Package org.openscience.cdk.charges
Class Polarizability
- java.lang.Object
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- org.openscience.cdk.charges.Polarizability
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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
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Constructor Summary
Constructors Constructor Description Polarizability()
Constructor for the Polarizability object.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
calculateBondPolarizability(IAtomContainer atomContainer, IBond bond)
calculate bond polarizability.double
calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom, boolean addExplicitH, int[][] distanceMatrix)
calculate effective atom polarizability.double
calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom, int influenceSphereCutOff, boolean addExplicitH)
calculate effective atom polarizability.double
calculateKJMeanMolecularPolarizability(IAtomContainer atomContainer)
calculates the mean molecular polarizability as described in paper of Kang and Jhorn.double
getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer, IAtom atom)
Gets the polarizabilitiyFactorForAtom.
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Method Detail
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getPolarizabilitiyFactorForAtom
public double getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer, IAtom atom)
Gets the polarizabilitiyFactorForAtom.- Parameters:
atomContainer
- AtomContaineratom
- atom for which the factor should become known- Returns:
- The polarizabilitiyFactorForAtom value
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calculateKJMeanMolecularPolarizability
public double calculateKJMeanMolecularPolarizability(IAtomContainer atomContainer)
calculates the mean molecular polarizability as described in paper of Kang and Jhorn.- Parameters:
atomContainer
- AtomContainer- Returns:
- polarizabilitiy
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calculateGHEffectiveAtomPolarizability
public double calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom, int influenceSphereCutOff, boolean addExplicitH)
calculate effective atom polarizability.- Parameters:
atomContainer
- IAtomContaineratom
- atom for which effective atom polarizability should be calculatedinfluenceSphereCutOff
- cut off for spheres which should taken into account for calculationaddExplicitH
- 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
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calculateGHEffectiveAtomPolarizability
public double calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom, boolean addExplicitH, int[][] distanceMatrix)
calculate effective atom polarizability.- Parameters:
atomContainer
- IAtomContaineratom
- atom for which effective atom polarizability should be calculatedaddExplicitH
- if set to true, then explicit H's will be added, otherwise it assumes that they have been added to the molecule before being calleddistanceMatrix
- 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
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calculateBondPolarizability
public double calculateBondPolarizability(IAtomContainer atomContainer, IBond bond)
calculate bond polarizability.- Parameters:
atomContainer
- AtomContainerbond
- Bond bond for which the polarizabilitiy should be calculated- Returns:
- polarizabilitiy
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