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

Class MDEDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
All Implemented Interfaces:
IDescriptor, IMolecularDescriptor
public class MDEDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
Calculates the Molecular Distance Edge descriptor described in [Liu, S. et. al.. Journal of Chemical Information and Computer Sciences. 1998. 38]. This class evaluates the 10 MDE descriptors described by Liu et al. and in addition it calculates variants where O and N are considered (as found in the DEDGE routine from ADAPT).
Table 1 - Description of the different MDE descriptors generated
MDEC-11 molecular distance edge between all primary carbons
MDEC-12 molecular distance edge between all primary and secondary carbons
MDEC-13 molecular distance edge between all primary and tertiary carbons
MDEC-14 molecular distance edge between all primary and quaternary carbons
MDEC-22 molecular distance edge between all secondary carbons
MDEC-23 molecular distance edge between all secondary and tertiary carbons
MDEC-24 molecular distance edge between all secondary and quaternary carbons
MDEC-33 molecular distance edge between all tertiary carbons
MDEC-34 molecular distance edge between all tertiary and quaternary carbons
MDEC-44 molecular distance edge between all quaternary carbons
MDEO-11 molecular distance edge between all primary oxygens
MDEO-12 molecular distance edge between all primary and secondary oxygens
MDEO-22 molecular distance edge between all secondary oxygens
MDEN-11 molecular distance edge between all primary nitrogens
MDEN-12 molecular distance edge between all primary and secondary nitrogens
MDEN-13 molecular distance edge between all primary and tertiary niroqens
MDEN-22 molecular distance edge between all secondary nitroqens
MDEN-23 molecular distance edge between all secondary and tertiary nitrogens
MDEN-33 molecular distance edge between all tertiary nitrogens
Author:
Rajarshi Guha
Dictionary pointer(s):
mde in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:mde]
Source code:
main
Belongs to CDK module:
qsarmolecular
Created on:
2006-09-18

  • Field Details

  • Constructor Details

    • MDEDescriptor

      public MDEDescriptor()

  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Returns a Map 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 WeightDescriptor object.
      Specified by:
      setParameters in interface IDescriptor
      Parameters:
      params - The new parameters value
      Throws:
      CDKException - if more than 1 parameter is specified or if the parameter is not of type String
      See Also:

    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the WeightDescriptor 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 container)
      Calculate the weight of specified element type in the supplied IAtomContainer.
      Specified by:
      calculate in interface IMolecularDescriptor
      Parameters:
      container - The AtomContainer for which this descriptor is to be calculated. If 'H' is specified as the element symbol make sure that the AtomContainer has hydrogens.
      Returns:
      The total weight of atoms of the specified element type

    • 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 WeightDescriptor object.
      Specified by:
      getParameterNames in interface IDescriptor
      Returns:
      The parameterNames value

    • getParameterType

      public Object getParameterType(String name)
      Gets the parameterType attribute of the WeightDescriptor object.
      Specified by:
      getParameterType in interface IDescriptor
      Parameters:
      name - Description of the Parameter
      Returns:
      An Object whose class is that of the parameter requested

    • initialise

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