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

Class TargetProcessor

java.lang.Object

org.openscience.cdk.smsd.algorithm.mcgregor.TargetProcessor

@Deprecated
public class TargetProcessor
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.

Class to handle mappings of target molecule based on the query.

Author:

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

Source code:

main

Belongs to CDK module:

smsd

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	TargetProcessor(List<String> cTab1Copy, List<String> cTab2Copy, String[] signArray, int neighborBondnumB, int setBondnumB, List<Integer> iBondNeighborsB, List<String> cBondNeighborsB, int newNeighborNumA, List<Integer> newINeighborsA, List<String> newCNeighborsA)	Deprecated.

Method Summary

Modifier and Type	Method	Description
protected int	getBondNumB()	Deprecated.
protected List<String>	getCTab1()	Deprecated.
protected List<String>	getCTab2()	Deprecated.
protected int	getNeighborBondNumB()	Deprecated.
protected void	process(int setNumB, List<Integer> unmappedAtomsMolB, int newMappingSize, List<Integer> iBondSetB, List<String> cBondSetB, List<Integer> newMapping, int counter, List<Integer> newIBondSetB, List<String> newCBondSetB)	Deprecated.
protected void	process(IAtomContainer target, List<Integer> unmappedAtomsMolB, int mappingSize, List<Integer> iBondSetB, List<String> cBondSetB, List<Integer> mappedAtoms, int counter)	Deprecated.

Methods inherited from class java.lang.Object

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

Constructor Detail

TargetProcessor

protected TargetProcessor(List<String> cTab1Copy,
                          List<String> cTab2Copy,
                          String[] signArray,
                          int neighborBondnumB,
                          int setBondnumB,
                          List<Integer> iBondNeighborsB,
                          List<String> cBondNeighborsB,
                          int newNeighborNumA,
                          List<Integer> newINeighborsA,
                          List<String> newCNeighborsA)

Deprecated.

Parameters:

cTab1Copy -

cTab2Copy -

signArray -

neighborBondnumB -

setBondnumB -

iBondNeighborsB -

cBondNeighborsB -

newNeighborNumA -

newINeighborsA -

newCNeighborsA -

Method Detail

process

protected void process(IAtomContainer target,
                       List<Integer> unmappedAtomsMolB,
                       int mappingSize,
                       List<Integer> iBondSetB,
                       List<String> cBondSetB,
                       List<Integer> mappedAtoms,
                       int counter)

Deprecated.

process

protected void process(int setNumB,
                       List<Integer> unmappedAtomsMolB,
                       int newMappingSize,
                       List<Integer> iBondSetB,
                       List<String> cBondSetB,
                       List<Integer> newMapping,
                       int counter,
                       List<Integer> newIBondSetB,
                       List<String> newCBondSetB)

Deprecated.

Parameters:

setNumB -

unmappedAtomsMolB -

newMappingSize -

iBondSetB -

cBondSetB -

newMapping -

counter -

newIBondSetB -

newCBondSetB -

getCTab1

protected List<String> getCTab1()

Deprecated.

Returns:

getCTab2

protected List<String> getCTab2()

Deprecated.

Returns:

getNeighborBondNumB

protected int getNeighborBondNumB()

Deprecated.

Returns:

number of remaining molecule A bonds after the clique search, which are neighbors of the MCS

getBondNumB

protected int getBondNumB()

Deprecated.

Returns:

number of remaining molecule A bonds after the clique search, which aren't neighbors