public class BondChangeCalculator extends AbstractChangeCalculator implements IChangeCalculator
Constructor and Description |
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BondChangeCalculator(org.openscience.cdk.interfaces.IReaction reaction,
boolean generate2D,
boolean generate3D) |
Modifier and Type | Method and Description |
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java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> |
getAtomAtomMappings() |
java.util.List<BondChange> |
getBondChangeList() |
java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> |
getBondCleavedReactant() |
java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> |
getBondFormedProduct() |
java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> |
getBondOrderProduct() |
java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> |
getBondOrderReactant() |
java.lang.Iterable<AtomStereoChangeInformation> |
getConformationChangeList() |
BEMatrix |
getEductBEMatrix() |
int |
getEnergyDelta() |
IPatternFingerprinter |
getFormedCleavedWFingerprint() |
AtomAtomMappingContainer |
getMappingContainer() |
java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> |
getMappingMap() |
java.util.Map<java.lang.String,java.util.Collection<java.lang.String>> |
getMoleculeMoleculeTransformationPairs() |
IPatternFingerprinter |
getOrderChangesWFingerprint() |
BEMatrix |
getProductBEMatrix() |
org.openscience.cdk.interfaces.IReaction |
getReaction() |
java.util.Map<java.lang.Integer,IPatternFingerprinter> |
getReactionCenterFormedCleavedFingerprint() |
java.util.Collection<ReactionCenterFragment> |
getReactionCenterFragmentList() |
java.util.Map<java.lang.Integer,IPatternFingerprinter> |
getReactionCenterOrderChangeFingerprint() |
java.util.Collection<org.openscience.cdk.interfaces.IAtom> |
getReactionCenterSet() |
java.util.Map<java.lang.Integer,IPatternFingerprinter> |
getReactionCenterStereoChangeFingerprint() |
IPatternFingerprinter |
getReactionCenterWFingerprint()
Return Reaction center Fingerprint
|
java.util.Collection<MoleculeMoleculePair> |
getReactionCentreTransformationPairs()
Return the list of Molecule Molecule Transformation List
|
org.openscience.cdk.interfaces.IReaction |
getReactionWithCompressUnChangedHydrogens() |
RMatrix |
getRMatrix() |
java.util.Map<org.openscience.cdk.interfaces.IAtom,java.lang.String> |
getStereoCenterAtomsProduct() |
java.util.Map<org.openscience.cdk.interfaces.IAtom,java.lang.String> |
getStereoCenterAtomsReactant() |
java.util.List<AtomStereoChangeInformation> |
getStereoChangeList() |
IPatternFingerprinter |
getStereoChangesWFingerprint() |
int |
getTotalBondBreakingEnergy() |
int |
getTotalSmallestFragmentSize() |
boolean |
hasRMatrix() |
void |
printBMatrix() |
void |
printEMatrix() |
void |
printRMatrix() |
java.lang.String |
toString()
Print the atom changes
|
void |
writeBMatrix(java.io.File outputFile) |
void |
writeBondChanges(java.io.File bondChangeInfoFile)
Print the atom changes
|
void |
writeEMatrix(java.io.File outputFile) |
void |
writeRMatrix(java.io.File outputFile) |
getMolMolPair
canonicalise, circularFragment, getAtomContainer, getAtomContainer, getAtomIndexByID, getAtoms, getBondOrderSign, getCanonicalisedBondChangePattern, getCanonisedBondChangePattern, getCircularFragment, getCircularReactionPatternFingerprints, getCircularSMILES, getMoleculeID, getMoleculeID, getNeighbourBondOrderCountFromRing, getSignature, getSmallestRingSet, getSMILES, getSMILES, initializeMolecule, setCircularFingerprints, setCircularSignatureFingerprints, setFragmentMatches, setReactionCenterMatches
printBEMatrix, printReactionMatrix, writeBEMatrix, writeReactionMatrix
public BondChangeCalculator(org.openscience.cdk.interfaces.IReaction reaction, boolean generate2D, boolean generate3D) throws java.lang.Exception
reaction
- generate2D
- generate3D
- java.lang.Exception
public BEMatrix getEductBEMatrix()
getEductBEMatrix
in interface IChangeCalculator
public BEMatrix getProductBEMatrix()
getProductBEMatrix
in interface IChangeCalculator
public RMatrix getRMatrix()
getRMatrix
in interface IChangeCalculator
public void printBMatrix()
printBMatrix
in interface IChangeCalculator
public void printEMatrix()
printEMatrix
in interface IChangeCalculator
public void printRMatrix()
printRMatrix
in interface IChangeCalculator
public void writeBMatrix(java.io.File outputFile)
writeBMatrix
in interface IChangeCalculator
outputFile
- public void writeEMatrix(java.io.File outputFile)
writeEMatrix
in interface IChangeCalculator
outputFile
- public void writeRMatrix(java.io.File outputFile)
writeRMatrix
in interface IChangeCalculator
outputFile
- public boolean hasRMatrix()
hasRMatrix
in interface IChangeCalculator
public java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> getMappingMap()
getMappingMap
in interface IChangeCalculator
public java.util.List<BondChange> getBondChangeList()
getBondChangeList
in interface IChangeCalculator
public IPatternFingerprinter getOrderChangesWFingerprint() throws org.openscience.cdk.exception.CDKException
getOrderChangesWFingerprint
in class AbstractChangeCalculator
org.openscience.cdk.exception.CDKException
public IPatternFingerprinter getStereoChangesWFingerprint() throws org.openscience.cdk.exception.CDKException
getStereoChangesWFingerprint
in class AbstractChangeCalculator
org.openscience.cdk.exception.CDKException
public IPatternFingerprinter getFormedCleavedWFingerprint() throws org.openscience.cdk.exception.CDKException
getFormedCleavedWFingerprint
in class AbstractChangeCalculator
org.openscience.cdk.exception.CDKException
public IPatternFingerprinter getReactionCenterWFingerprint() throws org.openscience.cdk.exception.CDKException
getReactionCenterWFingerprint
in class AbstractChangeCalculator
org.openscience.cdk.exception.CDKException
public java.lang.String toString()
toString
in class java.lang.Object
public void writeBondChanges(java.io.File bondChangeInfoFile) throws java.io.IOException
writeBondChanges
in class AbstractChangeCalculator
bondChangeInfoFile
- java.io.IOException
public java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> getBondFormedProduct()
getBondFormedProduct
in class AbstractChangeCalculator
public java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> getBondCleavedReactant()
getBondCleavedReactant
in class AbstractChangeCalculator
public java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> getBondOrderReactant()
getBondOrderReactant
in class AbstractChangeCalculator
public java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> getBondOrderProduct()
getBondOrderProduct
in class AbstractChangeCalculator
public java.util.Map<org.openscience.cdk.interfaces.IAtom,java.lang.String> getStereoCenterAtomsReactant()
getStereoCenterAtomsReactant
in class AbstractChangeCalculator
public java.util.Map<org.openscience.cdk.interfaces.IAtom,java.lang.String> getStereoCenterAtomsProduct()
getStereoCenterAtomsProduct
in class AbstractChangeCalculator
public org.openscience.cdk.interfaces.IReaction getReactionWithCompressUnChangedHydrogens()
getReactionWithCompressUnChangedHydrogens
in class AbstractChangeCalculator
public org.openscience.cdk.interfaces.IReaction getReaction() throws java.lang.Exception
getReaction
in class AbstractChangeCalculator
java.lang.Exception
public java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> getAtomAtomMappings()
getAtomAtomMappings
in class AbstractChangeCalculator
public AtomAtomMappingContainer getMappingContainer()
getMappingContainer
in interface IChangeCalculator
public int getTotalBondBreakingEnergy() throws org.openscience.cdk.exception.CDKException
org.openscience.cdk.exception.CDKException
public int getEnergyDelta()
public java.util.List<AtomStereoChangeInformation> getStereoChangeList()
getStereoChangeList
in interface IChangeCalculator
public java.lang.Iterable<AtomStereoChangeInformation> getConformationChangeList()
getConformationChangeList
in interface IChangeCalculator
public java.util.Map<java.lang.Integer,IPatternFingerprinter> getReactionCenterFormedCleavedFingerprint()
public java.util.Map<java.lang.Integer,IPatternFingerprinter> getReactionCenterOrderChangeFingerprint()
public java.util.Map<java.lang.Integer,IPatternFingerprinter> getReactionCenterStereoChangeFingerprint()
public java.util.Collection<org.openscience.cdk.interfaces.IAtom> getReactionCenterSet()
getReactionCenterSet
in interface IChangeCalculator
public java.util.Collection<ReactionCenterFragment> getReactionCenterFragmentList()
getReactionCenterFragmentList
in class AbstractChangeCalculator
public java.util.Collection<MoleculeMoleculePair> getReactionCentreTransformationPairs()
AbstractChangeCalculator
getReactionCentreTransformationPairs
in class AbstractChangeCalculator
public java.util.Map<java.lang.String,java.util.Collection<java.lang.String>> getMoleculeMoleculeTransformationPairs()
getMoleculeMoleculeTransformationPairs
in class AbstractChangeCalculator
public int getTotalSmallestFragmentSize()