Unifying user experience (UX) across OpenFE and external OpenFE-based protocols

[ijpulidos]

Following our recent protocol developer meeting, we want to kick off a discussion on unifying the user experience (UX) across different OpenFE protocols, as well as external integrations like eliantiudic/atom-openfe.

Our goal is to enable users to seamlessly utilize diverse protocols without friction. To achieve this, we propose drafting a set of unified UX guidelines and standards that can accommodate various use cases and protocol architectures.

We would love to get the community's input on:

• Core pain points in the current multi-protocol workflow.
• Design principles we should prioritize for a consistent look and feel.
• How to best structure these guidelines so they are easy for external developers to adopt.

Please share your thoughts, use cases, or suggestions below!

[ijpulidos]

Personally, I'd like to highlight the need of a more unified user interface (UI). Such as that the current command line interface (CLI) can be flexible and generic enough to run different protocols and extract and analyze results from them. This is probably something that needs to be gradually implemented, but having some UI and underlying API design thought from the beginning around the possibility of running different protocols and extracting results from them.

• Maybe a flag to specify the protocol or maybe subcommands for each protocol
• TOML (or analogous) readable and extensible configuration files for settings for the CLI/UI. That way we can take advantage of having specific sections and subsections for protocols. Think of a [septop.settings] section or [HybridTopology.charge_settings] section or similarly
• Results object that can be inspected to know what protocol and what parameters were used, on top of getting the free energy estimates.
• UI (CLI command) to allow extending and resuming simulations, independent of the protocol, as possible.
• UI/CLI API that enables protocol developers to extend it in their own code bases. I don't know what's the best practice for this, but something like "UI plugins".

These are just ideas that I'm brainstorming, each of these need more details and revision.