Hi Maria,
Output 11 is certainly wrong (the SMARTS generated is incorrect).
I suspect this is happening because the molecule "coa" (input 3 in your
notebook) is constructed from SMARTS and includes ~ bonds (which match any
bond type). I almost think that the MCS code should be generated to fail in
these cases. Do you really need to construct the input molecules from
SMARTS?
Best,
-greg
On Tue, Jul 5, 2016 at 6:52 AM, Marta Stepniewska-Dziubinska <
[email protected]> wrote:
> Hi all,
>
> I got a very surprising error: RDKit generated a SMARTS string that it
> cannot parse. Here's my code: https://goo.gl/ETvjjT
>
> In order to explain the code: I create a structural pattern with SMARTS.
> It's a strange pattern, I admit, but I was able to find it in my
> molecule. I then try to use FindMCS for the pattern and the molecule,
> and I get some results, but the smartsString is incorrect. I see some
> inexplicable commas before several bonds, and when I remove them I get a
> valid SMARTS and a reasonable structure.
>
> I'm using RDKit 2016.03.1 and conda 4.0.4 on Ubuntu 14.04.
>
> Best,
> Marta
>
>
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