Class MajorMicrospeciesAccessorPlugin

    • Field Detail

      • ionizer

        protected chemaxon.calculations.pka.Ionizer ionizer
    • Constructor Detail

      • MajorMicrospeciesAccessorPlugin

        public MajorMicrospeciesAccessorPlugin()
        Constructor. Creates the ionizer object.
    • Method Detail

      • 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
      • 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