Releases: chaidiscovery/chai-lab
Releases · chaidiscovery/chai-lab
v0.2.1: efficient weight loading + document MSA
What's Changed
Major changes:
- MSA usage is now documented, and an example pipeline is provided.
- More efficient weight loading + support for devices other than
cuda:0
PRs:
- Update README to highlight MSA usage. by @wukevin in #121
- Clarify MSA documentation by @wukevin in #129
- update weights by @arogozhnikov in #144
- change weight loading schema by @arogozhnikov in #145
Minor:
- Fix typo by @jackdent in #122
- report "downloading x" only when it is actially downloaded by @arogozhnikov in #134
Full Changelog: v0.2.0...v0.2.1
Contributors
jackdent, wukevin, and arogozhnikov
Assets 2
v0.2.0: documentation and tools to create MSA contexts
What's Changed
Major:
Minor:
- document envvar CHAI_DOWNLOADS_DIR by @arogozhnikov in #115
- fix race conditions during downloads by @arogozhnikov in #114
- Update technical report link by @jackdent in #105 #112
- resize image to have proper h/w ratio on all devices by @arogozhnikov in #106
- Add bibtex record for citation by @arogozhnikov in #107 #108
- remove redundant check by @arogozhnikov in #116
- Correct grammar in README by @jackdent in #119
- bump version by @arogozhnikov in #120
Full Changelog: v0.1.0...v0.2.0
Contributors
jackdent, wukevin, and arogozhnikov
Assets 2
v0.1.0
Main changes:
- demand unique names for entities, change of output format to simplify future changes
- more strict validation of user inputs
- report main metrics, saved in .npz
- fixed bug with additional oxygen in non-standard residues
- support python 3.10
- more efficient inference of ESM in complexes
What's Changed
- chore: update utils.py by @eltociear in #1
- move ESM to/from GPU once per complex, not once per chain by @arogozhnikov in #5
- Add pLDDT to pdb files by @jacquesboitreaud in #8
- Update lab.chaidiscovery.com screenshot by @jackdent in #11
- Warn user about potentially wrong EntityType by @arogozhnikov in #9
- Write confidence scores with model outputs by @jacquesboitreaud in #12
- support python 3.10 by @arogozhnikov in #15
- run pytest in CI by @arogozhnikov in #16
- Add plot of MSA coverage by @wukevin in #24
- Improve PDB output by @vreis in #34
- Naming, comments, change default installation method to use github version by @arogozhnikov in #39
- explicitly mention in readme requirement for bfloat16 by @arogozhnikov in #44
- streamline computation of clashes by @arogozhnikov in #43
- Write predictions in cif format by @jacquesboitreaud in #45
- Empty cache before we run folding by @wukevin in #47
- Fix for cases where tokenization failed by @wukevin in #54
- change default path for esm, provide envvar to control download location by @arogozhnikov in #61
- Remove OXT atom in non-standard residues by @jacquesboitreaud in #62
- Change of input/output formats by @arogozhnikov in #60
- add pre-commit to verify license headers in python files by @arogozhnikov in #68
- bump version to 0.1.0 by @arogozhnikov in #78
New Contributors
- @eltociear made their first contribution in #1
- @arogozhnikov made their first contribution in #5
- @jacquesboitreaud made their first contribution in #8
- @jackdent made their first contribution in #11
- @wukevin made their first contribution in #24
- @vreis made their first contribution in #34
Full Changelog: v0.0.1...v0.1.0
Contributors
vreis, jackdent, and 4 other contributors