Class 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 Detail

      • StructGenMatcher

        public StructGenMatcher()
        Constructor for the StructGenMatcher object.
    • Method Detail

      • 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