org.openscience.cdk.atomtype

Class MMFF94AtomTypeMatcher

java.lang.Object

org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher

All Implemented Interfaces:

IAtomTypeMatcher

public class MMFF94AtomTypeMatcher
extends Object
implements IAtomTypeMatcher

Class implements methods to assign mmff94 atom types for a specific atom in an molecule. The full list of mmff94 atom types is defined in the file cdk/config/data/mmff94_atomtypes.xml.

Author:

cho

Created on:

2005-18-07

Constructor Summary

Constructors

Constructor and Description
MMFF94AtomTypeMatcher() Constructor for the MMFF94AtomTypeMatcher object.

Method Summary

Methods

Modifier and Type	Method and Description
IAtomType[]	findMatchingAtomType(IAtomContainer atomContainer) Method that assigns atom types to atoms in the given atom container.
IAtomType	findMatchingAtomType(IAtomContainer atomContainer, IAtom atomInterface) Assign the mmff94 atom type to a given atom.

Methods inherited from class java.lang.Object

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

Constructor Detail

MMFF94AtomTypeMatcher

public MMFF94AtomTypeMatcher()

Constructor for the MMFF94AtomTypeMatcher object.

Method Detail

findMatchingAtomType

@TestMethod(value="testFindMatchingAtomType_IAtomContainer")
public IAtomType[] findMatchingAtomType(IAtomContainer atomContainer)
                                 throws CDKException

Description copied from interface: IAtomTypeMatcher

Method that assigns atom types to atoms in the given atom container.

Specified by:

findMatchingAtomType 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 atomInterface)
                               throws CDKException

Assign the mmff94 atom type to a given atom. Before this method can be called the following has to be done: atomContainer=(AtomContainer)atomTypeTools.assignAtomTypePropertiesToAtom(new Molecule(atomContainer));

Specified by:

findMatchingAtomType in interface IAtomTypeMatcher

Parameters:

atomContainer - AtomContainer

atomInterface - the target atom

Returns:

the matching AtomType (AtomType class)

Throws:

CDKException - Description of the Exception