Class RDFProtonDescriptor_G3R

All Implemented Interfaces:
IAtomicDescriptor, IDescriptor

public class RDFProtonDescriptor_G3R extends AbstractAtomicDescriptor implements IAtomicDescriptor
This class calculates G3R 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. This method only calculates values for protons bonded to specific types of rings or via non-rotatable bonds. From the original manuscript: "To account for axial and equatorial positions of protons bonded to cyclohexane-like rings, g3(r) was used"
Parameters for this descriptor:
Name Default Description
checkAromaticity false True is the aromaticity has to be checked
This class is affected by these bug(s):
Dictionary pointer(s):
rdfProtonCalculatedValues in the Descriptors Dictionary [qsar-descriptors:rdfProtonCalculatedValues]
Source code:
Belongs to CDK module:
Created on:
  • Constructor Details

    • RDFProtonDescriptor_G3R

      public RDFProtonDescriptor_G3R()
      Constructor for the RDFProtonDescriptor object
  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Gets the specification attribute of the RDFProtonDescriptor_G3R object
      Specified by:
      getSpecification in interface IDescriptor
      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
      params - Parameters are the proton position and a boolean (true if you need to detect aromaticity)
      CDKException - Possible Exceptions
      See Also:
    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the RDFProtonDescriptor object
      Specified by:
      getParameters in interface IDescriptor
      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
      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
      atom - An IAtom for which this descriptor should be calculated
      varAtomContainerSet - TODO
      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
      The parameterNames value
    • getParameterType

      public Object getParameterType(String name)
      Gets the parameterType attribute of the RDFProtonDescriptor object
      Specified by:
      getParameterType in interface IDescriptor
      name - Description of the Parameter
      The parameterType value
    • initialise

      public void initialise(IChemObjectBuilder builder)
      Default implementation of initialise allows optional override.
      Specified by:
      initialise in interface IDescriptor
      builder - chem object build