├── .codecov.yml ├── .github ├── CONTRIBUTING.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ └── autoTest.yml ├── .gitignore ├── .gitmodules ├── .img ├── RestraintMaker_logo_withBackground.png ├── pyMol_Wiz_export.png ├── pyMol_Wiz_instructions.png ├── pyMol_Wiz_menu.png ├── pyMol_Wiz_optimize.png ├── pyMol_Wiz_optimize_grid.png ├── pyMol_Wiz_select.png └── pyMol_Wiz_start.png ├── .lgtm.yml ├── CODE_OF_CONDUCT.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── devtools ├── README.md ├── conda-envs │ ├── dev_env.yaml │ ├── environment_windows.yaml │ └── test_env.yaml ├── pymol_writeOutGromosCnf.py └── scripts │ └── create_conda_env.py ├── docs ├── .buildinfo ├── .img │ ├── RestraintMaker_logo_withBackground.png │ ├── pyMol_Wiz_export.png │ ├── pyMol_Wiz_optimize.png │ ├── pyMol_Wiz_optimize_grid.png │ ├── pyMol_Wiz_select.png │ └── pyMol_Wiz_start.png ├── .nojekyll ├── _modules │ ├── index.html │ └── restraintmaker │ │ ├── algorithm │ │ ├── Filter.html │ │ ├── Optimizer.html │ │ └── Selection.html │ │ ├── interface_Pymol │ │ ├── RestraintMaker_Logic.html │ │ ├── RestraintMaker_Pymol.html │ │ └── pymol_utilities │ │ │ ├── program_states.html │ │ │ ├── pymol_utitlities.html │ │ │ └── qt_dialogs.html │ │ ├── io │ │ ├── Exporter.html │ │ ├── Files │ │ │ ├── Gromacs_files.html │ │ │ ├── Gromos_blocks.html │ │ │ └── Gromos_files.html │ │ └── Importer.html │ │ ├── restraintMaker.html │ │ ├── test │ │ ├── test_exporter.html │ │ ├── test_importer.html │ │ ├── test_optimizer.html │ │ └── test_restraintMaker_PyMol.html │ │ ├── tools_Rdkit │ │ └── Rdkit_Functions.html │ │ └── utils │ │ ├── Types.html │ │ └── Utilities.html ├── _source │ ├── modules.html │ ├── restraintmaker.algorithm.html │ ├── restraintmaker.html │ ├── restraintmaker.interface_Pymol.html │ ├── restraintmaker.interface_Pymol.pymol_utilities.html │ ├── restraintmaker.io.Files.html │ ├── restraintmaker.io.html │ ├── restraintmaker.test.html │ ├── restraintmaker.test.test_files.html │ ├── restraintmaker.tools_Rdkit.html │ └── restraintmaker.utils.html ├── _sources │ ├── _source │ │ ├── modules.rst.txt │ │ ├── restraintmaker.algorithm.rst.txt │ │ ├── restraintmaker.interface_Pymol.pymol_utilities.rst.txt │ │ ├── restraintmaker.interface_Pymol.rst.txt │ │ ├── restraintmaker.io.Files.rst.txt │ │ ├── restraintmaker.io.rst.txt │ │ ├── restraintmaker.rst.txt │ │ ├── restraintmaker.test.rst.txt │ │ ├── restraintmaker.test.test_files.rst.txt │ │ ├── restraintmaker.tools_Rdkit.rst.txt │ │ └── restraintmaker.utils.rst.txt │ ├── examples │ │ ├── example_script_execution.ipynb.txt │ │ └── index.rst.txt │ ├── index.rst.txt │ └── introduction.rst.txt ├── _static │ ├── README.md │ ├── basic.css │ ├── css │ │ ├── badge_only.css │ │ ├── fonts │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ ├── fontawesome-webfont.woff2 │ │ │ ├── lato-bold-italic.woff │ │ │ ├── lato-bold-italic.woff2 │ │ │ ├── lato-bold.woff │ │ │ ├── lato-bold.woff2 │ │ │ ├── lato-normal-italic.woff │ │ │ ├── lato-normal-italic.woff2 │ │ │ ├── lato-normal.woff │ │ │ └── lato-normal.woff2 │ │ └── theme.css │ ├── doctools.js │ ├── documentation_options.js │ ├── file.png │ ├── jquery-3.5.1.js │ ├── jquery.js │ ├── js │ │ ├── badge_only.js │ │ ├── html5shiv-printshiv.min.js │ │ ├── html5shiv.min.js │ │ └── theme.js │ ├── language_data.js │ ├── minus.png │ ├── plus.png │ ├── pygments.css │ ├── searchtools.js │ ├── underscore-1.13.1.js │ └── underscore.js ├── examples │ ├── example_script_execution.html │ ├── example_script_execution.ipynb │ └── index.html ├── genindex.html ├── index.html ├── introduction.html ├── objects.inv ├── py-modindex.html ├── search.html ├── searchindex.js └── sphinx_project │ ├── Makefile │ ├── _source │ └── restraintmaker.interface_Pymol.pymol_utilities.rst │ ├── _static │ └── README.md │ ├── _templates │ └── README.md │ ├── build_docs.sh │ ├── conf.py │ ├── examples │ ├── examples │ ├── example_script_execution.ipynb │ └── index.rst │ ├── index.rst │ └── make.bat ├── examples ├── example_gui_execution.py ├── example_script_execution.ipynb └── publication │ ├── a_benchmark_algorithms │ ├── build_particleClouds.py │ ├── comparison_bruteF_vs_maxGraph.py │ └── plot_data.ipynb │ └── b_ATB_solvationFreeEnergies │ ├── ATB_molecules │ ├── molID_1045 │ │ ├── 54A7.ifp │ │ ├── G277.top │ │ ├── G277_GROMOS11_54A7_unitedatom.mtb │ │ ├── G277_unitedatom_optimised_geometry.g96 │ │ └── G277_unitedatom_optimised_geometry.pdb │ ├── molID_1181 │ │ ├── 54A7.ifp │ │ ├── M097.top │ │ ├── M097_GROMOS11_54A7_unitedatom.mtb │ │ ├── M097_unitedatom_optimised_geometry.g96 │ │ └── M097_unitedatom_optimised_geometry.pdb │ ├── molID_1922 │ │ ├── 54A7.ifp │ │ ├── 8018.top │ │ ├── 8018_GROMOS11_54A7_unitedatom.mtb │ │ ├── 8018_unitedatom_optimised_geometry.g96 │ │ ├── 8018_unitedatom_optimised_geometry.pdb │ │ └── M097.top │ ├── molID_26135 │ │ ├── 54A7.ifp │ │ ├── 6J29.top │ │ ├── 6J29_GROMOS11_54A7_unitedatom.mtb │ │ ├── 6J29_unitedatom_optimised_geometry.g96 │ │ └── 6J29_unitedatom_optimised_geometry.pdb │ ├── molID_2905 │ │ ├── 54A7.ifp │ │ ├── S002.top │ │ ├── S002_GROMOS11_54A7_unitedatom.mtb │ │ ├── S002_unitedatom_optimised_geometry.g96 │ │ └── S002_unitedatom_optimised_geometry.pdb │ ├── molID_30212 │ │ ├── 54A7.ifp │ │ ├── TVVS.top │ │ ├── TVVS_GROMOS11_54A7_unitedatom.mtb │ │ ├── TVVS_unitedatom_optimised_geometry.g96 │ │ └── TVVS_unitedatom_optimised_geometry.pdb │ ├── molID_30253 │ │ ├── 54A7.ifp │ │ ├── E1VB.top │ │ ├── E1VB_GROMOS11_54A7_unitedatom.mtb │ │ ├── E1VB_unitedatom_optimised_geometry.g96 │ │ └── E1VB_unitedatom_optimised_geometry.pdb │ ├── molID_30491 │ │ ├── 54A7.ifp │ │ ├── 6KET.top │ │ ├── 6KET_GROMOS11_54A7_unitedatom.mtb │ │ ├── 6KET_allatom_optimised_geometry.g96 │ │ └── 6KET_unitedatom_optimised_geometry.pdb │ ├── molID_3348 │ │ ├── 54A7.ifp │ │ ├── M030.top │ │ ├── M030_GROMOS11_54A7_unitedatom.mtb │ │ ├── M030_unitedatom_optimised_geometry.g96 │ │ └── M030_unitedatom_optimised_geometry.pdb │ ├── molID_3596 │ │ ├── 54A7.ifp │ │ ├── M218.top │ │ ├── M218_GROMOS11_54A7_unitedatom.mtb │ │ ├── M218_unitedatom_optimised_geometry.g96 │ │ └── M218_unitedatom_optimised_geometry.pdb │ ├── molID_647 │ │ ├── 54A7.ifp │ │ ├── F313.top │ │ ├── F313_GROMOS11_54A7_unitedatom.mtb │ │ ├── F313_unitedatom_optimised_geometry.g96 │ │ └── F313_unitedatom_optimised_geometry.pdb │ ├── molID_8021 │ │ ├── 54A7.ifp │ │ ├── _O6T.top │ │ ├── _O6T_GROMOS11_54A7_unitedatom.mtb │ │ ├── _O6T_unitedatom_optimised_geometry.g96 │ │ └── _O6T_unitedatom_optimised_geometry.pdb │ ├── molID_8028 │ │ ├── 54A7.ifp │ │ ├── _O70.top │ │ ├── _O70_GROMOS11_54A7_unitedatom.mtb │ │ ├── _O70_unitedatom_optimised_geometry.g96 │ │ └── _O70_unitedatom_optimised_geometry.pdb │ ├── molID_8029 │ │ ├── 54A7.ifp │ │ ├── _O71.top │ │ ├── _O71_GROMOS11_54A7_unitedatom.mtb │ │ ├── _O71_unitedatom_optimised_geometry.g96 │ │ └── _O71_unitedatom_optimised_geometry.pdb │ ├── molID_824 │ │ ├── 54A7.ifp │ │ ├── G078.top │ │ ├── G078_GROMOS11_54A7_unitedatom.mtb │ │ ├── G078_unitedatom_optimised_geometry.g96 │ │ └── G078_unitedatom_optimised_geometry.pdb │ ├── molID_9378 │ │ ├── 54A7.ifp │ │ ├── _P8I.top │ │ ├── _P8I_GROMOS11_54A7_unitedatom.mtb │ │ ├── _P8I_unitedatom_optimised_geometry.g96 │ │ └── _P8I_unitedatom_optimised_geometry.pdb │ ├── molID_984 │ │ ├── 54A7.ifp │ │ ├── G209.top │ │ ├── G209_GROMOS11_54A7_unitedatom.mtb │ │ ├── G209_unitedatom_optimised_geometry.g96 │ │ └── G209_unitedatom_optimised_geometry.pdb │ └── solv.mtb │ ├── sets │ ├── build_gromos_singleligand_files.py │ ├── generate_multi_state_gromos_files.ipynb │ ├── generate_pairwise_state_gromos_files.ipynb │ ├── multistate │ │ ├── easy_6 │ │ │ ├── easy_6.cnf │ │ │ ├── easy_6.disres │ │ │ ├── easy_6.pdb │ │ │ ├── easy_6.ptp │ │ │ ├── easy_6.top │ │ │ ├── easy_6_box.pdb │ │ │ ├── easy_6_grid.png │ │ │ ├── easy_6_overlay.png │ │ │ ├── easy_6_solv.pdb │ │ │ ├── easy_6_spc.cnf │ │ │ └── solv_emin │ │ │ │ ├── easy_6_emin.cnf │ │ │ │ ├── easy_6_emin.imd │ │ │ │ ├── easy_6_emin.omd │ │ │ │ ├── easy_6_emin.por │ │ │ │ ├── easy_6_emin.rpf │ │ │ │ ├── easy_6_emin.trc │ │ │ │ └── easy_6_emin.tre │ │ ├── flat_10 │ │ │ ├── flat_10.cnf │ │ │ ├── flat_10.disres │ │ │ ├── flat_10.pdb │ │ │ ├── flat_10.ptp │ │ │ ├── flat_10.top │ │ │ ├── flat_10_box.pdb │ │ │ ├── flat_10_grid.png │ │ │ ├── flat_10_overlay.png │ │ │ ├── flat_10_solv.pdb │ │ │ ├── flat_10_spc.cnf │ │ │ └── solv_emin │ │ │ │ ├── flat_10_emin.cnf │ │ │ │ ├── flat_10_emin.imd │ │ │ │ ├── flat_10_emin.omd │ │ │ │ ├── flat_10_emin.por │ │ │ │ ├── flat_10_emin.rpf │ │ │ │ ├── flat_10_emin.trc │ │ │ │ └── flat_10_emin.tre │ │ ├── generate_disres.py │ │ └── prepare_distance_restraints.py │ ├── pairwise │ │ ├── 6KET_F313 │ │ │ ├── 6KET_F313.cnf │ │ │ ├── 6KET_F313.disres │ │ │ ├── 6KET_F313.pdb │ │ │ ├── 6KET_F313.por │ │ │ ├── 6KET_F313.ptp │ │ │ ├── 6KET_F313.rfp │ │ │ ├── 6KET_F313.top │ │ │ ├── 6KET_F313_box.cnf │ │ │ ├── 6KET_F313_box.pdb │ │ │ ├── 6KET_F313_grid.png │ │ │ ├── 6KET_F313_overlay.png │ │ │ ├── 6KET_F313_restraints.png │ │ │ ├── 6KET_F313_solv.pdb │ │ │ └── 6KET_F313_spc.cnf │ │ ├── 6KET_G277 │ │ │ ├── 6KET_G277.cnf │ │ │ ├── 6KET_G277.disres │ │ │ ├── 6KET_G277.pdb │ │ │ ├── 6KET_G277.por │ │ │ ├── 6KET_G277.ptp │ │ │ ├── 6KET_G277.rfp │ │ │ ├── 6KET_G277.top │ │ │ ├── 6KET_G277_box.cnf │ │ │ ├── 6KET_G277_box.pdb │ │ │ ├── 6KET_G277_grid.png │ │ │ ├── 6KET_G277_overlay.png │ │ │ ├── 6KET_G277_restraints.png │ │ │ ├── 6KET_G277_solv.pdb │ │ │ └── 6KET_G277_spc.cnf │ │ ├── 6KET__O6T │ │ │ ├── 6KET__O6T.cnf │ │ │ ├── 6KET__O6T.disres │ │ │ ├── 6KET__O6T.pdb │ │ │ ├── 6KET__O6T.por │ │ │ ├── 6KET__O6T.ptp │ │ │ ├── 6KET__O6T.rfp │ │ │ ├── 6KET__O6T.top │ │ │ ├── 6KET__O6T_box.cnf │ │ │ ├── 6KET__O6T_box.pdb │ │ │ ├── 6KET__O6T_grid.png │ │ │ ├── 6KET__O6T_overlay.png │ │ │ ├── 6KET__O6T_restraints.png │ │ │ ├── 6KET__O6T_solv.pdb │ │ │ └── 6KET__O6T_spc.cnf │ │ ├── F313_G277 │ │ │ ├── F313_G277.cnf │ │ │ ├── F313_G277.disres │ │ │ ├── F313_G277.pdb │ │ │ ├── F313_G277.por │ │ │ ├── F313_G277.ptp │ │ │ ├── F313_G277.rfp │ │ │ ├── F313_G277.top │ │ │ ├── F313_G277_box.cnf │ │ │ ├── F313_G277_box.pdb │ │ │ ├── F313_G277_grid.png │ │ │ ├── F313_G277_overlay.png │ │ │ ├── F313_G277_restraints.png │ │ │ ├── F313_G277_solv.pdb │ │ │ └── F313_G277_spc.cnf │ │ ├── F313__O6T │ │ │ ├── F313__O6T.cnf │ │ │ ├── F313__O6T.disres │ │ │ ├── F313__O6T.pdb │ │ │ ├── F313__O6T.por │ │ │ ├── F313__O6T.ptp │ │ │ ├── F313__O6T.rfp │ │ │ ├── F313__O6T.top │ │ │ ├── F313__O6T_box.cnf │ │ │ ├── F313__O6T_box.pdb │ │ │ ├── F313__O6T_grid.png │ │ │ ├── F313__O6T_overlay.png │ │ │ ├── F313__O6T_restraints.png │ │ │ ├── F313__O6T_solv.pdb │ │ │ └── F313__O6T_spc.cnf │ │ ├── G277__O6T │ │ │ ├── G277__O6T.cnf │ │ │ ├── G277__O6T.disres │ │ │ ├── G277__O6T.pdb │ │ │ ├── G277__O6T.por │ │ │ ├── G277__O6T.ptp │ │ │ ├── G277__O6T.rfp │ │ │ ├── G277__O6T.top │ │ │ ├── G277__O6T_box.cnf │ │ │ ├── G277__O6T_box.pdb │ │ │ ├── G277__O6T_grid.png │ │ │ ├── G277__O6T_overlay.png │ │ │ ├── G277__O6T_restraints.png │ │ │ ├── G277__O6T_solv.pdb │ │ │ └── G277__O6T_spc.cnf │ │ ├── M030_6J29 │ │ │ ├── M030_6J29.cnf │ │ │ ├── M030_6J29.disres │ │ │ ├── M030_6J29.pdb │ │ │ ├── M030_6J29.por │ │ │ ├── M030_6J29.ptp │ │ │ ├── M030_6J29.rfp │ │ │ ├── M030_6J29.top │ │ │ ├── M030_6J29_box.cnf │ │ │ ├── M030_6J29_box.pdb │ │ │ ├── M030_6J29_grid.png │ │ │ ├── M030_6J29_overlay.png │ │ │ ├── M030_6J29_restraints.png │ │ │ ├── M030_6J29_solv.pdb │ │ │ └── M030_6J29_spc.cnf │ │ ├── M030_6KET │ │ │ ├── M030_6KET.cnf │ │ │ ├── M030_6KET.disres │ │ │ ├── M030_6KET.pdb │ │ │ ├── M030_6KET.por │ │ │ ├── M030_6KET.ptp │ │ │ ├── M030_6KET.rfp │ │ │ ├── M030_6KET.top │ │ │ ├── M030_6KET_box.cnf │ │ │ ├── M030_6KET_box.pdb │ │ │ ├── M030_6KET_grid.png │ │ │ ├── M030_6KET_overlay.png │ │ │ ├── M030_6KET_restraints.png │ │ │ ├── M030_6KET_solv.pdb │ │ │ └── M030_6KET_spc.cnf │ │ ├── M030_8018 │ │ │ ├── M030_8018.cnf │ │ │ ├── M030_8018.disres │ │ │ ├── M030_8018.pdb │ │ │ ├── M030_8018.por │ │ │ ├── M030_8018.ptp │ │ │ ├── M030_8018.rfp │ │ │ ├── M030_8018.top │ │ │ ├── M030_8018_box.cnf │ │ │ ├── M030_8018_box.pdb │ │ │ ├── M030_8018_grid.png │ │ │ ├── M030_8018_overlay.png │ │ │ ├── M030_8018_restraints.png │ │ │ ├── M030_8018_solv.pdb │ │ │ └── M030_8018_spc.cnf │ │ ├── M030_E1VB │ │ │ ├── M030_E1VB.cnf │ │ │ ├── M030_E1VB.disres │ │ │ ├── M030_E1VB.pdb │ │ │ ├── M030_E1VB.por │ │ │ ├── M030_E1VB.ptp │ │ │ ├── M030_E1VB.rfp │ │ │ ├── M030_E1VB.top │ │ │ ├── M030_E1VB_box.cnf │ │ │ ├── M030_E1VB_box.pdb │ │ │ ├── M030_E1VB_greedy_shortest.disres │ │ │ ├── M030_E1VB_greedy_shortest_restraints.png │ │ │ ├── M030_E1VB_grid.png │ │ │ ├── M030_E1VB_overlay.png │ │ │ ├── M030_E1VB_restraints.png │ │ │ ├── M030_E1VB_solv.pdb │ │ │ └── M030_E1VB_spc.cnf │ │ ├── M030_F313 │ │ │ ├── M030_F313.cnf │ │ │ ├── M030_F313.disres │ │ │ ├── M030_F313.pdb │ │ │ ├── M030_F313.por │ │ │ ├── M030_F313.ptp │ │ │ ├── M030_F313.rfp │ │ │ ├── M030_F313.top │ │ │ ├── M030_F313_box.cnf │ │ │ ├── M030_F313_box.pdb │ │ │ ├── M030_F313_grid.png │ │ │ ├── M030_F313_overlay.png │ │ │ ├── M030_F313_restraints.png │ │ │ ├── M030_F313_solv.pdb │ │ │ └── M030_F313_spc.cnf │ │ ├── M030_G078 │ │ │ ├── M030_G078.cnf │ │ │ ├── M030_G078.disres │ │ │ ├── M030_G078.pdb │ │ │ ├── M030_G078.por │ │ │ ├── M030_G078.ptp │ │ │ ├── M030_G078.rfp │ │ │ ├── M030_G078.top │ │ │ ├── M030_G078_box.cnf │ │ │ ├── M030_G078_box.pdb │ │ │ ├── M030_G078_grid.png │ │ │ ├── M030_G078_overlay.png │ │ │ ├── M030_G078_restraints.png │ │ │ ├── M030_G078_solv.pdb │ │ │ └── M030_G078_spc.cnf │ │ ├── M030_G277 │ │ │ ├── M030_G277.cnf │ │ │ ├── M030_G277.disres │ │ │ ├── M030_G277.pdb │ │ │ ├── M030_G277.por │ │ │ ├── M030_G277.ptp │ │ │ ├── M030_G277.rfp │ │ │ ├── M030_G277.top │ │ │ ├── M030_G277_box.cnf │ │ │ ├── M030_G277_box.pdb │ │ │ ├── M030_G277_grid.png │ │ │ ├── M030_G277_overlay.png │ │ │ ├── M030_G277_restraints.png │ │ │ ├── M030_G277_solv.pdb │ │ │ └── M030_G277_spc.cnf │ │ ├── M030_M097 │ │ │ ├── M030_M097.cnf │ │ │ ├── M030_M097.disres │ │ │ ├── M030_M097.pdb │ │ │ ├── M030_M097.por │ │ │ ├── M030_M097.ptp │ │ │ ├── M030_M097.rfp │ │ │ ├── M030_M097.top │ │ │ ├── M030_M097_box.cnf │ │ │ ├── M030_M097_box.pdb │ │ │ ├── M030_M097_grid.png │ │ │ ├── M030_M097_overlay.png │ │ │ ├── M030_M097_restraints.png │ │ │ ├── M030_M097_solv.pdb │ │ │ └── M030_M097_spc.cnf │ │ ├── M030_M218 │ │ │ ├── M030_M218.cnf │ │ │ ├── M030_M218.disres │ │ │ ├── M030_M218.pdb │ │ │ ├── M030_M218.por │ │ │ ├── M030_M218.ptp │ │ │ ├── M030_M218.rfp │ │ │ ├── M030_M218.top │ │ │ ├── M030_M218_box.cnf │ │ │ ├── M030_M218_box.pdb │ │ │ ├── M030_M218_grid.png │ │ │ ├── M030_M218_overlay.png │ │ │ ├── M030_M218_restraints.png │ │ │ ├── M030_M218_solv.pdb │ │ │ └── M030_M218_spc.cnf │ │ ├── M030_TVVS │ │ │ ├── M030_TVVS.cnf │ │ │ ├── M030_TVVS.disres │ │ │ ├── M030_TVVS.pdb │ │ │ ├── M030_TVVS.por │ │ │ ├── M030_TVVS.ptp │ │ │ ├── M030_TVVS.rfp │ │ │ ├── M030_TVVS.top │ │ │ ├── M030_TVVS_box.cnf │ │ │ ├── M030_TVVS_box.pdb │ │ │ ├── M030_TVVS_grid.png │ │ │ ├── M030_TVVS_overlay.png │ │ │ ├── M030_TVVS_restraints.png │ │ │ ├── M030_TVVS_solv.pdb │ │ │ └── M030_TVVS_spc.cnf │ │ ├── M030__O6T │ │ │ ├── M030__O6T.cnf │ │ │ ├── M030__O6T.disres │ │ │ ├── M030__O6T.pdb │ │ │ ├── M030__O6T.por │ │ │ ├── M030__O6T.ptp │ │ │ ├── M030__O6T.rfp │ │ │ ├── M030__O6T.top │ │ │ ├── M030__O6T_box.cnf │ │ │ ├── M030__O6T_box.pdb │ │ │ ├── M030__O6T_grid.png │ │ │ ├── M030__O6T_overlay.png │ │ │ ├── M030__O6T_restraints.png │ │ │ ├── M030__O6T_solv.pdb │ │ │ └── M030__O6T_spc.cnf │ │ ├── M030__O70 │ │ │ ├── M030__O70.cnf │ │ │ ├── M030__O70.disres │ │ │ ├── M030__O70.pdb │ │ │ ├── M030__O70.por │ │ │ ├── M030__O70.ptp │ │ │ ├── M030__O70.rfp │ │ │ ├── M030__O70.top │ │ │ ├── M030__O70_box.cnf │ │ │ ├── M030__O70_box.pdb │ │ │ ├── M030__O70_grid.png │ │ │ ├── M030__O70_overlay.png │ │ │ ├── M030__O70_restraints.png │ │ │ ├── M030__O70_solv.pdb │ │ │ └── M030__O70_spc.cnf │ │ ├── M030__O71 │ │ │ ├── M030__O71.cnf │ │ │ ├── M030__O71.disres │ │ │ ├── M030__O71.pdb │ │ │ ├── M030__O71.por │ │ │ ├── M030__O71.ptp │ │ │ ├── M030__O71.rfp │ │ │ ├── M030__O71.top │ │ │ ├── M030__O71_box.cnf │ │ │ ├── M030__O71_box.pdb │ │ │ ├── M030__O71_greedy_shortest.disres │ │ │ ├── M030__O71_greedy_shortest_restraints.png │ │ │ ├── M030__O71_grid.png │ │ │ ├── M030__O71_overlay.png │ │ │ ├── M030__O71_restraints.png │ │ │ ├── M030__O71_solv.pdb │ │ │ └── M030__O71_spc.cnf │ │ ├── M030__P8I │ │ │ ├── M030__P8I.cnf │ │ │ ├── M030__P8I.disres │ │ │ ├── M030__P8I.pdb │ │ │ ├── M030__P8I.por │ │ │ ├── M030__P8I.ptp │ │ │ ├── M030__P8I.rfp │ │ │ ├── M030__P8I.top │ │ │ ├── M030__P8I_box.cnf │ │ │ ├── M030__P8I_box.pdb │ │ │ ├── M030__P8I_grid.png │ │ │ ├── M030__P8I_overlay.png │ │ │ ├── M030__P8I_restraints.png │ │ │ ├── M030__P8I_solv.pdb │ │ │ └── M030__P8I_spc.cnf │ │ ├── M030_ligs_tree.png │ │ ├── M097_6KET │ │ │ ├── M097_6KET.cnf │ │ │ ├── M097_6KET.disres │ │ │ ├── M097_6KET.pdb │ │ │ ├── M097_6KET.por │ │ │ ├── M097_6KET.ptp │ │ │ ├── M097_6KET.rfp │ │ │ ├── M097_6KET.top │ │ │ ├── M097_6KET_box.cnf │ │ │ ├── M097_6KET_box.pdb │ │ │ ├── M097_6KET_grid.png │ │ │ ├── M097_6KET_overlay.png │ │ │ ├── M097_6KET_restraints.png │ │ │ ├── M097_6KET_solv.pdb │ │ │ └── M097_6KET_spc.cnf │ │ ├── M097_F313 │ │ │ ├── M097_F313.cnf │ │ │ ├── M097_F313.disres │ │ │ ├── M097_F313.pdb │ │ │ ├── M097_F313.por │ │ │ ├── M097_F313.ptp │ │ │ ├── M097_F313.rfp │ │ │ ├── M097_F313.top │ │ │ ├── M097_F313_box.cnf │ │ │ ├── M097_F313_box.pdb │ │ │ ├── M097_F313_grid.png │ │ │ ├── M097_F313_overlay.png │ │ │ ├── M097_F313_restraints.png │ │ │ ├── M097_F313_solv.pdb │ │ │ └── M097_F313_spc.cnf │ │ ├── M097_G277 │ │ │ ├── M097_G277.cnf │ │ │ ├── M097_G277.disres │ │ │ ├── M097_G277.pdb │ │ │ ├── M097_G277.por │ │ │ ├── M097_G277.ptp │ │ │ ├── M097_G277.rfp │ │ │ ├── M097_G277.top │ │ │ ├── M097_G277_box.cnf │ │ │ ├── M097_G277_box.pdb │ │ │ ├── M097_G277_grid.png │ │ │ ├── M097_G277_overlay.png │ │ │ ├── M097_G277_restraints.png │ │ │ ├── M097_G277_solv.pdb │ │ │ └── M097_G277_spc.cnf │ │ ├── M097__O6T │ │ │ ├── M097__O6T.cnf │ │ │ ├── M097__O6T.disres │ │ │ ├── M097__O6T.pdb │ │ │ ├── M097__O6T.por │ │ │ ├── M097__O6T.ptp │ │ │ ├── M097__O6T.rfp │ │ │ ├── M097__O6T.top │ │ │ ├── M097__O6T_box.cnf │ │ │ ├── M097__O6T_box.pdb │ │ │ ├── M097__O6T_grid.png │ │ │ ├── M097__O6T_overlay.png │ │ │ ├── M097__O6T_restraints.png │ │ │ ├── M097__O6T_solv.pdb │ │ │ └── M097__O6T_spc.cnf │ │ ├── S002_M030 │ │ │ ├── S002_M030.cnf │ │ │ ├── S002_M030.disres │ │ │ ├── S002_M030.pdb │ │ │ ├── S002_M030.por │ │ │ ├── S002_M030.ptp │ │ │ ├── S002_M030.rfp │ │ │ ├── S002_M030.top │ │ │ ├── S002_M030_box.cnf │ │ │ ├── S002_M030_box.pdb │ │ │ ├── S002_M030_grid.png │ │ │ ├── S002_M030_overlay.png │ │ │ ├── S002_M030_restraints.png │ │ │ ├── S002_M030_solv.pdb │ │ │ └── S002_M030_spc.cnf │ │ └── prepare_distance_restraints.py │ ├── resn_lib.lib │ └── selection_process │ └── utils_test_set_ATB.py ├── restraintmaker ├── __init__.py ├── algorithm │ ├── Filter.py │ ├── Optimizer.py │ ├── Selection.py │ └── __init__.py ├── interface_Pymol │ ├── RestraintMaker_Logic.py │ ├── RestraintMaker_Pymol.py │ ├── __init__.py │ └── pymol_utilities │ │ ├── __init__.py │ │ ├── program_states.py │ │ ├── pymol_utitlities.py │ │ └── qt_dialogs.py ├── io │ ├── Exporter.py │ ├── Files │ │ ├── Gromacs_files.py │ │ ├── Gromos_blocks.py │ │ ├── Gromos_files.py │ │ └── __init__.py │ ├── Importer.py │ └── __init__.py ├── restraintMaker.py ├── test │ ├── __init__.py │ ├── pickle_input_test_file.py │ ├── test_exporter.py │ ├── test_files │ │ ├── IO │ │ │ ├── in_5ligs_disres.dat │ │ │ ├── in_5ligs_disres.p │ │ │ ├── in_7ligs_disres.dat │ │ │ └── in_7ligs_disres.p │ │ ├── __init__.py │ │ ├── optimizers │ │ │ ├── in_atom_list.p │ │ │ ├── out_bruteForce_optimizer.p │ │ │ ├── out_cog_MAD_optimizer.p │ │ │ ├── out_longestShortest_MAD_optimizer.p │ │ │ └── out_prim_optimizer.p │ │ ├── test_systems │ │ │ ├── systemA │ │ │ │ └── CHK1_5Ligs.pdb │ │ │ ├── systemB │ │ │ │ └── BRD4_7Ligs.pdb │ │ │ ├── systemC │ │ │ │ └── PNMT_9ligs.pdb │ │ │ ├── systemD │ │ │ │ └── FXR_21ligs.pdb │ │ │ ├── systemE │ │ │ │ └── single_CHK1 │ │ │ │ │ ├── KL1.pdb │ │ │ │ │ ├── KL17.pdb │ │ │ │ │ ├── KL19.pdb │ │ │ │ │ ├── KL20.pdb │ │ │ │ │ └── KL21.pdb │ │ │ └── systemF │ │ │ │ └── single_BRD4 │ │ │ │ ├── 3MXF.pdb │ │ │ │ ├── 3U5L.pdb │ │ │ │ ├── 4E96.pdb │ │ │ │ ├── 4J3I.pdb │ │ │ │ ├── 4LYS.pdb │ │ │ │ ├── 4LYW.pdb │ │ │ │ └── 4MR3.pdb │ │ └── test_tmp_file.pdb │ ├── test_importer.py │ ├── test_optimizer.py │ └── test_restraintMaker_PyMol.py ├── tools_Rdkit │ ├── Rdkit_Functions.py │ ├── __init__.py │ └── _visualizations.py 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