org.openscience.cdk.charges
Class GasteigerMarsiliPartialCharges

java.lang.Object
  org.openscience.cdk.charges.GasteigerMarsiliPartialCharges

All Implemented Interfaces:

IChargeCalculator, IElectronicPropertyCalculator

@TestClass(value="org.openscience.cdk.charges.GasteigerMarsiliPartialChargesTest")
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

Keywords:

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

Created on:

2004-11-03

Belongs to CDK module:

charges

Source code:

cdk-1.4.x

Constructor Summary

GasteigerMarsiliPartialCharges()
Constructor for the GasteigerMarsiliPartialCharges object

Method Summary

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

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

Constructor Detail

GasteigerMarsiliPartialCharges

public GasteigerMarsiliPartialCharges()

Constructor for the GasteigerMarsiliPartialCharges object

Method Detail

setChiCatHydrogen

@TestMethod(value="testSetChiCatHydrogen_Double")
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

@TestMethod(value="testSetMaxGasteigerDamp_Double")
public void setMaxGasteigerDamp(double damp)

Sets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object

Parameters:

damp - The new maxGasteigerDamp value

setMaxGasteigerIters

@TestMethod(value="testSetMaxGasteigerIters_Double")
public void setMaxGasteigerIters(double iters)

Sets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object

Parameters:

iters - The new maxGasteigerIters value

getChiCatHydrogen

@TestMethod(value="testGetChiCatHydrogen")
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

@TestMethod(value="testGetMaxGasteigerDamp")
public double getMaxGasteigerDamp()

Gets the maxGasteigerDamp attribute of the GasteigerMarsiliPartialCharges object

Returns:

The new maxGasteigerDamp value

getMaxGasteigerIters

@TestMethod(value="testGetMaxGasteigerIters")
public double getMaxGasteigerIters()

Gets the maxGasteigerIters attribute of the GasteigerMarsiliPartialCharges object

Returns:

The new maxGasteigerIters value

assignGasteigerMarsiliSigmaPartialCharges

@TestMethod(value="testAssignGasteigerMarsiliSigmaPartialCharges_IAtomContainer_Boolean")
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

@TestMethod(value="testCalculateCharges_IAtomContainer")
public void calculateCharges(IAtomContainer container)
                      throws CDKException

Specified by:

calculateCharges in interface IElectronicPropertyCalculator

Throws:

CDKException

getStepSize

@TestMethod(value="testGetStepSize")
public int getStepSize()

Get the StepSize attribute of the GasteigerMarsiliPartialCharges object

Returns:

STEP_SIZE

setStepSize

@TestMethod(value="testSetStepSize")
public void setStepSize(int step)

Set the StepSize attribute of the GasteigerMarsiliPartialCharges object

Parameters:

step -

assignGasteigerSigmaMarsiliFactors

@TestMethod(value="testAssignGasteigerSigmaMarsiliFactors_IAtomContainer")
public double[] assignGasteigerSigmaMarsiliFactors(IAtomContainer ac)

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