Package chemaxon.marvin.calculations

Class StereoisomerPlugin

  • All Implemented Interfaces:
    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

    • Constructor Detail

      • StereoisomerPlugin

        public StereoisomerPlugin()
        Deprecated.

    • Method Detail

      • 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

      • 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

      • 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

      • 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:
        getResultTypes()

      • 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