Openmm pypi#24
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In the original set of ligand AMBER parameterisations done by Moriarty & Case, the -NH2 group of guanine was incorrectly assigned as NH3. This commit corrects that for all current ligands in the components dictionary containing "guanosine" in their name. The underlying issue is a wider one affecting various other ligands; correcting this completely needs a more considered, general approach.
Forcefield loading was previously happening in a separate thread managed by `ThreadPoolExecutor` to reduce impact on main-thread performance. For unknown reasons, this seems to *very* rarely lead to a segmentation fault when loading the pickled force field. The good news is that the hit to performance is minimal - I added this threaded approach at a time when all the ligand definitions were pre-loaded into the main force field making it very slow to instantiate. Now that ligands are only added as-needed, startup time is essentially negligible.
Documentation says that it resets back to the original ffXML files, but it was only resetting back to the cached *pickle* file.
The RCSB ligand-expo server recently stopped serving these templates describing various amino acid residue protonation variants. Since they're currently used by ISOLDE's code for rebuilding incomplete residues, I'm bundling in an offline version of this template subset.
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