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>
Source code:
main
Belongs to CDK module:
smsd
  • 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