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 Details

    • AminoAcidCountDescriptor

      public AminoAcidCountDescriptor()
      Constructor for the AromaticAtomsCountDescriptor object.

  • Method Details

    • 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

      public Object[] getParameters()
      Gets the parameters attribute of the AminoAcidsCountDescriptor object.
      Specified by:
      getParameters in interface IDescriptor
      Returns:
      The parameters value
      See Also:

    • 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:

    • 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