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

Class PiContactDetectionDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractAtomPairDescriptor
org.openscience.cdk.qsar.descriptors.atompair.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 Details

    • PiContactDetectionDescriptor

      public PiContactDetectionDescriptor()
      Constructor for the PiContactDetectionDescriptor object.

  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Gets the specification attribute of the PiContactDetectionDescriptor 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 PiContactDetectionDescriptor object.
      Specified by:
      setParameters in interface IDescriptor
      Parameters:
      params - Parameters contains a boolean (true if is needed a checkAromaticity)
      Throws:
      CDKException - Description of the Exception
      See Also:

    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the PiContactDetectionDescriptor 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 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