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

Class BasicGroupCountDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.BasicGroupCountDescriptor
All Implemented Interfaces:
IDescriptor, IMolecularDescriptor
public class BasicGroupCountDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
Returns the number of basic groups. The list of basic groups is defined by this SMARTS "[$([NH2]-[CX4])]", "[$([NH](-[CX4])-[CX4])]", "[$(N(-[CX4])(-[CX4])-[CX4])]", "[$([*;+;!$(*~[*;-])])]", "[$(N=C-N)]", and "[$(N-C=N)]" originally presented in JOELib [Wegner, J. K., Data Mining und Graph Mining auf molekularen Graphen - Cheminformatik und molekulare Kodierungen f\"{u}r ADME/Tox QSAR Analysen, 2006, ?Institute?].
Author:
egonw
Dictionary pointer(s):
acidicGroupCount in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:acidicGroupCount]
Source code:
main
Belongs to CDK module:
qsarmolecular

  • Constructor Details

  • Method Details

    • initialise

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

    • getSpecification

      public DescriptorSpecification getSpecification()
      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 for this descriptor. Must be done before calling calculate as the parameters influence the calculation outcome.
      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()
      Returns the current parameter values. If not parameters have been set, it must return the default parameters. The method returns null or a zero-length Object[] array if the descriptor does not have any parameters.
      Specified by:
      getParameters in interface IDescriptor
      Returns:
      An array of Object containing the parameter default values
      See Also:

    • getDescriptorNames

      public String[] getDescriptorNames()
      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 atomContainer)
      Calculates the descriptor value for the given IAtomContainer.
      Specified by:
      calculate in interface IMolecularDescriptor
      Parameters:
      atomContainer - An IAtomContainer for which this descriptor should be calculated
      Returns:
      An object of DescriptorValue that contain the calculated value as well as specification details

    • 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.

      Additionally, the length indicated by the result type must match the actual length of a descriptor calculated with the current parameters. Typically, the length of array result types vary with the values of the parameters. See IDescriptor for more details.

      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()
      Returns the names of the parameters for this descriptor. The method returns null or a zero-length Object[] array if the descriptor does not have any parameters.
      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)
      Returns a class matching that of the parameter with the given name. May only return null for when 'name' does not match any parameters returned by the getParameters() method.
      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