org.openscience.cdk.qsar.descriptors.atomic
Class InductiveAtomicSoftnessDescriptor

java.lang.Object
  org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor

All Implemented Interfaces:

IAtomicDescriptor, IDescriptor

@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptorTest")
public class InductiveAtomicSoftnessDescriptor
extends Object
implements IAtomicDescriptor

Inductive atomic softness of an atom in a polyatomic system can be defined as charge delocalizing ability. Only works with 3D coordinates, which must be calculated beforehand.

This descriptor uses these parameters: Name Default Description no parameters

Author:

mfe4

Belongs to the set:

qsar-descriptors

Created on:

2004-11-03

Belongs to CDK module:

qsaratomic

Dictionary pointer(s):

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

Source code:

cdk-1.4.x

Constructor Summary

InductiveAtomicSoftnessDescriptor()
Constructor for the InductiveAtomicSoftnessDescriptor object

Method Summary

DescriptorValue	calculate(IAtom atom, IAtomContainer ac) It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
String[]	getParameterNames() Gets the parameterNames attribute of the InductiveAtomicSoftnessDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the InductiveAtomicSoftnessDescriptor object
Object	getParameterType(String name) Gets the parameterType attribute of the InductiveAtomicSoftnessDescriptor object.
DescriptorSpecification	getSpecification() Gets the specification attribute of the InductiveAtomicSoftnessDescriptor object
void	setParameters(Object[] params) This descriptor does have any parameter.

Methods inherited from class java.lang.Object

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

Constructor Detail

InductiveAtomicSoftnessDescriptor

public InductiveAtomicSoftnessDescriptor()
                                  throws IOException,
                                         ClassNotFoundException

Constructor for the InductiveAtomicSoftnessDescriptor object

Throws:

IOException - Description of the Exception

ClassNotFoundException - Description of the Exception

Method Detail

getSpecification

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

Gets the specification attribute of the InductiveAtomicSoftnessDescriptor object

Specified by:

getSpecification in interface IDescriptor

Returns:

The specification value

setParameters

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

This descriptor does have any parameter.

Specified by:

setParameters in interface IDescriptor

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 InductiveAtomicSoftnessDescriptor object

Specified by:

getParameters in interface IDescriptor

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

Specified by:

getDescriptorNames in interface IDescriptor

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)

It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.

Specified by:

calculate in interface IAtomicDescriptor

Parameters:

atom - The IAtom for which the DescriptorValue is requested

ac - AtomContainer

Returns:

a double with polarizability of the heavy atom

getParameterNames

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

Gets the parameterNames attribute of the InductiveAtomicSoftnessDescriptor object.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

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

Gets the parameterType attribute of the InductiveAtomicSoftnessDescriptor object.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

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