Package 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]
Created on:
2004-11-13

  • Constructor Details

    • AtomCountDescriptor

      public AtomCountDescriptor()
      Constructor for the AtomCountDescriptor 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 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

      public Object[] getParameters()
      Gets the parameters attribute of the AtomCountDescriptor 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 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