[gmx-developers] dssp

[Alexey Shvetsov]

Hi all!

I had some plans about writing dssp tool for gromacs using c++ gromacs 
api for it, is it still needed?

Mark Abraham писал 09-07-2013 00:28:
> 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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>>> gmx-developers at gromacs.org
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-- 
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, 
Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru