Package chemaxon.marvin.calculations

Class ChargePlugin

  • All Implemented Interfaces:
    chemaxon.license.Licensable
    @PublicAPI
public class ChargePlugin
extends MajorMicrospeciesAccessorPlugin
    Plugin class for partial charge calculation. Sigma, pi and total charge values can be calculated by this plugin. For formal charge calculation use the following methods: MoleculeGraph.getFormalCharge(), MolAtom.getCharge().

    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
    ChargePlugin plugin = new ChargePlugin();

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

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

    // run the calculation
    plugin.run();

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

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

    • Constructor Detail

      • ChargePlugin

        public ChargePlugin()
        Constructor. Creates the charge calculator object.

    • 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. Charge parameters and value ranges:
        • type: sigma,pi,total, formalcharge, "atomicformalcharge", aromaticsystem, aromaticsystemsigma,aromaticsystempi, aromaticring, aromaticringsigma, aromaticringpi
        • precision: 0-8 or inf (number of displayed fractional digits, inf for unrounded value)
        • implh: true or false - true if implicit H data should be shown
        • 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 charge should be calculated with resonant structures
        Since:
        Marvin 4.1

      • handlesMultiFragmentMolecules

        public boolean handlesMultiFragmentMolecules()
        Description copied from class: CalculatorPlugin
        Returns true if the plugin handles multifragment molecules, false otherwise. In the latter case the plugin takes the fragment with more atoms if a multifragment molecule is given as input. The default implementation returns false.
        Overrides:
        handlesMultiFragmentMolecules in class CalculatorPlugin
        Returns:
        true if the plugin handles multifragment molecules, false otherwise

      • 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

      • getFormalCharge

        public int getFormalCharge()
        Returns the formal charge of the molecule.
        Returns:
        the formal charge of the molecule
        Since:
        Marvin 5.2
        See Also:
        MoleculeGraph.getFormalCharge()

      • getFormalCharge

        public int getFormalCharge​(int index)
        Returns the formal charge of a specified atom.
        Parameters:
        index - is the atom index
        Returns:
        the formal charge of a specified atom
        Since:
        Marvin 5.2
        See Also:
        MolAtom.getCharge()

      • getTotalCharge

        public double getTotalCharge​(int index)
        Returns the total charge of a specified atom. Total charge is the sum of partial charges on the atom.
        Parameters:
        index - is the atom index
        Returns:
        the total charge of a specified atom, Double.NaN for implicit H-s
        Since:
        Marvin 3.4.1
        See Also:
        MolAtom.getCharge(), MoleculeGraph.getFormalCharge()

      • getSigmaCharge

        public double getSigmaCharge​(int index)
        Returns the sigma charge of a specified atom.
        Parameters:
        index - is the atom index
        Returns:
        the sigma charge of a specified atom, Double.NaN for implicit H-s
        Since:
        Marvin 3.4.1

      • getPiCharge

        public double getPiCharge​(int index)
        Returns the pi charge of a specified atom.
        Parameters:
        index - is the atom index
        Returns:
        the pi charge of a specified atom, Double.NaN for implicit H-s
        Since:
        Marvin 3.4.1

      • getResultantImplicitHCharge

        public double getResultantImplicitHCharge​(int index)
        Returns the implicit H charge around a central atom
        Parameters:
        index - is the central atom index
        Returns:
        the implicit H charge around the central atom
        Since:
        Marvin 3.5

      • getAromaticSystemCharge

        public double getAromaticSystemCharge​(int index)
        Returns the total partial charge of the aromatic system containing the specified atom.
        Parameters:
        index - is the atom index
        Returns:
        the total partial charge of the aromatic system containing the specified atom
        Since:
        Marvin 3.5

      • getAromaticSystemCharge

        public double getAromaticSystemCharge​(int index,
                                      int chgtype)
        Returns the partial charge of the aromatic system containing the specified atom.
        Parameters:
        index - is the atom index
        chgtype - is the charge type: 0 - total, 1 - sigma, 2 - pi
        Returns:
        the total partial charge of the aromatic system containing the specified atom
        Since:
        Marvin 4.1

      • getAromaticRingCharge

        public double getAromaticRingCharge​(int index)
        Returns the total partial charge of the smallest aromatic ring containing the specified atom.
        Parameters:
        index - is the atom index
        Returns:
        the total partial charge of the smallest aromatic ring containing the specified atom
        Since:
        Marvin 3.5

      • getAromaticRingCharge

        public double getAromaticRingCharge​(int index,
                                    int chgtype)
        Returns the partial charge of the smallest aromatic ring containing the specified atom.
        Parameters:
        index - is the atom index
        chgtype - is the charge type: 0 - total, 1 - sigma, 2 - pi
        Returns:
        the total partial charge of the smallest aromatic ring containing the specified atom
        Since:
        Marvin 4.1

      • getResultTypes

        public Object[] getResultTypes()
        Returns the result types (possible types: "sigma", "pi", "total").
        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. Charge 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. Charge returns the required charge value as a Double object.
        Overrides:
        getResult in class CalculatorPlugin
        Parameters:
        type - is the result type ("total", "pi", "sigma", "implh", ...)
        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. Charge returns the rounded charge 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