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:

master

Belongs to CDK module:

structgen

Created on:

2006-09-22

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
IAtomType	findMatchingAtomType(IAtomContainer atomContainer, IAtom atom) Finds the AtomType matching the Atom's element symbol, formal charge and hybridization state.
IAtomType[]	findMatchingAtomTypes(IAtomContainer atomContainer) Method that assigns atom types to atoms in the given atom container.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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