Class FractionalPSADescriptor

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

public class FractionalPSADescriptor extends Object implements IMolecularDescriptor
Polar surface area expressed as a ratio to molecular size. Calculates tpsaEfficiency, which is to TPSADescriptor / molecular weight, in units of square Angstroms per Dalton. Other related descriptors may also be useful to add, e.g. ratio of polar to hydrophobic surface area.
Dictionary pointer(s):
fractionalPSA in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:fractionalPSA]
Source code:
main
Belongs to CDK module:
qsarmolecular
Keywords:
volume, descriptor
  • Constructor Details

    • FractionalPSADescriptor

      public FractionalPSADescriptor()
  • 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()
      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()
      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 mol)
      Calculates the topological polar surface area and expresses it as a ratio to molecule size.
      Specified by:
      calculate in interface IMolecularDescriptor
      Parameters:
      mol - The IAtomContainer whose volume is to be calculated
      Returns:
      descriptor(s) retaining to polar surface area
    • 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