I'm looking to parse a large .sdf file and put it into a CSV.

The only software I could find that parses .sdf files is OpenBabel's Pybel, but it won't properly install for my El Capitan, for either python2.7 or 3.+ (it's an open issue, and might hopefully be fixed with the next release).

Are there any other languages/OSS that can easily parse this file? As well, if there aren't, is there a recommended operating system I could spin up with VirtualBox that will easily run OpenBabel/Pybel?

1 Answer 1


The OpenEyes library supports reading from MOD SD Files and writing to .csv files as you can see here along with a large number of others of course.

#!/usr/bin/env python
from openeye.oechem import *

ifs = oemolistream()
ofs = oemolostream()


for mol in ifs.GetOEGraphMols():
    OEWriteMolecule(ofs, mol)

It may be a good idea to follow the advice on setting up a virtual-env.

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