OK, thanks. So definitely using version 3.1 as expected. I tried Geoff's suggestion and that works fine. In fact any mode, even fastest generates something reasonable. But instead of that, using mol.make3D() gives the garbled structures with interlocked rings.
Tim On Tue, Oct 26, 2021 at 7:52 PM Stefano Forli via OpenBabel-discuss < openbabel-discuss@lists.sourceforge.net> wrote: > The easiest way to get the version would be this: > > from openbabel import openbabel as ob > print(ob.OBReleaseVersion()) > > > On 10/22/21 06:46, Tim Dudgeon wrote: > > I think I'm using 3.1, but can't be totally sure. > > How do you ask this from python? I can't see any obvious way. > > Tim > > > > On Tue, Oct 19, 2021 at 7:22 PM Geoffrey Hutchison < > geoff.hutchi...@gmail.com <mailto:geoff.hutchi...@gmail.com>> wrote: > > > > > I'm having problems when generating 3D molecules using the Python > bindings. > > > This may be a result of the molecule containing charges, but I'm > not certain about this. > > > > I haven't seen that problem (interlocking rings) in a long time. Are > you sure your Python bindings are using OB 3.1? > > > > You can also try something like this: > > > > gen3d = openbabel.OBOp.FindType("gen3D") > > gen3d.Do(mymol.OBMol, "--best") > > > > -Geoff > > > > > > > > _______________________________________________ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > -- > > Stefano Forli, PhD > > Associate Professor > Dept. of Integrative Structural > and Computational Biology, MB-112A > Scripps Research > 10550 North Torrey Pines Road > La Jolla, CA 92037-1000, USA. > > tel: +1 (858)784-2055 > email: fo...@scripps.edu > https://forlilab.org > > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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