Package chemaxon.marvin.calculations

Class RefractivityPlugin

java.lang.Object
chemaxon.marvin.plugin.CalculatorPlugin
chemaxon.marvin.calculations.RefractivityPlugin
All Implemented Interfaces:
TaggedCalculator, chemaxon.license.Licensable
@PublicApi public class RefractivityPlugin extends CalculatorPlugin
Plugin class for refractivity calculation. Both the incremental values for atoms and the overal refractivity value for the molecule can be calculated by this plugin.

API usage example: 

    // read input molecule
    MolImporter mi = new MolImporter("test.mol");
    Molecule mol = mi.read();
    mi.close();

    // create plugin
    RefractivityPlugin plugin = new RefractivityPlugin();

    // set double precision for string conversion (optional)
    plugin.setDoublePrecision(3);

    // set target molecule
    plugin.setMolecule(mol);

    // run the calculation
    plugin.run();

    // get molecular refractivity
    double refractivity = plugin.getRefractivity();
    System.out.println("molecular refractivity: "+plugin.format(refractivity));

    // get refractivity increments values for each atom
    String str = "";
    int count = mol.getAtomCount();
    for (int i=0; i < count; ++i) {
       double increment = plugin.getRefractivityIncrement(i);
       str += plugin.format(increment);
       str += ";";
    }
    System.out.println("refractivity increments for atoms: "+str);

For concurrent plugin example applications using ChemAxon's concurrent framework, refer to the Concurrent plugin examples.

  • Constructor Details

    • RefractivityPlugin

      public RefractivityPlugin()
      Constructor. Creates the refractivity calculator object.

  • Method Details

    • getProductName

      public String getProductName()
      Returns the product identifier of the plugin as given by LicenseManager.
      Specified by:
      getProductName in class CalculatorPlugin
      Returns:
      The identifier LicenseManager.REFRACTIVITY_PLUGIN

    • setParameters

      public void setParameters(Properties params) throws PluginException
      Sets the input parameters for the plugin. Refractivity parameters and value ranges:
      • precision: 0-8 or inf (number of displayed fractional digits, inf for unrounded value)
      • type: increments,refractivity
      • h: true or false (display increments on H atoms)
      Overrides:
      setParameters in class CalculatorPlugin
      Parameters:
      params - is the parameter table
      Throws:
      PluginException - on error

    • checkMolecule

      public void checkMolecule(Molecule mol) throws PluginException
      Checks the input molecule. Throws exception if the molecule is RxnMolecule, if the molecule contains R-groups or if the molecule consists of more than one fragments.
      Overrides:
      checkMolecule in class CalculatorPlugin
      Parameters:
      mol - is the input molecule
      Throws:
      PluginException - with error message for the user if the molecule is refused

    • setInputMolecule

      protected void setInputMolecule(Molecule mol) throws PluginException
      Sets the input molecule.
      Specified by:
      setInputMolecule in class CalculatorPlugin
      Parameters:
      mol - is the (standardized) input molecule
      Throws:
      PluginException - on error

    • run

      public boolean run() throws PluginException
      Runs the refractivity calculation.
      Specified by:
      run in class CalculatorPlugin
      Returns:
      true if the calculation was successful, false on calculation problems
      Throws:
      PluginException - on error
      See Also:

    • getErrorMessage

      public String getErrorMessage()
      Returns the calculation error information message if run() returned false (calculation error): hydrogen valence error.
      Overrides:
      getErrorMessage in class CalculatorPlugin
      Returns:
      the calculation error information message

    • getRefractivity

      public double getRefractivity()
      Returns the refractivity value. The refractivity calculation should be run beforehand by run().
      Returns:
      the refractivity value

    • getRefractivityIncrement

      public double getRefractivityIncrement(int index)
      Returns the refractivity increment for a given atom. The refractivity calculation should be run beforehand by run().
      Parameters:
      index - is the atom index
      Returns:
      the refractivity increment for a given atom

    • getRefractivityHIncrement

      public double getRefractivityHIncrement(int index)
      Returns the refractivity increment on the H atoms attached to a given atom. The refractivity calculation should be run beforehand by run().
      Parameters:
      index - is the atom index
      Returns:
      the refractivity increment on the H atoms attached to a given atom

    • getResultTypes

      public Object[] getResultTypes()
      Returns the result types. Possible result types: refractivity,increments,inch
      Overrides:
      getResultTypes in class CalculatorPlugin
      Returns:
      the result types

    • getTypeString

      public String getTypeString(Object type)
      Returns a string representation of the given type.
      Overrides:
      getTypeString in class CalculatorPlugin
      Parameters:
      type - is the type object
      Returns:
      the type string

    • getResultDomain

      public int getResultDomain(Object type)
      Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE. Returns CalculatorPlugin.ATOM for type "increments" or "inch" and CalculatorPlugin.MOLECULE otherwise.
      Overrides:
      getResultDomain in class CalculatorPlugin
      Parameters:
      type - is the result type
      Returns:
      CalculatorPlugin.MOLECULE or CalculatorPlugin.ATOM
      See Also:

    • getResultCount

      public int getResultCount(Object type)
      Returns the number of result items for the given result key. Refractivity returns the atom count for types "increments" and "inch" 1 otherwise.
      Overrides:
      getResultCount in class CalculatorPlugin
      Parameters:
      type - is the result type
      Returns:
      the number of result items
      See Also:

    • getResult

      public Object getResult(Object type, int index) throws PluginException
      Returns the result item for the specified key and index. Refractivity returns the required refractivity value or atomic increment as a Double object.
      Overrides:
      getResult in class CalculatorPlugin
      Parameters:
      type - is the result type
      index - is the result index
      Returns:
      the result item for the specified key and index
      Throws:
      PluginException - if the result cannot be returned
      See Also:

    • getResultAsString

      public String getResultAsString(Object type, int index, Object result) throws PluginException
      Returns the specified result in String format. Refractivity returns the rounded refractivity value in string format: the value is rounded using the 'precision' input parameter that determines the number of fractional digits displayed.
      Overrides:
      getResultAsString in class CalculatorPlugin
      Parameters:
      type - is the result type
      index - is the result index
      result - is the result item
      Returns:
      the specified result in String format
      Throws:
      PluginException - if an invalid result item is given

    • getResultMolecule

      public Molecule getResultMolecule() throws PluginException
      Returns the result molecule for display. Atomic results are stored in atom extra labels (MolAtom.getExtraLabel()). Molecular results are stored in molecule properties with keys being the result types (MPropHandler.convertToString(MPropertyContainer, String)).
      Overrides:
      getResultMolecule in class CalculatorPlugin
      Returns:
      the result molecule
      Throws:
      PluginException - on error
      Since:
      Marvin 4.0

    • standardize

      public void standardize(Molecule mol)
      Standardizes the molecule. This is done by performing the transformations necessary to run the plugin (e.g. aromatize, dehydrogenize, bring nitro groups to common form). Apart from the default standardization (aromatize and nitro) removes explicit hydrogens. TODO: replace by call to chemaxon.standardizer.Standardizer
      Overrides:
      standardize in class CalculatorPlugin
      Parameters:
      mol - is the molecule to be standardized