Package org.openscience.cdk.qsar.descriptors.molecular

Class AminoAcidCountDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractMolecularDescriptor

org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class AminoAcidCountDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor

Class that returns the number of each amino acid in an atom container.

Parameters for this descriptor:

Name	Default	Description
		no parameters

Returns 20 values with names of the form nX, where X is the short versio of the amino acid name

Author:

egonw

Dictionary pointer(s):

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

Source code:

main

Belongs to CDK module:

qsarprotein

Created on:

2006-01-15

Constructor Summary

Constructors

Constructor	Description
AminoAcidCountDescriptor()	Constructor for the AromaticAtomsCountDescriptor object.

Method Summary

Modifier and Type	Method	Description
DescriptorValue	calculate(IAtomContainer ac)	Determine the number of amino acids groups the supplied 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 AromaticAtomsCountDescriptor object.
Object[]	getParameters()	Gets the parameters attribute of the AminoAcidsCountDescriptor object.
Object	getParameterType(String name)	Gets the parameterType attribute of the AromaticAtomsCountDescriptor 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 AminoAcidsCountDescriptor object.

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

AminoAcidCountDescriptor

public AminoAcidCountDescriptor()

Constructor for the AromaticAtomsCountDescriptor 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 AminoAcidsCountDescriptor object.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameters value

Throws:

CDKException - if more than one parameter or a non-Boolean parameter is specified

See Also:

getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the AminoAcidsCountDescriptor 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 ac)

Determine the number of amino acids groups the supplied IAtomContainer.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

ac - The IAtomContainer for which this descriptor is to be calculated

Returns:

the number of aromatic atoms of this AtomContainer

See Also:

setParameters(java.lang.Object[])

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 AromaticAtomsCountDescriptor object.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the AromaticAtomsCountDescriptor 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

initialise

public void initialise(IChemObjectBuilder builder)

Default implementation of initialise allows optional override.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object build