Export canonical flat format in MarvinJS

Hello everyone,

marvin for JS is an outstanding tool. I'm planing to use it for testing of our students. I'm looking for a way to easily compare their drawing to right answer(both drawn in MarvinJS with webservices). The issue I have is that I can't find a reasonable format to do my matching. Let me tell you about formats:

1. Inchi - is canonical, which is key assumption, but in the export to this format I'm missing certain layers. There is a string called 'auxinfo' instead, with stereo and other position information,but this section seems not canonical, ie not suitable for comparison


2. Smiles - can be exported as 'cxsmiles' which should be canonical, but the stereo info seems to be gone(verified by export/import)ie not suitable for comparison


3. Smarts - seems to export all the stereo chemistry, but it's not canonical,ie not suitable for comparison


4. No more flat formats - I simply can't compare mrv or mdl and others

As I said, I need to compare 2 strings if they match (some easy logic can be implemented, but I don't want to implement my own canonization algorithm   )

Can anybody point me to any direction how to achieve this, please?  any Ideas?

Thank you

Martin

Dear Martin,

Sorry for the late answer. Indeed, if you need the coordinates you should use MRV or Mol format, since smiles does not contains the 2D coordinates. If you  need the (R/S or E/Z) stereo information only, CXSMILES can be a good solution. You can compare MRVs or MOL files with the help of  JChem Webservice. Please see the API documentation here: https://restdemo.chemaxon.com/apidocs/ and let us know if any other question arises.

Best regards,

Efi

Dear efi,

thank you for your answer. I managed to find the solution using smiles. since I don't need the coordination, but I need stereo info the smiles format seems to be a good way to do this. 

I've created a bad test suite, so the assumptions in the original post about smiles are misleading.

Smiles are canonical and stereo is handled well.

Thank you for your advice Martin