org.openscience.cdk.smsd.algorithm.matchers

Class DefaultVFAtomMatcher

java.lang.Object

org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher

All Implemented Interfaces:

VFAtomMatcher

Deprecated.

This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. 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 DefaultVFAtomMatcher
extends Object
implements VFAtomMatcher

Checks if atom is matching between query and target molecules.

Author:

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

Source code:

master

Belongs to CDK module:

smsd

Constructor Summary

Constructors

Constructor and Description
DefaultVFAtomMatcher() Deprecated. Constructor
DefaultVFAtomMatcher(IAtomContainer queryContainer, IAtom atom, boolean shouldMatchBonds) Deprecated. Constructor
DefaultVFAtomMatcher(IAtomContainer queryContainer, IAtom template, int blockedPositions, boolean shouldMatchBonds) Deprecated. Constructor
DefaultVFAtomMatcher(IQueryAtom smartQueryAtom, IQueryAtomContainer container) Deprecated. Constructor

Method Summary

Modifier and Type	Method and Description
boolean	isBondMatchFlag() Deprecated.
boolean	matches(TargetProperties targetContainer, IAtom targetAtom) Deprecated.
void	setBondMatchFlag(boolean shouldMatchBonds) Deprecated.
void	setMaximumNeighbors(int maximum) Deprecated.
void	setSymbol(String symbol) Deprecated.

Methods inherited from class java.lang.Object

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

Constructor Detail

DefaultVFAtomMatcher

public DefaultVFAtomMatcher()

Deprecated.

Constructor

DefaultVFAtomMatcher

public DefaultVFAtomMatcher(IAtomContainer queryContainer,
                            IAtom atom,
                            boolean shouldMatchBonds)

Deprecated.

Constructor

Parameters:

queryContainer - query atom container

atom - query atom

shouldMatchBonds - bond matching flag

DefaultVFAtomMatcher

public DefaultVFAtomMatcher(IQueryAtom smartQueryAtom,
                            IQueryAtomContainer container)

Deprecated.

Constructor

Parameters:

smartQueryAtom - query atom

container -

DefaultVFAtomMatcher

public DefaultVFAtomMatcher(IAtomContainer queryContainer,
                            IAtom template,
                            int blockedPositions,
                            boolean shouldMatchBonds)

Deprecated.

Constructor

Parameters:

queryContainer - query atom container

template - query atom

blockedPositions -

shouldMatchBonds - bond matching flag

Method Detail

isBondMatchFlag

public boolean isBondMatchFlag()

Deprecated.

Returns:

the shouldMatchBonds

setBondMatchFlag

public final void setBondMatchFlag(boolean shouldMatchBonds)

Deprecated.

Parameters:

shouldMatchBonds - the shouldMatchBonds to set

setMaximumNeighbors

public void setMaximumNeighbors(int maximum)

Deprecated.

Parameters:

maximum - numbers of connected atoms allowed

setSymbol

public void setSymbol(String symbol)

Deprecated.

Parameters:

symbol -

matches

public boolean matches(TargetProperties targetContainer,
                       IAtom targetAtom)

Deprecated.

Specified by:

matches in interface VFAtomMatcher