Hi Noel, thank you, that's very helpful. That document is the first stop when I'm migrating stuff, but I completely missed the concept, since I was looking for an explicit mention of that function. Although, from what's written there, I assumed that:
OBMol.UnsetFlag(OB_PH_CORRECTED_MOL) wold now become: OBMol.SetFlag(OB_PH_CORRECTED_MOL, False) But this does not seem to work, at least in Python, suggesting that SetFlag() takes still only a single argument. Any clues? Besides, I am suspecting this API change might be behind the serious issue of the nitrogens with 5 bonds. I've tried reproducing it with two versions of obabel, 2.4.1 and 3.1.0, and the results are attached. Same thing with Python, when testing the code I'm porting from 2 to 3, I noticed the regression is there, too. This is a major showstopper for us, so if there's a way to fix it or work around it, I'll be happy to know. Thanks, S On 9/16/21 12:51 AM, Noel O'Boyle wrote:
Hi Stefano, Most of the changes in 3.0 are described at https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html#molecule-atom-and-bond-flags <https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html#molecule-atom-and-bond-flags>. In short, OBMol::SetPartialChargesPerceived(false). The rationale for this change is described at https://github.com/openbabel/openbabel/pull/1951 <https://github.com/openbabel/openbabel/pull/1951>. Regards, Noel On Wed, 15 Sept 2021 at 18:11, Stefano Forli <fo...@scripps.edu <mailto:fo...@scripps.edu>> wrote: Hi, I'm cleaning up some of our code that was written for v.2 and I found something I don't know how to port to the new version. When assigning Gasteiger charges, it was possible to force the recalculation from scratch for molecules that already had charges by using the method OBMol::UnsetPartialChargesPerceived() The method is still listed in the comments in molchrg.cpp, but it's not in the OBMol anymore. I've tried looking for alternatives, possibly using the OBMol::UnsetFlag() method, but no luck. Any suggestions? Thank you! S--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 <mailto:fo...@scripps.edu> https://forlilab.org <https://forlilab.org> _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net <mailto:OpenBabel-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss <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
ammonium_OB2.mol2
Description: chemical/mol2
ammonium_OB3.mol2
Description: chemical/mol2
ammonium.xyz
Description: Xmol XYZ data
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