├── 1_state_2_generation ├── .DS_Store ├── 1_loop_helix_loop_reshaping │ ├── .DS_Store │ ├── 1smg_cleaned.pdb │ ├── calculate_reshaped_helix_RMSD.py │ ├── insertion_points.json │ ├── screen_compatible_loop_helix_loop_units.py │ ├── screen_single_insertion_loop_helix_loop_units.py │ └── select_linkers.py ├── 2_single_state_design │ ├── .DS_Store │ ├── 1_mutate_metal_ligands.py │ ├── 2_run_design_info_file_generator.py │ ├── 3_single_state_design.py │ └── design_info_file_generator.py └── 3_rosetta_abinitio │ ├── .DS_Store │ ├── 1_run_ab_initio_frag_generator.py │ ├── 2_ab_initio_frag_dependencies.py │ ├── 3_ab_initio_frag_func_lib.py │ ├── 4_run_biased_frag_generator.py │ ├── 5_biased_frag_generator.py │ ├── 6_run_biased_ff.py │ ├── placeholder_seqs │ └── standard.wghts ├── 2_multi_state_design ├── .DS_Store ├── 1_ProteinMPNN_scripts │ ├── .DS_Store │ └── submit_weighted_biased_homomer.sh └── 2_ColabFold │ ├── .DS_Store │ ├── 1_make_pt_mut_fastas.py │ ├── 2_run_colabfold.py │ ├── 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