Class ChemicalFilters

java.lang.Object
org.openscience.cdk.smsd.filters.ChemicalFilters

@Deprecated public class ChemicalFilters 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 that ranks MCS final solution according to the chemical rules.
Author:
Syed Asad Rahman <asad@ebi.ac.uk>
Source code:
main
Belongs to CDK module:
smsd
  • Constructor Details

    • ChemicalFilters

      public ChemicalFilters(List<Map<Integer,Integer>> allMCS, List<Map<IAtom,IAtom>> allAtomMCS, Map<Integer,Integer> firstSolution, Map<IAtom,IAtom> firstAtomMCS, IAtomContainer sourceMol, IAtomContainer targetMol)
      Deprecated.
      This class has all the three chemical filters supported by the SMSD. i.e ring matches, bond energy etc
      1. a: Bond energy,
      2. b: Fragment count,
      3. c: Stereo matches
      Parameters:
      allMCS -
      allAtomMCS -
      firstSolution -
      firstAtomMCS -
      sourceMol -
      targetMol -
  • Method Details

    • sortResultsByStereoAndBondMatch

      public void sortResultsByStereoAndBondMatch() throws CDKException
      Deprecated.
      Sort MCS solution by stereo and bond type matches.
      Throws:
      CDKException
    • sortResultsByFragments

      public void sortResultsByFragments()
      Deprecated.
      Sort solution by ascending order of the fragment count.
    • sortResultsByEnergies

      public void sortResultsByEnergies() throws CDKException
      Deprecated.
      Sort MCS solution by bond breaking energy.
      Throws:
      CDKException
    • getSortedEnergy

      public List<Double> getSortedEnergy()
      Deprecated.
      Return sorted energy in ascending order.
      Returns:
      sorted bond breaking energy
    • getSortedFragment

      public List<Integer> getSortedFragment()
      Deprecated.
      Return sorted fragment in ascending order of the size.
      Returns:
      sorted fragment count
    • getStereoMatches

      public List<Double> getStereoMatches()
      Deprecated.
      Return Stereo matches in descending order.
      Returns:
      sorted stereo matches
    • convertOrder

      public static IBond.Order convertOrder(double srcOrder)
      Deprecated.
      Get bond order value as IBond.Order.
      Parameters:
      srcOrder - numerical bond order
      Returns:
      the bond order type for the given numerical bond order
    • convertBondOrder

      public static int convertBondOrder(IBond bond)
      Deprecated.
      Get bond order value as int value.
      Parameters:
      bond - The IBond for which the order is returned.
      Returns:
      1 for a single bond, 2 for a double bond, 3 for a triple bond, 4 for a quadruple bond, and 0 for any other bond type.
    • convertBondStereo

      public static int convertBondStereo(IBond bond)
      Deprecated.
      Get stereo value as integer
      Parameters:
      bond -
    • convertStereo

      public static IBond.Stereo convertStereo(int stereoValue)
      Deprecated.
      Get stereo value as Stereo enum
      Parameters:
      stereoValue -