VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Dec 02 2021 - 10:04:56 CST

Hi FX, I just tested building your plugin together with VMD on CentOS 7
Linux, which supports C++11 in full and is the same OS that John used to
create the Linux builds of VMD 1.9.4 alpha that we're all using:
https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
I also included the typical dependencies (OpenGL, CUDA, OptiX RTX, OSPRay,
..) that John also uses in his official builds.

Your code builds okay, with nothing special worth mentioning. I'll contact
you privately with a couple of usage questions, since I'm unfamiliar with
the CIF format, but have colleagues who would benefit from your plugin.

For future record, I copied your file into molfile_plugin/src, downloaded
the GEMMI repository into the molfile_plugin folder, and used the attached
patch for the plugin tree. It is a good idea to also build VMD itself with
C++11, for which a companion patch is available here
<https://urldefense.com/v3/__https://raw.githubusercontent.com/giacomofiorin/vmd-patches/master/c*2B*2B11/c*2B*2B11.diff__;JSUlJQ!!DZ3fjg!s6un4bHnuPcTmk2knQAu6SfgVB1cAWVhpfyIGawnMpiHQkgY4-lTWZ8T0LI63GDXDg$ >.
The above are fairly straightforward steps, but are worth mentioning anyway
for reproducibility purposes (the UIUC license prevents distributing full
packages, especially with modifications).

John, I sincerely hope that the above can help you in your effort *before*
you finalize 1.9.4.

Giacomo

On Thu, Dec 2, 2021 at 12:38 AM John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> In addition what Axel mentions, I'm working out finalizing things
> on VMD 1.9.4, and for sure this will be the last release I plan to do
> with any compilers that are pre-C++11. Already both of the recent
> MacOS and Windows builds are using C++11 compilers, so it's really only
> some of the linux builds for older systems that I'm dealing with now.
> I'll at least take a shot at the idea of including the CIF plugin on
> the platforms with the C++11 toolchains, but my time is short, so if I
> hit any snags, then the alternative (for VMD 1.9.4) may be to do as
> Axel suggests, or I may manually insert the plugin for the cases where
> it's solid. I hope to followup on this very shortly as I begin making
> the "beta" builds before the relase.
>
> Best,
> John
>
> On Wed, Dec 01, 2021 at 11:26:19PM -0500, Axel Kohlmeyer wrote:
> > you can always produce binaries for just the plugin to be loaded
> > dynamically, which is not causing any licensing issues.
> > I've been distributing a plugin for a (now obsolete) HOOMD file format
> > separately (because it required an additional library)
> > with Linux and Windows binaries for many years.
> > On Wed, Dec 1, 2021 at 5:47 AM FX <[1]fxcoudert_at_gmail.com> wrote:
> >
> > Hi John, hi VMD users,
> >
> > I am wondering if it would be possible to include the CIF molfile
> > plugin, that I tried to contribute, in the alpha builds? I have met
> many
> > colleagues would say it would be useful to them. I know there were
> > questions because it uses C++11, but I am sure at least on macOS
> Intel
> > and ARM (where the system compiler supports C++11 since macOS 10.9,
> > released 7 years ago) the dependency would not be a problem.
> >
> > PS: I would gladly make the effort to distribute such builds
> myself, but
> > this would be in violation of the VMD license :(
> >
> > Best regards,
> > FX
> >
> > --
> > Dr. François-Xavier Coudert
> > Senior Researcher / Directeur de Recherche CNRS at Chimie ParisTech
> > Professeur attaché ENS / PSL University
> > Webpage:
> > [2]
> https://urldefense.com/v3/__https://www.coudert.name/__;!!DZ3fjg!vkU2nNUOVBtIl5dauRx0eItH6gR5rwwCbGWFQpd9_R3c6LrbexhCXtXZemZuhbAZ9A$
> >
> > > Le 4 avr. 2020 à 18:10, FX <[3]fxcoudert_at_gmail.com> a écrit :
> > >
> > > Hi everyone,
> > >
> > > Attached is an updated version of the CIF molfile plugin, which is
> > improved in several ways:
> > >
> > > - it can read multiple groups (frames) from the same CIF file, if
> they
> > have the same number of atoms
> > > - it ignores leading groups with zero atoms (usually used for
> > comments, for example in files from the ICSD database)
> > > - it can now write coordinates in CIF format
> > >
> > > Iâ**d love to get feedback from users about it, but I donâ**t
> really
> > know how. If you use my 64-bit macOS build, you can find the
> compiled
> > plugin here
> > ([4]
> https://urldefense.com/v3/__https://www.dropbox.com/s/0bq444sympgqm42/cifplugin.so.gz?dl=0__;!!DZ3fjg!vkU2nNUOVBtIl5dauRx0eItH6gR5rwwCbGWFQpd9_R3c6LrbexhCXtXZemYVfikqrQ$
> > ), download it, and install it inside the app (put it inside the
> VMD app
> > bundle, so its path is "VMD
> >
> 1.9.4a38.app/Contents/vmd/plugins/MACOSXX86_64/molfile/cifplugin.soâ**)
> > >
> > > Maybe once it gets into the official â**alphaâ** builds from VMD,
> we
> > can get more testing exposure. Not sure what the timeline is for a
> > future build, or for a 1.9.4 release.
> > >
> > > Best regards,
> > > FX
> > >
> > > --
> > > Dr. François-Xavier Coudert
> > > Senior Researcher / Directeur de Recherche CNRS
> > > at the Institut de Recherche de Chimie Paris
> > > Professeur attaché ENS / PSL University
> > > Webpage:
> > [5]
> https://urldefense.com/v3/__https://www.coudert.name/__;!!DZ3fjg!vkU2nNUOVBtIl5dauRx0eItH6gR5rwwCbGWFQpd9_R3c6LrbexhCXtXZemZuhbAZ9A$
> >
> > --
> > Dr. Axel Kohlmeyer  [6]akohlmey_at_gmail.com  [7]https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!s6un4bHnuPcTmk2knQAu6SfgVB1cAWVhpfyIGawnMpiHQkgY4-lTWZ8T0LKZZNZxVw$
> > College of Science & Technology, Temple University, Philadelphia PA,
> USA
> > International Centre for Theoretical Physics, Trieste. Italy.
> >
> > References
> >
> > Visible links
> > 1. mailto:fxcoudert_at_gmail.com
> > 2.
> https://urldefense.com/v3/__https://www.coudert.name/__;!!DZ3fjg!vkU2nNUOVBtIl5dauRx0eItH6gR5rwwCbGWFQpd9_R3c6LrbexhCXtXZemZuhbAZ9A$
> > 3. mailto:fxcoudert_at_gmail.com
> > 4.
> https://urldefense.com/v3/__https://www.dropbox.com/s/0bq444sympgqm42/cifplugin.so.gz?dl=0__;!!DZ3fjg!vkU2nNUOVBtIl5dauRx0eItH6gR5rwwCbGWFQpd9_R3c6LrbexhCXtXZemYVfikqrQ$
> > 5.
> https://urldefense.com/v3/__https://www.coudert.name/__;!!DZ3fjg!vkU2nNUOVBtIl5dauRx0eItH6gR5rwwCbGWFQpd9_R3c6LrbexhCXtXZemZuhbAZ9A$
> > 6. mailto:akohlmey_at_gmail.com
> > 7.
> https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!ofmzhFhG8C3BwF8gpySDnOAniGk_IT312ZS6K8Idm0T2wGpaAqXCkuDyj3bPMq8CpQ$
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>