Class PartialSigmaChargeDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractAtomicDescriptor
org.openscience.cdk.qsar.descriptors.atomic.PartialSigmaChargeDescriptor
All Implemented Interfaces:
IAtomicDescriptor, IDescriptor

public class PartialSigmaChargeDescriptor extends AbstractAtomicDescriptor
The calculation of sigma partial charges in sigma-bonded systems of an heavy atom was made by Marsilli-Gasteiger. It is implemented with the Partial Equalization of Orbital Electronegativity (PEOE).
Parameters for this descriptor:
Name Default Description
maxIterations 0 Number of maximum iterations
Author:
Miguel Rojas
See Also:
Dictionary pointer(s):
partialSigmaCharge in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:partialSigmaCharge]
Source code:
main
Belongs to CDK module:
qsaratomic
Created on:
2006-04-15
  • Constructor Details

    • PartialSigmaChargeDescriptor

      public PartialSigmaChargeDescriptor()
      Constructor for the PartialSigmaChargeDescriptor object
  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Gets the specification attribute of the PartialSigmaChargeDescriptor object
      Returns:
      The specification value
    • setParameters

      public void setParameters(Object[] params) throws CDKException
      Sets the parameters attribute of the PartialSigmaChargeDescriptor object
      Parameters:
      params - Number of maximum iterations
      Throws:
      CDKException - Description of the Exception
      See Also:
    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the PartialSigmaChargeDescriptor object
      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
      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 PartialSigmaChargeDescriptor object
      Returns:
      The parameterNames value
    • getParameterType

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