Package org.openscience.cdk.atomtype

Class StructGenMatcher

java.lang.Object
org.openscience.cdk.atomtype.StructGenMatcher
All Implemented Interfaces:
IAtomTypeMatcher
public class StructGenMatcher extends Object implements IAtomTypeMatcher
AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol. This atom type matcher takes into account formal charge and number of implicit hydrogens, and requires bond orders to be given.

This class uses the cdk/config/data/structgen_atomtypes.xml list. If there is not an atom type defined for the tested atom, then null is returned.

Author:
egonw
Source code:
main
Belongs to CDK module:
structgen
Created on:
2006-09-22

  • Constructor Details

    • StructGenMatcher

      public StructGenMatcher()
      Constructor for the StructGenMatcher object.

  • Method Details

    • findMatchingAtomTypes

      public IAtomType[] findMatchingAtomTypes(IAtomContainer atomContainer) throws CDKException
      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 atom) throws CDKException
      Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.
      Specified by:
      findMatchingAtomType in interface IAtomTypeMatcher
      Parameters:
      atomContainer - AtomContainer
      atom - the target atom
      Returns:
      the matching AtomType
      Throws:
      CDKException - Exception thrown if something goes wrong