But we have learned that RDKit can do the imparsable....
-P.
On Tue, Jul 5, 2016 at 6:14 AM, Marta Stępniewska-Dziubińska <
[email protected]> wrote:
> Hi Greg,
>
> To be honest, I expected it to fail :)
>
> I want to find structures with a defined topology, but allow for
> different bond types. My first idea was to use SMARTS with ~ bonds,
> and it works fine with GetSubstructMatch.
> I don't really need MCS, I just used it to check different patterns.
> But I expected that FindMCS will throw an exception, rather than
> produce SMARTS it cannot parse.
>
> Best,
> Marta
>
>
> 2016-07-05 11:32 GMT+02:00 Greg Landrum <[email protected]>:
> > 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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