Package org.openscience.cdk.smsd.algorithm.matchers

Class DefaultVFAtomMatcher

java.lang.Object
org.openscience.cdk.smsd.algorithm.matchers.DefaultVFAtomMatcher
All Implemented Interfaces:
VFAtomMatcher
@Deprecated public class DefaultVFAtomMatcher extends Object implements VFAtomMatcher
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 Details

    • DefaultVFAtomMatcher

      public DefaultVFAtomMatcher()
      Deprecated.
      Constructor

    • DefaultVFAtomMatcher

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

    • DefaultVFAtomMatcher

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

    • DefaultVFAtomMatcher

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

  • Method Details

    • 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 -

    • matches

      public boolean matches(TargetProperties targetContainer, IAtom targetAtom)
      Deprecated.
      Specified by:
      matches in interface VFAtomMatcher