded templates is a substructure in the given
Molecule and returns all matched substructures in a IAtomContainerSet.
|
double |
OverlapResolver.getOverlapScore(IAtomContainer ac,
Vector overlappingAtoms,
Vector overlappingBonds)
Calculates a score based on the overlap of atoms and intersection of bonds.
|
IAtomContainer |
AtomPlacer.getPlacedAtoms(IAtomContainer ac)
Get all the placed atoms in an AtomContainer
|
String |
AtomPlacer.listNumbers(IAtomContainer mol,
IAtomContainer ac)
Returns a string with the numbers of all atoms in an AtomContainer relative
to a given molecule.
|
String |
AtomPlacer.listNumbers(IAtomContainer mol,
Vector ac)
Returns a string with the numbers of all atoms in a Vector relative to a
given molecule.
|
String |
AtomPlacer.listPlaced(IAtomContainer ac)
Returns a string with the numbers of all placed atoms in an AtomContainer
|
boolean |
TemplateHandler.mapTemplateExact(IAtomContainer molecule)
Checks if one of the loaded templates is isomorph to the given
Molecule.
|
boolean |
TemplateHandler.mapTemplates(IAtomContainer molecule)
Checks if one of the loaded templates is a substructure in the given
Molecule.
|
void |
AtomPlacer.markNotPlaced(IAtomContainer ac)
Marks all the atoms in the given AtomContainer as not placed
|
void |
AtomPlacer.markPlaced(IAtomContainer ac)
Marks all the atoms in the given AtomContainer as placed
|
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 |
RingPlacer.placeFusedRing(IRing ring,
IAtomContainer sharedAtoms,
javax.vecmath.Point2d sharedAtomsCenter,
javax.vecmath.Vector2d ringCenterVector,
double bondLength)
Generated coordinates for a given ring, which is fused to another ring.
|
void |
HydrogenPlacer.placeHydrogens2D(IAtomContainer atomContainer,
double bondLength) |
void |
HydrogenPlacer.placeHydrogens2D(IAtomContainer atomContainer,
IAtom atom) |
void |
HydrogenPlacer.placeHydrogens2D(IAtomContainer atomContainer,
IAtom atom,
double bondLength) |
void |
AtomPlacer.placeLinearChain(IAtomContainer atomContainer,
javax.vecmath.Vector2d initialBondVector,
double bondLength)
Places the atoms in a linear chain.
|
void |
RingPlacer.placeRing(IRing ring,
IAtomContainer sharedAtoms,
javax.vecmath.Point2d sharedAtomsCenter,
javax.vecmath.Vector2d ringCenterVector,
double bondLength)
Generated coordinates for a given ring.
|
void |
RingPlacer.placeSpiroRing(IRing ring,
IAtomContainer sharedAtoms,
javax.vecmath.Point2d sharedAtomsCenter,
javax.vecmath.Vector2d ringCenterVector,
double bondLength)
Generated coordinates for a given ring, which is connected to a spiro ring.
|
IAtomContainer |
TemplateHandler.removeMolecule(IAtomContainer molecule) |
double |
OverlapResolver.resolveOverlap(IAtomContainer ac,
IRingSet sssr)
Main method to be called to resolve overlap situations.
|
void |
AtomPlacer.setMolecule(IAtomContainer molecule)
Sets the molecule the AtomPlacer currently works with
|
boolean |
AtomPlacer.shouldBeLinear(IAtom atom,
IAtomContainer molecule) |
Modifier and Type | Method and Description |
---|---|
org.xmlcml.cml.element.CMLMolecule |
Convertor.cdkAtomContainerToCMLMolecule(IAtomContainer structure) |
org.xmlcml.cml.element.CMLAtom |
Convertor.cdkAtomToCMLAtom(IAtomContainer container,
IAtom cdkAtom) |
void |
QSARCustomizer.customize(IAtomContainer molecule,
Object nodeToAdd) |
void |
PDBAtomCustomizer.customize(IAtomContainer molecule,
Object nodeToAdd) |
void |
MDMoleculeCustomizer.customize(IAtomContainer molecule,
Object nodeToAdd)
Customize Molecule
|
void |
ICMLCustomizer.customize(IAtomContainer molecule,
Object nodeToAdd)
Customized the nodeToAdd for the given Molecule.
|
Modifier and Type | Class and Description |
---|---|
class |
ChargeGroup
A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.
|
class |
MDMolecule |
class |
Residue
A residue is a named, numbered collection of atoms in an MDMolecule.
|
Constructor and Description |
---|
ChargeGroup(IAtomContainer container,
int number,
MDMolecule parentMolecule)
Constructor to create a ChargeGroup based on an AC, a number, and a MDMolecule.
|
MDMolecule(IAtomContainer container) |
Residue(IAtomContainer container,
int number,
MDMolecule parentMolecule)
Constructor to create a Residue based on an AC, a number, and a MDMolecule.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
TemplateExtractor.createAnyAtomAtomContainer(IAtomContainer atomContainer) |
IAtomContainer |
AtomTetrahedralLigandPlacer3D.getPlacedAtomsInAtomContainer(IAtom atom,
IAtomContainer ac)
Gets all placed neighbouring atoms of a atom
|
IAtomContainer |
AtomPlacer3D.getPlacedHeavyAtoms(IAtomContainer molecule,
IAtom atom)
Gets the placed Heavy Atoms connected to an atom.
|
IAtomContainer |
TemplateHandler3D.getTemplateAt(int position)
Gets the templateAt attribute of the TemplateHandler object
|
IAtomContainer |
AtomTetrahedralLigandPlacer3D.getUnsetAtomsInAtomContainer(IAtom atom,
IAtomContainer ac)
Gets the unsetAtomsInAtomContainer attribute of the
AtomTetrahedralLigandPlacer3D object
|
IAtomContainer |
AtomPlacer3D.markPlaced(IAtomContainer ac)
Mark all atoms in chain as placed (CDKConstant ISPLACED)
|
IAtomContainer |
TemplateExtractor.resetFlags(IAtomContainer ac) |
Modifier and Type | Method and Description |
---|---|
void |
AtomTetrahedralLigandPlacer3D.add3DCoordinatesForSinglyBondedLigands(IAtomContainer atomContainer)
Generate coordinates for all atoms which are singly bonded and have no
coordinates.
|
boolean |
AtomPlacer3D.allHeavyAtomsPlaced(IAtomContainer ac)
True is all the atoms in the given AtomContainer have been placed
|
IAtomContainer |
TemplateExtractor.createAnyAtomAtomContainer(IAtomContainer atomContainer) |
int[] |
AtomPlacer3D.findHeavyAtomsInChain(IAtomContainer molecule,
IAtomContainer chain)
Count and find first heavy atom(s) (non Hydrogens) in a chain.
|
javax.vecmath.Point3d |
AtomPlacer3D.geometricCenterAllPlacedAtoms(IAtomContainer molecule)
Calculates the geometric center of all placed atoms in the atomcontainer
|
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) |
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
|
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) |
void |
TemplateHandler3D.mapTemplates(IAtomContainer ringSystems,
double NumberOfRingAtoms)
Checks if one of the loaded templates is a substructure in the given
Molecule.
|
IAtomContainer |
AtomPlacer3D.markPlaced(IAtomContainer ac)
Mark all atoms in chain as placed (CDKConstant ISPLACED)
|
int |
AtomPlacer3D.numberOfUnplacedHeavyAtoms(IAtomContainer ac)
Gets numberOfUnplacedHeavyAtoms (no Flag ISPLACED, no Hydrogens)
|
void |
AtomPlacer3D.placeAliphaticHeavyChain(IAtomContainer molecule,
IAtomContainer chain)
Method assigns 3Dcoordinates to the heavy atoms in an aliphatic chain
|
IAtomContainer |
TemplateExtractor.resetFlags(IAtomContainer ac) |
void |
AtomPlacer3D.zmatrixChainToCartesian(IAtomContainer molecule,
boolean flag_branched)
Takes the given Z Matrix coordinates and converts them to cartesian coordinates.
|
Modifier and Type | Class and Description |
---|---|
class |
NNAminoAcid
Deprecated.
Use the
AminoAcid instead. |
class |
NNAtomContainer
Deprecated.
Use the
AtomContainer instead. |
class |
NNBioPolymer
Deprecated.
Use the
BioPolymer instead. |
class |
NNCrystal
Deprecated.
Use the
Crystal instead. |
class |
NNMolecule
Deprecated.
Use the
Molecule instead. |
class |
NNMonomer
Deprecated.
Use the
Monomer instead. |
class |
NNPDBMonomer
Deprecated.
Use the
PDBMonomer instead. |
class |
NNPDBPolymer
Deprecated.
Use the
PDBPolymer instead. |
class |
NNPolymer
Deprecated.
Use the
Polymer instead. |
class |
NNRing
Deprecated.
Use the
Ring instead. |
class |
NNStrand
Deprecated.
Use the
Strand instead. |
Constructor and Description |
---|
NNAtomContainer(IAtomContainer container)
Deprecated.
|
NNCrystal(IAtomContainer container)
Deprecated.
|
NNMolecule(IAtomContainer container)
Deprecated.
|
NNRing(IAtomContainer atomContainer)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
static IAtomContainer |
SMSDNormalizer.convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
|
static IAtomContainer |
SMSDNormalizer.removeHydrogensAndPreserveAtomID(IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
|
Modifier and Type | Method and Description |
---|---|
static void |
SMSDNormalizer.aromatizeMolecule(IAtomContainer mol)
This function finds rings and uses aromaticity detection code to
aromatize the molecule.
|
static IAtomContainer |
SMSDNormalizer.convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
|
static int |
SMSDNormalizer.getExplicitHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
Returns The number of explicit hydrogens for a given IAtom.
|
static int |
SMSDNormalizer.getHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
The summed implicit + explicit hydrogens of the given IAtom.
|
static int |
SMSDNormalizer.getImplicitHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
Returns The number of Implicit Hydrogen Count for a given IAtom.
|
static IMolecule |
SMSDNormalizer.makeDeepCopy(IAtomContainer container)
Returns deep copy of the molecule
|
static boolean |
Normalizer.normalize(IAtomContainer ac,
Document doc)
The method takes an xml files like the following:
<replace-set> <replace>O=N=O</replace> <replacement>[O-][N+]=O</replacement> </replace-set> All parts in ac which are the same as replace will be changed according to replacement. |
static void |
SMSDNormalizer.percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Convenience method to perceive atom types for all
IAtom s in the
IAtomContainer , using the CDKAtomTypeMatcher . |
static IAtomContainer |
SMSDNormalizer.removeHydrogensAndPreserveAtomID(IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
|
Modifier and Type | Class and Description |
---|---|
class |
PharmacophoreQuery
Represents a colleciton of pharmacophore groups and constraints.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PharmacophoreMatcher.matches(IAtomContainer atomContainer)
Performs the pharmacophore matching.
|
boolean |
PharmacophoreMatcher.matches(IAtomContainer atomContainer,
boolean initializeTarget)
Performs the pharmacophore matching.
|
Modifier and Type | Class and Description |
---|---|
class |
PDBMonomer
Represents the idea of an monomer as used in PDB files.
|
class |
PDBPolymer
An entry in the PDB database.
|
class |
PDBStrand
An entry in the PDB database.
|
Modifier and Type | Method and Description |
---|---|
void |
AbstractAtomicDescriptor.cacheDescriptorValue(IAtom atom,
IAtomContainer container,
IDescriptorResult value)
Caches a DescriptorValue for a given IAtom.
|
void |
AbstractBondDescriptor.cacheDescriptorValue(IBond bond,
IAtomContainer container,
IDescriptorResult doubleResult)
Caches a DescriptorValue for a given IBond.
|
DescriptorValue |
IMolecularDescriptor.calculate(IAtomContainer container)
Calculates the descriptor value for the given IAtomContainer.
|
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.
|
DescriptorValue |
IBondDescriptor.calculate(IBond bond,
IAtomContainer atomContainer)
Calculates the descriptor value for the given IBond.
|
boolean |
AbstractBondDescriptor.isCachedAtomContainer(IAtomContainer container)
Returns true if the cached IDescriptorResult's are for the given IAtomContainer.
|
boolean |
AbstractAtomicDescriptor.isCachedAtomContainer(IAtomContainer container)
Returns true if the cached IDescriptorResult's are for the given IAtomContainer.
|
void |
DescriptorEngine.process(IAtomContainer molecule)
Calculates all available (or only those specified) descriptors for a molecule.
|
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
VdWRadiusDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculate the Van der Waals radius of an atom.
|
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 |
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_GSR.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
RDFProtonDescriptor_GHR_topol.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
RDFProtonDescriptor_GHR.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
RDFProtonDescriptor_GDR.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
RDFProtonDescriptor_G3R.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
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 |
ProtonAffinityHOSEDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the protonation affinity of an atom.
|
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 |
PeriodicTablePositionDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the period of an atom.
|
DescriptorValue |
PartialTChargePEOEDescriptor.calculate(IAtom atom,
IAtomContainer ac)
The method returns partial total charges assigned to an heavy atom through PEOE method.
|
DescriptorValue |
PartialTChargeMMFF94Descriptor.calculate(IAtom atom,
IAtomContainer ac)
The method returns partial charges assigned to an heavy atom through MMFF94 method.
|
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 |
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 |
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 |
IPAtomicLearningDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the ionization potential of an atom.
|
DescriptorValue |
IPAtomicHOSEDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the ionization potential 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 |
InductiveAtomicHardnessDescriptor.calculate(IAtom atom,
IAtomContainer ac)
It is needed to call the addExplicitHydrogensToSatisfyValency method from
the class tools.HydrogenAdder, and 3D coordinates.
|
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 |
DistanceToAtomDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculate the 3D distance between two atoms.
|
DescriptorValue |
CovalentRadiusDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculate the Covalent radius of an atom.
|
DescriptorValue |
BondsToAtomDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculate the number of bonds on the shortest path between two atoms.
|
DescriptorValue |
AtomValenceDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the valence of an atom.
|
DescriptorValue |
AtomHybridizationVSEPRDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the hybridization of an atom.
|
DescriptorValue |
AtomHybridizationDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the hybridization of an atom.
|
DescriptorValue |
AtomDegreeDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the number of not-H substituents of an atom.
|
DescriptorValue |
RDFProtonDescriptor_GSR.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GHR_topol.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GHR.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GDR.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 |
---|---|
DescriptorValue |
IPBondLearningDescriptor.calculate(IBond bond,
IAtomContainer atomContainer)
This method calculates the ionization potential of a bond.
|
DescriptorValue |
BondSigmaElectronegativityDescriptor.calculate(IBond aBond,
IAtomContainer atomContainer)
The method calculates the sigma electronegativity of a given bond
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
BondPartialTChargeDescriptor.calculate(IBond bond,
IAtomContainer ac)
The method calculates the bond total Partial charge of a given bond
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
BondPartialSigmaChargeDescriptor.calculate(IBond bond,
IAtomContainer ac)
The method calculates the bond-sigma Partial charge of a given bond
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
BondPartialPiChargeDescriptor.calculate(IBond bond,
IAtomContainer ac)
The method calculates the bond-pi Partial charge of a given bond
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
|
DescriptorValue |
AtomicNumberDifferenceDescriptor.calculate(IBond bond,
IAtomContainer ac) |
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
ZagrebIndexDescriptor.calculate(IAtomContainer atomContainer)
Evaluate the Zagreb Index for a molecule.
|
DescriptorValue |
XLogPDescriptor.calculate(IAtomContainer atomContainer)
Calculates the xlogP for an atom container.
|
DescriptorValue |
WienerNumbersDescriptor.calculate(IAtomContainer atomContainer)
Calculate the Wiener numbers.
|
DescriptorValue |
WHIMDescriptor.calculate(IAtomContainer container)
Calculates 11 directional and 6 non-directional WHIM descriptors for.
|
DescriptorValue |
WeightedPathDescriptor.calculate(IAtomContainer container)
Calculates the weighted path descriptors.
|
DescriptorValue |
WeightDescriptor.calculate(IAtomContainer container)
Calculate the weight of specified element type in the supplied
IAtomContainer . |
DescriptorValue |
VAdjMaDescriptor.calculate(IAtomContainer atomContainer)
calculates the VAdjMa descriptor for an atom container
|
DescriptorValue |
VABCDescriptor.calculate(IAtomContainer atomContainer)
Calculates the descriptor value using the
VABCVolume class. |
DescriptorValue |
TPSADescriptor.calculate(IAtomContainer atomContainer)
Calculates the TPSA for an atom container.
|
DescriptorValue |
RuleOfFiveDescriptor.calculate(IAtomContainer mol)
the method take a boolean checkAromaticity: if the boolean is true, it means that
aromaticity has to be checked.
|
DescriptorValue |
RotatableBondsCountDescriptor.calculate(IAtomContainer ac)
The method calculates the number of rotatable bonds of an atom container.
|
DescriptorValue |
PetitjeanShapeIndexDescriptor.calculate(IAtomContainer container)
Calculates the two Petitjean shape indices.
|
DescriptorValue |
PetitjeanNumberDescriptor.calculate(IAtomContainer atomContainer)
Evaluate the descriptor for the molecule.
|
DescriptorValue |
MomentOfInertiaDescriptor.calculate(IAtomContainer container)
Calculates the 3 MI's, 3 ration and the R_gyr value.
|
DescriptorValue |
MDEDescriptor.calculate(IAtomContainer container)
Calculate the weight of specified element type in the supplied
IAtomContainer . |
DescriptorValue |
MannholdLogPDescriptor.calculate(IAtomContainer atomContainer)
Calculates the Mannhold LogP for an atom container.
|
DescriptorValue |
LongestAliphaticChainDescriptor.calculate(IAtomContainer atomContainer)
Calculate the count of atoms of the longest aliphatic chain in the supplied
AtomContainer . |
DescriptorValue |
LengthOverBreadthDescriptor.calculate(IAtomContainer atomContainer)
Evaluate the descriptor for the molecule.
|
DescriptorValue |
LargestPiSystemDescriptor.calculate(IAtomContainer container)
Calculate the count of atoms of the largest pi system in the supplied
AtomContainer . |
DescriptorValue |
LargestChainDescriptor.calculate(IAtomContainer atomContainer)
Calculate the count of atoms of the largest chain in the supplied
IAtomContainer . |
DescriptorValue |
KierHallSmartsDescriptor.calculate(IAtomContainer container)
This method calculates occurrences of the Kier & Hall E-state fragments.
|
DescriptorValue |
KappaShapeIndicesDescriptor.calculate(IAtomContainer container)
calculates the kier shape indices for an atom container
|
DescriptorValue |
IPMolecularLearningDescriptor.calculate(IAtomContainer atomContainer)
It calculates the first ionization energy of a molecule.
|
DescriptorValue |
HybridizationRatioDescriptor.calculate(IAtomContainer container)
Calculate sp3/sp2 hybridization ratio in the supplied
IAtomContainer . |
DescriptorValue |
HBondDonorCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the number of H bond donors.
|
DescriptorValue |
HBondAcceptorCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the number of H bond acceptors.
|
DescriptorValue |
GravitationalIndexDescriptor.calculate(IAtomContainer container)
Calculates the 9 gravitational indices.
|
DescriptorValue |
FragmentComplexityDescriptor.calculate(IAtomContainer container)
Calculate the complexity in the supplied
AtomContainer . |
DescriptorValue |
FMFDescriptor.calculate(IAtomContainer container)
Calculates the FMF descriptor value for the given
IAtomContainer . |
DescriptorValue |
EccentricConnectivityIndexDescriptor.calculate(IAtomContainer container)
Calculates the eccentric connectivity
|
DescriptorValue |
CPSADescriptor.calculate(IAtomContainer atomContainer)
Evaluates the 29 CPSA descriptors using Gasteiger-Marsilli charges.
|
DescriptorValue |
ChiPathDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
ChiPathClusterDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
ChiClusterDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
ChiChainDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
CarbonTypesDescriptor.calculate(IAtomContainer container)
Calculates the 9 carbon types descriptors
|
DescriptorValue |
BPolDescriptor.calculate(IAtomContainer container)
This method calculate the sum of the absolute value of
the difference between atomic polarizabilities of all bonded atoms in the molecule
|
DescriptorValue |
BondCountDescriptor.calculate(IAtomContainer container)
This method calculate the number of bonds of a given type in an atomContainer
|
DescriptorValue |
BCUTDescriptor.calculate(IAtomContainer container)
Calculates the three classes of BCUT descriptors.
|
DescriptorValue |
BasicGroupCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the descriptor value for the given IAtomContainer.
|
DescriptorValue |
AutocorrelationDescriptorPolarizability.calculate(IAtomContainer container)
This method calculate the ATS Autocorrelation descriptor.
|
DescriptorValue |
AutocorrelationDescriptorMass.calculate(IAtomContainer atomContainer)
This method calculate the ATS Autocorrelation descriptor.
|
DescriptorValue |
AutocorrelationDescriptorCharge.calculate(IAtomContainer atomContainer) |
DescriptorValue |
AtomCountDescriptor.calculate(IAtomContainer container)
This method calculate the number of atoms of a given type in an
IAtomContainer . |
DescriptorValue |
AromaticBondsCountDescriptor.calculate(IAtomContainer atomContainer)
Calculate the count of aromatic atoms in the supplied
IAtomContainer . |
DescriptorValue |
AromaticAtomsCountDescriptor.calculate(IAtomContainer atomContainer)
Calculate the count of aromatic atoms in the supplied
IAtomContainer . |
DescriptorValue |
APolDescriptor.calculate(IAtomContainer container)
Calculate the sum of atomic polarizabilities in an
IAtomContainer . |
DescriptorValue |
AminoAcidCountDescriptor.calculate(IAtomContainer ac)
Determine the number of amino acids groups the supplied
IAtomContainer . |
DescriptorValue |
ALOGPDescriptor.calculate(IAtomContainer atomContainer)
The AlogP descriptor.
|
DescriptorValue |
AcidicGroupCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the descriptor value for the given IAtomContainer.
|
DescriptorValue |
IPMolecularLearningDescriptor.calculatePlus(IAtomContainer container)
It calculates the 1,2,..
|
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
TaeAminoAcidDescriptor.calculate(IAtomContainer container)
Calculates the 147 TAE descriptors for amino acids.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
RendererModel.getClipboardContent()
Returns the atoms and bonds on the Renderer2D clipboard.
|
IAtomContainer |
RendererModel.getExternalSelectedPart()
Get externally selected atoms.
|
Modifier and Type | Method and Description |
---|---|
List<IGenerator<IAtomContainer>> |
AtomContainerRenderer.getGenerators()
Returns a
List of IGenerator s for this renderer. |
Modifier and Type | Method and Description |
---|---|
static Rectangle2D |
BoundsCalculator.calculateBounds(IAtomContainer atomContainer)
Calculate the bounding rectangle for an atom container.
|
Rectangle |
AtomContainerRenderer.calculateDiagramBounds(IAtomContainer atomContainer)
Given a
IChemObject , calculates the bounding rectangle in screen
space. |
Rectangle |
AtomContainerRenderer.paint(IAtomContainer atomContainer,
IDrawVisitor drawVisitor)
Paint an IChemObject.
|
void |
AtomContainerRenderer.paint(IAtomContainer atomContainer,
IDrawVisitor drawVisitor,
Rectangle2D bounds,
boolean resetCenter)
Paint a molecule (an IAtomContainer).
|
void |
RendererModel.setClipboardContent(IAtomContainer content)
Sets the atoms and bonds on the Renderer2D clipboard.
|
void |
RendererModel.setExternalSelectedPart(IAtomContainer externalSelectedPart)
Set externally selected atoms.
|
void |
AtomContainerRenderer.setScale(IAtomContainer atomContainer)
Set the scale for an IAtomContainer.
|
void |
AtomContainerRenderer.setup(IAtomContainer atomContainer,
Rectangle screen)
Setup the transformations necessary to draw this Atom Container.
|
Constructor and Description |
---|
AtomContainerRenderer(List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager)
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
|
AtomContainerRenderer(RendererModel rendererModel,
List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager) |
ChemModelRenderer(List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager)
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
|
ChemModelRenderer(List<IGenerator<IAtomContainer>> generators,
List<IGenerator<IReaction>> reactionGenerators,
IFontManager fontManager) |
MoleculeSetRenderer(List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager)
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
|
MoleculeSetRenderer(RendererModel rendererModel,
List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager) |
ReactionRenderer(List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager)
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
|
ReactionRenderer(List<IGenerator<IAtomContainer>> generators,
List<IGenerator<IReaction>> reactionGenerators,
IFontManager fontManager)
A renderer that draws
IReaction s with the passed IGenerator
for both IAtomContainer and IReaction content. |
ReactionRenderer(RendererModel rendererModel,
List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager) |
ReactionSetRenderer(List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager)
A renderer that generates diagrams using the specified
generators and manages fonts with the supplied font manager.
|
ReactionSetRenderer(List<IGenerator<IAtomContainer>> generators,
List<IGenerator<IReaction>> reactionGenerators,
IFontManager fontManager)
A renderer that generates diagrams using the specified
generators for
IAtomContainer s and IReactionSet s
and manages fonts with the supplied font manager. |
ReactionSetRenderer(RendererModel rendererModel,
List<IGenerator<IAtomContainer>> generators,
IFontManager fontManager) |
Modifier and Type | Method and Description |
---|---|
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 |
RadicalGenerator.generate(IAtomContainer container,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
LonePairGenerator.generate(IAtomContainer container,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
BasicSceneGenerator.generate(IAtomContainer ac,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
BasicGenerator.generate(IAtomContainer ac,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
BasicBondGenerator.generate(IAtomContainer container,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
BasicAtomGenerator.generate(IAtomContainer container,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
AtomNumberGenerator.generate(IAtomContainer container,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
IRenderingElement |
AtomContainerBoundsGenerator.generate(IAtomContainer container,
RendererModel model)
Converts a
IChemObject from the chemical data model into
something that can be drawn in the chemical drawing. |
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.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
IChemObjectSelection.getConnectedAtomContainer()
Make an IAtomContainer where all the bonds
only have atoms that are in the selection.
|
Modifier and Type | Method and Description |
---|---|
static IAtomContainer |
RingPartitioner.convertToAtomContainer(IRingSet ringSet)
Converts a RingSet to an AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
IRingSet |
AllRingsFinderMod.findAllRings(IAtomContainer atomContainer)
Returns a ringset containing all rings in the given AtomContainer
Calls
AllRingsFinderMod.findAllRings(org.openscience.cdk.interfaces.IAtomContainer, Integer) with max ring size argument set to null (=unlimited ring sizes) |
IRingSet |
AllRingsFinder.findAllRings(IAtomContainer atomContainer)
Returns a ringset containing all rings in the given AtomContainer
Calls
AllRingsFinder.findAllRings(IAtomContainer, Integer) with max ring size argument set to null (=unlimited ring sizes) |
IRingSet |
AllRingsFinderMod.findAllRings(IAtomContainer atomContainer,
Integer maxRingSize)
Returns a ringset containing all rings up to a provided maximum size in a given AtomContainer
|
IRingSet |
AllRingsFinder.findAllRings(IAtomContainer atomContainer,
Integer maxRingSize)
Returns a ringset containing all rings up to a provided maximum size in a given AtomContainer
|
IRingSet |
AllRingsFinderMod.findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer)
Fings the set of all rings in a molecule
Calls
AllRingsFinderMod.findAllRingsInIsolatedRingSystem(org.openscience.cdk.interfaces.IAtomContainer,Integer) with max ring size argument set to null (=unlimited ring sizes) |
IRingSet |
AllRingsFinder.findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer)
Fings the set of all rings in a molecule
Calls
AllRingsFinder.findAllRingsInIsolatedRingSystem(IAtomContainer,Integer) with max ring size argument set to null (=unlimited ring sizes) |
IRingSet |
AllRingsFinderMod.findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer,
Integer maxRingSize)
Finds the set of all rings in a molecule
|
IRingSet |
AllRingsFinder.findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer,
Integer maxRingSize)
Finds the set of all rings in a molecule
|
String |
Path.toString(IAtomContainer ac) |
Constructor and Description |
---|
SSSRFinder(IAtomContainer container)
Constructs a SSSRFinder for a specified molecule.
|
Modifier and Type | Method and Description |
---|---|
static IAtomContainer |
MoleculeSignature.fromSignatureString(String signatureString,
IChemObjectBuilder coBuilder)
Builder for molecules (rather, for atom containers) from signature
strings.
|
IAtomContainer |
MoleculeFromSignatureBuilder.getAtomContainer()
Gets the atom container.
|
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 . |
AtomSignature(int atomIndex,
IAtomContainer molecule)
Create an atom signature starting at
atomIndex . |
AtomSignature(int atomIndex,
int height,
signature.AbstractVertexSignature.InvariantType invariantType,
IAtomContainer molecule)
Create an atom signature starting at
atomIndex , with maximum
height of height , and using a particular invariant type. |
AtomSignature(int atomIndex,
int height,
IAtomContainer molecule)
Create an atom signature starting at
atomIndex and with a
maximum height of height . |
MoleculeSignature(IAtomContainer molecule)
Creates a signature that represents this molecule.
|
SignatureQuotientGraph(IAtomContainer atomContainer)
Construct a quotient graph from the symmetry classes generated from the
atom container.
|
SignatureQuotientGraph(IAtomContainer atomContainer,
int height)
Construct a quotient graph using symmetry classes defined by signatures
of height
height . |
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
AtomContainer.clone()
Clones this AtomContainer object and its content.
|
IAtomContainer |
AtomContainerSet.getAtomContainer(int number)
Returns the AtomContainer at position
number in the
container. |
IAtomContainer |
FragmentAtom.getFragment() |
Modifier and Type | Method and Description |
---|---|
Iterable<IAtomContainer> |
AtomContainerSet.atomContainers()
Get an iterator for this AtomContainerSet.
|
Iterable<IAtomContainer> |
MoleculeSet.molecules()
Returns the array of Molecules of this container.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainer.add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
MoleculeSet.addAtomContainer(IAtomContainer atomContainer)
Adds an atomContainer to this container.
|
void |
AtomContainerSet.addAtomContainer(IAtomContainer atomContainer)
Adds an atomContainer to this container.
|
void |
MoleculeSet.addAtomContainer(IAtomContainer atomContainer,
double multiplier)
Adds an atomContainer to this container with the given
multiplier.
|
void |
AtomContainerSet.addAtomContainer(IAtomContainer atomContainer,
double multiplier)
Adds an atomContainer to this container with the given
multiplier.
|
boolean |
RingSet.contains(IAtomContainer ring)
Checks for presence of a ring in this RingSet.
|
Double |
AtomContainerSet.getMultiplier(IAtomContainer container)
Returns the multiplier of the given AtomContainer.
|
void |
AtomContainer.remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
AtomContainerSet.removeAtomContainer(IAtomContainer atomContainer)
Removes an AtomContainer from this container.
|
void |
AtomContainerSet.replaceAtomContainer(int position,
IAtomContainer container)
Replace the AtomContainer at a specific position (array has to be large enough).
|
void |
FragmentAtom.setFragment(IAtomContainer fragment) |
boolean |
AtomContainerSet.setMultiplier(IAtomContainer container,
Double multiplier)
Sets the coefficient of a AtomContainer to a given value.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainerSet.sortAtomContainers(Comparator<IAtomContainer> comparator)
Sort the AtomContainers and multipliers using a provided Comparator
|
Constructor and Description |
---|
AtomContainer(IAtomContainer container)
Constructs an AtomContainer with a copy of the atoms and electronContainers
of another AtomContainer (A shallow copy, i.e., with the same objects as in
the original AtomContainer).
|
Crystal(IAtomContainer container)
Constructs a new crystal with zero length cell axis
and adds the atoms in the AtomContainer as cell content.
|
Molecule(IAtomContainer container)
Constructs a Molecule with
a shallow copy of the atoms and bonds of an AtomContainer.
|
Ring(IAtomContainer atomContainer)
Constructs a ring from the atoms in an IAtomContainer object.
|
Modifier and Type | Method and Description |
---|---|
static float |
DistanceMoment.calculate(IAtomContainer query,
IAtomContainer target)
Evaluate the 3D similarity between two molecules.
|
static float[] |
DistanceMoment.generateMoments(IAtomContainer atomContainer)
Evaluate the 12 descriptors used to characterize the 3D shape of a molecule.
|
Modifier and Type | Method and Description |
---|---|
String |
SmilesGenerator.createChiralSMILES(IAtomContainer molecule,
boolean[] doubleBondConfiguration)
Generate canonical and chiral SMILES from the
molecule . |
String |
SmilesGenerator.createSMILES(IAtomContainer molecule)
Generate canonical SMILES from the
molecule . |
String |
SmilesGenerator.createSMILES(IAtomContainer molecule,
boolean chiral,
boolean[] doubleBondConfiguration)
Generate canonical SMILES from the
molecule . |
String |
SmilesGenerator.createSMILESWithoutCheckForMultipleMolecules(IAtomContainer molecule,
boolean chiral,
boolean[] doubleBondConfiguration)
Generate canonical SMILES from the
molecule . |
boolean |
SmilesGenerator.isValidDoubleBondConfiguration(IAtomContainer container,
IBond bond)
Tells if a certain bond is center of a valid double bond configuration.
|
Modifier and Type | Method and Description |
---|---|
boolean |
SMARTSQueryTool.matches(IAtomContainer atomContainer)
Perform a SMARTS match and check whether the query is present in the target molecule.
|
boolean |
SMARTSQueryTool.matches(IAtomContainer atomContainer,
boolean forceInitialization)
Perform a SMARTS match and check whether the query is present in the target molecule.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
Isomorphism.getProductMolecule()
Returns modified target molecule on which mapping was
performed.
|
IAtomContainer |
Isomorphism.getReactantMolecule()
Returns modified query molecule on which mapping was
performed.
|
Modifier and Type | Method and Description |
---|---|
void |
Isomorphism.init(IAtomContainer reactant,
IAtomContainer product,
boolean removeHydrogen,
boolean cleanAndConfigureMolecule)
initialize query and target molecules.
|
void |
Isomorphism.init(IQueryAtomContainer reactant,
IAtomContainer product) |
static Map<IBond,IBond> |
Isomorphism.makeBondMapOfAtomMap(IAtomContainer ac1,
IAtomContainer ac2,
Map<IAtom,IAtom> mapping)
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)
Returns bond maps between source and target molecules based on the atoms
|
Modifier and Type | Method and Description |
---|---|
static boolean |
DefaultMatcher.isAtomMatch(AtomMatcher atomMatcher1,
AtomMatcher atomMatcher2,
IAtomContainer ac2,
IBond bondA2,
boolean shouldMatchBonds) |
static boolean |
DefaultMatcher.isBondMatch(BondMatcher bondMatcher,
IAtomContainer ac2,
IBond bondA2,
boolean shouldMatchBonds) |
boolean |
DefaultRGraphAtomMatcher.matches(IAtomContainer targetContainer,
IAtom targetAtom) |
boolean |
DefaultMCSPlusAtomMatcher.matches(IAtomContainer targetContainer,
IAtom targetAtom) |
boolean |
AtomMatcher.matches(IAtomContainer container,
IAtom atom) |
boolean |
DefaultBondMatcher.matches(IAtomContainer targetContainer,
IBond targetBond) |
boolean |
BondMatcher.matches(IAtomContainer container,
IBond atom) |
Constructor and Description |
---|
DefaultBondMatcher(IAtomContainer queryMol,
IBond queryBond,
boolean shouldMatchBonds)
Constructor
|
DefaultMCSPlusAtomMatcher(IAtomContainer queryContainer,
IAtom atom,
boolean shouldMatchBonds)
Constructor
|
DefaultMCSPlusAtomMatcher(IAtomContainer queryContainer,
IAtom template,
int blockedPositions,
boolean shouldMatchBonds)
Constructor
|
DefaultRGraphAtomMatcher(IAtomContainer queryContainer,
IAtom atom,
boolean shouldMatchBonds)
Constructor
|
DefaultRGraphAtomMatcher(IAtomContainer queryContainer,
IAtom template,
int blockedPositions,
boolean shouldMatchBonds)
Constructor
|
DefaultVFAtomMatcher(IAtomContainer queryContainer,
IAtom atom,
boolean shouldMatchBonds)
Constructor
|
DefaultVFAtomMatcher(IAtomContainer queryContainer,
IAtom template,
int blockedPositions,
boolean shouldMatchBonds)
Constructor
|
DefaultVFBondMatcher(IAtomContainer queryMol,
IBond queryBond,
boolean shouldMatchBonds)
Constructor
|
Constructor and Description |
---|
McGregor(IAtomContainer source,
IAtomContainer target,
List<List<Integer>> _mappings,
boolean shouldMatchBonds)
Constructor for the McGregor algorithm.
|
McGregor(IQueryAtomContainer source,
IAtomContainer target,
List<List<Integer>> _mappings)
Constructor for the McGregor algorithm.
|
Modifier and Type | Method and Description |
---|---|
void |
MCSPlusHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
Constructor and Description |
---|
GenerateCompatibilityGraph(IAtomContainer source,
IAtomContainer target,
boolean shouldMatchBonds)
Generates a compatibility graph between two molecules
|
Modifier and Type | Method and Description |
---|---|
static IAtomContainer |
CDKRMapHandler.getSource()
Returns source molecule
|
static IAtomContainer |
CDKRMapHandler.getTarget()
Returns target molecule
|
static IAtomContainer |
CDKMCS.project(List<CDKRMap> rMapList,
IAtomContainer graph,
int key)
Projects atom list of CDKRMap on atom molecule.
|
Modifier and Type | Method and Description |
---|---|
static List<IAtomContainer> |
CDKMCS.getOverlaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Returns all the maximal common substructure between 2 atom containers.
|
static ArrayList<IAtomContainer> |
CDKMCS.projectList(List<List<CDKRMap>> rMapsList,
IAtomContainer graph,
int key)
Projects atom list of RMapsList on atom molecule.
|
Modifier and Type | Method and Description |
---|---|
static CDKRGraph |
CDKMCS.buildRGraph(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Builds the CDKRGraph ( resolution graph ), from two atomContainer
(description of the two molecules to compare)
This is the interface point between the CDK model and
the generic MCSS algorithm based on the RGRaph.
|
void |
CDKRMapHandler.calculateIsomorphs(IAtomContainer Molecule1,
IAtomContainer Molecule2,
boolean shouldMatchBonds)
This function calculates only one solution (exact) because we are looking at the
molecules which are exactly same in terms of the bonds and atoms determined by the
Fingerprint
|
void |
CDKRMapHandler.calculateOverlapsAndReduce(IAtomContainer Molecule1,
IAtomContainer Molecule2,
boolean shouldMatchBonds)
This function calculates all the possible combinations of MCS
|
void |
CDKRMapHandler.calculateOverlapsAndReduceExactMatch(IAtomContainer Molecule1,
IAtomContainer Molecule2,
boolean shouldMatchBonds)
This function calculates only one solution (exact) because we are looking at the
molecules which are exactly same in terms of the bonds and atoms determined by the
Fingerprint
|
void |
CDKRMapHandler.calculateSubGraphs(IAtomContainer Molecule1,
IAtomContainer Molecule2,
boolean shouldMatchBonds)
This function calculates only one solution (exact) because we are looking at the
molecules which are exactly same in terms of the bonds and atoms determined by the
Fingerprint
|
static List<CDKRMap> |
CDKMCS.checkSingleAtomCases(IAtomContainer sourceGraph,
IAtomContainer targetGraph)
Checks for single atom cases before doing subgraph/isomorphism search
|
static BitSet |
CDKMCS.getBitSet(IAtomContainer atomContainer)
Transforms an AtomContainer into atom BitSet (which's size = number of bondA1
in the atomContainer, all the bit are set to true).
|
static List<CDKRMap> |
CDKMCS.getIsomorphAtomsMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Returns the first isomorph 'atom mapping' found for targetGraph in sourceGraph.
|
static List<CDKRMap> |
CDKMCS.getIsomorphMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Returns the first isomorph mapping found or null.
|
static List<List<CDKRMap>> |
CDKMCS.getIsomorphMaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Returns all the isomorph 'mappings' found between two
atom containers.
|
static List<IAtomContainer> |
CDKMCS.getOverlaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Returns all the maximal common substructure between 2 atom containers.
|
static List<CDKRMap> |
CDKMCS.getSubgraphAtomsMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Returns the first subgraph 'atom mapping' found for targetGraph in sourceGraph.
|
static List<List<CDKRMap>> |
CDKMCS.getSubgraphAtomsMaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Returns all subgraph 'atom mappings' found for targetGraph in sourceGraph.
|
static List<CDKRMap> |
CDKMCS.getSubgraphMap(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Returns the first subgraph 'bondA1 mapping' found for targetGraph in sourceGraph.
|
static List<List<CDKRMap>> |
CDKMCS.getSubgraphMaps(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Returns all the subgraph 'bondA1 mappings' found for targetGraph in sourceGraph.
|
static boolean |
CDKMCS.isIsomorph(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Tests if sourceGraph and targetGraph are isomorph.
|
static boolean |
CDKMCS.isSubgraph(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
boolean shouldMatchBonds)
Tests if targetGraph atom subgraph of sourceGraph.
|
static List<CDKRMap> |
CDKMCS.makeAtomsMapOfBondsMap(List<CDKRMap> list,
IAtomContainer sourceGraph,
IAtomContainer targetGraph)
This makes atom map of matching atoms out of atom map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
|
static List<List<CDKRMap>> |
CDKMCS.makeAtomsMapsOfBondsMaps(List<List<CDKRMap>> list,
IAtomContainer sourceGraph,
IAtomContainer targetGraph)
This makes maps of matching atoms out of atom maps of matching bonds as produced by the get(Subgraph|Ismorphism)Maps methods.
|
static IAtomContainer |
CDKMCS.project(List<CDKRMap> rMapList,
IAtomContainer graph,
int key)
Projects atom list of CDKRMap on atom molecule.
|
static ArrayList<IAtomContainer> |
CDKMCS.projectList(List<List<CDKRMap>> rMapsList,
IAtomContainer graph,
int key)
Projects atom list of RMapsList on atom molecule.
|
static List<List<CDKRMap>> |
CDKMCS.search(IAtomContainer sourceGraph,
IAtomContainer targetGraph,
BitSet sourceBitSet,
BitSet targetBitSet,
boolean findAllStructure,
boolean findAllMap,
boolean shouldMatchBonds)
General Rgraph parsing method (usually not used directly)
This method is the entry point for the recursive search
adapted to the atom container input.
|
void |
CDKSubGraphHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
void |
CDKMCSHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
static void |
CDKRMapHandler.setSource(IAtomContainer aSource)
Set source molecule
|
static void |
CDKRMapHandler.setTarget(IAtomContainer aTarget)
Set target molecule
|
Modifier and Type | Method and Description |
---|---|
void |
SingleMappingHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
Modifier and Type | Method and Description |
---|---|
void |
VFlibTurboHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
void |
VFlibSubStructureHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
void |
VFlibMCSHandler.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
Constructor and Description |
---|
TargetProperties(IAtomContainer container) |
Modifier and Type | Method and Description |
---|---|
int |
IMapper.countMaps(IAtomContainer target)
Returns solution map count.
|
Map<INode,IAtom> |
IMapper.getFirstMap(IAtomContainer target)
Returns first solution map.
|
List<Map<INode,IAtom>> |
IMapper.getMaps(IAtomContainer target)
Returns all solution map.
|
boolean |
IMapper.hasMap(IAtomContainer molecule)
checks if a map exits for a molecule.
|
Modifier and Type | Method and Description |
---|---|
int |
VFMCSMapper.countMaps(IAtomContainer target)
Returns solution map count.
|
int |
VFMapper.countMaps(IAtomContainer target)
Returns solution map count.
|
Map<INode,IAtom> |
VFMCSMapper.getFirstMap(IAtomContainer target)
Returns first solution map.
|
Map<INode,IAtom> |
VFMapper.getFirstMap(IAtomContainer target)
Returns first solution map.
|
List<Map<INode,IAtom>> |
VFMCSMapper.getMaps(IAtomContainer target)
Returns all solution map.
|
List<Map<INode,IAtom>> |
VFMapper.getMaps(IAtomContainer target)
Returns all solution map.
|
boolean |
VFMCSMapper.hasMap(IAtomContainer targetMolecule)
checks if a map exits for a molecule.
|
boolean |
VFMapper.hasMap(IAtomContainer targetMolecule)
checks if a map exits for a molecule.
|
Constructor and Description |
---|
VFMapper(IAtomContainer queryMolecule,
boolean bondMatcher) |
VFMCSMapper(IAtomContainer queryMolecule,
boolean bondMatcher) |
Constructor and Description |
---|
QueryCompiler(IAtomContainer molecule,
boolean shouldMatchBonds)
Construct query object from the molecule
|
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)
This class has all the three chemical filters supported by the SMSD.
|
Modifier and Type | Method and Description |
---|---|
abstract IAtomContainer |
AbstractMCS.getProductMolecule()
Returns modified target molecule on which mapping was
performed.
|
abstract IAtomContainer |
AbstractMCS.getReactantMolecule()
Returns modified query molecule on which mapping was
performed.
|
Modifier and Type | Method and Description |
---|---|
abstract void |
AbstractMCS.init(IAtomContainer source,
IAtomContainer target,
boolean removeHydrogen,
boolean cleanAndConfigureMolecule)
initialize query and target molecules.
|
abstract void |
AbstractMCS.init(IQueryAtomContainer source,
IAtomContainer target)
initialize query and target molecules.
|
void |
IMCSBase.set(IQueryAtomContainer source,
IAtomContainer target)
Initialise the query and target molecule.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
MoleculeSignatureLabellingAdaptor.getCanonicalMolecule(IAtomContainer container) |
IAtomContainer |
ICanonicalMoleculeLabeller.getCanonicalMolecule(IAtomContainer container) |
IAtomContainer |
CanonicalLabellingAdaptor.getCanonicalMolecule(IAtomContainer container) |
IAtomContainer |
AtomContainerAtomPermutor.next() |
static IAtomContainer |
AtomContainerAtomPermutor.permute(int[] p,
IAtomContainer atomContainer) |
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
MoleculeSignatureLabellingAdaptor.getCanonicalMolecule(IAtomContainer container) |
IAtomContainer |
ICanonicalMoleculeLabeller.getCanonicalMolecule(IAtomContainer container) |
IAtomContainer |
CanonicalLabellingAdaptor.getCanonicalMolecule(IAtomContainer container) |
int[] |
MoleculeSignatureLabellingAdaptor.getCanonicalPermutation(IAtomContainer container) |
int[] |
ICanonicalMoleculeLabeller.getCanonicalPermutation(IAtomContainer container) |
int[] |
CanonicalLabellingAdaptor.getCanonicalPermutation(IAtomContainer container) |
static IAtomContainer |
AtomContainerAtomPermutor.permute(int[] p,
IAtomContainer atomContainer) |
String |
AtomContainerPrinter.toString(IAtomContainer atomContainer) |
Constructor and Description |
---|
AtomContainerAtomPermutor(IAtomContainer atomContainer) |
Modifier and Type | Method and Description |
---|---|
void |
RingFilter.filterAtoms(IAtomContainer molecule,
Collection<IAtom> atoms) |
Collection<List<IAtom>> |
RingFinder.findRings(IAtomContainer molecule)
Returns Collection of atoms in Rings based on Hanser Ring Finding method
|
Collection<List<IAtom>> |
HanserRingFinder.findRings(IAtomContainer molecule)
Returns a collection of rings.
|
IRingSet |
RingFinder.getRingSet(IAtomContainer molecule)
Returns CDK object Ring set based on Hanser Ring Finding method
|
IRingSet |
HanserRingFinder.getRingSet(IAtomContainer molecule)
Returns Ring set based on Hanser Ring Finding method
|
Constructor and Description |
---|
PathGraph(IAtomContainer molecule) |
Modifier and Type | Method and Description |
---|---|
static IAtomContainer |
MoleculeSanityCheck.checkAndCleanMolecule(IAtomContainer molecule)
Modules for cleaning a molecule
|
static IAtomContainer |
ExtAtomContainerManipulator.convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
|
IAtomContainer |
MolHandler.getMolecule()
Returns the modified container
|
static IAtomContainer |
ExtAtomContainerManipulator.makeDeepCopy(IAtomContainer container)
Retrurns deep copy of the molecule
|
Modifier and Type | Method and Description |
---|---|
static void |
ExtAtomContainerManipulator.aromatizeMolecule(IAtomContainer mol)
This function finds rings and uses aromaticity detection code to
aromatize the molecule.
|
static IAtomContainer |
MoleculeSanityCheck.checkAndCleanMolecule(IAtomContainer molecule)
Modules for cleaning a molecule
|
static void |
MoleculeSanityCheck.configure(IAtomContainer mol)
Fixes Aromaticity of the molecule
i.e.
|
static IAtomContainer |
ExtAtomContainerManipulator.convertExplicitToImplicitHydrogens(IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
|
static int |
ExtAtomContainerManipulator.getExplicitHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
Returns The number of explicit hydrogens for a given IAtom.
|
static int |
ExtAtomContainerManipulator.getHydrogenCount(IAtomContainer atomContainer,
IAtom atom)
The summed implicit + explicit hydrogens of the given IAtom.
|
static IAtomContainer |
ExtAtomContainerManipulator.makeDeepCopy(IAtomContainer container)
Retrurns deep copy of the molecule
|
static void |
ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Convenience method to perceive atom types for all
IAtom s in the
IAtomContainer , using the CDKAtomTypeMatcher . |
static IMolecule |
ExtAtomContainerManipulator.removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer atomContainer)
Returns IAtomContainer without Hydrogen.
|
Constructor and Description |
---|
MolHandler(IAtomContainer container,
boolean removeHydrogen,
boolean cleanMolecule)
Creates a new instance of MolHandler
|
Modifier and Type | Method and Description |
---|---|
void |
RandomGenerator.mutate(IAtomContainer ac)
Randomly chooses four atoms and alters the bonding
pattern between them according to rules described
in "Faulon, JCICS 1996, 36, 731".
|
void |
SingleStructureRandomGenerator.setAtomContainer(IAtomContainer ac)
Sets the AtomContainer attribute of the SingleStructureRandomGenerator object.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
PartialFilledStructureMerger.generate(IAtomContainerSet atomContainers)
Randomly generates a single, connected, correctly bonded structure from
a number of fragments.
|
Modifier and Type | Method and Description |
---|---|
List<IAtomContainer> |
CrossoverMachine.doCrossover(IAtomContainer dad,
IAtomContainer mom)
Performs the n point crossover of two
IAtomContainer . |
Modifier and Type | Method and Description |
---|---|
List<IAtomContainer> |
CrossoverMachine.doCrossover(IAtomContainer dad,
IAtomContainer mom)
Performs the n point crossover of two
IAtomContainer . |
Constructor and Description |
---|
ChemGraph(IAtomContainer chrom) |
Modifier and Type | Method and Description |
---|---|
List<IAtomContainer> |
InChITautomerGenerator.getTautomers(IAtomContainer molecule)
Public method to get tautomers for an input molecule, based on the InChI which will be calculated by jniinchi.
|
List<IAtomContainer> |
InChITautomerGenerator.getTautomers(IAtomContainer inputMolecule,
String inchi)
Overloaded
InChITautomerGenerator.getTautomers(IAtomContainer) to get tautomers for an input molecule with the InChI already
provided as input argument. |
Modifier and Type | Method and Description |
---|---|
List<IAtomContainer> |
InChITautomerGenerator.getTautomers(IAtomContainer molecule)
Public method to get tautomers for an input molecule, based on the InChI which will be calculated by jniinchi.
|
List<IAtomContainer> |
InChITautomerGenerator.getTautomers(IAtomContainer inputMolecule,
String inchi)
Overloaded
InChITautomerGenerator.getTautomers(IAtomContainer) to get tautomers for an input molecule with the InChI already
provided as input argument. |
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
StructureResonanceGenerator.getContainer(IMolecule molecule,
IAtom atom)
Get the container which the atom is found on resonance from a IMolecule.
|
IAtomContainer |
StructureResonanceGenerator.getContainer(IMolecule molecule,
IBond bond)
Get the container which the bond is found on resonance from a IMolecule.
|
Modifier and Type | Method and Description |
---|---|
void |
CDKHydrogenAdder.addImplicitHydrogens(IAtomContainer container)
Sets implicit hydrogen counts for all atoms in the given IAtomContainer.
|
void |
CDKHydrogenAdder.addImplicitHydrogens(IAtomContainer container,
IAtom atom)
Sets the implicit hydrogen count for the indicated IAtom in the given IAtomContainer.
|
boolean |
SmilesValencyChecker.allSaturated(IAtomContainer ac) |
boolean |
SaturationChecker.allSaturated(IAtomContainer ac) |
boolean |
LonePairElectronChecker.allSaturated(IAtomContainer ac)
Determines of all atoms on the AtomContainer have
the right number the lone pair electrons.
|
int |
SmilesValencyChecker.calculateNumberOfImplicitHydrogens(IAtom atom,
IAtomContainer container) |
int |
SaturationChecker.calculateNumberOfImplicitHydrogens(IAtom atom,
IAtomContainer container)
Calculate the number of missing hydrogens by substracting 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.
|
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)
|
static double[] |
IonizationPotentialTool.getQSARs(IAtomContainer container,
IAtom atom)
Get the results of 7 qsar descriptors been applied.
|
static double[] |
IonizationPotentialTool.getQSARs(IAtomContainer container,
IBond bond)
Get the results of 7 qsar descriptors been applied.
|
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 |
SmilesValencyChecker.isSaturated(IAtomContainer container)
Determines of all atoms on the AtomContainer are saturated.
|
boolean |
SaturationChecker.isSaturated(IAtomContainer container)
Determines of all atoms on the AtomContainer are saturated.
|
boolean |
LonePairElectronChecker.isSaturated(IAtomContainer container)
Determines of all atoms on the AtomContainer have the
right number the lone pair electrons.
|
boolean |
IValencyChecker.isSaturated(IAtomContainer ac) |
boolean |
CDKValencyChecker.isSaturated(IAtomContainer atomContainer) |
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 |
LonePairElectronChecker.isSaturated(IAtom atom,
IAtomContainer ac)
Checks if an Atom is saturated their lone pair electrons
by comparing it with known AtomTypes.
|
boolean |
IValencyChecker.isSaturated(IAtom atom,
IAtomContainer container) |
boolean |
CDKValencyChecker.isSaturated(IAtom atom,
IAtomContainer container) |
boolean |
SmilesValencyChecker.isSaturated(IBond bond,
IAtomContainer atomContainer)
Returns whether a bond is saturated.
|
boolean |
SaturationChecker.isSaturated(IBond bond,
IAtomContainer atomContainer)
Returns whether a bond is saturated.
|
boolean |
SmilesValencyChecker.isUnsaturated(IBond bond,
IAtomContainer atomContainer)
Returns whether a bond is unsaturated.
|
boolean |
SaturationChecker.isUnsaturated(IBond bond,
IAtomContainer atomContainer)
Returns whether a bond is unsaturated.
|
void |
SaturationChecker.newSaturate(IAtomContainer atomContainer)
Saturates a molecule by setting appropriate bond orders.
|
boolean |
SaturationChecker.newSaturate(IBond[] bonds,
IAtomContainer atomContainer)
Saturates a set of Bonds in an AtomContainer.
|
boolean |
SaturationChecker.newSaturate(IBond bond,
IAtomContainer atomContainer)
Saturate atom by adjusting its bond orders.
|
static double |
IonizationPotentialTool.predictIP(IAtomContainer container,
IAtom atom)
Method which is predict the Ionization Potential from given atom.
|
static double |
IonizationPotentialTool.predictIP(IAtomContainer container,
IBond bond)
Method which is predict the Ionization Potential from given atom.
|
void |
SmilesValencyChecker.saturate(IAtomContainer atomContainer)
Saturates a molecule by setting appropriate bond orders.
|
void |
SaturationChecker.saturate(IAtomContainer atomContainer)
The method is known to fail for certain compounds.
|
void |
LonePairElectronChecker.saturate(IAtomContainer atomContainer)
Saturates a molecule by setting appropriate number lone pair electrons.
|
void |
IDeduceBondOrderTool.saturate(IAtomContainer ac) |
void |
LonePairElectronChecker.saturate(IAtom atom,
IAtomContainer ac)
Saturates an IAtom by adding the appropriate number lone pairs.
|
boolean |
SmilesValencyChecker.saturate(IBond[] bonds,
IAtomContainer atomContainer)
Saturates a set of Bonds in an AtomContainer.
|
boolean |
SmilesValencyChecker.saturateByIncreasingBondOrder(IBond bond,
IAtomContainer atomContainer)
Tries to saturate a bond by increasing its bond orders by 1.0.
|
void |
SaturationChecker.saturateRingSystems(IAtomContainer atomContainer) |
void |
SaturationChecker.unsaturate(IAtomContainer atomContainer)
Resets the bond orders of all atoms to 1.0.
|
void |
SaturationChecker.unsaturateBonds(IAtomContainer container)
Resets the bond order of the Bond to 1.0.
|
Modifier and Type | Method and Description |
---|---|
static IAtomContainer |
AtomContainerManipulator.createAllCarbonAllSingleNonAromaticBondAtomContainer(IAtomContainer atomContainer)
Generates a cloned atomcontainer with all atoms being carbon, all bonds being single non-aromatic
|
static IAtomContainer |
ChemModelManipulator.createNewMolecule(IChemModel chemModel)
Adds a new Molecule to the MoleculeSet inside a given ChemModel.
|
static IAtomContainer |
AtomContainerManipulator.extractSubstructure(IAtomContainer atomContainer,
int... atomIndices)
Extract a substructure from an atom container, in the form of a new
cloned atom container with only the atoms with indices in atomIndices and
bonds that connect these atoms.
|
static IAtomContainer |
RingSetManipulator.getAllInOneContainer(IRingSet ringSet)
Puts all rings of a ringSet in a single atomContainer
|
static IAtomContainer |
MolecularFormulaManipulator.getAtomContainer(IMolecularFormula formula)
Method that actually does the work of convert the IMolecularFormula
to IAtomContainer.
|
static IAtomContainer |
MolecularFormulaManipulator.getAtomContainer(IMolecularFormula formula,
IAtomContainer atomContainer)
Method that actually does the work of convert the IMolecularFormula
to IAtomContainer given a IAtomContainer.
|
static IAtomContainer |
AtomContainerManipulator.getIntersection(IAtomContainer container1,
IAtomContainer container2)
Compares this AtomContainer with another given AtomContainer and returns
the Intersection between them.
|
static IAtomContainer |
AtomContainerSetManipulator.getRelevantAtomContainer(IAtomContainerSet containerSet,
IAtom atom) |
static IAtomContainer |
AtomContainerSetManipulator.getRelevantAtomContainer(IAtomContainerSet containerSet,
IBond bond) |
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 |
ChemModelManipulator.getRelevantAtomContainer(IChemModel chemModel,
IBond bond)
Retrieves the first IAtomContainer containing a given IBond from an
IChemModel.
|
static IAtomContainer |
MoleculeSetManipulator.getRelevantAtomContainer(IMoleculeSet moleculeSet,
IAtom atom) |
static IAtomContainer |
MoleculeSetManipulator.getRelevantAtomContainer(IMoleculeSet moleculeSet,
IBond bond) |
static IAtomContainer |
ReactionManipulator.getRelevantAtomContainer(IReaction reaction,
IAtom atom) |
static IAtomContainer |
ReactionManipulator.getRelevantAtomContainer(IReaction reaction,
IBond bond) |
static IAtomContainer |
ReactionSetManipulator.getRelevantAtomContainer(IReactionSet set,
IAtom atom) |
static IAtomContainer |
ReactionSetManipulator.getRelevantAtomContainer(IReactionSet set,
IBond bond) |
static IAtomContainer |
AtomContainerManipulator.removeHydrogens(IAtomContainer atomContainer)
Produces an AtomContainer without explicit Hs but with H count from one with Hs.
|
static IAtomContainer |
AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded(IAtomContainer ac)
Produces an AtomContainer without explicit Hs but with H count from one with Hs.
|
Modifier and Type | Method and Description |
---|---|
static List<IAtomContainer> |
AtomContainerSetManipulator.getAllAtomContainers(IAtomContainerSet set)
Returns all the AtomContainer's of a MoleculeSet.
|
static List<IAtomContainer> |
ChemFileManipulator.getAllAtomContainers(IChemFile file)
Returns all the AtomContainer's of a ChemFile.
|
static List<IAtomContainer> |
ChemModelManipulator.getAllAtomContainers(IChemModel chemModel)
Returns all the AtomContainer's of a ChemModel.
|
static List<IAtomContainer> |
ChemSequenceManipulator.getAllAtomContainers(IChemSequence sequence)
Returns all the AtomContainer's of a ChemSequence.
|
static List<IAtomContainer> |
MoleculeSetManipulator.getAllAtomContainers(IMoleculeSet set)
Returns all the AtomContainer's of a MoleculeSet.
|
static List<IAtomContainer> |
ReactionManipulator.getAllAtomContainers(IReaction reaction)
Returns all the AtomContainer's of a Reaction.
|
static List<IAtomContainer> |
ReactionSetManipulator.getAllAtomContainers(IReactionSet set)
Returns all the AtomContainer's of a Reaction.
|
static List<IAtomContainer> |
RingSetManipulator.getAllAtomContainers(IRingSet set)
Returns all the AtomContainer's in a RingSet.
|
Modifier and Type | Method and Description |
---|---|
static void |
AtomContainerManipulator.clearAtomConfigurations(IAtomContainer container)
This method will reset all atom configuration to UNSET.
|
int |
AtomContainerComparatorBy2DCenter.compare(IAtomContainer a,
IAtomContainer b)
Compare two AtomContainers based on their 2D position.
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int |
AtomContainerComparator.compare(IAtomContainer o1,
IAtomContainer o2) |
static void |
AtomContainerManipulator.convertImplicitToExplicitHydrogens(IAtomContainer atomContainer)
Adds explicit hydrogens (without coordinates) to the IAtomContainer,
equaling the number of set implicit hydrogens.
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static int |
AtomContainerManipulator.countExplicitHydrogens(IAtomContainer atomContainer,
IAtom atom)
Count explicit hydrogens.
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static int |
AtomContainerManipulator.countHydrogens(IAtomContainer atomContainer,
IAtom atom) |
static IAtomContainer |
AtomContainerManipulator.createAllCarbonAllSingleNonAromaticBondAtomContainer(IAtomContainer atomContainer)
Generates a cloned atomcontainer with all atoms being carbon, all bonds being single non-aromatic
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static IAtomContainer |
AtomContainerManipulator.extractSubstructure(IAtomContainer atomContainer,
int... atomIndices)
Extract a substructure from an atom container, in the form of a new
cloned atom container with only the atoms with indices in atomIndices and
bonds that connect these atoms.
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static List<String> |
AtomContainerManipulator.getAllIDs(IAtomContainer mol) |
static IAtom[] |
AtomContainerManipulator.getAtomArray(IAtomContainer container)
Constructs an array of Atom objects from an AtomContainer.
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static IAtom |
AtomContainerManipulator.getAtomById(IAtomContainer ac,
String id)
Returna an atom in an atomcontainer identified by id
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static IAtomContainer |
MolecularFormulaManipulator.getAtomContainer(IMolecularFormula formula,
IAtomContainer atomContainer)
Method that actually does the work of convert the IMolecularFormula
to IAtomContainer given a IAtomContainer.
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static IAtomParity |
AtomContainerManipulator.getAtomParity(IAtomContainer container,
IAtom atom)
Helper methods that works through the stereo elements of the given atom container
and returns if the atom parity for the given atom, if one is defined.
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static IBond[] |
AtomContainerManipulator.getBondArray(IAtomContainer container)
Constructs an array of Bond objects from an AtomContainer.
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static double |
AtomContainerManipulator.getBondOrderSum(IAtomContainer container,
IAtom atom)
Returns the sum of the bond order equivalents for a given IAtom.
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static IElectronContainer[] |
AtomContainerManipulator.getElectronContainerArray(IAtomContainer container)
Constructs an array of Bond objects from an AtomContainer.
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static List<IAtom> |
AtomContainerManipulator.getHeavyAtoms(IAtomContainer container)
Returns a set of nodes excluding all the hydrogens.
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static IAtomContainer |
AtomContainerManipulator.getIntersection(IAtomContainer container1,
IAtomContainer container2)
Compares this AtomContainer with another given AtomContainer and returns
the Intersection between them.
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static IBond.Order |
AtomContainerManipulator.getMaximumBondOrder(IAtomContainer container) |
static IMolecularFormula |
MolecularFormulaManipulator.getMolecularFormula(IAtomContainer atomContainer)
Method that actually does the work of convert the atomContainer
to IMolecularFormula.
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static IMolecularFormula |
MolecularFormulaManipulator.getMolecularFormula(IAtomContainer atomContainer,
IMolecularFormula formula)
Method that actually does the work of convert the atomContainer
to IMolecularFormula given a IMolecularFormula.
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static double |
AtomContainerManipulator.getNaturalExactMass(IAtomContainer atomContainer)
Returns the molecular mass of the IAtomContainer.
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static IReactionSet |
ReactionSetManipulator.getRelevantReactions(IReactionSet reactSet,
IAtomContainer molecule)
Get all Reactions object containing a Molecule from a set of Reactions.
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static IReactionSet |
ReactionSetManipulator.getRelevantReactionsAsProduct(IReactionSet reactSet,
IAtomContainer molecule)
Get all Reactions object containing a Molecule as a Product from a set of
Reactions.
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static IReactionSet |
ReactionSetManipulator.getRelevantReactionsAsReactant(IReactionSet reactSet,
IAtomContainer molecule)
Get all Reactions object containing a Molecule as a Reactant from a set
of Reactions.
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static int |
AtomContainerManipulator.getSingleBondEquivalentSum(IAtomContainer container)
Returns the sum of bond orders, where a single bond counts as one
single bond equivalent, a double as two, etc.
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static double |
AtomContainerManipulator.getTotalCharge(IAtomContainer atomContainer)
Get the summed charge of all atoms in an AtomContainer
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static double |
AtomContainerManipulator.getTotalExactMass(IAtomContainer atomContainer)
Get the summed exact mass of all atoms in an AtomContainer.
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static int |
AtomContainerManipulator.getTotalFormalCharge(IAtomContainer atomContainer)
Get the total formal charge on a molecule.
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static int |
AtomContainerManipulator.getTotalHydrogenCount(IAtomContainer atomContainer)
Count the total number of hydrogens (implicit and explicit).
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static double |
AtomContainerManipulator.getTotalNaturalAbundance(IAtomContainer atomContainer)
Get the summed natural abundance of all atoms in an AtomContainer
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static int |
AtomContainerManipulator.getTotalNegativeFormalCharge(IAtomContainer atomContainer)
Get the total formal negative charge on a molecule.
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static int |
AtomContainerManipulator.getTotalPositiveFormalCharge(IAtomContainer atomContainer)
Get the total positive formal charge on a molecule.
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static IChemModel |
ChemModelManipulator.newChemModel(IAtomContainer atomContainer)
Create a new ChemModel containing an IAtomContainer.
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static void |
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(IAtomContainer container)
Convenience method to perceive atom types for all
IAtom s in the
IAtomContainer , using the CDKAtomTypeMatcher . |
static void |
AtomContainerManipulator.percieveAtomTypesAndConfigureUnsetProperties(IAtomContainer container)
Convenience method to perceive atom types for all
IAtom s in the
IAtomContainer , using the CDKAtomTypeMatcher . |
static IAtomContainer |
AtomContainerManipulator.removeHydrogens(IAtomContainer atomContainer)
Produces an AtomContainer without explicit Hs but with H count from one with Hs.
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static IAtomContainer |
AtomContainerManipulator.removeHydrogensPreserveMultiplyBonded(IAtomContainer ac)
Produces an AtomContainer without explicit Hs but with H count from one with Hs.
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static boolean |
AtomContainerManipulator.replaceAtomByAtom(IAtomContainer container,
IAtom atom,
IAtom newAtom) |
static void |
AtomContainerManipulator.setAtomProperties(IAtomContainer container,
Object propKey,
Object propVal)
Sets a property on all
Atom s in the given container. |
static void |
AtomContainerManipulator.unregisterAtomListeners(IAtomContainer container)
A method to remove AtomListeners.
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static void |
AtomContainerManipulator.unregisterElectronContainerListeners(IAtomContainer container)
A method to remove ElectronContainerListeners.
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Modifier and Type | Method and Description |
---|---|
ValidationReport |
ValidatorEngine.validateAtomContainer(IAtomContainer subject) |
ValidationReport |
IValidator.validateAtomContainer(IAtomContainer subject) |
ValidationReport |
AbstractValidator.validateAtomContainer(IAtomContainer subject) |