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

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

Hi Kovas,

Thank you so much for pointing me to this github issues page and for
sharing your code! It is very helpful.

I'm having a bit of trouble with the 'react_atom_idx' property. Where did
this get set initially? If I try to run your code as written on the github
page, it does not recognize this key.

Thank you!

Best,
Jennifer

On Thu, Sep 28, 2017 at 5:06 PM Kovas Palunas <kov...@ar...>
wrote:

> 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
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rdkit_rdkit_issues_1269&d=DwMFAg&c=WO-RGvefibhHBZq3fL85hQ&r=UPzYrSHLXjnX3tYn90C8Ljjzb-yfrb1UtMOxOFh-tKk&m=hXZ3O7Hw9kEXazs6L_WExNyi7ezPgiZXuii8kvqDRA8&s=eJJg7q8uOJQMmNIHUCyRODhdtFsi_ZXhch3Dn74wk08&e=>
>
> 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 <jen...@fa...>
> *Sent:* Thursday, September 28, 2017 11:47:53 AM
> *To:* rdk...@li...
> *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])
>       *'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
>
>