On Sat, Sep 25, 2021 at 5:05 PM Alexander Ploumistos <alex.ploumistos@xxxxxxxxx> wrote: > > I will try with a Fedora 34 VM later and report back. I got pretty much the same results on F34. I think xdrawchem works better with Open Babel 3 than it does with Open Babel 2, at least as far as structure cleanup goes (I installed the current version in F34). With Open Babel 2, SMILES output is also asterisks and trying InChi output crashes the program, so nothing changed there. gnome-chemistry-utils programs can't find the required shared object files in F34 either. I built the latest avogadro2 and avogadro2-libs from the srpm in your copr for F34 and I hit some graphical glitches again. On Wayland, Avogadro2 for X11 has a transparent canvas, whereas the other one (I guess Wayland) doesn't, but as soon as I add a fourth atom to the drawing, it crashes: /usr/include/c++/11/bits/stl_vector.h:1045: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](std::vector<_Tp, _Alloc>::size_type) [with _Tp = Eigen::Matrix<double, 3, 1>; _Alloc = std::allocator<Eigen::Matrix<double, 3, 1> >; std::vector<_Tp, _Alloc>::reference = Eigen::Matrix<double, 3, 1>&; std::vector<_Tp, _Alloc>::size_type = long unsigned int]: Assertion '__n < this->size()' failed. Aborted (core dumped) However, when given a badly drawn propene or propane molecule, the structure optimization works fine. On X, I did not get the transparent canvas, but I got the crash at the fourth atom. I was able to open some of my existing files though, with up to several thousand atoms and the structure optimization worked fine after I had deformed them. At least any issues are not from Open Babel 3 (I guess). _______________________________________________ devel mailing list -- devel@xxxxxxxxxxxxxxxxxxxxxxx To unsubscribe send an email to devel-leave@xxxxxxxxxxxxxxxxxxxxxxx Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@xxxxxxxxxxxxxxxxxxxxxxx Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
