org.openscience.cdk.qsar.descriptors.bond

Class BondPartialSigmaChargeDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractBondDescriptor

org.openscience.cdk.qsar.descriptors.bond.BondPartialSigmaChargeDescriptor

All Implemented Interfaces:

IBondDescriptor, IDescriptor

public class BondPartialSigmaChargeDescriptor
extends AbstractBondDescriptor

The calculation of bond-sigma Partial charge is calculated determining the difference the Partial Sigma Charge on atoms A and B of a bond. Based in Gasteiger Charge.

Parameters for this descriptor:

Name	Default	Description
bondPosition	0	The position of the target bond

Author:

Miguel Rojas

See Also:

PartialSigmaChargeDescriptor

Dictionary pointer(s):

bondPartialSigmaCharge in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:bondPartialSigmaCharge]

Source code:

master

Belongs to CDK module:

qsarbond

Created on:

2006-05-08

Constructor Summary

Constructors

Constructor and Description
BondPartialSigmaChargeDescriptor() Constructor for the BondPartialSigmaChargeDescriptor object.

Method Summary

Modifier and Type	Method and Description
DescriptorValue	calculate(IBond bond, IAtomContainer ac) The method calculates the bond-sigma Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
String[]	getParameterNames() Gets the parameterNames attribute of the BondPartialSigmaChargeDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the BondPartialSigmaChargeDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the BondPartialSigmaChargeDescriptor object.
DescriptorSpecification	getSpecification() Gets the specification attribute of the BondPartialSigmaChargeDescriptor object.
void	initialise(IChemObjectBuilder builder) Default implementation of initialise allows optional override.
void	setParameters(Object[] params) This descriptor does have any parameter.

Methods inherited from class org.openscience.cdk.qsar.AbstractBondDescriptor

cacheDescriptorValue, getCachedDescriptorValue, isCachedAtomContainer

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.qsar.IDescriptor

initialise

Constructor Detail

BondPartialSigmaChargeDescriptor

public BondPartialSigmaChargeDescriptor()

Constructor for the BondPartialSigmaChargeDescriptor object.

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Gets the specification attribute of the BondPartialSigmaChargeDescriptor object.

Returns:

The specification value

setParameters

public void setParameters(Object[] params)
                   throws CDKException

This descriptor does have any parameter.

Parameters:

params - An array of Object containing the parameters for this descriptor

Throws:

CDKException - if invalid number of type of parameters are passed to it

See Also:

IDescriptor.getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the BondPartialSigmaChargeDescriptor object.

Returns:

The parameters value

See Also:

setParameters(java.lang.Object[])

getDescriptorNames

public String[] getDescriptorNames()

Description copied from interface: IDescriptor

Returns an array of names for each descriptor value calculated. Many descriptors return multiple values. In general it is useful for the descriptor to indicate the names for each value. In many cases, these names can be as simple as X1, X2, ..., XN where X is a prefix and 1, 2, ..., N are the indices. On the other hand it is also possible to return other arbitrary names, which should be documented in the Javadocs for the descriptor (e.g., the CPSA descriptor). Note that by default if a descriptor returns a single value (such as ALOGPDescriptor the return array will have a single element

Returns:

An array of descriptor names, equal in length to the number of descriptor calculated..

calculate

public DescriptorValue calculate(IBond bond,
                                 IAtomContainer ac)

The method calculates the bond-sigma Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

Parameters:

ac - AtomContainer

bond - A IBond for which this descriptor should be calculated

Returns:

return the sigma electronegativity

getParameterNames

public String[] getParameterNames()

Gets the parameterNames attribute of the BondPartialSigmaChargeDescriptor object.

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the BondPartialSigmaChargeDescriptor object.

Parameters:

name - Description of the Parameter

Returns:

An Object of class equal to that of the parameter being requested

initialise

public void initialise(IChemObjectBuilder builder)

Default implementation of initialise allows optional override.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object build