├── .gitignore ├── CHANGELOG.md ├── README.md ├── Tools ├── cgenff_charmm2gmx_py3.py ├── rest1.sh └── rest2.sh ├── align_utils.py ├── all_classes.py ├── analyze_results.py ├── config ├── defaults.ini └── internal.ini ├── dist ├── collect_results_from_xvg └── collect_results_from_xvg.py ├── docking_readers ├── autodock4_loader.py ├── generic_loader.py ├── pdb_loader.py ├── superimpose_loader.py └── vina_loader.py ├── docs ├── Manual.pdf ├── PyAutoFEP logo.svg └── tutorial01 │ ├── PyAutoFEP Tutorial 01.pdf │ ├── README.md │ └── workdir.tgz ├── generate_perturbation_map.py ├── merge_topologies.py ├── mol_util.py ├── os_util.py ├── prepare_dual_topology.py ├── process_user_input.py ├── savestate_util.py ├── templates ├── lambdas.ini ├── mdp │ ├── charmm_nosc │ │ ├── complex │ │ │ ├── md.mdp │ │ │ ├── min01.mdp │ │ │ ├── min02.mdp │ │ │ ├── min03.mdp │ │ │ ├── npt.mdp │ │ │ ├── nve.mdp │ │ │ └── nvt.mdp │ │ └── water │ │ │ ├── md.mdp │ │ │ ├── min01.mdp │ │ │ ├── min02.mdp │ │ │ ├── npt.mdp │ │ │ ├── nve.mdp │ │ │ └── nvt.mdp │ └── default_nosc │ │ ├── complex │ │ ├── md.mdp │ │ ├── min01.mdp │ │ ├── min02.mdp │ │ ├── min03.mdp │ │ ├── npt.mdp │ │ ├── nve.mdp │ │ └── nvt.mdp │ │ └── water │ │ ├── md.mdp │ │ ├── min01.mdp │ │ ├── min02.mdp │ │ ├── npt.mdp │ │ ├── nve.mdp │ │ └── nvt.mdp └── output_files_data.ini └── tests ├── __init__.py ├── test_align_ligands.py ├── test_data ├── align_ligands_autodock4 │ ├── 1dvwb_altered.pdb │ ├── FXR_10.dlg │ ├── FXR_12.dlg │ ├── FXR_receptor.pdbqt │ └── results_autodock4.pkl ├── align_ligands_generic │ ├── 1dvwb.pdb │ ├── 1dvwb_altered.pdb │ ├── FXR_10.pdb │ ├── FXR_12.pdb │ └── result_generic.pkl ├── align_ligands_pdb │ ├── 1dvwb.pdb │ ├── 1dvwb_altered.pdb │ ├── FXR_10.pdb │ ├── FXR_12.pdb │ ├── results_pdb1.pkl │ └── results_pdb2.pkl ├── align_ligands_superimpose │ ├── 1dvwb.pdb │ ├── 1dvwb_altered.pdb │ ├── FXR_10.mol2 │ ├── FXR_10_ref.mol2 │ ├── FXR_10_ref.pdb │ ├── FXR_10_result.pdb │ └── FXR_12.mol2 ├── find_mcs_3d │ ├── azithromycin.mol2 │ ├── azithromycin_diastero1.mol2 │ ├── azithromycin_diastero2.mol2 │ ├── galactose.mol2 │ └── glucose.mol2 ├── gromacs_index │ ├── 3ekv.pdb │ ├── 3ekv_gmx.ndx │ ├── 3ekv_gmx_protlig.ndx │ ├── 3ekv_mdanalysis.ndx │ └── 3ekv_mdanalysis_aroundlig.ndx ├── merge_topology_3d │ ├── galactose.mol2 │ ├── galactose.top │ ├── glucose.mol2 │ ├── glucose.top │ ├── mola.pdb │ └── molb.pdb └── parse_ligands_data │ ├── dirs │ ├── FXR_10 │ │ ├── FXR_10.mol2 │ │ └── FXR_10.top │ └── FXR_12 │ │ ├── FXR_12.mol2 │ │ └── FXR_12.top │ ├── files_only │ ├── FXR_10.mol2 │ ├── FXR_10.top │ ├── FXR_12.mol2 │ └── FXR_12.top │ ├── inputfile.txt │ ├── molecules_test1.pkl │ └── molecules_test2.pkl ├── test_detect_solute_molecule_name.py ├── test_find_mcs.py ├── test_mol_util_obmol_to_rwmol.py ├── test_os_util.py ├── test_parse_input_molecules.py ├── test_prepare_dual_topology.py └── test_read_small_molecule_from_pdbqt.py /.gitignore: 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