Hi Greg,
It helped a lot ! Now it works.
A good occasion for me to learn more about while loops usage :)
Thank you so much,
LF
> On 24 Jun 2018, at 5:07 PM, Greg Landrum <[email protected]> wrote:
>
> Hi Louis Felix,
>
> The trick is to feed the products of the reaction back in as reactants and
> then stop as soon as the reaction doesn't produce any products. Here's a
> short illustration using your reaction:
>
> In [11]: m =
> Chem.MolFromSmiles('O=C1[C@@](C)(OC(CC)=O)[C@@]2([H])[C@]([C@H](OC(C3=CC=CC=C3)=O)C[C@@]4([H])[C@]2(C)C4(C
> ...:
> )C)(COC(C)=O)[C@H](OC(C)=O)[C@@]5([H])[C@@H](OC(C)=O)[C@@H](C)C[C@@]51OC(CCC)=O')
>
> In [12]: while 1:
> ...: ps = rxn.RunReactants((m,))
> ...: if not ps:
> ...: break
> ...: m = ps[0][0]
> ...:
>
> In [13]: print(Chem.MolToSmiles(m))
> C[C@H]1C[C@]2(O)C(=O)[C@@](C)(O)[C@@H]3[C@]4(C)[C@H](C[C@@H](O)[C@@]3(CO)[C@H](O)[C@H]2[C@H]1O)C4(C)C
>
> I hope this helps,
> -greg
>
>
>
> On Sat, Jun 23, 2018 at 2:54 AM Louis-Félix Nothias
> <[email protected] <mailto:[email protected]>> wrote:
> Hello,
>
> I would need a bit of help setting a SMART reaction with RDKit.
> This is pretty basic. I just want to hydrolyse the esters of an input
> molecules with the RunReactants function .
> So far, I have the following SMART reaction, and it works, but for only one
> ester at a time (6 product pairs produced here).
> Could you please indicate a strategy to remove all the esters from the input
> compound, rather than only one ?
>
> Thank you very much for your help,
>
> Louis Felix
>
> ```
> from rdkit import rdBase, Chem
> from rdkit.Chem import AllChem, Draw
>
> rxn = AllChem.ReactionFromSmarts('[C:1][O:2]C([C,c])=O>>[C:1][OH:2].O=[C][C]')
> m =
> Chem.MolFromSmiles('O=C1[C@@](C)(OC(CC)=O)[C@@]2([H])[C@]([C@H](OC(C3=CC=CC=C3)=O)C[C@@]4([H])[C@]2(C)C4(C)C)(COC(C)=O)[C@H](OC(C)=O)[C@@]5([H])[C@@H](OC(C)=O)[C@@H](C)C[C@@]51OC(CCC)=O')
> products = rxn.RunReactants((m,))
>
> ——
>
>
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