├── LICENSE ├── README.md ├── create_fragment_library.py ├── database ├── AA_alphabet.pdb ├── backbone_frags │ ├── 3helix.pdb │ ├── 5helix.pdb │ └── 7helix.pdb ├── bb_dep_rotlibs │ ├── arg.bbdep.rotamers.lib │ ├── asn.bbdep.rotamers.lib │ ├── asp.bbdep.rotamers.lib │ ├── cys.bbdep.rotamers.lib │ ├── gln.bbdep.rotamers.lib │ ├── glu.bbdep.rotamers.lib │ ├── his.bbdep.rotamers.lib │ ├── ile.bbdep.rotamers.lib │ ├── leu.bbdep.rotamers.lib │ ├── lys.bbdep.rotamers.lib │ ├── met.bbdep.rotamers.lib │ ├── phe.bbdep.rotamers.lib │ ├── pro.bbdep.rotamers.lib │ ├── ser.bbdep.rotamers.lib │ ├── thr.bbdep.rotamers.lib │ ├── trp.bbdep.rotamers.lib │ ├── tyr.bbdep.rotamers.lib │ └── val.bbdep.rotamers.lib ├── channel_placeholder │ ├── 310_polygly.pdb │ ├── 310_small.pdb │ ├── doublehelix.pdb │ ├── helix_cone_long.pdb │ ├── helix_cone_short.pdb │ └── sheet.pdb └── potentials.py ├── examples ├── inputs │ ├── 5an7.pdb │ └── in.json ├── motif_library_generation.sh └── structure_generation.sh ├── scripts └── helper_scripts │ ├── extract_md_scores.py │ ├── md_analysis.py │ ├── md_starter.py │ └── predict_protein_ligand.py ├── structure_generation.py └── utils ├── clash_detection.py ├── coupled_moves.xml ├── default_md_20ns.mdp ├── fastrelax.xml ├── fr_constrained.xml ├── fragment_extraction.py ├── hbond_analysis.xml ├── identify_positions_for_rotamer_insertion.py ├── molfile_to_params.py └── rosetta_py ├── __init__.py ├── __pycache__ ├── __init__.cpython-310.pyc ├── __init__.cpython-311.pyc ├── __init__.cpython-312.pyc ├── __init__.cpython-38.pyc └── __init__.cpython-39.pyc ├── io ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-310.pyc │ ├── __init__.cpython-311.pyc │ ├── __init__.cpython-312.pyc │ ├── __init__.cpython-38.pyc │ ├── __init__.cpython-39.pyc │ ├── mdl_molfile.cpython-310.pyc │ ├── mdl_molfile.cpython-311.pyc │ ├── mdl_molfile.cpython-312.pyc │ ├── mdl_molfile.cpython-38.pyc │ └── mdl_molfile.cpython-39.pyc ├── mdl_molfile.py └── pdb.py └── utility ├── ForkManager.py 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