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

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

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class AminoAcidCountDescriptor
extends java.lang.Object
implements IMolecularDescriptor

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

This descriptor uses these parameters:

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

Belongs to the set:

qsar-descriptors

Created on:

2006-01-15

Belongs to CDK module:

qsarprotein

Dictionary pointer(s):

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

Source code:

revision 11707

Constructor Summary

AminoAcidCountDescriptor()
Constructor for the AromaticAtomsCountDescriptor object.

Method Summary

DescriptorValue	calculate(IAtomContainer ac) Determine the number of amino acids groups the supplied IAtomContainer.
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() Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.
java.lang.Object[]	getParameters() Gets the parameters attribute of the AminoAcidsCountDescriptor object.
java.lang.Object	getParameterType(java.lang.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	setParameters(java.lang.Object[] params) Sets the parameters attribute of the AminoAcidsCountDescriptor object.

Methods inherited from class java.lang.Object

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

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(java.lang.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 java.lang.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

@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..

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 java.lang.String[] getParameterNames()

Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

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