Package org.openscience.cdk.charges

Class GasteigerPEPEPartialCharges

java.lang.Object

org.openscience.cdk.charges.GasteigerPEPEPartialCharges

All Implemented Interfaces:

IChargeCalculator, IElectronicPropertyCalculator

public class GasteigerPEPEPartialCharges
extends Object
implements IChargeCalculator

The calculation of the Gasteiger (PEPE) partial charges is based on [Saller, H., Quantitative Emperische Modelle fur Elektronische Effekte in Pi-Systemen und fur die Chemische Reaktivitat, 1985, ?Institute?]. This class doesn't implement the original method of the Marsili but the method based on H. Saller which is described from Petra manual version 2.6

They are calculated by generating all valence bond (resonance) structures for this system and then weighting them on the basis of pi-orbital electronegativities and formal considerations based on PEPE (Partial Equalization of pi-electronegativity).

Author:

Miguel Rojas

See Also:

GasteigerMarsiliPartialCharges

Source code:

main

Belongs to CDK module:

charges

Keywords:

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

Created on:

2006-05-14

Constructor Summary

Constructors

Constructor	Description
GasteigerPEPEPartialCharges()	Constructor for the GasteigerPEPEPartialCharges object.

Method Summary

Modifier and Type	Method	Description
IAtomContainer	assignGasteigerPiPartialCharges(IAtomContainer ac, boolean setCharge)	Main method which assigns Gasteiger partial pi charges.
double[][]	assignrPiMarsilliFactors(IAtomContainerSet setAc)	Method which stores and assigns the factors a,b,c and CHI+.
void	calculateCharges(IAtomContainer container)
int	getMaxGasteigerIters()	Gets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges object.
int	getMaxResoStruc()	Gets the maximum resonance structures to be searched.
int	getStepSize()	Get the StepSize attribute of the GasteigerMarsiliPartialCharges object.
void	setMaxGasteigerIters(int iters)	Sets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges object.
void	setMaxResoStruc(int numbReson)	Sets the maximum resonance structures to be searched.
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

GasteigerPEPEPartialCharges

public GasteigerPEPEPartialCharges()

Constructor for the GasteigerPEPEPartialCharges object.

Method Detail

setMaxGasteigerIters

public void setMaxGasteigerIters(int iters)

Sets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges object.

Parameters:

iters - The new maxGasteigerIters value

setMaxResoStruc

public void setMaxResoStruc(int numbReson)

Sets the maximum resonance structures to be searched.

Parameters:

numbReson - The number of resonance Structures to be searched

getMaxGasteigerIters

public int getMaxGasteigerIters()

Gets the maxGasteigerIters attribute of the GasteigerPEPEPartialCharges object.

Returns:

The new maxGasteigerIters value

getMaxResoStruc

public int getMaxResoStruc()

Gets the maximum resonance structures to be searched.

Returns:

the maximum number of resonance structures that will be returned

assignGasteigerPiPartialCharges

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

Main method which assigns Gasteiger partial pi charges.

Parameters:

ac - AtomContainer

setCharge - currently unused

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 -

assignrPiMarsilliFactors

public double[][] assignrPiMarsilliFactors(IAtomContainerSet setAc)

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

Returns:

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