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* initial commit * try to fix file refs * ruff, polish pypi README.md and add citations (#2) * run formatter * add gitignore, update pyproject.toml, update readme, remove warning, update draw * vibe-coded to desired interface, need to check correctness of inference scripts now, probably a better LLM can simplify * read mol * remove old inference scripts * new inference * fixes * working (to be polished) * Simplify everything, change the pyproject.toml * py3dmol to dev * revert old readme.md * .. * note the extra uma * batching * saving * not clari-csp * hydrogens always added * hydrogens always added * oom bug * seed everything, remove a todo * --model flag * rm unused * save blank config * revert * fable fixes everything * clarify the batched input * colab and molab * working delete and add * changes * margins * .. * ketcher inside molab * smiles text input too * filter clashing * polish * note the clashing checks * note clashes * more updates and clarifications * finishing touches * bump to old python version * bump v * molab: install clari from PyPI, drop editable path source The editable path source pointed uv at a local checkout that doesn't exist in molab's sandbox, so the notebook failed to start. Resolve clari from PyPI like the other dependencies. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> * .. * from marimo * working on molab * fixed * molab badge --------- Co-authored-by: alstonlo <alston@mit.edu> Co-authored-by: Austin Cheng <auhcheng@gmail.com> Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
* sync molab * more fps in the gif * ruff
…t cifs immediately after sampling
* change flags and checkpoint loading * filter clashing * bump v * some bug fixes * ruff format * debloat scripts * fixes * more fixes for molab * simpler resampling * bump * update docs
* change flags and checkpoint loading * filter clashing * bump v * some bug fixes * ruff format * debloat scripts * fixes * more fixes for molab * simpler resampling * bump * update docs
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New PR to squash prior PRs and remove messy commit history.