org.openscience.cdk.atomtype
Class StructGenAtomTypeGuesser

java.lang.Object
  extended by org.openscience.cdk.atomtype.StructGenAtomTypeGuesser
All Implemented Interfaces:
IAtomTypeGuesser

public class StructGenAtomTypeGuesser
extends Object
implements IAtomTypeGuesser

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
Created on:
2006-09-22
Belongs to CDK module:
structgen
Source code:
HEAD

Constructor Summary
StructGenAtomTypeGuesser()
          Constructor for the StructGenMatcher object.
 
Method Summary
 List<IAtomType> possibleAtomTypes(IAtomContainer atomContainer, IAtom atom)
          Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

StructGenAtomTypeGuesser

public StructGenAtomTypeGuesser()
Constructor for the StructGenMatcher object.

Method Detail

possibleAtomTypes

public List<IAtomType> possibleAtomTypes(IAtomContainer atomContainer,
                                         IAtom atom)
                                  throws CDKException
Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.

Specified by:
possibleAtomTypes in interface IAtomTypeGuesser
Parameters:
atomContainer - AtomContainer
atom - the target atom
Returns:
the matching AtomType
Throws:
CDKException - Exception thrown if something goed wrong