Markush Enumeration plugin API : 

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(m.toFormat("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(enumerated[i].toFormat("smiles"));
         // ...
     }
 }
================================ 

I want to create new molecules from scaffold molecule in java code. 

but there is no information for how can i set the R-group compounds. 

Hi,

You should build a so-called Markush structure or R-group molecule before you use the enumeration plugin. An RgMolecule is composed of a scaffold structure (see setRoot() method) and R-group definitions (see addRgroup() method). Both methods take Molecule objects as parameter, which can be imported from various formats (SDF/MOL, MRV, smiles, etc.) or can be built from scratch using the API of the class.

Example:

RgMolecule rgmol = new RgMolecule();
Molecule scaffold = ...
rgmol.setRoot(scaffold);
Molecule r1a = ...
Molecule r1b = ...
Molecule r1c = ...
rgmol.addRgroup(1, r1a);
rgmol.addRgroup(1, r1b);
rgmol.addRgroup(1, r1c);
Molecule r2a = ...
Molecule r2b = ...
rgmol.addRgroup(2, r2a);
rgmol.addRgroup(2, r2b);

This example builds an RgMolecule with a scaffold (which should contain R1 and R2 atoms) and adds 3 definition member molecules to R1 group and two members to R2.

I hope this helps.

Péter Kovács

Thank you for your kind answer.

The answer is very helpful to me. 

but, I still don't know that how can I apply the R-group molecule code to enumeration plugin code.

Could you please explain the method using enumeration code?

You can build a Markush structure using the "Build R-group" code example from here

https://www.chemaxon.com/marvin-archive/6.1.3/marvin/help/developer/core/appendix.html

and you can insert the created rgMol in the corresponding part of the enumeration example, to generate the compounds represented by your Markush structure.

// Create plugin
 MarkushEnumerationPlugin plugin = new MarkushEnumerationPlugin();
 
 // Set target molecule
 plugin.setMolecule(rgMol);