[Debichem-devel] Bug#826069: Adding avogadro to med-bio or replacing ghemical by avogadro in med-bio task

[Michael Banck]

On Sat, Dec 02, 2017 at 09:10:50AM +0100, Andreas Tille wrote:
> in my attempt to move all packages mentioned in our task list to SVN I
> stumled upon ghemical.  The Debichem team considered the removal of
> ghemical which is not maintained upstream any more.  I'm not convinced
> since according to popcon it has more users as several other packages in
> the med-bio task.  When reading bug #826069 I was wondering whether
> those users are not affected and can easily use the package.  The other
> thing I learned from that bug report is that avogadro might be a
> sensible addition for med-bio - may be a replacement.
> 
> I do not work with modelling molecules neither I'm a biologist so I need
> input what might be the most sensible thing to do for our target user
> group.

I think avogadro-1.x is miles ahead of ghemical in every regard, not
least maintenance. It does tend to crash from time to time on me when I
click randomly, but maybe that is fixed in the latest 1.2 release; I'm
not using it frequently these days.

The only thing ghemical has going for it is the fact it can do (very
trivial) quantum chemistry computations directly via MPQC - but I doubt
any biologist would be very interested in them. Avogadro has a
force-field based geometry optimizer (as does ghemical), which is
probably more useful.

There's the problem of one/some of the authors deciding to rewrite
everything as avogadro-2.x and then apparently running out of steam so
the way forward is a bit unclear; avogadro-2.x should probably be a
different source package for now.

Also, for biologists, maybe PyMOL is the even better alternative; but it
has a pretty ugly TKInter inteface; it has been ported to PyQT recently,
but the vendor has not released that as open source yet.


Michael