LICENSE
README.md
pyproject.toml
src/atlasfold/__init__.py
src/atlasfold/pretrained.py
src/atlasfold/runner.py
src/atlasfold/runner_multimer.py
src/atlasfold.egg-info/PKG-INFO
src/atlasfold.egg-info/SOURCES.txt
src/atlasfold.egg-info/dependency_links.txt
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src/atlasfold/cli/__init__.py
src/atlasfold/cli/__main__.py
src/atlasfold/cli/monomer.py
src/atlasfold/cli/multigpu.py
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src/atlasfold/common/ccd.py
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src/atlasfold/configs/__init__.py
src/atlasfold/configs/atlasfold.py
src/atlasfold/configs/atlasfold_multimer.py
src/atlasfold/data/__init__.py
src/atlasfold/data/cif_factory.py
src/atlasfold/data/fasta.py
src/atlasfold/data/mmseq2.py
src/atlasfold/model/__init__.py
src/atlasfold/model/model.py
src/atlasfold/model/model_multimer.py
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src/atlasfold/model/network/diffusion_head.py
src/atlasfold/model/network/diffusion_transformer.py
src/atlasfold/model/network/distogram_head.py
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src/atlasfold/model/network/rel_pos_encoding.py
src/atlasfold/model/network/template.py
src/atlasfold/model/network/trunk.py
src/atlasfold/model/network/primitives/__init__.py
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src/atlasfold/model/network/primitives/normalization.py
src/atlasfold/model/network/primitives/transition.py
src/atlasfold/model/network/primitives/triangle_update.py
src/atlasfold/model/utils/__init__.py
src/atlasfold/model/utils/confidence_metrics.py
src/atlasfold/train/__init__.py
src/atlasfold/train/config.py
src/atlasfold/train/losses/__init__.py
src/atlasfold/train/losses/confidence.py
src/atlasfold/train/losses/diffusion.py
src/atlasfold/train/losses/distogram.py
src/atlasfold/train/monomer/__init__.py
src/atlasfold/train/monomer/cropper.py
src/atlasfold/train/monomer/datamodule.py
src/atlasfold/train/monomer/dataset.py
src/atlasfold/train/monomer/model_train.py
src/atlasfold/train/monomer/structure_alignment.py
src/atlasfold/train/monomer/train_module.py
src/atlasfold/train/monomer/validation_metrics.py
src/atlasfold/train/multimer/__init__.py
src/atlasfold/train/multimer/cropper.py
src/atlasfold/train/multimer/datamodule.py
src/atlasfold/train/multimer/dataset.py
src/atlasfold/train/multimer/model_train.py
src/atlasfold/train/multimer/train_alignment.py
src/atlasfold/train/multimer/train_module.py
src/atlasfold/train/multimer/validation_metrics.py
src/atlasfold/train/utils/__init__.py
src/atlasfold/train/utils/dl_sampler.py
src/atlasfold/train/utils/ema.py
src/atlasfold/train/utils/gradient_logging.py
src/atlasfold/train/utils/lr_scheduler.py
src/atlasfold/train/utils/kernels/__init__.py
src/atlasfold/train/utils/kernels/cdist.py
src/atlasfold/utils/__init__.py
src/atlasfold/utils/checkpointing.py
src/atlasfold/utils/kernel.py
src/atlasfold/utils/misc.py
src/atlasfold/utils/rasa.py
src/atlasfold/utils/torch_utils.py
src/atlasfold/utils/geometry/__init__.py
src/atlasfold/utils/geometry/metrics.py
src/atlasfold/utils/geometry/random_augment.py
src/atlasfold/utils/geometry/rigid_align.py
src/atlaslm/__init__.py
src/atlaslm/alphabet.py
src/atlaslm/model.py
src/atlaslm/pretrained.py
src/atlaslm/layers/__init__.py
src/atlaslm/layers/attention.py
src/atlaslm/layers/regression_head.py
src/atlaslm/layers/rotary.py
src/atlaslm/layers/transformer_stack.py