Class HBondAcceptorCountDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
All Implemented Interfaces:
IDescriptor, IMolecularDescriptor

public class HBondAcceptorCountDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
This descriptor calculates the number of hydrogen bond acceptors using a slightly simplified version of the PHACIR atom types. The following groups are counted as hydrogen bond acceptors:
  • any oxygen where the formal charge of the oxygen is non-positive (i.e. formal charge ≤ 0) except
    1. an aromatic ether oxygen (i.e. an ether oxygen that is adjacent to at least one aromatic carbon)
    2. an oxygen that is adjacent to a nitrogen
  • any nitrogen where the formal charge of the nitrogen is non-positive (i.e. formal charge ≤ 0) except
    1. a nitrogen that is adjacent to an oxygen
Returns a single value named nHBAcc.
Parameters for this descriptor:
Name Default Description
checkAromaticity false true if the aromaticity has to be checked

This descriptor works properly with AtomContainers whose atoms contain implicit hydrogens or explicit hydrogens.

Author:
ulif
Dictionary pointer(s):
hBondacceptors in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:hBondacceptors]
Source code:
main
Belongs to CDK module:
qsarmolecular
Created on:
2005-22-07
  • Constructor Details

    • HBondAcceptorCountDescriptor

      public HBondAcceptorCountDescriptor()
      Constructor for the HBondAcceptorCountDescriptor object
  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Gets the specification attribute of the HBondAcceptorCountDescriptor 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 HBondAcceptorCountDescriptor object.
      Specified by:
      setParameters in interface IDescriptor
      Parameters:
      params - a boolean true means that aromaticity has to be checked
      Throws:
      CDKException - Description of the Exception
      See Also:
    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the HBondAcceptorCountDescriptor 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 atomContainer)
      Calculates the number of H bond acceptors.
      Specified by:
      calculate in interface IMolecularDescriptor
      Parameters:
      atomContainer - AtomContainer
      Returns:
      number of H bond acceptors
    • 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 HBondAcceptorCountDescriptor object.
      Specified by:
      getParameterNames in interface IDescriptor
      Returns:
      The parameterNames value
    • getParameterType

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