I made PyMOL run on web-browsers (WASM port)

[yakomaxa]

Dear PyMOL developers.

First of all, thank you for maintaining this wonderful software.

I'm a bioinformatician in Japan, and I have been trying to port PyMOL to Web-assembly (WASM). I've successfully ported it using Pyodide, and now my PyMOL (the internal GUI part) runs on modern browsers like Chrome and Firefox with the help of a bit of javascript code. Though it's still under development, I want to share this with the community. However, I'm hesitating to share because I'm unsure about two things:

(1) Is it acceptable to distribute PyMOL wasm binary by myself, especially naming it "PyMOL-wasm" or something like that?
(2) How should I distribute the source code? I considered making a pull request for PyMOL main, but I guess my modifications are large and also out of the main branch's scope, so I'm hesitating about this, too.

On (1) point, I sent an email to Schrodinger Inc. months ago for confirmations, but there are no replies.

I created this discussion to ask you (developers here) what would be the best way to share this work. I hope you'll be interested in this work, and any suggestions and questions will be appreciated.

Best regards,
Koya Sakuma @yakomaxa

[JarrettSJohnson]

Hi Koya, we look forward to seeing the progress of your work! Excited to see what you have. At this moment, feel free to distribute the binaries; PyMOL-wasm sounds fine.

As far as merging the project in, let's experiment with having it separate from the main repository at least for now. Depending on your implementation, if pymol-open-source itself has to be modified, perhaps keep it as a fork. But if it's unmodified, perhaps as a submodule is better? For projects similar we've had to this, it's inevitable for the main repo to also include some changes to accommodate the implementation for that project, and we'll usually be open to PRs for those as long as the changes are easily maintainable not intrusive.

[yakomaxa]

Hi Jarrett. Thank you for responding to this discussion and letting me distribute the binary! Making binary available allows me to open a simple website on the GitHub page for a demonstration. Please wait a moment for me to construct the website.

As for source code, I now store the source code for the wasm port in my private repo, which can be disclosed at any time. I separated it from the forked repo to make it easy to make modifications when I started this project. With some effort, this source code (or modified parts) can be again merged to the fork of the latest original repo.

In my implementation, pymol-open-source has to be modified. I've made (I believe) these modifications conditional using ifdef so that it will be compatible with the usual pymol build. However, this also needs extra packages, changes on setup.py, and so on for compilation. I'm considering how to deal with these parts now. Any suggestions on these issues will help. When we solve these issues, the source code can be safely imported into the forked repository, and I can create a pull request with it. Before it, I'll keep my version in my repo and try to merge it to the forked repo for ease of following updates in the main.

[yakomaxa]

Hi, I've opened this project's repo and demo page! The repo only contains binary and html/JavaScript at this moment. The demo page remains quite primitive and will be updated.

Repository:
https://github.com/yakomaxa/PyMOL-Wasm

Demo page:
https://yakomaxa.github.io/PyMOL-Wasm

I checked the interactions with the PyMOL window on my machine, which will be improved for other platforms.

It is worth noting that the current implementation cannot follow the changes in window size after launching the PyMOL process. I will also improve this in the future.

I appreciate any comments on this project. Please post it to the repo's issues and discussions.