├── .gitignore ├── .gitmodules ├── README.md ├── conditional ├── __init__.py ├── bpf.py ├── components │ ├── __init__.py │ ├── observation_generator.py │ └── particle_filter.py ├── fpssmc.py ├── mcgdiff.py ├── smcdiff.py ├── tds.py └── wrapper.py ├── config ├── config.yaml ├── experiment │ ├── conditional_method │ │ ├── bpf.yaml │ │ ├── fpssmc.yaml │ │ ├── mcgdiff.yaml │ │ ├── replacement.yaml │ │ ├── smcdiff.yaml │ │ ├── tds-distance.yaml │ │ ├── tds-frame-distance.yaml │ │ ├── tds-mask.yaml │ │ └── tds.yaml │ ├── debug_gpu_stats.yaml │ ├── evaluate_samples.yaml │ ├── motif │ │ ├── 1BCF.yaml │ │ ├── 1PRW.yaml │ │ ├── 1QJG.yaml │ │ ├── 1YCR.yaml │ │ ├── 2KL8.yaml │ │ ├── 3IXT.yaml │ │ ├── 4JHW.yaml │ │ ├── 5IUS.yaml │ │ ├── 5TPN.yaml │ │ ├── 5TRV_long.yaml │ │ ├── 5TRV_med.yaml │ │ ├── 5TRV_short.yaml │ │ ├── 5WN9.yaml │ │ ├── 5YUI.yaml │ │ ├── 6E6R_long.yaml │ │ ├── 6E6R_med.yaml │ │ ├── 6E6R_short.yaml │ │ ├── 6EXZ_long.yaml │ │ ├── 6EXZ_med.yaml │ │ ├── 6EXZ_short.yaml │ │ ├── 6X93.yaml │ │ ├── 7MRX_128.yaml │ │ ├── 7MRX_60.yaml │ │ ├── 7MRX_85.yaml │ │ ├── il7ra_gc.yaml │ │ └── rsv_site4.yaml │ ├── multi_motif │ │ ├── 1PRW_four.yaml │ │ ├── 1PRW_two.yaml │ │ ├── 2B5I.yaml │ │ ├── 3BIK+3BP5.yaml │ │ ├── 3NTN.yaml │ │ └── 4JHW+5WN9.yaml │ ├── none.yaml │ ├── sample_given_motif.yaml │ ├── sample_given_motif_and_symmetry.yaml │ ├── sample_given_multiple_motifs.yaml │ ├── sample_given_symmetry.yaml │ ├── sample_unconditional.yaml │ └── symmetric_motif │ │ └── 7UHB.yaml └── model │ ├── genie-scope-128.yaml │ └── genie-scope-256.yaml ├── data ├── README.md ├── motif_problems │ ├── 1BCF.pdb │ ├── 1PRW.pdb │ ├── 1QJG.pdb │ ├── 1Y6K.pdb │ ├── 1YCR.pdb │ ├── 2KL8.pdb │ ├── 2W0Z.pdb │ ├── 3IXT.pdb │ ├── 3O41.pdb │ ├── 4JHW.pdb │ ├── 4ZYP.pdb │ ├── 5IUS.pdb │ ├── 5TPN.pdb │ ├── 5TRV.pdb │ ├── 5WN9.pdb │ ├── 5YUI.pdb │ ├── 6E6R.pdb │ ├── 6EXZ.pdb │ ├── 6J6J.pdb │ ├── 6VW1.pdb │ ├── 6X93.pdb │ ├── 7MRX.pdb │ ├── 7N3T.pdb │ ├── 7N3T_double.pdb │ ├── benchmark.csv │ └── il7ra_gc.pdb ├── multi_motif_problems │ ├── 1PRW.pdb │ ├── 2B5I.pdb │ ├── 3BIK.pdb │ ├── 3BP5.pdb │ ├── 3NTN.pdb │ ├── 4JHW.pdb │ ├── 5WN9.pdb │ └── benchmark.csv └── symmetric_motif_problems │ └── 7UHB.pdb ├── experiments ├── __init__.py └── experiments.py ├── main.py ├── model ├── __init__.py ├── diffusion.py └── genie.py ├── outputs └── README.md ├── protein ├── alignment.py └── frames.py ├── requirements.txt ├── scripts └── generate_motif_configs.py └── utils ├── path.py ├── pdb.py ├── registry.py ├── resampling.py └── symmetry.py /.gitignore: -------------------------------------------------------------------------------- 1 | submodules/* 2 | **/**/__pycache__ 3 | -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/matsagad/mres-project/HEAD/.gitmodules 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