Hi Marco,
I took a look at the code. It expects that there is only a single SMARTS, so
there's no way to get what you want.
The SMARTS handling code only touches <50 lines of code. It does not seem that
hard to have it take multiple --cut-smarts, apply each of the cuts, find the
unique union of those cuts, and work with them.
Could you add that as a issue in the mmpdb tracker?
It is in principle possible to merge two fragment files together and index the
result. However, it would be difficult to use the indexed database for analysis
purposes, because any input/query structure would use the single SMARTS pattern
defined in the database.
Best regards,
Andrew
da...@dalkescientific.com
> On Aug 29, 2019, at 15:55, Marco Stenta <marco.ste...@gmail.com> wrote:
>
> Dear Colleagues,
> I am looking for matched molecular pairs in a set of compounds using a custom
> definition of the bonds to be cut, because I am interested in a small set of
> transformations, that I define as SMARTS in the fragmentation step.
> It would be ideal to define the smirks, but I guess that is not possible.
> Is it possible, however, to define alternative cut schemes with --cut-smarts
> keyword,
>
> Would it be possible to define multiple SMARTS in the same fragmentation run?
> or, alternatively, merge the .fragment file obtained from each of these runs
> (each with a different smarts option)
>
> thanks a lot in advance.
>
> Kind regards,
> Marco
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