public final class BondChangeAnnotator extends StereoCenteralityTool
Modifier and Type | Field and Description |
---|---|
protected boolean |
generate2DCoordinates |
protected boolean |
generate3DCoordinates |
protected AtomAtomMappingContainer |
mapping |
protected BEMatrix |
productBE |
protected org.openscience.cdk.interfaces.IRingSet |
queryRingSet |
protected BEMatrix |
reactantBE |
protected RMatrix |
reactionMatrix |
protected org.openscience.cdk.interfaces.IRingSet |
targetRingSet |
Modifier | Constructor and Description |
---|---|
protected |
BondChangeAnnotator(org.openscience.cdk.interfaces.IReaction reaction,
boolean withoutHydrogen,
boolean generate2D,
boolean generate3D) |
Modifier and Type | Method and Description |
---|---|
java.util.List<BondChange> |
getBondChangeList() |
java.util.List<AtomStereoChangeInformation> |
getConformationChangeList() |
BEMatrix |
getEductBEMatrix() |
AtomAtomMappingContainer |
getMappingContainer() |
java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> |
getMappingMap() |
BEMatrix |
getProductBEMatrix() |
java.util.Collection<org.openscience.cdk.interfaces.IAtom> |
getReactionCenterSet() |
RMatrix |
getRMatrix() |
java.util.List<AtomStereoChangeInformation> |
getStereoChangeList() |
boolean |
hasRMatrix() |
int |
isAlternateKekuleChange(org.openscience.cdk.interfaces.IBond affectedBondReactants,
org.openscience.cdk.interfaces.IBond affectedBondProducts) |
int |
isKekuleEffect(org.openscience.cdk.interfaces.IBond affectedBondReactants,
org.openscience.cdk.interfaces.IBond affectedBondProducts) |
protected void |
markBondChanges()
set bond change flag
|
void |
printBMatrix() |
void |
printEMatrix() |
void |
printRMatrix() |
java.lang.String |
toString() |
void |
writeBMatrix(java.io.File outputFile) |
void |
writeEMatrix(java.io.File outputFile) |
void |
writeRMatrix(java.io.File outputFile) |
getChirality2D, getChirality2D
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
protected final boolean generate3DCoordinates
protected final boolean generate2DCoordinates
protected final AtomAtomMappingContainer mapping
protected final BEMatrix reactantBE
protected final BEMatrix productBE
protected final RMatrix reactionMatrix
protected final org.openscience.cdk.interfaces.IRingSet queryRingSet
protected final org.openscience.cdk.interfaces.IRingSet targetRingSet
protected BondChangeAnnotator(org.openscience.cdk.interfaces.IReaction reaction, boolean withoutHydrogen, boolean generate2D, boolean generate3D) throws java.lang.Exception
reaction
- with Atom-Atom Mapping produced by Reactor classwithoutHydrogen
- generate2D
- generate3D
- java.lang.Exception
public AtomAtomMappingContainer getMappingContainer()
public BEMatrix getEductBEMatrix()
public java.util.List<BondChange> getBondChangeList()
public java.util.Collection<org.openscience.cdk.interfaces.IAtom> getReactionCenterSet()
public java.util.List<AtomStereoChangeInformation> getStereoChangeList()
public BEMatrix getProductBEMatrix()
public java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> getMappingMap()
public RMatrix getRMatrix()
public boolean hasRMatrix()
public void printBMatrix()
public java.util.List<AtomStereoChangeInformation> getConformationChangeList()
public void writeBMatrix(java.io.File outputFile)
outputFile
- public void printEMatrix()
public void writeEMatrix(java.io.File outputFile)
outputFile
- public void printRMatrix()
public void writeRMatrix(java.io.File outputFile)
outputFile
- protected void markBondChanges() throws java.lang.Exception
java.lang.Exception
public int isKekuleEffect(org.openscience.cdk.interfaces.IBond affectedBondReactants, org.openscience.cdk.interfaces.IBond affectedBondProducts)
affectedBondReactants
- affectedBondProducts
- public int isAlternateKekuleChange(org.openscience.cdk.interfaces.IBond affectedBondReactants, org.openscience.cdk.interfaces.IBond affectedBondProducts)
affectedBondReactants
- affectedBondProducts
- public java.lang.String toString()
toString
in class java.lang.Object