Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Z _ __post_init__() (bonafide.utils.molecule_vault.MolVault method) __repr__() (bonafide.utils.molecule_vault.MolVault method) _abc_impl (bonafide.utils.input_validation.ValidateAlfabet attribute) (bonafide.utils.input_validation.ValidateBonafideAutocorrelation attribute) (bonafide.utils.input_validation.ValidateBonafideConstant attribute) (bonafide.utils.input_validation.ValidateBonafideDistance attribute) (bonafide.utils.input_validation.ValidateBonafideFunctionalGroup attribute) (bonafide.utils.input_validation.ValidateBonafideOxidationState attribute) (bonafide.utils.input_validation.ValidateBonafideSymmetry attribute) (bonafide.utils.input_validation.ValidateDbstep attribute) (bonafide.utils.input_validation.ValidateDscribeAcsf attribute) (bonafide.utils.input_validation.ValidateDscribeCoulombMatrix attribute) (bonafide.utils.input_validation.ValidateDscribeLmbtr attribute) (bonafide.utils.input_validation.ValidateDscribeSoap attribute) (bonafide.utils.input_validation.ValidateDummy attribute) (bonafide.utils.input_validation.ValidateKallisto attribute) (bonafide.utils.input_validation.ValidateMendeleev attribute) (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume attribute) (bonafide.utils.input_validation.ValidateMorfeusConeAndSolidAngle attribute) (bonafide.utils.input_validation.ValidateMorfeusDispersion attribute) (bonafide.utils.input_validation.ValidateMorfeusLocalForce attribute) (bonafide.utils.input_validation.ValidateMorfeusPyramidalization attribute) (bonafide.utils.input_validation.ValidateMorfeusSasa attribute) (bonafide.utils.input_validation.ValidateMultiwfnBondAnalysis attribute) (bonafide.utils.input_validation.ValidateMultiwfnCdft attribute) (bonafide.utils.input_validation.ValidateMultiwfnFuzzy attribute) (bonafide.utils.input_validation.ValidateMultiwfnMisc attribute) (bonafide.utils.input_validation.ValidateMultiwfnOrbital attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) (bonafide.utils.input_validation.ValidateMultiwfnRootData attribute) (bonafide.utils.input_validation.ValidateMultiwfnSurface attribute) (bonafide.utils.input_validation.ValidateMultiwfnTopology attribute) (bonafide.utils.input_validation.ValidatePsi4 attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) (bonafide.utils.input_validation.ValidateXtb attribute) _abs_diff() (bonafide.features.autocorrelation._Bonafide2DAtomAutocorrelation static method) _add_custom_functional_groups() (bonafide.features.functional_group.Bonafide2DAtomFunctionalGroupMatch method) _Alfabet2DBond (class in bonafide.features.alfabet_) _analyze_rings() (bonafide.features.rdkit_atom._Rdkit2DAtomRingInfo method) (bonafide.features.rdkit_bond._Rdkit2DBondRingInfo method) _atom_feature_indices_2D (bonafide._bonafide._AtomBondFeaturizer attribute) (bonafide._bonafide_utils._AtomBondFeaturizerUtils attribute) _atom_feature_indices_3D (bonafide._bonafide._AtomBondFeaturizer attribute) (bonafide._bonafide_utils._AtomBondFeaturizerUtils attribute) _AtomBondFeaturizer (class in bonafide._bonafide) _AtomBondFeaturizerUtils (class in bonafide._bonafide_utils) _attach_electronic_structure() (bonafide._bonafide._AtomBondFeaturizer method) _attach_energy() (bonafide._bonafide._AtomBondFeaturizer method) _attach_smiles() (bonafide._bonafide._AtomBondFeaturizer method) _BaseMixin (class in bonafide.utils.base_mixin) _Bonafide2DAtomAutocorrelation (class in bonafide.features.autocorrelation) _Bonafide2DAtomIsSpiroBridgehead (class in bonafide.features.spiro_bridgehead) _BonafideAtomDistance (class in bonafide.features.distance) _BonafideBondDistance (class in bonafide.features.distance) _bond_feature_indices_2D (bonafide._bonafide._AtomBondFeaturizer attribute) (bonafide._bonafide_utils._AtomBondFeaturizerUtils attribute) _bond_feature_indices_3D (bonafide._bonafide._AtomBondFeaturizer attribute) (bonafide._bonafide_utils._AtomBondFeaturizerUtils attribute) _calculate_electronic_structure() (bonafide._bonafide._AtomBondFeaturizer method) _calculate_global_descriptors_fmo() (bonafide.features.multiwfn_cdft._Multiwfn3DAtomCdftLocal method) (bonafide.features.xtb_fukui_misc._Xtb3DAtomFukuiMisc method) _calculate_global_descriptors_redox() (bonafide.utils.cdft_redox_mixin.CdftLocalRedoxMixin method) _cast_reduced_props_to_mol() (bonafide.utils.feature_output.FeatureOutput method) _check_atom_indices() (bonafide._bonafide_utils._AtomBondFeaturizerUtils method) _check_bond_indices() (bonafide._bonafide_utils._AtomBondFeaturizerUtils method) _check_config_dict() (bonafide._bonafide._AtomBondFeaturizer method) _check_electronic_structure_data() (bonafide.features.multiwfn_cdft._Multiwfn3DAtomCdftLocal method) (bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedFukui method) _check_energy_data() (bonafide.utils.cdft_redox_mixin.CdftLocalRedoxMixin method) _check_feature_indices() (bonafide._bonafide_utils._AtomBondFeaturizerUtils method) _check_is_2D() (bonafide._bonafide_utils._AtomBondFeaturizerUtils method) _check_is_initialized() (bonafide._bonafide_utils._AtomBondFeaturizerUtils method) _check_is_of_type() (bonafide._bonafide_utils._AtomBondFeaturizerUtils method) _check_is_str_in_list() (bonafide._bonafide_utils._AtomBondFeaturizerUtils method) _check_renumbering_list() (in module bonafide.utils.helper_functions_chemistry) _check_requirements() (bonafide.utils.base_featurizer.BaseFeaturizer method) (bonafide.utils.base_single_point.BaseSinglePoint method) _check_xtb_method() (bonafide.features.xtb_fukui_misc._Xtb3DAtomFukuiMisc method) _check_xtb_version() (in module bonafide.utils.dependencies) _clear_feature_cache() (bonafide._bonafide._AtomBondFeaturizer method) _clear_mols() (bonafide.utils.feature_output.FeatureOutput method) _clrk_exists() (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace method) _Dbstep3DAtom (class in bonafide.features.dbstep_) _determine_bonds() (bonafide._bonafide._AtomBondFeaturizer method) _DistanceMatrixMixin (class in bonafide.features.distance) _Dscribe3DAtom (class in bonafide.features.dscribe_) _err (bonafide.utils.base_featurizer.BaseFeaturizer attribute) _extract_energy_from_mol_object() (bonafide.utils.molecule_vault.MolVault static method) _extract_energy_from_xyz_block() (bonafide.utils.molecule_vault.MolVault static method) _feature_config (bonafide._bonafide._AtomBondFeaturizer attribute) (bonafide._bonafide_utils._AtomBondFeaturizerUtils attribute) _feature_info (bonafide._bonafide._AtomBondFeaturizer attribute) (bonafide._bonafide_utils._AtomBondFeaturizerUtils attribute) _feature_info_df (bonafide._bonafide._AtomBondFeaturizer attribute) _fill_missing_features() (bonafide.utils.feature_output.FeatureOutput method) _format_orbital_idx() (bonafide.features.multiwfn_orbital._Multiwfn3DAtomMoContribution method) _from_cache() (bonafide.utils.base_featurizer.BaseFeaturizer method) _functional_groups_smarts (bonafide._bonafide._AtomBondFeaturizer attribute) (bonafide.features.functional_group.Bonafide2DAtomFunctionalGroupMatch attribute) _get_attribute_data() (bonafide.features.mendeleev_._Mendeleev2DAtom method) _get_autocorrelation_vector() (bonafide.features.autocorrelation._Bonafide2DAtomAutocorrelation method) _get_configs() (bonafide._bonafide_utils._AtomBondFeaturizerUtils method) _get_distance() (bonafide.features.multiwfn_topology_bond._Multiwfn3DBondTopology static method) _get_distance_matrix_2D() (bonafide.features.distance._DistanceMatrixMixin method) _get_distance_matrix_3D() (bonafide.features.distance._DistanceMatrixMixin method) _get_en_data() (bonafide.features.mendeleev_._Mendeleev2DAtom method) _get_feature_df() (bonafide.utils.feature_output.FeatureOutput method) _get_fukuis() (bonafide.features.xtb_fukui_misc._Xtb3DAtomFukuiMisc method) _get_program_filetype() (bonafide.features.morfeus_local_force._Morfeus3DBondLocalForce method) _get_property_vector() (bonafide.features.autocorrelation._Bonafide2DAtomAutocorrelation method) _get_rank_idx() (bonafide.features.symmetric_sites.Bonafide2DBondIsSymmetricTo static method) _get_relative_bond_position() (bonafide.features.multiwfn_topology_bond._Multiwfn3DBondTopology static method) _get_relative_energies() (bonafide.utils.molecule_vault.MolVault method) _get_renumbering_list() (in module bonafide.utils.helper_functions_chemistry) _get_solvent_input_string() (bonafide.utils.sp_psi4.Psi4SP static method) _get_spiro_bridgehead() (bonafide.features.spiro_bridgehead._Bonafide2DAtomIsSpiroBridgehead method) _get_structure_input_string() (bonafide.utils.sp_psi4.Psi4SP static method) _get_time_stamp() (bonafide.log_file_analysis.LogFileAnalyzer method) _init_directory (bonafide._bonafide._AtomBondFeaturizer attribute) _init_logging() (bonafide._bonafide._AtomBondFeaturizer method) _Kallisto3DAtom (class in bonafide.features.kallisto_) _keep_output_files (bonafide._bonafide._AtomBondFeaturizer attribute) (bonafide.utils.base_mixin._BaseMixin attribute) (bonafide.utils.base_single_point.BaseSinglePoint attribute) _kronecker_delta() (bonafide.features.autocorrelation._Bonafide2DAtomAutocorrelation static method) _list_features() (bonafide._bonafide._AtomBondFeaturizer method) _load_config_file() (bonafide._bonafide._AtomBondFeaturizer method) _load_feature_info_file() (bonafide._bonafide._AtomBondFeaturizer method) _loc (bonafide._bonafide._AtomBondFeaturizer attribute) (bonafide._bonafide_utils._AtomBondFeaturizerUtils attribute) _LowdinAlphaBetaMixin (class in bonafide.features.multiwfn_population) _LowdinMixin (class in bonafide.features.multiwfn_spin_population) _mean() (bonafide.features.autocorrelation._Bonafide2DAtomAutocorrelation static method) _Mendeleev2DAtom (class in bonafide.features.mendeleev_) _modify_settings_ini() (in module bonafide.utils.driver) _Morfeus3DAtomBV (class in bonafide.features.morfeus_bv) _Morfeus3DAtomDispersion (class in bonafide.features.morfeus_dispersion) _Morfeus3DAtomSASA (class in bonafide.features.morfeus_sasa) _Morfeus3DBondLocalForce (class in bonafide.features.morfeus_local_force) _MullikenAlphaBetaMixin (class in bonafide.features.multiwfn_population) _MullikenBickelhauptAlphaBetaMixin (class in bonafide.features.multiwfn_population) _MullikenMixin (class in bonafide.features.multiwfn_spin_population) _MullikenRosSchuitAlphaBetaMixin (class in bonafide.features.multiwfn_population) _MullikenStoutPolitzerAlphaBetaMixin (class in bonafide.features.multiwfn_population) _Multiwfn3DAtomCdftCondensedFukui (class in bonafide.features.multiwfn_fukui) _Multiwfn3DAtomCdftCondensedOrbitalWeightedFukui (class in bonafide.features.multiwfn_fukui) _Multiwfn3DAtomCdftLocal (class in bonafide.features.multiwfn_cdft) _Multiwfn3DAtomConnectivity (class in bonafide.features.multiwfn_connectivity) _Multiwfn3DAtomForce (class in bonafide.features.multiwfn_forces) _Multiwfn3DAtomMoContribution (class in bonafide.features.multiwfn_orbital) _Multiwfn3DAtomPopulationAnalysis (class in bonafide.features.multiwfn_population_analysis) _Multiwfn3DAtomSurface (class in bonafide.features.multiwfn_surface) _Multiwfn3DAtomTopology (class in bonafide.features.multiwfn_topology_atom) _Multiwfn3DBond (class in bonafide.features.multiwfn_bond_misc) _Multiwfn3DBondOrder (class in bonafide.features.multiwfn_bond) _Multiwfn3DBondTopology (class in bonafide.features.multiwfn_topology_bond) _Multiwfn3DFuzzySpace (class in bonafide.features.multiwfn_fuzzy_space) _Multiwfn3DHilbertSpace (class in bonafide.features.multiwfn_hilbert_space) _namespace (bonafide._bonafide._AtomBondFeaturizer attribute) (bonafide._bonafide_utils._AtomBondFeaturizerUtils attribute) _out (bonafide.utils.base_featurizer.BaseFeaturizer attribute) _output_directory (bonafide._bonafide._AtomBondFeaturizer attribute) _parse_delocalization_matrix() (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace method) _parse_localization_index_block() (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace method) _periodic_table (bonafide._bonafide._AtomBondFeaturizer attribute) (bonafide.features.mendeleev_._Mendeleev2DAtom attribute) (bonafide.features.oxidation_state.Bonafide2DAtomOxidationState attribute) _postprocess_df() (bonafide.utils.feature_output.FeatureOutput method) _process_feature_info_dict() (bonafide._bonafide._AtomBondFeaturizer method) _pull_from_periodic_table() (bonafide.features.mendeleev_._Mendeleev2DAtom method) _Qmdesc2DAtom (class in bonafide.features.qmdesc_) _Qmdesc2DBond (class in bonafide.features.qmdesc_) _Rdkit2DAtomRingInfo (class in bonafide.features.rdkit_atom) _Rdkit2DBondRingInfo (class in bonafide.features.rdkit_bond) _read_atom_prop_file() (bonafide.features.multiwfn_topology_atom._Multiwfn3DAtomTopology method) _read_cp_prop_file() (bonafide.features.multiwfn_topology_bond._Multiwfn3DBondTopology method) _read_file() (bonafide.log_file_analysis.LogFileAnalyzer method) _read_fmo_energies() (in module bonafide.utils.global_properties) _read_functional_group_smarts() (bonafide.features.functional_group.Bonafide2DAtomFunctionalGroupMatch method) _read_output_file() (bonafide.features.alfabet_._Alfabet2DBond method) (bonafide.features.kallisto_._Kallisto3DAtom method) (bonafide.features.multiwfn_bond._Multiwfn3DBondOrder method) (bonafide.features.multiwfn_bond_misc._Multiwfn3DBond method) (bonafide.features.multiwfn_connectivity._Multiwfn3DAtomConnectivity method) (bonafide.features.multiwfn_forces._Multiwfn3DAtomForce method) (bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedOrbitalWeightedFukui method) (bonafide.features.multiwfn_misc.Multiwfn3DAtomEnergyIndex method) (bonafide.features.multiwfn_orbital._Multiwfn3DAtomMoContribution method) (bonafide.features.multiwfn_population_analysis._Multiwfn3DAtomPopulationAnalysis method) (bonafide.features.multiwfn_surface._Multiwfn3DAtomSurface method) (bonafide.features.xtb_fukui_misc._Xtb3DAtomFukuiMisc method) _read_output_file2() (bonafide.features.multiwfn_population_analysis._Multiwfn3DAtomPopulationAnalysis method) (bonafide.features.multiwfn_surface._Multiwfn3DAtomSurface method) (bonafide.features.xtb_fukui_misc._Xtb3DAtomFukuiMisc method) _read_output_file3() (bonafide.features.multiwfn_population_analysis._Multiwfn3DAtomPopulationAnalysis method) (bonafide.features.multiwfn_surface._Multiwfn3DAtomSurface method) _read_output_file4() (bonafide.features.multiwfn_population_analysis._Multiwfn3DAtomPopulationAnalysis method) _read_output_file5() (bonafide.features.multiwfn_population_analysis._Multiwfn3DAtomPopulationAnalysis method) _read_output_file_atom() (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace method) (bonafide.features.multiwfn_hilbert_space._Multiwfn3DHilbertSpace method) _read_output_file_atom2() (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace method) _read_output_file_atom3() (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace method) _read_output_file_bond() (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace method) (bonafide.features.multiwfn_hilbert_space._Multiwfn3DHilbertSpace method) _read_output_file_clrk() (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace method) _read_xtb_output() (bonafide.utils.sp_xtb.XtbSP method) _rearrange_feature_indices() (bonafide._bonafide_utils._AtomBondFeaturizerUtils method) _reduce_conformer_data() (bonafide.utils.feature_output.FeatureOutput method) _render_mol_3D() (bonafide.utils.molecule_vault.MolVault method) _return_features() (bonafide._bonafide._AtomBondFeaturizer method) _run_calculation() (bonafide.features.distance._BonafideAtomDistance method) (bonafide.features.distance._BonafideBondDistance method) (bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedFukui method) _run_clean_up() (bonafide.utils.sp_xtb.XtbSP static method) _run_dbstep() (bonafide.features.dbstep_._Dbstep3DAtom method) _run_featurization() (bonafide._bonafide._AtomBondFeaturizer method) _run_kallisto() (bonafide.features.kallisto_._Kallisto3DAtom method) _run_morfeus() (bonafide.features.morfeus_bv._Morfeus3DAtomBV method) (bonafide.features.morfeus_dispersion._Morfeus3DAtomDispersion method) (bonafide.features.morfeus_sasa._Morfeus3DAtomSASA method) _run_multiwfn() (bonafide.features.multiwfn_bond._Multiwfn3DBondOrder method) (bonafide.features.multiwfn_bond_misc._Multiwfn3DBond method) (bonafide.features.multiwfn_connectivity._Multiwfn3DAtomConnectivity method) (bonafide.features.multiwfn_forces._Multiwfn3DAtomForce method) (bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedOrbitalWeightedFukui method) (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace method) (bonafide.features.multiwfn_hilbert_space._Multiwfn3DHilbertSpace method) (bonafide.features.multiwfn_misc.Multiwfn3DAtomEnergyIndex method) (bonafide.features.multiwfn_orbital._Multiwfn3DAtomMoContribution method) (bonafide.features.multiwfn_population_analysis._Multiwfn3DAtomPopulationAnalysis method) (bonafide.features.multiwfn_surface._Multiwfn3DAtomSurface method) (bonafide.features.multiwfn_topology_atom._Multiwfn3DAtomTopology method) (bonafide.features.multiwfn_topology_bond._Multiwfn3DBondTopology method) _run_qmdesc() (bonafide.features.qmdesc_._Qmdesc2DAtom method) (bonafide.features.qmdesc_._Qmdesc2DBond method) _run_xtb() (bonafide.features.xtb_fukui_misc._Xtb3DAtomFukuiMisc method) _save_output_files() (bonafide.utils.base_mixin._BaseMixin method) _save_output_files2() (bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedFukui method) _save_values() (bonafide.features.morfeus_local_force._Morfeus3DBondLocalForce method) _set_atom_bond_properties() (in module bonafide.utils.helper_functions_chemistry) _set_feature() (bonafide._bonafide._AtomBondFeaturizer method) _set_options() (bonafide._bonafide._AtomBondFeaturizer method) _setup_output_directory() (bonafide._bonafide._AtomBondFeaturizer method) _setup_work_dir() (bonafide.utils.base_mixin._BaseMixin method) _StandardizeStrMixin (class in bonafide.utils.input_validation) _to_cache() (bonafide.utils.base_featurizer.BaseFeaturizer method) _transfer_atom_bond_properties() (in module bonafide.utils.helper_functions_chemistry) _validate_and_format_smarts_df() (bonafide.features.functional_group.Bonafide2DAtomFunctionalGroupMatch method) _validate_atom_indices() (bonafide.features.morfeus_bv._Morfeus3DAtomBV method) (bonafide.features.morfeus_dispersion._Morfeus3DAtomDispersion method) _validate_sdf() (in module bonafide.utils.io_) _validate_xyz() (in module bonafide.utils.io_) _ValidateIterableIntOptionMixin (class in bonafide.utils.input_validation) _ValidateSpeciesMixin (class in bonafide.utils.input_validation) _wrap_fukui() (bonafide.features.xtb_cdft._Xtb3DAtomCdftLocal method) _wrap_fukui_dual() (bonafide.features.multiwfn_cdft._Multiwfn3DAtomCdftLocal method) _wrap_fukui_minus() (bonafide.features.multiwfn_cdft._Multiwfn3DAtomCdftLocal method) _wrap_fukui_plus() (bonafide.features.multiwfn_cdft._Multiwfn3DAtomCdftLocal method) _wrap_fukui_zero() (bonafide.features.multiwfn_cdft._Multiwfn3DAtomCdftLocal method) _write_input_file() (bonafide.features.dbstep_._Dbstep3DAtom method) (bonafide.features.dscribe_._Dscribe3DAtom method) (bonafide.features.kallisto_._Kallisto3DAtom method) (bonafide.features.multiwfn_bond_misc._Multiwfn3DBond method) (bonafide.features.multiwfn_connectivity._Multiwfn3DAtomConnectivity method) _Xtb3DAtomCdftLocal (class in bonafide.features.xtb_cdft) _Xtb3DAtomFukuiMisc (class in bonafide.features.xtb_fukui_misc) A acc (bonafide.utils.input_validation.ValidateXtb attribute) (bonafide.utils.sp_xtb.XtbSP attribute) add_custom_featurizer() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] addmetals (bonafide.features.dbstep_._Dbstep3DAtom attribute) (bonafide.utils.input_validation.ValidateDbstep attribute) Alfabet2DBondBondDissociationEnergy (class in bonafide.features.alfabet_) Alfabet2DBondBondDissociationFreeEnergy (class in bonafide.features.alfabet_) alle (bonafide.features.mendeleev_.Mendeleev2DAtomZeff attribute) (bonafide.utils.input_validation.ValidateMendeleev attribute) angstrom (bonafide.features.kallisto_._Kallisto3DAtom attribute) (bonafide.utils.input_validation.ValidateKallisto attribute) atom_bond_idx (bonafide.utils.base_featurizer.BaseFeaturizer attribute) atom_constant (bonafide.features.constant_feature.Bonafide2DAtomConstantFeature attribute) (bonafide.utils.input_validation.ValidateBonafideConstant attribute) AtomBondFeaturizer (class in bonafide.bonafide), [1] atomic_radii (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeChelpg attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMerzKollmann attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgTwoStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannTwoStage attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) attach_electronic_structure() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] attach_energy() (bonafide.bonafide.AtomBondFeaturizer method), [1] attach_smiles() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] average (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeSoap attribute) B BaseFeaturizer (class in bonafide.utils.base_featurizer) BaseSinglePoint (class in bonafide.utils.base_single_point) basis (bonafide.utils.input_validation.ValidatePsi4 attribute) (bonafide.utils.sp_psi4.Psi4SP attribute) bind_smiles_with_xyz() (in module bonafide.utils.helper_functions_chemistry) bonafide._bonafide module bonafide._bonafide_utils module bonafide.bonafide module, [1] bonafide.features.alfabet_ module bonafide.features.autocorrelation module bonafide.features.constant_feature module bonafide.features.dbstep_ module bonafide.features.distance module bonafide.features.dscribe_ module bonafide.features.functional_group module bonafide.features.kallisto_ module bonafide.features.mendeleev_ module bonafide.features.morfeus_bv module bonafide.features.morfeus_dispersion module bonafide.features.morfeus_local_force module bonafide.features.morfeus_sasa module bonafide.features.multiwfn_bond module bonafide.features.multiwfn_bond_misc module bonafide.features.multiwfn_cdft module bonafide.features.multiwfn_connectivity module bonafide.features.multiwfn_forces module bonafide.features.multiwfn_fukui module bonafide.features.multiwfn_fuzzy_space module bonafide.features.multiwfn_hilbert_space module bonafide.features.multiwfn_misc module bonafide.features.multiwfn_orbital module bonafide.features.multiwfn_partial_charge module bonafide.features.multiwfn_population module bonafide.features.multiwfn_population_analysis module bonafide.features.multiwfn_spin_population module bonafide.features.multiwfn_surface module bonafide.features.multiwfn_topology_atom module bonafide.features.multiwfn_topology_bond module bonafide.features.oxidation_state module bonafide.features.qmdesc_ module bonafide.features.rdkit_atom module bonafide.features.rdkit_bond module bonafide.features.rdkit_fingerprint module bonafide.features.spiro_bridgehead module bonafide.features.symmetric_sites module bonafide.features.xtb_cdft module bonafide.features.xtb_fukui_misc module bonafide.log_file_analysis module bonafide.utils.base_featurizer module bonafide.utils.base_mixin module bonafide.utils.base_single_point module bonafide.utils.cdft_redox_mixin module bonafide.utils.constants module bonafide.utils.custom_featurizer_input_validation module bonafide.utils.dependencies module bonafide.utils.driver module bonafide.utils.environment module bonafide.utils.feature_factories module bonafide.utils.feature_output module bonafide.utils.global_properties module bonafide.utils.helper_functions module bonafide.utils.helper_functions_chemistry module bonafide.utils.helper_functions_output module bonafide.utils.input_validation module bonafide.utils.io_ module bonafide.utils.logging_format module bonafide.utils.molecule_vault module bonafide.utils.multiwfn_properties module bonafide.utils.sp_psi4 module bonafide.utils.sp_xtb module bonafide.utils.string_formatting module Bonafide2DAtomAtomsBeyondXBonds (class in bonafide.features.distance) Bonafide2DAtomAtomsWithinXBonds (class in bonafide.features.distance) Bonafide2DAtomAtomsXBondsAway (class in bonafide.features.distance) Bonafide2DAtomAutocorrelationAbsDifference (class in bonafide.features.autocorrelation) Bonafide2DAtomAutocorrelationDifference (class in bonafide.features.autocorrelation) Bonafide2DAtomAutocorrelationMean (class in bonafide.features.autocorrelation) Bonafide2DAtomAutocorrelationProduct (class in bonafide.features.autocorrelation) Bonafide2DAtomAutocorrelationScaledAbsDifference (class in bonafide.features.autocorrelation) Bonafide2DAtomAutocorrelationScaledDifference (class in bonafide.features.autocorrelation) Bonafide2DAtomAutocorrelationScaledMean (class in bonafide.features.autocorrelation) Bonafide2DAtomAutocorrelationScaledProduct (class in bonafide.features.autocorrelation) Bonafide2DAtomAutocorrelationScaledSum (class in bonafide.features.autocorrelation) Bonafide2DAtomAutocorrelationSum (class in bonafide.features.autocorrelation) Bonafide2DAtomBondsBeyondXBonds (class in bonafide.features.distance) Bonafide2DAtomBondsWithinXBonds (class in bonafide.features.distance) Bonafide2DAtomConstantFeature (class in bonafide.features.constant_feature) Bonafide2DAtomDistanceToAllAtomsMax (class in bonafide.features.distance) Bonafide2DAtomDistanceToAllAtomsMean (class in bonafide.features.distance) Bonafide2DAtomDistanceToAllBondsMax (class in bonafide.features.distance) Bonafide2DAtomDistanceToAllBondsMean (class in bonafide.features.distance) Bonafide2DAtomFractionAtomsBeyondXBonds (class in bonafide.features.distance) Bonafide2DAtomFractionAtomsWithinXBonds (class in bonafide.features.distance) Bonafide2DAtomFractionAtomsXBondsAway (class in bonafide.features.distance) Bonafide2DAtomFractionBondsBeyondXBonds (class in bonafide.features.distance) Bonafide2DAtomFractionBondsWithinXBonds (class in bonafide.features.distance) Bonafide2DAtomFunctionalGroupMatch (class in bonafide.features.functional_group) Bonafide2DAtomIsBridgehead (class in bonafide.features.spiro_bridgehead) Bonafide2DAtomIsSpiro (class in bonafide.features.spiro_bridgehead) Bonafide2DAtomIsSymmetricTo (class in bonafide.features.symmetric_sites) Bonafide2DAtomNAtomsBeyondXBonds (class in bonafide.features.distance) Bonafide2DAtomNAtomsWithinXBonds (class in bonafide.features.distance) Bonafide2DAtomNAtomsXBondsAway (class in bonafide.features.distance) Bonafide2DAtomNBondsBeyondXBonds (class in bonafide.features.distance) Bonafide2DAtomNBondsWithinXBonds (class in bonafide.features.distance) Bonafide2DAtomOxidationState (class in bonafide.features.oxidation_state) Bonafide2DBondAtomsBeyondXBonds (class in bonafide.features.distance) Bonafide2DBondAtomsWithinXBonds (class in bonafide.features.distance) Bonafide2DBondAtomsXBondsAway (class in bonafide.features.distance) Bonafide2DBondBondsBeyondXBonds (class in bonafide.features.distance) Bonafide2DBondBondsWithinXBonds (class in bonafide.features.distance) Bonafide2DBondConstantFeature (class in bonafide.features.constant_feature) Bonafide2DBondDistanceToAllAtomsMax (class in bonafide.features.distance) Bonafide2DBondDistanceToAllAtomsMean (class in bonafide.features.distance) Bonafide2DBondDistanceToAllBondsMax (class in bonafide.features.distance) Bonafide2DBondDistanceToAllBondsMean (class in bonafide.features.distance) Bonafide2DBondFractionAtomsBeyondXBonds (class in bonafide.features.distance) Bonafide2DBondFractionAtomsWithinXBonds (class in bonafide.features.distance) Bonafide2DBondFractionAtomsXBondsAway (class in bonafide.features.distance) Bonafide2DBondFractionBondsBeyondXBonds (class in bonafide.features.distance) Bonafide2DBondFractionBondsWithinXBonds (class in bonafide.features.distance) Bonafide2DBondIsSymmetricTo (class in bonafide.features.symmetric_sites) Bonafide2DBondNAtomsBeyondXBonds (class in bonafide.features.distance) Bonafide2DBondNAtomsWithinXBonds (class in bonafide.features.distance) Bonafide2DBondNAtomsXBondsAway (class in bonafide.features.distance) Bonafide2DBondNBondsBeyondXBonds (class in bonafide.features.distance) Bonafide2DBondNBondsWithinXBonds (class in bonafide.features.distance) Bonafide3DAtomAtomsBeyondXAngstrom (class in bonafide.features.distance) Bonafide3DAtomAtomsWithinXAngstrom (class in bonafide.features.distance) Bonafide3DAtomBondsBeyondXAngstrom (class in bonafide.features.distance) Bonafide3DAtomBondsWithinXAngstrom (class in bonafide.features.distance) Bonafide3DAtomDistanceToAllAtomsMax (class in bonafide.features.distance) Bonafide3DAtomDistanceToAllAtomsMean (class in bonafide.features.distance) Bonafide3DAtomDistanceToAllBondsMax (class in bonafide.features.distance) Bonafide3DAtomDistanceToAllBondsMean (class in bonafide.features.distance) Bonafide3DAtomFractionAtomsBeyondXAngstrom (class in bonafide.features.distance) Bonafide3DAtomFractionAtomsWithinXAngstrom (class in bonafide.features.distance) Bonafide3DAtomFractionBondsBeyondXAngstrom (class in bonafide.features.distance) Bonafide3DAtomFractionBondsWithinXAngstrom (class in bonafide.features.distance) Bonafide3DAtomNAtomsBeyondXAngstrom (class in bonafide.features.distance) Bonafide3DAtomNAtomsWithinXAngstrom (class in bonafide.features.distance) Bonafide3DAtomNBondsBeyondXAngstrom (class in bonafide.features.distance) Bonafide3DAtomNBondsWithinXAngstrom (class in bonafide.features.distance) Bonafide3DBondAtomsBeyondXAngstrom (class in bonafide.features.distance) Bonafide3DBondAtomsWithinXAngstrom (class in bonafide.features.distance) Bonafide3DBondBondsBeyondXAngstrom (class in bonafide.features.distance) Bonafide3DBondBondsWithinXAngstrom (class in bonafide.features.distance) Bonafide3DBondDistanceToAllAtomsMax (class in bonafide.features.distance) Bonafide3DBondDistanceToAllAtomsMean (class in bonafide.features.distance) Bonafide3DBondDistanceToAllBondsMax (class in bonafide.features.distance) Bonafide3DBondDistanceToAllBondsMean (class in bonafide.features.distance) Bonafide3DBondFractionAtomsBeyondXAngstrom (class in bonafide.features.distance) Bonafide3DBondFractionAtomsWithinXAngstrom (class in bonafide.features.distance) Bonafide3DBondFractionBondsBeyondXAngstrom (class in bonafide.features.distance) Bonafide3DBondFractionBondsWithinXAngstrom (class in bonafide.features.distance) Bonafide3DBondNAtomsBeyondXAngstrom (class in bonafide.features.distance) Bonafide3DBondNAtomsWithinXAngstrom (class in bonafide.features.distance) Bonafide3DBondNBondsBeyondXAngstrom (class in bonafide.features.distance) Bonafide3DBondNBondsWithinXAngstrom (class in bonafide.features.distance) bond_constant (bonafide.features.constant_feature.Bonafide2DBondConstantFeature attribute) (bonafide.utils.input_validation.ValidateBonafideConstant attribute) box_extension_chelpg (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeChelpg attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgTwoStage attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) branchedPaths (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintRdkit attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintRdkit attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) bv_ (bonafide.features.morfeus_bv._Morfeus3DAtomBV attribute) C calculate() (bonafide.features.alfabet_._Alfabet2DBond method) (bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationAbsDifference method) (bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationDifference method) (bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationMean method) (bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationProduct method) (bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationScaledAbsDifference method) (bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationScaledDifference method) (bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationScaledMean method) (bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationScaledProduct method) (bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationScaledSum method) (bonafide.features.autocorrelation.Bonafide2DAtomAutocorrelationSum method) (bonafide.features.constant_feature.Bonafide2DAtomConstantFeature method) (bonafide.features.constant_feature.Bonafide2DBondConstantFeature method) (bonafide.features.dbstep_.Dbstep3DAtomBuriedVolume method) (bonafide.features.dbstep_.Dbstep3DAtomFractionBuriedShellVolume method) (bonafide.features.dbstep_.Dbstep3DAtomFractionBuriedVolume method) (bonafide.features.distance.Bonafide2DAtomAtomsBeyondXBonds method) (bonafide.features.distance.Bonafide2DAtomAtomsWithinXBonds method) (bonafide.features.distance.Bonafide2DAtomAtomsXBondsAway method) (bonafide.features.distance.Bonafide2DAtomBondsBeyondXBonds method) (bonafide.features.distance.Bonafide2DAtomBondsWithinXBonds method) (bonafide.features.distance.Bonafide2DAtomDistanceToAllAtomsMax method) (bonafide.features.distance.Bonafide2DAtomDistanceToAllAtomsMean method) (bonafide.features.distance.Bonafide2DAtomDistanceToAllBondsMax method) (bonafide.features.distance.Bonafide2DAtomDistanceToAllBondsMean method) (bonafide.features.distance.Bonafide2DAtomFractionAtomsBeyondXBonds method) (bonafide.features.distance.Bonafide2DAtomFractionAtomsWithinXBonds method) (bonafide.features.distance.Bonafide2DAtomFractionAtomsXBondsAway method) (bonafide.features.distance.Bonafide2DAtomFractionBondsBeyondXBonds method) (bonafide.features.distance.Bonafide2DAtomFractionBondsWithinXBonds method) (bonafide.features.distance.Bonafide2DAtomNAtomsBeyondXBonds method) (bonafide.features.distance.Bonafide2DAtomNAtomsWithinXBonds method) (bonafide.features.distance.Bonafide2DAtomNAtomsXBondsAway method) (bonafide.features.distance.Bonafide2DAtomNBondsBeyondXBonds method) (bonafide.features.distance.Bonafide2DAtomNBondsWithinXBonds method) (bonafide.features.distance.Bonafide2DBondAtomsBeyondXBonds method) (bonafide.features.distance.Bonafide2DBondAtomsWithinXBonds method) (bonafide.features.distance.Bonafide2DBondAtomsXBondsAway method) (bonafide.features.distance.Bonafide2DBondBondsBeyondXBonds method) (bonafide.features.distance.Bonafide2DBondBondsWithinXBonds method) (bonafide.features.distance.Bonafide2DBondDistanceToAllAtomsMax method) (bonafide.features.distance.Bonafide2DBondDistanceToAllAtomsMean method) (bonafide.features.distance.Bonafide2DBondDistanceToAllBondsMax method) (bonafide.features.distance.Bonafide2DBondDistanceToAllBondsMean method) (bonafide.features.distance.Bonafide2DBondFractionAtomsBeyondXBonds method) (bonafide.features.distance.Bonafide2DBondFractionAtomsWithinXBonds method) (bonafide.features.distance.Bonafide2DBondFractionAtomsXBondsAway method) (bonafide.features.distance.Bonafide2DBondFractionBondsBeyondXBonds method) (bonafide.features.distance.Bonafide2DBondFractionBondsWithinXBonds method) (bonafide.features.distance.Bonafide2DBondNAtomsBeyondXBonds method) (bonafide.features.distance.Bonafide2DBondNAtomsWithinXBonds method) (bonafide.features.distance.Bonafide2DBondNAtomsXBondsAway method) (bonafide.features.distance.Bonafide2DBondNBondsBeyondXBonds method) (bonafide.features.distance.Bonafide2DBondNBondsWithinXBonds method) (bonafide.features.distance.Bonafide3DAtomAtomsBeyondXAngstrom method) (bonafide.features.distance.Bonafide3DAtomAtomsWithinXAngstrom method) (bonafide.features.distance.Bonafide3DAtomBondsBeyondXAngstrom method) (bonafide.features.distance.Bonafide3DAtomBondsWithinXAngstrom method) (bonafide.features.distance.Bonafide3DAtomDistanceToAllAtomsMax method) (bonafide.features.distance.Bonafide3DAtomDistanceToAllAtomsMean method) (bonafide.features.distance.Bonafide3DAtomDistanceToAllBondsMax method) (bonafide.features.distance.Bonafide3DAtomDistanceToAllBondsMean method) (bonafide.features.distance.Bonafide3DAtomFractionAtomsBeyondXAngstrom method) (bonafide.features.distance.Bonafide3DAtomFractionAtomsWithinXAngstrom method) (bonafide.features.distance.Bonafide3DAtomFractionBondsBeyondXAngstrom method) (bonafide.features.distance.Bonafide3DAtomFractionBondsWithinXAngstrom method) (bonafide.features.distance.Bonafide3DAtomNAtomsBeyondXAngstrom method) (bonafide.features.distance.Bonafide3DAtomNAtomsWithinXAngstrom method) (bonafide.features.distance.Bonafide3DAtomNBondsBeyondXAngstrom method) (bonafide.features.distance.Bonafide3DAtomNBondsWithinXAngstrom method) (bonafide.features.distance.Bonafide3DBondAtomsBeyondXAngstrom method) (bonafide.features.distance.Bonafide3DBondAtomsWithinXAngstrom method) (bonafide.features.distance.Bonafide3DBondBondsBeyondXAngstrom method) (bonafide.features.distance.Bonafide3DBondBondsWithinXAngstrom method) (bonafide.features.distance.Bonafide3DBondDistanceToAllAtomsMax method) (bonafide.features.distance.Bonafide3DBondDistanceToAllAtomsMean method) (bonafide.features.distance.Bonafide3DBondDistanceToAllBondsMax method) (bonafide.features.distance.Bonafide3DBondDistanceToAllBondsMean method) (bonafide.features.distance.Bonafide3DBondFractionAtomsBeyondXAngstrom method) (bonafide.features.distance.Bonafide3DBondFractionAtomsWithinXAngstrom method) (bonafide.features.distance.Bonafide3DBondFractionBondsBeyondXAngstrom method) (bonafide.features.distance.Bonafide3DBondFractionBondsWithinXAngstrom method) (bonafide.features.distance.Bonafide3DBondNAtomsBeyondXAngstrom method) (bonafide.features.distance.Bonafide3DBondNAtomsWithinXAngstrom method) (bonafide.features.distance.Bonafide3DBondNBondsBeyondXAngstrom method) (bonafide.features.distance.Bonafide3DBondNBondsWithinXAngstrom method) (bonafide.features.dscribe_.Dscribe3DAtomAtomCenteredSymmetryFunction method) (bonafide.features.dscribe_.Dscribe3DAtomAtomicCoulombVector method) (bonafide.features.dscribe_.Dscribe3DAtomLocalManyBodyTensorRepresentation method) (bonafide.features.dscribe_.Dscribe3DAtomSmoothOverlapOfAtomicPositions method) (bonafide.features.functional_group.Bonafide2DAtomFunctionalGroupMatch method) (bonafide.features.kallisto_.Kallisto3DAtomCoordinationNumber method) (bonafide.features.kallisto_.Kallisto3DAtomPartialCharge method) (bonafide.features.kallisto_.Kallisto3DAtomPolarizability method) (bonafide.features.kallisto_.Kallisto3DAtomProximityShell method) (bonafide.features.kallisto_.Kallisto3DAtomRelativePolarizability method) (bonafide.features.kallisto_.Kallisto3DAtomVdwRadius method) (bonafide.features.mendeleev_.Mendeleev2DAtomAtomicRadius method) (bonafide.features.mendeleev_.Mendeleev2DAtomAtomicRadiusRahm method) (bonafide.features.mendeleev_.Mendeleev2DAtomAtomicVolume method) (bonafide.features.mendeleev_.Mendeleev2DAtomAtomicWeight method) (bonafide.features.mendeleev_.Mendeleev2DAtomBlock method) (bonafide.features.mendeleev_.Mendeleev2DAtomC6 method) (bonafide.features.mendeleev_.Mendeleev2DAtomC6Gb method) (bonafide.features.mendeleev_.Mendeleev2DAtomCas method) (bonafide.features.mendeleev_.Mendeleev2DAtomCovalentRadiusBragg method) (bonafide.features.mendeleev_.Mendeleev2DAtomCovalentRadiusCordero method) (bonafide.features.mendeleev_.Mendeleev2DAtomCovalentRadiusPyykko method) (bonafide.features.mendeleev_.Mendeleev2DAtomCovalentRadiusPyykkoDouble method) (bonafide.features.mendeleev_.Mendeleev2DAtomCovalentRadiusPyykkoTriple method) (bonafide.features.mendeleev_.Mendeleev2DAtomDensity method) (bonafide.features.mendeleev_.Mendeleev2DAtomDipolePolarizability method) (bonafide.features.mendeleev_.Mendeleev2DAtomEconf method) (bonafide.features.mendeleev_.Mendeleev2DAtomElectronAffinity method) (bonafide.features.mendeleev_.Mendeleev2DAtomElectrophilicity method) (bonafide.features.mendeleev_.Mendeleev2DAtomEnAllen method) (bonafide.features.mendeleev_.Mendeleev2DAtomEnAllredRochow method) (bonafide.features.mendeleev_.Mendeleev2DAtomEnCottrellSutton method) (bonafide.features.mendeleev_.Mendeleev2DAtomEnGhosh method) (bonafide.features.mendeleev_.Mendeleev2DAtomEnGordy method) (bonafide.features.mendeleev_.Mendeleev2DAtomEnMartynovBatsanov method) (bonafide.features.mendeleev_.Mendeleev2DAtomEnMiedema method) (bonafide.features.mendeleev_.Mendeleev2DAtomEnMulliken method) (bonafide.features.mendeleev_.Mendeleev2DAtomEnNagle method) (bonafide.features.mendeleev_.Mendeleev2DAtomEnPauling method) (bonafide.features.mendeleev_.Mendeleev2DAtomEnSanderson method) (bonafide.features.mendeleev_.Mendeleev2DAtomEvaporationHeat method) (bonafide.features.mendeleev_.Mendeleev2DAtomFirstIonizationEnergy method) (bonafide.features.mendeleev_.Mendeleev2DAtomFusionHeat method) (bonafide.features.mendeleev_.Mendeleev2DAtomGasBasicity method) (bonafide.features.mendeleev_.Mendeleev2DAtomGroupId method) (bonafide.features.mendeleev_.Mendeleev2DAtomHardness method) (bonafide.features.mendeleev_.Mendeleev2DAtomHeatOfFormation method) (bonafide.features.mendeleev_.Mendeleev2DAtomInchi method) (bonafide.features.mendeleev_.Mendeleev2DAtomIsMonoisotopic method) (bonafide.features.mendeleev_.Mendeleev2DAtomIsRadioactive method) (bonafide.features.mendeleev_.Mendeleev2DAtomLatticeConstant method) (bonafide.features.mendeleev_.Mendeleev2DAtomLatticeStructure method) (bonafide.features.mendeleev_.Mendeleev2DAtomMeltingPoint method) (bonafide.features.mendeleev_.Mendeleev2DAtomMetallicRadius method) (bonafide.features.mendeleev_.Mendeleev2DAtomMetallicRadiusC12 method) (bonafide.features.mendeleev_.Mendeleev2DAtomMiedemaElectronDensity method) (bonafide.features.mendeleev_.Mendeleev2DAtomMiedemaMolarVolume method) (bonafide.features.mendeleev_.Mendeleev2DAtomMolarHeatCapacity method) (bonafide.features.mendeleev_.Mendeleev2DAtomName method) (bonafide.features.mendeleev_.Mendeleev2DAtomNValenceElectrons method) (bonafide.features.mendeleev_.Mendeleev2DAtomPeriod method) (bonafide.features.mendeleev_.Mendeleev2DAtomPettiforNumber method) (bonafide.features.mendeleev_.Mendeleev2DAtomProtonAffinity method) (bonafide.features.mendeleev_.Mendeleev2DAtomSoftness method) (bonafide.features.mendeleev_.Mendeleev2DAtomSpecificHeatCapacity method) (bonafide.features.mendeleev_.Mendeleev2DAtomThermalConductivity method) (bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadius method) (bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadiusAlvarez method) (bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadiusBatsanov method) (bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadiusBondi method) (bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadiusDreiding method) (bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadiusMm3 method) (bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadiusRt method) (bonafide.features.mendeleev_.Mendeleev2DAtomVdwRadiusUff method) (bonafide.features.mendeleev_.Mendeleev2DAtomZeff method) (bonafide.features.morfeus_bv.Morfeus3DAtomBuriedVolume method) (bonafide.features.morfeus_bv.Morfeus3DAtomBuriedVolumeOctants method) (bonafide.features.morfeus_bv.Morfeus3DAtomBuriedVolumeQuadrants method) (bonafide.features.morfeus_bv.Morfeus3DAtomDistalVolume method) (bonafide.features.morfeus_bv.Morfeus3DAtomDistalVolumeOctants method) (bonafide.features.morfeus_bv.Morfeus3DAtomDistalVolumeQuadrants method) (bonafide.features.morfeus_bv.Morfeus3DAtomFractionBuriedVolume method) (bonafide.features.morfeus_bv.Morfeus3DAtomFractionBuriedVolumeOctants method) (bonafide.features.morfeus_bv.Morfeus3DAtomFractionBuriedVolumeQuadrants method) (bonafide.features.morfeus_bv.Morfeus3DAtomFractionFreeVolume method) (bonafide.features.morfeus_bv.Morfeus3DAtomFractionFreeVolumeOctants method) (bonafide.features.morfeus_bv.Morfeus3DAtomFractionFreeVolumeQuadrants method) (bonafide.features.morfeus_bv.Morfeus3DAtomFreeVolume method) (bonafide.features.morfeus_bv.Morfeus3DAtomFreeVolumeOctants method) (bonafide.features.morfeus_bv.Morfeus3DAtomFreeVolumeQuadrants method) (bonafide.features.morfeus_bv.Morfeus3DAtomMolecularVolumeOctants method) (bonafide.features.morfeus_bv.Morfeus3DAtomMolecularVolumeQuadrants method) (bonafide.features.morfeus_dispersion.Morfeus3DAtomPInt method) (bonafide.features.morfeus_dispersion.Morfeus3DAtomPMax method) (bonafide.features.morfeus_dispersion.Morfeus3DAtomPMin method) (bonafide.features.morfeus_local_force._Morfeus3DBondLocalForce method) (bonafide.features.morfeus_sasa.Morfeus3DAtomSasAtomArea method) (bonafide.features.morfeus_sasa.Morfeus3DAtomSasFractionAtomArea method) (bonafide.features.multiwfn_bond.Multiwfn3DBondBondOrderFuzzy method) (bonafide.features.multiwfn_bond.Multiwfn3DBondBondOrderLaplacian method) (bonafide.features.multiwfn_bond.Multiwfn3DBondBondOrderMayer method) (bonafide.features.multiwfn_bond.Multiwfn3DBondBondOrderMulliken method) (bonafide.features.multiwfn_bond.Multiwfn3DBondBondOrderWiberg method) (bonafide.features.multiwfn_bond.Multiwfn3DBondIntrinsicBondStrengthIndex method) (bonafide.features.multiwfn_bond_misc._Multiwfn3DBond method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalElectrophilicityFmo method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalElectrophilicityRedox method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHardnessMinusFmo method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHardnessMinusRedox method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHardnessPlusFmo method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHardnessPlusRedox method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHardnessZeroFmo method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHardnessZeroRedox method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHyperhardnessFmo method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHyperhardnessRedox method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHypersoftnessFmo method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalHypersoftnessRedox method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalNucleophilicityFmo method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalNucleophilicityRedox method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalRelativeElectrophilicity method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalRelativeNucleophilicity method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalSoftnessMinusFmo method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalSoftnessMinusRedox method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalSoftnessPlusFmo method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalSoftnessPlusRedox method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalSoftnessZeroFmo method) (bonafide.features.multiwfn_cdft.Multiwfn3DAtomCdftLocalSoftnessZeroRedox method) (bonafide.features.multiwfn_connectivity._Multiwfn3DAtomConnectivity method) (bonafide.features.multiwfn_forces._Multiwfn3DAtomForce method) (bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedFukuiDual method) (bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedFukuiMinus method) (bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedFukuiPlus method) (bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedFukuiZero method) (bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedOrbitalWeightedFukuiDual method) (bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedOrbitalWeightedFukuiMinus method) (bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedOrbitalWeightedFukuiPlus method) (bonafide.features.multiwfn_fukui.Multiwfn3DAtomCdftCondensedOrbitalWeightedFukuiZero method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceAtomicElectronicSpatialExtent method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceAtomicValence method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceAtomicValenceAlpha method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceAtomicValenceBeta method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceCondensedLinearResponseKernelMatrixElement method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceContributionToSystemDipoleMoment method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceContributionToSystemDipoleMomentNorm method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceDipoleMoment method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceDipoleMomentNorm method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceIntegrationDescriptor method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceIntegrationDescriptorAbsRelative method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceIntegrationDescriptorRelative method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceLocalizationIndex method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceLocalizationIndexAlpha method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceLocalizationIndexBeta method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceMonopoleMoment method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceOctopoleMomentMagnitude method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceQuadrupoleMomentMagnitude method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DAtomFuzzySpaceTracelessQuadrupoleMomentTensorMagnitude method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DBondFuzzySpaceCondensedLinearResponseKernelMatrixElement method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DBondFuzzySpaceOverlapIntegrationDescriptor method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DBondFuzzySpaceOverlapIntegrationDescriptorNegative method) (bonafide.features.multiwfn_fuzzy_space.Multiwfn3DBondFuzzySpaceOverlapIntegrationDescriptorPositive method) (bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMoment method) (bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentElectrons method) (bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentElectronsNorm method) (bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentNorm method) (bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentNuclearCharge method) (bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentNuclearChargeNorm method) (bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceDipoleMoment method) (bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceDipoleMomentNorm method) (bonafide.features.multiwfn_hilbert_space.Multiwfn3DAtomHilbertSpaceLocalPopulationNumber method) (bonafide.features.multiwfn_hilbert_space.Multiwfn3DBondHilbertSpaceContributionToSystemDipoleMoment method) (bonafide.features.multiwfn_hilbert_space.Multiwfn3DBondHilbertSpaceContributionToSystemDipoleMomentNorm method) (bonafide.features.multiwfn_hilbert_space.Multiwfn3DBondHilbertSpaceDipoleMoment method) (bonafide.features.multiwfn_hilbert_space.Multiwfn3DBondHilbertSpaceDipoleMomentNorm method) (bonafide.features.multiwfn_hilbert_space.Multiwfn3DBondHilbertSpaceOverlapPopulation method) (bonafide.features.multiwfn_misc.Multiwfn3DAtomEnergyIndex method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMulliken method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenAlpha method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenBeta method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenRosSchuit method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenRosSchuitAlpha method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenRosSchuitBeta method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenStoutPolitzer method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenStoutPolitzerAlpha method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionOccupiedMullikenStoutPolitzerBeta method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMulliken method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenAlpha method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenBeta method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenRosSchuit method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenRosSchuitAlpha method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenRosSchuitBeta method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenStoutPolitzer method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenStoutPolitzerAlpha method) (bonafide.features.multiwfn_orbital.Multiwfn3DAtomMoContributionUnoccupiedMullikenStoutPolitzerBeta method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeBecke method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeChelpg method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeCm5 method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeCm5Scaled1point2 method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeCorrectedHirshfeld method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeEem method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeHirshfeld method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeLowdin method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMerzKollmann method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMulliken method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMullikenBickelhaupt method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMullikenRosSchuit method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMullikenStoutPolitzer method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgOneStage method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgTwoStage method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannOneStage method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannTwoStage method) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeVdd method) (bonafide.features.multiwfn_population._LowdinAlphaBetaMixin method) (bonafide.features.multiwfn_population._MullikenAlphaBetaMixin method) (bonafide.features.multiwfn_population._MullikenBickelhauptAlphaBetaMixin method) (bonafide.features.multiwfn_population._MullikenRosSchuitAlphaBetaMixin method) (bonafide.features.multiwfn_population._MullikenStoutPolitzerAlphaBetaMixin method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdin method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinD method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinF method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinG method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinH method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinP method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationLowdinS method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMulliken method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenBickelhaupt method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenD method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenF method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenG method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenH method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenP method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenRosSchuit method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenS method) (bonafide.features.multiwfn_population.Multiwfn3DAtomPopulationMullikenStoutPolitzer method) (bonafide.features.multiwfn_spin_population._LowdinMixin method) (bonafide.features.multiwfn_spin_population._MullikenMixin method) (bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationMullikenBickelhaupt method) (bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationMullikenRosSchuit method) (bonafide.features.multiwfn_spin_population.Multiwfn3DAtomSpinPopulationMullikenStoutPolitzer method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceAverageLocalIonizationEnergyMax method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceAverageLocalIonizationEnergyMean method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceAverageLocalIonizationEnergyMin method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDelocalizationRangeFunctionMax method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDelocalizationRangeFunctionMean method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDelocalizationRangeFunctionMin method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDensityMax method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDensityMean method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDensityMin method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectrostaticPotentialBalanceOfCharges method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectrostaticPotentialBalanceOfChargesTimesVariance method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectrostaticPotentialInternalChargeSeparation method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectrostaticPotentialMax method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectrostaticPotentialMean method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectrostaticPotentialMin method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceLocalElectronAffinityMax method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceLocalElectronAffinityMean method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceLocalElectronAffinityMin method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceLocalElectronAttachmentEnergyMax method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceLocalElectronAttachmentEnergyMean method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceLocalElectronAttachmentEnergyMin method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceOrbitalOverlapLengthFunctionMax method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceOrbitalOverlapLengthFunctionMean method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceOrbitalOverlapLengthFunctionMin method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceSignSecondLargestEigenvalueElectronDensityHessianMax method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceSignSecondLargestEigenvalueElectronDensityHessianMean method) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceSignSecondLargestEigenvalueElectronDensityHessianMin method) (bonafide.features.multiwfn_topology_atom._Multiwfn3DAtomTopology method) (bonafide.features.multiwfn_topology_bond._Multiwfn3DBondTopology method) (bonafide.features.oxidation_state.Bonafide2DAtomOxidationState method) (bonafide.features.qmdesc_._Qmdesc2DAtom method) (bonafide.features.qmdesc_._Qmdesc2DBond method) (bonafide.features.rdkit_atom.Rdkit2DAtomAtomicNumber method) (bonafide.features.rdkit_atom.Rdkit2DAtomAtomMapNumber method) (bonafide.features.rdkit_atom.Rdkit2DAtomChiralTag method) (bonafide.features.rdkit_atom.Rdkit2DAtomDegree method) (bonafide.features.rdkit_atom.Rdkit2DAtomEstate method) (bonafide.features.rdkit_atom.Rdkit2DAtomExplicitValence method) (bonafide.features.rdkit_atom.Rdkit2DAtomFormalCharge method) (bonafide.features.rdkit_atom.Rdkit2DAtomGasteigerCharge method) (bonafide.features.rdkit_atom.Rdkit2DAtomHybridization method) (bonafide.features.rdkit_atom.Rdkit2DAtomImplicitValence method) (bonafide.features.rdkit_atom.Rdkit2DAtomIsAromatic method) (bonafide.features.rdkit_atom.Rdkit2DAtomIsotope method) (bonafide.features.rdkit_atom.Rdkit2DAtomLabuteAsaContribution method) (bonafide.features.rdkit_atom.Rdkit2DAtomMass method) (bonafide.features.rdkit_atom.Rdkit2DAtomNeighboringAtomsIndices method) (bonafide.features.rdkit_atom.Rdkit2DAtomNeighboringAtomsMapNumbers method) (bonafide.features.rdkit_atom.Rdkit2DAtomNeighboringBondsIndices method) (bonafide.features.rdkit_atom.Rdkit2DAtomNExplicitH method) (bonafide.features.rdkit_atom.Rdkit2DAtomNImplicitH method) (bonafide.features.rdkit_atom.Rdkit2DAtomNNeighbors method) (bonafide.features.rdkit_atom.Rdkit2DAtomNoImplicit method) (bonafide.features.rdkit_atom.Rdkit2DAtomNRadicalElectrons method) (bonafide.features.rdkit_atom.Rdkit2DAtomRingInfo method) (bonafide.features.rdkit_atom.Rdkit2DAtomRingInfoAromaticCarbocycle method) (bonafide.features.rdkit_atom.Rdkit2DAtomRingInfoAromaticHeterocycle method) (bonafide.features.rdkit_atom.Rdkit2DAtomRingInfoNonaromaticCarbocycle method) (bonafide.features.rdkit_atom.Rdkit2DAtomRingInfoNonaromaticHeterocycle method) (bonafide.features.rdkit_atom.Rdkit2DAtomSymbol method) (bonafide.features.rdkit_atom.Rdkit2DAtomTotalDegree method) (bonafide.features.rdkit_atom.Rdkit2DAtomTotalNH method) (bonafide.features.rdkit_atom.Rdkit2DAtomTotalValence method) (bonafide.features.rdkit_atom.Rdkit2DAtomTpsaContribution method) (bonafide.features.rdkit_atom.Rdkit2DAtomWildmanCrippenLogpContribution method) (bonafide.features.rdkit_atom.Rdkit3DAtomCoordinates method) (bonafide.features.rdkit_bond.Rdkit2DBondBeginAtomIndex method) (bonafide.features.rdkit_bond.Rdkit2DBondBeginAtomMapNumber method) (bonafide.features.rdkit_bond.Rdkit2DBondBondOrder method) (bonafide.features.rdkit_bond.Rdkit2DBondBondType method) (bonafide.features.rdkit_bond.Rdkit2DBondEndAtomIndex method) (bonafide.features.rdkit_bond.Rdkit2DBondEndAtomMapNumber method) (bonafide.features.rdkit_bond.Rdkit2DBondIsAromatic method) (bonafide.features.rdkit_bond.Rdkit2DBondIsConjugated method) (bonafide.features.rdkit_bond.Rdkit2DBondNeighboringAtomsIndices method) (bonafide.features.rdkit_bond.Rdkit2DBondNeighboringAtomsMapNumbers method) (bonafide.features.rdkit_bond.Rdkit2DBondNeighboringBondsIndices method) (bonafide.features.rdkit_bond.Rdkit2DBondNNeighbors method) (bonafide.features.rdkit_bond.Rdkit2DBondRingInfo method) (bonafide.features.rdkit_bond.Rdkit2DBondRingInfoAromaticCarbocycle method) (bonafide.features.rdkit_bond.Rdkit2DBondRingInfoAromaticHeterocycle method) (bonafide.features.rdkit_bond.Rdkit2DBondRingInfoNonaromaticCarbocycle method) (bonafide.features.rdkit_bond.Rdkit2DBondRingInfoNonaromaticHeterocycle method) (bonafide.features.rdkit_bond.Rdkit2DBondStereo method) (bonafide.features.rdkit_bond.Rdkit2DBondValenceContributionBeginAtom method) (bonafide.features.rdkit_bond.Rdkit2DBondValenceContributionEndAtom method) (bonafide.features.rdkit_bond.Rdkit3DBondBondLength method) (bonafide.features.rdkit_bond.Rdkit3DBondCoordinatesBeginAtom method) (bonafide.features.rdkit_bond.Rdkit3DBondCoordinatesCenter method) (bonafide.features.rdkit_bond.Rdkit3DBondCoordinatesEndAtom method) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintAtomPair method) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintFeatureMorgan method) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintMorgan method) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintRdkit method) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintTopologicalTorsion method) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintAtomPair method) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintFeatureMorgan method) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintMorgan method) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintRdkit method) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintTopologicalTorsion method) (bonafide.features.spiro_bridgehead._Bonafide2DAtomIsSpiroBridgehead method) (bonafide.features.symmetric_sites.Bonafide2DAtomIsSymmetricTo method) (bonafide.features.symmetric_sites.Bonafide2DBondIsSymmetricTo method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalElectrophilicityFmo method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalElectrophilicityRedox method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHardnessMinusFmo method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHardnessMinusRedox method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHardnessPlusFmo method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHardnessPlusRedox method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHardnessZeroFmo method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHardnessZeroRedox method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHyperhardnessFmo method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHyperhardnessRedox method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHypersoftnessFmo method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalHypersoftnessRedox method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalNucleophilicityFmo method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalNucleophilicityRedox method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalRelativeElectrophilicity method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalRelativeNucleophilicity method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalSoftnessMinusFmo method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalSoftnessMinusRedox method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalSoftnessPlusFmo method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalSoftnessPlusRedox method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalSoftnessZeroFmo method) (bonafide.features.xtb_cdft.Xtb3DAtomCdftLocalSoftnessZeroRedox method) (bonafide.features.xtb_fukui_misc.Xtb3DAtomC6DispersionCoefficient method) (bonafide.features.xtb_fukui_misc.Xtb3DAtomCdftCondensedFukuiDual method) (bonafide.features.xtb_fukui_misc.Xtb3DAtomCdftCondensedFukuiMinus method) (bonafide.features.xtb_fukui_misc.Xtb3DAtomCdftCondensedFukuiPlus method) (bonafide.features.xtb_fukui_misc.Xtb3DAtomCdftCondensedFukuiZero method) (bonafide.features.xtb_fukui_misc.Xtb3DAtomPartialChargeHueckel method) (bonafide.features.xtb_fukui_misc.Xtb3DAtomPolarizability method) (bonafide.utils.sp_psi4.Psi4SP method) (bonafide.utils.sp_xtb.XtbSP method) calculate_electronic_structure() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] calculate_global_cdft_descriptors_fmo() (in module bonafide.utils.global_properties) calculate_global_cdft_descriptors_redox() (in module bonafide.utils.global_properties) CdftLocalRedoxMixin (class in bonafide.utils.cdft_redox_mixin) ch_equivalence_constraint_resp (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgTwoStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannTwoStage attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) charge (bonafide.features.kallisto_._Kallisto3DAtom attribute) (bonafide.utils.base_mixin._BaseMixin attribute) (bonafide.utils.base_single_point.BaseSinglePoint attribute) check_dependency_env() (in module bonafide.utils.dependencies) check_dependency_path() (in module bonafide.utils.dependencies) check_iterable_option() (bonafide.utils.input_validation._ValidateIterableIntOptionMixin method) check_string_in_last_line() (bonafide.log_file_analysis.LogFileAnalyzer method) clean_properties() (bonafide.utils.molecule_vault.MolVault method) clean_up() (in module bonafide.utils.helper_functions) clear_atom_feature_cache() (bonafide.bonafide.AtomBondFeaturizer method), [1] clear_bond_feature_cache() (bonafide.bonafide.AtomBondFeaturizer method), [1] clear_feature_cache_() (bonafide.utils.molecule_vault.MolVault method) cntype (bonafide.features.kallisto_._Kallisto3DAtom attribute) (bonafide.utils.input_validation.ValidateKallisto attribute) compare_conformers() (bonafide.utils.molecule_vault.MolVault method) config_data_validator() (in module bonafide.utils.input_validation) conformer_idx (bonafide.features.distance._DistanceMatrixMixin attribute) (bonafide.utils.base_featurizer.BaseFeaturizer attribute) (bonafide.utils.cdft_redox_mixin.CdftLocalRedoxMixin attribute) conformer_name (bonafide.utils.base_featurizer.BaseFeaturizer attribute) (bonafide.utils.base_mixin._BaseMixin attribute) (bonafide.utils.base_single_point.BaseSinglePoint attribute) connectivity_index_threshold (bonafide.features.multiwfn_connectivity._Multiwfn3DAtomConnectivity attribute) (bonafide.utils.input_validation.ValidateMultiwfnBondAnalysis attribute) convergence_threshold_resp (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgTwoStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannTwoStage attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) coordinates (bonafide.features.kallisto_._Kallisto3DAtom attribute) (bonafide.utils.base_mixin._BaseMixin attribute) (bonafide.utils.base_single_point.BaseSinglePoint attribute) countBounds (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintAtomPair attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintFeatureMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintRdkit attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintTopologicalTorsion attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintAtomPair attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintFeatureMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintRdkit attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintTopologicalTorsion attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) countSimulation (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintAtomPair attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintFeatureMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintRdkit attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintTopologicalTorsion attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintAtomPair attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintFeatureMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintRdkit attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintTopologicalTorsion attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) custom_featurizer_data_validator() (in module bonafide.utils.custom_featurizer_input_validation) custom_groups (bonafide.features.functional_group.Bonafide2DAtomFunctionalGroupMatch attribute) (bonafide.utils.input_validation.ValidateBonafideFunctionalGroup attribute) D Dbstep3DAtomBuriedVolume (class in bonafide.features.dbstep_) Dbstep3DAtomFractionBuriedShellVolume (class in bonafide.features.dbstep_) Dbstep3DAtomFractionBuriedVolume (class in bonafide.features.dbstep_) density (bonafide.features.morfeus_bv._Morfeus3DAtomBV attribute) (bonafide.features.morfeus_dispersion._Morfeus3DAtomDispersion attribute) (bonafide.features.morfeus_sasa._Morfeus3DAtomSASA attribute) (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume attribute) (bonafide.utils.input_validation.ValidateMorfeusConeAndSolidAngle attribute) (bonafide.utils.input_validation.ValidateMorfeusDispersion attribute) (bonafide.utils.input_validation.ValidateMorfeusSasa attribute) depth (bonafide.features.autocorrelation._Bonafide2DAtomAutocorrelation attribute) (bonafide.utils.input_validation.ValidateBonafideAutocorrelation attribute) determine_bonds() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] dimensionality (bonafide._bonafide_utils._AtomBondFeaturizerUtils attribute) dispersion_ (bonafide.features.morfeus_dispersion._Morfeus3DAtomDispersion attribute) distal_volume_method (bonafide.features.morfeus_bv._Morfeus3DAtomBV attribute) (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume attribute) distal_volume_sasa_density (bonafide.features.morfeus_bv._Morfeus3DAtomBV attribute) (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume attribute) Dscribe3DAtomAtomCenteredSymmetryFunction (class in bonafide.features.dscribe_) Dscribe3DAtomAtomicCoulombVector (class in bonafide.features.dscribe_) Dscribe3DAtomLocalManyBodyTensorRepresentation (class in bonafide.features.dscribe_) Dscribe3DAtomSmoothOverlapOfAtomicPositions (class in bonafide.features.dscribe_) E eem_parameters (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeEem attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) electronic_struc_n (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeEem attribute) (bonafide.utils.base_mixin._BaseMixin attribute) electronic_struc_n_minus1 (bonafide.utils.base_mixin._BaseMixin attribute) electronic_struc_n_plus1 (bonafide.utils.base_mixin._BaseMixin attribute) electronic_struc_type_n (bonafide.features.morfeus_local_force._Morfeus3DBondLocalForce attribute) elements (bonafide.features.kallisto_._Kallisto3DAtom attribute) (bonafide.utils.base_mixin._BaseMixin attribute) (bonafide.utils.base_single_point.BaseSinglePoint attribute) en_scale (bonafide.features.oxidation_state.Bonafide2DAtomOxidationState attribute) (bonafide.utils.input_validation.ValidateBonafideOxidationState attribute) energy_n (bonafide.utils.cdft_redox_mixin.CdftLocalRedoxMixin attribute) energy_n_minus1 (bonafide.utils.cdft_redox_mixin.CdftLocalRedoxMixin attribute) energy_n_plus1 (bonafide.utils.cdft_redox_mixin.CdftLocalRedoxMixin attribute) engine_name (bonafide.utils.base_single_point.BaseSinglePoint attribute) ensemble_dimensionality (bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedFukui attribute) Environment (class in bonafide.utils.environment) esp_type (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeChelpg attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMerzKollmann attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgTwoStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannTwoStage attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) etemp (bonafide.utils.input_validation.ValidateXtb attribute) (bonafide.utils.sp_xtb.XtbSP attribute) etemp_native (bonafide.utils.input_validation.ValidateXtb attribute) exclude (bonafide.features.dbstep_._Dbstep3DAtom attribute) (bonafide.utils.input_validation.ValidateDbstep attribute) exclude_atoms (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeChelpg attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMerzKollmann attribute) (bonafide.utils.input_validation.ValidateMultiwfnFuzzy attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) excluded_atoms (bonafide.features.morfeus_bv._Morfeus3DAtomBV attribute) (bonafide.features.morfeus_dispersion._Morfeus3DAtomDispersion attribute) (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume attribute) (bonafide.utils.input_validation.ValidateMorfeusDispersion attribute) (bonafide.utils.input_validation.ValidateMorfeusPyramidalization attribute) external_driver() (in module bonafide.utils.driver) extract_energy_from_string() (in module bonafide.utils.io_) extraction_mode (bonafide.utils.base_featurizer.BaseFeaturizer attribute) F feature_cache (bonafide.utils.base_featurizer.BaseFeaturizer attribute) feature_cache_n_minus1 (bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedFukui attribute) feature_cache_n_plus1 (bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedFukui attribute) feature_dimensionality (bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedFukui attribute) feature_info (bonafide.utils.input_validation._ValidateIterableIntOptionMixin attribute) (bonafide.utils.input_validation.ValidateBonafideAutocorrelation attribute) feature_name (bonafide.utils.base_featurizer.BaseFeaturizer attribute) feature_type (bonafide.utils.base_featurizer.BaseFeaturizer attribute) FeatureOutput (class in bonafide.utils.feature_output) featurize_atoms() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] featurize_bonds() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] fitting_points_settings_merz_kollmann (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMerzKollmann attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannTwoStage attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) flatten_dict() (in module bonafide.utils.helper_functions) format() (bonafide.utils.logging_format.IndentationFormatter method) fpSize (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintAtomPair attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintFeatureMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintRdkit attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintTopologicalTorsion attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintAtomPair attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintFeatureMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintRdkit attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintTopologicalTorsion attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) from_periodic_table() (in module bonafide.utils.helper_functions_chemistry) G g2_params (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeAcsf attribute) g3_params (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeAcsf attribute) g4_params (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeAcsf attribute) g5_params (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeAcsf attribute) geometry_function (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeLmbtr attribute) get_atom_bond_mapping_dicts() (in module bonafide.utils.helper_functions_chemistry) get_charge_from_mol_object() (in module bonafide.utils.helper_functions_chemistry) get_elements() (bonafide.utils.molecule_vault.MolVault method) get_energy_based_reduced_features() (in module bonafide.utils.helper_functions_output) get_fmo_energies_multiwfn() (in module bonafide.utils.global_properties) get_function_or_method_name() (in module bonafide.utils.helper_functions) get_level_log_messages() (bonafide.log_file_analysis.LogFileAnalyzer method) get_molecular_formula() (in module bonafide.utils.helper_functions_chemistry) get_non_energy_based_reduced_features() (in module bonafide.utils.helper_functions_output) get_results() (bonafide.utils.feature_output.FeatureOutput method) get_ring_classification() (in module bonafide.utils.helper_functions_chemistry) get_time_for_individual_features() (bonafide.log_file_analysis.LogFileAnalyzer method) get_total_runtime() (bonafide.log_file_analysis.LogFileAnalyzer method) get_total_time_for_atom_featurization() (bonafide.log_file_analysis.LogFileAnalyzer method) get_total_time_for_bond_featurization() (bonafide.log_file_analysis.LogFileAnalyzer method) global_feature_cache (bonafide.features.distance._DistanceMatrixMixin attribute) (bonafide.utils.base_mixin._BaseMixin attribute) (bonafide.utils.cdft_redox_mixin.CdftLocalRedoxMixin attribute) grid (bonafide.features.dbstep_._Dbstep3DAtom attribute) (bonafide.utils.input_validation.ValidateDbstep attribute) grid_max (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeLmbtr attribute) grid_min (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeLmbtr attribute) grid_n (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeLmbtr attribute) grid_point_spacing (bonafide.features.multiwfn_surface._Multiwfn3DAtomSurface attribute) (bonafide.utils.input_validation.ValidateMultiwfnSurface attribute) grid_sigma (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeLmbtr attribute) grid_spacing_chelpg (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeChelpg attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgTwoStage attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) H homo_minus (bonafide.features.multiwfn_orbital._Multiwfn3DAtomMoContribution attribute) (bonafide.utils.input_validation.ValidateMultiwfnOrbital attribute) I ibis_igm_type (bonafide.features.multiwfn_bond.Multiwfn3DBondIntrinsicBondStrengthIndex attribute) (bonafide.utils.input_validation.ValidateMultiwfnBondAnalysis attribute) ibsi_grid (bonafide.features.multiwfn_bond.Multiwfn3DBondIntrinsicBondStrengthIndex attribute) (bonafide.utils.input_validation.ValidateMultiwfnBondAnalysis attribute) imag_cutoff (bonafide.features.morfeus_local_force._Morfeus3DBondLocalForce attribute) (bonafide.utils.input_validation.ValidateMorfeusLocalForce attribute) include_hs (bonafide.features.morfeus_bv._Morfeus3DAtomBV attribute) (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume attribute) includeAtomMaps (bonafide.features.symmetric_sites.Bonafide2DAtomIsSymmetricTo attribute) (bonafide.features.symmetric_sites.Bonafide2DBondIsSymmetricTo attribute) (bonafide.utils.input_validation.ValidateBonafideSymmetry attribute) includeChirality (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintAtomPair attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintFeatureMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintTopologicalTorsion attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintAtomPair attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintFeatureMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintTopologicalTorsion attribute) (bonafide.features.symmetric_sites.Bonafide2DAtomIsSymmetricTo attribute) (bonafide.features.symmetric_sites.Bonafide2DBondIsSymmetricTo attribute) (bonafide.utils.input_validation.ValidateBonafideSymmetry attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) includeChiralPresence (bonafide.features.symmetric_sites.Bonafide2DAtomIsSymmetricTo attribute) (bonafide.features.symmetric_sites.Bonafide2DBondIsSymmetricTo attribute) (bonafide.utils.input_validation.ValidateBonafideSymmetry attribute) included_atoms (bonafide.features.morfeus_dispersion._Morfeus3DAtomDispersion attribute) (bonafide.utils.input_validation.ValidateMorfeusDispersion attribute) includeIsotopes (bonafide.features.symmetric_sites.Bonafide2DAtomIsSymmetricTo attribute) (bonafide.features.symmetric_sites.Bonafide2DBondIsSymmetricTo attribute) (bonafide.utils.input_validation.ValidateBonafideSymmetry attribute) IndentationFormatter (class in bonafide.utils.logging_format) initialize_mol() (bonafide.utils.molecule_vault.MolVault method) input_type (bonafide.utils.molecule_vault.MolVault attribute) integration_grid (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace attribute) (bonafide.utils.input_validation.ValidateMultiwfnFuzzy attribute) iterable_option (bonafide.features.autocorrelation._Bonafide2DAtomAutocorrelation attribute) (bonafide.features.multiwfn_cdft._Multiwfn3DAtomCdftLocal attribute) (bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedFukui attribute) (bonafide.utils.input_validation._ValidateIterableIntOptionMixin attribute) (bonafide.utils.input_validation.ValidateBonafideAutocorrelation attribute) (bonafide.utils.input_validation.ValidateMultiwfnCdft attribute) iterations (bonafide.utils.input_validation.ValidateXtb attribute) (bonafide.utils.sp_xtb.XtbSP attribute) K Kallisto3DAtomCoordinationNumber (class in bonafide.features.kallisto_) Kallisto3DAtomPartialCharge (class in bonafide.features.kallisto_) Kallisto3DAtomPolarizability (class in bonafide.features.kallisto_) Kallisto3DAtomProximityShell (class in bonafide.features.kallisto_) Kallisto3DAtomRelativePolarizability (class in bonafide.features.kallisto_) Kallisto3DAtomVdwRadius (class in bonafide.features.kallisto_) kallisto_driver() (in module bonafide.utils.driver) key_level (bonafide.features.functional_group.Bonafide2DAtomFunctionalGroupMatch attribute) (bonafide.utils.input_validation.ValidateBonafideFunctionalGroup attribute) L l_max (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeSoap attribute) length_scale (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDelocalizationRangeFunctionMax attribute) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDelocalizationRangeFunctionMean attribute) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceElectronDelocalizationRangeFunctionMin attribute) (bonafide.utils.input_validation.ValidateMultiwfnSurface attribute) list_atom_features() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] list_bond_features() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] local_force_ (bonafide.features.morfeus_local_force._Morfeus3DBondLocalForce attribute) LogFileAnalyzer (class in bonafide.log_file_analysis) lumo_plus (bonafide.features.multiwfn_orbital._Multiwfn3DAtomMoContribution attribute) (bonafide.utils.input_validation.ValidateMultiwfnOrbital attribute) M matrix_parser() (in module bonafide.utils.helper_functions) maxDistance (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintAtomPair attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintAtomPair attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) maxiter (bonafide.utils.input_validation.ValidatePsi4 attribute) (bonafide.utils.sp_psi4.Psi4SP attribute) maxPath (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintRdkit attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintRdkit attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) memory (bonafide.utils.input_validation.ValidatePsi4 attribute) (bonafide.utils.sp_psi4.Psi4SP attribute) Mendeleev2DAtomAtomicRadius (class in bonafide.features.mendeleev_) Mendeleev2DAtomAtomicRadiusRahm (class in bonafide.features.mendeleev_) Mendeleev2DAtomAtomicVolume (class in bonafide.features.mendeleev_) Mendeleev2DAtomAtomicWeight (class in bonafide.features.mendeleev_) Mendeleev2DAtomBlock (class in bonafide.features.mendeleev_) Mendeleev2DAtomC6 (class in bonafide.features.mendeleev_) Mendeleev2DAtomC6Gb (class in bonafide.features.mendeleev_) Mendeleev2DAtomCas (class in bonafide.features.mendeleev_) Mendeleev2DAtomCovalentRadiusBragg (class in bonafide.features.mendeleev_) Mendeleev2DAtomCovalentRadiusCordero (class in bonafide.features.mendeleev_) Mendeleev2DAtomCovalentRadiusPyykko (class in bonafide.features.mendeleev_) Mendeleev2DAtomCovalentRadiusPyykkoDouble (class in bonafide.features.mendeleev_) Mendeleev2DAtomCovalentRadiusPyykkoTriple (class in bonafide.features.mendeleev_) Mendeleev2DAtomDensity (class in bonafide.features.mendeleev_) Mendeleev2DAtomDipolePolarizability (class in bonafide.features.mendeleev_) Mendeleev2DAtomEconf (class in bonafide.features.mendeleev_) Mendeleev2DAtomElectronAffinity (class in bonafide.features.mendeleev_) Mendeleev2DAtomElectrophilicity (class in bonafide.features.mendeleev_) Mendeleev2DAtomEnAllen (class in bonafide.features.mendeleev_) Mendeleev2DAtomEnAllredRochow (class in bonafide.features.mendeleev_) Mendeleev2DAtomEnCottrellSutton (class in bonafide.features.mendeleev_) Mendeleev2DAtomEnGhosh (class in bonafide.features.mendeleev_) Mendeleev2DAtomEnGordy (class in bonafide.features.mendeleev_) Mendeleev2DAtomEnMartynovBatsanov (class in bonafide.features.mendeleev_) Mendeleev2DAtomEnMiedema (class in bonafide.features.mendeleev_) Mendeleev2DAtomEnMulliken (class in bonafide.features.mendeleev_) Mendeleev2DAtomEnNagle (class in bonafide.features.mendeleev_) Mendeleev2DAtomEnPauling (class in bonafide.features.mendeleev_) Mendeleev2DAtomEnSanderson (class in bonafide.features.mendeleev_) Mendeleev2DAtomEvaporationHeat (class in bonafide.features.mendeleev_) Mendeleev2DAtomFirstIonizationEnergy (class in bonafide.features.mendeleev_) Mendeleev2DAtomFusionHeat (class in bonafide.features.mendeleev_) Mendeleev2DAtomGasBasicity (class in bonafide.features.mendeleev_) Mendeleev2DAtomGroupId (class in bonafide.features.mendeleev_) Mendeleev2DAtomHardness (class in bonafide.features.mendeleev_) Mendeleev2DAtomHeatOfFormation (class in bonafide.features.mendeleev_) Mendeleev2DAtomInchi (class in bonafide.features.mendeleev_) Mendeleev2DAtomIsMonoisotopic (class in bonafide.features.mendeleev_) Mendeleev2DAtomIsRadioactive (class in bonafide.features.mendeleev_) Mendeleev2DAtomLatticeConstant (class in bonafide.features.mendeleev_) Mendeleev2DAtomLatticeStructure (class in bonafide.features.mendeleev_) Mendeleev2DAtomMeltingPoint (class in bonafide.features.mendeleev_) Mendeleev2DAtomMetallicRadius (class in bonafide.features.mendeleev_) Mendeleev2DAtomMetallicRadiusC12 (class in bonafide.features.mendeleev_) Mendeleev2DAtomMiedemaElectronDensity (class in bonafide.features.mendeleev_) Mendeleev2DAtomMiedemaMolarVolume (class in bonafide.features.mendeleev_) Mendeleev2DAtomMolarHeatCapacity (class in bonafide.features.mendeleev_) Mendeleev2DAtomName (class in bonafide.features.mendeleev_) Mendeleev2DAtomNValenceElectrons (class in bonafide.features.mendeleev_) Mendeleev2DAtomPeriod (class in bonafide.features.mendeleev_) Mendeleev2DAtomPettiforNumber (class in bonafide.features.mendeleev_) Mendeleev2DAtomProtonAffinity (class in bonafide.features.mendeleev_) Mendeleev2DAtomSoftness (class in bonafide.features.mendeleev_) Mendeleev2DAtomSpecificHeatCapacity (class in bonafide.features.mendeleev_) Mendeleev2DAtomThermalConductivity (class in bonafide.features.mendeleev_) Mendeleev2DAtomVdwRadius (class in bonafide.features.mendeleev_) Mendeleev2DAtomVdwRadiusAlvarez (class in bonafide.features.mendeleev_) Mendeleev2DAtomVdwRadiusBatsanov (class in bonafide.features.mendeleev_) Mendeleev2DAtomVdwRadiusBondi (class in bonafide.features.mendeleev_) Mendeleev2DAtomVdwRadiusDreiding (class in bonafide.features.mendeleev_) Mendeleev2DAtomVdwRadiusMm3 (class in bonafide.features.mendeleev_) Mendeleev2DAtomVdwRadiusRt (class in bonafide.features.mendeleev_) Mendeleev2DAtomVdwRadiusUff (class in bonafide.features.mendeleev_) Mendeleev2DAtomZeff (class in bonafide.features.mendeleev_) method (bonafide.features.mendeleev_.Mendeleev2DAtomZeff attribute) (bonafide.features.morfeus_local_force._Morfeus3DBondLocalForce attribute) (bonafide.features.xtb_fukui_misc._Xtb3DAtomFukuiMisc attribute) (bonafide.utils.base_single_point.BaseSinglePoint attribute) (bonafide.utils.input_validation.ValidateMendeleev attribute) (bonafide.utils.input_validation.ValidateMorfeusLocalForce attribute) (bonafide.utils.input_validation.ValidateMorfeusPyramidalization attribute) (bonafide.utils.input_validation.ValidatePsi4 attribute) (bonafide.utils.input_validation.ValidateXtb attribute) minDistance (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintAtomPair attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintAtomPair attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) minPath (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintRdkit attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintRdkit attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) MKL_NUM_THREADS (bonafide.utils.input_validation.ValidateXtb attribute) model_config (bonafide.utils.input_validation.ValidateAlfabet attribute) (bonafide.utils.input_validation.ValidateBonafideAutocorrelation attribute) (bonafide.utils.input_validation.ValidateBonafideConstant attribute) (bonafide.utils.input_validation.ValidateBonafideDistance attribute) (bonafide.utils.input_validation.ValidateBonafideFunctionalGroup attribute) (bonafide.utils.input_validation.ValidateBonafideOxidationState attribute) (bonafide.utils.input_validation.ValidateBonafideSymmetry attribute) (bonafide.utils.input_validation.ValidateDbstep attribute) (bonafide.utils.input_validation.ValidateDscribeAcsf attribute) (bonafide.utils.input_validation.ValidateDscribeCoulombMatrix attribute) (bonafide.utils.input_validation.ValidateDscribeLmbtr attribute) (bonafide.utils.input_validation.ValidateDscribeSoap attribute) (bonafide.utils.input_validation.ValidateDummy attribute) (bonafide.utils.input_validation.ValidateKallisto attribute) (bonafide.utils.input_validation.ValidateMendeleev attribute) (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume attribute) (bonafide.utils.input_validation.ValidateMorfeusConeAndSolidAngle attribute) (bonafide.utils.input_validation.ValidateMorfeusDispersion attribute) (bonafide.utils.input_validation.ValidateMorfeusLocalForce attribute) (bonafide.utils.input_validation.ValidateMorfeusPyramidalization attribute) (bonafide.utils.input_validation.ValidateMorfeusSasa attribute) (bonafide.utils.input_validation.ValidateMultiwfnBondAnalysis attribute) (bonafide.utils.input_validation.ValidateMultiwfnCdft attribute) (bonafide.utils.input_validation.ValidateMultiwfnFuzzy attribute) (bonafide.utils.input_validation.ValidateMultiwfnMisc attribute) (bonafide.utils.input_validation.ValidateMultiwfnOrbital attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) (bonafide.utils.input_validation.ValidateMultiwfnRootData attribute) (bonafide.utils.input_validation.ValidateMultiwfnSurface attribute) (bonafide.utils.input_validation.ValidateMultiwfnTopology attribute) (bonafide.utils.input_validation.ValidatePsi4 attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) (bonafide.utils.input_validation.ValidateXtb attribute) module bonafide._bonafide bonafide._bonafide_utils bonafide.bonafide, [1] bonafide.features.alfabet_ bonafide.features.autocorrelation bonafide.features.constant_feature bonafide.features.dbstep_ bonafide.features.distance bonafide.features.dscribe_ bonafide.features.functional_group bonafide.features.kallisto_ bonafide.features.mendeleev_ bonafide.features.morfeus_bv bonafide.features.morfeus_dispersion bonafide.features.morfeus_local_force bonafide.features.morfeus_sasa bonafide.features.multiwfn_bond bonafide.features.multiwfn_bond_misc bonafide.features.multiwfn_cdft bonafide.features.multiwfn_connectivity bonafide.features.multiwfn_forces bonafide.features.multiwfn_fukui bonafide.features.multiwfn_fuzzy_space bonafide.features.multiwfn_hilbert_space bonafide.features.multiwfn_misc bonafide.features.multiwfn_orbital bonafide.features.multiwfn_partial_charge bonafide.features.multiwfn_population bonafide.features.multiwfn_population_analysis bonafide.features.multiwfn_spin_population bonafide.features.multiwfn_surface bonafide.features.multiwfn_topology_atom bonafide.features.multiwfn_topology_bond bonafide.features.oxidation_state bonafide.features.qmdesc_ bonafide.features.rdkit_atom bonafide.features.rdkit_bond bonafide.features.rdkit_fingerprint bonafide.features.spiro_bridgehead bonafide.features.symmetric_sites bonafide.features.xtb_cdft bonafide.features.xtb_fukui_misc bonafide.log_file_analysis bonafide.utils.base_featurizer bonafide.utils.base_mixin bonafide.utils.base_single_point bonafide.utils.cdft_redox_mixin bonafide.utils.constants bonafide.utils.custom_featurizer_input_validation bonafide.utils.dependencies bonafide.utils.driver bonafide.utils.environment bonafide.utils.feature_factories bonafide.utils.feature_output bonafide.utils.global_properties bonafide.utils.helper_functions bonafide.utils.helper_functions_chemistry bonafide.utils.helper_functions_output bonafide.utils.input_validation bonafide.utils.io_ bonafide.utils.logging_format bonafide.utils.molecule_vault bonafide.utils.multiwfn_properties bonafide.utils.sp_psi4 bonafide.utils.sp_xtb bonafide.utils.string_formatting mol (bonafide.features.distance._DistanceMatrixMixin attribute) (bonafide.utils.base_featurizer.BaseFeaturizer attribute) mol_inputs (bonafide.utils.molecule_vault.MolVault attribute) mol_vault (bonafide._bonafide._AtomBondFeaturizer attribute) (bonafide._bonafide_utils._AtomBondFeaturizerUtils attribute) (bonafide.utils.base_single_point.BaseSinglePoint attribute) MolVault (class in bonafide.utils.molecule_vault) Morfeus3DAtomBuriedVolume (class in bonafide.features.morfeus_bv) Morfeus3DAtomBuriedVolumeOctants (class in bonafide.features.morfeus_bv) Morfeus3DAtomBuriedVolumeQuadrants (class in bonafide.features.morfeus_bv) Morfeus3DAtomDistalVolume (class in bonafide.features.morfeus_bv) Morfeus3DAtomDistalVolumeOctants (class in bonafide.features.morfeus_bv) Morfeus3DAtomDistalVolumeQuadrants (class in bonafide.features.morfeus_bv) Morfeus3DAtomFractionBuriedVolume (class in bonafide.features.morfeus_bv) Morfeus3DAtomFractionBuriedVolumeOctants (class in bonafide.features.morfeus_bv) Morfeus3DAtomFractionBuriedVolumeQuadrants (class in bonafide.features.morfeus_bv) Morfeus3DAtomFractionFreeVolume (class in bonafide.features.morfeus_bv) Morfeus3DAtomFractionFreeVolumeOctants (class in bonafide.features.morfeus_bv) Morfeus3DAtomFractionFreeVolumeQuadrants (class in bonafide.features.morfeus_bv) Morfeus3DAtomFreeVolume (class in bonafide.features.morfeus_bv) Morfeus3DAtomFreeVolumeOctants (class in bonafide.features.morfeus_bv) Morfeus3DAtomFreeVolumeQuadrants (class in bonafide.features.morfeus_bv) Morfeus3DAtomMolecularVolumeOctants (class in bonafide.features.morfeus_bv) Morfeus3DAtomMolecularVolumeQuadrants (class in bonafide.features.morfeus_bv) Morfeus3DAtomPInt (class in bonafide.features.morfeus_dispersion) Morfeus3DAtomPMax (class in bonafide.features.morfeus_dispersion) Morfeus3DAtomPMin (class in bonafide.features.morfeus_dispersion) Morfeus3DAtomSasAtomArea (class in bonafide.features.morfeus_sasa) Morfeus3DAtomSasFractionAtomArea (class in bonafide.features.morfeus_sasa) Morfeus3DBondLocalForceConstant (class in bonafide.features.morfeus_local_force) Morfeus3DBondLocalFrequency (class in bonafide.features.morfeus_local_force) multiplicity (bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedFukui attribute) (bonafide.utils.base_mixin._BaseMixin attribute) (bonafide.utils.base_single_point.BaseSinglePoint attribute) Multiwfn3DAtomCdftCondensedFukuiDual (class in bonafide.features.multiwfn_fukui) Multiwfn3DAtomCdftCondensedFukuiMinus (class in bonafide.features.multiwfn_fukui) Multiwfn3DAtomCdftCondensedFukuiPlus (class in bonafide.features.multiwfn_fukui) Multiwfn3DAtomCdftCondensedFukuiZero (class in bonafide.features.multiwfn_fukui) Multiwfn3DAtomCdftCondensedOrbitalWeightedFukuiDual (class in bonafide.features.multiwfn_fukui) Multiwfn3DAtomCdftCondensedOrbitalWeightedFukuiMinus (class in bonafide.features.multiwfn_fukui) Multiwfn3DAtomCdftCondensedOrbitalWeightedFukuiPlus (class in bonafide.features.multiwfn_fukui) Multiwfn3DAtomCdftCondensedOrbitalWeightedFukuiZero (class in bonafide.features.multiwfn_fukui) Multiwfn3DAtomCdftLocalElectrophilicityFmo (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalElectrophilicityRedox (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalHardnessMinusFmo (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalHardnessMinusRedox (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalHardnessPlusFmo (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalHardnessPlusRedox (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalHardnessZeroFmo (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalHardnessZeroRedox (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalHyperhardnessFmo (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalHyperhardnessRedox (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalHypersoftnessFmo (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalHypersoftnessRedox (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalNucleophilicityFmo (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalNucleophilicityRedox (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalRelativeElectrophilicity (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalRelativeNucleophilicity (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalSoftnessMinusFmo (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalSoftnessMinusRedox (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalSoftnessPlusFmo (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalSoftnessPlusRedox (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalSoftnessZeroFmo (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomCdftLocalSoftnessZeroRedox (class in bonafide.features.multiwfn_cdft) Multiwfn3DAtomConnectivityIndex (class in bonafide.features.multiwfn_connectivity) Multiwfn3DAtomConnectivityIndexInteger (class in bonafide.features.multiwfn_connectivity) Multiwfn3DAtomEnergyIndex (class in bonafide.features.multiwfn_misc) Multiwfn3DAtomForceHellmannFeynman (class in bonafide.features.multiwfn_forces) Multiwfn3DAtomForceHellmannFeynmanElectrons (class in bonafide.features.multiwfn_forces) Multiwfn3DAtomForceHellmannFeynmanNuclearCharges (class in bonafide.features.multiwfn_forces) Multiwfn3DAtomFuzzySpaceAtomicElectronicSpatialExtent (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceAtomicValence (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceAtomicValenceAlpha (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceAtomicValenceBeta (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceCondensedLinearResponseKernelMatrixElement (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceContributionToSystemDipoleMoment (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceContributionToSystemDipoleMomentNorm (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceDipoleMoment (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceDipoleMomentNorm (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceIntegrationDescriptor (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceIntegrationDescriptorAbsRelative (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceIntegrationDescriptorRelative (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceLocalizationIndex (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceLocalizationIndexAlpha (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceLocalizationIndexBeta (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceMonopoleMoment (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceOctopoleMomentMagnitude (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceQuadrupoleMomentMagnitude (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomFuzzySpaceTracelessQuadrupoleMomentTensorMagnitude (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMoment (class in bonafide.features.multiwfn_hilbert_space) Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentElectrons (class in bonafide.features.multiwfn_hilbert_space) Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentElectronsNorm (class in bonafide.features.multiwfn_hilbert_space) Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentNorm (class in bonafide.features.multiwfn_hilbert_space) Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentNuclearCharge (class in bonafide.features.multiwfn_hilbert_space) Multiwfn3DAtomHilbertSpaceContributionToSystemDipoleMomentNuclearChargeNorm (class in bonafide.features.multiwfn_hilbert_space) Multiwfn3DAtomHilbertSpaceDipoleMoment (class in bonafide.features.multiwfn_hilbert_space) Multiwfn3DAtomHilbertSpaceDipoleMomentNorm (class in bonafide.features.multiwfn_hilbert_space) Multiwfn3DAtomHilbertSpaceLocalPopulationNumber (class in bonafide.features.multiwfn_hilbert_space) Multiwfn3DAtomMoContributionOccupiedMulliken (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionOccupiedMullikenAlpha (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionOccupiedMullikenBeta (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionOccupiedMullikenRosSchuit (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionOccupiedMullikenRosSchuitAlpha (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionOccupiedMullikenRosSchuitBeta (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionOccupiedMullikenStoutPolitzer (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionOccupiedMullikenStoutPolitzerAlpha (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionOccupiedMullikenStoutPolitzerBeta (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionUnoccupiedMulliken (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionUnoccupiedMullikenAlpha (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionUnoccupiedMullikenBeta (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionUnoccupiedMullikenRosSchuit (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionUnoccupiedMullikenRosSchuitAlpha (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionUnoccupiedMullikenRosSchuitBeta (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionUnoccupiedMullikenStoutPolitzer (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionUnoccupiedMullikenStoutPolitzerAlpha (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomMoContributionUnoccupiedMullikenStoutPolitzerBeta (class in bonafide.features.multiwfn_orbital) Multiwfn3DAtomPartialChargeBecke (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeChelpg (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeCm5 (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeCm5Scaled1point2 (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeCorrectedHirshfeld (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeEem (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeHirshfeld (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeLowdin (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeMerzKollmann (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeMulliken (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeMullikenBickelhaupt (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeMullikenRosSchuit (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeMullikenStoutPolitzer (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeRespChelpgOneStage (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeRespChelpgTwoStage (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeRespMerzKollmannOneStage (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeRespMerzKollmannTwoStage (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPartialChargeVdd (class in bonafide.features.multiwfn_partial_charge) Multiwfn3DAtomPopulationLowdin (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinD (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinDAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinDBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinF (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinFAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinFBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinG (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinGAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinGBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinH (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinHAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinHBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinP (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinPAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinPBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinS (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinSAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationLowdinSBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMulliken (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenBickelhaupt (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenBickelhauptAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenBickelhauptBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenD (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenDAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenDBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenF (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenFAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenFBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenG (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenGAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenGBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenH (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenHAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenHBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenP (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenPAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenPBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenRosSchuit (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenRosSchuitAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenRosSchuitBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenS (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenSAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenSBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenStoutPolitzer (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenStoutPolitzerAlpha (class in bonafide.features.multiwfn_population) Multiwfn3DAtomPopulationMullikenStoutPolitzerBeta (class in bonafide.features.multiwfn_population) Multiwfn3DAtomSpinPopulationLowdin (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationLowdinD (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationLowdinF (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationLowdinG (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationLowdinH (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationLowdinP (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationLowdinS (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationMulliken (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationMullikenBickelhaupt (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationMullikenD (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationMullikenF (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationMullikenG (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationMullikenH (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationMullikenP (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationMullikenRosSchuit (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationMullikenS (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSpinPopulationMullikenStoutPolitzer (class in bonafide.features.multiwfn_spin_population) Multiwfn3DAtomSurfaceAverageLocalIonizationEnergyMax (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceAverageLocalIonizationEnergyMean (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceAverageLocalIonizationEnergyMin (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceElectronDelocalizationRangeFunctionMax (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceElectronDelocalizationRangeFunctionMean (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceElectronDelocalizationRangeFunctionMin (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceElectronDensityMax (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceElectronDensityMean (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceElectronDensityMin (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceElectrostaticPotentialBalanceOfCharges (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceElectrostaticPotentialBalanceOfChargesTimesVariance (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceElectrostaticPotentialInternalChargeSeparation (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceElectrostaticPotentialMax (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceElectrostaticPotentialMean (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceElectrostaticPotentialMin (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceLocalElectronAffinityMax (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceLocalElectronAffinityMean (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceLocalElectronAffinityMin (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceLocalElectronAttachmentEnergyMax (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceLocalElectronAttachmentEnergyMean (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceLocalElectronAttachmentEnergyMin (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceOrbitalOverlapLengthFunctionMax (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceOrbitalOverlapLengthFunctionMean (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceOrbitalOverlapLengthFunctionMin (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceSignSecondLargestEigenvalueElectronDensityHessianMax (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceSignSecondLargestEigenvalueElectronDensityHessianMean (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomSurfaceSignSecondLargestEigenvalueElectronDensityHessianMin (class in bonafide.features.multiwfn_surface) Multiwfn3DAtomTopologyAverageLocalIonizationEnergy (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyDeltaGHirshfeld (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyDeltaGPromolecular (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyElectronDensity (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyElectronDensityAlpha (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyElectronDensityBeta (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyElectronDensityEllipticity (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyElectronLocalizationFunction (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyElectrostaticPotential (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyElectrostaticPotentialElectrons (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyElectrostaticPotentialNuclearCharges (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyEnergyDensity (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyEtaIndex (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyGradientComponentsXYZ (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyGradientNorm (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyHamiltonianKineticEnergy (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyHessianDeterminant (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyHessianEigenvalues (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyInteractionRegionIndicator (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyLagrangianKineticEnergy (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyLaplacianComponentsXYZ (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyLaplacianOfElectronDensity (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyLaplacianTotal (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyLocalInformationEntropy (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyLocalizedOrbitalLocator (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyPotentialEnergyDensity (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyReducedDensityGradient (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyReducedDensityGradientPromolecular (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologySignSecondLargestEigenvalueElectronDensityHessian (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologySignSecondLargestEigenvalueElectronDensityHessianPromolecular (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologySpinDensity (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DAtomTopologyVdwPotential (class in bonafide.features.multiwfn_topology_atom) Multiwfn3DBondBondOrderFuzzy (class in bonafide.features.multiwfn_bond) Multiwfn3DBondBondOrderLaplacian (class in bonafide.features.multiwfn_bond) Multiwfn3DBondBondOrderMayer (class in bonafide.features.multiwfn_bond) Multiwfn3DBondBondOrderMulliken (class in bonafide.features.multiwfn_bond) Multiwfn3DBondBondOrderWiberg (class in bonafide.features.multiwfn_bond) Multiwfn3DBondCoordinatesCenterOfMass (class in bonafide.features.multiwfn_bond_misc) Multiwfn3DBondCoordinatesCenterOfNuclearCharges (class in bonafide.features.multiwfn_bond_misc) Multiwfn3DBondElectrostaticInteractionEnergyNuclearCharges (class in bonafide.features.multiwfn_bond_misc) Multiwfn3DBondFuzzySpaceCondensedLinearResponseKernelMatrixElement (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DBondFuzzySpaceOverlapIntegrationDescriptor (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DBondFuzzySpaceOverlapIntegrationDescriptorNegative (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DBondFuzzySpaceOverlapIntegrationDescriptorPositive (class in bonafide.features.multiwfn_fuzzy_space) Multiwfn3DBondGyrationRadius (class in bonafide.features.multiwfn_bond_misc) Multiwfn3DBondHilbertSpaceContributionToSystemDipoleMoment (class in bonafide.features.multiwfn_hilbert_space) Multiwfn3DBondHilbertSpaceContributionToSystemDipoleMomentNorm (class in bonafide.features.multiwfn_hilbert_space) Multiwfn3DBondHilbertSpaceDipoleMoment (class in bonafide.features.multiwfn_hilbert_space) Multiwfn3DBondHilbertSpaceDipoleMomentNorm (class in bonafide.features.multiwfn_hilbert_space) Multiwfn3DBondHilbertSpaceOverlapPopulation (class in bonafide.features.multiwfn_hilbert_space) Multiwfn3DBondIntrinsicBondStrengthIndex (class in bonafide.features.multiwfn_bond) Multiwfn3DBondTopologyBcpAverageLocalIonizationEnergy (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpCoordinates (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpDeltaGHirshfeld (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpDeltaGPromolecular (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpDistanceEndAtom (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpDistanceStartAtom (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpElectronDensity (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpElectronDensityAlpha (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpElectronDensityBeta (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpElectronDensityEllipticity (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpElectronLocalizationFunction (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpElectrostaticPotential (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpElectrostaticPotentialElectrons (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpElectrostaticPotentialNuclearCharges (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpEnergyDensity (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpEtaIndex (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpGradientComponentsXYZ (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpGradientNorm (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpHamiltonianKineticEnergy (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpHessianDeterminant (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpHessianEigenvalues (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpInteractionRegionIndicator (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpLagrangianKineticEnergy (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpLaplacianComponentsXYZ (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpLaplacianOfElectronDensity (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpLaplacianTotal (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpLocalInformationEntropy (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpLocalizedOrbitalLocator (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpPotentialEnergyDensity (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpReducedDensityGradient (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpReducedDensityGradientPromolecular (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpRelativeBondPosition (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpSignSecondLargestEigenvalueElectronDensityHessian (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpSignSecondLargestEigenvalueElectronDensityHessianPromolecular (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpSpinDensity (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyBcpVdwPotential (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyCpIndex (class in bonafide.features.multiwfn_topology_bond) Multiwfn3DBondTopologyCpType (class in bonafide.features.multiwfn_topology_bond) multiwfn_driver() (in module bonafide.utils.driver) N n_bonds_cutoff (bonafide.features.distance._BonafideAtomDistance attribute) (bonafide.features.distance._BonafideBondDistance attribute) (bonafide.utils.input_validation.ValidateBonafideDistance attribute) n_iterations_becke_partition (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeBecke attribute) (bonafide.utils.input_validation.ValidateMultiwfnFuzzy attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) n_iterations_resp (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgTwoStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannTwoStage attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) n_max (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeSoap attribute) n_points_angstrom2_merz_kollmann (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeMerzKollmann attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannTwoStage attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) namespace (bonafide.utils.molecule_vault.MolVault attribute) neighbor_distance_cutoff (bonafide.features.multiwfn_topology_bond._Multiwfn3DBondTopology attribute) (bonafide.utils.input_validation.ValidateMultiwfnTopology attribute) noH (bonafide.features.dbstep_._Dbstep3DAtom attribute) (bonafide.utils.input_validation.ValidateDbstep attribute) normalization (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeLmbtr attribute) normalize_gaussians (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeLmbtr attribute) NUM_THREADS (bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedFukui attribute) (bonafide.utils.input_validation.ValidateMultiwfnBondAnalysis attribute) (bonafide.utils.input_validation.ValidateMultiwfnCdft attribute) (bonafide.utils.input_validation.ValidateMultiwfnFuzzy attribute) (bonafide.utils.input_validation.ValidateMultiwfnMisc attribute) (bonafide.utils.input_validation.ValidateMultiwfnOrbital attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) (bonafide.utils.input_validation.ValidateMultiwfnRootData attribute) (bonafide.utils.input_validation.ValidateMultiwfnSurface attribute) (bonafide.utils.input_validation.ValidateMultiwfnTopology attribute) num_threads (bonafide.utils.input_validation.ValidatePsi4 attribute) (bonafide.utils.sp_psi4.Psi4SP attribute) numBitsPerFeature (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintRdkit attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintRdkit attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) O OMP_MAX_ACTIVE_LEVELS (bonafide.utils.input_validation.ValidateXtb attribute) OMP_NUM_THREADS (bonafide.utils.input_validation.ValidateXtb attribute) OMP_STACKSIZE (bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedFukui attribute) (bonafide.utils.input_validation.ValidateMultiwfnBondAnalysis attribute) (bonafide.utils.input_validation.ValidateMultiwfnCdft attribute) (bonafide.utils.input_validation.ValidateMultiwfnFuzzy attribute) (bonafide.utils.input_validation.ValidateMultiwfnMisc attribute) (bonafide.utils.input_validation.ValidateMultiwfnOrbital attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) (bonafide.utils.input_validation.ValidateMultiwfnRootData attribute) (bonafide.utils.input_validation.ValidateMultiwfnSurface attribute) (bonafide.utils.input_validation.ValidateMultiwfnTopology attribute) (bonafide.utils.input_validation.ValidateXtb attribute) orbital_overlap_edr_option (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceOrbitalOverlapLengthFunctionMax attribute) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceOrbitalOverlapLengthFunctionMean attribute) (bonafide.features.multiwfn_surface.Multiwfn3DAtomSurfaceOrbitalOverlapLengthFunctionMin attribute) (bonafide.utils.input_validation.ValidateMultiwfnSurface attribute) ow_delta (bonafide.features.multiwfn_fukui._Multiwfn3DAtomCdftCondensedOrbitalWeightedFukui attribute) (bonafide.utils.input_validation.ValidateMultiwfnCdft attribute) P partitioning_scheme (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace attribute) (bonafide.utils.input_validation.ValidateMultiwfnFuzzy attribute) print_options() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] probe_radius (bonafide.features.morfeus_sasa._Morfeus3DAtomSASA attribute) (bonafide.utils.input_validation.ValidateMorfeusSasa attribute) project_imag (bonafide.features.morfeus_local_force._Morfeus3DBondLocalForce attribute) (bonafide.utils.input_validation.ValidateMorfeusLocalForce attribute) prune_ensemble_by_energy() (bonafide.utils.molecule_vault.MolVault method) Psi4SP (class in bonafide.utils.sp_psi4) python_interpreter_path (bonafide.features.alfabet_._Alfabet2DBond attribute) (bonafide.utils.input_validation.ValidateAlfabet attribute) Q Qmdesc2DAtomFukuiDual (class in bonafide.features.qmdesc_) Qmdesc2DAtomFukuiMinus (class in bonafide.features.qmdesc_) Qmdesc2DAtomFukuiPlus (class in bonafide.features.qmdesc_) Qmdesc2DAtomNmrChemicalShift (class in bonafide.features.qmdesc_) Qmdesc2DAtomPartialCharge (class in bonafide.features.qmdesc_) Qmdesc2DBondBondLength (class in bonafide.features.qmdesc_) Qmdesc2DBondBondOrder (class in bonafide.features.qmdesc_) R r (bonafide.features.dbstep_._Dbstep3DAtom attribute) (bonafide.utils.input_validation.ValidateDbstep attribute) r_cut (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeAcsf attribute) (bonafide.utils.input_validation.ValidateDscribeSoap attribute) radii (bonafide.features.morfeus_bv._Morfeus3DAtomBV attribute) (bonafide.features.morfeus_dispersion._Morfeus3DAtomDispersion attribute) (bonafide.features.morfeus_sasa._Morfeus3DAtomSASA attribute) (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume attribute) (bonafide.utils.input_validation.ValidateMorfeusConeAndSolidAngle attribute) (bonafide.utils.input_validation.ValidateMorfeusDispersion attribute) (bonafide.utils.input_validation.ValidateMorfeusPyramidalization attribute) (bonafide.utils.input_validation.ValidateMorfeusSasa attribute) radii_scale (bonafide.features.morfeus_bv._Morfeus3DAtomBV attribute) (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume attribute) radii_type (bonafide.features.morfeus_bv._Morfeus3DAtomBV attribute) (bonafide.features.morfeus_dispersion._Morfeus3DAtomDispersion attribute) (bonafide.features.morfeus_sasa._Morfeus3DAtomSASA attribute) (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume attribute) (bonafide.utils.input_validation.ValidateMorfeusConeAndSolidAngle attribute) (bonafide.utils.input_validation.ValidateMorfeusDispersion attribute) (bonafide.utils.input_validation.ValidateMorfeusSasa attribute) radius (bonafide.features.morfeus_bv._Morfeus3DAtomBV attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintFeatureMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintFeatureMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintMorgan attribute) (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) radius_becke_partition (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeBecke attribute) (bonafide.utils.input_validation.ValidateMultiwfnFuzzy attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) radius_cutoff (bonafide.features.distance._BonafideAtomDistance attribute) (bonafide.features.distance._BonafideBondDistance attribute) (bonafide.utils.input_validation.ValidateBonafideDistance attribute) rbf (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeSoap attribute) Rdkit2DAtomAtomicNumber (class in bonafide.features.rdkit_atom) Rdkit2DAtomAtomMapNumber (class in bonafide.features.rdkit_atom) Rdkit2DAtomChiralTag (class in bonafide.features.rdkit_atom) Rdkit2DAtomDegree (class in bonafide.features.rdkit_atom) Rdkit2DAtomEstate (class in bonafide.features.rdkit_atom) Rdkit2DAtomExplicitValence (class in bonafide.features.rdkit_atom) Rdkit2DAtomFormalCharge (class in bonafide.features.rdkit_atom) Rdkit2DAtomGasteigerCharge (class in bonafide.features.rdkit_atom) Rdkit2DAtomGasteigerHCharge (class in bonafide.features.rdkit_atom) Rdkit2DAtomHybridization (class in bonafide.features.rdkit_atom) Rdkit2DAtomImplicitValence (class in bonafide.features.rdkit_atom) Rdkit2DAtomIsAromatic (class in bonafide.features.rdkit_atom) Rdkit2DAtomIsotope (class in bonafide.features.rdkit_atom) Rdkit2DAtomLabuteAsaContribution (class in bonafide.features.rdkit_atom) Rdkit2DAtomMass (class in bonafide.features.rdkit_atom) Rdkit2DAtomNeighboringAtomsIndices (class in bonafide.features.rdkit_atom) Rdkit2DAtomNeighboringAtomsMapNumbers (class in bonafide.features.rdkit_atom) Rdkit2DAtomNeighboringBondsIndices (class in bonafide.features.rdkit_atom) Rdkit2DAtomNExplicitH (class in bonafide.features.rdkit_atom) Rdkit2DAtomNImplicitH (class in bonafide.features.rdkit_atom) Rdkit2DAtomNNeighbors (class in bonafide.features.rdkit_atom) Rdkit2DAtomNoImplicit (class in bonafide.features.rdkit_atom) Rdkit2DAtomNRadicalElectrons (class in bonafide.features.rdkit_atom) Rdkit2DAtomRingInfo (class in bonafide.features.rdkit_atom) Rdkit2DAtomRingInfoAromaticCarbocycle (class in bonafide.features.rdkit_atom) Rdkit2DAtomRingInfoAromaticHeterocycle (class in bonafide.features.rdkit_atom) Rdkit2DAtomRingInfoNonaromaticCarbocycle (class in bonafide.features.rdkit_atom) Rdkit2DAtomRingInfoNonaromaticHeterocycle (class in bonafide.features.rdkit_atom) Rdkit2DAtomRootedCountFingerprintAtomPair (class in bonafide.features.rdkit_fingerprint) Rdkit2DAtomRootedCountFingerprintFeatureMorgan (class in bonafide.features.rdkit_fingerprint) Rdkit2DAtomRootedCountFingerprintMorgan (class in bonafide.features.rdkit_fingerprint) Rdkit2DAtomRootedCountFingerprintRdkit (class in bonafide.features.rdkit_fingerprint) Rdkit2DAtomRootedCountFingerprintTopologicalTorsion (class in bonafide.features.rdkit_fingerprint) Rdkit2DAtomRootedFingerprintAtomPair (class in bonafide.features.rdkit_fingerprint) Rdkit2DAtomRootedFingerprintFeatureMorgan (class in bonafide.features.rdkit_fingerprint) Rdkit2DAtomRootedFingerprintMorgan (class in bonafide.features.rdkit_fingerprint) Rdkit2DAtomRootedFingerprintRdkit (class in bonafide.features.rdkit_fingerprint) Rdkit2DAtomRootedFingerprintTopologicalTorsion (class in bonafide.features.rdkit_fingerprint) Rdkit2DAtomSymbol (class in bonafide.features.rdkit_atom) Rdkit2DAtomTotalDegree (class in bonafide.features.rdkit_atom) Rdkit2DAtomTotalNH (class in bonafide.features.rdkit_atom) Rdkit2DAtomTotalValence (class in bonafide.features.rdkit_atom) Rdkit2DAtomTpsaContribution (class in bonafide.features.rdkit_atom) Rdkit2DAtomWildmanCrippenLogpContribution (class in bonafide.features.rdkit_atom) Rdkit2DAtomWildmanCrippenMrContribution (class in bonafide.features.rdkit_atom) Rdkit2DBondBeginAtomIndex (class in bonafide.features.rdkit_bond) Rdkit2DBondBeginAtomMapNumber (class in bonafide.features.rdkit_bond) Rdkit2DBondBondOrder (class in bonafide.features.rdkit_bond) Rdkit2DBondBondType (class in bonafide.features.rdkit_bond) Rdkit2DBondEndAtomIndex (class in bonafide.features.rdkit_bond) Rdkit2DBondEndAtomMapNumber (class in bonafide.features.rdkit_bond) Rdkit2DBondIsAromatic (class in bonafide.features.rdkit_bond) Rdkit2DBondIsConjugated (class in bonafide.features.rdkit_bond) Rdkit2DBondNeighboringAtomsIndices (class in bonafide.features.rdkit_bond) Rdkit2DBondNeighboringAtomsMapNumbers (class in bonafide.features.rdkit_bond) Rdkit2DBondNeighboringBondsIndices (class in bonafide.features.rdkit_bond) Rdkit2DBondNNeighbors (class in bonafide.features.rdkit_bond) Rdkit2DBondRingInfo (class in bonafide.features.rdkit_bond) Rdkit2DBondRingInfoAromaticCarbocycle (class in bonafide.features.rdkit_bond) Rdkit2DBondRingInfoAromaticHeterocycle (class in bonafide.features.rdkit_bond) Rdkit2DBondRingInfoNonaromaticCarbocycle (class in bonafide.features.rdkit_bond) Rdkit2DBondRingInfoNonaromaticHeterocycle (class in bonafide.features.rdkit_bond) Rdkit2DBondStereo (class in bonafide.features.rdkit_bond) Rdkit2DBondValenceContributionBeginAtom (class in bonafide.features.rdkit_bond) Rdkit2DBondValenceContributionEndAtom (class in bonafide.features.rdkit_bond) Rdkit3DAtomCoordinates (class in bonafide.features.rdkit_atom) Rdkit3DBondBondLength (class in bonafide.features.rdkit_bond) Rdkit3DBondCoordinatesBeginAtom (class in bonafide.features.rdkit_bond) Rdkit3DBondCoordinatesCenter (class in bonafide.features.rdkit_bond) Rdkit3DBondCoordinatesEndAtom (class in bonafide.features.rdkit_bond) read_input() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] read_mol_energies() (bonafide.utils.molecule_vault.MolVault method) read_mol_object() (in module bonafide.utils.io_) read_prop_file() (in module bonafide.utils.multiwfn_properties) read_sd_file() (in module bonafide.utils.io_) read_smarts() (in module bonafide.utils.io_) read_smiles() (in module bonafide.utils.io_) read_xyz_file() (in module bonafide.utils.io_) real_space_function (bonafide.features.multiwfn_fuzzy_space._Multiwfn3DFuzzySpace attribute) (bonafide.utils.input_validation.ValidateMultiwfnFuzzy attribute) reduce_to_canonical (bonafide.features.symmetric_sites.Bonafide2DAtomIsSymmetricTo attribute) (bonafide.features.symmetric_sites.Bonafide2DBondIsSymmetricTo attribute) (bonafide.utils.input_validation.ValidateBonafideSymmetry attribute) render_mol() (bonafide.utils.molecule_vault.MolVault method) reset_environment() (bonafide.utils.environment.Environment method) restraint_one_stage_resp (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgTwoStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannTwoStage attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) restraint_stage1_resp (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgTwoStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannTwoStage attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) restraint_stage2_resp (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgTwoStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannTwoStage attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) results (bonafide.utils.base_featurizer.BaseFeaturizer attribute) return_atom_features() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] return_bond_features() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] run() (bonafide.utils.base_single_point.BaseSinglePoint method) run_workflow() (bonafide.features.autocorrelation._Bonafide2DAtomAutocorrelation method) S sasa_ (bonafide.features.morfeus_sasa._Morfeus3DAtomSASA attribute) save_hessian (bonafide.features.morfeus_local_force._Morfeus3DBondLocalForce attribute) (bonafide.utils.input_validation.ValidateMorfeusLocalForce attribute) scale_factor (bonafide.utils.input_validation.ValidateMorfeusPyramidalization attribute) scalevdw (bonafide.features.dbstep_._Dbstep3DAtom attribute) (bonafide.utils.input_validation.ValidateDbstep attribute) scaling_exponent (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeCoulombMatrix attribute) scan (bonafide.features.dbstep_._Dbstep3DAtom attribute) (bonafide.utils.input_validation.ValidateDbstep attribute) set_charge() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] set_environment() (bonafide.utils.environment.Environment method) set_multiplicity() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] set_options() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] show_molecule() (bonafide._bonafide._AtomBondFeaturizer method) (bonafide.bonafide.AtomBondFeaturizer method), [1] sigma (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeSoap attribute) size (bonafide.features.kallisto_._Kallisto3DAtom attribute) (bonafide.utils.input_validation.ValidateKallisto attribute) solvent (bonafide.utils.base_single_point.BaseSinglePoint attribute) (bonafide.utils.input_validation.ValidatePsi4 attribute) (bonafide.utils.input_validation.ValidateXtb attribute) solvent_model (bonafide.utils.input_validation.ValidateXtb attribute) (bonafide.utils.sp_xtb.XtbSP attribute) solvent_model_solver (bonafide.utils.input_validation.ValidatePsi4 attribute) (bonafide.utils.sp_psi4.Psi4SP attribute) species (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeAcsf attribute) (bonafide.utils.input_validation.ValidateDscribeLmbtr attribute) (bonafide.utils.input_validation.ValidateDscribeSoap attribute) standardize_string() (in module bonafide.utils.helper_functions) standardize_strings() (bonafide.utils.input_validation._StandardizeStrMixin class method) state (bonafide.utils.base_single_point.BaseSinglePoint attribute) step_size (bonafide.features.multiwfn_topology_bond._Multiwfn3DBondTopology attribute) (bonafide.utils.input_validation.ValidateMultiwfnTopology attribute) surface_definition (bonafide.features.multiwfn_surface._Multiwfn3DAtomSurface attribute) (bonafide.utils.input_validation.ValidateMultiwfnSurface attribute) surface_iso_value (bonafide.features.multiwfn_surface._Multiwfn3DAtomSurface attribute) (bonafide.utils.input_validation.ValidateMultiwfnSurface attribute) T tightness_resp (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespChelpgTwoStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannOneStage attribute) (bonafide.features.multiwfn_partial_charge.Multiwfn3DAtomPartialChargeRespMerzKollmannTwoStage attribute) (bonafide.utils.input_validation.ValidateMultiwfnPopulation attribute) torsionAtomCount (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintTopologicalTorsion attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintTopologicalTorsion attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) U update_boltzmann_weights() (bonafide.utils.molecule_vault.MolVault method) use2D (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintAtomPair attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintAtomPair attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) useBondOrder (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintRdkit attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintRdkit attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) useBondTypes (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintFeatureMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintFeatureMorgan attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintMorgan attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) useHs (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedCountFingerprintRdkit attribute) (bonafide.features.rdkit_fingerprint.Rdkit2DAtomRootedFingerprintRdkit attribute) (bonafide.utils.input_validation.ValidateRdkitFingerprint attribute) V validate_atomic_radii() (bonafide.utils.input_validation.ValidateMultiwfnPopulation class method) validate_average() (bonafide.utils.input_validation.ValidateDscribeSoap class method) validate_cntype() (bonafide.utils.input_validation.ValidateKallisto class method) validate_count_bounds() (bonafide.utils.input_validation.ValidateRdkitFingerprint class method) validate_custom_groups() (bonafide.utils.input_validation.ValidateBonafideFunctionalGroup class method) validate_distal_volume_method() (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume class method) validate_eem_parameters() (bonafide.utils.input_validation.ValidateMultiwfnPopulation class method) validate_en_scale() (bonafide.utils.input_validation.ValidateBonafideOxidationState class method) validate_esp_type() (bonafide.utils.input_validation.ValidateMultiwfnPopulation class method) validate_exclude() (bonafide.utils.input_validation.ValidateDbstep class method) validate_fitting_points_settings_merz_kollmann() (bonafide.utils.input_validation.ValidateMultiwfnPopulation class method) validate_geometry_function() (bonafide.utils.input_validation.ValidateDscribeLmbtr class method) validate_ibis_igm_type() (bonafide.utils.input_validation.ValidateMultiwfnBondAnalysis class method) validate_ibsi_grid() (bonafide.utils.input_validation.ValidateMultiwfnBondAnalysis class method) validate_integration_grid() (bonafide.utils.input_validation.ValidateMultiwfnFuzzy class method) validate_iterable_option_after() (bonafide.utils.input_validation.ValidateMultiwfnCdft class method) validate_iterable_option_before() (bonafide.utils.input_validation._ValidateIterableIntOptionMixin class method) (bonafide.utils.input_validation.ValidateMultiwfnCdft class method) validate_key_level() (bonafide.utils.input_validation.ValidateBonafideFunctionalGroup class method) validate_memory() (bonafide.utils.input_validation.ValidatePsi4 class method) validate_method() (bonafide.utils.input_validation.ValidateMendeleev class method) (bonafide.utils.input_validation.ValidateMorfeusLocalForce class method) (bonafide.utils.input_validation.ValidateMorfeusPyramidalization class method) (bonafide.utils.input_validation.ValidateXtb class method) validate_normalization() (bonafide.utils.input_validation.ValidateDscribeLmbtr class method) validate_orbital_overlap_edr_option() (bonafide.utils.input_validation.ValidateMultiwfnSurface class method) validate_params() (bonafide.utils.input_validation.ValidateDscribeAcsf class method) validate_partitioning_scheme() (bonafide.utils.input_validation.ValidateMultiwfnFuzzy class method) validate_radii_type() (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume class method) (bonafide.utils.input_validation.ValidateMorfeusConeAndSolidAngle class method) (bonafide.utils.input_validation.ValidateMorfeusDispersion class method) (bonafide.utils.input_validation.ValidateMorfeusSasa class method) validate_radius_becke_partition() (bonafide.utils.input_validation.ValidateMultiwfnFuzzy class method) (bonafide.utils.input_validation.ValidateMultiwfnPopulation class method) validate_rbf() (bonafide.utils.input_validation.ValidateDscribeSoap class method) validate_real_space_function() (bonafide.utils.input_validation.ValidateMultiwfnFuzzy class method) validate_scan() (bonafide.utils.input_validation.ValidateDbstep class method) validate_size_after() (bonafide.utils.input_validation.ValidateKallisto class method) validate_size_before() (bonafide.utils.input_validation.ValidateKallisto class method) validate_solvent() (bonafide.utils.input_validation.ValidatePsi4 class method) (bonafide.utils.input_validation.ValidateXtb class method) validate_solvent_model() (bonafide.utils.input_validation.ValidateXtb class method) validate_solvent_model_solver() (bonafide.utils.input_validation.ValidatePsi4 class method) validate_species_after() (bonafide.utils.input_validation._ValidateSpeciesMixin class method) validate_species_before() (bonafide.utils.input_validation._ValidateSpeciesMixin class method) validate_surface_definition() (bonafide.utils.input_validation.ValidateMultiwfnSurface class method) validate_vdwtype() (bonafide.utils.input_validation.ValidateKallisto class method) validate_weighting_function() (bonafide.utils.input_validation.ValidateDscribeLmbtr class method) validate_xtb_home() (bonafide.utils.input_validation.ValidateXtb class method) ValidateAlfabet (class in bonafide.utils.input_validation) ValidateBonafideAutocorrelation (class in bonafide.utils.input_validation) ValidateBonafideConstant (class in bonafide.utils.input_validation) ValidateBonafideDistance (class in bonafide.utils.input_validation) ValidateBonafideFunctionalGroup (class in bonafide.utils.input_validation) ValidateBonafideOxidationState (class in bonafide.utils.input_validation) ValidateBonafideSymmetry (class in bonafide.utils.input_validation) ValidateDbstep (class in bonafide.utils.input_validation) ValidateDscribeAcsf (class in bonafide.utils.input_validation) ValidateDscribeCoulombMatrix (class in bonafide.utils.input_validation) ValidateDscribeLmbtr (class in bonafide.utils.input_validation) ValidateDscribeSoap (class in bonafide.utils.input_validation) ValidateDummy (class in bonafide.utils.input_validation) ValidateKallisto (class in bonafide.utils.input_validation) ValidateMendeleev (class in bonafide.utils.input_validation) ValidateMorfeusBuriedVolume (class in bonafide.utils.input_validation) ValidateMorfeusConeAndSolidAngle (class in bonafide.utils.input_validation) ValidateMorfeusDispersion (class in bonafide.utils.input_validation) ValidateMorfeusLocalForce (class in bonafide.utils.input_validation) ValidateMorfeusPyramidalization (class in bonafide.utils.input_validation) ValidateMorfeusSasa (class in bonafide.utils.input_validation) ValidateMultiwfnBondAnalysis (class in bonafide.utils.input_validation) ValidateMultiwfnCdft (class in bonafide.utils.input_validation) ValidateMultiwfnFuzzy (class in bonafide.utils.input_validation) ValidateMultiwfnMisc (class in bonafide.utils.input_validation) ValidateMultiwfnOrbital (class in bonafide.utils.input_validation) ValidateMultiwfnPopulation (class in bonafide.utils.input_validation) ValidateMultiwfnRootData (class in bonafide.utils.input_validation) ValidateMultiwfnSurface (class in bonafide.utils.input_validation) ValidateMultiwfnTopology (class in bonafide.utils.input_validation) ValidatePsi4 (class in bonafide.utils.input_validation) ValidateRdkitFingerprint (class in bonafide.utils.input_validation) ValidateXtb (class in bonafide.utils.input_validation) vdwtype (bonafide.features.kallisto_._Kallisto3DAtom attribute) (bonafide.utils.input_validation.ValidateKallisto attribute) vshell (bonafide.features.dbstep_._Dbstep3DAtom attribute) (bonafide.utils.input_validation.ValidateDbstep attribute) W weighting_function (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeLmbtr attribute) weighting_scale (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeLmbtr attribute) weighting_threshold (bonafide.features.dscribe_._Dscribe3DAtom attribute) (bonafide.utils.input_validation.ValidateDscribeLmbtr attribute) work_dir_name (bonafide.utils.base_mixin._BaseMixin attribute) write_sd_file() (in module bonafide.utils.io_) write_xyz_file_from_coordinates_array() (in module bonafide.utils.io_) X Xtb3DAtomC6DispersionCoefficient (class in bonafide.features.xtb_fukui_misc) Xtb3DAtomCdftCondensedFukuiDual (class in bonafide.features.xtb_fukui_misc) Xtb3DAtomCdftCondensedFukuiMinus (class in bonafide.features.xtb_fukui_misc) Xtb3DAtomCdftCondensedFukuiPlus (class in bonafide.features.xtb_fukui_misc) Xtb3DAtomCdftCondensedFukuiZero (class in bonafide.features.xtb_fukui_misc) Xtb3DAtomCdftLocalElectrophilicityFmo (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalElectrophilicityRedox (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalHardnessMinusFmo (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalHardnessMinusRedox (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalHardnessPlusFmo (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalHardnessPlusRedox (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalHardnessZeroFmo (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalHardnessZeroRedox (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalHyperhardnessFmo (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalHyperhardnessRedox (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalHypersoftnessFmo (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalHypersoftnessRedox (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalNucleophilicityFmo (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalNucleophilicityRedox (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalRelativeElectrophilicity (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalRelativeNucleophilicity (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalSoftnessMinusFmo (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalSoftnessMinusRedox (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalSoftnessPlusFmo (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalSoftnessPlusRedox (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalSoftnessZeroFmo (class in bonafide.features.xtb_cdft) Xtb3DAtomCdftLocalSoftnessZeroRedox (class in bonafide.features.xtb_cdft) Xtb3DAtomPartialChargeHueckel (class in bonafide.features.xtb_fukui_misc) Xtb3DAtomPolarizability (class in bonafide.features.xtb_fukui_misc) xtb_driver() (in module bonafide.utils.driver) XTBHOME (bonafide.utils.input_validation.ValidateXtb attribute) XtbSP (class in bonafide.utils.sp_xtb) xz_plane_atoms (bonafide.features.morfeus_bv._Morfeus3DAtomBV attribute) (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume attribute) Z z_axis_atoms (bonafide.features.morfeus_bv._Morfeus3DAtomBV attribute) (bonafide.utils.input_validation.ValidateMorfeusBuriedVolume attribute)