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

java.lang.Object
  org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptor

All Implemented Interfaces:

IBondDescriptor, IDescriptor

@TestClass(value="org.openscience.cdk.qsar.descriptors.bond.AtomicNumberDifferenceDescriptorTest")
public class AtomicNumberDifferenceDescriptor
extends Object
implements IBondDescriptor

Describes the imbalance in atomic number of the IBond.

Author:

Egon Willighagen

Belongs to the set:

qsar-descriptors

Created on:

2007-12-29

Belongs to CDK module:

qsarbond

Dictionary pointer(s):

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

Source code:

cdk-1.4.x

Constructor Summary

AtomicNumberDifferenceDescriptor()

Method Summary

DescriptorValue	calculate(IBond bond, IAtomContainer ac) Calculates the descriptor value for the given IBond.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
String[]	getParameterNames() Returns the names of the parameters for this descriptor.
Object[]	getParameters() Returns the current parameter values.
Object	getParameterType(String name) Returns a class matching that of the parameter with the given name.
DescriptorSpecification	getSpecification() Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
void	setParameters(Object[] params) Sets the parameters for this descriptor.

Methods inherited from class java.lang.Object

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

Constructor Detail

AtomicNumberDifferenceDescriptor

public AtomicNumberDifferenceDescriptor()

Method Detail

getSpecification

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

Description copied from interface: IDescriptor

Returns a IImplementationSpecification which specifies which descriptor is implemented by this class. These fields are used in the map:

• Specification-Reference: refers to an entry in a unique dictionary
• Implementation-Title: anything
• Implementation-Identifier: a unique identifier for this version of this class
• Implementation-Vendor: CDK, JOELib, or anything else

Specified by:

getSpecification in interface IDescriptor

Returns:

An object containing the descriptor specification

setParameters

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

Description copied from interface: IDescriptor

Sets the parameters for this descriptor. Must be done before calling calculate as the parameters influence the calculation outcome.

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()

Description copied from interface: IDescriptor

Returns the current parameter values. If not parameters have been set, it must return the default parameters. The method returns null or a zero-length Object[] array if the descriptor does not have any parameters.

Specified by:

getParameters in interface IDescriptor

Returns:

An array of Object containing the parameter default values

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

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_IBond_IAtomContainer,testDescriptor1,testDescriptor2")
public DescriptorValue calculate(IBond bond,
                                                 IAtomContainer ac)

Description copied from interface: IBondDescriptor

Calculates the descriptor value for the given IBond.

Specified by:

calculate in interface IBondDescriptor

Parameters:

bond - A IBond for which this descriptor should be calculated

ac - The molecule containing the bond

Returns:

An object of DescriptorValue that contain the calculated value as well as specification details

getParameterNames

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

Description copied from interface: IDescriptor

Returns the names of the parameters for this descriptor. The method returns null or a zero-length Object[] array if the descriptor does not have any parameters.

Specified by:

getParameterNames in interface IDescriptor

Returns:

An array of String containing the names of the parameters that this descriptor can accept.

getParameterType

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

Description copied from interface: IDescriptor

Returns a class matching that of the parameter with the given name. May only return null for when 'name' does not match any parameters returned by the getParameters() method.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - The name of the parameter whose type is requested

Returns:

An Object of the class corresponding to the parameter with the supplied name