Package org.openscience.cdk.qsar.descriptors.atompair

Class PiContactDetectionDescriptor

  • All Implemented Interfaces:
    IAtomPairDescriptor, IDescriptor
    public class PiContactDetectionDescriptor
extends AbstractAtomPairDescriptor
implements IAtomPairDescriptor
    This class checks if two atoms have pi-contact (this is true when there is one and the same conjugated pi-system which contains both atoms, or directly linked neighbours of the atoms). Only conjugated systems with more than 2 atoms are considered.
    Parameters for this descriptor:
    Name Default Description
    firstAtom 0 The position of the first atom
    secondAtom 0 The position of the second atom
    checkAromaticity false True is the aromaticity has to be checked
    Author:
    mfe4
    Dictionary pointer(s):
    piContact in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:piContact]
    Source code:
    main
    Belongs to CDK module:
    qsarmolecular
    Created on:
    2004-11-03

    • Constructor Detail

      • PiContactDetectionDescriptor

        public PiContactDetectionDescriptor()
        Constructor for the PiContactDetectionDescriptor 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 first,
                                 IAtom second,
                                 IAtomContainer atomContainer)
        The method returns if two atoms have pi-contact.
        Specified by:
        calculate in interface IAtomPairDescriptor
        Parameters:
        atomContainer - AtomContainer
        first - The first IAtom of the pair for which this descriptor should be calculated
        second - The second IAtom of the pair for which this descriptor should be calculated
        Returns:
        true if the atoms have pi-contact

      • getParameterNames

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

      • getParameterType

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