Package chemaxon.marvin.calculations

Class StereoisomerPlugin

java.lang.Object
chemaxon.marvin.plugin.CalculatorPlugin
chemaxon.marvin.calculations.StereoisomerPlugin
All Implemented Interfaces:
TaggedCalculator, chemaxon.license.Licensable
@Deprecated @PublicAPI public class StereoisomerPlugin extends CalculatorPlugin
Deprecated.
Plugin class for stereoisomer calculation. * Data types:
  • "structure"
  • "structures"
  • "count"

API usage example: 

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

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

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

 // set parameters for calculation
 plugin.setStereoisomerismType(StereoisomerPlugin.TETRAHEDRAL);
 plugin.setMaxNumberOfStereoisomers(2048); // if not set all stereoisomers are generated

 // run the calculation
 plugin.run();

 // get results
 Molecule[] stereoisomers = plugin.getStereoisomers();
 int stereoisomerCount = plugin.getStereoisomerCount();
 for (Molecule m : stereoisomers) { // or:  m = plugin.getStereoisomer(i);
     // do something with molecule ...
 }

 // do something with the results ...

Note: Stereoisomer plugin does not handle enhanced stereo information. Enhanced stereo information is cleared before generating the stereoisomers.

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

Use StereoisomerEnumeration instead. This class is scheduled for removal in June 2015.
Since:
Marvin 4.1 03/07/2006

  • Field Details

  • Constructor Details

    • StereoisomerPlugin

      public StereoisomerPlugin()
      Deprecated.

  • Method Details

    • getProductName

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

    • handlesMultiFragmentMolecules

      public boolean handlesMultiFragmentMolecules()
      Deprecated.
      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.
      Overrides:
      handlesMultiFragmentMolecules in class CalculatorPlugin
      Returns:
      true if the plugin handles multifragment molecules, false otherwise

    • setProgressMonitor

      public void setProgressMonitor(MProgressMonitor pmon)
      Deprecated.
      Sets a progress monitor 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 observer object, may be null

    • setParameters

      public void setParameters(Properties params) throws PluginException
      Deprecated.
      Sets the input parameters for the plugin. Parameters and value ranges:
      • type: structure,structures,count
      • generateall: if true all stereoisomers are generated (default: true)
      • maxstereoisomers: maximum number of stereoisomers to generate, if generateall option is set to false (default: 2048)
      • verify3D: if true generated stereoisomers are checked for a valid 3D conformation (default: false)
      • in3D: if true stereoisomers are checked for a valid 3D conformation and stored in 3D (default: false)
      Overrides:
      setParameters in class CalculatorPlugin
      Parameters:
      params - is the parameter table
      Throws:
      PluginException - on error

    • isIn3D

      public boolean isIn3D()
      Deprecated.
      Returns true if structures are returned in 3D.
      Returns:
      true if structures are returned in 3D
      Since:
      Marvin 5.0

    • setProtectTetrahedralStereo

      public void setProtectTetrahedralStereo(boolean protect)
      Deprecated.
      Sets the protection of tetrahedral stereo centers: if true then stereo configuration of tetrahedral stereo centers with preset stereo information will not be changed. Default: false.
      Parameters:
      protect - is true if preset tetrahedral stereo centers should be protected
      Since:
      Marvin 5.2.3

    • setProtectDoubleBondStereo

      public void setProtectDoubleBondStereo(boolean protect)
      Deprecated.
      Sets double bond stereo protection: if true then the stereo configuration of double bonds with preset stereo information will not be changed. Default: false.
      Parameters:
      protect - is true if preset double bond stereo information should be protected
      Since:
      Marvin 5.2.3

    • checkMolecule

      public void checkMolecule(Molecule mol) throws PluginException
      Deprecated.
      Checks the input molecule. Throws exception if the molecule is RxnMolecule or if the molecule contains R-groups.
      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
      Deprecated.
      Sets the input molecule.
      Specified by:
      setInputMolecule in class CalculatorPlugin
      Parameters:
      mol - is the input molecule
      Throws:
      PluginException - on error

    • isChiralCenter

      public boolean isChiralCenter(int a)
      Deprecated.
      Determines if an atom can be a tetrahedral stereogenic center.
      Parameters:
      a - index of the atom
      Returns:
      true if the atom is stereogenic.

    • chiralCenterCount

      public int chiralCenterCount()
      Deprecated.
      Calculates the number of tetrahedral stereogenic centers. This function identifies two chiral centers in 1,4-dimethylcyclohexane, which does not contain asymmetric atoms.
      Returns:
      number of tetrahedral stereogenic center atoms

    • setMaxNumberOfStereoisomers

      public void setMaxNumberOfStereoisomers(int n)
      Deprecated.
      Sets the maxinum number of stereoisomers to be generated. If not set the plugin generates all stereoisomers of the molecule. It is recommended to use when there are too much stereoisomers to fit to the memory.
      Parameters:
      n - is the number of stereoisomers to be generated

    • setStereoisomerismType

      public void setStereoisomerismType(int itype)
      Deprecated.
      Sets which type of stereoiseomers should be generated. Available values:
      • TETRAHEDRAL : tetrahedral stereoisomers are generated
      • DOUBLE_BOND : double bond stereoisomers are generated
      • BOTH : tetrahedral and double bond stereoisomers are generated (in fact tetrahedral stereoisomers of double bond stereoisomers are generated)
      Parameters:
      itype - is the stereoisomerism type (represented by an integer constant)

    • setCheck3DStereo

      public void setCheck3DStereo(boolean c)
      Deprecated.
      Sets the 3D stereo conformation checking of the structure.
      Parameters:
      c - if true structure is checked for a valid stereo conformation.

    • setIn3D

      public void setIn3D(boolean b)
      Deprecated.
      Sets to display the molecule in 3D.
      Parameters:
      b - if true structure is displayed in 3D

    • getResultSource

      public chemaxon.marvin.plugin.PluginMDocSource getResultSource() throws PluginException
      Deprecated.
      Returns the result as a document source object. This is useful for displaying the molecules in a viewer dynamically as they become available instead of collecting all results before display.
      Overrides:
      getResultSource in class CalculatorPlugin
      Returns:
      the document source interface
      Throws:
      PluginException - on error
      Since:
      Marvin 5.0

    • getStereoisomerCount

      public int getStereoisomerCount()
      Deprecated.
      Returns the number of different stereoisomers.
      Returns:
      the number of different stereoisomers

    • getStereoisomer

      public Molecule getStereoisomer(int index)
      Deprecated.
      Returns a stereoisomer.
      Parameters:
      index - is the index of the stereoisomer
      Returns:
      a stereoisomer

    • getStereoisomers

      public Molecule[] getStereoisomers()
      Deprecated.
      Returns the stereoisomers in a Molecule[] array.
      Returns:
      stereoisomers

    • run

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

    • getResultTypes

      public Object[] getResultTypes()
      Deprecated.
      Returns the result types.
      Overrides:
      getResultTypes in class CalculatorPlugin
      Returns:
      the result types

    • getTypeString

      public String getTypeString(Object type)
      Deprecated.
      Returns a string representation of the given type.
      Overrides:
      getTypeString in class CalculatorPlugin
      Parameters:
      type - is the type object
      Returns:
      the type string

    • getResultDomain

      public int getResultDomain(Object type)
      Deprecated.
      Returns the calculation domain.
      Overrides:
      getResultDomain in class CalculatorPlugin
      Parameters:
      type - is the result type
      Returns:
      the calculation domain
      See Also:

    • getResultCount

      public int getResultCount(Object type)
      Deprecated.
      Returns the number of result items for the given result key.
      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
      Deprecated.
      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
      Deprecated.
      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

    • getWarningMessage

      public String getWarningMessage()
      Deprecated.
      Returns a warning message if there are no stereoisomers, null otherwise.
      Overrides:
      getWarningMessage in class CalculatorPlugin
      Returns:
      a warning message if stereoisomer calculation aborted

    • standardize

      public void standardize(Molecule mol)
      Deprecated.
      Clears enhanced stereo information.
      Overrides:
      standardize in class CalculatorPlugin
      Parameters:
      mol - is the molecule to be standardized

    • tags

      public Set<CalculatorTag> tags()
      Deprecated.
      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