├── .github └── workflows │ └── codeql.yml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── SECURITY.md ├── SUPPORT.md ├── __init__.py ├── configs ├── equivariant_nvp.yaml ├── gaussian_baseline.yaml ├── gaussian_density_transformer.yaml ├── kernel_cheb_transformer_nvp.yaml ├── kernel_transformer_nvp.yaml ├── local_transformer_nvp.yaml ├── transformer_cvae.yaml ├── transformer_nvp.yaml └── transformer_nvp_posenc.yaml ├── dataloader.py ├── datasets ├── __init__.py ├── iterable_datasets.py ├── lmdb_dataset.py └── pdb_sampler.py ├── equivariance ├── __init__.py ├── equivariance_transforms.py └── equivariance_utils.py ├── evaluate.py ├── evaluate_o2.py ├── exploration.py ├── loss_configs.py ├── losses.py ├── model_configs.py ├── model_constructor.py ├── modules ├── __init__.py ├── baselines.py ├── custom_transformer_nvp.py ├── dense_equivariant_nvp.py ├── layers │ ├── __init__.py │ ├── custom_attention_encoder.py │ ├── custom_self_attention.py │ ├── custom_transformer_block.py │ ├── dense_equivariant_coupling_layer.py │ ├── equivariant_features_basis.py │ ├── feature_processor.py │ ├── kernel_attention.py │ ├── kernel_self_attention.py │ ├── local_self_attention.py │ ├── mlp.py │ ├── nvp.py │ ├── rff_position_encoder.py │ └── transformer_block.py ├── model_wrappers │ ├── __init__.py │ ├── base.py │ ├── conditional_vae.py │ ├── density_model_base.py │ ├── flow.py │ ├── gaussian_density.py │ └── point_estimate.py ├── transformer_gaussian_density.py └── transformer_nvp.py ├── notebooks ├── Paper │ ├── conditional-plots.ipynb │ ├── speed-up-exploration.ipynb │ ├── speed-up-mcmc.ipynb │ ├── tica-2AA-plots.ipynb │ └── tica-4AA-plots.ipynb └── analysis │ ├── 4AA-evaluations-conditional.ipynb │ ├── 4AA-sample-trajectory-evaluation.ipynb │ └── Torsion analysis Ala2.ipynb ├── preprocess_lmdb.py ├── profile.py ├── sample.py ├── sample_trajectory.py ├── setenv.sh ├── simulation ├── README.md ├── __init__.py ├── amulet_configs │ ├── sim-2AA-large.yaml │ ├── sim-4AA-huge.yaml │ ├── sim-4AA-large.yaml │ └── sim-t1b-huge.yaml ├── checknpz.py ├── checkpointing.py ├── create_linear_protein.py ├── create_random_peptides.py ├── create_trajectory_from_npz.py ├── md.py ├── npzreporter.py ├── pdbfix.py ├── pymol_make_movie.py ├── sample_openmm.py ├── simulate_trajectory.py ├── testdata │ ├── alanine-dipeptide.pdb │ ├── implicit-2olx-traj-arrays.npz │ ├── implicit-2olx-traj-cpu-arrays.npz │ ├── implicit-2olx-traj-cpu-state0.pdb │ ├── implicit-2olx-traj-state0.pdb │ ├── implicit-2olx-traj.pdb │ └── implicit-2olx.pdb └── tests │ ├── __init__.py │ ├── test_checknpz.py │ ├── test_md.py │ └── test_npzreporter.py ├── testdata ├── 1rcx.pdb ├── 5hr5.pdb ├── 6wle.pdb ├── 6zg3.pdb ├── 7alr.pdb ├── 7d0k.pdb ├── 7k9b.pdb ├── AF-O97980-F1-model_v1-traj-state0.pdb ├── AF-P0C6P0-F1-model_v1-traj-state0.pdb ├── benzene.xyz ├── output │ ├── 1hgv-traj-arrays.npz │ ├── 1hgv-traj-state0.pdb │ ├── 1hgv-traj.pdb │ ├── 2olx-traj-arrays.npz │ ├── 2olx-traj-state0.pdb │ └── 2olx-traj.pdb ├── smallest_molecule │ ├── 2olx-traj-arrays.npz │ └── 2olx-traj-state0.pdb ├── smallest_molecule_equivariant │ ├── 2olx-traj-arrays.npz │ └── 2olx-traj-state0.pdb └── waterbox-2olx-small.pdb ├── tests ├── __init__.py ├── assets.py ├── conftest.py ├── test_batching.py ├── test_chirality.py ├── test_config_utils.py ├── test_dataloaders.py ├── test_dataset_utils.py ├── test_distributional_equivariance.py ├── test_evaluation_utils.py ├── test_kernel_attention.py ├── test_lmdb_distributed_sampler.py ├── test_lmdb_trajectory_dataset.py ├── test_local_attention.py ├── test_losses.py ├── test_openmm_bridge.py ├── test_rff.py ├── test_se3_transforms.py ├── test_torsion_utils.py ├── test_training_utils.py ├── test_transformer_cvae.py └── utils.py ├── timewarp-environment.yml ├── train.py ├── train_deepspeed.py ├── training_config.py ├── utilities ├── __init__.py ├── benchmarks │ ├── __init__.py │ └── blobstorage-benchmark.py ├── cache.py ├── common.py ├── config_utils.py ├── createdby.py ├── deepspeed_utils.py ├── delayed_reporter.py ├── distributed_iterable_dataset.py ├── downloadable_dataset.py ├── experiment_summary.py ├── fixtures.py ├── hash.py ├── lazy_unpickler.py ├── lmdb_utils.py ├── logger.py ├── logging.py ├── mock_amlt_utils.py ├── model_utils.py ├── moments.py ├── mongo_utils.py ├── pytest_utils.py ├── random.py ├── rest_utils.py ├── run_metadata_utils.py ├── self_caches.py ├── tables │ ├── README.md │ ├── __init__.py │ ├── base.py │ ├── mongo.py │ └── pandas.py └── training_utils.py ├── utils ├── __init__.py ├── chirality.py ├── config_utils.py ├── dataset_utils.py ├── deepspeed_lr_scheduler.py ├── energy_utils.py ├── evaluation_utils.py ├── evaluation_utils_o2.py ├── graph_utils.py ├── loss_utils.py ├── molecule_utils.py ├── openmm │ ├── __init__.py │ ├── openmm_bridge.py │ └── openmm_provider.py ├── sampling_utils.py ├── tica_utils.py ├── torsion_utils.py └── training_utils.py └── visualise ├── README.md ├── 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