[Rdkit-discuss] How to number the outputs of a reaction?

[Jennifer W. <jen...@fa...>]

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])
      *'O=CN([C:4])[C:6]'*

I would like the product to be fully labeled, so I get this on the last
line instead.
      *'[O:2]=[C:1][N:5]([C:4])[C:6]'*

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

Best,
Jennifer