Package org.openscience.cdk.charges

Class Polarizability

java.lang.Object
org.openscience.cdk.charges.Polarizability
public class Polarizability extends Object
Calculation of the polarizability of a molecule by the method of Kang and Jhon and Gasteiger based on [Kang, Y.K. and Jhon, M.S.. Theoretica Chimica Acta. 1982. 61] and [Gasteiger, J. and Hutchings, M.G.. J. Amer. Chem. Soc.. 1984. 106] Limitations in parameterization of atoms: H, Csp3, Csp2, Csp2arom, Csp3, Nsp3, Nsp2, Nsp3, P, Osp3 and Osp2. Aromaticity must be calculated beforehand.
Author:
chhoppe
Source code:
main
Belongs to CDK module:
charges
Keywords:
polarizability
Created on:
2004-11-03

  • Constructor Details

    • Polarizability

      public Polarizability()
      Constructor for the Polarizability object.

  • Method Details

    • getPolarizabilitiyFactorForAtom

      public double getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer, IAtom atom)
      Gets the polarizabilitiyFactorForAtom.
      Parameters:
      atomContainer - AtomContainer
      atom - atom for which the factor should become known
      Returns:
      The polarizabilitiyFactorForAtom value

    • calculateKJMeanMolecularPolarizability

      public double calculateKJMeanMolecularPolarizability(IAtomContainer atomContainer)
      calculates the mean molecular polarizability as described in paper of Kang and Jhorn.
      Parameters:
      atomContainer - AtomContainer
      Returns:
      polarizabilitiy

    • calculateGHEffectiveAtomPolarizability

      public double calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom, int influenceSphereCutOff, boolean addExplicitH)
      calculate effective atom polarizability.
      Parameters:
      atomContainer - IAtomContainer
      atom - atom for which effective atom polarizability should be calculated
      influenceSphereCutOff - cut off for spheres which should taken into account for calculation
      addExplicitH - if set to true, then explicit H's will be added, otherwise it assumes that they have been added to the molecule before being called
      Returns:
      polarizabilitiy

    • calculateGHEffectiveAtomPolarizability

      public double calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom, boolean addExplicitH, int[][] distanceMatrix)
      calculate effective atom polarizability.
      Parameters:
      atomContainer - IAtomContainer
      atom - atom for which effective atom polarizability should be calculated
      addExplicitH - if set to true, then explicit H's will be added, otherwise it assumes that they have been added to the molecule before being called
      distanceMatrix - an n x n matrix of topological distances between all the atoms in the molecule. if this argument is non-null, then BFS will not be used and instead path lengths will be looked up. This form of the method is useful, if it is being called for multiple atoms in the same molecule
      Returns:
      polarizabilitiy

    • calculateBondPolarizability

      public double calculateBondPolarizability(IAtomContainer atomContainer, IBond bond)
      calculate bond polarizability.
      Parameters:
      atomContainer - AtomContainer
      bond - Bond bond for which the polarizabilitiy should be calculated
      Returns:
      polarizabilitiy