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

Class MDEDescriptor

  • All Implemented Interfaces:
    IDescriptor, IMolecularDescriptor
    public class MDEDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor
    Calculates the Molecular Distance Edge descriptor described in [Liu, S. et. al.. Journal of Chemical Information and Computer Sciences. 1998. 38]. This class evaluates the 10 MDE descriptors described by Liu et al. and in addition it calculates variants where O and N are considered (as found in the DEDGE routine from ADAPT).
    Table 1 - Description of the different MDE descriptors generated
    MDEC-11 molecular distance edge between all primary carbons
    MDEC-12 molecular distance edge between all primary and secondary carbons
    MDEC-13 molecular distance edge between all primary and tertiary carbons
    MDEC-14 molecular distance edge between all primary and quaternary carbons
    MDEC-22 molecular distance edge between all secondary carbons
    MDEC-23 molecular distance edge between all secondary and tertiary carbons
    MDEC-24 molecular distance edge between all secondary and quaternary carbons
    MDEC-33 molecular distance edge between all tertiary carbons
    MDEC-34 molecular distance edge between all tertiary and quaternary carbons
    MDEC-44 molecular distance edge between all quaternary carbons
    MDEO-11 molecular distance edge between all primary oxygens
    MDEO-12 molecular distance edge between all primary and secondary oxygens
    MDEO-22 molecular distance edge between all secondary oxygens
    MDEN-11 molecular distance edge between all primary nitrogens
    MDEN-12 molecular distance edge between all primary and secondary nitrogens
    MDEN-13 molecular distance edge between all primary and tertiary niroqens
    MDEN-22 molecular distance edge between all secondary nitroqens
    MDEN-23 molecular distance edge between all secondary and tertiary nitrogens
    MDEN-33 molecular distance edge between all tertiary nitrogens
    Author:
    Rajarshi Guha
    Dictionary pointer(s):
    mde in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:mde]
    Source code:
    main
    Belongs to CDK module:
    qsarmolecular
    Created on:
    2006-09-18

    • Constructor Detail

      • MDEDescriptor

        public MDEDescriptor()

    • 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 WeightDescriptor object.
        Specified by:
        setParameters in interface IDescriptor
        Parameters:
        params - The new parameters value
        Throws:
        CDKException - if more than 1 parameter is specified or if 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)
        Calculate the weight of specified element type in the supplied IAtomContainer.
        Specified by:
        calculate in interface IMolecularDescriptor
        Parameters:
        container - The AtomContainer for which this descriptor is to be calculated. If 'H' is specified as the element symbol make sure that the AtomContainer has hydrogens.
        Returns:
        The total weight of atoms of the specified element type

      • 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 WeightDescriptor object.
        Specified by:
        getParameterNames in interface IDescriptor
        Returns:
        The parameterNames value

      • getParameterType

        public Object getParameterType​(String name)
        Gets the parameterType attribute of the WeightDescriptor 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