Package chemaxon.marvin.calculations

Class MajorMicrospeciesAccessorPlugin

java.lang.Object
chemaxon.marvin.plugin.CalculatorPlugin
chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
All Implemented Interfaces:
TaggedCalculator, chemaxon.license.Licensable
Direct Known Subclasses:
ChargePlugin, HBDAPlugin, HuckelAnalysisPlugin, MSAPlugin, OrbitalElectronegativityPlugin, PolarizabilityPlugin, TPSAPlugin
@PublicApi public abstract class MajorMicrospeciesAccessorPlugin extends CalculatorPlugin
Common base class for all plugins with possible major microspecies input.

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

Since:
Marvin 4.0.2

  • Field Details

    • ionizer

      protected chemaxon.calculations.pka.Ionizer ionizer

  • Constructor Details

    • MajorMicrospeciesAccessorPlugin

      protected MajorMicrospeciesAccessorPlugin()
      Constructor. Creates the ionizer object.

  • Method Details

    • isLicensed

      public boolean isLicensed()
      Description copied from class: CalculatorPlugin
      Returns true if the plugin is licensed. The license checking is based on the product name, returned by CalculatorPlugin.getProductName().
      Specified by:
      isLicensed in interface chemaxon.license.Licensable
      Overrides:
      isLicensed in class CalculatorPlugin
      Returns:
      true if the plugin is licensed

    • setParameters

      public void setParameters(Properties params) throws PluginException
      Sets the input parameters for the plugin. The parameters and value ranges:
      • pH: major microspecies on given pH is taken as input molecule if omitted then the input molecule is taken as it is
      • microspecies: "true" if major microspecies should be taken as input molecule (corresponds to 'take major microspecies' GUI checkbox)
      • msdistr: "true" if microspecies distributions should be calculated (default: "false")
      Overrides:
      setParameters in class CalculatorPlugin
      Parameters:
      params - is the parameter table
      Throws:
      PluginException - on error

    • setChemicalTermsArgument

      @Deprecated protected void setChemicalTermsArgument(String arg) throws PluginException
      Deprecated.
      Description copied from class: CalculatorPlugin
      Sets the argument string as specified in Chemical Terms expressions. This method may only be called from CalculatorPlugin.setChemicalTermsParameters(Properties, String).
      Overrides:
      setChemicalTermsArgument in class CalculatorPlugin
      Parameters:
      arg - The argument, never null. Its meaning is implementation-dependent.
      Throws:
      PluginException - on error

    • setpH

      public void setpH(double pH)
      Sets the pH: major microspecies on given pH is taken as input molecule if set to Double.NaN then the input molecule is taken as it is.
      Parameters:
      pH - is the pH value

    • getpH

      public double getpH()
      Returns the pH where the major microspecies should be taken. Returns Double.NaN if no microspecies calculation required.
      Overrides:
      getpH in class CalculatorPlugin
      Returns:
      the pH where the major microspecies should be taken or Double.NaN if no microspecies calculation

    • createModifiedInputMolecule

      protected final Molecule createModifiedInputMolecule(Molecule mol)
      Returns the molecule form with largest distribution. Returns a microspecies with largest distribution on a given pH if getpH() returns a value different from Double.NaN, otherwise returns the input molecule itself.
      Overrides:
      createModifiedInputMolecule in class CalculatorPlugin
      Parameters:
      mol - is the input molecule
      Returns:
      the molecule form with largest distribution
      Throws:
      PluginException - on access error

    • getErrorMessage

      public String getErrorMessage()
      Returns the calculation error information message or the empty string if there is no error.
      Overrides:
      getErrorMessage in class CalculatorPlugin
      Returns:
      the calculation error information message

    • getIonizerErrorMessage

      public String getIonizerErrorMessage()
      Returns the calculation error information message or the empty string if there is no error.
      Returns:
      the calculation error information message

    • checkMolecule

      public void checkMolecule(Molecule mol) throws PluginException
      Checks the input molecule. Throws exception if the molecule molecule contains R-groups.
      Overrides:
      checkMolecule in class CalculatorPlugin
      Parameters:
      mol - is the input molecule
      Throws:
      PluginException - with error message for the user if the molecule is refused

    • standardize

      public void standardize(Molecule mol)
      Standardizes the molecule. Adds dehydrogenization to default standardization in case when major microsepcies calculation required.
      Overrides:
      standardize in class CalculatorPlugin
      Parameters:
      mol - is the molecule to be standardized