Dear all,
Andrew's fix for the wildcard atom representation in RDKit 2018.3 has just
been incorporated into the main mmpdb branch. If you download the latest
version of mmpdb, it should now work with with the current version and also
with previous RDKit versions.
Note that you have to rebuild your mmp database if you switch from a pre
2018 version of RDKit to a 2018+ version.
Bests,
Christian
*Dr. Christian Kramer*
Computer-Aided Drug Design (CADD) Senior Scientist
F. Hoffmann-La Roche Ltd
Pharma Research and Early Development
Bldg. 092/8.56 C
CH-4070 Basel
Phone +41 61 682 2471
mailto: christian.kra...@roche.com
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On Tue, May 8, 2018 at 4:04 PM, Andrew Dalke <da...@dalkescientific.com>
wrote:
> Dear Marco,
>
> > On May 7, 2018, at 23:59, Marco Stenta <marco.ste...@gmail.com> wrote:
> > I had some time to set an environment for it and test it: it works fine,
> as far as my tests go. I will switch to this version and to the latest
> RDKIT now.
>
> Thanks for the feedback. Someone else sent me a private email also saying
> it worked. I'll put together the final changes for a 2.1 release, and see
> about making it accessible from PyPI so "pip install mmpdb" will work.
>
> > some questions:
> > Is there any plan to:
> > include MCS as a fragmentation method?
> > extend to matched series?
> > include "fuzzy" environment definitions based on pharmacophores (as BI
> people did)?
>
> I know of no plans for that.
>
> As a consultant, my answer is more along the lines of "are you willing to
> pay for it?" :)
>
> It won't be cheap.
>
> Speaking of which, many thanks to Roche because they funded this work,
> just like that previously funded me to develop the MCS code that is now in
> RDKit.
>
>
> > I am currently using the database file to explore the rules mainly via
> visual inspection through spotfire by means of a series of joins to
> generate suitable tables: would anybody be interested in this (also helping
> improving it)?
>
> I hope you find others and are able to get this out there.
>
> One of the reasons for developing what eventually became mmpdb 2.0 is to
> make this sort of viewer possible.
>
> That is, the unreleased mmpdb 1.0 didn't have canonical attachment point
> assignment, resulting in up to 6 different ways to represent a 3-cut
> fragment. This made it technically challenging to the simple sorts of
> analyses that mmpdb 2.0 does now, and impossible to visualize meaningfully.
>
> Cheers,
>
> Andrew
> da...@dalkescientific.com
>
>
>
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