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

Class PartialPiChargeDescriptor

  • All Implemented Interfaces:
    IAtomicDescriptor, IDescriptor
    public class PartialPiChargeDescriptor
extends AbstractAtomicDescriptor

    The calculation of pi partial charges in pi-bonded systems of an heavy atom was made by Saller-Gasteiger. It is based on the qualitative concept of resonance and implemented with the Partial Equalization of Pi-Electronegativity (PEPE).

    Parameters for this descriptor:
    Name Default Description
    maxIterations 0 Number of maximum iterations
    Author:
    Miguel Rojas
    See Also:
    GasteigerPEPEPartialCharges
    Dictionary pointer(s):
    partialPiCharge in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:partialPiCharge]
    Source code:
    main
    Belongs to CDK module:
    qsaratomic
    Created on:
    2006-04-15

    • Constructor Detail

      • PartialPiChargeDescriptor

        public PartialPiChargeDescriptor()
        Constructor for the PartialPiChargeDescriptor object

    • Method Detail

      • getSpecification

        public DescriptorSpecification getSpecification()
        Gets the specification attribute of the PartialPiChargeDescriptor object
        Returns:
        The specification value

      • setParameters

        public void setParameters​(Object[] params)
                   throws CDKException
        Sets the parameters attribute of the PartialPiChargeDescriptor object
        Parameters:
        params - 1:Number of maximum iterations, 2: checking lone pair electrons, 3: number of maximum resonance structures to be searched.
        Throws:
        CDKException - Description of the Exception
        See Also:
        IDescriptor.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
        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 apha partial charges assigned to an heavy atom through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder. For this method will be only possible if the heavy atom has single bond.
        Parameters:
        atom - The IAtom for which the DescriptorValue is requested
        ac - AtomContainer
        Returns:
        Value of the alpha partial charge

      • getParameterNames

        public String[] getParameterNames()
        Gets the parameterNames attribute of the PartialPiChargeDescriptor object
        Returns:
        The parameterNames value

      • getParameterType

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