Package org.openscience.cdk.qsar.descriptors.molecular

Class MomentOfInertiaDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
All Implemented Interfaces:
IDescriptor, IMolecularDescriptor
public class MomentOfInertiaDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
A descriptor that calculates the moment of inertia and radius of gyration. Moment of inertia (MI) values characterize the mass distribution of a molecule. Related to the MI values, ratios of the MI values along the three principal axes are also well know modeling variables. This descriptor calculates the MI values along the X, Y and Z axes as well as the ratio's X/Y, X/Z and Y/Z. Finally it also calculates the radius of gyration of the molecule. The descriptor generates 7 values in the following order
  • MOMI-X - MI along X axis
  • MOMI-Y - MI along Y axis
  • MOMI-Z - MI along Z axis
  • MOMI-XY - X/Y
  • MOMI-XZ - X/Z
  • MOMI-YZ Y/Z
  • MOMI-R - Radius of gyration
One important aspect of the algorithm is that if the eigenvalues of the MI tensor are below 1e-3, then the ratio's are set to a default of 1000.
Parameters for this descriptor:
Name Default Description
no parameters
Author:
Rajarshi Guha
Dictionary pointer(s):
momentOfInertia in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:momentOfInertia]
Source code:
main
Belongs to CDK module:
qsarmolecular
Keywords:
moment of inertia
Created on:
2005-02-07

  • Constructor Details

    • MomentOfInertiaDescriptor

      public MomentOfInertiaDescriptor()

  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Description copied from interface: IDescriptor
      Returns a IImplementationSpecification which specifies which descriptor is implemented by this class. These fields are used in the map:
      • Specification-Reference: refers to an entry in a unique dictionary
      • Implementation-Title: anything
      • Implementation-Identifier: a unique identifier for this version of this class
      • Implementation-Vendor: CDK, JOELib, or anything else
      Specified by:
      getSpecification in interface IDescriptor
      Returns:
      An object containing the descriptor specification

    • setParameters

      public void setParameters(Object[] params) throws CDKException
      Sets the parameters attribute of the MomentOfInertiaDescriptor object.
      Specified by:
      setParameters in interface IDescriptor
      Parameters:
      params - The new parameters value
      Throws:
      CDKException - Description of the Exception
      See Also:

    • getParameters

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

    • getParameterNames

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

    • getParameterType

      public Object getParameterType(String name)
      Gets the parameterType attribute of the MomentOfInertiaDescriptor object.
      Specified by:
      getParameterType in interface IDescriptor
      Parameters:
      name - Description of the Parameter
      Returns:
      The parameterType value

    • calculate

      public DescriptorValue calculate(IAtomContainer container)
      Calculates the 3 MI's, 3 ration and the R_gyr value. The molecule should have hydrogens
      Specified by:
      calculate in interface IMolecularDescriptor
      Parameters:
      container - Parameter is the atom container.
      Returns:
      An ArrayList containing 7 elements in the order described above

    • getDescriptorResultType

      public IDescriptorResult getDescriptorResultType()
      Returns the specific type of the DescriptorResult object. The return value from this method really indicates what type of result will be obtained from the DescriptorValue object. Note that the same result can be achieved by interrogating the DescriptorValue object; this method allows you to do the same thing, without actually calculating the descriptor.
      Specified by:
      getDescriptorResultType in interface IMolecularDescriptor
      Returns:
      an object that implements the IDescriptorResult interface indicating the actual type of values returned by the descriptor in the DescriptorValue object

    • initialise

      public void initialise(IChemObjectBuilder builder)
      Default implementation of initialise allows optional override.
      Specified by:
      initialise in interface IDescriptor
      Parameters:
      builder - chem object build