VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 01 2021 - 23:38:29 CST

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]http://goo.gl/1wk0
> 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/