Re: [PyMOL] Running pymol without launching window in batch

2025-01-12 Thread Saurabh Gayali 
Apart from others' reply, I believe pymol will run .pml files while python
will run .py files.

Regards,
Saurabh Gayali


--

*Saurabh Gayali*
Business Analyst [Excelra], Former Research Scientist [IGIB]
[email protected] / +91 8800412916
Bangalore, India


On Tue, Dec 10, 2024 at 3:11 AM Yarrow Madrona 
wrote:

> I'm trying to run pymol in batch mode without launching the window. I am
> running PyMOL 3.1.1.
>
> Here is my code for an example script (test.py). I'm trying to run before
> running the real script. In the command line I enter:
> pymol -cq test.py
>
>
> from pymol import cmd
> import time
>
> def main():
> print("Starting PyMOL batch processing...")
> cmd.load("3gbn.pdb")
> do_stuff()
> print("Loaded 3gbn.pdb")
> time.sleep(25) # Ensure commands are processed
> cmd.quit()
>
> if __name__ == "__main_":
> main()
> I don't get any output. If I type:
> pymol -c test.py
> It appears that pymol starts and closes:
>
> [image: image.png]
>
> Any help on how to run a python script with pymol in batch without opening
> the GUI would be appreciated.
> Yarrow
>
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Re: [PyMOL] Running pymol without launching window in batch

2025-01-06 Thread Gruber, Karl ([email protected]) 
Dear Yarrow,

The problem in your script is the `if __name__ == "__main__"` clause.

When the script is run using `pymol -cqk test.py`, __name__ refers to the 
string "pymol".

The following script fetches a structure from the PDB and saves a PNG image. 
Run it using `pymol -cqk test.py -- `. (The flag -k prevents loading 
pymolrc and plugins.)

```python
from pymol import cmd


def main(pdb_id: str) -> None:
print(f"Loading PDB-ID {pdb_id.upper()}")
cmd.fetch(pdb_id)
png_file_name = f"{pdb_id}.png"
print(f"Writting image to {png_file_name}")
cmd.png(png_file_name)


if __name__ == "pymol":
import sys

pdb_id = sys.argv[1]
main(pdb_id)
```

Best regards,

Karl

On 06.01.2025, at 18:04, Florian Nachon  wrote:


Hello,

It is much easier than that.

Make a pymol script, for example, test.pml:

#
load 3gbn.pdb
select Selection1, resi 80:115
save Selection1.cif, Selection1
quit
#

then run it with the -c option :
pymol test.pml -c

If you want to pass an argument, like the filename of a pdb file to be directly 
opened, then use the -cp option.

Florian

On 9 Dec 2024, at 22:38, Yarrow Madrona  wrote:

I'm trying to run pymol in batch mode without launching the window. I am 
running PyMOL 3.1.1.

Here is my code for an example script (test.py). I'm trying to run before 
running the real script. In the command line I enter:
pymol -cq test.py


from pymol import cmd
import time

def main():
print("Starting PyMOL batch processing...")
cmd.load("3gbn.pdb")
do_stuff()
print("Loaded 3gbn.pdb")
time.sleep(25) # Ensure commands are processed
cmd.quit()

if __name__ == "__main_":
main()
I don't get any output. If I type:
pymol -c test.py
It appears that pymol starts and closes:



Any help on how to run a python script with pymol in batch without opening the 
GUI would be appreciated.
Yarrow

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Re: [PyMOL] Running pymol without launching window in batch

2025-01-06 Thread Florian Nachon 

Hello,

It is much easier than that.

Make a pymol script, for example, test.pml:

#
load 3gbn.pdb
select Selection1, resi 80:115
save Selection1.cif, Selection1
quit
#

then run it with the -c option : 
pymol test.pml -c

If you want to pass an argument, like the filename of a pdb file to be directly 
opened, then use the -cp option.

Florian

> On 9 Dec 2024, at 22:38, Yarrow Madrona  wrote:
> 
> I'm trying to run pymol in batch mode without launching the window. I am 
> running PyMOL 3.1.1.
> 
> Here is my code for an example script (test.py). I'm trying to run before 
> running the real script. In the command line I enter:
> pymol -cq test.py
> 
> 
> from pymol import cmd
> import time
> 
> def main():
> print("Starting PyMOL batch processing...")
> cmd.load("3gbn.pdb")
> do_stuff()
> print("Loaded 3gbn.pdb")
> time.sleep(25)  # Ensure commands are processed
> cmd.quit()
> 
> if __name__ == "__main_":
> main()
> I don't get any output. If I type:
> pymol -c test.py
> It appears that pymol starts and closes:
> 
> 
> 
> Any help on how to run a python script with pymol in batch without opening 
> the GUI would be appreciated.
> Yarrow
> 
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> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/[email protected]
> Unsubscribe: 
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

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