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

Class SmallRingDescriptor

java.lang.Object
org.openscience.cdk.qsar.descriptors.molecular.SmallRingDescriptor
All Implemented Interfaces:
IDescriptor, IMolecularDescriptor
public class SmallRingDescriptor extends Object implements IMolecularDescriptor
Small ring descriptors: these are based on enumeration of all the small rings (sizes 3 to 9) in a molecule, which can be obtained quickly and deterministically. Returns these values
  1. nSmallRings - total number of small rings (of size 3 through 9)
  2. nAromRings - total number of small aromatic rings
  3. nRingBlocks - total number of distinct ring blocks
  4. nAromBlocks - total number of aromatically connected components
  5. nRings3 - total number of 3-membered rings
  6. nRings4 - total number of 4-membered rings
  7. nRings5 - total number of 5-membered rings
  8. nRings6 - total number of 6-membered rings
  9. nRings7 - total number of 7-membered rings
  10. nRings8 - total number of 8-membered rings
  11. nRings9 - total number of 9-membered rings
Dictionary pointer(s):
smallrings in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:smallrings]
Source code:
main
Belongs to CDK module:
qsarmolecular
Keywords:
smallrings, descriptor

  • Constructor Details

    • SmallRingDescriptor

      public SmallRingDescriptor()

  • Method Details

    • initialise

      public void initialise(IChemObjectBuilder builder)
      Description copied from interface: IDescriptor
      Initialise the descriptor with the specified chem object builder. This allows descriptors that required domain objects, such as for SMARTS queries to initialise correctly. If you do not need domain objects then this method does not need to be implemented.
      Specified by:
      initialise in interface IDescriptor
      Parameters:
      builder - chem object builder to use with this descriptor

    • getSpecification

      public DescriptorSpecification getSpecification()
      Fetch descriptor specification.
      Specified by:
      getSpecification in interface IDescriptor
      Returns:
      An object containing the descriptor specification

    • setParameters

      public void setParameters(Object[] params) throws CDKException
      Set parameters: ignored, there are none.
      Specified by:
      setParameters in interface IDescriptor
      Parameters:
      params - An array of Object containing the parameters for this descriptor
      Throws:
      CDKException - if invalid number of type of parameters are passed to it
      See Also:

    • getParameters

      public Object[] getParameters()
      Get parameters: returns empty array, there are none.
      Specified by:
      getParameters in interface IDescriptor
      Returns:
      An array of Object containing the parameter default values
      See Also:

    • getDescriptorNames

      public String[] getDescriptorNames()
      Returns the names of the descriptors made available by this class.
      Specified by:
      getDescriptorNames in interface IDescriptor
      Returns:
      An array of descriptor names, equal in length to the number of descriptor calculated..

    • getDescriptorResultType

      public IDescriptorResult getDescriptorResultType()
      Returns a placeholder with the descriptor size and type.
      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

    • getParameterNames

      public String[] getParameterNames()
      Get parameters: empty, there are none.
      Specified by:
      getParameterNames in interface IDescriptor
      Returns:
      An array of String containing the names of the parameters that this descriptor can accept.

    • getParameterType

      public Object getParameterType(String name)
      Parameter types: there aren't any.
      Specified by:
      getParameterType in interface IDescriptor
      Parameters:
      name - The name of the parameter whose type is requested
      Returns:
      An Object of the class corresponding to the parameter with the supplied name

    • calculate

      public DescriptorValue calculate(IAtomContainer mol)
      Performs the calculation: the graph will be analyzed and ring information will be determined and wrapped up into descriptors.
      Specified by:
      calculate in interface IMolecularDescriptor
      Parameters:
      mol - the atoms and bonds that make up the molecular object
      Returns:
      the various ring-based descriptors generated