Package chemaxon.marvin.calculations

Class MSAPlugin

java.lang.Object
chemaxon.marvin.plugin.CalculatorPlugin
chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
chemaxon.marvin.calculations.MSAPlugin
All Implemented Interfaces:
TaggedCalculator, chemaxon.license.Licensable
@PublicApi public class MSAPlugin extends MajorMicrospeciesAccessorPlugin
Plugin class for molecular surface area calculation. Both the incremental values for atoms and the overal surface area for the molecule can be calculated by this plugin.

Reference:

  1. Ferrara, P,. Apostolakis J., Caflisch A., Proteins 2002, 46, 24-33

API usage example: 

 try (MolImporter mi = new MolImporter("test.mol")) {
    // read input molecule
    Molecule mol = mi.read();

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

    // optional: take major microspecies at pH=7.4
    plugin.setpH(7.4);

    // set surface area type (default: VAN_DER_WAALS)
    plugin.setSurfaceAreaType(SOLVENT);

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

    // run the calculation
    plugin.run();

    // get result
    double area = plugin.getSurfaceArea();

    // print result
    System.out.println("Solvent accessible surface area (pH=7.4): "+area);
 }

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

Since:
Marvin 4.1

  • Field Details

    • VAN_DER_WAALS

      public static final int VAN_DER_WAALS
      Surface area type: 3D van der Waals surface area.
      See Also:

    • SOLVENT

      public static final int SOLVENT
      Surface area type: 3D solvent accessible surface area.
      See Also:

  • Constructor Details

    • MSAPlugin

      public MSAPlugin()
      Constructor. Creates the MSA 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.GEOMETRY_PLUGIN_GROUP

    • setParameters

      public void setParameters(Properties params) throws PluginException
      Sets the input parameters for the plugin. MSA parameters and value ranges:
      • precision: 0-8 or inf (number of displayed fractional digits, inf for unrounded value)
      • type: "vanderwaals", "solvent" (default: "vanderwaals")
      • increments: "true" if surface increments should be returned (for 3D surface ("vanderwaals", "solvent") only)
      • 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

    • setSurfaceAreaType

      public void setSurfaceAreaType(int saType)
      Sets surface area calculation type: VAN_DER_WAALS or SOLVENT. The surface area is returned by getSurfaceArea(). The atomic increments and the 3D molecule can also be enquired by getAtomicSurfaceAreaIncrement(int) and get3DMolecule(). Default: VAN_DER_WAALS.
      Parameters:
      saType - is VAN_DER_WAALS or SOLVENT

    • checkMolecule

      public void checkMolecule(Molecule mol) throws PluginException
      Checks the input molecule. Throws exception if the molecule is RxnMolecule, if the molecule contains R-groups or if the molecule consists of more than one fragments.
      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 (standardized) input molecule
      Throws:
      PluginException - on error

    • run

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

    • getErrorMessage

      public String getErrorMessage()
      Returns the calculation error information message if run() returned false (calculation error). This implementation returns the empty string.
      Overrides:
      getErrorMessage in class MajorMicrospeciesAccessorPlugin
      Returns:
      the calculation error information message

    • getResultTypes

      public Object[] getResultTypes()
      Returns the result types. Possible result types: "vanderwaals", "solvent", "increments".
      Overrides:
      getResultTypes in class CalculatorPlugin
      Returns:
      the result types

    • getResultDomain

      public int getResultDomain(Object type)
      Returns the calculation domain CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULE in case of increments .
      Overrides:
      getResultDomain in class CalculatorPlugin
      Parameters:
      type - is the result type
      Returns:
      CalculatorPlugin.MOLECULE
      See Also:

    • getResultCount

      public int getResultCount(Object type)
      Returns the number of result items for the given result key. TPSA returns 1 for surface area, the atom count for increments.
      Overrides:
      getResultCount in class CalculatorPlugin
      Parameters:
      type - is the result type
      Returns:
      the number of result items
      See Also:

    • setSolventRadius

      public void setSolventRadius(double r)
      Sets solvent radius. Default: 1.4 Angstrom.

    • getSurfaceArea

      public double getSurfaceArea()
      Returns the surface area, calculation type is previously set in setSurfaceAreaType(int). Default: VAN_DER_WAALS.
      Returns:
      the surface area

    • getVDWSA

      public double getVDWSA()
      Returns van der Waals surface area. Calculation type must be set to VAN_DER_WAALS using setSurfaceAreaType(int), and the alculation should be run beforehand by run()
      Returns:
      van der Waals surface area
      Since:
      Marvin 5.0

    • getASA

      public double getASA()
      Returns water accessible surface area calculated using a radius of 1.4 A for the water molecule. Calculation type must be set to SOLVENT using setSurfaceAreaType(int), and the calculation should be run beforehand by run()
      Returns:
      water accessible surface area
      Since:
      Marvin 5.0

    • getASAPlus

      public double getASAPlus()
      Returns water accessible surface area of all atoms with positive partial charge (strictly greater than 0). Calculation type must be set to SOLVENT using setSurfaceAreaType(int), and the calculation should be run beforehand by run()
      Returns:
      water accessible surface area of all atoms with positive partial charge
      Since:
      Marvin 5.0

    • getASANegative

      public double getASANegative()
      Returns water accessible surface area of all atoms with negative partial charge (strictly less than 0). Calculation type must be set to SOLVENT using setSurfaceAreaType(int), and the calculation should be run beforehand by run()
      Returns:
      water accessible surface area of all atoms with negative partial charge
      Since:
      Marvin 5.0

    • getASAHydrophobic

      public double getASAHydrophobic()
      Returns water accessible surface area of all hydrophobic (|qi|invalid input: '<'0.125) atoms. Calculation type must be set to SOLVENT using setSurfaceAreaType(int), and the calculation should be run beforehand by run()
      Returns:
      water accessible surface area of all hydrophobic atoms
      Since:
      Marvin 5.0

    • getASAPolar

      public double getASAPolar()
      Returns water accessible surface area of all polar (|qi|>=0.125) atoms. Calculation type must be set to SOLVENT using setSurfaceAreaType(int), and the calculation should be run beforehand by run()
      Returns:
      water accessible surface area of all polar atoms
      Since:
      Marvin 5.0

    • getAtomicSurfaceAreaIncrement

      public double getAtomicSurfaceAreaIncrement(int index)
      Returns the 3D surface area increments. Calculated only if surface area type is set to SOLVENT or VAN_DER_WAALS in setSurfaceAreaType(int).
      Parameters:
      index - is the atom index
      Returns:
      the surface area increment for the specified atom index

    • get3DMolecule

      public Molecule get3DMolecule()
      Returns the 3D molecule used in 3D surface area calculation. Can be called only if surface area type is set to SOLVENT or VAN_DER_WAALS in setSurfaceAreaType(int).
      Returns:
      the 3D molecule used in 3D surface area calculation

    • getResult

      public Object getResult(Object type, int index) throws PluginException
      Returns the result item for the specified key and index.
      Overrides:
      getResult in class CalculatorPlugin
      Parameters:
      type - is the result type
      index - is the result index
      Returns:
      the result item for the specified key 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

    • getDisplayMolecule

      protected Molecule getDisplayMolecule()
      Returns the molecule object to be used for GUI display. This is the 3D molecule returned by get3DMolecule().
      Overrides:
      getDisplayMolecule in class CalculatorPlugin
      Returns:
      the molecule object to be used for GUI display

    • 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

    • 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

    • isMultiThreadedRunEnabled

      public boolean isMultiThreadedRunEnabled()
      For internal use only.
      Overrides:
      isMultiThreadedRunEnabled in class CalculatorPlugin
      Returns:
      true if multi-threaded run is enabled

    • 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