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

Class QueryProcessor

java.lang.Object

org.openscience.cdk.smsd.algorithm.mcgregor.QueryProcessor

@Deprecated
public class QueryProcessor
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 query molecule.

Author:

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

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	QueryProcessor(List<String> cTab1Copy, List<String> cTab2Copy, String[] signArray, int neighborBondnumA, int setBondnumA, List<Integer> iBondNeighborsA, List<String> cBondNeighborsA, int mappingSize, List<Integer> iBondSetA, List<String> cBondSetA)	Deprecated. Query molecule

Method Summary

Modifier and Type	Method	Description
protected int	getBondNumA()	Deprecated.
protected List<String>	getCTab1()	Deprecated.
protected List<String>	getCTab2()	Deprecated.
protected int	getNeighborBondNumA()	Deprecated.
protected void	process(int setNumA, int setNumB, List<Integer> iBondSetA, List<Integer> iBondSetB, List<Integer> unmappedAtomsMolA, List<Integer> newMapping, int counter)	Deprecated.
protected void	process(IAtomContainer query, IAtomContainer target, List<Integer> unmappedAtomsMolA, List<Integer> mappedAtoms, int counter)	Deprecated.
protected void	process(IQueryAtomContainer query, IAtomContainer target, List<Integer> unmappedAtomsMolA, 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 Details

QueryProcessor

protected QueryProcessor(List<String> cTab1Copy,
 List<String> cTab2Copy,
 String[] signArray,
 int neighborBondnumA,
 int setBondnumA,
 List<Integer> iBondNeighborsA,
 List<String> cBondNeighborsA,
 int mappingSize,
 List<Integer> iBondSetA,
 List<String> cBondSetA)

Deprecated.

Query molecule

Parameters:

cTab1Copy -

cTab2Copy -

signArray -

neighborBondnumA -

setBondnumA -

iBondNeighborsA -

cBondNeighborsA -

mappingSize -

iBondSetA -

cBondSetA -

Method Details

process

protected void process(IAtomContainer query,
 IAtomContainer target,
 List<Integer> unmappedAtomsMolA,
 List<Integer> mappedAtoms,
 int counter)

Deprecated.

Parameters:

query -

target -

unmappedAtomsMolA -

mappedAtoms -

counter -

process

protected void process(IQueryAtomContainer query,
 IAtomContainer target,
 List<Integer> unmappedAtomsMolA,
 List<Integer> mappedAtoms,
 int counter)

Deprecated.

Parameters:

query -

target -

unmappedAtomsMolA -

mappedAtoms -

counter -

process

protected void process(int setNumA,
 int setNumB,
 List<Integer> iBondSetA,
 List<Integer> iBondSetB,
 List<Integer> unmappedAtomsMolA,
 List<Integer> newMapping,
 int counter)

Deprecated.

Parameters:

setNumA -

setNumB -

iBondSetA -

iBondSetB -

unmappedAtomsMolA -

newMapping -

counter -

getCTab1

protected List<String> getCTab1()

Deprecated.

Returns:

cTabQuery copy

getCTab2

protected List<String> getCTab2()

Deprecated.

Returns:

cTabTarget Copy

getNeighborBondNumA

protected int getNeighborBondNumA()

Deprecated.

Returns:

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

getBondNumA

protected int getBondNumA()

Deprecated.

Returns:

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