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

Class HBondAcceptorCountDescriptor

  • All Implemented Interfaces:
    IDescriptor, IMolecularDescriptor
    public class HBondAcceptorCountDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor
    This descriptor calculates the number of hydrogen bond acceptors using a slightly simplified version of the PHACIR atom types. The following groups are counted as hydrogen bond acceptors:
    • any oxygen where the formal charge of the oxygen is non-positive (i.e. formal charge ≤ 0) except
      1. an aromatic ether oxygen (i.e. an ether oxygen that is adjacent to at least one aromatic carbon)
      2. an oxygen that is adjacent to a nitrogen
    • any nitrogen where the formal charge of the nitrogen is non-positive (i.e. formal charge ≤ 0) except
      1. a nitrogen that is adjacent to an oxygen
    Returns a single value named nHBAcc.
    Parameters for this descriptor:
    Name Default Description
    checkAromaticity false true if the aromaticity has to be checked

    This descriptor works properly with AtomContainers whose atoms contain implicit hydrogens or explicit hydrogens.

    Author:
    ulif
    Dictionary pointer(s):
    hBondacceptors in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:hBondacceptors]
    Source code:
    main
    Belongs to CDK module:
    qsarmolecular
    Created on:
    2005-22-07

    • Constructor Detail

      • HBondAcceptorCountDescriptor

        public HBondAcceptorCountDescriptor()
        Constructor for the HBondAcceptorCountDescriptor object

    • Method Detail

      • 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..

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

      • getParameterType

        public Object getParameterType​(String name)
        Gets the parameterType attribute of the HBondAcceptorCountDescriptor object.
        Specified by:
        getParameterType in interface IDescriptor
        Parameters:
        name - Description of the Parameter
        Returns:
        The parameterType value

      • initialise

        public void initialise​(IChemObjectBuilder builder)
        Default implementation of initialise allows optional override.
        Specified by:
        initialise in interface IDescriptor
        Parameters:
        builder - chem object build