Package chemaxon.marvin.calculations

Class HBDAPlugin

java.lang.Object
chemaxon.marvin.plugin.CalculatorPlugin
chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
chemaxon.marvin.calculations.HBDAPlugin
All Implemented Interfaces:
TaggedCalculator, 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
 Molecule mol = null;
 try (MolImporter mi = new MolImporter("target.mol")) {
     mol = mi.read();
 }

 // 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.getAcceptorSiteCount();
 int molecularDonorCount = plugin.getDonorSiteCount();
 // 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.getAcceptorSiteCount(i);
     int atomicDonorCount = plugin.getDonorSiteCount(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.

  • Field Details

  • Constructor Details

    • HBDAPlugin

      public HBDAPlugin()
      Constructor. Creates the calculator object.

  • Method Details

    • 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

    • getProductName

      public String getProductName()
      Returns the product identifier of the plugin as given by LicenseManager.
      Specified by:
      getProductName in class CalculatorPlugin
      Returns:
      The identifier LicenseManager.HBDA_PLUGIN

    • 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

    • setMsCalc

      public void setMsCalc(boolean mscalc)
      Sets microspecies calculation.
      Parameters:
      mscalc - is true if microspecies calculation required
      Since:
      Marvin 3.5.1
      See Also:

    • isMsCalc

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

    • 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 MajorMicrospeciesAccessorPlugin
      Parameters:
      mol - is the input molecule
      Throws:
      PluginException - with error message for the user if the molecule is refused

    • setInputMolecule

      protected void setInputMolecule(Molecule mol) throws PluginException
      Sets the input molecule.
      Specified by:
      setInputMolecule in class CalculatorPlugin
      Parameters:
      mol - is the input molecule
      Throws:
      PluginException - on error

    • 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

    • run

      public boolean run() throws PluginException
      Runs the charge calculation.
      Specified by:
      run in class CalculatorPlugin
      Returns:
      true if the calculation was successful, false on calculation error
      Throws:
      PluginException - on error
      See Also:

    • 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()

    • getAcceptorCount

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public int getAcceptorCount(int index)
      Deprecated, for removal: This API element is subject to removal in a future version.
      Use getAcceptorSiteCount() instead!

    • 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

    • getDonorCount

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public int getDonorCount(int index)
      Deprecated, for removal: This API element is subject to removal in a future version.
      Use getDonorSiteCount(int) instead!

    • 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

    • getAcceptorCount

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public int getAcceptorCount()
      Deprecated, for removal: This API element is subject to removal in a future version.
      Use getAcceptorSiteCount() instead.

    • getAcceptorSiteCount

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

    • getDonorCount

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public int getDonorCount()
      Deprecated, for removal: This API element is subject to removal in a future version.
      Use getDonorSiteCount() instead!

    • 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

    • getResultTypes

      public Object[] getResultTypes()
      Returns the result types. The possible types are described in setParameters(Properties params).
      Overrides:
      getResultTypes in class CalculatorPlugin
      Returns:
      the result types

    • setGUIMode

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) protected void setGUIMode(boolean guimode)
      Deprecated, for removal: This API element is subject to removal in a future version.
      No longer used.
      Sets GUI mode.
      Parameters:
      guimode - is true if GUI mode

    • getResultDomain

      public int getResultDomain(Object type)
      Returns the calculation domain CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE. HBDA returns CalculatorPlugin.ATOM for types "acc" and "don", CalculatorPlugin.MOLECULE for types "accsitecount", "donsitecount", "acceptorcount", "donorcount", and returns CalculatorPlugin.MOLECULE for type "msacc" and "msdon".
      Overrides:
      getResultDomain in class CalculatorPlugin
      Parameters:
      type - is the result type
      Returns:
      the domain as described above
      See Also:

    • 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:

    • 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:

    • 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

    • getResultMolecule

      public Molecule getResultMolecule() throws PluginException
      Returns the result molecule for display. Atomic results are stored in atom extra labels ( MolAtom.getExtraLabel()). Molecular results are stored in molecule properties with keys being the result types ( MPropHandler.convertToString(MPropertyContainer, String)).
      Overrides:
      getResultMolecule in class CalculatorPlugin
      Returns:
      the result molecule
      Throws:
      PluginException - on error
      Since:
      Marvin 4.0

    • tags

      public Set<CalculatorTag> tags()
      Description copied from interface: TaggedCalculator
      Returns the set of tags reported by this calculator. The same tags should be returned unless the calculator is modified using a mutator method, e.g. if some settings are changed.

      New tags can be introduced and reported in the future by existing calculators, so do not depend on the exact set of reported tags, only check for the presence of certain tags.

      Returns:
      the tags