openfe

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Protein models without protons get protonated without user input

2

Reported by an OpenFE partner yesterday - passing a model with only polar hydrogens leads to hydrogens being automatically added.

IAlibay

Cli protocol settings via yaml input

2

Checklist * [ ] Added a ``news`` entry ## Developers certificate of origin - [ ] I certify that this contribution is covered by the MIT License [here](https://github.com/OpenFreeEnergy/openfe/blob/main/LICENSE) and the...

richardjgowers

OpenMMSolvation: Support for non-cubic boxes and defined box properties

4

Fixes #585 In this PR: - Allows for defining the additional openmm keywords to addSolvent - New OpenMM solvation settings + docstring ## Developers certificate of origin - [x] I...

IAlibay

Allow for multiple alchemical waters

4

From today's Perses-OpenFE call - it might be good, once we've finished up validating the alchemical water code, to see if we can support net charge changes > 1.

IAlibay

Doc string clarification request

4

In [HybridTopologyFactory,](https://github.com/OpenFreeEnergy/openfe/blob/b1a7c062ae0e8565808ce49ebb97995195372d7c/openfe/protocols/openmm_rfe/_rfe_utils/relative.py#L20) there's an option which seems important but for which we can't fully understand the doc string. Specifically: ``` interpolate_old_and_new_14s : bool, default False Whether to turn off interactions...

davidlmobley

[docs] userguide, how to visualise various things in a notebook

1

- [ ] Add userguide docs on "how do I visualise a mapping, network, etc..."

IAlibay

As a "good practice" thing, and to ensure we don't have to rely on flaky git logging we should add an `AUTHORS` file that: - Has a list of historical...

IAlibay

We're using both in the repo, we should pick one and stick to it.

richardjgowers

add cuda DeviceIndex in engine_settings

1

Please add cuda DeviceIndex settings, similar to the Openmm Platform module, for easy operation on multi graphics card machines

jingqiong

Un-vendor `toolkit_registry_manager`

1

## Developers certificate of origin - [x] I certify that this contribution is covered by the MIT License [here](https://github.com/OpenFreeEnergy/openfe/blob/main/LICENSE) and the **Developer Certificate of Origin** at . I came across...

mattwthompson