How can i get the markush structures from marvin js?

How can i get the markush structures from marvin js?

Setting scaffold and R-groups is done in editor  and then i want to get generated structures in java code. 

Hi, 

I am sorry, but I think that I do not understand exactly what you need.
Could you give a little more detail about your workflow and about  what you would like to achieve by using Marvin JS?

Here you can find some online examples that might be useful: https://marvinjs-demo.chemaxon.com/latest/examples/index.html

Thank you in advance.

Best regards,
Eszter 

In Marvin JS, I draw scaffold structure and R-groups.

then, I used "get the mol" code in order to get the generated structures (markush enumeration) by scaffold and R-groups. 

// get mol button

	$("#btn-getmol").on("click", function (e) {

		marvinSketcherInstance.exportStructure("mrv").then(function(source) {

			$("#molsource").text(source);

		}, function(error) {

			alert("Molecule export failed:"+error);	

		});

	});

 but, the structure that obtained by this code is not markush structure.

i want to know how can i perform "Markush enumeration" in MarvinJS.

thank you for your help.  

Hi, 

Thank you for the details. 

You cannot enumerate markush structures directly with Marvin JS, however there are two options to make it possible with other ChemAxon-tools:

The exportstructure() function, you used, results in an mrv source. Mrv and other chemical formats are possible to be enumerated via Markush Enumeration Plugin or by using JChem Web Services.

For the first option please find an example code snippet, and the test file attached, for the latter, please find the JChem Web Services API documentation here: https://restdemo.chemaxon.com/apidocs/#markushAnalysis 

(The relevant information starts with: 9. Markush enumeration.)

 If you have more questions about these products, please do not hesitate to contact us.

Best regards,
Eszter 

i try to get markush structure like below code.

<%

response.setContentType("text/html;charset=UTF-8");

String strMol = request.getParameter("mol");

MolImporter mi = new MolImporter(new ByteArrayInputStream(strMol.getBytes()));
Molecule objMol = mi.read();
mi.close();

MarkushEnumerationPlugin Mp = new MarkushEnumerationPlugin();
Mp.setMolecule(objMol);
Mp.run();

long size = Mp.getStructureCount();
if(size != -1 && size <= Integer.MAX_VALUE){
    Molecule[] enumerated = Mp.getStructures();
    for(int i =0; i < enumerated.length; i++){
        System.out.println(enumerated.toFormat("smiles"));
    }
}

%>

In this code,

strMol ="

MJ150504                      

 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.3551    2.9351    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0696    2.5226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0696    1.6974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3551    1.2848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6405    1.6974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6405    2.5226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3551    3.7602    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
   -0.9259    1.2848    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
    1.4176   -0.0107    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4508   -2.5678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7364   -2.9803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7364   -3.8054    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4508   -4.2179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1653   -3.8054    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1653   -2.9803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  1  1  0  0  0  0
  1  7  1  0  0  0  0
  5  8  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 10  1  0  0  0  0
M  RGP  2   7   1   8   2
M  END"

 

and then, the output is just "O.C1=CC=CC=C1.

• C1=CC=CC(
• )=C1"
  
  

  give me some feedback, please..

  
  

   

  
  

  thank you for your help.

Hi, 

The problem is that Mol V2000 format only supports R-group labels, but not the R-group definitions, thus in your source there is nothing to enumerate. (If you import it to Marvin JS or another chemical editor, you can check this : there is no R-group definition on the canvas.)

You need to use mrv format or mol types which support R-group definitions (e.g., MDL RG file). 

I attach an mrv source with your structure. This should work with your code.

I hope, this will help.

Best regards,
Eszter