Hi, I apologize sincerely since I imagine this comes up often on the
mailing list.
I'm basically wondering if it's possible to import just the `core`
functionality from a chimerax installation into a custom python environment
and bypass the GUI and the binary completely.
Example: I don't think it matters whether it's linux, mac, or source build,
but let's say i installed a clean chimerax via my package manager (`yay i
chimerax`). It's at `/opt/chimerax` and looks like this:
(venv) ᢹ ritual.rtviii[ /opt/chimerax ] ls -la
total 24
drwxr-xr-x 6 root root 4096 May 1 16:08 .
drwxr-xr-x 10 root root 4096 May 1 16:58 ..
drwxr-xr-x 4 root root 4096 May 1 16:51 bin
drwxr-xr-x 8 root root 4096 May 1 16:51 include
drwxr-xr-x 4 root root 4096 May 1 16:51 lib
drwxr-xr-x 6 root root 4096 May 1 16:51 share
If I launch `chimerax` at the command line, i get a functional GUI etc. It
works. I create a fresh custom `virtualenv` with the same python that this
chimerax ships:
virtualenv --python='/opt/chimerax/bin/python3.11' venv
Then i do something ugly in the name of science: i symlink the chimerax
folder from the installation into my virtualenv:
ln -s /opt/chimerax/lib/python3.11/site-packages/chimerax
/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/chimerax
i also tried:
for P in $(ls /opt/chimerax/lib/python3.11/site-packages/); do ln -s
/opt/chimerax/lib/python3.11/site-packages/$P /home/rtviii/dev/try_chimerax/
venv/lib/python3.11/site-packages/$P; done
This enables me to import chimerax modules into my python code that uses
this virtualenv:
```/home/rtviii/dev/try_chimerax/test.py
from chimerax.core.commands import run
from chimerax.core.session import Session
import chimerax.mmcif.mmcif as mmcif
s = Session("Hi")
print(s)
run(s,"open 1ubq.cif")
```
However, this is where i'm struggling a little to use any actual
functionality (especially interested in cutting, merging structures and
operations treating density maps and mmcif structures) because the Session
wouldn't initialize well:
```
<chimerax.core.session.Session object at 0x70472673b5d0>
NOTE: Traceback (most recent call last):
File "/home/rtviii/dev/try_chimerax/test.py", line 9, in <module>
run(s,"open 1ubq.cif")
File "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/chimerax/core/commands/cli.py",
line 2849, in run
_compute_available_commands(session)
File
"/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/chimerax/core/commands/cli.py",
line 2431, in _compute_available_commands
ts.register_available_commands(session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no
attribute'register_available_commands'
BUG: AttributeError: 'NoneType' object has no
attribute'register_available_commands'
File "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2431, in
_compute_available_commands
ts.register_available_commands(session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_See log for complete Python traceback._
```
I had some success with a similar approach in PyMol in this regard, but
can't quite get this to work in ChimeraX. I really appreciate any advice
for achieving this scripting decoupling from GUI/binary if that's possible
at all:
- either how to "pull in" ChimeraX library code properly (i realize mine is
an ugly hack)
- how to use library code otherwise
- how to bypass the dependence of a lot of commands on the Session object
or how to initialize it outside of the gui properly: an example of how to
use selections to open a local density map and perform a smoothing, for
example.
Kindest regards and huge thanks for the monumental application.
Artem,
UBC Vancouver
