Modifier and Type | Method and Description |
---|---|
AtomAtomMapping |
BaseMapping.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<AtomAtomMapping> |
BaseMapping.getAllAtomMapping()
Returns all plausible mappings between query and target molecules
Each map in the list has atom-atom equivalence of the mappings
between query and target molecule i.e.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<java.util.Map<org.openscience.cdk.interfaces.IBond,org.openscience.cdk.interfaces.IBond>> |
BaseMapping.makeBondMapsOfAtomMaps(org.openscience.cdk.interfaces.IAtomContainer ac1,
org.openscience.cdk.interfaces.IAtomContainer ac2,
java.util.List<AtomAtomMapping> mappings)
Returns bond maps between sourceAtomCount and targetAtomCount molecules
based on the atoms
|
Modifier and Type | Method and Description |
---|---|
AtomAtomMapping |
MCSPlusHandler.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<AtomAtomMapping> |
MCSPlusHandler.getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
Modifier and Type | Method and Description |
---|---|
AtomAtomMapping |
CDKMCSHandler.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
AtomAtomMapping |
CDKSubGraphHandler.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<AtomAtomMapping> |
CDKMCSHandler.getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
java.util.List<AtomAtomMapping> |
CDKSubGraphHandler.getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
Modifier and Type | Method and Description |
---|---|
AtomAtomMapping |
SingleMappingHandler.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<AtomAtomMapping> |
SingleMappingHandler.getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
Modifier and Type | Method and Description |
---|---|
AtomAtomMapping |
VF2MCS.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
AtomAtomMapping |
VF2Sub.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<AtomAtomMapping> |
VF2MCS.getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
java.util.List<AtomAtomMapping> |
VF2Sub.getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
Modifier and Type | Method and Description |
---|---|
protected java.util.List<AtomAtomMapping> |
MCSSeedGenerator.addKochCliques() |
java.util.List<AtomAtomMapping> |
MCSSeedGenerator.call() |
Modifier and Type | Method and Description |
---|---|
AtomAtomMapping |
VF2.getFirstAtomMapping() |
Modifier and Type | Method and Description |
---|---|
java.util.List<AtomAtomMapping> |
VF2.getAllAtomMapping() |
Modifier and Type | Method and Description |
---|---|
protected java.util.List<AtomAtomMapping> |
ChemicalFilters.getMCSList() |
Modifier and Type | Method and Description |
---|---|
java.lang.Double |
EnergyFilter.sortResults(java.util.Map<java.lang.Integer,AtomAtomMapping> allAtomEnergyMCS,
java.util.Map<java.lang.Integer,java.lang.Double> energySelectionMap) |
java.lang.Double |
StereoFilter.sortResults(java.util.Map<java.lang.Integer,AtomAtomMapping> allStereoAtomMCS,
java.util.Map<java.lang.Integer,java.lang.Double> stereoScoreMap) |
java.lang.Integer |
FragmentFilter.sortResults(java.util.Map<java.lang.Integer,AtomAtomMapping> allFragmentAtomMCS,
java.util.Map<java.lang.Integer,java.lang.Integer> fragmentScoreMap) |
T |
IChemicalFilter.sortResults(java.util.Map<java.lang.Integer,AtomAtomMapping> allAtomMCS,
java.util.Map<java.lang.Integer,T> selectionMap)
Calculates a score for each MCS, and sorts the results on that score,
returning the best.
|
Modifier and Type | Method and Description |
---|---|
AtomAtomMapping |
IAtomMapping.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
AtomAtomMapping |
IResults.getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<AtomAtomMapping> |
IAtomMapping.getAllAtomMapping()
Returns all plausible mappings between query and target molecules
Each map in the list has atom-atom equivalence of the mappings
between query and target molecule i.e.
|
java.util.List<AtomAtomMapping> |
IResults.getAllAtomMapping()
Returns all plausible mappings between query and target molecules.
|
Modifier and Type | Method and Description |
---|---|
AtomAtomMapping |
BestMatchContainer.getAtomMatch(int indexI,
int indexJ)
String IKey = substrateIndex + "_" + productIndex;
|
Modifier and Type | Method and Description |
---|---|
void |
BestMatchContainer.putBestMapping(int indexI,
int indexJ,
AtomAtomMapping matchingAtoms)
String IKey = substrateIndex + "_" + productIndex;
|
Modifier and Type | Method and Description |
---|---|
AtomAtomMapping |
MCSSolution.getAtomAtomMapping() |
Constructor and Description |
---|
MCSSolution(int queryPosition,
int targetPosition,
org.openscience.cdk.interfaces.IAtomContainer queryContainer,
org.openscience.cdk.interfaces.IAtomContainer targetContainer,
AtomAtomMapping aam) |
Modifier and Type | Method and Description |
---|---|
abstract AtomAtomMapping |
BestMatch.getAtomMatch(int indexI,
int indexJ)
String IKey = substrateIndex + "_" + productIndex;
|
Modifier and Type | Method and Description |
---|---|
abstract void |
BestMatch.putBestMapping(int indexI,
int indexJ,
AtomAtomMapping matchingAtoms)
String IKey = substrateIndex + "_" + productIndex;
|
Modifier and Type | Method and Description |
---|---|
void |
ImageGenerator.addImages(org.openscience.cdk.interfaces.IAtomContainer query,
org.openscience.cdk.interfaces.IAtomContainer target,
java.lang.String label,
AtomAtomMapping maxac) |