org.openscience.cdk.atomtype

Class StructGenAtomTypeGuesser

java.lang.Object

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

Source code:

master

Belongs to CDK module:

structgen

Created on:

2006-09-22

Constructor Summary

Constructors

Constructor and Description
StructGenAtomTypeGuesser() Constructor for the StructGenMatcher object.

Method Summary

Modifier and Type	Method and Description
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

clone, equals, finalize, 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 goes wrong