org.openscience.cdk.charges

Class Polarizability

java.lang.Object

org.openscience.cdk.charges.Polarizability

@TestClass(value="org.openscience.cdk.charges.PolarizabilityTest")
public class Polarizability
extends Object

Calculation of the polarizability of a molecule by the method of Kang and Jhon and Gasteiger based on and Limitations in parameterization of atoms: H, Csp3, Csp2, Csp2arom, Csp3, Nsp3, Nsp2, Nsp3, P, Osp3 and Osp2. Aromaticity must be calculated beforehand.

Author:

chhoppe

Keywords:

polarizability

Created on:

2004-11-03

Constructor Summary

Constructors

Constructor and Description
Polarizability() Constructor for the Polarizability object

Method Summary

Methods

Modifier and Type	Method and 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

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Polarizability

public Polarizability()

Constructor for the Polarizability object

Method Detail

getPolarizabilitiyFactorForAtom

@TestMethod(value="testGetPolarizabilitiyFactorForAtom_IAtomContainer_IAtom")
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

@TestMethod(value="testCalculateKJMeanMolecularPolarizability")
public double calculateKJMeanMolecularPolarizability(IAtomContainer atomContainer)

calculates the mean molecular polarizability as described in paper of Kang and Jhorn

Parameters:

atomContainer - AtomContainer

Returns:

polarizabilitiy

calculateGHEffectiveAtomPolarizability

@TestMethod(value="testCalculateGHEffectiveAtomPolarizability_IAtomContainer_IAtom_Int_Boolean")
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

@TestMethod(value="testCalculateGHEffectiveAtomPolarizability_IAtomContainer_IAtom_Boolean_IntInt")
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

@TestMethod(value="testCalculateBondPolarizability_IAtomContainer_IBond")
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