W10: Avogadro week(s)
Finally, all three bugfix commits have been taken up by Debian, Ubuntu and Fedora maintainers. After the important matters have been taken care of, I'm focusing on extending Avogadro, already as part as this year's GSoC work (the application to which I'm discussing with its developer).
- A huge optimization to bond perception, which makes importing PDB files an order of magnitude faster.
- A fix for metals in PDB files not being loaded properly.
- Support for formal charges in CML (and thus also SMILES, etc.), CJSON, SDF and, in a rudimentary form (detects cations in e.g. some drugs), PDB.
- An optimization in secondary structure perception, that makes PDB import much faster when combined with other optimizations.
Right now I'm rewriting a part of Avogadro's code; the reason is, molecules in Avogadro contain some atom and bond information, as well as a graph data structure. I added some extra metadata to speed up many operations, but Geoff suggested that I move that into the graph (which makes sense). Problem is, the molecule code wasn't relying on that graph in the slightest, and trying to do so revealed it's basically nonfunctional... So a small optimization turned refactoring has now become a full-fledged rewrite :)
I've also finished my third 3D-printable PCB manufacturing device prototype. Hopefully I'll be able to try it within the coming days and report the results on Hackaday.io.