Package org.openscience.cdk.atomtype

Class MM2AtomTypeMatcher

java.lang.Object

org.openscience.cdk.atomtype.MM2AtomTypeMatcher

All Implemented Interfaces:

IAtomTypeMatcher

@Deprecated
public class MM2AtomTypeMatcher
extends Object
implements IAtomTypeMatcher

Deprecated.

Incomplete and error prone - use at your own risk.

Class implements methods to assign mmff94 atom types for a specific atom in an molecule.

Author:

cho

Source code:

main

Belongs to CDK module:

extra

Created on:

2005-18-07

Constructor Summary

Constructors

Constructor	Description
MM2AtomTypeMatcher()	Deprecated. Constructor for the MMFF94AtomTypeMatcher object.

Method Summary

Modifier and Type	Method	Description
IAtomType	findMatchingAtomType(IAtomContainer atomContainer, IAtom atomInterface)	Deprecated. Assign the mm2 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

MM2AtomTypeMatcher

public MM2AtomTypeMatcher()

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 mm2 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