org.openscience.cdk.smsd.algorithm.mcgregor

Class McGregor

java.lang.Object

org.openscience.cdk.smsd.algorithm.mcgregor.McGregor

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 final class McGregor
extends Object

Class which reports MCS solutions based on the McGregor algorithm published in 1982.

The SMSD algorithm is described in this paper. please refer Rahman et.al. 2009 [Rahman, S.A. and Bashton, M. and Holliday, G.L. and Schrader, R. and Thornton, J.M. , Small Molecule Subgraph Detector (SMSD) Toolkit, Journal of Cheminformatics, 2009, 1:12, doi:10.1186/1758-2946-1-12].

Author:

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

Source code:

master

Belongs to CDK module:

smsd

Constructor Summary

Constructors

Constructor and Description
McGregor(IAtomContainer source, IAtomContainer target, List<List<Integer>> mappings, boolean shouldMatchBonds) Deprecated. Constructor for the McGregor algorithm.
McGregor(IQueryAtomContainer source, IAtomContainer target, List<List<Integer>> mappings) Deprecated. Constructor for the McGregor algorithm.

Method Summary

Methods

Modifier and Type	Method and Description
List<List<Integer>>	getMappings() Deprecated. Returns computed mappings.
int	getMCSSize() Deprecated. Returns MCS size.
boolean	isNewMatrix() Deprecated. Checks if its a new Matrix.
void	setNewMatrix(boolean newMatrix) Deprecated. set a new Matrix.
void	startMcGregorIteration(int largestMappingSize, List<Integer> cliqueVector, List<Integer> compGraphNodes) Deprecated. Start McGregor search and extend the mappings if possible.
void	startMcGregorIteration(int largestMappingSize, Map<Integer,Integer> presentMapping) Deprecated. Start McGregor search and extend the mappings if possible.

Methods inherited from class java.lang.Object

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

Constructor Detail

McGregor

public McGregor(IAtomContainer source,
        IAtomContainer target,
        List<List<Integer>> mappings,
        boolean shouldMatchBonds)

Deprecated.

Constructor for the McGregor algorithm.

Parameters:

source -

target -

mappings -

shouldMatchBonds -

McGregor

public McGregor(IQueryAtomContainer source,
        IAtomContainer target,
        List<List<Integer>> mappings)

Deprecated.

Constructor for the McGregor algorithm.

Parameters:

source -

target -

mappings -

Method Detail

startMcGregorIteration

public void startMcGregorIteration(int largestMappingSize,
                          Map<Integer,Integer> presentMapping)
                            throws IOException

Deprecated.

Start McGregor search and extend the mappings if possible.

Parameters:

largestMappingSize -

presentMapping -

Throws:

IOException

startMcGregorIteration

public void startMcGregorIteration(int largestMappingSize,
                          List<Integer> cliqueVector,
                          List<Integer> compGraphNodes)
                            throws IOException

Deprecated.

Start McGregor search and extend the mappings if possible.

Parameters:

largestMappingSize -

cliqueVector -

compGraphNodes -

Throws:

IOException

getMappings

public List<List<Integer>> getMappings()

Deprecated.

Returns computed mappings.

Returns:

mappings

getMCSSize

public int getMCSSize()

Deprecated.

Returns MCS size.

Returns:

MCS size

isNewMatrix

public boolean isNewMatrix()

Deprecated.

Checks if its a new Matrix.

Returns:

the newMatrix

setNewMatrix

public void setNewMatrix(boolean newMatrix)

Deprecated.

set a new Matrix.

Parameters:

newMatrix - the newMatrix to set