Version 2.1.0 adds the AlphaFold-Multimer model and fixes a number of issues reported in the last few months.
Change log:
- [new feature] AlphaFold-Multimer data pipeline, model and metrics have been added. Use
model_preset=multimerto run with AlphaFold-Multimer. - [change] AlphaFold-Multimer no longer pre-processes the features via TensorFlow but instead does it in the JAX module code.
- Added a note and a check that the directory with data is outside the AlphaFold repository for faster Docker builds (thanks @jamespeapen).
- Advertise Python 3.7, 3.8, 3.9, 3.10 in setup.py (thanks @anukaal).
- Added an FAQ explaining that the Colab on free tier can time out (thanks @mooingcat).
- Stop using hardcoded
/tmp, instead use$TMPDIR(thanks @meson800, @EricDeveaud). - Make run_docker fully configurable via flags:
data_dir,docker_image_name,output_dir(thanks @akors, @chrisroat). - Look for stereo_chemical_props.txt relative to the residue_constants module (thanks @rjgildea).
- Crop UniRef90 MSA to 10,000 sequences to prevent hitting the 2 GB proto field limit and use less memory (thanks @biohegedus and @chrisroat).
- Finding third party tool binaries is now more robust and gives you better errors if any are missing (thanks @FanchTheSystem).
- Refactor and a few fixes and usability improvements in the AlphaFold Colab.