<p dir="ltr">That would certainly be one way around the problem! :-) Feel free!</p>
<p dir="ltr">Mark</p>
<div class="gmail_quote">On Jul 9, 2013 9:14 AM, "Alexey Shvetsov" <<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all!<br>
<br>
I had some plans about writing dssp tool for gromacs using c++ gromacs api for it, is it still needed?<br>
<br>
Mark Abraham писал <a href="tel:09-07-2013%2000" value="+46907201300" target="_blank">09-07-2013 00</a>:28:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Gert and I have had some discussion off list. DSSP is available under<br>
the Boost license, which is probably fine to work with LGPLv2.1 (but I<br>
haven't looked into details). It turns out the DSSP webpage was in<br>
need of an update - the new source is indeed freely available. It's<br>
under 100K, too, so that could be acceptable IMO.<br>
<br>
Unfortunately, it requires C++0x and four link-time Boost libraries,<br>
which is rather beyond the planned requirements for GROMACS 5.0 (C++98<br>
and very limited include-only Boost libraries). In theory, we could<br>
detect all that (or just try it and see) to do an optional internal<br>
build of dssp, but I think there are probably too few users with all<br>
the dependencies satisfied who want do_dssp and who would otherwise<br>
have generated email traffic through being unable to download a binary<br>
or set an environment variable.<br>
<br>
Debian and Gentoo have new-generation dssp pacakges, so it is<br>
reasonable to add the couple of lines of CMake detection for the dssp<br>
or mkdssp executables in the obvious places, rather than hard-code<br>
/opt/local/bin/dssp (or whatever we do now). We could have a CMake<br>
option (off by default) to download and install a dssp binary, but I'm<br>
not very keen on that.<br>
<br>
Mark<br>
<br>
<br>
On Mon, Jul 8, 2013 at 5:32 PM, Mark Abraham <<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Gert, cc gmx-developers,<br>
<br>
We do feel your pain - we get such emails too!<br>
<br>
Our do_dssp tool requires the user either install dssp as<br>
/usr/local/bin/dssp, or set the DSSP environment variable to point at<br>
the installed dssp binary. This is one source of problems - users<br>
often aren't savvy enough to do either correctly. Another source of<br>
problems has been the change of invocation syntax with newer versions<br>
of dssp. Installations of GROMACS 4.5 and earlier cannot cope with the<br>
newer syntax if that's what is used by the dssp that the user has<br>
installed. Unfortunately we can't do anything about that<br>
retrospectively.<br>
<br>
GROMACS 4.6 supports both dssp syntaxes, and defaults to using the new<br>
syntax. This causes problems if they have an old dssp, but that<br>
problem is probably not frequent! Anyway, as installations of earlier<br>
GROMACS and DSSP versions die out, those problems will go away. We<br>
still need a mechanism to find the dssp binary, though, and since<br>
there's no reliable place to look for one at configure or run time,<br>
there's no really good solution.<br>
<br>
The solution with the least ongoing impact would be to bundle the dssp<br>
source code and call it directly, which would also make these analyses<br>
much faster for GROMACS users. That would require that we can get and<br>
distribute the dssp source code under a license compatible with ours<br>
(LGPL v2.1). We cannot do so with FFTW source, for example, because<br>
they only make it available under GPL. Just being "open source" is not<br>
enough, unfortunately.<br>
<br>
If such a license is not acceptable to you, we could consider an<br>
option for our build system that downloads a Linux binary from your<br>
FTP site and installs it alongside GROMACS. That's similar to an<br>
existing feature we have for letting the user download and build FFTW<br>
as part of the GROMACS build. Such an option would have to be disabled<br>
by default, and so I think that could be more work than its reward.<br>
<br>
Regards,<br>
<br>
Mark<br>
<br>
On Mon, Jul 8, 2013 at 9:08 AM, Bert de Groot <<a href="mailto:bgroot@gwdg.de" target="_blank">bgroot@gwdg.de</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
I got the message below from Gert Vriend. My impression is that it would be<br>
easiest to incorporate the new, open source, algorithm of dssp into do_dssp.<br>
That will alleviate all of the version incompatibility issues, as well as<br>
file format issues.<br>
<br>
cheers<br>
<br>
Bert<br>
<br>
<br>
<br>
About once a week I get mails from people who have difficulties using DSSP.<br>
Every time it takes me three mails before I found out that this is a Gromacs<br>
user.<br>
<br>
We made a new DSSP about a year ago, and this TOTALLY REWRITTEN DSSP is now<br>
open source. Would it be possible that anybody from the Gromacs team looks<br>
at DSSP and tells us what to do to make it usable for the Gromacs community?<br>
<br>
I think this is especially important since the PDB format will stop to be<br>
used by the PDB on 1-1-2014, so everybody MUST start using the new DSSP by<br>
that time anyway.<br>
<br>
Greetings<br>
Gert<br>
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</blockquote></blockquote></blockquote>
<br>
-- <br>
Best Regards,<br>
Alexey 'Alexxy' Shvetsov<br>
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia<br>
Department of Molecular and Radiation Biophysics<br>
Gentoo Team Ru<br>
Gentoo Linux Dev<br>
mailto:<a href="mailto:alexxyum@gmail.com" target="_blank">alexxyum@gmail.com</a><br>
mailto:<a href="mailto:alexxy@gentoo.org" target="_blank">alexxy@gentoo.org</a><br>
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</blockquote></div>