org.openscience.cdk.qsar.descriptors.molecular

Class FractionalCSP3Descriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractMolecularDescriptor

org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class FractionalCSP3Descriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor

An implementation of the Fractional CSP3 descriptor described in (Lovering, Frank et. al.. J. Med. Chem.. 2009. 52). This descriptor is characterizing non-flatness of a molecule. This descriptor returns a single double value, labeled as "Fsp3"

Author:

Kazuya Ujihara

Dictionary pointer(s):

Fsp3 in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:Fsp3]

Belongs to CDK module:

qsarmolecular

Constructor Summary

Constructors

Constructor and Description
FractionalCSP3Descriptor()

Method Summary

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtomContainer mol) Calculates the Fsp3 descriptor value for the given IAtomContainer.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
IDescriptorResult	getDescriptorResultType() Returns the specific type of the Fsp3 descriptor value.
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	initialise(IChemObjectBuilder builder) Default implementation of initialise allows optional override.
void	setParameters(Object[] params) Sets the parameters for this descriptor.

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

clone

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.qsar.IDescriptor

initialise

Constructor Detail

FractionalCSP3Descriptor

public FractionalCSP3Descriptor()

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

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

getParameterNames

public String[] getParameterNames()

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 Object getParameterType(String name)

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

setParameters

public void setParameters(Object[] params)
                   throws CDKException

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

public Object[] getParameters()

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[])

calculate

public DescriptorValue calculate(IAtomContainer mol)

Calculates the Fsp³ descriptor value for the given IAtomContainer.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

mol - An IAtomContainer for which this descriptor should be calculated

Returns:

An object of DescriptorValue that contains the calculated Fsp³ descriptor value

getDescriptorResultType

public IDescriptorResult getDescriptorResultType()

Returns the specific type of the Fsp3 descriptor value. The Fsp3 descriptor is a single, double value.

Specified by:

getDescriptorResultType in interface IMolecularDescriptor

Returns:

an instance of the DoubleResultType

getDescriptorNames

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 descriptor (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..

initialise

public void initialise(IChemObjectBuilder builder)

Default implementation of initialise allows optional override.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object build