Class IsProtonInAromaticSystemDescriptor

All Implemented Interfaces:
IAtomicDescriptor, IDescriptor

public class IsProtonInAromaticSystemDescriptor extends AbstractAtomicDescriptor implements IAtomicDescriptor
This descriptor returns 1 if the protons is directly bonded to an aromatic system, it returns 2 if the distance between aromatic system and proton is 2 bonds, and it return 0 for other positions. It is needed to use addExplicitHydrogensToSatisfyValency method.
Parameters for this descriptor:
Name Default Description
checkAromaticity false True is the aromaticity has to be checked
Dictionary pointer(s):
isProtonInAromaticSystem in the Descriptors Dictionary [qsar-descriptors:isProtonInAromaticSystem]
Source code:
Belongs to CDK module:
Created on:
  • Constructor Details

    • IsProtonInAromaticSystemDescriptor

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

    • getSpecification

      public DescriptorSpecification getSpecification()
      Gets the specification attribute of the IsProtonInAromaticSystemDescriptor object
      Specified by:
      getSpecification in interface IDescriptor
      The specification value
    • setParameters

      public void setParameters(Object[] params) throws CDKException
      Sets the parameters attribute of the IsProtonInAromaticSystemDescriptor object
      Specified by:
      setParameters in interface IDescriptor
      params - The new parameters value
      CDKException - Possible Exceptions
      See Also:
    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the IsProtonInAromaticSystemDescriptor 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 atomContainer)
      The method is a proton descriptor that evaluate if a proton is bonded to an aromatic system or if there is distance of 2 bonds. It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
      Specified by:
      calculate in interface IAtomicDescriptor
      atom - The IAtom for which the DescriptorValue is requested
      atomContainer - AtomContainer
      true if the proton is bonded to an aromatic atom.
    • getParameterNames

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

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