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

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
    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 Detail

      • IsProtonInAromaticSystemDescriptor

        public IsProtonInAromaticSystemDescriptor()
        Constructor for the IsProtonInAromaticSystemDescriptor object

    • Method Detail

      • 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