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

[Kovas P. <kov...@ar...>]

There should be a post in there about changing the RDKit C++ code to make that property available.  It's a very small change!


 - Kovas


________________________________
From: Jennifer Wei <jen...@fa...>
Sent: Friday, September 29, 2017 10:51:02 AM
To: Kovas Palunas; rdk...@li...
Subject: Re: [Rdkit-discuss] How to number the outputs of a reaction?

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...<mailto: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...<mailto:jen...@fa...>>
Sent: Thursday, September 28, 2017 11:47:53 AM
To: rdk...@li...<mailto: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