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

Class StabilizationPlusChargeDescriptor

  • All Implemented Interfaces:
    IAtomicDescriptor, IDescriptor
    public class StabilizationPlusChargeDescriptor
extends AbstractAtomicDescriptor
implements IAtomicDescriptor
    The stabilization of the positive charge (e.g.) obtained in the polar breaking of a bond is calculated from the sigma- and lone pair-electronegativity values of the atoms that are in conjugation to the atoms obtaining the charges. The method is based following [Saller, H., Quantitative Emperische Modelle fur Elektronische Effekte in Pi-Systemen und fur die Chemische Reaktivitat, 1985, ?Institute?]. The value is calculated looking for resonance structures which can stabilize the charge.
    Parameters for this descriptor:
    Name Default Description
    maxIterations 0 Number of maximum iterations
    Author:
    Miguel Rojas Cherto
    See Also:
    StabilizationCharges
    Source code:
    main
    Belongs to CDK module:
    qsaratomic
    Created on:
    2008-104-31

    • Constructor Detail

      • StabilizationPlusChargeDescriptor

        public StabilizationPlusChargeDescriptor()
        Constructor for the StabilizationPlusChargeDescriptor 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 container)
        The method calculates the stabilization of charge of a given atom 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
        container - AtomContainer
        Returns:
        return the stabilization value

      • getParameterNames

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

      • getParameterType

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