Package chemaxon.marvin.calculations

Class StructuralFrameworksPlugin

java.lang.Object
chemaxon.marvin.plugin.CalculatorPlugin
chemaxon.marvin.calculations.StructuralFrameworksPlugin
All Implemented Interfaces:
TaggedCalculator, chemaxon.license.Licensable
@PublicAPI public class StructuralFrameworksPlugin extends CalculatorPlugin
Plugin class to calculate Bemis-Murcko and other structural scaffolds of input molecules. The plugin inside executes a series of atomic (not in chemical sense) operations which are accessible to the user. The configuration which is set either by setParameters(Properties) or by the individual setters. The operation chain is set up according to the actual configuration by getHost(boolean).

API usage example: 

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

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

    // set framework type
    plugin.setType(StructuralFrameworksPlugin.FrameworkTypes.bemismurcko );

    // process only the largest fragment
    plugin.setLfin( true );

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

    // run the calculation
    plugin.run();

    // get result
    Molecule result = plugin.getResultMolecule()

    // print result
    System.out.println("Bemis-Murcko framework in SMILES format: "+result.toFormat("smiles") );

  • Constructor Details

    • StructuralFrameworksPlugin

      public StructuralFrameworksPlugin()

  • Method Details

    • setVerbosePrinter

      public void setVerbosePrinter(StructuralFrameworksPlugin.VerbosePrinter verb)
      Set or clear verbose printer Verbose messages will be sent to the verbose printer to ease debugging
      Parameters:
      verb - Verbose printer. Use null to clear verbose.

    • checkMolecule

      public void checkMolecule(Molecule mol) throws PluginException
      Checks the input molecule. Throws exception if the molecule is not accepted as input molecule, otherwise does nothing (simply returns). In addition to the default implementation (which refuses query molecules, molecules with SRU S-groups, molecules with multicenter S-groups and molecules with coordinate bonds) this method will check if Frameworks can be executed on the structure.

      Currently the following cases (in addition to the default behavior) fail:

      • mcs Framework calculation needs at least two disconnected fragments. If the molecule contains no atoms or consists of one connected fragment exception is thrown.
      Overrides:
      checkMolecule in class CalculatorPlugin
      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
      Set input molecule to process
      Specified by:
      setInputMolecule in class CalculatorPlugin
      Parameters:
      mol - Input molecule
      Throws:
      PluginException

    • canRepeat

      public boolean canRepeat()
      Description copied from class: CalculatorPlugin
      Returns true if repeatedly running the same plugin object while getting the results on the GUI is allowed, false otherwise. For internal use.
      Overrides:
      canRepeat in class CalculatorPlugin
      Returns:
      true if allowed, false otherwise

    • standardize

      public void standardize(Molecule mol)
      Standardize input molecule
      Standardization currently ungroups SGroups
      Overrides:
      standardize in class CalculatorPlugin
      Parameters:
      mol - Input molecule to standardize

    • run

      public boolean run() throws PluginException
      Run calculation
      Specified by:
      run in class CalculatorPlugin
      Returns:
      true if success
      Throws:
      PluginException
      See Also:

    • getResultMolecule

      public Molecule getResultMolecule() throws PluginException
      Get result structure
      Overrides:
      getResultMolecule in class CalculatorPlugin
      Returns:
      The calculated framework
      Throws:
      PluginException

    • handlesMultiFragmentMolecules

      public boolean handlesMultiFragmentMolecules()
      This plugin handles multifrag molecules.
      Overrides:
      handlesMultiFragmentMolecules in class CalculatorPlugin
      Returns:
      true

    • setKeepSingleAtom

      public void setKeepSingleAtom(boolean b)
      Set behavior on acyclic input
      Parameters:
      b - If set true then a single atom will be assigned to acyclic fragments. If false then acyclic fragments will be projected to empty structures

    • setFormat

      public void setFormat(String f)
      Set output format used by CalculatorPlugin.getResultAsString(int, Object)
      Parameters:
      f - Output format to use

    • setLfin

      public void setLfin(boolean b)
      Set handling option for multi fragment (disconnected) inputs
      Parameters:
      b - If set true then the calculation will run only on the largest input fragment. Note that this necessarily yields the largest scaffold

    • setLfout

      public void setLfout(boolean b)
      Set handling option for multi fragment (disconnected) results. Note that disconnected result can be caused by disconnected input or by further modifications of the scaffold generation algorithm
      Parameters:
      b - If set true then only the largest calculated scaffold will be returned. Note that the returned scaffold not necessarily calculated from the largest fragment.

    • setType

      public void setType(StructuralFrameworksPlugin.FrameworkTypes ft)
      Set framework type to calculate.

      Note that default framework type is Bemis-Murcko

      Parameters:
      ft - Framework to calculate

    • setPruneIn

      public void setPruneIn(boolean b)
      Set prunein parameter
      Parameters:
      b - If true then input will be generalizes

    • setPruneOut

      public void setPruneOut(boolean b)
      Set pruneout parameter
      Parameters:
      b - If true then result will be generalized

    • setHydrogenize

      public void setHydrogenize(boolean b)
      Set hydrogenize parameter
      Parameters:
      b - If true then input will be hydrogenized

    • setDehydrogenize

      public void setDehydrogenize(boolean b)
      Set dehydrogenize parameter
      Parameters:
      b - If true then explicit hydrogens will be removed from the input

    • setOeqcheck

      public void setOeqcheck(boolean b)
      Set oeqcheck parameter
      Parameters:
      b - If true then eqivalent result fragments will be filtered

    • setParameters

      public void setParameters(Properties params) throws PluginException
      Sets the input parameters for the plugin Accepted parameters:
      • type: [bmf|mcs|sssr|cssr|allringsystems|largestringsystem| largestring|keep] Framework calculation type
        • bmf: Bemis-Murcko framework
        • bmfl: Bemis-Murcko loose framework
        • mcs: Pairwise Maximum Common Substructure
        • sssr: SSSR
        • cssr: CSSR
        • allringsystems: all fused ring systems
        • largestringsystem: largest fused ring system
        • largestring: largest ring
        • keep: no framework reduction; useful for testing pre/post process
      • keepsingleatom: [true|false] If set true then a single atom will be assigned to acyclic fragments. If false then acyclic fragments will be projected to empty structures
      • lfin: [true|false] If set true then the calculation will run only on the largest input fragment. Note that this necessarily yields the largest scaffold
      • lfout: [true|false] If set true then only the largest calculated scaffold will be returned. Note that the returned scaffold not necessarily calculated from the largest fragment.
      • prunein: [true|false] Generalize input
      • pruneout: [true|false] Generalize output
      • hydrogenize: [true|false] Add explicit hydrogens
      • dehydrogenize: [true|false] Remove explicit hydrogens
      • oeqcheck: [true|false] Remove equivalent output fragments
      • format: format to use for string export
      Overrides:
      setParameters in class CalculatorPlugin
      Parameters:
      params - parameter table
      Throws:
      PluginException

    • getProductName

      public String getProductName()
      Description copied from class: CalculatorPlugin
      Returns the product identifier of the plugin as given by LicenseManager. The name is used by the CalculatorPlugin.isLicensed() method.
      Specified by:
      getProductName in class CalculatorPlugin
      Returns:
      product identifier or a default string

    • getResultDomain

      public int getResultDomain(Object type)
      Description copied from class: CalculatorPlugin
      Returns the calculation domain CalculatorPlugin.ATOM, CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULES. The default implementation returns CalculatorPlugin.MOLECULE.
      Overrides:
      getResultDomain in class CalculatorPlugin
      Parameters:
      type - is the result type
      Returns:
      the calculation domain
      See Also:

    • getResultTypes

      public Object[] getResultTypes()
      Description copied from class: CalculatorPlugin
      Returns the result types. The default implementation returns null.
      Overrides:
      getResultTypes in class CalculatorPlugin
      Returns:
      the result types

    • getResultCount

      public int getResultCount()
      Description copied from class: CalculatorPlugin
      Returns the number of result items for the first result type.
      Overrides:
      getResultCount in class CalculatorPlugin
      Returns:
      the number of result items
      See Also:

    • getResult

      public Molecule getResult() throws PluginException
      Throws:
      PluginException

    • getResult

      public Object getResult(Object type, int index) throws PluginException
      Description copied from class: CalculatorPlugin
      Returns the result item for the specified type and index. The default implementation returns null.
      Overrides:
      getResult in class CalculatorPlugin
      Parameters:
      type - is the result type
      index - is the result index
      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
      Get a calculation result (returned by getResultMolecule() after a run() call in the given format setFormat(String)
      Overrides:
      getResultAsString in class CalculatorPlugin
      Parameters:
      type - this parameter is ignored
      index - this patameter is ignored
      result - result given by getResultMolecule()
      Returns:
      String representatin in the given format
      Throws:
      PluginException

    • 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