VizFold zarr archive for inference traces (issue #39), ksuleimanova#64
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ksuleimanova wants to merge 56 commits into
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VizFold zarr archive for inference traces (issue #39), ksuleimanova#64ksuleimanova wants to merge 56 commits into
ksuleimanova wants to merge 56 commits into
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Add instruction for how to get vizfold working.
…n directory The cell magic change is so the need for the Bask kernel is removed. Instead, a generic Python kernel can be used instead. The Conda install dir change is so different directories can be used if your home directory is too small
Updated installation instructions for AlphaFold, including new data directory paths and changes to the installation process.
Update install.ipynb and README.md
Add Mamba solver
Clarified instructions for loading Conda and using the OpenFold environment in Jupyter.
Update README with clearer Conda and Jupyter instructions
Update installation instructions for Jupyter kernel
Added verbose flag '-vvv' to various conda and pip commands for detailed output during installation.
Added verbose logging to Conda activation steps.
Updated installation commands to reduce verbosity in output.
Enhance installation script with verbose output
- Implemented a Python pipeline to intercept and patch the pretrained `esmfold_3B_v1.pt` checkpoint. - Resolved cross architecture weight incompatibilities (Meta ESM Issue #435) by mapping legacy Invariant Point Attention (IPA) tensor keys to align with the modern OpenFold/VizFold state dictionary (e.g., updating `.weight` to `.linear.weight`). - Added an inference testing script to validate the environment setup and patched weights. - Verified GPU accelerated forward pass execution using some test sequences which successfully output a properly formatted `.pdb` coordinate file.
… integration Implements ESMFold inference as a proper vizfold/backends/ package that fully integrates with VizFold's existing attention capture pipeline, replacing the earlier esmfold/ prototype scripts.
Add files via upload
Move mamba's command into env and add to readme
- Tested by removing my working conda environment and reinstalling using notebook. - Covers OpenFold and ESMFold installation
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Methods 8 and 9 mentioned in pr #62 completed in file vizfold_to_zarr.py
Hyperparameter optimization with grid search in file openfold_sweep_to_zarr.py