org.openscience.cdk.atomtype

Class MM2AtomTypeMatcher

java.lang.Object

org.openscience.cdk.atomtype.MM2AtomTypeMatcher

All Implemented Interfaces:

IAtomTypeMatcher

public class MM2AtomTypeMatcher
extends Object
implements IAtomTypeMatcher

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

Author:

cho

Created on:

2005-18-07

Constructor Summary

Constructors

Constructor and Description
MM2AtomTypeMatcher() 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 mm2 atom type to a given atom.

Methods inherited from class java.lang.Object

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

Constructor Detail

MM2AtomTypeMatcher

public MM2AtomTypeMatcher()

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 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