Package chemaxon.marvin.calculations

Class OrbitalElectronegativityPlugin

  • All Implemented Interfaces:
    chemaxon.license.Licensable
    @PublicAPI
public class OrbitalElectronegativityPlugin
extends MajorMicrospeciesAccessorPlugin
    Plugin class for orbital electronegativity calculation. Sigma anf pi orbital electronegativity values can be calculated by this plugin.

    References:

    1. J.Gasteiger and M.Marsili: Tetrahedron Vol. 36. , pp. 3219-3288 (1980)
    2. M.Marsili and J.Gasteiger: International Symposium on Aromaticity, Dubrovnik, Yugoslavia , Sept (1979), Croat.Chim.Acta. (1979)
    3. Steven L. Dixon and Peter C. Jurs: J.Comp.Chem., Vol.13. No.4, 492-504 (1992)
    4. W.J.Mortier, K.V.Genechten and J.Gasteiger: J.Am.Chem.Soc., Vol. 107,829-835 (1985)

    API usage example: 

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

    // read target molecule
    MolImporter mi = new MolImporter(new ByteArrayInputStream("Clc1cc(Cl)c(Cl)cc1".getBytes()));
    Molecule mol = mi.read();
    mi.close();

    // optional: take major microspecies at pH=7.4
    // skip this if you want to calculate orbital electronegativity for the input molecule as it is
    plugin.setpH(7.4);

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

    // run the calculation
    plugin.run();

    // get orbital electronegativity values for each atom
    int count = mol.getAtomCount();
    for (int i=0; i < count; ++i) {
          double sigmaoen = plugin.getSigmaOen(i);
          if (!Double.isNaN(sigmaoen)) {
              System.out.println("sigma orbital electronegativity for atom "+(i+1)+": "+sigmaoen);
          }
    }

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

    Since:
    Marvin 4.1, 07/25/2006

    • Constructor Detail

      • OrbitalElectronegativityPlugin

        public OrbitalElectronegativityPlugin()
        Constructor.

    • Method Detail

      • isLicensed

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

      • setParameters

        public void setParameters​(Properties params)
                   throws PluginException
        Sets the input parameters for the plugin. Orbital electronegativity parameters and value ranges:
        • type: sigma,pi
        • precision: 0-8 or inf (number of displayed fractional digits, inf for unrounded value)
        • resonance: true or false - true if calculate with resonant structures (default: false)
        • pH: major microspecies on given pH is taken as input molecule if omitted then the input molecule is taken as it is
        Overrides:
        setParameters in class MajorMicrospeciesAccessorPlugin
        Parameters:
        params - is the parameter table
        Throws:
        PluginException - on error

      • setTakeResonantStructures

        public void setTakeResonantStructures​(boolean resonance)
        Sets calculation with resonant structures. Default: false.
        Parameters:
        resonance - is true if orbital electornegativity should be calculated with resonant structures

      • getErrorMessage

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

      • getSigmaOEN

        public double getSigmaOEN​(int index)
        Returns the sigma orbital electronegativity of a specified atom.
        Parameters:
        index - is the atom index
        Returns:
        the sigma orbital electronegativity of a specified atom

      • getPiOEN

        public double getPiOEN​(int index)
        Returns the pi orbital electronegativity of a specified atom.
        Parameters:
        index - is the atom index
        Returns:
        the pi orbital electronegativity of a specified atom

      • getResultTypes

        public Object[] getResultTypes()
        Returns the result types (possible types: "sigma", "pi").
        Overrides:
        getResultTypes in class CalculatorPlugin
        Returns:
        the result types

      • getResultCount

        public int getResultCount​(Object type)
        Returns the number of result items for the given result type. Orbital electornegativity plugin returns the atom count.
        Overrides:
        getResultCount in class CalculatorPlugin
        Parameters:
        type - is the result type
        Returns:
        the number of result items
        See Also:
        getResultTypes()

      • 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

      • getResult

        public Object getResult​(Object type,
                        int index)
                 throws PluginException
        Returns the result item for the specified type and index. Orbital electornegativity plugin returns the required Orbital electornegativity value as a Double object.
        Overrides:
        getResult in class CalculatorPlugin
        Parameters:
        type - is the result type ("sigma" or "pi")
        index - is the atom index
        Returns:
        the result item for the specified type and index
        Throws:
        PluginException - if the result cannot be returned
        See Also:
        getResultTypes()

      • getResultAsString

        public String getResultAsString​(Object type,
                                int index,
                                Object result)
                         throws PluginException
        Returns the specified result in String format.
        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