Package chemaxon.marvin.calculations

Class HBDAPlugin

  • All Implemented Interfaces:
    chemaxon.license.Licensable
    @PublicAPI
public class HBDAPlugin
extends MajorMicrospeciesAccessorPlugin
    Plugin class for H bond acceptor/donor calculation.

    API usage example: 

     // create plugin
 HBDAPlugin plugin = new HBDAPlugin();
 
 // set plugin parameters
 plugin.setDoublePrecision(2);
 plugin.setpHLower(2.0);
 plugin.setpHUpper(12.0);
 plugin.setpHStep(2.0);
 
 // optional: take major microspecies at pH=7.4
 // skip this if you want to calculate HBDA for the input molecule as it is
 plugin.setpH(7.4);
 
 // read target molecule
 MolImporter mi = new MolImporter("target.mol");
 Molecule mol = mi.read();
 mi.close();
 
 // set target molecule
 plugin.setMolecule(mol);
 
 // run the calculation
 plugin.run();
 
 // get results
 
 // average acceptor/donor counts by microspecies distributions at given pH-s
 double[] pHs = plugin.getpHs();
 double[] msacc = plugin.getMsAcceptorCounts();
 double[] msdon = plugin.getMsDonorCounts();
 
 System.out.println("pH\tmsacc\tmsdon");
 for (int i = 0; i < pHs.length; ++i) {
     System.out.println("" + plugin.format(pHs[i]) + "\t" + plugin.format(msacc[i]) + "\t"
            + plugin.format(msdon[i]));
 }
 
 // molecular data
 // with multiplicity
 int molecularAcceptorCount = plugin.getAcceptorCount();
 int molecularDonorCount = plugin.getDonorCount();
 // without multiplicity
 int molecularAcceptorAtomCount = plugin.getAcceptorAtomCount();
 int molecularDonorAtomCount = plugin.getDonorAtomCount();
 System.out.println();
 System.out.println("Acceptor count with multiplicity: " + molecularAcceptorCount);
 System.out.println("Donor count with multiplicity: " + molecularDonorCount);
 System.out.println("Acceptor count without multiplicity: " + molecularAcceptorAtomCount);
 System.out.println("Donor count without multiplicity: " + molecularDonorAtomCount);
 
 // atomic data
 System.out.println();
 System.out.println("Atom\tAcceptor count\tDonor count");
 int count = mol.getAtomCount();
 for (int i = 0; i < count; ++i) {
 
     // atomic acceptor/donor count with multiplicity
     int atomicAcceptorCount = plugin.getAcceptorCount(i);
     int atomicDonorCount = plugin.getDonorCount(i);
 
     if (atomicAcceptorCount != -1) { // -1 means H atom
        System.out.println("" + (i + 1) + "\t" + atomicAcceptorCount + "\t" + atomicDonorCount);
     }
 }

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

    • Constructor Detail

      • HBDAPlugin

        public HBDAPlugin()
        Constructor. Creates the 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:
          • acc: atomic acceptors
          • don: atomic donors
          • accsitecount: molecular acceptor count with multiplicity
          • donsitecount: molecular donor count with multiplicity
          • acceptorcount: molecular acceptor atom count without multiplicity
          • donorcount: molecular donor atom count without multiplicity
          • msacc: average acceptor count over microspecies by pH
          • msdon: average donor count over microspecies by pH
          • excludesulfur: exclude sulfur atoms from acceptors
        • precision: 0-8 or inf (number of displayed fractional digits, inf for unrounded value)
        • lower: pH lower limit (default: 0.0)
        • upper: pH upper limit (default: 14.0)
        • count: pH step count between lower and upper limits (default: 0.5)
        Overrides:
        setParameters in class MajorMicrospeciesAccessorPlugin
        Parameters:
        params - is the parameter table
        Throws:
        PluginException - on error

      • setpHLower

        public void setpHLower​(double lower)
        Sets pH lower limit for the calculation of microspecies distributions. Also activates the calculation of microspecies distributions. The default value is 0.0.
        Parameters:
        lower - is the pH lower limit
        Since:
        Marvin 3.5.1

      • setpHUpper

        public void setpHUpper​(double upper)
        Sets pH upper limit for the calculation of microspecies distributions. Also activates the calculation of microspecies distributions. The default value is 14.0.
        Parameters:
        upper - is the pH upper limit
        Since:
        Marvin 3.5.1

      • setpHStep

        public void setpHStep​(double step)
        Sets pH step for the calculation of microspecies distributions. Also activates the calculation of microspecies distributions. The default value is 0.5.
        Parameters:
        step - is the pH step
        Since:
        Marvin 3.5.1

      • isMsCalc

        protected boolean isMsCalc()
        Returns true if microspecies calculation.
        Overrides:
        isMsCalc in class CalculatorPlugin
        Returns:
        true if microspecies calculation

      • setExcludeSulfur

        public void setExcludeSulfur​(boolean e)
        Sets if sulfur atom should be excluded from hydrogen bond acceptors. Default: true
        Parameters:
        e - if true then sulfur atom is not considered to be hydrogen bond acceptor.
        Since:
        Marvin 5.3

      • setExcludeHalogens

        public void setExcludeHalogens​(boolean e)
        Sets if halogens should be excluded from hydrogen bond acceptors. Default: true
        Parameters:
        e - if true then halogens are not considered to be hydrogen bond acceptor.
        Since:
        Marvin 5.3.2

      • 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

      • getWarningMessage

        public String getWarningMessage()
        Returns the calculation warning information message if no H-bond donor/acceptor atoms found, returns the empty string otherwise.
        Overrides:
        getWarningMessage in class CalculatorPlugin
        Returns:
        the calculation warning information message

      • getpHs

        public double[] getpHs()
        Returns the pH array.
        Returns:
        the pH array

      • getMsAcceptorCounts

        public double[] getMsAcceptorCounts()
        Returns the average acceptor counts over the microspecies distribution for different pH-s. The pH array is returned by getpHs() and determined by the "lower", "upper" and "step" plugin parameters.
        Returns:
        the average acceptor counts over the microspecies distribution for pH-s returned by getpHs()

      • getMsDonorCounts

        public double[] getMsDonorCounts()
        Returns the average donor counts over the microspecies distribution for different pH-s. The pH array is returned by getpHs() and determined by the "lower", "upper" and "step" plugin parameters.
        Returns:
        the average donor counts over the microspecies distribution for pH-s returned by getpHs()

      • getAcceptorSiteCount

        public int getAcceptorSiteCount​(int index)
        Returns the atomic acceptor count corresponding to the specified atom index.
        Parameters:
        index - is the atom index
        Returns:
        the atomic acceptor count, -1 for H atoms

      • getDonorSiteCount

        public int getDonorSiteCount​(int index)
        Returns the atomic donor count corresponding to the specified atom index.
        Parameters:
        index - is the atom index
        Returns:
        the atomic donor count, -1 for H atoms

      • getAcceptorSiteCount

        public int getAcceptorSiteCount()
        Returns the overall acceptor count (with multiplicity) in the molecule.
        Returns:
        the overall acceptor count (with multiplicity) in the molecule

      • getDonorSiteCount

        public int getDonorSiteCount()
        Returns the overall donor count (with multiplicity) in the molecule.
        Returns:
        the overall donor count (with multiplicity) in the molecule

      • getAcceptorAtomCount

        public int getAcceptorAtomCount()
        Returns the overall acceptor atom count (without multiplicity) in the molecule.
        Returns:
        the overall acceptor atom count (without multiplicity) in the molecule

      • getDonorAtomCount

        public int getDonorAtomCount()
        Returns the overall donor atom count (without multiplicity) in the molecule.
        Returns:
        the overall donor atom count (without multiplicity) in the molecule

      • setGUIMode

        @Deprecated
protected void setGUIMode​(boolean guimode)
        Deprecated.
        Sets GUI mode.
        Parameters:
        guimode - is true if GUI mode

      • getResultCount

        public int getResultCount​(Object type)
        Returns the number of result items for the given result type. Returns the atom count for types "acc" and "don", 1 otherwise.
        Overrides:
        getResultCount in class CalculatorPlugin
        Parameters:
        type - is the result type
        Returns:
        the number of result items
        See Also:
        getResultTypes()

      • getResult

        public Object getResult​(Object type,
                        int index)
                 throws PluginException
        Returns the result item for the specified type and index. HBDA returns the (pH, acceptor/donor count) arrays for types "msacceptor" and "msdonor" as a double[2][] with the 0-th element being the pH array and the 1-st element being the acceptor/donor count array. For types "acc" and "don" HBDA returns the acceptor/donor count corresponding to the specified atom index. For types "accsitecount" and "donsitecount" HBDA returns the sum of the atomic values. cc * @see #getResultTypes()
        Overrides:
        getResult in class CalculatorPlugin
        Parameters:
        type - is the result type ("acc", "don", "msacc", "msdon", "accsitecount", "donsitecount", "acceptorcount", "donorcount")
        index - is the atom index for types "acc", "don", N/A for "msacc", "msdon", "accsitecount", "donsitecount", "acceptorcount", "donorcount"
        Returns:
        the result item for the specified type and index
        Throws:
        PluginException - if the result cannot be returned
        See Also:
        CalculatorPlugin.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

      • getResultAsRGB

        public int getResultAsRGB​(Object type,
                          int index,
                          Object result)
                   throws PluginException
        Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue). Returns "red" for acceptor "blue" for donor.
        Overrides:
        getResultAsRGB in class CalculatorPlugin
        Parameters:
        type - is the result type
        index - is the result index
        result - is the result item
        Returns:
        the specified result in color as int
        Throws:
        PluginException - if an invalid result item is given

      • getResultsAsRGB

        public long getResultsAsRGB​(Object type,
                            int index,
                            Object result)
                     throws PluginException
        Returns the specified result color(s) as int format (alpha<<24 + red<<16 + green<<8 + blue). Returns "red" for acceptor "blue" for donor.
        Overrides:
        getResultsAsRGB in class CalculatorPlugin
        Parameters:
        type - is the result type
        index - is the result index
        result - is the result item
        Returns:
        the specified result in color as int
        Throws:
        PluginException - if an invalid result item is given

      • getResultsAsString

        public String getResultsAsString​(Object type,
                                 int index,
                                 Object result)
                          throws PluginException
        Returns the specified result in GUI-specific String format: A for acceptor, D for donor.
        Overrides:
        getResultsAsString 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

      • 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

      • isNegligibleResult

        public boolean isNegligibleResult​(Object type,
                                  int index,
                                  Object result)
                           throws PluginException
        Returns whether the result can be ignored. Returns true for microspecies acceptor/donor count below EPSILON. Returns false for all other results.
        Overrides:
        isNegligibleResult in class CalculatorPlugin
        Parameters:
        type - is the result type
        index - is the result index
        result - is the result object
        Returns:
        true for microspecies acceptor/donor count below EPSILON
        Throws:
        PluginException