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

Class ProtonAffinityHOSEDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractAtomicDescriptor
org.openscience.cdk.qsar.descriptors.atomic.ProtonAffinityHOSEDescriptor
All Implemented Interfaces:
IAtomicDescriptor, IDescriptor
public class ProtonAffinityHOSEDescriptor extends AbstractAtomicDescriptor
This class returns the proton affinity of an atom containing.
Parameters for this descriptor:
Name Default Description
no parameters
Author:
Miguel Rojas
Dictionary pointer(s):
protonaffinity in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:protonaffinity]
Source code:
main
Belongs to CDK module:
qsaratomic
Created on:
2006-05-26

  • Constructor Details

    • ProtonAffinityHOSEDescriptor

      public ProtonAffinityHOSEDescriptor()
      Constructor for the ProtonAffinityDescriptor object.

  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Gets the specification attribute of the ProtonAffinityDescriptor object
      Returns:
      The specification value

    • setParameters

      public void setParameters(Object[] params) throws CDKException
      This descriptor does have any parameter.
      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 ProtonAffinityDescriptor 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 container)
      This method calculates the protonation affinity of an atom.
      Parameters:
      atom - The IAtom to protonate
      container - Parameter is the IAtomContainer.
      Returns:
      The protonation affinity. Not possible the ionization.

    • getParameterNames

      public String[] getParameterNames()
      Gets the parameterNames attribute of the ProtonAffinityDescriptor object.
      Returns:
      The parameterNames value

    • getParameterType

      public Object getParameterType(String name)
      Gets the parameterType attribute of the ProtonAffinityDescriptor object.
      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