Package org.openscience.cdk.smsd.algorithm.mcsplus

Class GenerateCompatibilityGraph

java.lang.Object

org.openscience.cdk.smsd.algorithm.mcsplus.GenerateCompatibilityGraph

@Deprecated
public final class GenerateCompatibilityGraph
extends Object

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 generates compatibility graph between query and target molecule. It also markes edges in the compatibility graph as c-edges or d-edges.

Author:

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

Source code:

main

Belongs to CDK module:

smsd

Constructor Summary

Constructors

Constructor	Description
GenerateCompatibilityGraph()	Deprecated. Default constructor added
GenerateCompatibilityGraph(IAtomContainer source, IAtomContainer target, boolean shouldMatchBonds)	Deprecated. Generates a compatibility graph between two molecules

Method Summary

Modifier and Type	Method	Description
void	clear()	Deprecated.
protected void	clearCEgdes()	Deprecated.
protected void	clearCompGraphNodes()	Deprecated.
protected void	clearCompGraphNodesCZero()	Deprecated.
protected void	clearDEgdes()	Deprecated.
protected int	compatibilityGraph()	Deprecated. Generate Compatibility Graph Nodes Bond Insensitive
protected int	compatibilityGraphCEdgeZero()	Deprecated. compatibilityGraphCEdgeZero is used to build up of the edges of the compatibility graph BIS
protected int	compatibilityGraphNodes()	Deprecated. Generate Compatibility Graph Nodes
protected Integer	compatibilityGraphNodesIfCEdgeIsZero()	Deprecated. compGraphNodesCZero is used to build up of the edges of the compatibility graph
protected int	getCEdgesSize()	Deprecated.
List<Integer>	getCEgdes()	Deprecated.
protected List<Integer>	getCompGraphNodes()	Deprecated.
protected List<Integer>	getCompGraphNodesCZero()	Deprecated.
protected int	getDEdgesSize()	Deprecated.
protected List<Integer>	getDEgdes()	Deprecated.
boolean	isMatchBond()	Deprecated.
protected void	resetCEdgesSize()	Deprecated.
protected void	resetDEdgesSize()	Deprecated.
void	setMatchBond(boolean shouldMatchBonds)	Deprecated.

Methods inherited from class java.lang.Object

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

Constructor Detail

GenerateCompatibilityGraph

public GenerateCompatibilityGraph()

Deprecated.

Default constructor added

GenerateCompatibilityGraph

public GenerateCompatibilityGraph(IAtomContainer source,
                                  IAtomContainer target,
                                  boolean shouldMatchBonds)
                           throws IOException

Deprecated.

Generates a compatibility graph between two molecules

Parameters:

source -

target -

shouldMatchBonds -

Throws:

IOException

Method Detail

compatibilityGraphNodes

protected int compatibilityGraphNodes()
                               throws IOException

Deprecated.

Generate Compatibility Graph Nodes

Returns:

Throws:

IOException

compatibilityGraph

protected int compatibilityGraph()
                          throws IOException

Deprecated.

Generate Compatibility Graph Nodes Bond Insensitive

Returns:

Throws:

IOException

compatibilityGraphNodesIfCEdgeIsZero

protected Integer compatibilityGraphNodesIfCEdgeIsZero()
                                                throws IOException

Deprecated.

compGraphNodesCZero is used to build up of the edges of the compatibility graph

Returns:

Throws:

IOException

compatibilityGraphCEdgeZero

protected int compatibilityGraphCEdgeZero()
                                   throws IOException

Deprecated.

compatibilityGraphCEdgeZero is used to build up of the edges of the compatibility graph BIS

Returns:

Throws:

IOException

getCEgdes

public List<Integer> getCEgdes()

Deprecated.

getDEgdes

protected List<Integer> getDEgdes()

Deprecated.

getCompGraphNodes

protected List<Integer> getCompGraphNodes()

Deprecated.

getCEdgesSize

protected int getCEdgesSize()

Deprecated.

getDEdgesSize

protected int getDEdgesSize()

Deprecated.

getCompGraphNodesCZero

protected List<Integer> getCompGraphNodesCZero()

Deprecated.

clearCEgdes

protected void clearCEgdes()

Deprecated.

clearDEgdes

protected void clearDEgdes()

Deprecated.

clearCompGraphNodes

protected void clearCompGraphNodes()

Deprecated.

clearCompGraphNodesCZero

protected void clearCompGraphNodesCZero()

Deprecated.

resetCEdgesSize

protected void resetCEdgesSize()

Deprecated.

resetDEdgesSize

protected void resetDEdgesSize()

Deprecated.

clear

public void clear()

Deprecated.

isMatchBond

public boolean isMatchBond()

Deprecated.

Returns:

the shouldMatchBonds

setMatchBond

public void setMatchBond(boolean shouldMatchBonds)

Deprecated.

Parameters:

shouldMatchBonds - the shouldMatchBonds to set