Hi Tim, Many of these options are just wrappers around API functions, so it's worthwhile taking a look at the API documentation. In this case, here's the link to the relevant docs:
http://openbabel.org/api/2.3/classOpenBabel_1_1OBPhModel.shtml Regards, - Noel On Thu, 11 Apr 2019 at 16:11, Tim Dudgeon <tdudgeon...@gmail.com> wrote: > Another Python options question. > I can use the protonation option on the CLI: > > > echo "C1=C(NC=N1)C[C@@H](C(=O)O)N" | obabel -i smi -o mol -p 3 > But I can't figure it out with the Python API: > > > import openbabel > > > > obConversion = openbabel.OBConversion() > > obConversion.SetInAndOutFormats("smi", "mol") > > mol = openbabel.OBMol() > > obConversion.AddOption("p", obConversion.GENOPTIONS, "3.0") > > obConversion.ReadString(mol, "C1=C(NC=N1)C[C@@H](C(=O)O)N") > > output = obConversion.WriteString(mol) > > print output > Output is generated but it's not protonated. Same if using OUTOPTIONS > instead of GENOPTIONS. > > Is the use of the options in Python documented anywhere? > > > > > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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