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:
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 Details

    • GasteigerPEPEPartialCharges

      public GasteigerPEPEPartialCharges()
      Constructor for the GasteigerPEPEPartialCharges object.
  • Method Details

    • 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