Re: Providing components.cif.gz [Was: Re: DeepMind’s AI Advanced Protein Structure Prediction tool Open Sourced]
Hi Maarten,
On 2021-09-08 22:50, Maarten L. Hekkelman wrote:
>
> Op 8-9-2021 om 09:07 schreef Andrius Merkys:
>> I am aware of solutions to similar problems, for example, libcifpp
>> package, which keeps an up-to-date mmcif_pdbx_v50.dic.gz at
>> /var/cache/libcifpp/mmcif_pdbx_v50.dic.gz. This could work for
>> components.cif.gz as well, but my main concern is whether keeping
>> system-wide components.cif.gz up-to-date is what every user would want.
>
> The latest incarnation of libcifpp already caches a copy of
> components.cif.gz in the exact same location. Not in Debian yet, will
> upload when I have the time.
>
> The way I do it in libcifpp is place a distribution provided copy in
> /usr/share/libcifpp/ I also install a script that weekly fetches a fresh
> copy that is then installed in /var/cache/libcifpp. For both the mmcif
> dictionary as well as the CCD components.cif file.
>
> The update script runs only when the accompanying settings file
> /etc/libcifpp.conf contains the line 'update = yes'.
>
> The installation of this script is also a dpkg configuration option.
That is great news! I think I will use libcifpp-provided
components.cif.gz as a fallback for the time being. Most likely I will
stick with the distribution-provided copy, but it is probably best
inquiring the OpenStructure/ProMod3 community about what they deem to be
the best approach. Nevertheless, I will ask about an environment
variable to control the choice.
> I thought that covered all cases.
>
> But I would not mind having a system wide service to update data files
> like these. Perhaps with a log with version info, so you can look up
> what version was used at what date.
Indeed, it would be nice to find a generic solution, but this might be
tricky. There are conflicting needs of stability (no updates), freshness
(updates every day) and multi-user support (no updates and updates
everyday all at once on the same machine). The only solution I can think
of now is keeping all the downloaded versions with version/date in their
names like:
/var/cache/pdb/components/components-20210814.cif.gz
/var/cache/pdb/components/components-20210820.cif.gz
/var/cache/pdb/components/components-20210826.cif.gz
...
(maybe /var/cache/pdb/components/components.cif.gz symlink to the latest)
Then a user would use environment variable, say, PDB_COMPONENTS to point
to a file with version in its name should they need a specific stable
database, and would use /var/cache/pdb/components/components.cif.gz
should they need the most up-to-date one.
Does this sound reasonable?
Best,
Andrius
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