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

Class RotatableBondsCountDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
All Implemented Interfaces:
IDescriptor, IMolecularDescriptor
public class RotatableBondsCountDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
The number of rotatable bonds is given by the SMARTS specified by Daylight on SMARTS tutorial

Parameters for this descriptor:
Name Default Description
includeTerminals false True if terminal bonds are included
excludeAmides false True if amide C-N bonds should be excluded
Returns a single value named nRotB
Author:
mfe4
Dictionary pointer(s):
rotatableBondsCount in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:rotatableBondsCount]
Source code:
main
Belongs to CDK module:
qsarmolecular
Keywords:
bond count, rotatable, descriptor
Created on:
2004-11-03

  • Constructor Details

    • RotatableBondsCountDescriptor

      public RotatableBondsCountDescriptor()
      Constructor for the RotatableBondsCountDescriptor object

  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Gets the specification attribute of the RotatableBondsCountDescriptor 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 RotatableBondsCountDescriptor object
      Specified by:
      setParameters in interface IDescriptor
      Parameters:
      params - a boolean true means that terminal atoms must be included in the count
      Throws:
      CDKException - Description of the Exception
      See Also:

    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the RotatableBondsCountDescriptor 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(IAtomContainer ac)
      The method calculates the number of rotatable bonds of an atom container. If the boolean parameter is set to true, terminal bonds are included.
      Specified by:
      calculate in interface IMolecularDescriptor
      Parameters:
      ac - AtomContainer
      Returns:
      number of rotatable bonds

    • 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

    • getParameterNames

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

    • getParameterType

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