├── .DS_Store ├── DiffAffinity.py ├── README.md ├── SidechainDiff_test.sh ├── SidechainDiff_train.sh ├── VERSION ├── config ├── architecture │ ├── concat.yaml │ └── embed.yaml ├── base │ ├── default.yaml │ ├── normal.yaml │ └── uniform.yaml ├── beta_schedule │ ├── constant.yaml │ ├── linear.yaml │ ├── quadratic.yaml │ └── triangle.yaml ├── dataset │ ├── dirac.yaml │ ├── earthquake.yaml │ ├── fire.yaml │ ├── flood.yaml │ ├── langevin.yaml │ ├── mix_vmf.yaml │ ├── uniform.yaml │ ├── vmf.yaml │ ├── volcanoe.yaml │ ├── wrapnormmix.yaml │ └── wrapped.yaml ├── embedding │ ├── laplacian_eigenfunction.yaml │ └── none.yaml ├── experiment │ ├── earth_data.yaml │ ├── earthquake.yaml │ ├── fire.yaml │ ├── flood.yaml │ ├── hyperboloid.yaml │ ├── poincare.yaml │ ├── s2_toy.yaml │ ├── so3.yaml │ ├── tn.yaml │ └── volcanoe.yaml ├── flow │ ├── brownian.yaml │ ├── cnf.yaml │ ├── langevin.yaml │ └── vp.yaml ├── generator │ ├── ambient.yaml │ ├── canonical.yaml │ ├── div_free.yaml │ ├── eigen.yaml │ ├── lie_algebra.yaml │ ├── torus.yaml │ └── transport.yaml ├── logger │ ├── all.yaml │ ├── csv.yaml │ └── wandb.yaml ├── loss │ ├── dsm0.yaml │ ├── dsms.yaml │ ├── dsmv.yaml │ ├── ism.yaml │ ├── logp.yaml │ ├── moser.yaml │ └── ssm.yaml ├── main.yaml ├── manifold │ ├── hyperbolic.yaml │ ├── nsphere.yaml │ ├── s1.yaml │ ├── so3.yaml │ └── tn.yaml ├── model │ ├── cnf.yaml │ ├── exp_sgm.yaml │ ├── moser.yaml │ ├── rsgm.yaml │ ├── stereo_sgm.yaml │ └── tanhexp_sgm.yaml ├── optim │ └── adam.yaml ├── pushf │ ├── default.yaml │ ├── moser.yaml │ └── sde.yaml ├── scheduler │ ├── cosine.yaml │ ├── r3cosine.yaml │ ├── ramp.yaml │ ├── rcosine.yaml │ └── rloglinear.yaml ├── server │ ├── base.yaml │ ├── debug_ziz.yaml │ ├── local.yaml │ └── ziz.yaml └── transform │ ├── exp.yaml │ ├── id.yaml │ ├── stereo.yaml │ └── tanhexp.yaml ├── context_generator ├── configs │ ├── common │ │ ├── data_train_pdbredo_chain.yml │ │ └── data_val_pdbredo_chain.yml │ ├── inference │ │ ├── 6m0j.yml │ │ └── 7FAE_RBD_Fv_mutation.yml │ └── train │ │ ├── da_ddg_skempi.yml │ │ └── diff.yml ├── datasets │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-39.pyc │ │ ├── pdbredo_chain.cpython-39.pyc │ │ └── skempi.cpython-39.pyc │ ├── pdbredo_chain.py │ └── skempi.py ├── models │ ├── __pycache__ │ │ ├── da_ddg.cpython-39.pyc │ │ ├── da_encoder.cpython-39.pyc │ │ ├── da_encoder_nobias.cpython-39.pyc │ │ ├── rde_ddg.cpython-39.pyc │ │ ├── rde_encoder.cpython-39.pyc │ │ └── rde_encoder_nobias.cpython-39.pyc │ ├── da_ddg.py │ ├── da_encoder.py │ └── da_encoder_nobias.py ├── modules │ ├── common │ │ ├── __pycache__ │ │ │ ├── geometry.cpython-39.pyc │ │ │ └── layers.cpython-39.pyc │ │ ├── all_atom.py │ │ ├── geometry.py │ │ └── layers.py │ ├── encoders │ │ ├── __pycache__ │ │ │ ├── attn.cpython-39.pyc │ │ │ ├── pair.cpython-39.pyc │ │ │ └── single.cpython-39.pyc │ │ ├── attn.py │ │ ├── pair.py │ │ └── single.py │ └── model │ │ ├── __pycache__ │ │ └── r3.cpython-39.pyc │ │ └── r3.py └── utils │ ├── __pycache__ │ ├── data.cpython-39.pyc │ ├── misc.cpython-39.pyc │ ├── skempi.cpython-39.pyc │ └── train.cpython-39.pyc │ ├── data.py │ ├── misc.py │ ├── protein │ ├── __pycache__ │ │ ├── constants.cpython-39.pyc │ │ ├── icoord.cpython-39.pyc │ │ ├── parsers.cpython-39.pyc │ │ └── residue_constants.cpython-39.pyc │ ├── constants.py │ ├── icoord.py │ ├── parsers.py │ └── residue_constants.py │ ├── skempi.py │ ├── train.py │ └── transforms │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-39.pyc │ ├── _base.cpython-39.pyc │ ├── corrupt_chi.cpython-39.pyc │ ├── mask.cpython-39.pyc │ ├── noise.cpython-39.pyc │ ├── patch.cpython-39.pyc │ ├── select_atom.cpython-39.pyc │ └── select_chain.cpython-39.pyc │ ├── _base.py │ ├── corrupt_chi.py │ ├── mask.py │ ├── noise.py │ ├── patch.py │ ├── select_atom.py │ └── select_chain.py ├── data ├── .gitignore ├── 7FAE_RBD_Fv.pdb ├── DDG_6m0j.csv ├── get_pdbredo.sh ├── get_skempi_v2.sh ├── pdbredo_clusters.txt └── pdbredo_splits.txt ├── figures └── RDGM.png ├── gen_pdb.py ├── main.py ├── parse_atom14.ipynb ├── prediction.py ├── requirements.txt ├── riemannian_score_sde ├── datasets │ ├── __init__.py │ ├── earth.py │ ├── mixture.py │ └── simple.py ├── losses.py ├── models │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-39.pyc │ │ ├── distribution.cpython-39.pyc │ │ ├── embedding.cpython-39.pyc │ │ ├── transform.cpython-39.pyc │ │ └── vector_field.cpython-39.pyc │ ├── distribution.py │ ├── embedding.py │ ├── transform.py │ └── vector_field.py ├── sampling.py ├── sde.py └── utils │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-39.pyc │ ├── normalization.cpython-39.pyc │ └── vis.cpython-39.pyc │ ├── normalization.py │ └── vis.py ├── run.py ├── score_sde ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-39.pyc │ ├── losses.cpython-39.pyc │ ├── ode.cpython-39.pyc │ ├── sampling.cpython-39.pyc │ ├── schedule.cpython-39.pyc │ └── sde.cpython-39.pyc ├── datasets │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-39.pyc │ │ ├── mixture.cpython-39.pyc │ │ ├── split.cpython-39.pyc │ │ └── tensordataset.cpython-39.pyc │ ├── mixture.py │ ├── split.py │ └── tensordataset.py ├── likelihood.py ├── losses.py ├── models │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-39.pyc │ │ ├── architecture.cpython-39.pyc │ │ ├── flow.cpython-39.pyc │ │ ├── mlp.cpython-39.pyc │ │ ├── model.cpython-39.pyc │ │ └── transform.cpython-39.pyc │ ├── architecture.py │ ├── distribution.py │ ├── flow.py │ ├── layers │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-39.pyc │ │ │ └── layers.cpython-39.pyc │ │ └── layers.py │ ├── mlp.py │ ├── model.py │ ├── normalization.py │ └── transform.py ├── ode.py ├── optim.py ├── sampling.py ├── schedule.py ├── sde.py └── utils │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-39.pyc │ ├── cfg.cpython-39.pyc │ ├── data.cpython-39.pyc │ ├── jax.cpython-39.pyc │ ├── random.cpython-39.pyc │ ├── registry.cpython-39.pyc │ ├── schedule.cpython-39.pyc │ ├── training.cpython-39.pyc │ └── typing.cpython-39.pyc │ ├── cfg.py │ ├── data.py │ ├── jax.py │ ├── loggers_pl │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-39.pyc │ │ ├── base.cpython-39.pyc │ │ ├── csv_log.cpython-39.pyc │ │ ├── utilities.cpython-39.pyc │ │ └── wandb.cpython-39.pyc │ ├── base.py │ ├── csv_log.py │ ├── utilities.py │ └── wandb.py │ ├── random.py │ ├── registry.py │ ├── schedule.py │ ├── training.py │ └── typing.py ├── scripts ├── abdb │ └── download_data.py ├── approximate_forward.py ├── basalisk_calc_angles.py ├── blender │ ├── mesh_utils.py │ └── render_utils.py ├── deploy │ ├── config.sh │ ├── make_venv.sh │ ├── setup_ssh_keys_on_zizgpus.sh │ ├── sync_keys.sh │ └── sync_venv.sh ├── diffusion_sphere │ ├── blender_diffusion_sphere_stills.py │ └── make_diffusion_sphere_plot_data.py ├── examples │ ├── 1D_example.py │ ├── 1D_example2.py │ ├── diffusion.ipynb │ ├── diffusion2.ipynb │ ├── earth_datasets.py │ ├── s2_example.py │ └── so3.ipynb ├── gaussian_pushforward │ └── make_gaussian_pushforward_data.py ├── gaussian_random_walk │ └── make_grw_data.py ├── gaussian_random_walk_step │ └── make_grw_step_data.py ├── horizontal_vs_vertical.py ├── hyperbolic │ └── make_hyperbolic_data.py ├── kent │ ├── agg_results.py │ ├── config.yaml │ ├── kent_model.py │ └── run_kent.py ├── make_fisher_data.py ├── plot_diffusion.py ├── pull_earth_results.py ├── pull_scaling_results.py ├── sabdab │ └── download_data.py ├── so3_results.py ├── test_abdb.py ├── test_heat_kernel.py ├── test_hyperbolic.py ├── test_hyperbolic2.py ├── test_sabdab.py └── utils.py ├── setup.py └── tests ├── test_divergence.py ├── test_haiku.py ├── test_likelihood.py ├── test_likelihood_transform.py ├── test_registry.py ├── test_transform.py └── test_vmf.py /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TianZhuAI4S/DiffAffinity/HEAD/.DS_Store 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