org.openscience.cdk.qsar.descriptors.atomic

Class PartialSigmaChargeDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractAtomicDescriptor

org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor

All Implemented Interfaces:

IAtomicDescriptor, IDescriptor

@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptorTest")
public class PartialSigmaChargeDescriptor
extends AbstractAtomicDescriptor

The calculation of sigma partial charges in sigma-bonded systems of an heavy atom was made by Marsilli-Gasteiger. It is implemented with the Partial Equalization of Orbital Electronegativity (PEOE).

This descriptor uses these parameters:

Name	Default	Description
maxIterations	0	Number of maximum iterations

Author:

Miguel Rojas

See Also:

GasteigerMarsiliPartialCharges

Belongs to the set:

qsar-descriptors

Created on:

2006-04-15

Constructor Summary

Constructors

Constructor and Description
PartialSigmaChargeDescriptor() Constructor for the PartialSigmaChargeDescriptor object

Method Summary

Methods

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtom atom, IAtomContainer ac) The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili 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 PartialSigmaChargeDescriptor object
Object[]	getParameters() Gets the parameters attribute of the PartialSigmaChargeDescriptor object
Object	getParameterType(String name) Gets the parameterType attribute of the PartialSigmaChargeDescriptor object
DescriptorSpecification	getSpecification() Gets the specification attribute of the PartialSigmaChargeDescriptor object
void	setParameters(Object[] params) Sets the parameters attribute of the PartialSigmaChargeDescriptor object

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

cacheDescriptorValue, getCachedDescriptorValue, isCachedAtomContainer

Methods inherited from class java.lang.Object

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

Constructor Detail

PartialSigmaChargeDescriptor

public PartialSigmaChargeDescriptor()

Constructor for the PartialSigmaChargeDescriptor object

Method Detail

getSpecification

@TestMethod(value="testGetSpecification")
public DescriptorSpecification getSpecification()

Gets the specification attribute of the PartialSigmaChargeDescriptor object

Returns:

The specification value

setParameters

@TestMethod(value="testSetParameters_arrayObject")
public void setParameters(Object[] params)
                   throws CDKException

Sets the parameters attribute of the PartialSigmaChargeDescriptor object

Parameters:

params - Number of maximum iterations

Throws:

CDKException - Description of the Exception

See Also:

IDescriptor.getParameters()

getParameters

@TestMethod(value="testGetParameters")
public Object[] getParameters()

Gets the parameters attribute of the PartialSigmaChargeDescriptor object

Returns:

The parameters value

See Also:

IDescriptor.setParameters(java.lang.Object[])

getDescriptorNames

@TestMethod(value="testNamesConsistency")
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 decsriptor (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

@TestMethod(value="testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtom atom,
                                        IAtomContainer ac)

The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder. For this method will be only possible if the heavy atom has single bond.

Parameters:

atom - The IAtom for which the DescriptorValue is requested

ac - AtomContainer

Returns:

Value of the alpha partial charge

getParameterNames

@TestMethod(value="testGetParameterNames")
public String[] getParameterNames()

Gets the parameterNames attribute of the PartialSigmaChargeDescriptor object

Returns:

The parameterNames value

getParameterType

@TestMethod(value="testGetParameterType_String")
public Object getParameterType(String name)

Gets the parameterType attribute of the PartialSigmaChargeDescriptor object

Parameters:

name - Description of the Parameter

Returns:

The parameterType value