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

Class StabilizationPlusChargeDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractAtomicDescriptor
org.openscience.cdk.qsar.descriptors.atomic.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:
Source code:
main
Belongs to CDK module:
qsaratomic
Created on:
2008-104-31

  • Constructor Details

    • StabilizationPlusChargeDescriptor

      public StabilizationPlusChargeDescriptor()
      Constructor for the StabilizationPlusChargeDescriptor object

  • Method Details

    • getSpecification

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

    • setParameters

      public void setParameters(Object[] params) throws CDKException
      Sets the parameters attribute of the StabilizationPlusChargeDescriptor object
      Specified by:
      setParameters in interface IDescriptor
      Parameters:
      params - 1: max iterations (optional, defaults to 20)
      Throws:
      CDKException - Description of the Exception
      See Also:

    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the StabilizationPlusChargeDescriptor 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)
      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