Package org.openscience.cdk.smsd.algorithm.mcgregor

Class McgregorHelper

java.lang.Object

org.openscience.cdk.smsd.algorithm.mcgregor.McgregorHelper

@Deprecated
public class McgregorHelper
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.

Helper Class for McGregor algorithm. The second part of the program extents the mapping by the McGregor algorithm in case, that not all atoms of molecule A and molecule B are mapped by the clique approach.

Author:

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

Source code:

main

Belongs to CDK module:

smsd

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	McgregorHelper(boolean mappingCheckFlag, int mappedAtomCount, List<Integer> mappedAtomsOrg, int neighborBondNumA, int neighborBondNumB, List<Integer> iBondNeighborAtomsA, List<Integer> iBondNeighborAtomsB, List<String> cBondNeighborsA, List<String> cBondNeighborsB, int setNumA, int setNumB, List<Integer> iBondSetA, List<Integer> iBondSetB, List<String> cBondSetA, List<String> cBondSetB)	Deprecated. Stores the variables

Method Summary

Modifier and Type	Method	Description
protected List<String>	getcBondNeighborsA()	Deprecated.
protected List<String>	getcBondNeighborsB()	Deprecated.
protected List<String>	getCBondSetA()	Deprecated.
protected List<String>	getCBondSetB()	Deprecated.
protected List<Integer>	getiBondNeighborAtomsA()	Deprecated.
protected List<Integer>	getiBondNeighborAtomsB()	Deprecated.
protected List<Integer>	getIBondSetA()	Deprecated.
protected List<Integer>	getIBondSetB()	Deprecated.
protected int	getMappedAtomCount()	Deprecated.
protected List<Integer>	getMappedAtomsOrg()	Deprecated.
protected int	getNeighborBondNumA()	Deprecated.
protected int	getNeighborBondNumB()	Deprecated.
protected int	getSetNumA()	Deprecated.
protected boolean	isMappingCheckFlag()	Deprecated.

Methods inherited from class java.lang.Object

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

Constructor Detail

McgregorHelper

protected McgregorHelper(boolean mappingCheckFlag,
                         int mappedAtomCount,
                         List<Integer> mappedAtomsOrg,
                         int neighborBondNumA,
                         int neighborBondNumB,
                         List<Integer> iBondNeighborAtomsA,
                         List<Integer> iBondNeighborAtomsB,
                         List<String> cBondNeighborsA,
                         List<String> cBondNeighborsB,
                         int setNumA,
                         int setNumB,
                         List<Integer> iBondSetA,
                         List<Integer> iBondSetB,
                         List<String> cBondSetA,
                         List<String> cBondSetB)

Deprecated.

Stores the variables

Parameters:

mappingCheckFlag -

mappedAtomCount -

mappedAtomsOrg -

neighborBondNumA -

neighborBondNumB -

iBondNeighborAtomsA -

iBondNeighborAtomsB -

cBondNeighborsA -

cBondNeighborsB -

setNumA -

setNumB -

iBondSetA -

iBondSetB -

cBondSetA -

cBondSetB -

Method Detail

getCBondSetA

protected List<String> getCBondSetA()

Deprecated.

Returns:

the cBondSetA

getCBondSetB

protected List<String> getCBondSetB()

Deprecated.

Returns:

the cBondSetB

isMappingCheckFlag

protected boolean isMappingCheckFlag()

Deprecated.

Returns:

the mappingCheckFlag

getMappedAtomCount

protected int getMappedAtomCount()

Deprecated.

Returns:

the mappedAtomCount

getMappedAtomsOrg

protected List<Integer> getMappedAtomsOrg()

Deprecated.

Returns:

the mappedAtomsOrg

getNeighborBondNumA

protected int getNeighborBondNumA()

Deprecated.

Returns:

the neighborBondNumA

getNeighborBondNumB

protected int getNeighborBondNumB()

Deprecated.

Returns:

the neighborBondNumB

getiBondNeighborAtomsA

protected List<Integer> getiBondNeighborAtomsA()

Deprecated.

Returns:

the iBondNeighborAtomsA

getiBondNeighborAtomsB

protected List<Integer> getiBondNeighborAtomsB()

Deprecated.

Returns:

the iBondNeighborAtomsB

getcBondNeighborsA

protected List<String> getcBondNeighborsA()

Deprecated.

Returns:

the cBondNeighborsA

getcBondNeighborsB

protected List<String> getcBondNeighborsB()

Deprecated.

Returns:

the cBondNeighborsB

getSetNumA

protected int getSetNumA()

Deprecated.

Returns:

the setNumA

getIBondSetA

protected List<Integer> getIBondSetA()

Deprecated.

Returns:

the iBondSetA

getIBondSetB

protected List<Integer> getIBondSetB()

Deprecated.

Returns:

the iBondSetB