LICENSE
README.md
requirements.txt
setup.py
configs/__init__.py
configs/configs_base.py
configs/configs_data.py
configs/configs_inference.py
protenix/__init__.py
protenix.egg-info/PKG-INFO
protenix.egg-info/SOURCES.txt
protenix.egg-info/dependency_links.txt
protenix.egg-info/entry_points.txt
protenix.egg-info/requires.txt
protenix.egg-info/top_level.txt
protenix/config/__init__.py
protenix/config/config.py
protenix/config/extend_types.py
protenix/data/__init__.py
protenix/data/ccd.py
protenix/data/constants.py
protenix/data/data_pipeline.py
protenix/data/dataloader.py
protenix/data/dataset.py
protenix/data/featurizer.py
protenix/data/filter.py
protenix/data/infer_data_pipeline.py
protenix/data/json_maker.py
protenix/data/json_parser.py
protenix/data/json_to_feature.py
protenix/data/msa_featurizer.py
protenix/data/msa_utils.py
protenix/data/parser.py
protenix/data/substructure_perms.py
protenix/data/tokenizer.py
protenix/data/utils.py
protenix/metrics/__init__.py
protenix/metrics/clash.py
protenix/metrics/lddt_metrics.py
protenix/metrics/rmsd.py
protenix/model/__init__.py
protenix/model/generator.py
protenix/model/loss.py
protenix/model/protenix.py
protenix/model/sample_confidence.py
protenix/model/utils.py
protenix/model/layer_norm/__init__.py
protenix/model/layer_norm/layer_norm.py
protenix/model/layer_norm/torch_ext_compile.py
protenix/model/layer_norm/kernel/compat.h
protenix/model/layer_norm/kernel/layer_norm_cuda.cpp
protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu
protenix/model/layer_norm/kernel/type_shim.h
protenix/model/modules/__init__.py
protenix/model/modules/confidence.py
protenix/model/modules/diffusion.py
protenix/model/modules/embedders.py
protenix/model/modules/frames.py
protenix/model/modules/head.py
protenix/model/modules/pairformer.py
protenix/model/modules/primitives.py
protenix/model/modules/transformer.py
protenix/openfold_local/__init__.py
protenix/openfold_local/data/__init__.py
protenix/openfold_local/data/data_transforms.py
protenix/openfold_local/data/errors.py
protenix/openfold_local/data/mmcif_parsing.py
protenix/openfold_local/data/msa_identifiers.py
protenix/openfold_local/data/msa_pairing.py
protenix/openfold_local/data/parsers.py
protenix/openfold_local/data/templates.py
protenix/openfold_local/data/tools/__init__.py
protenix/openfold_local/data/tools/jackhmmer.py
protenix/openfold_local/data/tools/utils.py
protenix/openfold_local/model/__init__.py
protenix/openfold_local/model/dropout.py
protenix/openfold_local/model/outer_product_mean.py
protenix/openfold_local/model/primitives.py
protenix/openfold_local/model/triangular_attention.py
protenix/openfold_local/model/triangular_multiplicative_update.py
protenix/openfold_local/np/__init__.py
protenix/openfold_local/np/residue_constants.py
protenix/openfold_local/utils/__init__.py
protenix/openfold_local/utils/all_atom_multimer.py
protenix/openfold_local/utils/checkpointing.py
protenix/openfold_local/utils/chunk_utils.py
protenix/openfold_local/utils/feats.py
protenix/openfold_local/utils/precision_utils.py
protenix/openfold_local/utils/rigid_utils.py
protenix/openfold_local/utils/tensor_utils.py
protenix/openfold_local/utils/geometry/__init__.py
protenix/openfold_local/utils/geometry/quat_rigid.py
protenix/openfold_local/utils/geometry/rigid_matrix_vector.py
protenix/openfold_local/utils/geometry/rotation_matrix.py
protenix/openfold_local/utils/geometry/test_utils.py
protenix/openfold_local/utils/geometry/utils.py
protenix/openfold_local/utils/geometry/vector.py
protenix/openfold_local/utils/kernel/__init__.py
protenix/openfold_local/utils/kernel/attention_core.py
protenix/utils/__init__.py
protenix/utils/cropping.py
protenix/utils/distributed.py
protenix/utils/file_io.py
protenix/utils/geometry.py
protenix/utils/logger.py
protenix/utils/lr_scheduler.py
protenix/utils/metrics.py
protenix/utils/scatter_utils.py
protenix/utils/seed.py
protenix/utils/torch_utils.py
protenix/utils/training.py
protenix/utils/permutation/__init__.py
protenix/utils/permutation/atom_permutation.py
protenix/utils/permutation/permutation.py
protenix/utils/permutation/utils.py
protenix/utils/permutation/chain_permutation/__init__.py
protenix/utils/permutation/chain_permutation/heuristic.py
protenix/utils/permutation/chain_permutation/pocket_based_permutation.py
protenix/utils/permutation/chain_permutation/utils.py
protenix/web_service/__init__.py
protenix/web_service/colab_request_parser.py
protenix/web_service/colab_request_utils.py
protenix/web_service/dependency_url.py
protenix/web_service/prediction_visualization.py
protenix/web_service/viewer.py
runner/__init__.py
runner/batch_inference.py
runner/dumper.py
runner/ema.py
runner/inference.py
runner/msa_search.py
runner/train.py