Package org.openscience.cdk.qsar.descriptors.atomic

Class ProtonTotalPartialChargeDescriptor

  • All Implemented Interfaces:
    IAtomicDescriptor, IDescriptor
    public class ProtonTotalPartialChargeDescriptor
extends AbstractAtomicDescriptor
implements IAtomicDescriptor
    The calculation of partial charges of an heavy atom and its protons is based on Gasteiger Marsili (PEOE). This descriptor has no parameters. The result of this descriptor is a vector of 5 values, corresponding to a maximum of four protons for any given atom. If an atom has fewer than four protons, the remaining values are set to Double.NaN. Also note that the values for the neighbors are not returned in a particular order (though the order is fixed for multiple runs for the same atom).
    Author:
    mfe4
    Dictionary pointer(s):
    protonPartialCharge in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:protonPartialCharge]
    Source code:
    main
    Belongs to CDK module:
    qsaratomic
    Created on:
    2004-11-03

    • Constructor Detail

      • ProtonTotalPartialChargeDescriptor

        public ProtonTotalPartialChargeDescriptor()
        Constructor for the ProtonTotalPartialChargeDescriptor 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..

      • calculate

        public DescriptorValue calculate​(IAtom atom,
                                 IAtomContainer ac)
        The method returns partial charges assigned to an heavy atom and its protons through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
        Specified by:
        calculate in interface IAtomicDescriptor
        Parameters:
        atom - The IAtom for which the DescriptorValue is requested
        ac - AtomContainer
        Returns:
        an array of doubles with partial charges of [heavy, proton_1 ... proton_n]

      • getParameterNames

        public String[] getParameterNames()
        Gets the parameterNames attribute of the ProtonTotalPartialChargeDescriptor object
        Specified by:
        getParameterNames in interface IDescriptor
        Returns:
        The parameterNames value

      • getParameterType

        public Object getParameterType​(String name)
        Gets the parameterType attribute of the ProtonTotalPartialChargeDescriptor object
        Specified by:
        getParameterType in interface IDescriptor
        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