Dear Andrew, first of all — thank you so much for your feedback, both the technical and the legal parts. Your earlier comments about SDF and PDB parsing corner cases are incredibly valuable.
PyMOL has been one of my primary tools for 15 years, and I've always held it in deep respect. This project was born entirely out of a desire to contribute something to molecular visualization in the modern world — something fast, modular, and with qualities I've been missing in existing tools. And as a source of inspiration, I took the best one: PyMOL.
Of course I spent a lot of time reading and studying its code, and I openly took concepts and algorithms from it. I don't hide that — it's why the project carries the name it does, and it's why the README has had an Acknowledgments section since the very first commit: "Inspired by PyMOL, created by Warren Lyford DeLano. This is an independent reimplementation, not affiliated with Schrödinger, Inc."
You are absolutely right about the "clean-room" wording — I used it loosely, meaning "rewritten from scratch in a different language with a different architecture," not in the legal sense. That was misleading, and I've already removed it from the README.
You're also right that DSS or CE was a fairly direct port of PyMOL's algorithm, and it should carry proper attribution. At the same time, many other parts — surface generation, cartoon rendering, the shading pipeline — are done quite differently, and the gap keeps growing. But that doesn't excuse insufficient attribution where code was closely followed.
Going forward, I'm focusing on genuinely new functionality — Rust plugin system, web interface, novel shading models (try set shading_mode, skripkin!) — things the original PyMOL never had. But this is not an attempt to distance the project from DeLano's creation. It's a respectful continuation of his ideas in a completely new product.
Thank you again — your comments are making this project better.
PyMOL has been one of my primary tools for 15 years, and I've always held it in deep respect. This project was born entirely out of a desire to contribute something to molecular visualization in the modern world — something fast, modular, and with qualities I've been missing in existing tools. And as a source of inspiration, I took the best one: PyMOL.
Of course I spent a lot of time reading and studying its code, and I openly took concepts and algorithms from it. I don't hide that — it's why the project carries the name it does, and it's why the README has had an Acknowledgments section since the very first commit: "Inspired by PyMOL, created by Warren Lyford DeLano. This is an independent reimplementation, not affiliated with Schrödinger, Inc."
You are absolutely right about the "clean-room" wording — I used it loosely, meaning "rewritten from scratch in a different language with a different architecture," not in the legal sense. That was misleading, and I've already removed it from the README.
You're also right that DSS or CE was a fairly direct port of PyMOL's algorithm, and it should carry proper attribution. At the same time, many other parts — surface generation, cartoon rendering, the shading pipeline — are done quite differently, and the gap keeps growing. But that doesn't excuse insufficient attribution where code was closely followed.
Going forward, I'm focusing on genuinely new functionality — Rust plugin system, web interface, novel shading models (try set shading_mode, skripkin!) — things the original PyMOL never had. But this is not an attempt to distance the project from DeLano's creation. It's a respectful continuation of his ideas in a completely new product.
Thank you again — your comments are making this project better.