org.openscience.cdk.smsd.algorithm.mcsplus
Class MCSPlusHandler

java.lang.Object
  org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm
      org.openscience.cdk.smsd.algorithm.mcsplus.MCSPlusHandler

All Implemented Interfaces:

IMCSBase

@TestClass(value="org.openscience.cdk.smsd.SMSDBondSensitiveTest")
public class MCSPlusHandler
extends AbstractMCSAlgorithm
implements IMCSBase

This class acts as a handler class for MCSPlus algorithm. MCSPlus

Author:

Syed Asad Rahman

Belongs to CDK module:

smsd

Source code:

HEAD

Constructor Summary

MCSPlusHandler()
Constructor for the MCS Plus algorithm class

Method Summary

List<Map<IAtom,IAtom>>	getAllAtomMapping() Returns all plausible mappings between query and target molecules.
List<Map<Integer,Integer>>	getAllMapping() Returns all plausible mappings between query and target molecules.
Map<IAtom,IAtom>	getFirstAtomMapping() Returns one of the best matches with atoms mapped.
Map<Integer,Integer>	getFirstMapping() Returns one of the best matches with atom indexes mapped.
void	searchMCS(boolean shouldMatchBonds) Initialise the MCS search algorithm.
void	set(IQueryAtomContainer source, IAtomContainer target) Initialise the query and target molecule.
void	set(MolHandler source, MolHandler target) Initialise the query and target molecule.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MCSPlusHandler

public MCSPlusHandler()

Constructor for the MCS Plus algorithm class

Method Detail

set

@TestMethod(value="testSet_MolHandler_MolHandler")
public void set(MolHandler source,
                                MolHandler target)

Initialise the query and target molecule.

Specified by:

set in interface IMCSBase

Parameters:

source -

target -

set

@TestMethod(value="testSet_IQueryAtomContainer_MolHandler")
public void set(IQueryAtomContainer source,
                                IAtomContainer target)

Initialise the query and target molecule.

Specified by:

set in interface IMCSBase

Parameters:

source -

target -

searchMCS

@TestMethod(value="testSearchMCS")
public void searchMCS(boolean shouldMatchBonds)

Initialise the MCS search algorithm. Each MCS algorithm should contain this method. Function is called by the main program and serves as a starting point for the comparison procedure.

Specified by:

searchMCS in class AbstractMCSAlgorithm

Parameters:

shouldMatchBonds -

getAllMapping

@TestMethod(value="testSearchMCS")
public List<Map<Integer,Integer>> getAllMapping()

Returns all plausible mappings between query and target molecules. Each map in the list has atom-atom equivalence index of the mappings between query and target molecule i.e. map.getKey() for the query and map.getValue() for the target molecule

Specified by:

getAllMapping in interface IMCSBase

Returns:

All possible MCS Mapping Index

getFirstMapping

@TestMethod(value="testSearchMCS")
public Map<Integer,Integer> getFirstMapping()

Returns one of the best matches with atom indexes mapped.

Specified by:

getFirstMapping in interface IMCSBase

Returns:

Best Mapping Index

getAllAtomMapping

@TestMethod(value="testSearchMCS")
public List<Map<IAtom,IAtom>> 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. map.getKey() for the query and map.getValue() for the target molecule

Specified by:

getAllAtomMapping in interface IMCSBase

Returns:

All possible MCS atom Mappings

getFirstAtomMapping

@TestMethod(value="testSearchMCS")
public Map<IAtom,IAtom> getFirstAtomMapping()

Returns one of the best matches with atoms mapped.

Specified by:

getFirstAtomMapping in interface IMCSBase

Returns:

Best Atom Mapping