org.openscience.cdk.charges

Class InductivePartialCharges

java.lang.Object

org.openscience.cdk.charges.InductivePartialCharges

All Implemented Interfaces:

IChargeCalculator, IElectronicPropertyCalculator

public class InductivePartialCharges
extends Object
implements IChargeCalculator

The calculation of the inductive partial atomic charges and equalization of effective electronegativities is based on [Cherkasov, A., Inductive Electronegativity Scale. Iterative Calculation of Inductive Partial Charges, J. Chem. Inf. Comput. Sci., 2003, 43:2039-2047].

Author:

mfe4

Source code:

master

Belongs to CDK module:

charges

Keywords:

partial atomic charges, charge distribution, electronegativity

Created on:

2004-11-03

Constructor Summary

Constructors

Constructor and Description
InductivePartialCharges() Constructor for the InductivePartialCharges object.

Method Summary

Methods

Modifier and Type	Method and Description
IAtomContainer	assignInductivePartialCharges(IAtomContainer ac) Main method, set charge as atom properties.
void	calculateCharges(IAtomContainer container)
double	getAtomicSoftnessCore(IAtomContainer ac, int atomPosition) Gets the atomicSoftnessCore attribute of the InductivePartialCharges object.
double[]	getPaulingElectronegativities(IAtomContainer ac, boolean modified) Gets the paulingElectronegativities attribute of the InductivePartialCharges object.

Methods inherited from class java.lang.Object

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

Constructor Detail

InductivePartialCharges

public InductivePartialCharges()
                        throws IOException,
                               ClassNotFoundException

Constructor for the InductivePartialCharges object.

Throws:

IOException - Description of the Exception

ClassNotFoundException - Description of the Exception

Method Detail

assignInductivePartialCharges

public IAtomContainer assignInductivePartialCharges(IAtomContainer ac)
                                             throws Exception

Main method, set charge as atom properties.

Parameters:

ac - AtomContainer

Returns:

AtomContainer

Throws:

Exception - Description of the Exception

calculateCharges

public void calculateCharges(IAtomContainer container)
                      throws CDKException

Specified by:

calculateCharges in interface IElectronicPropertyCalculator

Throws:

CDKException

getPaulingElectronegativities

public double[] getPaulingElectronegativities(IAtomContainer ac,
                                     boolean modified)
                                       throws CDKException

Gets the paulingElectronegativities attribute of the InductivePartialCharges object.

Parameters:

ac - AtomContainer

modified - if true, some values are modified by following the reference

Returns:

The pauling electronegativities

Throws:

CDKException

getAtomicSoftnessCore

public double getAtomicSoftnessCore(IAtomContainer ac,
                           int atomPosition)
                             throws CDKException

Gets the atomicSoftnessCore attribute of the InductivePartialCharges object.

Parameters:

ac - AtomContainer

atomPosition - position of target atom

Returns:

The atomicSoftnessCore value

Throws:

CDKException - Description of the Exception