LICENSE
README.md
setup.py
configs/__init__.py
configs/configs_base.py
configs/configs_data.py
configs/configs_inference.py
configs/configs_model_type.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/constants.py
protenix/data/tokenizer.py
protenix/data/utils.py
protenix/data/constraint/__init__.py
protenix/data/constraint/constraint_featurizer.py
protenix/data/core/__init__.py
protenix/data/core/ccd.py
protenix/data/core/featurizer.py
protenix/data/core/filter.py
protenix/data/core/parser.py
protenix/data/core/substructure_perms.py
protenix/data/esm/__init__.py
protenix/data/esm/compute_esm.py
protenix/data/esm/esm_featurizer.py
protenix/data/inference/__init__.py
protenix/data/inference/infer_dataloader.py
protenix/data/inference/json_maker.py
protenix/data/inference/json_parser.py
protenix/data/inference/json_to_feature.py
protenix/data/msa/__init__.py
protenix/data/msa/msa_featurizer.py
protenix/data/msa/msa_utils.py
protenix/data/pipeline/__init__.py
protenix/data/pipeline/data_pipeline.py
protenix/data/pipeline/dataloader.py
protenix/data/pipeline/dataset.py
protenix/data/template/__init__.py
protenix/data/template/template_featurizer.py
protenix/data/template/template_parser.py
protenix/data/template/template_utils.py
protenix/data/tools/__init__.py
protenix/data/tools/common.py
protenix/data/tools/kalign.py
protenix/data/tools/search.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/model/tri_attention/__init__.py
protenix/model/tri_attention/autotune.py
protenix/model/tri_attention/autotune_helpers.py
protenix/model/tri_attention/backward.py
protenix/model/tri_attention/forward.py
protenix/model/tri_attention/op.py
protenix/model/triangular/__init__.py
protenix/model/triangular/layers.py
protenix/model/triangular/triangular.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/rna_msa_search.py
runner/template_search.py
runner/train.py
scripts/__init__.py
scripts/colabfold_msa.py
scripts/gen_ccd_cache.py
scripts/prepare_training_data.py
tests/__init__.py
tests/test_attention_pair_bias.py
tests/test_condition_transition.py
tests/test_diffusion_transformer.py
tests/test_esm_loading.py
tests/test_frame.py
tests/test_installation.py
tests/test_local_rearrange.py
tests/test_lr_schedule.py
tests/test_triton_compatibility.py
tests/test_utils.py
tests/test_weighted_rigid_align.py