Class MM2AtomTypeMatcher

java.lang.Object
org.openscience.cdk.atomtype.MM2AtomTypeMatcher
All Implemented Interfaces:
IAtomTypeMatcher

@Deprecated public class MM2AtomTypeMatcher extends Object implements IAtomTypeMatcher
Deprecated.
Incomplete and error prone - use at your own risk.
Class implements methods to assign mmff94 atom types for a specific atom in an molecule.
Author:
cho
Source code:
main
Belongs to CDK module:
extra
Created on:
2005-18-07
  • Constructor Details

    • MM2AtomTypeMatcher

      public MM2AtomTypeMatcher()
      Deprecated.
      Constructor for the MMFF94AtomTypeMatcher object.
  • Method Details

    • findMatchingAtomTypes

      public IAtomType[] findMatchingAtomTypes(IAtomContainer atomContainer) throws CDKException
      Deprecated.
      Description copied from interface: IAtomTypeMatcher
      Method that assigns atom types to atoms in the given atom container.
      Specified by:
      findMatchingAtomTypes in interface IAtomTypeMatcher
      Parameters:
      atomContainer - AtomContainer for which atom types are perceived
      Returns:
      The matching AtomType
      Throws:
      CDKException - when something went wrong with going through the AtomType's
    • findMatchingAtomType

      public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atomInterface) throws CDKException
      Deprecated.
      Assign the mm2 atom type to a given atom. Before this method can be called the following has to be done:
       atomContainer = (AtomContainer)atomTypeTools.assignAtomTypePropertiesToAtom(
         new Molecule(atomContainer)
       );
       
      Specified by:
      findMatchingAtomType in interface IAtomTypeMatcher
      Parameters:
      atomContainer - AtomContainer
      atomInterface - the target atom
      Returns:
      the matching AtomType (AtomType class)
      Throws:
      CDKException - Description of the Exception