├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── ckpt ├── .gitignore └── get_odesign_ckpt.sh ├── configs ├── data │ ├── _base.yaml │ ├── recentPDB_1536_sample384_0925.yaml │ └── weightedPDB_before2109_wopb_nometalc_0925.yaml ├── exp │ ├── _base.yaml │ ├── train_odesign_base_ligand_rigid.yaml │ ├── train_odesign_base_na_rigid.yaml │ ├── train_odesign_base_prot_flex.yaml │ └── train_odesign_base_prot_rigid.yaml ├── hydra │ └── default.yaml ├── inference.yaml ├── loss │ └── _base.yaml ├── lr_scheduler │ └── af3.yaml ├── model │ ├── _base.yaml │ └── odesign_base_default.yaml ├── optimizer │ └── adam.yaml └── train.yaml ├── data └── .gitignore ├── examples ├── ligand_design │ └── prot_binding_lig │ │ ├── 7v11_OQO_pocket.pdb │ │ └── odesign_input.json ├── na_design │ ├── prot_binding_rna │ │ ├── 8gxb-assembly1.cif │ │ └── odesign_input.json │ └── rna_bb │ │ └── odesign_input.json └── protein_design │ ├── atom_scaffold │ ├── M0129_1os7.pdb │ └── odesign_input.json │ ├── lig_binding_prot │ ├── 7bkc_FAD.cif │ └── odesign_input.json │ ├── motif_scaffold │ ├── 30_7UWL.pdb │ └── odesign_input.json │ └── prot_binding_prot │ ├── IL7Ra_complex.pdb │ └── odesign_input.json ├── imgs ├── odesign_design_mode.jpg ├── odesign_logo.svg ├── odesign_video.gif └── odesign_wechat_qr_code.jpg ├── inference_demo.sh ├── license_file_list.md ├── odesign.def ├── requirements.txt ├── scripts ├── inference.py └── train.py ├── src ├── api │ ├── _base.py │ ├── data_interface.py │ └── model_interface.py ├── data │ ├── dataloader.py │ └── dataset.py ├── model │ ├── modules │ │ ├── diffusion.py │ │ ├── embedders.py │ │ ├── feature_dims.py │ │ ├── frames.py │ │ ├── generator.py │ │ ├── head.py │ │ ├── invfold │ │ │ ├── .gitignore │ │ │ ├── __init__.py │ │ │ ├── environment.yml │ │ │ ├── evaluation_tools │ │ │ │ ├── ODesign.yaml │ │ │ │ ├── __init__.py │ │ │ │ ├── design_interface.py │ │ │ │ ├── inference_utils.py │ │ │ │ ├── tools.py │ │ │ │ └── utils │ │ │ │ │ ├── TMscore │ │ │ │ │ ├── TMscore.cpp │ │ │ │ │ ├── USalign │ │ │ │ │ ├── USalign_readme.txt │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── config_utils.py │ │ │ │ │ └── main_utils.py │ │ │ ├── requirements.txt │ │ │ └── src │ │ │ │ ├── __init__.py │ │ │ │ ├── datasets │ │ │ │ ├── __init__.py │ │ │ │ ├── featurizer.py │ │ │ │ └── featurizer_ligand.py │ │ │ │ ├── models │ │ │ │ ├── __init__.py │ │ │ │ ├── configs │ │ │ │ │ └── ODesign.yaml │ │ │ │ ├── odesign_ligand.py │ │ │ │ └── odesign_model.py │ │ │ │ ├── modules │ │ │ │ ├── __init__.py │ │ │ │ └── if_module.py │ │ │ │ └── tools │ │ │ │ ├── __init__.py │ │ │ │ ├── affine_utils.py │ │ │ │ ├── evaluation_tools.py │ │ │ │ └── logger.py │ │ ├── loss.py │ │ ├── pairformer.py │ │ ├── primitives.py │ │ ├── schedulers.py │ │ └── transformer.py │ └── odesign.py └── utils │ ├── data │ ├── ccd.py │ ├── constants.py │ ├── constraint_featurizer.py │ ├── cropping.py │ ├── data_pipeline.py │ ├── featurizer.py │ ├── file_io.py │ ├── filter.py │ ├── geometry.py │ ├── mask_generator.py │ ├── misc.py │ ├── msa_featurizer.py │ ├── msa_utils.py │ ├── parser.py │ ├── substructure_perms.py │ └── tokenizer.py │ ├── inference │ ├── dumper.py │ ├── infer_runner.py │ └── inference_utils.py │ ├── license_register.py │ ├── misc.py │ ├── model │ ├── misc.py │ ├── rmsd.py │ ├── scatter_utils.py │ └── torch_utils.py │ ├── openfold_local │ ├── README.md │ ├── __init__.py │ ├── data │ │ ├── __init__.py │ │ ├── data_transforms.py │ │ ├── errors.py │ │ ├── mmcif_parsing.py │ │ ├── msa_identifiers.py │ │ ├── msa_pairing.py │ │ ├── parsers.py │ │ ├── templates.py │ │ └── tools │ │ │ ├── __init__.py │ │ │ ├── jackhmmer.py │ │ │ └── utils.py │ ├── model │ │ ├── __init__.py │ │ ├── dropout.py │ │ ├── outer_product_mean.py │ │ ├── primitives.py │ │ ├── triangular_attention.py │ │ └── triangular_multiplicative_update.py │ ├── np │ │ ├── __init__.py │ │ └── residue_constants.py │ └── utils │ │ ├── __init__.py │ │ ├── all_atom_multimer.py │ │ ├── checkpointing.py │ │ ├── chunk_utils.py │ │ ├── feats.py │ │ ├── geometry │ │ ├── __init__.py │ │ ├── quat_rigid.py │ │ ├── rigid_matrix_vector.py │ │ ├── rotation_matrix.py │ │ ├── test_utils.py │ │ ├── utils.py │ │ └── vector.py │ │ ├── kernel │ │ ├── __init__.py │ │ ├── attention_core.py │ │ └── csrc │ │ │ ├── compat.h │ │ │ ├── softmax_cuda.cpp │ │ │ ├── softmax_cuda_kernel.cu │ │ │ └── softmax_cuda_stub.cpp │ │ ├── precision_utils.py │ │ ├── rigid_utils.py │ │ └── tensor_utils.py │ ├── permutation │ ├── atom_permutation.py │ ├── chain_permutation │ │ ├── __init__.py │ │ ├── heuristic.py │ │ ├── pocket_based_permutation.py │ │ └── utils.py │ ├── permutation.py │ └── utils.py │ └── train │ ├── distributed.py │ ├── lr_scheduler.py │ ├── metrics.py │ ├── optimizer.py │ └── train_runner.py └── train_demo.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/The-Institute-for-AI-Molecular-Design/ODesign/HEAD/.gitignore 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