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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