Package org.openscience.cdk.smsd.algorithm.vflib.map

Class VFMapper

java.lang.Object

org.openscience.cdk.smsd.algorithm.vflib.map.VFMapper

All Implemented Interfaces:

IMapper

@Deprecated
public class VFMapper
extends Object
implements IMapper

Deprecated.

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

This class finds MCS between query and target molecules using VF2 algorithm.

Author:

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

Source code:

main

Belongs to CDK module:

smsd

Constructor Summary

Constructors

Constructor	Description
VFMapper(IAtomContainer queryMolecule, boolean bondMatcher)	Deprecated.
VFMapper(IQuery query)	Deprecated.

Method Summary

Modifier and Type	Method	Description
int	countMaps(IAtomContainer target)	Deprecated. Returns solution map count.
int	countMaps(TargetProperties targetMolecule)	Deprecated. Returns solution map count.
Map<INode,IAtom>	getFirstMap(IAtomContainer target)	Deprecated. Returns first solution map.
Map<INode,IAtom>	getFirstMap(TargetProperties targetMolecule)	Deprecated. Returns first solution map.
List<Map<INode,IAtom>>	getMaps(IAtomContainer target)	Deprecated. Returns all solution map.
List<Map<INode,IAtom>>	getMaps(TargetProperties targetMolecule)	Deprecated. Returns all solution map.
protected static TimeManager	getTimeManager()	Deprecated.
protected static double	getTimeout()	Deprecated.
boolean	hasMap(IAtomContainer targetMolecule)	Deprecated. checks if a map exits for a molecule.
boolean	hasMap(TargetProperties targetMolecule)	Deprecated. checks if a map exits for a molecule.
static boolean	isTimeOut()	Deprecated.
protected static void	setTimeManager(TimeManager aTimeManager)	Deprecated.

Methods inherited from class java.lang.Object

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

Constructor Detail

VFMapper

public VFMapper(IQuery query)

Deprecated.

Parameters:

query -

VFMapper

public VFMapper(IAtomContainer queryMolecule,
                boolean bondMatcher)

Deprecated.

Parameters:

queryMolecule -

bondMatcher -

Method Detail

getTimeout

protected static double getTimeout()

Deprecated.

Returns:

the timeout

getTimeManager

protected static TimeManager getTimeManager()

Deprecated.

Returns:

the timeManager

setTimeManager

protected static void setTimeManager(TimeManager aTimeManager)

Deprecated.

Parameters:

aTimeManager - the timeManager to set

hasMap

public boolean hasMap(IAtomContainer targetMolecule)

Deprecated.

checks if a map exits for a molecule.

Specified by:

hasMap in interface IMapper

Parameters:

targetMolecule - targetMolecule graph

Returns:

true/false.

getMaps

public List<Map<INode,IAtom>> getMaps(IAtomContainer target)

Deprecated.

Returns all solution map.

Specified by:

getMaps in interface IMapper

Parameters:

target - molecule.

Returns:

get maps.

getFirstMap

public Map<INode,IAtom> getFirstMap(IAtomContainer target)

Deprecated.

Returns first solution map.

Specified by:

getFirstMap in interface IMapper

Parameters:

target -

Returns:

get first map.

countMaps

public int countMaps(IAtomContainer target)

Deprecated.

Returns solution map count.

Specified by:

countMaps in interface IMapper

Parameters:

target - target molecule.

Returns:

map count.

hasMap

public boolean hasMap(TargetProperties targetMolecule)

Deprecated.

checks if a map exits for a molecule.

Specified by:

hasMap in interface IMapper

Parameters:

targetMolecule - targetMolecule graph

Returns:

true/false.

getMaps

public List<Map<INode,IAtom>> getMaps(TargetProperties targetMolecule)

Deprecated.

Returns all solution map.

Specified by:

getMaps in interface IMapper

Parameters:

targetMolecule -

Returns:

get maps.

getFirstMap

public Map<INode,IAtom> getFirstMap(TargetProperties targetMolecule)

Deprecated.

Returns first solution map.

Specified by:

getFirstMap in interface IMapper

Parameters:

targetMolecule -

Returns:

get first map.

countMaps

public int countMaps(TargetProperties targetMolecule)

Deprecated.

Returns solution map count.

Specified by:

countMaps in interface IMapper

Parameters:

targetMolecule -

Returns:

map count.

isTimeOut

public static boolean isTimeOut()

Deprecated.