[gmx-developers] dssp

[Mark Abraham]

Gert and I have had some discussion off list. DSSP is available under
the Boost license, which is probably fine to work with LGPLv2.1 (but I
haven't looked into details). It turns out the DSSP webpage was in
need of an update - the new source is indeed freely available. It's
under 100K, too, so that could be acceptable IMO.

Unfortunately, it requires C++0x and four link-time Boost libraries,
which is rather beyond the planned requirements for GROMACS 5.0 (C++98
and very limited include-only Boost libraries). In theory, we could
detect all that (or just try it and see) to do an optional internal
build of dssp, but I think there are probably too few users with all
the dependencies satisfied who want do_dssp and who would otherwise
have generated email traffic through being unable to download a binary
or set an environment variable.

Debian and Gentoo have new-generation dssp pacakges, so it is
reasonable to add the couple of lines of CMake detection for the dssp
or mkdssp executables in the obvious places, rather than hard-code
/opt/local/bin/dssp (or whatever we do now). We could have a CMake
option (off by default) to download and install a dssp binary, but I'm
not very keen on that.

Mark


On Mon, Jul 8, 2013 at 5:32 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> Hi Gert, cc gmx-developers,
>
> We do feel your pain - we get such emails too!
>
> Our do_dssp tool requires the user either install dssp as
> /usr/local/bin/dssp, or set the DSSP environment variable to point at
> the installed dssp binary. This is one source of problems - users
> often aren't savvy enough to do either correctly. Another source of
> problems has been the change of invocation syntax with newer versions
> of dssp. Installations of GROMACS 4.5 and earlier cannot cope with the
> newer syntax if that's what is used by the dssp that the user has
> installed. Unfortunately we can't do anything about that
> retrospectively.
>
> GROMACS 4.6 supports both dssp syntaxes, and defaults to using the new
> syntax. This causes problems if they have an old dssp, but that
> problem is probably not frequent! Anyway, as installations of earlier
> GROMACS and DSSP versions die out, those problems will go away. We
> still need a mechanism to find the dssp binary, though, and since
> there's no reliable place to look for one at configure or run time,
> there's no really good solution.
>
> The solution with the least ongoing impact would be to bundle the dssp
> source code and call it directly, which would also make these analyses
> much faster for GROMACS users. That would require that we can get and
> distribute the dssp source code under a license compatible with ours
> (LGPL v2.1). We cannot do so with FFTW source, for example, because
> they only make it available under GPL. Just being "open source" is not
> enough, unfortunately.
>
> If such a license is not acceptable to you, we could consider an
> option for our build system that downloads a Linux binary from your
> FTP site and installs it alongside GROMACS. That's similar to an
> existing feature we have for letting the user download and build FFTW
> as part of the GROMACS build. Such an option would have to be disabled
> by default, and so I think that could be more work than its reward.
>
> Regards,
>
> Mark
>
> On Mon, Jul 8, 2013 at 9:08 AM, Bert de Groot <bgroot at gwdg.de> wrote:
>> Hi,
>>
>> I got the message below from Gert Vriend. My impression is that it would be
>> easiest to incorporate the new, open source, algorithm of dssp into do_dssp.
>> That will alleviate all of the version incompatibility issues, as well as
>> file format issues.
>>
>> cheers
>>
>> Bert
>>
>>
>>
>> About once a week I get mails from people who have difficulties using DSSP.
>> Every time it takes me three mails before I found out that this is a Gromacs
>> user.
>>
>> We made a new DSSP about a year ago, and this TOTALLY REWRITTEN DSSP is now
>> open source. Would it be possible that anybody from the Gromacs team looks
>> at DSSP and tells us what to do to make it usable for the Gromacs community?
>>
>> I think this is especially important since the PDB format will stop to be
>> used by the PDB on 1-1-2014, so everybody MUST start using the new DSSP by
>> that time anyway.
>>
>> Greetings
>> Gert
>> --
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