How to export standard inchi key ?

Hello,

 

I have following compound

inchi key : QXNRVGDNHDTVOL-UHFFFAOYSA-N

 smiles : CC1=CN2C(=NC(=N2)NC(C)CO)C=C1

 

I tried to import it into MarvinJS by smiles, then export directly without making any change, I have got

inchi key : QXNRVGDNHDTVOL-UHFFFAOYNA-N (different inchi key)

 smiles : CC(CO)NC1=NN2C=C(C)C=CC2=N1 (different smiles)

 

What configuration should I do to force export standard inchi key ? In order to get the same inchi key as my input. 

 

Thanks,

William

Hi William,

There a can be many different SMILES representations for the same molecule.
(If you are interested in SMILES representation in Marvin JS, please check this documentation: https://docs.chemaxon.com/display/docs/SMILES style="font-size: 13px;">).

In your case the molecule may contained some stereo information that resulted in the non-standard InChiKey export. Setting stereochemistry as absolute, should do the trick.

In this situation, by setting the "Absolute stereo" chiral flag *, and then exporting the InChiKey, you should get the expected InChiKey.

I hope this will solve the problem.

Best regards,
Eszter 

*(by right-clicking on the Canvas, and selecting "Absolut stereo (chiral)" option from the list)

Hello, 

 

Thanks, It can work, however, can this be configured from the server side ? Like always choose Absolut stereo (chiral) by default.

 

Regards,

Willliam

Hi William, 

If you have JChem Web Services installed, it could be also a good solution to convert the SMILES sources directly to InChiKey with the required settings. 
You can do this by sending a POST request to MolExport web service.

You can find the detailed description, and  try this call here:
https://restdemo.chemaxon.com/apidocs/#molExport   />

(The relevant part starts with: 8.1 Simple Format Conversion)

You can find the InChi/InChiKey export options here:

https://docs.chemaxon.com/display/docs/InChi+and+InChiKey+export+options

Best regards,
Eszter

 

Hello, 

 

Thank you for your help. I'm using the MarvinJS export structure API described here : https://marvinjs-demo.chemaxon.com/latest/jsdoc.html#marvin.Sketch.exportStructure()

 

I tried to set 'SAbs' as options, but seems not working, could you please be more specific which parameters should i pass ?

 

Regards,

William

Dear William,

Marvin JS editor exports structures to other formats with its default export parameters. That is why it did not work that you imported SMILES to the editor, and exported it as InChiKey at the first place.

As the exportStructure() function calls the editor's exporting mechanism, that should not work either.

For Marvin JS exportStructure()  function, you can only set whether exporting mrv with unique atom and bond id-s, and the visibility settings for images.

What could be a solution for you is to call molExport (or stringMolExport) web service directly. (For example via an ajax call.)

(https://restdemo.chemaxon.com/apidocs/#stringMolExport />The relevant part starts with: 8.1 Simple Format Conversion)

You need to send a POST request to molExport (or stringMolExport) web service with the following body for example:

{

    "structure": "CCCCC",

    "parameters": "inchikey:SAbs"

}

In the response of the service you should get the standard InChiKey.
(MolExporter web service recognises all the export options, you can find in the documentation: https://docs.chemaxon.com/display/docs/InChi+and+InChiKey+export+options) 

I hope this will help. 

Best regards,
Eszter 

Hello, Eszter

 

Thank you for your detailed explanation, that definitely helps.

 

Regards,

William

Hi William, 

If you need more information or if any further question arises, let us know.

Regards,
Eszter