Thank you Noel I will go down the path of using the subprocess support in Python.
As a different, but related question, is it true that the open babel conformer search routines are the ones used in Avogadro? Finally, if you have time: Do you know of any python-accessible scripts/code that can generate ring conformers (like chair, boat, twisted, etc.)? It appears that neither confab in Open Babel nor RDkit functions can do this. Cheers, Ryan -----Original Message----- From: Geoffrey Hutchison [mailto:geoff.hutchi...@gmail.com] Sent: Wednesday, February 25, 2015 3:24 PM To: Noel O'Boyle Cc: Renslow, Ryan S; openbabel-discuss@lists.sourceforge.net Subject: Re: [Open Babel] pybel/openbabel and use of confab > The operations are aimed at use from the command-line and so I would > recommend using Python's subprocess. Well, I think you can employ them in Python directly. This is untested, but something like this would work: >> confab = openbabel.OBOp.FindType("confab") confab.Do(myOBMol, >> "options") where "options" is a space-delimited set of options. Looking at the code, it seems like none of the Op classes actually parse the option text, which seems like a bug (i.e., a never-implemented feature). As Noel said, the src/ops/opconfab.cpp code is more-or-less command-line driven and using the subprocess support seems to be the best current approach. -Geoff ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
