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
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