org.openscience.cdk.charges

Class GasteigerMarsiliPartialCharges

java.lang.Object

org.openscience.cdk.charges.GasteigerMarsiliPartialCharges

All Implemented Interfaces:

IChargeCalculator, IElectronicPropertyCalculator

public class GasteigerMarsiliPartialCharges
extends Object
implements IChargeCalculator

The calculation of the Gasteiger Marsili (PEOE) partial charges is based on [Gasteiger, J. and Marsili, M., Iterative partial equalization of orbital elektronegativity - a rapid access to atomic charges, Tetrahedron, 1980, 36:3219-3288]. This class only implements the original method which only applies to σ-bond systems.

Author:

chhoppe, rojas

Source code:

master

Belongs to CDK module:

charges

Keywords:

partial atomic charges, charge distribution, electronegativities, partial equalization of orbital, PEOE

Created on:

2004-11-03

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
IAtomContainer	assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac, boolean setCharge) Main method which assigns Gasteiger Marisili partial sigma charges.
double[]	assignGasteigerSigmaMarsiliFactors(IAtomContainer ac) Method which stores and assigns the factors a,b,c and CHI+.
void	calculateCharges(IAtomContainer container)
double	getChiCatHydrogen() Gets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation.
double	getMaxGasteigerDamp() Gets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object.
double	getMaxGasteigerIters() Gets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object.
int	getStepSize() Get the StepSize attribute of the GasteigerMarsiliPartialCharges object.
void	setChiCatHydrogen(double chiCat) Sets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation.
void	setMaxGasteigerDamp(double damp) Sets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object.
void	setMaxGasteigerIters(double iters) Sets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object.
void	setStepSize(int step) Set the StepSize attribute of the GasteigerMarsiliPartialCharges object.

Methods inherited from class java.lang.Object

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

Constructor Detail

GasteigerMarsiliPartialCharges

public GasteigerMarsiliPartialCharges()

Constructor for the GasteigerMarsiliPartialCharges object.

Method Detail

setChiCatHydrogen

public void setChiCatHydrogen(double chiCat)

Sets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation.

Parameters:

chiCat - The new DEOC_HYDROGEN value

setMaxGasteigerDamp

public void setMaxGasteigerDamp(double damp)

Sets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object.

Parameters:

damp - The new maxGasteigerDamp value

setMaxGasteigerIters

public void setMaxGasteigerIters(double iters)

Sets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object.

Parameters:

iters - The new maxGasteigerIters value

getChiCatHydrogen

public double getChiCatHydrogen()

Gets chi_cat value for hydrogen, because H poses a special problem due to lack of possible second ionisation.

Returns:

The new DEOC_HYDROGEN value

getMaxGasteigerDamp

public double getMaxGasteigerDamp()

Gets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object.

Returns:

The new maxGasteigerDamp value

getMaxGasteigerIters

public double getMaxGasteigerIters()

Gets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object.

Returns:

The new maxGasteigerIters value

assignGasteigerMarsiliSigmaPartialCharges

public IAtomContainer assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac,
                                                       boolean setCharge)
                                                         throws Exception

Main method which assigns Gasteiger Marisili partial sigma charges.

Parameters:

ac - AtomContainer

setCharge - The Charge

Returns:

AtomContainer with partial charges

Throws:

Exception - Possible Exceptions

calculateCharges

public void calculateCharges(IAtomContainer container)
                      throws CDKException

Specified by:

calculateCharges in interface IElectronicPropertyCalculator

Throws:

CDKException

getStepSize

public int getStepSize()

Get the StepSize attribute of the GasteigerMarsiliPartialCharges object.

Returns:

STEP_SIZE

setStepSize

public void setStepSize(int step)

Set the StepSize attribute of the GasteigerMarsiliPartialCharges object.

Parameters:

step - size of the step

assignGasteigerSigmaMarsiliFactors

public double[] assignGasteigerSigmaMarsiliFactors(IAtomContainer ac)
                                            throws CDKException

Method which stores and assigns the factors a,b,c and CHI+.

Parameters:

ac - AtomContainer

Returns:

Array of doubles [a1,b1,c1,denom1,chi1,q1...an,bn,cn...] 1:Atom 1-n in AtomContainer

Throws:

CDKException