org.openscience.cdk.smsd.algorithm.vflib

Class VFlibMCSHandler

java.lang.Object

org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm

org.openscience.cdk.smsd.algorithm.vflib.VFlibMCSHandler

All Implemented Interfaces:

IMCSBase

Deprecated.

SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.

@Deprecated
public class VFlibMCSHandler
extends AbstractMCSAlgorithm
implements IMCSBase

This class should be used to find MCS between query graph and target graph. First the algorithm runs VF lib VFMCSMapper and reports MCS between run query and target graphs. Then these solutions are extended using McGregor McGregor algorithm where ever required.

Author:

Syed Asad Rahman <asad@ebi.ac.uk>

Source code:

master

Belongs to CDK module:

smsd

Constructor Summary

Constructors

Constructor and Description
VFlibMCSHandler() Deprecated. Constructor for an extended VF Algorithm for the MCS search

Method Summary

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

Methods inherited from class java.lang.Object

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

Constructor Detail

VFlibMCSHandler

public VFlibMCSHandler()

Deprecated.

Constructor for an extended VF Algorithm for the MCS search

Method Detail

searchMCS

public void searchMCS(boolean bondTypeMatch)

Deprecated.

Initialise the MCS search algorithm. Each MCS algorithm should contain this method.

Specified by:

searchMCS in class AbstractMCSAlgorithm

Parameters:

bondTypeMatch -

set

public void set(MolHandler reactant,
                MolHandler product)

Deprecated.

Initialise the query and target molecule. Set the VFLib MCS software

Specified by:

set in interface IMCSBase

Parameters:

reactant -

product -

set

public void set(IQueryAtomContainer source,
                IAtomContainer target)

Deprecated.

Initialise the query and target molecule.

Specified by:

set in interface IMCSBase

Parameters:

source -

target -

getAllAtomMapping

public List<Map<IAtom,IAtom>> getAllAtomMapping()

Deprecated.

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

getAllMapping

public List<Map<Integer,Integer>> getAllMapping()

Deprecated.

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

getFirstAtomMapping

public Map<IAtom,IAtom> getFirstAtomMapping()

Deprecated.

Returns one of the best matches with atoms mapped.

Specified by:

getFirstAtomMapping in interface IMCSBase

Returns:

Best Atom Mapping

getFirstMapping

public Map<Integer,Integer> getFirstMapping()

Deprecated.

Returns one of the best matches with atom indexes mapped.

Specified by:

getFirstMapping in interface IMCSBase

Returns:

Best Mapping Index

isBondMatchFlag

public boolean isBondMatchFlag()

Deprecated.

Returns:

the shouldMatchBonds

setBondMatchFlag

public void setBondMatchFlag(boolean shouldMatchBonds)

Deprecated.

Parameters:

shouldMatchBonds - the shouldMatchBonds to set