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

Class LongestAliphaticChainDescriptor

  • All Implemented Interfaces:
    IDescriptor, IMolecularDescriptor
    public class LongestAliphaticChainDescriptor
extends AbstractMolecularDescriptor
    Counts the number of atoms in the longest aliphatic chain.

    Parameters for this descriptor:
    Name Default Description
    checkRingSystem false True is the CDKConstant.ISINRING has to be set

    Returns a single value named nAtomLAC

    Author:
    chhoppe from EUROSCREEN, John Mayfield
    Dictionary pointer(s):
    largestAliphaticChain in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:largestAliphaticChain]
    Source code:
    main
    Belongs to CDK module:
    qsarmolecular
    Created on:
    2006-1-03

    • Constructor Detail

      • LongestAliphaticChainDescriptor

        public LongestAliphaticChainDescriptor()
        Constructor for the LongestAliphaticChainDescriptor 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
        Returns:
        An object containing the descriptor specification

      • setParameters

        public void setParameters​(Object[] params)
                   throws CDKException
        Sets the parameters attribute of the LongestAliphaticChainDescriptor object.

        This descriptor takes one parameter, which should be Boolean to indicate whether aromaticity has been checked (TRUE) or not (FALSE).

        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 LongestAliphaticChainDescriptor object.
        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
        Returns:
        An array of descriptor names, equal in length to the number of descriptor calculated..

      • calculate

        public DescriptorValue calculate​(IAtomContainer mol)
        Calculate the count of atoms of the longest aliphatic chain in the supplied IAtomContainer.

        The method require one parameter: if checkRingSyste is true the CDKConstant.ISINRING will be set

        Parameters:
        mol - The IAtomContainer for which this descriptor is to be calculated
        Returns:
        the number of atoms in the longest aliphatic chain 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.

        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 LongestAliphaticChainDescriptor object.
        Returns:
        The parameterNames value

      • getParameterType

        public Object getParameterType​(String name)
        Gets the parameterType attribute of the LongestAliphaticChainDescriptor object.
        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