Hi Jennifer,

I had this same issue a while back.  Here is an issue I posted about it on the 
github: https://github.com/rdkit/rdkit/issues/1269

I never did make the pull request mentioned in the issue, but all the code that 
does what you want should be in there.  Let me know if you have any other 
questions, I've spent a good amount of time on this problem.

 - Kovas

From: Jennifer Wei <jennifer...@fas.harvard.edu>
Sent: Thursday, September 28, 2017 11:47:53 AM
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] How to number the outputs of a reaction?

Hi All,

I am working with atom mapping for reactions. How do I get the correct atom 
mapping for my products?

I have tried the following:
>> rxn = 
>> rdChemReactions.ReactionFromSmarts('[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]')
>> rcts_lab = (Chem.MolFromSmiles('[C:1](=[O:2])[O:3]'), 
>> Chem.MolFromSmiles('[C:4][N:5][C:6]'))
>> pcts_lab = rxn.RunReactants(rcts_lab)
>> Chem.MolToSmiles(pcts_lab[0][0])

I would like the product to be fully labeled, so I get this on the last line 

Thank you in advance for any help you can provide me.


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