Running bash_profile commands with python

Question

In my bash terminal, I can run the following command:

$SCHRODINGER/run volume_calc.py -imae type.mae

and this works correctly.

I am then trying to run the same command in a python script; where I have tried the following approach:

import subprocess
subprocess.run(['$SCHRODINGER/run', 'volume_calc.py', '-imae', 'type.mae'])

which throws the error:

FileNotFoundError: [Errno 2] No such file or directory: '$SCHRODINGER/run'

I am confused what the issue could be, as I can run basic bash commands fine. Thank you for any help.

Answer 1

Environment variable expansion is not done by default using subprocess unless you pass the shell argument to the subprocess.run call. This will pass your arguments to a shell (eg bash ) which will handle the desired expansion and any other shell-like functionality.

Here's the code change necessary:

subprocess.run(['$SCHRODINGER/run', 'volume_calc.py', '-imae', 'type.mae'], shell=True)

Note that it is worth reading through the security considerations for using this given in the python documentation.