├── .github └── workflows │ └── codeql.yml ├── .gitignore ├── .gitmodules ├── .readthedocs.yaml ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── SECURITY.md ├── SUPPORT.md ├── distributional_graphormer ├── README.md ├── catalyst-adsorption │ ├── README.md │ ├── graphormer │ │ ├── __init__.py │ │ ├── criterions │ │ │ ├── __init__.py │ │ │ └── diffusion.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── algos.c │ │ │ ├── algos.pyx │ │ │ ├── collator.py │ │ │ ├── dataset.py │ │ │ ├── diff_datasets │ │ │ │ ├── diff_dataset.py │ │ │ │ └── oc_dataset.py │ │ │ └── wrapper.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ ├── graphormer_diff.py │ │ │ ├── graphormer_encoder.py │ │ │ └── oc_pbc.py │ │ ├── modules │ │ │ ├── __init__.py │ │ │ ├── droppath.py │ │ │ ├── graphormer_3d_layer.py │ │ │ ├── graphormer_graph_encoder.py │ │ │ ├── graphormer_graph_encoder_layer.py │ │ │ ├── graphormer_layers.py │ │ │ └── multihead_attention.py │ │ ├── optim │ │ │ ├── __init__.py │ │ │ └── layerwise_adam.py │ │ ├── pretrain │ │ │ └── __init__.py │ │ ├── tasks │ │ │ ├── __init__.py │ │ │ └── graph_diffusion.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ └── utils.py │ ├── install.sh │ ├── scripts │ │ ├── density.sh │ │ ├── sample.sh │ │ └── train.sh │ └── setup_cython.py ├── property-guided │ ├── README.md │ ├── graphormer │ │ ├── __init__.py │ │ ├── criterions │ │ │ ├── __init__.py │ │ │ └── diffusion.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── algos.c │ │ │ ├── algos.pyx │ │ │ ├── collator.py │ │ │ ├── dataset.py │ │ │ ├── diff_datasets │ │ │ │ ├── diff_dataset.py │ │ │ │ └── oc_dataset.py │ │ │ └── wrapper.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ ├── graphormer_diff.py │ │ │ ├── graphormer_encoder.py │ │ │ ├── m3gnet_utils.py │ │ │ ├── matbench_bandgap │ │ │ │ ├── checkpoint │ │ │ │ ├── m3gnet.data-00000-of-00001 │ │ │ │ ├── m3gnet.index │ │ │ │ └── m3gnet.json │ │ │ └── oc_pbc.py │ │ ├── modules │ │ │ ├── __init__.py │ │ │ ├── droppath.py │ │ │ ├── graphormer_3d_layer.py │ │ │ ├── graphormer_graph_encoder.py │ │ │ ├── graphormer_graph_encoder_layer.py │ │ │ ├── graphormer_layers.py │ │ │ └── multihead_attention.py │ │ ├── optim │ │ │ ├── __init__.py │ │ │ └── layerwise_adam.py │ │ ├── pretrain │ │ │ └── __init__.py │ │ ├── tasks │ │ │ ├── __init__.py │ │ │ └── graph_diffusion.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ └── utils.py │ ├── install.sh │ ├── scripts │ │ ├── sample.sh │ │ └── train.sh │ └── setup_cython.py ├── protein-ligand │ ├── README.md │ └── src │ │ ├── env.yml │ │ ├── evaluation │ │ ├── calc_rmsd.py │ │ ├── conform_rmsd.py │ │ ├── full_evaluation.sh │ │ ├── genlist.py │ │ └── single_datapoint_sampling.sh │ │ ├── examples │ │ └── diffusion │ │ │ └── train_cli.sh │ │ ├── graphormer │ │ ├── __init__.py │ │ ├── criterions │ │ │ ├── __init__.py │ │ │ └── diffusion.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── algos.pyx │ │ │ ├── collator.py │ │ │ ├── dataset.py │ │ │ ├── diff_datasets │ │ │ │ ├── diff_dataset.py │ │ │ │ └── md_dataset.py │ │ │ └── wrapper.py │ │ ├── models │ │ │ ├── __init__.py │ │ │ ├── diffusion │ │ │ │ ├── __init__.py │ │ │ │ ├── schedulers │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── ddpm.py │ │ │ │ │ └── legacy_scheduler.py │ │ │ │ └── utils │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── utils.py │ │ │ ├── graphormer_diff.py │ │ │ ├── graphormer_encoder.py │ │ │ └── model_utils.py │ │ ├── modules │ │ │ ├── __init__.py │ │ │ ├── graphormer_3d_layer.py │ │ │ ├── graphormer_graph_encoder.py │ │ │ ├── graphormer_graph_encoder_layer.py │ │ │ ├── graphormer_layers.py │ │ │ └── multihead_attention.py │ │ ├── optim │ │ │ ├── __init__.py │ │ │ └── layerwise_adam.py │ │ ├── tasks │ │ │ ├── __init__.py │ │ │ └── graph_diffusion.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ └── utils.py │ │ ├── install.sh │ │ ├── samplepdb │ │ ├── 16sys_md.csv │ │ └── cordinate2pdb.py │ │ └── setup_cython.py └── protein │ ├── .gitignore │ ├── .projectile │ ├── README.md │ ├── common │ ├── __init__.py │ ├── aa_vocab.py │ ├── config.py │ ├── logger.py │ └── util.py │ ├── data_provider │ ├── __init__.py │ ├── dataset.py │ ├── train_loader.py │ └── util.py │ ├── model │ ├── __init__.py │ ├── attention.py │ ├── base_model.py │ ├── geometry.py │ ├── main_model.py │ ├── pair_encoder.py │ ├── positional_encoding.py │ ├── so3.py │ └── structure_module.py │ ├── requirements.txt │ └── run_inference.py ├── docs ├── Datasets.rst ├── Installation-Guide.rst ├── Makefile ├── Overview.rst ├── Parameters.rst ├── Pretrained-Models.rst ├── Quick-Start.rst ├── Tutorisals.rst ├── conf.py ├── index.rst ├── logo-09.png ├── logo-10.png ├── make.bat └── requirements.txt ├── examples ├── customized_dataset │ └── customized_dataset.py ├── oc20 │ ├── README.md │ ├── oc20.sh │ └── ocp.gif └── property_prediction │ ├── README.md │ ├── hiv_pre.sh │ ├── pcqv1.sh │ ├── pcqv2.sh │ └── zinc.sh ├── graphormer ├── __init__.py ├── criterions │ ├── __init__.py │ ├── binary_logloss.py │ ├── l1_loss.py │ ├── mae_deltapos.py │ └── multiclass_cross_entropy.py ├── data │ ├── __init__.py │ ├── algos.pyx │ ├── collator.py │ ├── dataset.py │ ├── dgl_datasets │ │ ├── __init__.py │ │ ├── dgl_dataset.py │ │ └── dgl_dataset_lookup_table.py │ ├── ogb_datasets │ │ ├── __init__.py │ │ └── ogb_dataset_lookup_table.py │ ├── pyg_datasets │ │ ├── __init__.py │ │ ├── pyg_dataset.py │ │ └── pyg_dataset_lookup_table.py │ ├── smiles │ │ └── smiles_dataset.py │ └── wrapper.py ├── evaluate │ └── evaluate.py ├── models │ ├── __init__.py │ ├── graphormer.py │ └── graphormer_3d.py ├── modules │ ├── __init__.py │ ├── graphormer_graph_encoder.py │ ├── graphormer_graph_encoder_layer.py │ ├── graphormer_layers.py │ └── multihead_attention.py ├── pretrain │ └── __init__.py ├── tasks │ ├── __init__.py │ ├── graph_prediction.py │ └── is2re.py └── utils │ └── __init__.py └── install.sh /.github/workflows/codeql.yml: -------------------------------------------------------------------------------- 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