public class AbstractReactionLabeller
extends java.lang.Object
Constructor and Description |
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AbstractReactionLabeller() |
Modifier and Type | Method and Description |
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protected void |
atomAtomMap(org.openscience.cdk.interfaces.IAtomContainerSet original,
org.openscience.cdk.interfaces.IAtomContainerSet clone,
java.util.Map<org.openscience.cdk.interfaces.IAtomContainer,int[]> permutationMap,
java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> atomAtom) |
protected java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> |
atomAtomMap(org.openscience.cdk.interfaces.IReaction reaction,
org.openscience.cdk.interfaces.IReaction clone,
java.util.Map<org.openscience.cdk.interfaces.IAtomContainer,int[]> permutationMap) |
protected org.openscience.cdk.interfaces.IAtomContainerSet |
canoniseAtomContainerSet(org.openscience.cdk.interfaces.IAtomContainerSet moleculeSet,
ICanonicalMoleculeLabeller labeller,
java.util.Map<org.openscience.cdk.interfaces.IAtomContainer,int[]> permutationMap) |
protected void |
cloneAndSortMappings(org.openscience.cdk.interfaces.IReaction reaction,
org.openscience.cdk.interfaces.IReaction copyOfReaction,
java.util.Map<org.openscience.cdk.interfaces.IAtomContainer,int[]> permutationMap)
Clone and Sort the mappings based on the order of the first object in the
mapping (which is assumed to be the reactant).
|
protected org.openscience.cdk.interfaces.IMapping |
cloneMapping(org.openscience.cdk.interfaces.IMapping mapping,
java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> atomAtomMap) |
protected java.util.List<org.openscience.cdk.interfaces.IMapping> |
cloneMappings(org.openscience.cdk.interfaces.IReaction reaction,
java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> atomAtomMap) |
org.openscience.cdk.interfaces.IReaction |
labelReaction(org.openscience.cdk.interfaces.IReaction reaction,
ICanonicalMoleculeLabeller labeller) |
protected java.util.Map<org.openscience.cdk.interfaces.IChemObject,java.lang.Integer> |
makeIndexMap(org.openscience.cdk.interfaces.IReaction reaction) |
protected void |
sortMappings(org.openscience.cdk.interfaces.IReaction reaction,
java.util.List<org.openscience.cdk.interfaces.IMapping> map) |
protected void atomAtomMap(org.openscience.cdk.interfaces.IAtomContainerSet original, org.openscience.cdk.interfaces.IAtomContainerSet clone, java.util.Map<org.openscience.cdk.interfaces.IAtomContainer,int[]> permutationMap, java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> atomAtom)
original
- clone
- permutationMap
- atomAtom
- protected java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> atomAtomMap(org.openscience.cdk.interfaces.IReaction reaction, org.openscience.cdk.interfaces.IReaction clone, java.util.Map<org.openscience.cdk.interfaces.IAtomContainer,int[]> permutationMap)
reaction
- clone
- permutationMap
- protected java.util.List<org.openscience.cdk.interfaces.IMapping> cloneMappings(org.openscience.cdk.interfaces.IReaction reaction, java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> atomAtomMap)
reaction
- atomAtomMap
- protected org.openscience.cdk.interfaces.IMapping cloneMapping(org.openscience.cdk.interfaces.IMapping mapping, java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> atomAtomMap)
mapping
- atomAtomMap
- protected java.util.Map<org.openscience.cdk.interfaces.IChemObject,java.lang.Integer> makeIndexMap(org.openscience.cdk.interfaces.IReaction reaction)
reaction
- protected void cloneAndSortMappings(org.openscience.cdk.interfaces.IReaction reaction, org.openscience.cdk.interfaces.IReaction copyOfReaction, java.util.Map<org.openscience.cdk.interfaces.IAtomContainer,int[]> permutationMap)
reaction
- copyOfReaction
- permutationMap
- protected void sortMappings(org.openscience.cdk.interfaces.IReaction reaction, java.util.List<org.openscience.cdk.interfaces.IMapping> map)
reaction
- map
- protected org.openscience.cdk.interfaces.IAtomContainerSet canoniseAtomContainerSet(org.openscience.cdk.interfaces.IAtomContainerSet moleculeSet, ICanonicalMoleculeLabeller labeller, java.util.Map<org.openscience.cdk.interfaces.IAtomContainer,int[]> permutationMap)
moleculeSet
- labeller
- permutationMap
- public org.openscience.cdk.interfaces.IReaction labelReaction(org.openscience.cdk.interfaces.IReaction reaction, ICanonicalMoleculeLabeller labeller)
reaction
- labeller
-