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

Class DistanceToAtomDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractAtomicDescriptor
org.openscience.cdk.qsar.descriptors.atomic.DistanceToAtomDescriptor
All Implemented Interfaces:
IAtomicDescriptor, IDescriptor
public class DistanceToAtomDescriptor extends AbstractAtomicDescriptor implements IAtomicDescriptor
This class returns the 3D distance between two atoms. Only works with 3D coordinates, which must be calculated beforehand.
Parameters for this descriptor:
Name Default Description
focusPosition 0 The position of the second atom
Author:
mfe4
Dictionary pointer(s):
distanceToAtom in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:distanceToAtom]
Source code:
main
Belongs to CDK module:
qsaratomic
Created on:
2004-11-13

  • Constructor Details

    • DistanceToAtomDescriptor

      public DistanceToAtomDescriptor()
      Constructor for the DistanceToAtomDescriptor object

  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Gets the specification attribute of the DistanceToAtomDescriptor 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 DistanceToAtomDescriptor object
      Specified by:
      setParameters in interface IDescriptor
      Parameters:
      params - The parameter is the position to focus
      Throws:
      CDKException - Description of the Exception
      See Also:

    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the DistanceToAtomDescriptor 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 container)
      This method calculate the 3D distance between two atoms.
      Specified by:
      calculate in interface IAtomicDescriptor
      Parameters:
      atom - The IAtom for which the DescriptorValue is requested
      container - Parameter is the atom container.
      Returns:
      The number of bonds on the shortest path between two atoms

    • getParameterNames

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

    • getParameterType

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