org.openscience.cdk.qsar.descriptors.molecular

Class AtomCountDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractMolecularDescriptor

org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class AtomCountDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor

IDescriptor based on the number of atoms of a certain element type. It is possible to use the wild card symbol '*' as element type to get the count of all atoms.

Parameters for this descriptor:

Name	Default	Description
elementName	*	Symbol of the element we want to count

Returns a single value with name nX where X is the atomic symbol. If * is specified then the name is nAtom

Author:

mfe4

Dictionary pointer(s):

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

Source code:

master

Belongs to CDK module:

qsarmolecular

Created on:

2004-11-13

Constructor Summary

Constructors

Constructor and Description
AtomCountDescriptor() Constructor for the AtomCountDescriptor object.

Method Summary

Methods

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtomContainer container) This method calculate the number of atoms of a given type in an IAtomContainer.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
IDescriptorResult	getDescriptorResultType() Returns the specific type of the DescriptorResult object.
String[]	getParameterNames() Gets the parameterNames attribute of the AtomCountDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the AtomCountDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the AtomCountDescriptor object.
DescriptorSpecification	getSpecification() Returns a Map 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 attribute of the AtomCountDescriptor object.

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

AtomCountDescriptor

public AtomCountDescriptor()

Constructor for the AtomCountDescriptor object.

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

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

setParameters

public void setParameters(Object[] params)
                   throws CDKException

Sets the parameters attribute of the AtomCountDescriptor object.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameters value

Throws:

CDKException - if the number of parameters is greater than 1 or else the parameter is not of type String

See Also:

getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the AtomCountDescriptor object.

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

See Also:

setParameters(java.lang.Object[])

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..

calculate

public DescriptorValue calculate(IAtomContainer container)

This method calculate the number of atoms of a given type in an IAtomContainer.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

container - The atom container for which this descriptor is to be calculated

Returns:

Number of atoms of a certain type is returned.

getDescriptorResultType

public IDescriptorResult getDescriptorResultType()

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.

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

getParameterNames

public String[] getParameterNames()

Gets the parameterNames attribute of the AtomCountDescriptor object.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the AtomCountDescriptor object.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

An Object whose class is that of the parameter requested

initialise

public void initialise(IChemObjectBuilder builder)

Default implementation of initialise allows optional override.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object build