public class BaseMapping extends ChemicalFilters implements IAtomMapping
Constructor and Description |
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BaseMapping(org.openscience.cdk.interfaces.IAtomContainer mol1,
org.openscience.cdk.interfaces.IAtomContainer mol2,
boolean matchBonds,
boolean matchRings,
boolean matchAtomType) |
BaseMapping(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer mol1,
org.openscience.cdk.interfaces.IAtomContainer mol2) |
Modifier and Type | Method and Description |
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void |
clearMaps() |
java.util.List<AtomAtomMapping> |
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<java.util.Map<org.openscience.cdk.interfaces.IBond,org.openscience.cdk.interfaces.IBond>> |
getAllBondMaps() |
java.lang.Double |
getEnergyScore(int Key)
Returns summation energy score of the disorder if the MCS is removed
from the target and query graph.
|
double |
getEuclideanDistance()
Returns Euclidean Distance between query and target molecule.
|
AtomAtomMapping |
getFirstAtomMapping()
Returns one of the best matches with atoms mapped.
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java.lang.Integer |
getFragmentSize(int Key)
Returns number of fragment generated in the solution space,
if the MCS is removed from the target and query graph.
|
int |
getMappingCount()
Returns total mapping count 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.lang.Integer |
getStereoScore(int Key)
Returns a number which denotes the quality of the mcs.
|
double |
getTanimotoSimilarity()
Returns Tanimoto similarity between query and target molecules
(Score is between 0-min and 1-max).
|
boolean |
isMatchAtomType() |
protected boolean |
isMatchBonds()
Returns true if bond are to be matched.
|
protected boolean |
isMatchRings()
Returns true if rings are to be matched.
|
boolean |
isStereoMisMatch()
Returns true if mols have different stereo
chemistry else false if no stereo mismatch.
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boolean |
isSubgraph()
Returns true if Query is a subgraph of the Target.
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java.util.List<java.util.Map<org.openscience.cdk.interfaces.IBond,org.openscience.cdk.interfaces.IBond>> |
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
|
void |
setChemFilters(boolean stereoFilter,
boolean fragmentFilter,
boolean energyFilter)
initialize query and target molecules.
|
getMCSList, getSortedEnergy, getSortedFragment, getStereoMatches, sortResultsByEnergies, sortResultsByFragments, sortResultsByStereoAndBondMatch
getQuery, getTarget
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
toString
public BaseMapping(org.openscience.cdk.interfaces.IAtomContainer mol1, org.openscience.cdk.interfaces.IAtomContainer mol2, boolean matchBonds, boolean matchRings, boolean matchAtomType)
matchBonds
- matchRings
- matchAtomType
- mol1
- mol2
- public BaseMapping(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer mol1, org.openscience.cdk.interfaces.IAtomContainer mol2)
mol1
- mol2
- public void setChemFilters(boolean stereoFilter, boolean fragmentFilter, boolean energyFilter)
IAtomMapping
setChemFilters
in interface IAtomMapping
stereoFilter
- set true to rank the solutions as per stereo matchesfragmentFilter
- set true to return matches with minimum fragmentsenergyFilter
- set true to return matches with minimum bond changes
based on the bond breaking energypublic java.lang.Integer getFragmentSize(int Key)
IAtomMapping
getFragmentSize
in interface IAtomMapping
Key
- Index of the mapping solutionpublic java.lang.Integer getStereoScore(int Key)
IAtomMapping
getStereoScore
in interface IAtomMapping
Key
- Index of the mapping solutionpublic java.lang.Double getEnergyScore(int Key)
IAtomMapping
getEnergyScore
in interface IAtomMapping
Key
- Index of the mapping solutionpublic double getTanimotoSimilarity()
getTanimotoSimilarity
in interface IAtomMapping
public boolean isStereoMisMatch()
isStereoMisMatch
in interface IAtomMapping
public int getMappingCount()
IAtomMapping
getMappingCount
in interface IAtomMapping
public double getEuclideanDistance()
getEuclideanDistance
in interface IAtomMapping
public java.util.List<AtomAtomMapping> getAllAtomMapping()
getAllAtomMapping
in interface IAtomMapping
public AtomAtomMapping getFirstAtomMapping()
getFirstAtomMapping
in interface IAtomMapping
protected boolean isMatchBonds()
protected boolean isMatchRings()
public boolean isSubgraph()
public void clearMaps()
public java.util.List<java.util.Map<org.openscience.cdk.interfaces.IBond,org.openscience.cdk.interfaces.IBond>> getAllBondMaps()
public java.util.List<java.util.Map<org.openscience.cdk.interfaces.IBond,org.openscience.cdk.interfaces.IBond>> makeBondMapsOfAtomMaps(org.openscience.cdk.interfaces.IAtomContainer ac1, org.openscience.cdk.interfaces.IAtomContainer ac2, java.util.List<AtomAtomMapping> mappings)
ac1
- sourceAtomCount moleculeac2
- targetAtomCount moleculemappings
- mappings between sourceAtomCount and targetAtomCount
molecule atomspublic boolean isMatchAtomType()