public abstract class AbstractChangeCalculator extends Utility
Constructor and Description |
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AbstractChangeCalculator() |
Modifier and Type | Method and Description |
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abstract java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> |
getAtomAtomMappings() |
abstract java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> |
getBondCleavedReactant() |
abstract java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> |
getBondFormedProduct() |
abstract java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> |
getBondOrderProduct() |
abstract java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> |
getBondOrderReactant() |
abstract IPatternFingerprinter |
getFormedCleavedWFingerprint() |
abstract java.util.Map<java.lang.String,java.util.Collection<java.lang.String>> |
getMoleculeMoleculeTransformationPairs() |
protected static MoleculeMoleculePair |
getMolMolPair(org.openscience.cdk.interfaces.IAtom reactantAtom,
org.openscience.cdk.interfaces.IAtom productAtom,
org.openscience.cdk.interfaces.IAtomContainer atomContainerR,
org.openscience.cdk.interfaces.IAtomContainer atomContainerP) |
abstract IPatternFingerprinter |
getOrderChangesWFingerprint() |
abstract org.openscience.cdk.interfaces.IReaction |
getReaction() |
abstract java.util.Collection<ReactionCenterFragment> |
getReactionCenterFragmentList() |
abstract IPatternFingerprinter |
getReactionCenterWFingerprint() |
abstract java.util.Collection<MoleculeMoleculePair> |
getReactionCentreTransformationPairs()
Return the list of Molecule Molecule Transformation List
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abstract org.openscience.cdk.interfaces.IReaction |
getReactionWithCompressUnChangedHydrogens() |
abstract java.util.Map<org.openscience.cdk.interfaces.IAtom,java.lang.String> |
getStereoCenterAtomsProduct() |
abstract java.util.Map<org.openscience.cdk.interfaces.IAtom,java.lang.String> |
getStereoCenterAtomsReactant() |
abstract IPatternFingerprinter |
getStereoChangesWFingerprint() |
abstract void |
writeBondChanges(java.io.File bondChangeInfoFile)
Print the bond changes
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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 abstract java.util.Map<java.lang.String,java.util.Collection<java.lang.String>> getMoleculeMoleculeTransformationPairs()
public abstract java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> getBondCleavedReactant()
public abstract java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> getBondFormedProduct()
public abstract java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> getBondOrderProduct()
public abstract java.util.Map<org.openscience.cdk.interfaces.IBond,java.lang.String> getBondOrderReactant()
public abstract java.util.Map<org.openscience.cdk.interfaces.IAtom,java.lang.String> getStereoCenterAtomsProduct()
public abstract java.util.Map<org.openscience.cdk.interfaces.IAtom,java.lang.String> getStereoCenterAtomsReactant()
public abstract IPatternFingerprinter getFormedCleavedWFingerprint() throws org.openscience.cdk.exception.CDKException
org.openscience.cdk.exception.CDKException
public abstract IPatternFingerprinter getOrderChangesWFingerprint() throws org.openscience.cdk.exception.CDKException
org.openscience.cdk.exception.CDKException
public abstract IPatternFingerprinter getReactionCenterWFingerprint() throws org.openscience.cdk.exception.CDKException
org.openscience.cdk.exception.CDKException
public abstract java.util.Collection<ReactionCenterFragment> getReactionCenterFragmentList()
public abstract org.openscience.cdk.interfaces.IReaction getReaction() throws java.lang.Exception
java.lang.Exception
public abstract org.openscience.cdk.interfaces.IReaction getReactionWithCompressUnChangedHydrogens() throws java.lang.Exception
java.lang.Exception
public abstract IPatternFingerprinter getStereoChangesWFingerprint() throws org.openscience.cdk.exception.CDKException
org.openscience.cdk.exception.CDKException
public abstract java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> getAtomAtomMappings()
public abstract void writeBondChanges(java.io.File bondChangeInfoFile) throws java.io.IOException
bondChangeInfoFile
- java.io.IOException
public abstract java.util.Collection<MoleculeMoleculePair> getReactionCentreTransformationPairs()
protected static MoleculeMoleculePair getMolMolPair(org.openscience.cdk.interfaces.IAtom reactantAtom, org.openscience.cdk.interfaces.IAtom productAtom, org.openscience.cdk.interfaces.IAtomContainer atomContainerR, org.openscience.cdk.interfaces.IAtomContainer atomContainerP) throws java.lang.Exception
reactantAtom
- productAtom
- atomContainerR
- atomContainerP
- java.lang.Exception