├── .gitignore ├── LICENSE.txt ├── README.md ├── conda-recipe ├── build.sh ├── meta.yaml └── post-link.sh ├── data ├── .gitignore ├── filters.csv ├── legacy │ └── antibody_data.csv ├── split.csv └── structures │ ├── success_df.csv │ └── summary_df.csv ├── download.sh ├── dvc.lock ├── dvc.yaml ├── environment_cpu.yml ├── environment_gpu.yml ├── experiment_scripts ├── submit_base.sh ├── submit_language.sh └── submit_plddt.sh ├── init_conda_venv.sh ├── notebooks └── example.ipynb ├── noxfile.py ├── params.yaml ├── pinned-versions.txt ├── pyproject.toml ├── setup.cfg ├── setup.py └── src └── abodybuilder3 ├── .gitignore ├── __init__.py ├── dataloader.py ├── language ├── __init__.py └── model.py ├── lightning_module.py ├── loss ├── __init__.py ├── aligned_rmsd.py └── loss.py ├── openfold ├── __init__.py ├── config.py ├── data │ ├── __init__.py │ └── data_transforms.py ├── model │ ├── __init__.py │ ├── heads.py │ ├── primitives.py │ └── structure_module.py ├── np │ ├── __init__.py │ ├── protein.py │ ├── relax │ │ ├── __init__.py │ │ └── cleanup.py │ └── residue_constants.py ├── resources │ ├── __init__.py │ └── stereo_chemical_props.txt └── utils │ ├── __init__.py │ ├── checkpointing.py │ ├── chunk_utils.py │ ├── feats.py │ ├── kernel │ ├── __init__.py │ ├── attention_core.py │ └── csrc │ │ ├── compat.h │ │ ├── softmax_cuda.cpp │ │ ├── softmax_cuda_kernel.cu │ │ └── softmax_cuda_stub.cpp │ ├── loss.py │ ├── precision_utils.py │ ├── rigid_utils.py │ └── tensor_utils.py ├── py.typed ├── radam.py ├── stages ├── __init__.py ├── data │ ├── __init__.py │ ├── combine_data_dfs.py │ ├── filter_data.py │ ├── generate_data.py │ ├── generate_data.sh │ ├── generate_data_summary.py │ ├── generate_pdbs.py │ ├── language_model_embeddings.py │ └── split_data.py ├── finetune.py ├── inference.py └── train.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Exscientia/abodybuilder3/HEAD/.gitignore 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