Dear Colleagues,
I hope you are all safe and well at this extraordinary time.
This is a follow-up to messages I sent to the list in late 2013 and early 2014
regarding an old DOS-based program 'SMOG' (see CCL archives
http://www.ccl.net/cca/software/MS-DOS/SMOG/index.shtml and
http://pubs.acs.org/doi/abs/10.1021/ci950393z) that generates isomers given a
molecular formula and a set of structural constraints. Although the output is
in the form of a connection table it was not understood by other applications I
was aware of and I thought OpenBabel might work. However, at the time this was
not an option and Noel kindly provided me with a Python script (smog.py -
attached as a txt file) that took the SMOG output and generated SMILES. I
believe there was an intention to include this in future versions of Open Babel
but I appreciate there are many calls on time and I don't think this has yet
happened.
Fast forwarding seven years or so, during which my attention was taken by other
duties, I have now returned to working on the additional SMOG output I have
available and I naively thought I would be able to install current versions of
Open Babel and Python, fire up the script and everything would work as before.
Unfortunately, things didn't go quite to plan and the following is what
happened.
I Installed Anaconda Powershell and OpenBabel 3.0.0 and, I think, the bindings
('pip install -U openbabel') correctly.
I ran through the commands given in the 'Test the installation' box on
https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html
and obtained a structure in a separate window so it seemed that things were
working okay. I then ran smog.py as attached and got the following:
(base) PS C:\users\anthony\anaconda2> python smog.py myfile.res myoutputfile.smi
Traceback (most recent call last):
File "smog.py", line 5, in <module>
import pybel
ImportError: No module named pybel
Having looked at
https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html
again and also the 'Updating to Open Babel 3.0 from 2.x' page
(https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html), I
changed line 5 in smog.py from 'import pybel' to 'from openbabel import pybel'
and ran smog.py again with the following result:
(base) PS C:\users\anthony\anaconda2> python smog.py myfile.res myoutputfile.smi
Traceback (most recent call last):
File "smog.py", line 60, in <module>
for mol in readSMOG(options['inputfile']):
File "smog.py", line 41, in readSMOG
yield smog2mol(lines)
File "smog.py", line 16, in smog2mol
atm.SetAtomicNum(ob.cvar.etab.GetAtomicNum(element))
AttributeError: Unknown C global variable 'etab'
At this point I am well beyond my capabilities but I assume there have been
changes since version 2.x'ish that I used in the past and the global variable
'etab' and is absent. I did find 'etab' defined on line 468 at
https://github.com/openbabel/documentation/blob/master/pybel.py (dated 14 Oct
2012) but I don't know what to do with this information!
I guess this is a similar issue to one posted to the list at the end of May and
I'm hoping that someone can provide some assistance and, if it's possible, show
me how I can get the smog.py working again. Maybe this is my chance to learn
Python after all the times I've said I would...
My apologies for the lengthy post and many thanks for any assistance received,
Anthony
C. Anthony Lewis
Petroleum & Environmental Geochemistry Group & Centre for Chemical Sciences,
School of Geography, Earth and Environmental Sciences,
Plymouth University,
Plymouth, Devon PL4 8AA, U.K.
tel: +44 (0)1752 584554
email: [email protected]<mailto:[email protected]>
web: http://www.pegg.org.uk<http://www.pegg.org.uk/>
http://www.plymouth.ac.uk/chemistry
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from __future__ import print_function
import os
import sys
import pybel
ob = pybel.ob
def smog2mol(lines):
mol = ob.OBMol()
for line in lines:
atmnum = int(line[:3])
element = line[6:10].strip()
bonds = line[23:]
if atmnum > 0:
atm = ob.OBAtom()
atm.SetAtomicNum(ob.cvar.etab.GetAtomicNum(element))
mol.AddAtom(atm)
for i, b in enumerate(bonds):
if int(b):
mol.AddBond(mol.NumAtoms(), i+1, int(b))
else:
for i, n in enumerate(bonds):
for j in range(int(n)):
atm = ob.OBAtom()
atm.SetAtomicNum(ob.cvar.etab.GetAtomicNum(element))
mol.AddAtom(atm)
mol.AddBond(mol.NumAtoms(), i+1, 1)
return mol
def readSMOG(filename):
with open(filename) as f:
for line in f:
if line.startswith("Isomer"):
lines = []
while True:
temp = f.next().strip()
if not temp:
break
lines.append(temp)
yield smog2mol(lines)
def printhelp():
print("python smog.py inputfile outputfile")
sys.exit(1)
def handleargs(args):
options = {}
if len(args) != 3:
printhelp()
options['inputfile'] = sys.argv[1]
if not os.path.isfile(sys.argv[1]):
printhelp()
options['outputfile'] = sys.argv[2]
return options
if __name__ == "__main__":
options = handleargs(sys.argv)
output = pybel.Outputfile("smi", options['outputfile'], overwrite=True)
for mol in readSMOG(options['inputfile']):
m = pybel.Molecule(mol)
m.removeh()
output.write(m)
output.close()
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