public class AtomAtomMapping
extends java.lang.Object
implements java.io.Serializable
Constructor and Description |
---|
AtomAtomMapping(org.openscience.cdk.interfaces.IAtomContainer query,
org.openscience.cdk.interfaces.IAtomContainer target) |
Modifier and Type | Method and Description |
---|---|
void |
clear()
Clear mappings
|
boolean |
equals(java.lang.Object obj) |
org.openscience.cdk.interfaces.IAtomContainer |
getCommonFragment()
Returns common mapped fragment in the query molecule.
|
java.lang.String |
getCommonFragmentAsSMILES()
Returns Maximum Common Fragment between Query and Target as SMILES
|
int |
getCount()
Returns mapping size.
|
org.openscience.cdk.interfaces.IAtomContainer |
getMapCommonFragmentOnQuery()
Returns common mapped fragment in the query molecule.
|
org.openscience.cdk.interfaces.IAtomContainer |
getMapCommonFragmentOnTarget()
Returns common mapped fragment in the target molecule.
|
java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> |
getMappingsByAtoms()
Returns atom-atom mappings
|
java.util.Map<java.lang.Integer,java.lang.Integer> |
getMappingsByIndex()
Returns atom-atom index mappings
|
org.openscience.cdk.interfaces.IAtomContainer |
getQuery()
Returns query molecule
|
int |
getQueryIndex(org.openscience.cdk.interfaces.IAtom atom)
Returns atom index of the given atom in the query molecule
|
org.openscience.cdk.interfaces.IAtomContainer |
getTarget()
Returns target molecule
|
int |
getTargetIndex(org.openscience.cdk.interfaces.IAtom atom)
Returns atom index of the given atom in the target molecule
|
int |
hashCode() |
boolean |
isEmpty()
Returns true if 'query' is not isomorphic of 'target'.
|
void |
put(org.openscience.cdk.interfaces.IAtom atom1,
org.openscience.cdk.interfaces.IAtom atom2) |
java.lang.String |
toString()
Returns String.
|
public AtomAtomMapping(org.openscience.cdk.interfaces.IAtomContainer query, org.openscience.cdk.interfaces.IAtomContainer target)
query
- source moleculetarget
- target moleculepublic boolean equals(java.lang.Object obj)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object
public void put(org.openscience.cdk.interfaces.IAtom atom1, org.openscience.cdk.interfaces.IAtom atom2)
atom1
- atom2
- public java.lang.String toString()
toString
in class java.lang.Object
public boolean isEmpty()
public void clear()
public int getCount()
public java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtom> getMappingsByAtoms()
public java.util.Map<java.lang.Integer,java.lang.Integer> getMappingsByIndex()
public int getQueryIndex(org.openscience.cdk.interfaces.IAtom atom)
atom
- public int getTargetIndex(org.openscience.cdk.interfaces.IAtom atom)
atom
- public org.openscience.cdk.interfaces.IAtomContainer getQuery()
public org.openscience.cdk.interfaces.IAtomContainer getTarget()
public org.openscience.cdk.interfaces.IAtomContainer getMapCommonFragmentOnQuery() throws java.lang.CloneNotSupportedException
java.lang.CloneNotSupportedException
public org.openscience.cdk.interfaces.IAtomContainer getMapCommonFragmentOnTarget() throws java.lang.CloneNotSupportedException
java.lang.CloneNotSupportedException
public org.openscience.cdk.interfaces.IAtomContainer getCommonFragment() throws java.lang.CloneNotSupportedException
java.lang.CloneNotSupportedException
public java.lang.String getCommonFragmentAsSMILES() throws java.lang.CloneNotSupportedException, org.openscience.cdk.exception.CDKException
java.lang.CloneNotSupportedException
org.openscience.cdk.exception.CDKException