├── .gitignore ├── README.md ├── VFN-Diff ├── .gitignore ├── LICENSE ├── README.md ├── SE3-README.md ├── analysis │ ├── metrics.py │ ├── plotting.py │ └── utils.py ├── config │ ├── base.yaml │ ├── baseline.yaml │ ├── baseline_1gpu.yaml │ ├── baseline_1gpu_re.yaml │ ├── debug.yaml │ ├── icml_published.yaml │ ├── inference.yaml │ ├── pure_dsm.yaml │ └── vfn_full_4_4090.yaml ├── data │ ├── all_atom.py │ ├── chemical.py │ ├── errors.py │ ├── igso3.py │ ├── mmcif_parsing.py │ ├── parsers.py │ ├── pdb_data_loader.py │ ├── process_pdb_dataset.py │ ├── process_pdb_files.py │ ├── protein.py │ ├── r3_diffuser.py │ ├── residue_constants.py │ ├── se3_diffuser.py │ ├── so3_diffuser.py │ ├── so3_utils.py │ └── utils.py ├── experiments │ ├── inference_se3_diffusion.py │ ├── train_se3_diffusion.py │ └── utils.py ├── model │ ├── ipa_pytorch.py │ ├── layers.py │ ├── score_network.py │ └── vfn.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 ├── se3.yml ├── setup.py └── weian_script │ ├── baseline_1gpu.sh │ ├── baseline_1gpu_re.sh │ ├── icml_published.sh │ ├── process_data.sh │ └── vfn_full_4_gpu.sh ├── VFN-IF ├── .gitignore ├── Uni-Core │ ├── .gitignore │ ├── LICENSE │ ├── README.md │ ├── csrc │ │ ├── adam │ │ │ ├── adam_kernel.cu │ │ │ └── interface.cpp │ │ ├── layernorm │ │ │ ├── interface.cpp │ │ │ ├── interface_gamma_beta.cpp │ │ │ ├── layernorm.cu │ │ │ └── layernorm_backward.cu │ │ ├── multi_tensor │ │ │ ├── interface.cpp │ │ │ ├── multi_tensor_apply.cuh │ │ │ └── multi_tensor_l2norm_kernel.cu │ │ ├── rounding │ │ │ ├── fp32_to_bf16.cu │ │ │ └── interface.cpp │ │ ├── softmax_dropout │ │ │ ├── interface.cpp │ │ │ ├── softmax_dropout_kernel.cu │ │ │ └── softmax_fast.h │ │ ├── type_shim.h │ │ └── util.h │ ├── docker │ │ ├── cu116 │ │ │ └── Dockerfile │ │ └── rdma │ │ │ └── Dockerfile │ ├── examples │ │ └── bert │ │ │ ├── __init__.py │ │ │ ├── example_data │ │ │ ├── README.md │ │ │ ├── dict.txt │ │ │ └── preprocess.py │ │ │ ├── model.py │ │ │ ├── task.py │ │ │ └── train_bert_test.sh │ ├── requirements.txt │ ├── setup.py │ ├── tests │ │ └── test_softmax.py │ ├── unicore │ │ ├── __init__.py │ │ ├── checkpoint_utils.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── append_token_dataset.py │ │ │ ├── base_wrapper_dataset.py │ │ │ ├── bert_tokenize_dataset.py │ │ │ ├── data_utils.py │ │ │ ├── dictionary.py │ │ │ ├── from_numpy_dataset.py │ │ │ ├── iterators.py │ │ │ ├── lmdb_dataset.py │ │ │ ├── lru_cache_dataset.py │ │ │ ├── mask_tokens_dataset.py │ │ │ ├── nested_dictionary_dataset.py │ │ │ ├── num_samples_dataset.py │ │ │ ├── numel_dataset.py │ │ │ ├── pad_dataset.py │ │ │ ├── prepend_token_dataset.py │ │ │ ├── raw_dataset.py │ │ │ ├── sort_dataset.py │ │ │ ├── tokenize_dataset.py │ │ │ └── unicore_dataset.py │ │ ├── distributed │ │ │ ├── __init__.py │ │ │ ├── legacy_distributed_data_parallel.py │ │ │ ├── module_proxy_wrapper.py │ │ │ └── utils.py │ │ ├── logging │ │ │ ├── __init__.py │ │ │ ├── meters.py │ │ │ ├── metrics.py │ │ │ └── progress_bar.py │ │ ├── losses │ │ │ ├── __init__.py │ │ │ ├── cross_entropy.py │ │ │ ├── masked_lm.py │ │ │ └── unicore_loss.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ ├── distributed_unicore_model.py │ │ │ └── unicore_model.py │ │ ├── modules │ │ │ ├── __init__.py │ │ │ ├── layer_norm.py │ │ │ ├── multihead_attention.py │ │ │ ├── softmax_dropout.py │ │ │ ├── transformer_decoder.py │ │ │ ├── transformer_decoder_layer.py │ │ │ ├── transformer_encoder.py │ │ │ └── transformer_encoder_layer.py │ │ ├── nan_detector.py │ │ ├── optim │ │ │ ├── __init__.py │ │ │ ├── adadelta.py │ │ │ ├── adagrad.py │ │ │ ├── adam.py │ │ │ ├── dynamic_loss_scaler.py │ │ │ ├── fp16_optimizer.py │ │ │ ├── fused_adam.py │ │ │ ├── lr_scheduler │ │ │ │ ├── __init__.py │ │ │ │ ├── cosine_lr_scheduler.py │ │ │ │ ├── exponential_decay_schedule.py │ │ │ │ ├── fixed_schedule.py │ │ │ │ ├── inverse_square_root_schedule.py │ │ │ │ ├── pass_through.py │ │ │ │ ├── polynomial_decay_schedule.py │ │ │ │ ├── reduce_lr_on_plateau.py │ │ │ │ ├── tri_stage_lr_scheduler.py │ │ │ │ ├── triangular_lr_scheduler.py │ │ │ │ └── unicore_lr_scheduler.py │ │ │ ├── sgd.py │ │ │ └── unicore_optimizer.py │ │ ├── options.py │ │ ├── registry.py │ │ ├── tasks │ │ │ ├── __init__.py │ │ │ └── unicore_task.py │ │ ├── trainer.py │ │ ├── utils.py │ │ ├── version.py │ │ └── version.txt │ └── unicore_cli │ │ ├── __init__.py │ │ └── train.py ├── api │ ├── __init__.py │ ├── config.py │ ├── data │ │ ├── __init__.py │ │ ├── data_ops.py │ │ ├── msa_pairing.py │ │ ├── process.py │ │ ├── process_multimer.py │ │ ├── protein.py │ │ ├── residue_constants.py │ │ ├── stereo_chemical_props.txt │ │ └── utils.py │ ├── dataset.py │ ├── loss.py │ ├── losses │ │ ├── __init__.py │ │ ├── auxillary.py │ │ ├── chain_align.py │ │ ├── eval.py │ │ ├── fape.py │ │ ├── geometry.py │ │ ├── inverse.py │ │ ├── utils.py │ │ └── violation.py │ ├── model.py │ ├── modules │ │ ├── VFN.py │ │ ├── alphafold.py │ │ ├── attentions.py │ │ ├── auxillary_heads.py │ │ ├── common.py │ │ ├── confidence.py │ │ ├── denoise.py │ │ ├── embedders.py │ │ ├── evoformer.py │ │ ├── featurization.py │ │ ├── frame.py │ │ ├── inverse_module_utils │ │ │ ├── __init__.py │ │ │ ├── pifold_featurizer.py │ │ │ └── pifold_utils.py │ │ ├── prodesign_module.py │ │ ├── refine_module.py │ │ ├── refine_module_utils │ │ │ ├── __init__.py │ │ │ └── af_refine.py │ │ ├── structure_module.py │ │ ├── template.py │ │ └── triangle_multiplication.py │ └── utils │ │ ├── __init__.py │ │ └── layer_norm.py ├── dataset │ └── json │ │ └── CATH4.2 │ │ ├── eval_multi_label.json │ │ ├── eval_sample_weight.json │ │ ├── sd_train_sample_weight.json │ │ ├── train_multi_label.json │ │ └── train_sample_weight.json ├── docker │ └── Dockerfile ├── extra.py ├── readme.md ├── train.py ├── train_script │ ├── layers │ │ ├── x2_vecdirect_noedge_atom_gbf_nofeat_10l.sh │ │ ├── x2_vecdirect_noedge_atom_gbf_nofeat_12l.sh │ │ ├── x2_vecdirect_noedge_atom_gbf_nofeat_15l.sh │ │ ├── x2_vecdirect_noedge_atom_gbf_nofeat_5l.sh │ │ └── x2_vecdirect_noedge_atom_gbf_nofeat_8l.sh │ └── vec │ │ ├── x2_16vec_v2.sh │ │ └── x2_64vec_v2.sh ├── unifold │ ├── __init__.py │ ├── config.py │ ├── data │ │ ├── __init__.py │ │ ├── data_ops.py │ │ ├── msa_pairing.py │ │ ├── process.py │ │ ├── process_multimer.py │ │ ├── protein.py │ │ ├── residue_constants.py │ │ ├── stereo_chemical_props.txt │ │ └── utils.py │ ├── dataset.py │ ├── loss.py │ ├── losses │ │ ├── __init__.py │ │ ├── auxillary.py │ │ ├── chain_align.py │ │ ├── eval.py │ │ ├── fape.py │ │ ├── geometry.py │ │ ├── inverse.py │ │ ├── utils.py │ │ └── violation.py │ ├── model.py │ ├── modules │ │ ├── VFN.py │ │ ├── __init__.py │ │ ├── alphafold.py │ │ ├── attentions.py │ │ ├── auxillary_heads.py │ │ ├── common.py │ │ ├── confidence.py │ │ ├── denoise.py │ │ ├── embedders.py │ │ ├── evoformer.py │ │ ├── featurization.py │ │ ├── frame.py │ │ ├── inverse_module.py │ │ ├── inverse_module_utils │ │ │ ├── __init__.py │ │ │ ├── af_inverse.py │ │ │ ├── gragh_init_inverse.py │ │ │ ├── pifold_featurizer.py │ │ │ └── pifold_utils.py │ │ ├── prodesign_module.py │ │ ├── refine_module.py │ │ ├── refine_module_utils │ │ │ ├── __init__.py │ │ │ └── af_refine.py │ │ ├── structure_module.py │ │ ├── template.py │ │ └── triangle_multiplication.py │ ├── optim │ │ ├── __init__.py │ │ └── onecyclelr.py │ └── task.py └── zenodo.sh └── graph └── logo.png /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aim-uofa/VFN/HEAD/.gitignore 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