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

Class AtomHybridizationVSEPRDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractAtomicDescriptor
org.openscience.cdk.qsar.descriptors.atomic.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 Details

    • AtomHybridizationVSEPRDescriptor

      public AtomHybridizationVSEPRDescriptor()
      Constructor for the AtomHybridizationVSEPRDescriptor object

  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Gets the specification attribute of the AtomHybridizationVSEPRDescriptor object
      Specified by:
      getSpecification in interface IDescriptor
      Returns:
      The specification value

    • setParameters

      public void setParameters(Object[] params) throws CDKException
      This descriptor does have any parameter.
      Specified by:
      setParameters in interface IDescriptor
      Parameters:
      params - An array of Object containing the parameters for this descriptor
      Throws:
      CDKException - if invalid number of type of parameters are passed to it
      See Also:

    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the AtomHybridizationVSEPRDescriptor object
      Specified by:
      getParameters in interface IDescriptor
      Returns:
      The parameters value
      See Also:

    • 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