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
