org.openscience.cdk.atomtype
Class MMFF94AtomTypeMatcher

java.lang.Object
  extended by 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
Belongs to CDK module:
extra
Source code:
HEAD

Constructor Summary
MMFF94AtomTypeMatcher()
          Constructor for the MMFF94AtomTypeMatcher object.
 
Method Summary
 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