ContentsΒΆ
- mlchem
- Documentation
- Features
- Architecture
- Modules
- Installation
- Logging
- Compatibility checks (Python 3.12, 3.13, 3.14)
- Usage
- calculate rdkit descriptors for two molecules
- calculate chemotypes faster on larger datasets
- control ML verbosity in notebooks and development runs
- optional diagnostics for undersampling and y-scrambling
- calculate fingerprints
- pattern recognition
- de novo molecule generation and cleaning
- show pre-defined colour palette
- Building the documentation
- Contributing
- Third-Party Dependencies
- License
- Acknowledgements
- mlchem package
- chem and ml subpackages
- mlchem.chem package
- Subpackages
- Submodules
- mlchem.chem.manipulation module
MolCleanerinput_smiles_listinput_id_listdf_inputn_stepssmilesidsIsIsomericIsCanonicalIsKekuliseddf_accepteddf_rejected__init__()desalt_smiles()full_clean()initialise_smiles()neutralise_smiles()quality_checker()remove_carbon_ions()remove_inorganics()remove_mixtures()remove_organometallics()
MolGeneratorPatternRecognitionAtomsBaseBondsMolPatternsalpha_nitroalkane()check_acetylenic_carbon()check_acyl_halide()check_alanine()check_alcohol()check_aldehyde()check_alkali_metals()check_alkaline_earth_metals()check_alkyl_carbon()check_allenic_carbon()check_alpha_dicarbonyl()check_alpha_diketone()check_amide()check_amine()check_amine_primary()check_amine_quaternary()check_amine_secondary()check_amine_tertiary()check_aminoacid()check_anhydride()check_arginine()check_asparagine()check_aspartate()check_azide()check_azo()check_azoxy()check_beta_dicarbonyl()check_beta_diketone()check_boron_group_elements()check_bromine()check_carbamate()check_carbanion()check_carbocation()check_carbon()check_carbon_group_elements()check_carbonate_ester()check_carbonic_acid()check_carbonyl()check_carbosulphone()check_carbosulphoxide()check_carboxyl()check_chalcogens()check_chlorine()check_cyanamide()check_cyanate()check_cysteine()check_delta_dicarbonyl()check_diazo()check_disulphide()check_enamine()check_enol()check_ester()check_ether()check_fluorine()check_gamma_dicarbonyl()check_gamma_diketone()check_glutamate()check_glycine()check_haloalkane()check_haloalkane_primary()check_haloalkane_secondary()check_haloalkane_tertiary()check_haloalkene()check_halogen()check_halogen_carbon()check_halogen_nitrogen()check_halogen_oxygen()check_hbond_acceptors()check_hbond_acceptors_higher_than()check_hbond_acceptors_lower_than()check_hbond_donors()check_hbond_donors_higher_than()check_hbond_donors_lower_than()check_histidine()check_hydrazine()check_hydrazone()check_imide()check_imine()check_iminium()check_iodine()check_isocyanate()check_isoleucine()check_isonitrile()check_isothiocyanate()check_ketone()check_leucine()check_lysine()check_methionine()check_n_oxide()check_neg_charge_1()check_neg_charge_2()check_neg_charge_3()check_nitrate()check_nitrile()check_nitro()check_nitrogen()check_nitrogen_group_elements()check_nitroso()check_noble_gases()check_oxohalide()check_oxygen()check_pattern_aliphatic()check_pattern_aromatic()check_pattern_aromatic_substituent()check_phenylalanine()check_phosphoric_acid()check_phosphoric_ester()check_phosphorus()check_pos_charge_1()check_pos_charge_2()check_pos_charge_3()check_proline()check_serine()check_sulphamic_acid()check_sulphamic_ester()check_sulphenic_acid()check_sulphenic_ester()check_sulphide()check_sulphinic_acid()check_sulphinic_ester()check_sulphonamide()check_sulphone()check_sulphonic_acid()check_sulphonic_ester()check_sulphoxide()check_sulphur()check_sulphuric_acid()check_sulphuric_ester()check_thioaldehyde()check_thioanhydride()check_thiocarbamate()check_thiocarbonyl()check_thiocarboxylic()check_thiocyanate()check_thioester()check_thioketone()check_thiol()check_threonine()check_transition_metals()check_tryptophan()check_tyrosine()check_unbranched_rotatable_carbons()check_unbranched_rotatable_chain()check_unbranched_structure()check_valine()check_vinylic_carbon()check_zwitterion()
Ringscheck_heterocycle()check_heterocycle_N()check_heterocycle_O()check_heterocycle_S()check_macrocycle()check_meta_substituted_aromatic_r6()check_ortho_substituted_aromatic_r6()check_para_substituted_aromatic_r6()check_pattern_cyclic()check_pattern_cyclic_substituent()check_ring()check_ring_fusion()check_ring_size()
PropManagerAtomclear_atomprops()get_atomic_num()get_bonds()get_degree()get_explicit_valence()get_formal_charge()get_hybridisation()get_idx()get_implicit_valence()get_mass()get_neighbours()get_num_explicit_h()get_num_implicit_h()get_num_radical_electrons()get_tot_h()get_total_degree()get_total_valence()has_valence_violation()is_aromatic()is_in_ring()is_in_ring_size()set_atom_map_num()set_formal_charge()set_is_aromatic()set_num_explicit_h()set_num_radical_electrons()
BaseBondConformationMol
convert_molecule_string()create_molecule()detect_smarts_vs_smiles()generate_resonance()kekulise_smiles()mol_from_string()mol_to_binary()neutralise_mol()remove_smarts_pattern()smarts_from_string()smiles_from_smarts()smiles_to_inchi()unkekulise_smiles()
- mlchem.chem.manipulation module
- mlchem.ml package
- Subpackages
- mlchem.ml.feature_selection package
- mlchem.ml.modelling package
- mlchem.ml.preprocessing package
- Subpackages
- mlchem.helper module
LogCaptureadd_inchi_to_dataframe()assign_sign()bokeh_plot()coerce_log_level()compute_alpha()convert_rgb()convert_size()count_features()create_mask()create_progressive_column_names()create_smooth_gradient_circle()create_structure_files()dfs_to_excel()disable_estimator_parallelization()find_all_occurrences()flatten()generate_cartesian_product()generate_combination_cascade()generate_random_rgb()identify_df_duplicates()insert_string_piece()loadingbar()make_rgb_transparent()merge_dicts_with_duplicates()normalise_iterable()prepare_dataframe()prepare_datatable()process_custom_string()reset_string()resolve_n_jobs()show_png()size_ratio()sort_list_by_other_list()standardise_path()start_logging()suppress_warnings()try_except()validate_task_type()visualise_colour()visualise_colour_grid()
- mlchem.importables module
- mlchem.metrics module
AllBitSimilarity()AsymmetricSimilarity()BraunBlanquetSimilarity()CosineSimilarity()DiceSimilarity()FingerprintSimilarity()KulczynskiSimilarity()McConnaugheySimilarity()OffBitProjSimilarity()OnBitSimilarity()RogotGoldbergSimilarity()RusselSimilarity()SokalSimilarity()TanimotoSimilarity()TverskySimilarity()calculate_reliability_components()get_geometric_S()get_mcc()get_r2()get_rmse()get_sensitivity()get_specificity()rmse_to_std_ratio()
- mlchem.chem package
- chem and ml subpackages