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

Class ProtonTotalPartialChargeDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractAtomicDescriptor
org.openscience.cdk.qsar.descriptors.atomic.ProtonTotalPartialChargeDescriptor
All Implemented Interfaces:
IAtomicDescriptor, IDescriptor
public class ProtonTotalPartialChargeDescriptor extends AbstractAtomicDescriptor implements IAtomicDescriptor
The calculation of partial charges of an heavy atom and its protons is based on Gasteiger Marsili (PEOE). This descriptor has no parameters. The result of this descriptor is a vector of 5 values, corresponding to a maximum of four protons for any given atom. If an atom has fewer than four protons, the remaining values are set to Double.NaN. Also note that the values for the neighbors are not returned in a particular order (though the order is fixed for multiple runs for the same atom).
Author:
mfe4
Dictionary pointer(s):
protonPartialCharge in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:protonPartialCharge]
Source code:
main
Belongs to CDK module:
qsaratomic
Created on:
2004-11-03

  • Constructor Details

    • ProtonTotalPartialChargeDescriptor

      public ProtonTotalPartialChargeDescriptor()
      Constructor for the ProtonTotalPartialChargeDescriptor object

  • Method Details

    • getSpecification

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

    • setParameters

      public void setParameters(Object[] params) throws CDKException
      This descriptor does not have any parameter to be set.
      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 ProtonTotalPartialChargeDescriptor 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 ac)
      The method returns partial charges assigned to an heavy atom and its protons through Gasteiger Marsili 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
      ac - AtomContainer
      Returns:
      an array of doubles with partial charges of [heavy, proton_1 ... proton_n]

    • getParameterNames

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

    • getParameterType

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