public final class Isomorphism extends BaseMapping implements java.io.Serializable
This class implements the Isomorphism- a multipurpose structure comparison tool. It allows users to, i) find the maximal common substructure(s) (MCS); ii) perform the mapping of a substructure in another structure, and; iii) map two isomorphic structures.
It also comes with various published algorithms. The user is free to choose his favorite algorithm to perform MCS or substructure search. For example:
It also has a set of robust chemical filters (i.e. bond energy, fragment count, stereo & bond match) to sort the reported MCS solutions in a chemically relevant manner. Each comparison can be made with or without using the bond sensitive mode and with implicit or explicit hydrogens.
If you are using Isomorphism, please cite Rahman et.al. 2009 {
Constructor and Description |
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Isomorphism(org.openscience.cdk.interfaces.IAtomContainer query,
org.openscience.cdk.interfaces.IAtomContainer target,
Algorithm algorithmType,
boolean bondTypeFlag,
boolean matchRings,
boolean matchAtomType)
Initialize query and target molecules.
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Isomorphism(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query,
org.openscience.cdk.interfaces.IAtomContainer target,
Algorithm algorithmType)
Initialize query and target molecules.
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Modifier and Type | Method and Description |
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double |
getBondInSensitiveMcGregor() |
double |
getBondSensitiveMcGregorOut() |
boolean |
isSubgraph()
Returns true if Query is a subgraph of the Target.
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void |
setBondInSenSitiveMcGregor(double bondInSensitiveMcGregor) |
void |
setBondSenSitiveMcGregorOut(double bondSensitiveMcGregorOut) |
clearMaps, getAllAtomMapping, getAllBondMaps, getEnergyScore, getEuclideanDistance, getFirstAtomMapping, getFragmentSize, getMappingCount, getStereoScore, getTanimotoSimilarity, isMatchAtomType, isMatchBonds, isMatchRings, isStereoMisMatch, makeBondMapsOfAtomMaps, setChemFilters
getMCSList, getSortedEnergy, getSortedFragment, getStereoMatches, sortResultsByEnergies, sortResultsByFragments, sortResultsByStereoAndBondMatch
getQuery, getTarget
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
toString
public Isomorphism(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query, org.openscience.cdk.interfaces.IAtomContainer target, Algorithm algorithmType)
query
- query moleculetarget
- target molecule This is the algorithm factory and entry
port for all the MCS algorithm in the Isomorphism supported algorithm
org.openscience.cdk.smsd.interfaces.Algorithm
types: algorithmType
- org.openscience.cdk.smsd.interfaces.Algorithm
public Isomorphism(org.openscience.cdk.interfaces.IAtomContainer query, org.openscience.cdk.interfaces.IAtomContainer target, Algorithm algorithmType, boolean bondTypeFlag, boolean matchRings, boolean matchAtomType)
query
- query moltarget
- target mol This is the algorithm factory and entry port for
all the MCS algorithm in the Isomorphism supported algorithm
org.openscience.cdk.smsd.interfaces.Algorithm
types: algorithmType
- org.openscience.cdk.smsd.interfaces.Algorithm
bondTypeFlag
- Match bond types (i.e. double to double etc)matchRings
- Match ring atoms and ring sizematchAtomType
- public boolean isSubgraph()
BaseMapping
isSubgraph
in class BaseMapping
public double getBondSensitiveMcGregorOut()
public void setBondSenSitiveMcGregorOut(double bondSensitiveMcGregorOut)
bondSensitiveMcGregorOut
- the bondSensitiveMcGregorOut to setpublic double getBondInSensitiveMcGregor()
public void setBondInSenSitiveMcGregor(double bondInSensitiveMcGregor)
bondInSensitiveMcGregor
- the bondInSensitiveMcGregor to set