Package org.openscience.cdk.charges

Class AtomTypeCharges

java.lang.Object

org.openscience.cdk.charges.AtomTypeCharges

All Implemented Interfaces:

IChargeCalculator, IElectronicPropertyCalculator

public class AtomTypeCharges
extends Object
implements IChargeCalculator

Assigns charges to atom types.

Author:

chhoppe

Created on:

2004-11-03

Method Summary

Modifier and Type	Method	Description
void	calculateCharges(IAtomContainer container)
IAtomContainer	setCharges(IAtomContainer atomContainer)	Sets initial charges for atom types

Methods inherited from class java.lang.Object

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

Method Details

setCharges

public IAtomContainer setCharges(IAtomContainer atomContainer)
                          throws Exception

Sets initial charges for atom types. +1 for cationic atom types -1 for anionic atom types carboxylic oxygen -0.5 phosphorylic oxygen -0.66 sulfanilic oxygen -0.5 or to formal charge (which must be determined elsewhere or set manually) polycations are not handled by this approach

Parameters:

atomContainer - AtomContainer

Returns:

AtomContainer with set charges

Throws:

Exception - Description of the Exception

calculateCharges

public void calculateCharges(IAtomContainer container)
                      throws CDKException

Specified by:

calculateCharges in interface IElectronicPropertyCalculator

Throws:

CDKException