Matt Thompson
Matt Thompson
**Is your feature request related to a problem? Please describe.** Each parameter handler follows a similar pattern that can be reduced to the following steps: 1. Find matches via `self.find_matches`,...
We have `Molecule. compute_partial_charges_am1bcc` staged for official deprecated in version 0.11.0 after a few years of unofficial this-is-getting-removed-sometime-eventually deprecation, and also removal in 0.12.0. This issue is milestoned as a...
**Describe the bug** `UnassignedValenceParameterException` and its subclasses (`UnassignedBondParameterException`, `UnassignedAngleParameterException`, `UnassignedProperTorsionParameterException`) are stuffed with tuples of atoms when they're prepared inside of [`_check_all_valence_terms_assigned`](https://github.com/openforcefield/openff-toolkit/blob/7fdc181d6a4911f66a14341562f59927e9ef7f7a/openff/toolkit/typing/engines/smirnoff/parameters.py#L2339) via a [`unassigned_topology_atom_tuples`](https://github.com/openforcefield/openff-toolkit/blob/7fdc181d6a4911f66a14341562f59927e9ef7f7a/openff/toolkit/typing/engines/smirnoff/parameters.py#L2432) attribute. This exception is raised...
**Is your feature request related to a problem? Please describe.** While working on #1163, it struck me that the error message for [failing to load a force field ](https://github.com/openforcefield/openff-toolkit/blob/12f5e3b27c7c009923de908634690e7c8f4b2b64/openff/toolkit/typing/engines/smirnoff/forcefield.py#L1108-L1116)through plugins...
**Is your feature request related to a problem? Please describe.** The toolkit, and our software in general, should raise descriptive, custom exceptions instead of re-using built-in exceptions. **Describe the solution...
[graph-tool](https://graph-tool.skewed.de/) seems to be a more performant replacement for `networkx`. It is available on [`conda-forge`](https://anaconda.org/conda-forge/graph-tool), although it may or may not make our dependency footprint larger, i.e. > Depends: cairomm,...
**Is your feature request related to a problem? Please describe.** The author of `Molecule.nth_degree_neighbors` - yours truly - used an implementation that does not scale well with molecule size; computing...
Some ambiguous behavior can be reached if a molecule is loaded in with `allow_undefined_stereo=True`, which is commonly the case for loading in large molecule datasets and "just let me run...
In #1050 @j-wags and I re-encountered strange behavior relating to the `toolkit_registry` argument in some `Molecule` API points. The behavior is different if a `ToolkitWrapper` and `ToolkitRegistry` argument is passed...
Right now, `ToolkitRegistry.call` tries the requested method in each of its wrapped toolkits and if they _all_ fail, it raises a `ValueError` that squishes together the messages in each exception:...