program automatization

[Gribouillis]

Why do you write stderr=subprocess.PIPE if you don't use the subprocess' error output? I suggest

import os
import subprocess
import sys
cmd = ['/usr/share/apps/flexaid_temporal/Process_Ligand' , '-f']
for file in os.listdir('.'):
    if file.endswith('.pdb'):
        subprocess.call(cmd + [file])