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

Class IsProtonInAromaticSystemDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractAtomicDescriptor
org.openscience.cdk.qsar.descriptors.atomic.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
Author:
mfe4
Dictionary pointer(s):
isProtonInAromaticSystem in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:isProtonInAromaticSystem]
Source code:
main
Belongs to CDK module:
qsaratomic
Created on:
2004-11-03

  • 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
      Returns:
      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
      Parameters:
      params - The new parameters value
      Throws:
      CDKException - Possible Exceptions
      See Also:

    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the IsProtonInAromaticSystemDescriptor 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 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
      Parameters:
      atom - The IAtom for which the DescriptorValue is requested
      atomContainer - AtomContainer
      Returns:
      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
      Returns:
      The parameterNames value

    • getParameterType

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