Class McGregorChecks

java.lang.Object
org.openscience.cdk.smsd.algorithm.mcgregor.McGregorChecks

@Deprecated public class McGregorChecks 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 perform check/methods for McGregor class.
Author:
Syed Asad Rahman <asad@ebi.ac.uk>
Source code:
main
Belongs to CDK module:
smsd
  • Constructor Details

    • McGregorChecks

      public McGregorChecks()
      Deprecated.
  • Method Details

    • isFurtherMappingPossible

      protected static boolean isFurtherMappingPossible(IAtomContainer source, IAtomContainer target, int neighborBondNumA, int neighborBondNumB, List<Integer> iBondNeighborAtomsA, List<Integer> iBondNeighborAtomsB, List<String> cBondNeighborsA, List<String> cBondNeighborsB, boolean shouldMatchBonds)
      Deprecated.
      Parameters:
      source -
      target -
      neighborBondNumA -
      neighborBondNumB -
      iBondNeighborAtomsA -
      iBondNeighborAtomsB -
      cBondNeighborsA -
      cBondNeighborsB -
      shouldMatchBonds -
      Returns:
    • isMatchFeasible

      protected static boolean isMatchFeasible(IAtomContainer ac1, IBond bondA1, IAtomContainer ac2, IBond bondA2, boolean shouldMatchBonds)
      Deprecated.
    • searchCorrespondingAtom

      protected static int searchCorrespondingAtom(int mappedAtomsSize, int atomFromOtherMolecule, int molecule, List<Integer> mappedAtomsOrg)
      Deprecated.
      Parameters:
      mappedAtomsSize -
      atomFromOtherMolecule -
      molecule -
      mappedAtomsOrg -
      Returns:
    • isAtomMatch

      protected static boolean isAtomMatch(String g1A, String g2A, String g1B, String g2B)
      Deprecated.
      Parameters:
      g1A -
      g2A -
      g1B -
      g2B -
      Returns:
    • removeTreeStructure

      protected static int removeTreeStructure(BinaryTree curStruc)
      Deprecated.
    • removeRecurringMappings

      protected static List<Integer> removeRecurringMappings(List<Integer> atomMapping)
      Deprecated.
      Parameters:
      atomMapping -
      Returns:
    • removeRedundantArcs

      protected static void removeRedundantArcs(int row, int column, List<Integer> marcs, McgregorHelper mcGregorHelper)
      Deprecated.
      The function is called in function partsearch. The function is given a temporary matrix and a position (row/column) within this matrix. First the function sets all entries to zero, which can be exlcuded in respect to the current atom by atom matching. After this the function replaces all entries in the same row and column of the current position by zeros. Only the entry of the current position is set to one. Return value "count_arcsleft" counts the number of arcs, which are still in the matrix.
      Parameters:
      row -
      column -
      marcs -
      mcGregorHelper -
    • generateCSetCopy

      protected static List<String> generateCSetCopy(int bondNumber, List<String> cSet)
      Deprecated.
      Parameters:
      bondNumber -
      cSet -
      Returns:
    • generateCTabCopy

      protected static List<String> generateCTabCopy(IAtomContainer atomContainer) throws IOException
      Deprecated.
      Parameters:
      atomContainer -
      Returns:
      Throws:
      IOException
    • case1

      protected static boolean case1(int g1Atom, int g3Atom, int g4Atom, int rowAtom1, int rowAtom2, int columnAtom3, int columnAtom4)
      Deprecated.
      Parameters:
      g1Atom -
      g3Atom -
      g4Atom -
      rowAtom1 -
      rowAtom2 -
      columnAtom3 -
      columnAtom4 -
      Returns:
    • case2

      protected static boolean case2(int g2Atom, int g3Atom, int g4Atom, int rowAtom1, int rowAtom2, int columnAtom3, int columnAtom4)
      Deprecated.
      Parameters:
      g2Atom -
      g3Atom -
      g4Atom -
      rowAtom1 -
      rowAtom2 -
      columnAtom3 -
      columnAtom4 -
      Returns:
    • case3

      protected static boolean case3(int g1Atom, int g3Atom, int g2Atom, int rowAtom1, int rowAtom2, int columnAtom3, int columnAtom4)
      Deprecated.
      Parameters:
      g1Atom -
      g3Atom -
      g2Atom -
      rowAtom1 -
      rowAtom2 -
      columnAtom3 -
      columnAtom4 -
      Returns:
    • case4

      protected static boolean case4(int g1Atom, int g2Atom, int g4Atom, int rowAtom1, int rowAtom2, int columnAtom3, int columnAtom4)
      Deprecated.
      Parameters:
      g1Atom -
      g2Atom -
      g4Atom -
      rowAtom1 -
      rowAtom2 -
      columnAtom3 -
      columnAtom4 -
      Returns:
    • cases

      protected static boolean cases(int g1Atom, int g2Atom, int g3Atom, int g4Atom, int rowAtom1, int rowAtom2, int columnAtom3, int columnAtom4)
      Deprecated.
      Parameters:
      g1Atom -
      g2Atom -
      g3Atom -
      g4Atom -
      rowAtom1 -
      rowAtom2 -
      columnAtom3 -
      columnAtom4 -
      Returns:
    • setArcs

      protected static List<Integer> setArcs(IAtomContainer source, IAtomContainer target, int neighborBondNumA, int neighborBondNumB, List<Integer> iBondNeighborAtomsA, List<Integer> iBondNeighborAtomsB, List<String> cBondNeighborsA, List<String> cBondNeighborsB, List<Integer> modifiedARCS, boolean shouldMatchBonds)
      Deprecated.
      Parameters:
      source -
      target -
      neighborBondNumA -
      neighborBondNumB -
      iBondNeighborAtomsA -
      iBondNeighborAtomsB -
      cBondNeighborsA -
      cBondNeighborsB -
      modifiedARCS -
      shouldMatchBonds -
      Returns:
    • countArcsLeft

      protected static int countArcsLeft(List<Integer> tempmarcs, int neighborBondNumA, int neighborBondNumB)
      Deprecated.
      Parameters:
      tempmarcs -
      neighborBondNumA -
      neighborBondNumB -
      Returns:
    • changeCharBonds

      protected static int changeCharBonds(int correspondingAtom, String newSymbol, int neighborBondNum, IAtomContainer atomContainer, List<String> cBondNeighbors)
      Deprecated.
      Parameters:
      correspondingAtom -
      newSymbol -
      neighborBondNum -
      atomContainer -
      cBondNeighbors -
      Returns:
    • changeCharBonds

      protected static int changeCharBonds(int correspondingAtom, String newSymbol, int neighborBondNum, List<Integer> iBondNeighbors, List<String> cBondNeighbors)
      Deprecated.
      Parameters:
      correspondingAtom -
      newSymbol -
      neighborBondNum -
      iBondNeighbors -
      cBondNeighbors -
      Returns: