├── .flake8 ├── .github ├── codecov.yml ├── codeql-config.yml └── workflows │ ├── build.yaml │ ├── codeql.yml │ ├── pytest.yaml │ └── python-linter.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── LICENSE ├── MLmodel-reference.md ├── README.md ├── devtools └── conda-envs │ ├── mols.yml │ └── mols_minimal.yml ├── docs ├── Makefile ├── make.bat ├── scaling.csv └── source │ ├── Citation.rst │ ├── Classes.rst │ ├── Informatics.rst │ ├── Installation.rst │ ├── Scripts.rst │ ├── code_structure.png │ ├── conf.py │ ├── index.rst │ ├── logo.png │ ├── logo_enhanced.png │ └── tutorials │ └── development.rst ├── examples └── example-1.in ├── molSimplify ├── .gitignore ├── Bind │ ├── bicarbonate.mol │ ├── bind.dict │ ├── bisulfate.mol │ ├── bisulfite.mol │ ├── carbonmonoxide.mol │ ├── dihydrogenphosphate.mol │ ├── dihydrogenphosphite.mol │ ├── formate.mol │ ├── nitrate.mol │ ├── oxalate.mol │ ├── oxygen.mol │ ├── perchlorate.mol │ ├── test.smi.smi │ └── water.mol ├── Classes │ ├── .gitignore │ ├── README.md │ ├── __init__.py │ ├── atom3D.py │ ├── dft_obs.py │ ├── globalvars.py │ ├── helpers.py │ ├── ligand.py │ ├── mol2D.py │ ├── mol3D.py │ ├── monomer3D.py │ ├── partialcharges.py │ ├── protein3D.py │ ├── rundiag.py │ └── voxelgrid.py ├── Cores │ ├── Coporphyrin.mol │ ├── Crporphyrin.mol │ ├── Cuporphyrin.mol │ ├── Fe2O2.xyz │ ├── Feporphyrin.mol │ ├── Mnporphyrin.mol │ ├── N2OTS.xyz │ ├── Niporphyrin.mol │ ├── Scporphyrin.mol │ ├── Tiporphyrin.mol │ ├── Vporphyrin.mol │ ├── Znporphyrin.mol │ ├── cores.dict │ ├── cr4nh3o.xyz │ ├── fen4py.xyz │ ├── fen4pyO.xyz │ ├── fenh3O.xyz │ ├── ferrcore.xyz │ ├── ferrocene.mol │ ├── mn3nh3o.xyz │ ├── mn5nh3o.xyz │ └── zncat.xyz ├── Data │ ├── .tcdefinput.inp │ ├── ML.dat │ ├── MLS_FSR_for_inter.dat │ ├── MLS_FSR_for_inter2.dat │ ├── MLS_angle_for_click.dat │ ├── MLS_angle_for_inter.dat │ ├── MLS_angle_for_inter2.dat │ ├── MLS_angle_for_intra.dat │ ├── MLS_angle_for_intra2.dat │ ├── MLS_angle_for_oa.dat │ ├── ML_FSR_for_inter.dat │ ├── ML_FSR_for_inter2.dat │ ├── ML_bond_for_cat.dat │ ├── ML_bond_for_click.dat │ ├── ML_bond_for_inter.dat │ ├── ML_bond_for_inter2.dat │ ├── ML_bond_for_intra.dat │ ├── ML_bond_for_intra2.dat │ ├── ML_bond_for_oa.dat │ ├── bp1.dat │ ├── coordinations.dict │ ├── li.dat │ ├── no.dat │ ├── oct.dat │ ├── pbp.dat │ ├── spy.dat │ ├── sqap.dat │ ├── sqp.dat │ ├── tbp.dat │ ├── tdhd.dat │ ├── thd.dat │ ├── tpl.dat │ └── tpr.dat ├── Informatics │ ├── FeatureSetVisualization.ipynb │ ├── HFXsensitivity │ │ ├── __init__.py │ │ ├── measure_HFX_sensitivity_oxo_hat_reb_rel.py │ │ └── measure_HFX_stable.py │ ├── MOF │ │ ├── MOF_RAC_example.ipynb │ │ ├── MOF_descriptors.py │ │ ├── MOF_fragment_example.ipynb │ │ ├── MOF_functionalizer.py │ │ ├── MOF_functionalizer_v2.py │ │ ├── PBC_functions.py │ │ ├── README.md │ │ ├── __init__.py │ │ ├── atomic.py │ │ ├── cluster_extraction.py │ │ ├── fragment_MOFs_for_pormake.py │ │ ├── functional_group_dictionary.pkl │ │ ├── linker_rotation.py │ │ └── monofunctionalized_BDC │ │ │ ├── CO2H.xyz │ │ │ ├── OCF3.xyz │ │ │ ├── OCH3.xyz │ │ │ ├── README │ │ │ ├── SO3H.xyz │ │ │ ├── example_terachem_input.in │ │ │ └── index_information.py │ ├── Mol2Parser.py │ ├── RACassemble.py │ ├── __init__.py │ ├── active_learning │ │ ├── __init__.py │ │ └── expected_improvement.py │ ├── autocorrelation.py │ ├── coulomb_analyze.py │ ├── decoration_manager.py │ ├── geo_analyze.py │ ├── geometrics.py │ ├── geometrics_csd.json │ ├── graph_analyze.py │ ├── graph_racs.py │ ├── jupyter_vis.py │ ├── lacRACAssemble.py │ ├── misc_descriptors.py │ ├── organic_fingerprints.py │ ├── partialcharges.py │ ├── protein │ │ ├── activesite.py │ │ └── pymol_add_hs.py │ ├── py3Dmol_visualization.ipynb │ └── rac155_geo.py ├── Ligands │ ├── (1_methylbenzimidazol_2_yl)pyridine.xyz │ ├── .gitignore │ ├── 1-4-dimethyl-1-2-3-triazole.xyz │ ├── 12crown4.mol │ ├── Antipyrine.mol │ ├── BPAbipy.mol │ ├── Hpyrrole.mol │ ├── N-quinolinylbutyramidate.xyz │ ├── N-quinolinylmethylmethinylacetamidate.xyz │ ├── NMe2_-1.xyz │ ├── PCy3.mol │ ├── PMe3.xyz │ ├── PPh3.mol │ ├── Propyphenazone.mol │ ├── README │ ├── acac.mol │ ├── acacen.mol │ ├── acetate.smi │ ├── acetate.xyz │ ├── aceticacidbipyridine.mol │ ├── acetonitrile.mol │ ├── alanine.mol │ ├── alphabetizer.py │ ├── amine.mol │ ├── ammonia.mol │ ├── arginine.mol │ ├── asparagine.mol │ ├── aspartic_acid.mol │ ├── azide.mol │ ├── benzene.mol │ ├── benzene_pi.mol │ ├── benzenedithiol.mol │ ├── benzenethiol.mol │ ├── benzylisocy.mol │ ├── bidiazine.mol │ ├── bidiazole.mol │ ├── bifuran.mol │ ├── bihydrodiazine.mol │ ├── bihydrodiazole.mol │ ├── bihydrooxazine.mol │ ├── bihydrooxazole.mol │ ├── bihydrothiazine.mol │ ├── bihydrothiazole.mol │ ├── biimidazole.mol │ ├── bioxazole.mol │ ├── bipy.mol │ ├── bipyrazine.xyz │ ├── bipyrimidine.mol │ ├── bipyrrole.mol │ ├── bisnapthyridylpyridine.mol │ ├── bithiazole.mol │ ├── bromide.mol │ ├── bromide.smi │ ├── c2.mol │ ├── caprolactone.mol │ ├── carbonyl.mol │ ├── carboxyl.mol │ ├── cat.mol │ ├── chloride.mol │ ├── chloride.smi │ ├── chloropyridine.mol │ ├── co2.mol │ ├── corrolazine.mol │ ├── cs.mol │ ├── cyanate.xyz │ ├── cyanide.mol │ ├── cyanoaceticporphyrin.mol │ ├── cyanopyridine.mol │ ├── cyclam.mol │ ├── cyclen.mol │ ├── cyclopentadienyl.mol │ ├── cysteine.mol │ ├── diaminomethyl.mol │ ├── diazine.mol │ ├── diazole.mol │ ├── dicyanamide.mol │ ├── dihydrofuran.mol │ ├── dmap.xyz │ ├── dmf.mol │ ├── dmi.mol │ ├── dmpe.mol │ ├── dpmu.mol │ ├── dppe.mol │ ├── edta.mol │ ├── en.mol │ ├── ethanethiol.mol │ ├── ethanolamine.mol │ ├── ethbipy.mol │ ├── ethyl.mol │ ├── ethylamine.mol │ ├── ethylene.mol │ ├── ethylesteracac.mol │ ├── fluoride.mol │ ├── fluoride.smi │ ├── formaldehyde.mol │ ├── formamidate.xyz │ ├── formate.xyz │ ├── furan.mol │ ├── gitignore │ ├── glutamic_acid.mol │ ├── glutamine.mol │ ├── glycinate.mol │ ├── glycine.mol │ ├── h2s.mol │ ├── helium.mol │ ├── histidine.mol │ ├── hmpa.mol │ ├── hs-.mol │ ├── hydride.mol │ ├── hydrocarboxyacetylide.xyz │ ├── hydrocyanide.mol │ ├── hydrodiazine.mol │ ├── hydrodiazole.mol │ ├── hydrogensulfide.mol │ ├── hydroisocyanide.mol │ ├── hydrooxazine.mol │ ├── hydrooxazole.mol │ ├── hydrothiazine.mol │ ├── hydrothiazole.mol │ ├── hydroxyl.mol │ ├── imidazole.mol │ ├── imidazolidinone.mol │ ├── imine.mol │ ├── iminodiacetic.mol │ ├── iodide.mol │ ├── iodobenzene.xyz │ ├── isoleucine.mol │ ├── isothiocyanate.mol │ ├── leucine.mol │ ├── ligands.dict │ ├── lysine.mol │ ├── mebenzenedithiol.mol │ ├── mebim_py.xyz │ ├── mebim_pz.xyz │ ├── mebipy.mol │ ├── mecat.mol │ ├── methanal.mol │ ├── methanethiol.mol │ ├── methanol.mol │ ├── methionine.mol │ ├── methyl.mol │ ├── methylacetylide.xyz │ ├── methylamine.mol │ ├── methylazide.xyz │ ├── methylisocy.mol │ ├── methylpyridine.mol │ ├── n2.mol │ ├── n4py.xyz │ ├── nch.mol │ ├── nco-.mol │ ├── nethanolamine.mol │ ├── nitrate.mol │ ├── nitrite.mol │ ├── nitro.mol │ ├── nitrobipy.mol │ ├── nitroso.mol │ ├── nme3.mol │ ├── no-.mol │ ├── no2-.mol │ ├── noxygen.mol │ ├── ns-.mol │ ├── o-pyridylbenzene.xyz │ ├── o-pyridylphenylanion.xyz │ ├── o2-.mol │ ├── o2.xyz │ ├── och2.mol │ ├── oethanolamine.mol │ ├── ome2.mol │ ├── ooh.xyz │ ├── oxalate.mol │ ├── oxalate.smi │ ├── oxygen.mol │ ├── pentacyanocyclopentadienide.mol │ ├── pf3.mol2 │ ├── ph2-.mol │ ├── ph3.mol │ ├── phen.mol │ ├── phenacac.mol │ ├── phenalalanine.mol │ ├── phendione.mol │ ├── phenphen.mol │ ├── phenylbenzoxazole.mol │ ├── phenylcyc.mol │ ├── phenylenediamine.mol │ ├── phenylisocy.mol │ ├── phosacidbipy.mol │ ├── phosphine.mol │ ├── phosphorine.mol │ ├── phthalocyanine.mol │ ├── pme3o.mol │ ├── porphyrin.mol │ ├── pph3o.mol │ ├── proline.mol │ ├── propdiol.mol │ ├── propylene.mol │ ├── pyridine.mol │ ├── pyrimidone.mol │ ├── pyrrole.mol │ ├── quinoxalinedithiol.mol │ ├── s2-.mol │ ├── salen.mol │ ├── salphen.mol │ ├── serine.mol │ ├── simple_ligands.dict │ ├── sulfacidbipy.mol │ ├── tbucat.mol │ ├── tbuphisocy.mol │ ├── tbutylcyclen.mol │ ├── tbutylisocy.mol │ ├── tbutylthiol.mol │ ├── tcnoet.mol │ ├── tcnoetOH.mol │ ├── terpy.mol │ ├── tetrahydrofuran.mol │ ├── thiane.mol │ ├── thiazole.mol │ ├── thiocyanate.mol │ ├── thiol.mol │ ├── thiophene.mol │ ├── thiopyridine.mol │ ├── threonine.mol │ ├── tpp.mol │ ├── tricyanomethyl.mol │ ├── trifluoromethyl.mol │ ├── tryptophan.mol │ ├── tyrosine.mol │ ├── uthiol.mol │ ├── uthiolme2.mol │ ├── valine.mol │ ├── water.mol │ └── x.mol ├── README.md ├── SQLite │ └── molSimp.sqlite ├── Scripts │ ├── .gitignore │ ├── __init__.py │ ├── addtodb.py │ ├── align.py │ ├── cellbuilder.py │ ├── cellbuilder_tools.py │ ├── chains.py │ ├── convert_2to3.py │ ├── dbinteract.py │ ├── distgeom.py │ ├── enhanced_structgen.py │ ├── enhanced_structgen_functionality.py │ ├── findcorrelations.py │ ├── generator.py │ ├── geometry.py │ ├── inparse.py │ ├── io.py │ ├── isomers.py │ ├── jobgen.py │ ├── krr_prep.py │ ├── molSimplify_io.py │ ├── namegen.py │ ├── nn_prep.py │ ├── nx_helpers.py │ ├── oct_check_mols.py │ ├── periodic_QE.py │ ├── postmold.py │ ├── postmwfn.py │ ├── postparse.py │ ├── postproc.py │ ├── qcgen.py │ ├── rmsd.py │ ├── rungen.py │ ├── structgen.py │ ├── tf_nn_prep.py │ ├── tsgen.py │ └── uq_calibration.py ├── Substrates │ ├── 1-4-dimethyl-1-2-3-triazole.xyz │ ├── BCM_opt.xyz │ ├── DHA.xyz │ ├── N-quinolinylbutyramidate.xyz │ ├── N2.xyz │ ├── acetaldehyde.xyz │ ├── acetylene.xyz │ ├── benzene.mol │ ├── benzene.xyz │ ├── biphenyl.xyz │ ├── bromobenzene.xyz │ ├── cumene.xyz │ ├── cyclohexene.xyz │ ├── diphenylmethane.xyz │ ├── estrogen.xyz │ ├── ethane.xyz │ ├── ethylene.xyz │ ├── fluorene.xyz │ ├── formaldehyde.xyz │ ├── formicacid.xyz │ ├── iodobenzene.xyz │ ├── methane.xyz │ ├── methanol.xyz │ ├── methylazide.xyz │ ├── new.xyz │ ├── propane.xyz │ ├── propylene.xyz │ ├── propyne.xyz │ ├── substrates.dict │ ├── tert-butane.xyz │ ├── toluene.xyz │ ├── trunc.xyz │ └── xanthene.xyz ├── Unitcells │ ├── anatase_tio2.cif │ ├── gold.cif │ └── iron.cif ├── __init__.py ├── __main__.py ├── icons │ ├── chemdb.png │ ├── geoms │ │ ├── li.png │ │ ├── linear.png │ │ ├── oct.png │ │ ├── octahedral.png │ │ ├── pbp.png │ │ ├── pentagonal_bipyramidal.png │ │ ├── spy.png │ │ ├── sqap.png │ │ ├── sqp.png │ │ ├── square_planar.png │ │ ├── square_pyramidal.png │ │ ├── tbp.png │ │ ├── tetrahedral.png │ │ ├── thd.png │ │ ├── tpl.png │ │ ├── tpr.png │ │ ├── trigonal_bipyramidal.png │ │ ├── trigonal_planar.png │ │ └── trigonal_prismatic.png │ ├── geoms_labels │ │ ├── pure │ │ │ ├── li.png │ │ │ ├── oct.png │ │ │ ├── pbp.png │ │ │ ├── spy.png │ │ │ ├── sqp.png │ │ │ ├── tbp.png │ │ │ ├── thd.png │ │ │ ├── tpl.png │ │ │ └── tpr.png │ │ ├── vector │ │ │ ├── li.eps │ │ │ ├── oct.eps │ │ │ ├── pbp.eps │ │ │ ├── spy.eps │ │ │ ├── sqap.eps │ │ │ ├── sqp.eps │ │ │ ├── tbp.eps │ │ │ ├── thd.eps │ │ │ ├── tpl.eps │ │ │ └── tpr.eps │ │ └── wiki │ │ │ ├── li.png │ │ │ ├── oct.png │ │ │ ├── pbp.png │ │ │ ├── spy.png │ │ │ ├── sqp.png │ │ │ ├── tbp.png │ │ │ ├── thd.png │ │ │ ├── tpl.png │ │ │ └── tpr.png │ ├── hjklogo.png │ ├── icon.png │ ├── logo.png │ ├── logo_enhanced.png │ ├── logo_old.png │ ├── petachem.png │ ├── petachem2.png │ ├── petachem_full.png │ ├── pythonlogo.png │ ├── sge copy.png │ ├── sge.png │ ├── slurm.png │ ├── wft1.png │ ├── wft2 │ ├── wft2.png │ └── wft3.png ├── ml │ ├── __init__.py │ ├── kernels.py │ └── layers.py ├── plugindefines_reference.txt ├── python_krr │ ├── X_train_TS.csv │ ├── __init__.py │ ├── hat2_X_mean_std.csv │ ├── hat2_feature_names.csv │ ├── hat2_krr_model.pkl │ ├── hat2_y_mean_std.csv │ ├── hat_X_mean_std.csv │ ├── hat_feature_names.csv │ ├── hat_krr_X_train.csv │ ├── hat_krr_dual_coef.csv │ ├── hat_krr_model.pkl │ ├── hat_y_mean_std.csv │ ├── sklearn_models.py │ └── y_train_TS.csv ├── python_nn │ ├── .gitignore │ ├── ANN.py │ ├── __init__.py │ ├── clf_analysis_tool.py │ ├── dictionary_toolbox.py │ ├── ensemble_test.py │ ├── hs_center.csv │ ├── hs_scale.csv │ ├── ls_center.csv │ ├── ls_scale.csv │ ├── ms_hs_b1.csv │ ├── ms_hs_b2.csv │ ├── ms_hs_b3.csv │ ├── ms_hs_w1.csv │ ├── ms_hs_w2.csv │ ├── ms_hs_w3.csv │ ├── ms_ls_b1.csv │ ├── ms_ls_b2.csv │ ├── ms_ls_b3.csv │ ├── ms_ls_w1.csv │ ├── ms_ls_w2.csv │ ├── ms_ls_w3.csv │ ├── ms_slope_b1.csv │ ├── ms_slope_b2.csv │ ├── ms_slope_b3.csv │ ├── ms_slope_w1.csv │ ├── ms_slope_w2.csv │ ├── ms_slope_w3.csv │ ├── ms_split_b1.csv │ ├── ms_split_b2.csv │ ├── ms_split_b3.csv │ ├── ms_split_w1.csv │ ├── ms_split_w2.csv │ ├── ms_split_w3.csv │ ├── slope_center.csv │ ├── slope_scale.csv │ ├── split_center.csv │ ├── split_scale.csv │ ├── tf_ANN.py │ └── train_data.csv ├── sklearn_models │ ├── geo_static_clf │ │ └── geo_static_clf_model.h5 │ └── sc_staic_clf │ │ └── sc_static_clf_model.h5 ├── tf_nn │ ├── __init__.py │ ├── geo_static_clf │ │ ├── geo_static_clf_ensemble_spectro │ │ │ ├── spectro_all_geo_0.h5 │ │ │ ├── spectro_all_geo_1.h5 │ │ │ ├── spectro_all_geo_2.h5 │ │ │ ├── spectro_all_geo_3.h5 │ │ │ ├── spectro_all_geo_4.h5 │ │ │ ├── spectro_all_geo_5.h5 │ │ │ ├── spectro_all_geo_6.h5 │ │ │ ├── spectro_all_geo_7.h5 │ │ │ ├── spectro_all_geo_8.h5 │ │ │ └── spectro_all_geo_9.h5 │ │ ├── geo_static_clf_model.h5 │ │ ├── geo_static_clf_train_name.csv │ │ ├── geo_static_clf_train_x.csv │ │ ├── geo_static_clf_train_y.csv │ │ └── geo_static_clf_vars.csv │ ├── geos │ │ ├── hs_ii_bl_x.csv │ │ ├── hs_ii_bl_y.csv │ │ ├── hs_ii_model.h5 │ │ ├── hs_ii_model.json │ │ ├── hs_ii_vars.csv │ │ ├── hs_iii_bl_x.csv │ │ ├── hs_iii_bl_y.csv │ │ ├── hs_iii_model.h5 │ │ ├── hs_iii_model.json │ │ ├── hs_iii_vars.csv │ │ ├── ls_ii_bl_x.csv │ │ ├── ls_ii_bl_y.csv │ │ ├── ls_ii_model.h5 │ │ ├── ls_ii_model.json │ │ ├── ls_ii_vars.csv │ │ ├── ls_iii_bl_x.csv │ │ ├── ls_iii_bl_y.csv │ │ ├── ls_iii_model.h5 │ │ ├── ls_iii_model.json │ │ └── ls_iii_vars.csv │ ├── homolumo │ │ ├── gap_model.h5 │ │ ├── gap_model.json │ │ ├── gap_test_names.csv │ │ ├── gap_test_x.csv │ │ ├── gap_test_y.csv │ │ ├── gap_train_names.csv │ │ ├── gap_train_x.csv │ │ ├── gap_train_y.csv │ │ ├── gap_vars.csv │ │ ├── homo_model.h5 │ │ ├── homo_model.json │ │ ├── homo_test_names.csv │ │ ├── homo_test_x.csv │ │ ├── homo_test_y.csv │ │ ├── homo_train_names.csv │ │ ├── homo_train_x.csv │ │ ├── homo_train_y.csv │ │ └── homo_vars.csv │ ├── oxoandhomo │ │ ├── homo_empty_info.json │ │ ├── homo_empty_model.h5 │ │ ├── homo_empty_model.json │ │ ├── homo_empty_nocharge │ │ │ ├── homo_empty_info.json │ │ │ ├── homo_empty_model.h5 │ │ │ ├── homo_empty_model.json │ │ │ ├── homo_empty_test_names.csv │ │ │ ├── homo_empty_test_x.csv │ │ │ ├── homo_empty_test_y.csv │ │ │ ├── homo_empty_train_names.csv │ │ │ ├── homo_empty_train_x.csv │ │ │ ├── homo_empty_train_y.csv │ │ │ ├── homo_empty_val_names.csv │ │ │ ├── homo_empty_val_x.csv │ │ │ ├── homo_empty_val_y.csv │ │ │ └── homo_empty_vars.csv │ │ ├── homo_empty_test_names.csv │ │ ├── homo_empty_test_x.csv │ │ ├── homo_empty_test_y.csv │ │ ├── homo_empty_train_names.csv │ │ ├── homo_empty_train_x.csv │ │ ├── homo_empty_train_y.csv │ │ ├── homo_empty_val_names.csv │ │ ├── homo_empty_val_x.csv │ │ ├── homo_empty_val_y.csv │ │ ├── homo_empty_vars.csv │ │ ├── oxo20_info.json │ │ ├── oxo20_model.h5 │ │ ├── oxo20_model.json │ │ ├── oxo20_test_names.csv │ │ ├── oxo20_test_x.csv │ │ ├── oxo20_test_y.csv │ │ ├── oxo20_train_names.csv │ │ ├── oxo20_train_x.csv │ │ ├── oxo20_train_y.csv │ │ ├── oxo20_val_names.csv │ │ ├── oxo20_val_x.csv │ │ ├── oxo20_val_y.csv │ │ └── oxo20_vars.csv │ ├── oxocatalysis │ │ ├── hat_model.h5 │ │ ├── hat_model.json │ │ ├── hat_test_names.csv │ │ ├── hat_test_x.csv │ │ ├── hat_test_y.csv │ │ ├── hat_train_names.csv │ │ ├── hat_train_x.csv │ │ ├── hat_train_y.csv │ │ ├── hat_val_x.csv │ │ ├── hat_val_y.csv │ │ ├── hat_vars.csv │ │ ├── old │ │ │ ├── oxo_model.h5 │ │ │ ├── oxo_model.json │ │ │ ├── oxo_test_names.csv │ │ │ ├── oxo_test_x.csv │ │ │ ├── oxo_test_y.csv │ │ │ ├── oxo_train_names.csv │ │ │ ├── oxo_train_x.csv │ │ │ ├── oxo_train_y.csv │ │ │ └── oxo_vars.csv │ │ ├── oxo_model.h5 │ │ ├── oxo_model.json │ │ ├── oxo_test_names.csv │ │ ├── oxo_test_x.csv │ │ ├── oxo_test_y.csv │ │ ├── oxo_train_names.csv │ │ ├── oxo_train_x.csv │ │ ├── oxo_train_y.csv │ │ ├── oxo_val_x.csv │ │ ├── oxo_val_y.csv │ │ └── oxo_vars.csv │ ├── rescaling_data │ │ ├── gap_mean_x.csv │ │ ├── gap_mean_y.csv │ │ ├── gap_var_x.csv │ │ ├── gap_var_y.csv │ │ ├── geo_static_clf_mean_x.csv │ │ ├── geo_static_clf_mean_y.csv │ │ ├── geo_static_clf_var_x.csv │ │ ├── geo_static_clf_var_y.csv │ │ ├── hat_mean_x.csv │ │ ├── hat_mean_y.csv │ │ ├── hat_var_x.csv │ │ ├── hat_var_y.csv │ │ ├── homo_empty_mean_x.csv │ │ ├── homo_empty_mean_y.csv │ │ ├── homo_empty_nocharge │ │ │ ├── homo_empty_mean_x.csv │ │ │ ├── homo_empty_mean_y.csv │ │ │ ├── homo_empty_var_x.csv │ │ │ └── homo_empty_var_y.csv │ │ ├── homo_empty_var_x.csv │ │ ├── homo_empty_var_y.csv │ │ ├── homo_mean_x.csv │ │ ├── homo_mean_y.csv │ │ ├── homo_var_x.csv │ │ ├── homo_var_y.csv │ │ ├── hs_ii_mean_x.csv │ │ ├── hs_ii_mean_y.csv │ │ ├── hs_ii_var_x.csv │ │ ├── hs_ii_var_y.csv │ │ ├── hs_iii_mean_x.csv │ │ ├── hs_iii_mean_y.csv │ │ ├── hs_iii_var_x.csv │ │ ├── hs_iii_var_y.csv │ │ ├── ls_ii_mean_x.csv │ │ ├── ls_ii_mean_y.csv │ │ ├── ls_ii_var_x.csv │ │ ├── ls_ii_var_y.csv │ │ ├── ls_iii_mean_x.csv │ │ ├── ls_iii_mean_y.csv │ │ ├── ls_iii_var_x.csv │ │ ├── ls_iii_var_y.csv │ │ ├── old │ │ │ ├── oxo_mean_x.csv │ │ │ ├── oxo_mean_y.csv │ │ │ ├── oxo_var_x.csv │ │ │ └── oxo_var_y.csv │ │ ├── oxo20_mean_x.csv │ │ ├── oxo20_mean_y.csv │ │ ├── oxo20_var_x.csv │ │ ├── oxo20_var_y.csv │ │ ├── oxo_mean_x.csv │ │ ├── oxo_mean_y.csv │ │ ├── oxo_var_x.csv │ │ ├── oxo_var_y.csv │ │ ├── sc_static_clf_mean_x.csv │ │ ├── sc_static_clf_mean_y.csv │ │ ├── sc_static_clf_var_x.csv │ │ ├── sc_static_clf_var_y.csv │ │ ├── split_mean_x.csv │ │ ├── split_mean_y.csv │ │ ├── split_var_x.csv │ │ └── split_var_y.csv │ ├── sc_static_clf │ │ ├── sc_static_clf_model.h5 │ │ ├── sc_static_clf_train_name.csv │ │ ├── sc_static_clf_train_x.csv │ │ ├── sc_static_clf_train_y.csv │ │ ├── sc_static_clf_vars.csv │ │ └── sc_static_csl_ensemble_spectro │ │ │ ├── spectro_all_sc_0.h5 │ │ │ ├── spectro_all_sc_1.h5 │ │ │ ├── spectro_all_sc_2.h5 │ │ │ ├── spectro_all_sc_3.h5 │ │ │ ├── spectro_all_sc_4.h5 │ │ │ ├── spectro_all_sc_5.h5 │ │ │ ├── spectro_all_sc_6.h5 │ │ │ ├── spectro_all_sc_7.h5 │ │ │ ├── spectro_all_sc_8.h5 │ │ │ └── spectro_all_sc_9.h5 │ └── split │ │ ├── split_model.h5 │ │ ├── split_model.json │ │ ├── split_vars.csv │ │ ├── split_x.csv │ │ ├── split_y.csv │ │ └── train_names.csv └── utils │ ├── Graph_Hash.py │ ├── Importing_Functions.py │ ├── LigandBreakdown.py │ ├── __init__.py │ ├── decorators.py │ ├── metaclasses.py │ ├── nx_helpers.py │ ├── openbabel_helpers.py │ ├── tensorflow.py │ └── timer.py ├── pyproject.toml ├── tests ├── README.txt ├── helperFuncs.py ├── informatics │ ├── test_MOF_descriptors.py │ ├── test_MOF_functional_group_add.py │ ├── test_MOF_functional_group_add_v2.py │ ├── test_MOF_linker_rotation.py │ ├── test_PBC_functions.py │ ├── test_active_learning.py │ ├── test_coulomb_analyze.py │ └── test_graph_racs.py ├── ml │ ├── test_kernels.py │ └── test_layers.py ├── test_atom3D.py ├── test_autocorrelation.py ├── test_basic_imports.py ├── test_cli.py ├── test_decoration.py ├── test_distgeom.py ├── test_example_1.py ├── test_example_3.py ├── test_example_5.py ├── test_example_7.py ├── test_example_8.py ├── test_example_tbp.py ├── test_ff_xtb.py ├── test_geocheck_oct.py ├── test_geocheck_one_empty.py ├── test_geometry.py ├── test_inparse.py ├── test_io.py ├── test_jobgen.py ├── test_joption_pythonic.py ├── test_lig_load.py ├── test_ligand_assign.py ├── test_ligand_assign_consistent.py ├── test_ligand_class.py ├── test_ligand_from_mol_file.py ├── test_ligands.py ├── test_mol2D.py ├── test_mol3D.py ├── test_molcas_caspt2.py ├── test_molcas_casscf.py ├── test_old_ANNs.py ├── test_orca_ccsdt.py ├── test_orca_dft.py ├── test_qcgen.py ├── test_racs.py ├── test_rmsd.py ├── test_structgen_functions.py ├── test_tetrahedral.py ├── test_tutorial_10_part_one.py ├── test_tutorial_10_part_two.py ├── test_tutorial_2.py ├── test_tutorial_3.py ├── test_tutorial_4.py ├── test_tutorial_6.py ├── test_tutorial_8.py ├── test_tutorial_9_part_one.py ├── test_tutorial_9_part_two.py └── testresources │ ├── inputs │ ├── cif_files │ │ ├── Co_MOF_with_duplicate.cif │ │ ├── Co_MOF_with_overlap.cif │ │ ├── Co_MOF_with_solvent.cif │ │ ├── ETECIR_clean.cif │ │ ├── FAVGUH_clean.cif │ │ ├── FOKYIP_clean.cif │ │ ├── MIL-53.cif │ │ ├── NEXXIZ_clean.cif │ │ ├── SETDUS_clean.cif │ │ ├── TIRLIQ.cif │ │ ├── UXUPEK_clean.cif │ │ ├── UiO-66.cif │ │ ├── UiO-67.cif │ │ ├── VONBIK_clean.cif │ │ ├── YAHPON.cif │ │ ├── YICDAR_clean.cif │ │ ├── Zn_MOF_with_duplicate.cif │ │ ├── Zn_MOF_with_overlap.cif │ │ ├── Zn_MOF_with_solvent.cif │ │ ├── odac-21383.cif │ │ ├── odac-21433.cif │ │ ├── odac-21478.cif │ │ ├── odac-21735.cif │ │ ├── odac-21816.cif │ │ └── pd_test_tutorial_2.cif │ ├── edge_compounds │ │ ├── BUFLUM_comp_0.mol2 │ │ ├── BUHMID_comp_0.mol2 │ │ ├── COYXUM_comp_0.mol2 │ │ ├── COYYEX_comp_0.mol2 │ │ └── COYYIB_comp_0.mol2 │ ├── geocheck │ │ ├── H_transfer │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── all_flying_away │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── atom_ordering_mismatch │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── broken_ligands │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── catom_change │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── compact_bonding │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── iodide_radius │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── iodine_sulfur │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── ligand_assemble │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── ligand_bent │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── linear_broken │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── methane_trans │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── oct_comp_greedy │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── one_empty_bad │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── one_empty_good │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── rotational_group │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ ├── switch_test │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ │ └── triplebond_linear_broken │ │ │ ├── init.xyz │ │ │ └── opt.xyz │ ├── geometry_type │ │ ├── linear.xyz │ │ ├── octahedral.xyz │ │ ├── pentagonal_bipyramidal.xyz │ │ ├── pentagonal_planar.xyz │ │ ├── pentagonal_pyramidal.xyz │ │ ├── seesaw.xyz │ │ ├── square_antiprismatic.xyz │ │ ├── square_planar.xyz │ │ ├── square_pyramidal.xyz │ │ ├── t_shape.xyz │ │ ├── tetrahedral.xyz │ │ ├── tricapped_trigonal_prismatic.xyz │ │ ├── trigonal_bipyramidal.xyz │ │ ├── trigonal_planar.xyz │ │ ├── trigonal_prismatic.xyz │ │ └── trigonal_pyramidal.xyz │ ├── hapticity_compounds │ │ ├── BOWROX_comp_0.mol2 │ │ ├── BOXTEQ_comp_0.mol2 │ │ ├── BOXTIU_comp_0.mol2 │ │ ├── BOZHOQ_comp_2.mol2 │ │ ├── BOZHUW_comp_2.mol2 │ │ ├── BUFLUM_comp_0.mol2 │ │ ├── BUHMID_comp_0.mol2 │ │ ├── COYXUM_comp_0.mol2 │ │ ├── COYYEX_comp_0.mol2 │ │ └── COYYIB_comp_0.mol2 │ ├── in_files │ │ ├── bidentate.in │ │ ├── bidentate_v3.in │ │ ├── example_1.in │ │ ├── example_1_noff.in │ │ ├── example_3.in │ │ ├── example_3_noff.in │ │ ├── example_5.in │ │ ├── example_5_noff.in │ │ ├── example_5_v3.in │ │ ├── example_7.in │ │ ├── example_8.in │ │ ├── example_tbp.in │ │ ├── gfnff_NH3_BA.in │ │ ├── ligand_from_mol_file.in │ │ ├── molcas_caspt2.in │ │ ├── molcas_casscf.in │ │ ├── old_ANN.in │ │ ├── orca_ccsdt.in │ │ ├── orca_dft.in │ │ ├── tetrahedral_1.in │ │ ├── tetrahedral_2.in │ │ ├── tutorial_09_part_one.in │ │ ├── tutorial_09_part_two.in │ │ ├── tutorial_10_part_one.in │ │ ├── tutorial_10_part_two.in │ │ ├── tutorial_2.in │ │ ├── tutorial_3.in │ │ ├── tutorial_4_dissim.in │ │ ├── tutorial_4_human.in │ │ ├── tutorial_4_query.in │ │ ├── tutorial_6.in │ │ ├── tutorial_8_part_one.in │ │ ├── tutorial_8_part_two.in │ │ ├── xtb_ANC_fail.in │ │ ├── xtb_H2O_before.in │ │ ├── xtb_bipy_spin5.in │ │ ├── xtb_final_opt.in │ │ └── xtb_imidazole_BA.in │ ├── informatics │ │ ├── co_acac_en.mol2 │ │ ├── co_acac_en_water_hydrogensulfide.mol2 │ │ ├── fe_carbonyl_6.mol2 │ │ └── mn_furan_water_ammonia_furan_water_ammonia.mol2 │ ├── io │ │ ├── ADUYUV.mol2 │ │ ├── acac.mol │ │ ├── acac.mol2 │ │ ├── formaldehyde.mol2 │ │ ├── furan.mol │ │ ├── furan.mol2 │ │ ├── water.mol │ │ └── water.mol2 │ ├── ligand_assign_consistent │ │ ├── fe_acac_bipy_bipy.xyz │ │ └── fe_water_ammonia_carbonyl_formaldehyde_hydrogensulfide_hydrocyanide.xyz │ ├── ligand_class │ │ ├── acac_ref.mol2 │ │ └── fe_acac.mol2 │ ├── mol2_files │ │ ├── carbonyl.mol2 │ │ ├── fluorine.mol2 │ │ ├── phenylpyridine.mol2 │ │ └── porphine.mol2 │ ├── mol_files │ │ ├── caffeine.mol │ │ ├── pdms_unit.mol │ │ └── pdp.mol │ ├── net_files │ │ ├── HKUST-1_linker.net │ │ └── HKUST-1_sbu.net │ ├── qcgen │ │ └── FeH2O6.xyz │ ├── rmsd │ │ ├── BUWGOQ.xyz │ │ ├── BUWGOQ_final.xyz │ │ ├── BUWGOQ_final_reordered.xyz │ │ ├── BUWGOQ_noH.xyz │ │ ├── BUWGOQ_noH_final.xyz │ │ ├── example_1.xyz │ │ └── example_1_noff.xyz │ ├── sandwich_compounds │ │ ├── BOWROX_comp_0.mol2 │ │ ├── BOXTEQ_comp_0.mol2 │ │ ├── BOXTIU_comp_0.mol2 │ │ ├── BOZHOQ_comp_2.mol2 │ │ └── BOZHUW_comp_2.mol2 │ ├── tutorial_4 │ │ └── chembl_33_minimal.sdf │ └── xyz_files │ │ ├── BOWROX_comp_0.xyz │ │ ├── FIrpic.xyz │ │ ├── HKUST-1_linker.xyz │ │ ├── HKUST-1_sbu.xyz │ │ ├── UiO-66_sbu.xyz │ │ ├── benzene.xyz │ │ ├── bimetallic_al_complex.xyz │ │ ├── caffeine.xyz │ │ ├── co.xyz │ │ ├── co_acac_en_water_hydrogensulfide.xyz │ │ ├── cr3_f6_optimization.xyz │ │ ├── cr_acac_acac_bipy.xyz │ │ ├── far_co.xyz │ │ ├── fe_bipy_2_bifuran.xyz │ │ ├── fe_bipy_3.xyz │ │ ├── fe_carbonyl_6.xyz │ │ ├── fe_complex.xyz │ │ ├── fe_pyr_4_furan_2.xyz │ │ ├── fe_pyr_6.xyz │ │ ├── formaldehyde.xyz │ │ ├── in_complex.xyz │ │ ├── mn_furan_water_ammonia_furan_water_ammonia.xyz │ │ ├── ni_porphyrin_complex.xyz │ │ ├── pdms_unit.xyz │ │ ├── pdp.xyz │ │ ├── penicillin.xyz │ │ ├── phenanthroline.xyz │ │ ├── slab.xyz │ │ └── taurine.xyz │ └── refs │ ├── decorated_xyz │ └── mod_benzene.xyz │ ├── example │ ├── example_1.report │ ├── example_1.xyz │ ├── example_1_noff.report │ ├── example_1_noff.xyz │ ├── example_3.report │ ├── example_3.xyz │ ├── example_3_noff.report │ ├── example_3_noff.xyz │ ├── example_5.report │ ├── example_5.xyz │ ├── example_5_noff.report │ ├── example_5_noff.xyz │ ├── example_5_v3.report │ ├── example_5_v3.xyz │ ├── example_5_v3_noff.report │ ├── example_5_v3_noff.xyz │ ├── example_7.report │ ├── example_7.xyz │ ├── example_7_noff.report │ ├── example_7_noff.xyz │ ├── example_8.report │ ├── example_8.xyz │ ├── example_9.report │ ├── example_9.xyz │ ├── example_tbp.report │ └── example_tbp.xyz │ ├── geocheck │ ├── H_transfer │ │ └── ref.json │ ├── all_flying_away │ │ └── ref.json │ ├── atom_ordering_mismatch │ │ └── ref.json │ ├── broken_ligands │ │ └── ref.json │ ├── catom_change │ │ └── ref.json │ ├── compact_bonding │ │ └── ref.json │ ├── iodide_radius │ │ └── ref.json │ ├── iodine_sulfur │ │ └── ref.json │ ├── ligand_assemble │ │ └── ref.json │ ├── ligand_bent │ │ └── ref.json │ ├── linear_broken │ │ └── ref.json │ ├── methane_trans │ │ └── ref.json │ ├── oct_comp_greedy │ │ └── ref.json │ ├── one_empty_bad │ │ └── ref.json │ ├── one_empty_good │ │ └── ref.json │ ├── rotational_group │ │ └── ref.json │ ├── switch_test │ │ └── ref.json │ └── triplebond_linear_broken │ │ └── ref.json │ ├── gfnff │ ├── gfnff_NH3_BA.report │ └── gfnff_NH3_BA.xyz │ ├── graph_hash │ ├── benzene.txt │ ├── co.txt │ └── cr3_f6_optimization.txt │ ├── informatics │ ├── json │ │ ├── lig_racs_co_acac_en.json │ │ ├── lig_racs_fe_carbonyl_6.json │ │ ├── lig_racs_mn_furan_water_ammonia_furan_water_ammonia.json │ │ ├── racs_Co_acac_en_water_hydrogensulfide.json │ │ ├── racs_Fe_carbonyl_6.json │ │ └── racs_Mn_furan_water_ammonia_furan_water_ammonia.json │ └── mof │ │ ├── MOF_descriptors │ │ ├── ETECIR_clean │ │ │ ├── ETECIR_clean.json │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ └── sbu_descriptors.csv │ │ ├── FAVGUH_clean │ │ │ ├── FAVGUH_clean.json │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ └── sbu_descriptors.csv │ │ ├── FOKYIP_clean │ │ │ ├── FOKYIP_clean.json │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ └── sbu_descriptors.csv │ │ ├── NEXXIZ_clean │ │ │ ├── NEXXIZ_clean.json │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ └── sbu_descriptors.csv │ │ ├── SETDUS_clean │ │ │ ├── SETDUS_clean.json │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ └── sbu_descriptors.csv │ │ ├── TIRLIQ │ │ │ ├── TIRLIQ.json │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ └── sbu_descriptors.csv │ │ ├── UXUPEK_clean │ │ │ ├── UXUPEK_clean.json │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ └── sbu_descriptors.csv │ │ ├── VONBIK_clean │ │ │ ├── VONBIK_clean.json │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ └── sbu_descriptors.csv │ │ ├── YAHPON │ │ │ ├── YAHPON.json │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ └── sbu_descriptors.csv │ │ ├── YICDAR_clean │ │ │ ├── YICDAR_clean.json │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ └── sbu_descriptors.csv │ │ ├── odac-21383 │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ ├── odac-21383.json │ │ │ └── sbu_descriptors.csv │ │ ├── odac-21433 │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ ├── odac-21433.json │ │ │ └── sbu_descriptors.csv │ │ ├── odac-21478 │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ ├── odac-21478.json │ │ │ └── sbu_descriptors.csv │ │ ├── odac-21735 │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ ├── odac-21735.json │ │ │ └── sbu_descriptors.csv │ │ └── odac-21816 │ │ │ ├── lc_descriptors.csv │ │ │ ├── linker_descriptors.csv │ │ │ ├── odac-21816.json │ │ │ └── sbu_descriptors.csv │ │ ├── cif │ │ ├── Co_MOF_duplicate_fixed.cif │ │ ├── Co_MOF_overlap_fixed.cif │ │ ├── Co_MOF_solvent_removed.cif │ │ ├── MIL-53_rot_45-00.cif │ │ ├── UiO-66_rot_135-00.cif │ │ ├── UiO-66_rot_270-00.cif │ │ ├── UiO-66_rot_45-00.cif │ │ ├── UiO-67_rot_45-00.cif │ │ ├── Zn_MOF_duplicate_fixed.cif │ │ ├── Zn_MOF_overlap_fixed.cif │ │ ├── Zn_MOF_solvent_removed.cif │ │ ├── functionalized_UiO-66_CH3_1.cif │ │ ├── functionalized_UiO-66_CH3_2.cif │ │ ├── functionalized_UiO-66_CN_1.cif │ │ ├── functionalized_UiO-66_CN_2.cif │ │ ├── functionalized_UiO-66_F_1.cif │ │ ├── functionalized_UiO-66_F_2.cif │ │ ├── functionalized_UiO-66_I_1.cif │ │ ├── functionalized_UiO-66_I_2.cif │ │ ├── functionalized_UiO-66_NO2_1.cif │ │ ├── functionalized_UiO-66_NO2_2.cif │ │ ├── functionalized_UiO-66_OH_1.cif │ │ ├── functionalized_UiO-66_OH_2.cif │ │ └── test_write_cif.cif │ │ ├── functionalized_cifs_v2 │ │ ├── functionalized_UiO-66_Br_1.cif │ │ ├── functionalized_UiO-66_Br_2.cif │ │ ├── functionalized_UiO-66_CF3_1.cif │ │ ├── functionalized_UiO-66_CF3_2.cif │ │ ├── functionalized_UiO-66_CH3_1.cif │ │ ├── functionalized_UiO-66_CH3_2.cif │ │ ├── functionalized_UiO-66_CN_1.cif │ │ ├── functionalized_UiO-66_CN_2.cif │ │ ├── functionalized_UiO-66_COOH_1.cif │ │ ├── functionalized_UiO-66_COOH_2.cif │ │ ├── functionalized_UiO-66_Cl_1.cif │ │ ├── functionalized_UiO-66_Cl_2.cif │ │ ├── functionalized_UiO-66_F_1.cif │ │ ├── functionalized_UiO-66_F_2.cif │ │ ├── functionalized_UiO-66_NH2_1.cif │ │ ├── functionalized_UiO-66_NH2_2.cif │ │ ├── functionalized_UiO-66_NO2_1.cif │ │ ├── functionalized_UiO-66_NO2_2.cif │ │ ├── functionalized_UiO-66_OH_1.cif │ │ ├── functionalized_UiO-66_OH_2.cif │ │ ├── functionalized_UiO-66_SH_1.cif │ │ ├── functionalized_UiO-66_SH_2.cif │ │ ├── functionalized_UiO-66_sulfonic_1.cif │ │ └── functionalized_UiO-66_sulfonic_2.cif │ │ ├── json │ │ ├── FOKYIP_clean_all_atom_types.json │ │ ├── NEXXIZ_clean_all_atom_types.json │ │ ├── SETDUS_clean_all_atom_types.json │ │ ├── UXUPEK_clean_all_atom_types.json │ │ ├── VONBIK_clean_all_atom_types.json │ │ ├── YICDAR_clean_all_atom_types.json │ │ ├── test_findPaths.json │ │ ├── test_get_closed_subgraph_adj_matrix.json │ │ ├── test_get_closed_subgraph_linker_list.json │ │ ├── test_get_closed_subgraph_linker_subgraphlist.json │ │ ├── test_get_closed_subgraph_linkers.json │ │ └── test_get_closed_subgraph_remove_list.json │ │ ├── net │ │ ├── test_writeXYZandGraph.net │ │ └── test_writeXYZandGraph.xyz │ │ └── txt │ │ ├── FOKYIP_clean_adj_mat.txt │ │ ├── FOKYIP_clean_cpar.txt │ │ ├── FOKYIP_clean_distance_mat.txt │ │ ├── FOKYIP_clean_fcoords.txt │ │ ├── NEXXIZ_clean_adj_mat.txt │ │ ├── NEXXIZ_clean_cpar.txt │ │ ├── NEXXIZ_clean_distance_mat.txt │ │ ├── NEXXIZ_clean_fcoords.txt │ │ ├── SETDUS_clean_adj_mat.txt │ │ ├── SETDUS_clean_cpar.txt │ │ ├── SETDUS_clean_distance_mat.txt │ │ ├── SETDUS_clean_fcoords.txt │ │ ├── UXUPEK_clean_adj_mat.txt │ │ ├── UXUPEK_clean_cpar.txt │ │ ├── UXUPEK_clean_distance_mat.txt │ │ ├── UXUPEK_clean_fcoords.txt │ │ ├── VONBIK_clean_adj_mat.txt │ │ ├── VONBIK_clean_cpar.txt │ │ ├── VONBIK_clean_distance_mat.txt │ │ ├── VONBIK_clean_fcoords.txt │ │ ├── YICDAR_clean_adj_mat.txt │ │ ├── YICDAR_clean_cpar.txt │ │ ├── YICDAR_clean_distance_mat.txt │ │ └── YICDAR_clean_fcoords.txt │ ├── joption_pythonic_jobscript │ ├── json │ ├── test_autocorrelation │ │ ├── atom_only_autocorrelation │ │ │ ├── 0-5-10-15_3_False_True_False.json │ │ │ ├── 0-5-10-15_3_True_False_False.json │ │ │ ├── 0_2_True_False_False.json │ │ │ ├── 0_3_True_False_False.json │ │ │ ├── 5_3_False_False_False.json │ │ │ ├── 5_3_False_True_False.json │ │ │ ├── 5_3_False_True_True.json │ │ │ └── 5_3_True_False_False.json │ │ ├── atom_only_deltametric │ │ │ ├── 0-5-10-15_3_False_True_False.json │ │ │ ├── 0-5-10-15_3_True_False_False.json │ │ │ ├── 0_2_True_False_False.json │ │ │ ├── 0_3_True_False_False.json │ │ │ ├── 5_3_False_False_False.json │ │ │ ├── 5_3_False_True_False.json │ │ │ ├── 5_3_False_True_True.json │ │ │ └── 5_3_True_False_False.json │ │ ├── autocorrelation │ │ │ ├── 0_2_True_False_False.json │ │ │ ├── 0_3_True_False_False.json │ │ │ ├── 5_3_False_False_False.json │ │ │ ├── 5_3_False_True_False.json │ │ │ ├── 5_3_False_True_True.json │ │ │ └── 5_3_True_False_False.json │ │ ├── construct_property_vector │ │ │ ├── electronegativity.json │ │ │ ├── group_number.json │ │ │ ├── ident.json │ │ │ ├── nuclear_charge.json │ │ │ ├── polarizability.json │ │ │ ├── size.json │ │ │ └── topology.json │ │ ├── deltametric │ │ │ ├── 0_2_True_False_False.json │ │ │ ├── 0_3_True_False_False.json │ │ │ ├── 5_3_False_False_False.json │ │ │ ├── 5_3_False_True_False.json │ │ │ ├── 5_3_False_True_True.json │ │ │ └── 5_3_True_False_False.json │ │ ├── full_autocorrelation │ │ │ ├── group_number_3_False_False_False.json │ │ │ ├── ident_3_True_False_False.json │ │ │ ├── nuclear_charge_3_False_True_True.json │ │ │ ├── polarizability_3_False_True_False.json │ │ │ ├── size_3_True_False_False.json │ │ │ └── topology_2_True_False_False.json │ │ ├── generate_atomonly_autocorrelations │ │ │ ├── 0-5-10-15_3_False_False_True_False.json │ │ │ ├── 0-5-10-15_3_True_False_False_False.json │ │ │ ├── 0_2_True_False_False_False.json │ │ │ ├── 0_3_True_False_False_False.json │ │ │ ├── 5_3_False_False_False_False.json │ │ │ ├── 5_3_False_True_False_False.json │ │ │ ├── 5_3_False_True_True_True.json │ │ │ └── 5_3_True_False_False_False.json │ │ ├── generate_atomonly_deltametrics │ │ │ ├── 0-5-10-15_3_False_False_True_False.json │ │ │ ├── 0-5-10-15_3_True_False_False_False.json │ │ │ ├── 0_2_True_False_False_False.json │ │ │ ├── 0_3_True_False_False_False.json │ │ │ ├── 5_3_False_False_False_False.json │ │ │ ├── 5_3_False_True_False_False.json │ │ │ ├── 5_3_False_True_True_True.json │ │ │ └── 5_3_True_False_False_False.json │ │ ├── generate_full_complex_autocorrelations │ │ │ ├── 2_True_False_False_False_False_False.json │ │ │ ├── 3_False_False_False_False_False_False.json │ │ │ ├── 3_False_True_False_False_False_False.json │ │ │ ├── 3_False_True_True_False_False_False.json │ │ │ ├── 3_True_False_False_False_False_False.json │ │ │ ├── 3_True_False_False_False_True_False.json │ │ │ ├── 3_True_False_False_True_False_False.json │ │ │ └── 3_True_False_False_True_True_True.json │ │ ├── generate_metal_autocorrelations_1 │ │ │ ├── 2_True_False_False_False_False_False.json │ │ │ ├── 3_False_False_False_False_False_False.json │ │ │ ├── 3_False_True_False_False_False_False.json │ │ │ ├── 3_False_True_True_False_False_False.json │ │ │ ├── 3_True_False_False_False_False_False.json │ │ │ ├── 3_True_False_False_False_True_False.json │ │ │ ├── 3_True_False_False_True_False_False.json │ │ │ └── 3_True_False_False_True_True_True.json │ │ ├── generate_metal_autocorrelations_2 │ │ │ ├── 2_True_False_False_False_False_False.json │ │ │ ├── 3_False_False_False_False_False_False.json │ │ │ ├── 3_False_True_False_False_False_False.json │ │ │ ├── 3_False_True_True_False_False_False.json │ │ │ ├── 3_True_False_False_False_False_False.json │ │ │ ├── 3_True_False_False_False_True_False.json │ │ │ ├── 3_True_False_False_True_False_False.json │ │ │ └── 3_True_False_False_True_True_True.json │ │ ├── generate_metal_autocorrelations_3 │ │ │ ├── 2_True_False_False_False_False_False.json │ │ │ ├── 3_False_False_False_False_False_False.json │ │ │ ├── 3_False_True_False_False_False_False.json │ │ │ ├── 3_False_True_True_False_False_False.json │ │ │ ├── 3_True_False_False_False_False_False.json │ │ │ ├── 3_True_False_False_False_True_False.json │ │ │ ├── 3_True_False_False_True_False_False.json │ │ │ └── 3_True_False_False_True_True_True.json │ │ ├── generate_metal_deltametrics_1 │ │ │ ├── 2_True_False_False_False_False_False.json │ │ │ ├── 3_False_False_False_False_False_False.json │ │ │ ├── 3_False_True_False_False_False_False.json │ │ │ ├── 3_False_True_True_False_False_False.json │ │ │ ├── 3_True_False_False_False_False_False.json │ │ │ ├── 3_True_False_False_False_True_False.json │ │ │ ├── 3_True_False_False_True_False_False.json │ │ │ └── 3_True_False_False_True_True_True.json │ │ ├── generate_metal_deltametrics_2 │ │ │ ├── 2_True_False_False_False_False_False.json │ │ │ ├── 3_False_False_False_False_False_False.json │ │ │ ├── 3_False_True_False_False_False_False.json │ │ │ ├── 3_False_True_True_False_False_False.json │ │ │ ├── 3_True_False_False_False_False_False.json │ │ │ ├── 3_True_False_False_False_True_False.json │ │ │ ├── 3_True_False_False_True_False_False.json │ │ │ └── 3_True_False_False_True_True_True.json │ │ ├── generate_metal_deltametrics_3 │ │ │ ├── 2_True_False_False_False_False_False.json │ │ │ ├── 3_False_False_False_False_False_False.json │ │ │ ├── 3_False_True_False_False_False_False.json │ │ │ ├── 3_False_True_True_False_False_False.json │ │ │ ├── 3_True_False_False_False_False_False.json │ │ │ ├── 3_True_False_False_False_True_False.json │ │ │ ├── 3_True_False_False_True_False_False.json │ │ │ └── 3_True_False_False_True_True_True.json │ │ ├── get_descriptor_vector │ │ │ ├── 2_False_False_False_False_False_names.json │ │ │ ├── 2_False_False_False_False_False_vals.json │ │ │ ├── 3_False_False_False_False_False_names.json │ │ │ ├── 3_False_False_False_False_False_vals.json │ │ │ ├── 3_False_False_False_False_True_names.json │ │ │ ├── 3_False_False_False_False_True_vals.json │ │ │ ├── 3_False_False_True_False_False_names.json │ │ │ ├── 3_False_False_True_False_False_vals.json │ │ │ ├── 3_False_False_True_True_False_names.json │ │ │ ├── 3_False_False_True_True_False_vals.json │ │ │ ├── 3_True_False_False_False_False_names.json │ │ │ ├── 3_True_False_False_False_False_vals.json │ │ │ ├── 3_True_True_False_False_False_names.json │ │ │ ├── 3_True_True_False_False_False_vals.json │ │ │ ├── 3_True_True_True_True_True_names.json │ │ │ └── 3_True_True_True_True_True_vals.json │ │ ├── metal_only_autocorrelation_1 │ │ │ ├── group_number_3_False_False_False.json │ │ │ ├── ident_3_True_False_False.json │ │ │ ├── nuclear_charge_3_False_True_True.json │ │ │ ├── polarizability_3_False_True_False.json │ │ │ ├── size_3_True_False_False.json │ │ │ └── topology_2_True_False_False.json │ │ ├── metal_only_autocorrelation_2 │ │ │ ├── group_number_3_False_False_False.json │ │ │ ├── ident_3_True_False_False.json │ │ │ ├── nuclear_charge_3_False_True_True.json │ │ │ ├── polarizability_3_False_True_False.json │ │ │ ├── size_3_True_False_False.json │ │ │ └── topology_2_True_False_False.json │ │ ├── metal_only_autocorrelation_3 │ │ │ ├── group_number_3_False_False_False.json │ │ │ ├── ident_3_True_False_False.json │ │ │ ├── nuclear_charge_3_False_True_True.json │ │ │ ├── polarizability_3_False_True_False.json │ │ │ ├── size_3_True_False_False.json │ │ │ └── topology_2_True_False_False.json │ │ ├── metal_only_deltametric_1 │ │ │ ├── group_number_3_False_False_False.json │ │ │ ├── ident_3_True_False_False.json │ │ │ ├── nuclear_charge_3_False_True_True.json │ │ │ ├── polarizability_3_False_True_False.json │ │ │ ├── size_3_True_False_False.json │ │ │ └── topology_2_True_False_False.json │ │ ├── metal_only_deltametric_2 │ │ │ ├── group_number_3_False_False_False.json │ │ │ ├── ident_3_True_False_False.json │ │ │ ├── nuclear_charge_3_False_True_True.json │ │ │ ├── polarizability_3_False_True_False.json │ │ │ ├── size_3_True_False_False.json │ │ │ └── topology_2_True_False_False.json │ │ └── metal_only_deltametric_3 │ │ │ ├── group_number_3_False_False_False.json │ │ │ ├── ident_3_True_False_False.json │ │ │ ├── nuclear_charge_3_False_True_True.json │ │ │ ├── polarizability_3_False_True_False.json │ │ │ ├── size_3_True_False_False.json │ │ │ └── topology_2_True_False_False.json │ └── test_mol3D │ │ ├── assign_graph_from_net │ │ ├── HKUST-1_linker_graph.json │ │ └── HKUST-1_sbu_graph.json │ │ ├── convert2OBMol │ │ ├── caffeine_fc_False_OB_dict.json │ │ ├── caffeine_fc_True_OB_dict.json │ │ ├── cr3_f6_optimization_fc_False_OB_dict.json │ │ ├── cr3_f6_optimization_fc_True_OB_dict.json │ │ ├── taurine_fc_False_OB_dict.json │ │ └── taurine_fc_True_OB_dict.json │ │ ├── convert2OBMol2 │ │ ├── caffeine_OB_dict.json │ │ ├── caffeine_bo_mat.json │ │ ├── cr3_f6_optimization_OB_dict.json │ │ ├── cr3_f6_optimization_bo_mat.json │ │ ├── taurine_OB_dict.json │ │ └── taurine_bo_mat.json │ │ ├── createMolecularGraph │ │ ├── FIrpic_oct_False_graph.json │ │ ├── FIrpic_oct_True_graph.json │ │ ├── caffeine_oct_False_graph.json │ │ ├── caffeine_oct_True_graph.json │ │ ├── fe_complex_oct_False_graph.json │ │ └── fe_complex_oct_True_graph.json │ │ ├── deleteatom │ │ ├── FIrpic_bo_dict_False_graph_False.json │ │ ├── FIrpic_bo_dict_False_graph_True.json │ │ ├── FIrpic_bo_dict_True_graph_False.json │ │ ├── FIrpic_bo_dict_True_graph_True.json │ │ ├── penicillin_bo_dict_False_graph_False.json │ │ ├── penicillin_bo_dict_False_graph_True.json │ │ ├── penicillin_bo_dict_True_graph_False.json │ │ └── penicillin_bo_dict_True_graph_True.json │ │ ├── deleteatoms │ │ ├── FIrpic_bo_dict_False_graph_False.json │ │ ├── FIrpic_bo_dict_False_graph_True.json │ │ ├── FIrpic_bo_dict_True_graph_False.json │ │ ├── FIrpic_bo_dict_True_graph_True.json │ │ ├── penicillin_bo_dict_False_graph_False.json │ │ ├── penicillin_bo_dict_False_graph_True.json │ │ ├── penicillin_bo_dict_True_graph_False.json │ │ └── penicillin_bo_dict_True_graph_True.json │ │ ├── populateBOMatrix │ │ ├── benzene_bo_dict_False.json │ │ ├── benzene_bo_dict_True.json │ │ ├── benzene_molBOMat.json │ │ ├── caffeine_bo_dict_False.json │ │ ├── caffeine_bo_dict_True.json │ │ └── caffeine_molBOMat.json │ │ ├── readfrommol │ │ ├── pdms_unit_bo_dict.json │ │ ├── pdms_unit_bo_mat.json │ │ ├── pdms_unit_graph.json │ │ ├── pdp_bo_dict.json │ │ ├── pdp_bo_mat.json │ │ └── pdp_graph.json │ │ └── readfrommol2 │ │ ├── BOWROX_comp_0_bo_dict.json │ │ ├── BOWROX_comp_0_bo_mat.json │ │ ├── BOWROX_comp_0_graph.json │ │ ├── formaldehyde_bo_dict.json │ │ ├── formaldehyde_bo_mat.json │ │ └── formaldehyde_graph.json │ ├── ligand_from_mol │ ├── ligand_from_mol_file.report │ └── ligand_from_mol_file.xyz │ ├── molcas │ ├── molcas_caspt2.qcin │ ├── molcas_caspt2.report │ ├── molcas_caspt2.xyz │ ├── molcas_casscf.qcin │ ├── molcas_casscf.report │ └── molcas_casscf.xyz │ ├── old_ann │ ├── old_ANN.report │ └── old_ANN.xyz │ ├── orca │ ├── orca_ccsdt.qcin │ ├── orca_ccsdt.report │ ├── orca_ccsdt.xyz │ ├── orca_dft.qcin │ ├── orca_dft.report │ └── orca_dft.xyz │ ├── qcgen │ ├── gamgen │ │ └── FeH2O6 │ │ │ └── B3LYP │ │ │ └── gam.inp │ ├── mlpgen │ │ └── FeH2O6.mop │ ├── molcgen │ │ └── molcas.input │ ├── ogen │ │ └── orca.in │ ├── qgen │ │ └── FeH2O6 │ │ │ └── B3LYP │ │ │ └── qch.inp │ └── tcgen │ │ └── terachem_input │ ├── racs │ ├── generate_references.py │ ├── racs_Co_acac_en_water_hydrogensulfide.pickle │ ├── racs_Cr_acac_acac_bipy.pickle │ ├── racs_Fe_carbonyl_6.pickle │ └── racs_Mn_furan_water_ammonia_furan_water_ammonia.pickle │ ├── structgen │ └── structgen_complex.xyz │ ├── test_cli │ ├── fe_oct_2_water_6_s_5_conf_1.molinp │ ├── fe_oct_2_water_6_s_5_conf_1.report │ └── fe_oct_2_water_6_s_5_conf_1.xyz │ ├── tetrahedral │ ├── tetrahedral_1_noff.report │ ├── tetrahedral_1_noff.xyz │ ├── tetrahedral_2_noff.report │ └── tetrahedral_2_noff.xyz │ ├── tutorial │ ├── tutorial_09_part_one.report │ ├── tutorial_09_part_one.xyz │ ├── tutorial_09_part_two.report │ ├── tutorial_09_part_two.xyz │ ├── tutorial_10_part_one.report │ ├── tutorial_10_part_one.xyz │ ├── tutorial_10_part_two.report │ ├── tutorial_10_part_two.xyz │ ├── tutorial_2.xyz │ ├── tutorial_3.report │ ├── tutorial_3.xyz │ ├── tutorial_4 │ │ ├── dissimres.smi │ │ ├── simres.smi │ │ └── simres_human.smi │ ├── tutorial_6.xyz │ ├── tutorial_8_part_one.report │ ├── tutorial_8_part_one.xyz │ ├── tutorial_8_part_two.report │ ├── tutorial_8_part_two.xyz │ └── tutorial_qm9_part_one.xyz │ ├── write_tests │ ├── writemol2_test_ignoreX_False.mol2 │ ├── writemol2_test_ignoreX_True.mol2 │ ├── writexyz_test_withgraph_False_ignoreX_False_no_tabs_False.xyz │ ├── writexyz_test_withgraph_False_ignoreX_False_no_tabs_True.xyz │ ├── writexyz_test_withgraph_False_ignoreX_True_no_tabs_False.xyz │ └── writexyz_test_withgraph_True_ignoreX_False_no_tabs_False.xyz │ ├── xtb │ ├── xtb_ANC_fail.report │ ├── xtb_ANC_fail.xyz │ ├── xtb_H2O_before.report │ ├── xtb_H2O_before.xyz │ ├── xtb_bipy_spin5.report │ ├── xtb_bipy_spin5.xyz │ ├── xtb_final_opt.report │ ├── xtb_final_opt.xyz │ ├── xtb_imidazole_BA.report │ └── xtb_imidazole_BA.xyz │ └── xyz_files │ ├── CC(C)O.xyz │ └── pentacyanopentadienide.xyz └── workflows └── NandyJACSAu2022 ├── GeoFreeRAC.ipynb ├── bridge_functionalizer.py ├── frag_functionalizer.py ├── fragment_classes.py └── macrocycle_synthesis.py /.flake8: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hjkgrp/molSimplify/HEAD/.flake8 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