Package chemaxon.marvin.calculations

Class AlignmentPlugin

java.lang.Object
chemaxon.marvin.plugin.CalculatorPlugin
chemaxon.marvin.calculations.AlignmentPlugin
All Implemented Interfaces:
TaggedCalculator, chemaxon.license.Licensable
@PublicApi public final class AlignmentPlugin extends CalculatorPlugin
Plugin layer for the AlignmentAPI
Since:
Marvin 5.2

  • Field Details

  • Constructor Details

    • AlignmentPlugin

      public AlignmentPlugin()

  • Method Details

    • 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

    • 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

    • getResultTypes

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

    • setInputMolecule

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

    • setProgressMonitor

      public void setProgressMonitor(MProgressMonitor pmon)
      Sets a progress observer to be used in run() to display progress status. Short calculations may ignore the observer object. The default implementation does nothing.
      Overrides:
      setProgressMonitor in class CalculatorPlugin
      Parameters:
      pmon - is the progress monitor, may be null

    • getWarningMessage

      public String getWarningMessage()
      Returns the calculation warning information message.
      Overrides:
      getWarningMessage in class CalculatorPlugin
      Returns:
      the calculation warning information message

    • getResultMolecule

      public Molecule getResultMolecule() throws PluginException
      Description copied from class: CalculatorPlugin
      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

    • setAccuracyMode

      public void setAccuracyMode(AlignmentAccuracyMode acc) throws PluginException
      Throws:
      PluginException

    • setRingFlexibility

      public void setRingFlexibility(int size, int rotBondCount)
      If BOTH the two parameters is true for the ring then the ring is treated flexible.
      Parameters:
      size - atomcount above the ring is flexible
      rotBondCount - rotatable bond count in the ring above which the ring is flexible

    • setMinimumCommonSize

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public void setMinimumCommonSize(int mcsSize) throws PluginException
      Deprecated, for removal: This API element is subject to removal in a future version.
      No effect. Will be removed in later releases.
      Throws:
      PluginException

    • setParameters

      public void setParameters(Properties params) throws PluginException
      Sets the input parameters for the plugin.
      Overrides:
      setParameters in class CalculatorPlugin
      Parameters:
      params - is the parameter table
      Throws:
      PluginException - on error

    • run

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

    • getVolumeTanimoto

      public double getVolumeTanimoto()

    • standardize

      public void standardize(Molecule mol)
      Description copied from class: CalculatorPlugin
      Standardizes the molecule by performing the transformations necessary to run the plugin (aromatize, dehydrogenize, bring nitro groups to common form, ...). This implementation performs the following transformations:
      • aromatization
      • nitro group transformation: [O-:1][N+:2] >> [O:1]=[N:2], [NH1+:1][O-:2] >> [H:3][O:2][N:1]
      • sulphynil group transformation: [#6][S+:1]([#6])[#8-:2] >> [#6][S:1]([#6])=[O:2]
      To be overridden by subclasses that require other standardization (or none at all). TODO: replace by call to chemaxon.standardizer.Standardizer
      Overrides:
      standardize in class CalculatorPlugin
      Parameters:
      mol - is the molecule to be standardized