Class RDFProtonDescriptor_GHR_topol

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

public class RDFProtonDescriptor_GHR_topol extends AbstractAtomicDescriptor implements IAtomicDescriptor
This class calculates GHR topological proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74]. It only applies to (explicit) hydrogen atoms, requires aromaticity to be perceived (possibly done via a parameter), and needs 3D coordinates for all atoms.
Parameters for this descriptor:
Name Default Description
checkAromaticity false True is the aromaticity has to be checked
Author:
Federico
This class is affected by these bug(s):
1632419
Dictionary pointer(s):
rdfProtonCalculatedValues in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:rdfProtonCalculatedValues]
Source code:
main
Belongs to CDK module:
qsaratomic
Created on:
2006-12-11
  • Constructor Details

    • RDFProtonDescriptor_GHR_topol

      public RDFProtonDescriptor_GHR_topol()
      Constructor for the RDFProtonDescriptor object
  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Gets the specification attribute of the RDFProtonDescriptor_GHR_topol 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 RDFProtonDescriptor object
      Specified by:
      setParameters in interface IDescriptor
      Parameters:
      params - Parameters are the proton position and a boolean (true if you need to detect aromaticity)
      Throws:
      CDKException - Possible Exceptions
      See Also:
    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the RDFProtonDescriptor 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 varAtomContainerSet)
      Description copied from interface: IAtomicDescriptor
      Calculates the descriptor value for the given IAtom.
      Specified by:
      calculate in interface IAtomicDescriptor
      Parameters:
      atom - An IAtom for which this descriptor should be calculated
      varAtomContainerSet - TODO
      Returns:
      An object of DescriptorValue that contain the calculated value as well as specification details
    • calculate

      public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
    • getParameterNames

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

      public Object getParameterType(String name)
      Gets the parameterType attribute of the RDFProtonDescriptor object
      Specified by:
      getParameterType in interface IDescriptor
      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