org.openscience.cdk.qsar.descriptors.molecular
Class AutocorrelationDescriptorMass

java.lang.Object
  org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class AutocorrelationDescriptorMass
extends java.lang.Object
implements IMolecularDescriptor

This class calculates ATS autocorrelation descriptor, where the weight equal to the scaled atomic mass [Moreau G. and Broto P., The autocorrelation of a topological structure: A new molecular descriptor, Nouveau Journal de Chimie, 1980, ?:359-360].

Author:

Federico

Belongs to the set:

qsar-descriptors

Created on:

2007-02-08

Belongs to CDK module:

qsarmolecular

Source code:

revision 11707

Constructor Summary

AutocorrelationDescriptorMass()

Method Summary

DescriptorValue	calculate(IAtomContainer container) This method calculate the ATS Autocorrelation descriptor.
java.lang.String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
IDescriptorResult	getDescriptorResultType() Returns the specific type of the DescriptorResult object.
java.lang.String[]	getParameterNames() Returns the names of the parameters for this descriptor.
java.lang.Object[]	getParameters() Returns the current parameter values.
java.lang.Object	getParameterType(java.lang.String name) Returns a class matching that of the parameter with the given name.
DescriptorSpecification	getSpecification() Returns a Map which specifies which descriptor is implemented by this class.
void	setParameters(java.lang.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

AutocorrelationDescriptorMass

public AutocorrelationDescriptorMass()

Method Detail

calculate

public DescriptorValue calculate(IAtomContainer container)

This method calculate the ATS Autocorrelation descriptor.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

container - An IAtomContainer for which this descriptor should be calculated

Returns:

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

getParameterNames

public java.lang.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

public java.lang.Object getParameterType(java.lang.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

getParameters

public java.lang.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 java.lang.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..

getSpecification

public DescriptorSpecification getSpecification()

Description copied from interface: IDescriptor

Returns a Map 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

getDescriptorResultType

public IDescriptorResult getDescriptorResultType()

Description copied from interface: IMolecularDescriptor

Returns the specific type of the DescriptorResult object. The return value from this method really indicates what type of result will be obtained from the DescriptorValue object. Note that the same result can be achieved by interrogating the DescriptorValue object; this method allows you to do the same thing, without actually calculating the descriptor.

Additionally, the length indicated by the result type must match the actual length of a descriptor calculated with the current parameters. Typically, the length of array result types vary with the values of the parameters. See IDescriptor for more details.

Specified by:

getDescriptorResultType in interface IMolecularDescriptor

Returns:

an object that implements the IDescriptorResult interface indicating the actual type of values returned by the descriptor in the DescriptorValue object

setParameters

public void setParameters(java.lang.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()