org.openscience.cdk.charges

Class MMFF94PartialCharges

java.lang.Object

org.openscience.cdk.charges.MMFF94PartialCharges

All Implemented Interfaces:

IChargeCalculator, IElectronicPropertyCalculator

public class MMFF94PartialCharges
extends Object
implements IChargeCalculator

The calculation of the MMFF94 partial charges. Charges are stored as atom properties ("MMFF94charge") for an AtomContainer ac, values are calculated with:

  HydrogenAdder hAdder = new HydrogenAdder();
  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
  IAtomContainer ac = sp.parseSmiles("CC");
  hAdder.addExplicitHydrogensToSatisfyValency((Molecule)ac);
  MMFF94PartialCharges mmff = new MMFF94PartialCharges();
  mmff.assignMMFF94PartialCharges(ac);
  

and for each atom, the value is given by:

  ( (Double)atom.getProperty("MMFF94charge") ).doubleValue().
  

Note: This class delegates to Mmff and charges are also assigned directly to the atom attribute IAtom.getCharge().

Author:

mfe4, chhoppe

See Also:

Mmff.partialCharges(IAtomContainer)

Source code:

master

Belongs to CDK module:

forcefield

Created on:

2004-11-03

Field Summary

Fields

Modifier and Type	Field and Description
static String	MMFF_94_CHARGE

Constructor Summary

Constructors

Constructor and Description
MMFF94PartialCharges() Constructor for the MMFF94PartialCharges object

Method Summary

Methods

Modifier and Type	Method and Description
IAtomContainer	assignMMFF94PartialCharges(IAtomContainer ac) Main method which assigns MMFF94 partial charges
void	calculateCharges(IAtomContainer container)

Methods inherited from class java.lang.Object

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

Field Detail

MMFF_94_CHARGE

public static final String MMFF_94_CHARGE

See Also:

Constant Field Values

Constructor Detail

MMFF94PartialCharges

public MMFF94PartialCharges()

Constructor for the MMFF94PartialCharges object

Method Detail

assignMMFF94PartialCharges

public IAtomContainer assignMMFF94PartialCharges(IAtomContainer ac)
                                          throws CDKException

Main method which assigns MMFF94 partial charges

Parameters:

ac - AtomContainer

Returns:

AtomContainer with MMFF94 partial charges as atom properties

Throws:

CDKException

calculateCharges

public void calculateCharges(IAtomContainer container)
                      throws CDKException

Specified by:

calculateCharges in interface IElectronicPropertyCalculator

Throws:

CDKException