Package 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.. Tetrahedron. 1980. 36]. 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

  • Constructor Details

    • GasteigerMarsiliPartialCharges

      public GasteigerMarsiliPartialCharges()
      Constructor for the GasteigerMarsiliPartialCharges object.

  • Method Details

    • 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