├── Geom3D ├── dataloaders │ ├── __init__.py │ ├── dataloaders_AtomTriple.py │ ├── dataloaders_AtomTuple.py │ └── dataloaders_LEP.py ├── datasets │ ├── PDBBind_utils.py │ ├── __init__.py │ ├── datasets_3D.py │ ├── datasets_3D_Masking.py │ ├── datasets_3D_Radius.py │ ├── datasets_LBA.py │ ├── datasets_LBARadius.py │ ├── datasets_LEP.py │ ├── datasets_LEPRadius.py │ ├── datasets_MD17.py │ ├── datasets_MD17Radius.py │ ├── datasets_Molecule3D.py │ ├── datasets_QM9.py │ └── datasets_utils.py └── models │ ├── __init__.py │ ├── painn.py │ ├── painn_utils.py │ ├── schnet.py │ └── utils.py ├── LICENSE ├── README.md ├── examples ├── NCSN.py ├── config.py ├── finetune_lba.py ├── finetune_lep.py ├── finetune_md17.py ├── finetune_qm9.py ├── generate_Molecule3D.py ├── pretrain_3DInfoGraph.py ├── pretrain_ChargePrediction.py ├── pretrain_DistancePrediction.py ├── pretrain_GeoSSL.py ├── pretrain_Supervised.py ├── pretrain_TorsionAnglePrediction.py ├── run_finetune_lba.sh ├── run_finetune_lep.sh ├── run_finetune_md17.sh ├── run_finetune_qm9.sh ├── run_generate_GEOM.sh ├── run_pretrain_3DInfoGraph.sh ├── run_pretrain_3DInfoMax.sh ├── run_pretrain_ChargePrediction.sh ├── run_pretrain_DistancePrediction.sh ├── run_pretrain_GeoSSL.sh ├── run_pretrain_GraphMVP.sh ├── run_pretrain_PositionPerturbation.sh ├── run_pretrain_Supervised.sh ├── run_pretrain_TorsionAnglePrediction.sh ├── splitters.py └── util.py ├── fig └── pipeline.png └── scripts ├── finetune ├── submit_finetune_lba_lep_painn.sh ├── submit_finetune_lba_lep_schnet.sh ├── submit_finetune_md17_painn.sh ├── submit_finetune_md17_schnet.sh ├── submit_finetune_qm9_painn.sh ├── submit_finetune_qm9_schnet.sh └── submit_utils.sh ├── pretrain_GeoSSL_DDM └── submit_pretrain_GeoSSL_DDM.sh └── pretrain_baselines ├── submit_pretrain_3DInfoGraph.sh ├── submit_pretrain_ChargePrediction.sh ├── submit_pretrain_DistancePrediction.sh ├── submit_pretrain_GeoSSL_EBM_NCE.sh ├── submit_pretrain_GeoSSL_InfoNCE.sh ├── submit_pretrain_GeoSSL_RR.sh ├── 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