org.openscience.cdk.atomtype

Class MMFF94AtomTypeMatcher

java.lang.Object

org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher

All Implemented Interfaces:

IAtomTypeMatcher

Deprecated.

use the newer Mmff.assignAtomTypes()

@Deprecated
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

See Also:

Mmff

Source code:

master

Belongs to CDK module:

extra

Created on:

2005-18-07

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
IAtomType	findMatchingAtomType(IAtomContainer atomContainer, IAtom atomInterface) Deprecated. Assign the mmff94 atom type to a given atom.
IAtomType[]	findMatchingAtomTypes(IAtomContainer atomContainer) Deprecated. 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

MMFF94AtomTypeMatcher

public MMFF94AtomTypeMatcher()

Deprecated.

Constructor for the MMFF94AtomTypeMatcher object.

Method Detail

findMatchingAtomTypes

public IAtomType[] findMatchingAtomTypes(IAtomContainer atomContainer)
                                  throws CDKException

Deprecated.

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 atomInterface)
                               throws CDKException

Deprecated.

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