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

Class AtomHybridizationVSEPRDescriptor

  • All Implemented Interfaces:
    IAtomicDescriptor, IDescriptor
    public class AtomHybridizationVSEPRDescriptor
extends AbstractAtomicDescriptor
implements IAtomicDescriptor
    This class returns the hybridization of an atom.

    This class try to find a SIMPLE WAY the molecular geometry for following from Valence Shell Electron Pair Repulsion or VSEPR model and at the same time its hybridization of atoms in a molecule.

    The basic premise of the model is that the electrons are paired in a molecule and that the molecule geometry is determined only by the repulsion between the pairs. The geometry adopted by a molecule is then the one in which the repulsions are minimized.

    It counts the number of electron pairs in the Lewis dot diagram which are attached to an atom. Then uses the following table.

    Hybridisation states
    pairs on an atom hybridization of the atom geometry number for CDK.Constants
    2splinear1
    3sp^2trigonal planar2
    4sp^3tetrahedral3
    5sp^3dtrigonal bipyramid4
    6sp^3d^2octahedral5
    7sp^3d^3pentagonal bipyramid6
    8sp^3d^4square antiprim7
    9sp^3d^5tricapped trigonal prism8

    This table only works if the central atom is a p-block element (groups IIA through VIIIA), not a transition metal.

    Parameters for this descriptor
    Name Default Description
    no parameters
    Author:
    Miguel Rojas
    Dictionary pointer(s):
    atomHybridizationVSEPR in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:atomHybridizationVSEPR]
    Source code:
    main
    Belongs to CDK module:
    qsaratomic
    Created on:
    2005-03-24

    • Constructor Detail

      • AtomHybridizationVSEPRDescriptor

        public AtomHybridizationVSEPRDescriptor()
        Constructor for the AtomHybridizationVSEPRDescriptor 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)
        This method calculates the hybridization of an atom.
        Specified by:
        calculate in interface IAtomicDescriptor
        Parameters:
        atom - The IAtom for which the DescriptorValue is requested
        container - Parameter is the atom container.
        Returns:
        The hybridization

      • getParameterNames

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

      • getParameterType

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