├── .gitignore ├── CODE_OF_CONDUCT.md ├── LICENSE ├── NOTICE.md ├── README.md ├── SECURITY.md ├── SUPPORT.md ├── ado.yml ├── analysis ├── metrics.py └── utils.py ├── azure-pipelines.yml ├── cgmanifest.json ├── configs ├── _inference.yaml ├── base.yaml ├── datasets.yaml ├── inference_scaffolding.yaml ├── inference_scaffolding_guidance.yaml ├── inference_unconditional.yaml └── model.yaml ├── data ├── all_atom.py ├── datasets.py ├── errors.py ├── interpolant.py ├── parsers.py ├── pdb_dataloader.py ├── process_pdb_files.py ├── protein.py ├── protein_dataloader.py ├── residue_constants.py ├── so3_utils.py └── utils.py ├── experiments ├── inference_se3_flows.py ├── train_se3_flows.py └── utils.py ├── fm.yml ├── media ├── scaffolding.gif └── unconditional.gif ├── metadata ├── pdb.clusters ├── pdb_metadata.csv └── scope_metadata.csv ├── models ├── edge_feature_net.py ├── flow_model.py ├── flow_module.py ├── ipa_pytorch.py ├── node_feature_net.py └── utils.py ├── motif_scaffolding ├── benchmark.csv ├── save_motif_segments.py ├── targets │ ├── 1BCF_motif_segments.pkl │ ├── 1PRW_motif_segments.pkl │ ├── 1QJG_motif_segments.pkl │ ├── 1YCR_motif_segments.pkl │ ├── 2KL8_motif_segments.pkl │ ├── 3IXT_motif_segments.pkl │ ├── 4JHW_motif_segments.pkl │ ├── 5IUS_motif_segments.pkl │ ├── 5TPN_motif_segments.pkl │ ├── 5TRV_long_motif_segments.pkl │ ├── 5TRV_med_motif_segments.pkl │ ├── 5TRV_short_motif_segments.pkl │ ├── 5WN9_motif_segments.pkl │ ├── 5YUI_motif_segments.pkl │ ├── 6E6R_long_motif_segments.pkl │ ├── 6E6R_med_motif_segments.pkl │ ├── 6E6R_short_motif_segments.pkl │ ├── 6EXZ_long_motif_segments.pkl │ ├── 6EXZ_med_motif_segments.pkl │ ├── 6EXZ_short_motif_segments.pkl │ ├── 6X93_motif_segments.pkl │ ├── 7MRX_128_motif_segments.pkl │ ├── 7MRX_60_motif_segments.pkl │ ├── 7MRX_85_motif_segments.pkl │ ├── il7ra_gc_motif_segments.pkl │ └── rsv_site4_motif_segments.pkl ├── twisting.py ├── twisting_tds.py └── utils.py ├── openfold ├── config.py ├── data │ ├── __init__.py │ ├── data_modules.py │ ├── data_pipeline.py │ ├── data_transforms.py │ ├── errors.py │ ├── feature_pipeline.py │ ├── input_pipeline.py │ ├── mmcif_parsing.py │ ├── parsers.py │ ├── templates.py │ └── tools │ │ ├── __init__.py │ │ ├── hhblits.py │ │ ├── hhsearch.py │ │ ├── jackhmmer.py │ │ ├── kalign.py │ │ └── utils.py ├── model │ ├── __init__.py │ ├── dropout.py │ ├── embedders.py │ ├── evoformer.py │ ├── heads.py │ ├── model.py │ ├── msa.py │ ├── outer_product_mean.py │ ├── pair_transition.py │ ├── primitives.py │ ├── structure_module.py │ ├── template.py │ ├── torchscript.py │ ├── triangular_attention.py │ └── triangular_multiplicative_update.py ├── np │ ├── __init__.py │ ├── protein.py │ ├── relax │ │ ├── __init__.py │ │ ├── amber_minimize.py │ │ ├── cleanup.py │ │ ├── relax.py │ │ └── utils.py │ └── residue_constants.py ├── resources │ ├── __init__.py │ └── stereo_chemical_props.txt └── utils │ ├── argparse.py │ ├── callbacks.py │ ├── checkpointing.py │ ├── exponential_moving_average.py │ ├── feats.py │ ├── import_weights.py │ ├── logger.py │ ├── loss.py │ ├── lr_schedulers.py │ ├── precision_utils.py │ ├── rigid_utils.py │ ├── seed.py │ ├── superimposition.py │ ├── suppress_output.py │ ├── tensor_utils.py │ └── validation_metrics.py └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microsoft/protein-frame-flow/HEAD/.gitignore -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microsoft/protein-frame-flow/HEAD/CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microsoft/protein-frame-flow/HEAD/LICENSE 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