org.openscience.cdk.qsar.descriptors.bond
Class BondPartialPiChargeDescriptor

java.lang.Object
  org.openscience.cdk.qsar.AbstractBondDescriptor
      org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptor

All Implemented Interfaces:

IBondDescriptor, IDescriptor

@TestClass(value="org.openscience.cdk.qsar.descriptors.bond.BondPartialPiChargeDescriptorTest")
public class BondPartialPiChargeDescriptor
extends AbstractBondDescriptor

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

This descriptor uses these parameters:

Name	Default	Description
bondPosition	0	The position of the target bond

Author:

Miguel Rojas

See Also:

PartialPiChargeDescriptor

Belongs to the set:

qsar-descriptors

Created on:

2006-05-18

Belongs to CDK module:

qsarbond

Dictionary pointer(s):

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

Source code:

cdk-1.4.x

Constructor Summary

BondPartialPiChargeDescriptor()
Constructor for the BondPartialPiChargeDescriptor object

Method Summary

DescriptorValue	calculate(IBond bond, IAtomContainer ac) The method calculates the bond-pi 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 BondPartialPiChargeDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the BondPartialPiChargeDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the BondPartialPiChargeDescriptor object.
DescriptorSpecification	getSpecification() Gets the specification attribute of the BondPartialPiChargeDescriptor object
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

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

Constructor Detail

BondPartialPiChargeDescriptor

public BondPartialPiChargeDescriptor()

Constructor for the BondPartialPiChargeDescriptor object

Method Detail

getSpecification

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

Gets the specification attribute of the BondPartialPiChargeDescriptor object

Returns:

The specification value

setParameters

@TestMethod(value="testSetParameters_arrayObject")
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

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

Gets the parameters attribute of the BondPartialPiChargeDescriptor object.

Returns:

The parameters value

See Also:

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_IBond_IAtomContainer,testBondPiElectronegativityDescriptor,testBondPiElectronegativityDescriptor_Allyl_bromide")
public DescriptorValue calculate(IBond bond,
                                                 IAtomContainer ac)

The method calculates the bond-pi 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

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

Gets the parameterNames attribute of the BondPartialPiChargeDescriptor object.

Returns:

The parameterNames value

getParameterType

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

Gets the parameterType attribute of the BondPartialPiChargeDescriptor object.

Parameters:

name - Description of the Parameter

Returns:

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