org.openscience.cdk.qsar.descriptors.atomic

Class PartialTChargePEOEDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractAtomicDescriptor

org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor

All Implemented Interfaces:

IAtomicDescriptor, IDescriptor

public class PartialTChargePEOEDescriptor
extends AbstractAtomicDescriptor

The calculation of total partial charges of an heavy atom is based on Partial Equalization of Electronegativity method (PEOE-PEPE) from Gasteiger.

They are obtained by summation of the results of the calculations on sigma- and pi-charges.

Parameters for this descriptor:

Name	Default	Description
		no parameters

Author:

Miguel Rojas

See Also:

GasteigerMarsiliPartialCharges, GasteigerPEPEPartialCharges

Dictionary pointer(s):

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

Source code:

master

Belongs to CDK module:

qsaratomic

Created on:

2006-04-11

Constructor Summary

Constructors

Constructor and Description
PartialTChargePEOEDescriptor() Constructor for the PartialTChargePEOEDescriptor object

Method Summary

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtom atom, IAtomContainer ac) The method returns partial total charges assigned to an heavy atom through PEOE method.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
String[]	getParameterNames() Gets the parameterNames attribute of the PartialTChargePEOEDescriptor object
Object[]	getParameters() Gets the parameters attribute of the PartialTChargePEOEDescriptor object
Object	getParameterType(String name) Gets the parameterType attribute of the PartialTChargePEOEDescriptor object
DescriptorSpecification	getSpecification() Gets the specification attribute of the PartialTChargePEOEDescriptor object
void	initialise(IChemObjectBuilder builder) Default implementation of initialise allows optional override.
void	setParameters(Object[] params) This descriptor does not have any parameter to be set.

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

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

PartialTChargePEOEDescriptor

public PartialTChargePEOEDescriptor()

Constructor for the PartialTChargePEOEDescriptor object

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Gets the specification attribute of the PartialTChargePEOEDescriptor object

Returns:

The specification value

setParameters

public void setParameters(Object[] params)
                   throws CDKException

This descriptor does not have any parameter to be set.

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 PartialTChargePEOEDescriptor 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(IAtom atom,
                                 IAtomContainer ac)

The method returns partial total charges assigned to an heavy atom through PEOE method. It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

Parameters:

atom - The IAtom for which the DescriptorValue is requested

ac - AtomContainer

Returns:

an array of doubles with partial charges of [heavy, proton_1 ... proton_n]

getParameterNames

public String[] getParameterNames()

Gets the parameterNames attribute of the PartialTChargePEOEDescriptor object

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the PartialTChargePEOEDescriptor 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