[Tutor] Two Scripts, Same Commands, One Works, One Doesn't

[Stephen P. Molnar]

I am writing scripts to semi-automate some of my Quantum Chemistry 
software and have encountered a problem that has me baffled. The two 
scripts have the same form, the only difference being the commands. One 
script works, the other bombs.

The script that works is:

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
calc_pdbqt

Created on Mon May 13 09:50:54 2019

copyrignt (c) 2019 Stephen P. Molnar, Ph.D.  All rights reserved
"""

import subprocess
with open('ligand') as infile:
     ligand = infile.read().strip().split()
for nvar in ligand:
     command = ["./pythonsh", "./prepare_ligand4.py",
         "-l", nvar + ".mol2",
         "-o", nvar + ".pdbqt" ]
     proc = subprocess.Popen(command, stdout=subprocess.PIPE)
     out, err = proc.communicate()
     print(out)
     print(err)
     if proc.returncode:
         print ('Subprocess FAILED:', proc.command)


while the script that bombs is:

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
calc_pdf4

Created on Mon May 13 09:50:54 2019

copyrignt (c) 2019 Stephen P. Molnar, Ph.D.  All rights reserved
"""

import subprocess
with open('ligand') as infile:
     ligand = infile.read().strip().split()
for nvar in ligand:
     command = ["./pythonsh", "./prepare_pdf4.py",
         "-l", nvar + ".pdbqt",
         "-ro", nvar + ".dpf" ]
     proc = subprocess.Popen(command, stdout=subprocess.PIPE)
     out, err = proc.communicate()
     print(out)
     print(err)
     if proc.returncode:
         print ('Subprocess FAILED:', proc.command)

The errors are:

runfile('/home/comp/Apps/Models/1-NerveAgents/Ligands/calc_pdf.py', 
wdir='/home/comp/Apps/Models/1-NerveAgents/Ligands')
b''
None
/sdc1/Apps/MGLTools2-1.1/bin/python: can't open file 
'./prepare_pdf4.py': [Errno 2] No such file or directory
Traceback (most recent call last):

   File "<ipython-input-1-078e132fa938>", line 1, in <module>
runfile('/home/comp/Apps/Models/1-NerveAgents/Ligands/calc_pdf.py', 
wdir='/home/comp/Apps/Models/1-NerveAgents/Ligands')

   File 
"/home/comp/Apps/miniconda3/lib/python3.7/site-packages/spyder_kernels/customize/spydercustomize.py", 
line 824, in runfile
     execfile(filename, namespace)

   File 
"/home/comp/Apps/miniconda3/lib/python3.7/site-packages/spyder_kernels/customize/spydercustomize.py", 
line 110, in execfile
     exec(compile(f.read(), filename, 'exec'), namespace)

   File "/home/comp/Apps/Models/1-NerveAgents/Ligands/calc_pdf.py", line 
23, in <module>
     print ('Subprocess FAILED:', proc.command)

AttributeError: 'Popen' object has no attribute 'command'

I have attached the two scripts that are called and a test input file.

Googling has not helped me to find a solution and I would greatly 
appreciate your assistance.

Thanks in advance.

-- 
Stephen P. Molnar, Ph.D.          Life is a fuzzy set
www.molecular-modeling.net        Stochastic and multivariate
(614)312-7528(c)
Skype:  smolnar1