├── .gitignore ├── FMOkit ├── Atom.py ├── Fragment.py ├── System.py ├── __init__.py ├── config │ └── config.toml ├── hyb_carbon.py └── maeparser.py ├── LICENSE ├── README.md ├── examples ├── 1ioe-fmokit.inp ├── 1ioe-fmokit.out ├── 1ioe-pieda.tsv ├── 1ioe_pieda.ipynb ├── 1ioe_processed.cif ├── 5awl_pieda.ipynb ├── 5law-fmokit.inp ├── 5law-fmokit.out ├── 5law-pieda.tsv ├── 5law_pieda.ipynb ├── 5law_processed.cif ├── 5law_split-fmokit.out ├── 5law_split-pieda.tsv ├── 5law_split_ligand.cif ├── 5law_split_pieda.ipynb ├── 6fgl-fmokit.inp ├── 6fgl-fmokit.out ├── 6fgl-pieda.tsv ├── 6fgl_pieda.ipynb ├── 7w9n-addH.cif ├── 7w9n-fmokit.inp ├── 7w9n-fmokit.out ├── 7w9n-pieda.tsv ├── 7w9n_pieda.ipynb ├── 9cpd-fmokit.inp ├── 9cpd-fmokit.out ├── 9cpd-pieda.tsv ├── 9cpd_pieda.ipynb ├── 9cpd_processed.cif ├── prepare_complex-1IOE.ipynb ├── prepare_complex-1IOE.pdb ├── prepare_complex-5law.ipynb └── prepare_complex.ipynb ├── setup.py ├── tests ├── 1crn-addH.pdb ├── 1crn-fmo.inp ├── 1crn-fmo.out ├── 1crn.cif ├── 1crn.pdb ├── 1ioe.cif ├── 1ioe.mae ├── 1ioe_heavy.mae ├── 5awl-addH-capped.cif ├── 5awl-addH-capped.inp ├── 5awl-addH-dftbenergy.inp ├── 5awl-addH-dftbenergy.out ├── 5awl-addH-dftbenergy_pieda.csv ├── 5awl-addH-energy.inp ├── 5awl-addH-opt.inp ├── 5awl-addH.cif ├── 5awl-addH.inp ├── 5awl-addH.out ├── 5awl-addH.pdb ├── 5awl-addH_appendH.cif ├── 5awl-addH_fc.cif ├── 5awl-addH_mae.cif ├── 5awl-addH_pieda.csv ├── 5awl-appendHtest.inp ├── 5awl-fctest.inp ├── 5awl-fmo.inp ├── 5awl-fmo.out ├── 5awl-fmo_pieda.csv ├── 5awl-fmokit.inp ├── 5awl-fmokit.out ├── 5awl-longfrgnam.inp ├── 5awl-pieda.tsv ├── 5awl-s.inp ├── 5awl-ss.inp ├── 5awl.cif ├── 5awl.pdb ├── 6fgl_processed.cif ├── atom_test.py └── facio │ ├── 1crn-addH_R_pcm.inp │ ├── 1ioe_6-31Gs.inp │ ├── 1ioe_6-31Gss.inp │ ├── 1ioe_prepared.pdb │ ├── 1ioe_prepared_H.pdb │ ├── 5awl.pdb │ ├── 5awl_H.pdb │ ├── 5awl_H_R.inp │ ├── 5awl_H_R.pdb │ ├── 5awl_H_R_energy.inp │ ├── 5awl_H_R_energy.out │ ├── 6sm8.pdb │ ├── 6sm8_6-31Gs.inp │ ├── 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