Package chemaxon.calculations

Class MarkushEnumerationPlugin

java.lang.Object
chemaxon.calculations.CalculatorPlugin
chemaxon.calculations.MarkushEnumerationPlugin
All Implemented Interfaces:
TaggedCalculator, Licensable
@PublicApi public class MarkushEnumerationPlugin extends CalculatorPlugin
Plugin class for enumerating Markush molecules.

Input: a Markush structure.
Output: the number of possible enumerations and the enumerated molecules.

Note: Enumeration does not consider R-Logic conditions.

API usage examples:

  • Sequential enumeration: 
    
 // Create plugin
 MarkushEnumerationPlugin plugin = new MarkushEnumerationPlugin();

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

 // Run the calculation
 plugin.run();

 // 1. Get results one by one
 Molecule m = plugin.getNextStructure();
 while (m != null) {
     System.out.println(MolExporter.toFormat(m, "smiles"));
     // ...
     // Getting next enumerated molecule
     m = plugin.getNextStructure();
 }

 // OR
 // 2. Get results in an array
 long size = plugin.getStructureCount();
 if (size != -1 && size <= Integer.MAX_VALUE) {
     Molecule[] enumerated = plugin.getStructures();
     for (int i = 0; i < enumerated.length; i++) {
         System.out.println(MolExporter.toFormat(enumerated[i], "smiles"));
         // ...
     }
 }
  • Random enumeration: 
    
 // Create plugin
 MarkushEnumerationPlugin plugin = new MarkushEnumerationPlugin();

 // Set random enumeration
 plugin.setRandomEnumeration();

 // Set the number of random structures to generate
 plugin.setMaxStructureCount(10);

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

 // Run the calculation
 plugin.run();

 for (int i = 0; i < 10; i++) {
     Molecule m = plugin.getNextStructure();
     System.out.println(MolExporter.toFormat(m, "smiles"));
     // ...
 }

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

Since:
Marvin 5.0.3

  • Field Details

    • FILTER_VALENCE

      public static final MolFilter FILTER_VALENCE
      Filter constant: valence filter. Set this filter in setFilter(MolFilter) in order to reject molecules with valence errors.
      Since:
      Marvin 5.1
      See Also:

    • COLORING_NONE

      public static final int COLORING_NONE
      Constant for no hit coloring.
      Since:
      Marvin 5.1
      See Also:

    • COLORING_SCAFFOLD

      public static final int COLORING_SCAFFOLD
      Constant for scaffold coloring.
      Since:
      Marvin 5.1
      See Also:

    • COLORING_RGROUPS

      public static final int COLORING_RGROUPS
      Constant for R-group coloring.
      Since:
      Marvin 5.1
      See Also:

    • COLORING_ALL

      public static final int COLORING_ALL
      Constant for setting all coloring options, currently scaffold and R-groups.
      Since:
      Marvin 5.1
      See Also:

  • Constructor Details

    • MarkushEnumerationPlugin

      public MarkushEnumerationPlugin()
      Constructor.

  • Method Details