org.openscience.cdk.smsd.algorithm.matchers

Class DefaultRGraphAtomMatcher

java.lang.Object

org.openscience.cdk.smsd.algorithm.matchers.DefaultRGraphAtomMatcher

All Implemented Interfaces:

AtomMatcher

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 DefaultRGraphAtomMatcher
extends Object
implements AtomMatcher

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
DefaultRGraphAtomMatcher() Deprecated. Constructor
DefaultRGraphAtomMatcher(IAtomContainer queryContainer, IAtom atom, boolean shouldMatchBonds) Deprecated. Constructor
DefaultRGraphAtomMatcher(IAtomContainer queryContainer, IAtom template, int blockedPositions, boolean shouldMatchBonds) Deprecated. Constructor

Method Summary

Modifier and Type	Method and Description
boolean	isBondMatchFlag() Deprecated.
boolean	matches(IAtomContainer 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

DefaultRGraphAtomMatcher

public DefaultRGraphAtomMatcher()

Deprecated.

Constructor

DefaultRGraphAtomMatcher

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

Deprecated.

Constructor

Parameters:

queryContainer - query atom container

atom - query atom

shouldMatchBonds - bond matching flag

DefaultRGraphAtomMatcher

public DefaultRGraphAtomMatcher(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

matches

public boolean matches(IAtomContainer targetContainer,
                       IAtom targetAtom)

Deprecated.

Specified by:

matches in interface AtomMatcher

setMaximumNeighbors

public void setMaximumNeighbors(int maximum)

Deprecated.

Parameters:

maximum - numbers of connected atoms allowed

setSymbol

public void setSymbol(String symbol)

Deprecated.

Parameters:

symbol -