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Integration with VMD #27
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Hi Pallab, I'm working on getting offscreen rendering to an EGL buffer working so you can do everything from the module, but this is a low priority right now. |
Dear Robin,
I read your document on your own official page. Is it somehow possible to
attack the default python binary in the conda environment:
home/name/anaconda2/bin ?
When we run the command "vmd -python", can you tell me what python
interpreter it actually uses?
Your reply would be highly appreciated.
…On Wed, Jun 5, 2019 at 1:35 AM Robin Betz ***@***.***> wrote:
Hi Pallab,
You're right that without the usual VMD GUI the display module and others
(molrep, etc) aren't of much use. This interface is in the process of being
integrated into the main VMD codebase-- if you need these features you can
check out the main VMD CVS tree and compile it yourself.
I'm working on getting offscreen rendering to an EGL buffer working so you
can do everything from the module, but this is a low priority right now.
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It has been a while, but I believe it is whichever interpreter it was hooked up to at compile time. One could check via the contents of |
Um, yeah it's still showing up python2.5...
…On Wed 5 Jun, 2019, 10:12 PM Josh Vermaas, ***@***.***> wrote:
It has been a while, but I believe it is whichever interpreter it was
hooked up to at compile time. One could check via the contents of
sys.version
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Right, since it is using either the system python (ldd of the VMD executable links to a system python library) or a barebones python installation bundled in with the executable via static linkage. I think the default is the latter, so there isn't an easy way to replace your python library without a reinstall, which is why vmd-python is so awesome, as it takes alot of the guesswork out of building VMD on new systems. |
Yeah the vmd-python module is amazing, but the cmd it installs still have
the same problem we are talking about.
Anyway please continue, that integration part if possible, however that's
not necessary that much. Best of luck, from a python lover...
…On Wed 5 Jun, 2019, 10:34 PM Josh Vermaas, ***@***.***> wrote:
Right, since it is using either the system python (ldd of the VMD
executable links to a system python library) or a barebones python
installation bundled in with the executable via static linkage. I *think*
the default is the latter, so there isn't an easy way to replace your
python library without a reinstall, which is why vmd-python is so awesome,
as it takes alot of the guesswork out of building VMD on new systems.
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vmd-python is a Python module that exposes the molecular manipulation functions present in the main VMD program. It's not a full-featured VMD implementation or standalone program, and won't affect the interpreter used in VMD. It doesn't provide a vmd command or a vmd-python command---all it lets you do is run If you want a VMD installation with a Python interpreter, you'll have to compile VMD yourself and link against the python you want to use. Here's how I do it:
Hopefully this works. If not, let me know how I can help as I wrote this up pretty quickly. You'll probably want to get access to the VMD developer CVS tree for all the python functionality to be present. I'm also working on getting binary releases of these to be made available, but that won't be for a while. |
Please check your email I have attached one error image and another env file,
when I enter
make LINUXAMD64,
after sourcing my environmental variable file; this shows the following
error message. I am attaching my env file too. I mentioned tcl8.6 in my
vmd_me.sh file, but still the compiler is searching for tcl8.5.
…On Thu, Jun 6, 2019 at 11:39 PM Robin Betz ***@***.***> wrote:
vmd-python is a Python module that exposes the molecular manipulation
functions present in the main VMD program. It's not a full-featured VMD
implementation or standalone program, and won't affect the interpreter used
in VMD.
If you want a VMD installation with a Python interpreter, you'll have to
compile VMD yourself and link against the python you want to use. Here's
how I do it:
1.
Set the environment variables the build will use with a script.
[Here's mine(
https://gist.github.com/Eigenstate/361ef62e418aac2e3d5bb8a9a10d9c4a).
It builds against a conda installation of Python. See the comments for
which lines to change. Then source it: source source_me.sh
2.
In your VMD source directory $VMDDIR:
cd $VMDDIR/plugins
make LINUXAMD64
make distrib
1. Symlink the plugins installed directory into the main source
directory, then build cmd.
cd $VMDDIR/vmd ln -s $PLUGINDIR plugins make make install
Hopefully this works. If not, let me know how I can help as I wrote this
up pretty quickly. You'll probably want to get access to the VMD developer
CVS tree for all the python functionality to be present. I'm also working
on getting binary releases of these to be made available, but that won't be
for a while.
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please check this. |
Dear Developers,
How does the display function/module work? Do we have any kind of Display out from this module? The Actual VMD app is not integrated with this module. While installing via conda I didn't find it to install any other VMD app. Please suggest something...
Thanks,
Pallab
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