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

Class 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:
    main
    Belongs to CDK module:
    qsarmolecular
    Created on:
    2004-11-13

    • 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()

      • 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