├── .gitignore ├── LICENSE ├── README.md ├── code ├── add_chain_id.py ├── analysis.py ├── condor.py ├── database.py ├── energize.py ├── gb1_docking.py ├── prepare.py ├── process_run.py ├── query_pdb.py ├── rosetta_minimal.py ├── templates.py ├── utils.py └── variants.py ├── docking_args └── gb1_1fcc_condor_set_1.txt ├── energize_args ├── README.md ├── condor_set_1.txt ├── condor_set_2.txt └── example.txt ├── htcondor ├── package_env.sh ├── run_defs │ ├── README.md │ └── gb1_example_run.txt └── templates │ ├── energize.sub │ ├── osdf_python_distribution.txt │ ├── osdf_rosetta_distribution.txt │ ├── pass.txt │ ├── prepare.sub │ ├── run.sh │ └── run_prepare.sh ├── notebooks ├── osg │ ├── README.md │ ├── bash_scripts │ │ ├── generate_variants.sh │ │ ├── rosetta_download.sh │ │ ├── run_condor.sh │ │ ├── run_post_process.sh │ │ ├── run_prepare.sh │ │ └── run_variants.sh │ ├── condor │ │ ├── practice │ │ │ ├── helloworld.sh │ │ │ ├── output │ │ │ │ └── condor_logs │ │ │ │ │ └── .gitignore │ │ │ └── submit.sub │ │ └── rosetta │ │ │ ├── encrypt.sh │ │ │ ├── output │ │ │ └── condor_logs │ │ │ │ └── .gitignore │ │ │ ├── rosetta_download.sub │ │ │ ├── rosetta_minimal.py │ │ │ ├── run.sh │ │ │ └── utils.py │ ├── osg.ipynb │ ├── templates │ │ └── energize_run_template.txt │ └── utils.py └── parse_KosciolekAndJones.ipynb ├── pdb_files ├── KosciolekAndJones │ ├── README.md │ ├── fetch_pdbs.sh │ ├── loop_modeling │ │ ├── data │ │ │ ├── README.md │ │ │ ├── merge_logs.txt │ │ │ ├── remodel_checks.csv │ │ │ └── remodel_logs.txt │ │ ├── scripts │ │ │ ├── check_remodeled_structure.py │ │ │ ├── merge_structure_files.py │ │ │ ├── merge_structure_files_1rw7.py │ │ │ └── remodel_blueprint.py │ │ └── stragglers │ │ │ ├── README.md │ │ │ ├── list_stragglers.sh │ │ │ ├── remodel_checks.csv │ │ │ └── straggers_list.txt │ ├── pdb_list.txt │ ├── pone.0092197.s002.doc │ ├── prepare.sh │ ├── ready_set_1.txt │ ├── ready_set_2.txt │ ├── ready_set_3.txt │ └── ready_set_4.txt ├── README.md ├── prepared_pdb_files │ ├── 1FCC_dms.pdb │ ├── 1FCC_rosetta_best.pdb │ ├── 1a3a_remod_p.pdb │ ├── 1a6m_A_p.pdb │ ├── 1a70_A_p.pdb │ ├── 1aap_remod_p.pdb │ ├── 1aba_A_p.pdb │ ├── 1ag6_A_p.pdb │ ├── 1aoe_A_p.pdb │ ├── 1atl_remod_p.pdb │ ├── 1atz_remod_p.pdb │ ├── 1avs_remod_p.pdb │ ├── 1bdo_A_p.pdb │ ├── 1beb_remod_p.pdb │ ├── 1beh_remod_p.pdb │ ├── 1bkr_remod_p.pdb │ ├── 1brf_A_p.pdb │ ├── 1bsg_p.pdb │ ├── 1c44_A_p.pdb │ ├── 1c52_A_p.pdb │ ├── 1c52_remod_p.pdb │ ├── 1c9o_A_p.pdb │ ├── 1cc8_remod_p.pdb │ ├── 1chd_remod_p.pdb │ ├── 1cjw_A_p.pdb │ ├── 1cke_remod_p.pdb │ ├── 1ctf_remod_p.pdb │ ├── 1cxy_remod_p.pdb │ ├── 1czn_A_p.pdb │ ├── 1d0q_remod_p.pdb │ ├── 1d1q_remod_p.pdb │ ├── 1d4o_remod_p.pdb │ ├── 1dbx_remod_p.pdb │ ├── 1dix_p.pdb │ ├── 1dlw_A_p.pdb │ ├── 1dmg_remod_p.pdb │ ├── 1dqg_remod_p.pdb │ ├── 1dsx_A_p.pdb │ ├── 1eaz_remod_p.pdb │ ├── 1ej0_A_p.pdb │ ├── 1ej8_A_p.pdb │ ├── 1ek0_p.pdb │ ├── 1f6b_remod_p.pdb │ ├── 1fcy_A_p.pdb │ ├── 1fk5_A_p.pdb │ ├── 1fl0_remod_p.pdb │ ├── 1fna_A_p.pdb │ ├── 1fqt_remod_p.pdb │ ├── 1fvg_remod_p.pdb │ ├── 1fvk_remod_p.pdb │ ├── 1fx2_A_p.pdb │ ├── 1fx2_remod_p.pdb │ ├── 1g2r_remod_p.pdb │ ├── 1g9o_A_p.pdb │ ├── 1gbs_A_p.pdb │ ├── 1gfl_cm.pdb │ ├── 1gmi_remod_p.pdb │ ├── 1gmx_p.pdb │ ├── 1guu_remod_p.pdb │ ├── 1gz2_remod_p.pdb │ ├── 1gzc_A_p.pdb │ ├── 1h0p_A_p.pdb │ ├── 1h2e_A_p.pdb │ ├── 1h4x_remod_p.pdb │ ├── 1h98_remod_p.pdb │ ├── 1hdo_remod_p.pdb │ ├── 1hfc_remod_p.pdb │ ├── 1hh8_remod_p.pdb │ ├── 1htw_A_p.pdb │ ├── 1hxn_remod_p.pdb │ ├── 1i1j_remod_p.pdb │ ├── 1i1n_remod_p.pdb │ ├── 1i4j_p.pdb │ ├── 1i58_A_p.pdb │ ├── 1i5g_A_p.pdb │ ├── 1i71_A_p.pdb │ ├── 1ihz_remod_p.pdb │ ├── 1iib_remod_p.pdb │ ├── 1im5_remod_p.pdb │ ├── 1iwd_A_p.pdb │ ├── 1jbk_remod_p.pdb │ ├── 1jfu_remod_p.pdb │ ├── 1jfx_A_p.pdb │ ├── 1jkx_remod_p.pdb │ ├── 1jl1_remod_p.pdb │ ├── 1jo0_remod_p.pdb │ ├── 1jo8_A_p.pdb │ ├── 1jos_remod_p.pdb │ ├── 1jvw_remod_p.pdb │ ├── 1jwq_A_p.pdb │ ├── 1jyh_remod_p.pdb │ ├── 1k6k_remod_p.pdb │ ├── 1k7c_A_p.pdb │ ├── 1k7j_p.pdb │ ├── 1kid_remod_p.pdb │ ├── 1kq6_remod_p.pdb │ ├── 1kqr_remod_p.pdb │ ├── 1ktg_remod_p.pdb │ ├── 1ku3_remod_p.pdb │ ├── 1kw4_remod_p.pdb │ ├── 1lm4_remod_p.pdb │ ├── 1lo7_remod_p.pdb │ ├── 1lpy_remod_p.pdb │ ├── 1m4j_remod_p.pdb │ ├── 1m8a_remod_p.pdb │ ├── 1mk0_A_p.pdb │ ├── 1mug_remod_p.pdb │ ├── 1nb9_A_p.pdb │ ├── 1ne2_remod_p.pdb │ ├── 1nps_A_p.pdb │ ├── 1nrv_remod_p.pdb │ ├── 1ny1_remod_p.pdb │ ├── 1o1z_remod_p.pdb │ ├── 1p90_remod_p.pdb │ ├── 1pch_A_p.pdb │ ├── 1pko_remod_p.pdb │ ├── 1qf9_A_p.pdb │ ├── 1qjp_remod_p.pdb │ ├── 1ql0_A_p.pdb │ ├── 1r26_remod_p.pdb │ ├── 1roa_remod_p.pdb │ ├── 1rw1_p.pdb │ ├── 1rw7_remod_p.pdb │ ├── 1ryb_remod_p.pdb │ ├── 1smx_remod_p.pdb │ ├── 1svy_remod_p.pdb │ ├── 1t8k_A_p.pdb │ ├── 1tif_remod_p.pdb │ ├── 1tqg_A_p.pdb │ ├── 1tqh_remod_p.pdb │ ├── 1tzv_remod_p.pdb │ ├── 1vfy_remod_p.pdb │ ├── 1vhu_remod_p.pdb │ ├── 1vjk_remod_p.pdb │ ├── 1vmb_remod_p.pdb │ ├── 1vp6_remod_p.pdb │ ├── 1w0h_remod_p.pdb │ ├── 1whi_A_p.pdb │ ├── 1wjx_remod_p.pdb │ ├── 1wkc_remod_p.pdb │ ├── 1xdz_remod_p.pdb │ ├── 1xff_remod_p.pdb │ ├── 1xkr_remod_p.pdb │ ├── 2arc_remod_p.pdb │ ├── 2cua_remod_p.pdb │ ├── 2hs1_A_p.pdb │ ├── 2mhr_A_p.pdb │ ├── 2phy_A_p.pdb │ ├── 2qmt_p.pdb │ ├── 2tps_remod_p.pdb │ ├── 2vxn_remod_p.pdb │ ├── 3bor_remod_p.pdb │ ├── 3dqg_remod_p.pdb │ ├── 5ptp_p.pdb │ ├── 6qji_p.pdb │ ├── 6qji_p_trunc.pdb │ ├── 6qji_p_trunc_2022.pdb │ ├── AF-P60484-F1-model_v4_p.pdb │ ├── AF-P62993-F1-model_v4_trunc_p.pdb │ ├── AF-Q6SJ61-F1-model_v4_p.pdb │ ├── README.md │ ├── bgl3_cm_p.pdb │ ├── index.csv │ ├── pab1_cm.pdb │ └── ube4b_cm.pdb └── raw_pdb_files │ ├── 2qmt.pdb │ └── README.md ├── setup ├── clean_pdb_env.yml └── metl-sim_env.yml ├── templates ├── README.md ├── docking_wd_template │ ├── docking_minimize.xml │ ├── docking_minimize_fast.xml │ ├── mutate_template.xml │ ├── options_dock.txt │ ├── options_mutate.txt │ └── protein_dock_fast.sh ├── energize_wd_template │ ├── README.md │ ├── filter_3rd.xml │ ├── flags_centroid 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