Class DefaultMCSPlusAtomMatcher

  • All Implemented Interfaces:
    AtomMatcher

    @Deprecated
    public class DefaultMCSPlusAtomMatcher
    extends Object
    implements AtomMatcher
    Deprecated.
    This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.
    Checks if atom is matching between query and target molecules.
    Author:
    Syed Asad Rahman <asad@ebi.ac.uk>
    Source code:
    main
    Belongs to CDK module:
    smsd
    • Constructor Detail

      • DefaultMCSPlusAtomMatcher

        public DefaultMCSPlusAtomMatcher()
        Deprecated.
        Constructor
      • DefaultMCSPlusAtomMatcher

        public DefaultMCSPlusAtomMatcher​(IAtomContainer queryContainer,
                                         IAtom atom,
                                         boolean shouldMatchBonds)
        Deprecated.
        Constructor
        Parameters:
        queryContainer - query atom container
        atom - query atom
        shouldMatchBonds - bond matching flag
      • DefaultMCSPlusAtomMatcher

        public DefaultMCSPlusAtomMatcher​(IQueryAtom smartQueryAtom,
                                         IQueryAtomContainer container)
        Deprecated.
        Constructor
        Parameters:
        smartQueryAtom - query atom
        container -
      • DefaultMCSPlusAtomMatcher

        public DefaultMCSPlusAtomMatcher​(IAtomContainer queryContainer,
                                         IAtom template,
                                         int blockedPositions,
                                         boolean shouldMatchBonds)
        Deprecated.
        Constructor
        Parameters:
        queryContainer - query atom container
        template - query atom
        blockedPositions -
        shouldMatchBonds - bond matching flag
    • Method Detail

      • isBondMatchFlag

        public boolean isBondMatchFlag()
        Deprecated.
        Returns:
        the shouldMatchBonds
      • setBondMatchFlag

        public final void setBondMatchFlag​(boolean shouldMatchBonds)
        Deprecated.
        Parameters:
        shouldMatchBonds - the shouldMatchBonds to set
      • setMaximumNeighbors

        public void setMaximumNeighbors​(int maximum)
        Deprecated.
        Parameters:
        maximum - numbers of connected atoms allowed
      • setSymbol

        public void setSymbol​(String symbol)
        Deprecated.
        Parameters:
        symbol -