Class SybylAtomTypeMatcher

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

public class SybylAtomTypeMatcher extends Object implements IAtomTypeMatcher
Atom Type matcher for Sybyl atom types. It uses the CDKAtomTypeMatcher for perception and then maps CDK to Sybyl atom types.
Author:
egonw
Source code:
main
Belongs to CDK module:
atomtype
Keywords:
atom type, Sybyl
Created on:
2008-07-13
  • Method Details

    • getInstance

      public static SybylAtomTypeMatcher getInstance(IChemObjectBuilder builder)
      Returns an instance of this atom typer. It uses the given builder to create atom type objects.
      Parameters:
      builder - IChemObjectBuilder to use to create IAtomType instances.
      Returns:
      an instance of this atom type matcher.
    • findMatchingAtomTypes

      public IAtomType[] findMatchingAtomTypes(IAtomContainer atomContainer) throws CDKException
      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
      Sybyl atom type perception for a single atom. The molecular property aromaticity is not perceived; Aromatic carbons will, therefore, be perceived as C.2 and not C.ar. If the latter is required, please use findMatchingAtomType(IAtomContainer) instead.
      Specified by:
      findMatchingAtomType in interface IAtomTypeMatcher
      Parameters:
      atomContainer - the IAtomContainer in which the atom is found
      atom - the IAtom to find the atom type of
      Returns:
      the atom type perceived from the given atom
      Throws:
      CDKException - when something went wrong with going through the AtomType's