ContentsΒΆ
- Welcome to mlchem documentation!
- Installation
- Features
- Contributing
- License
- Acknowledgements
- mlchem package
- chem and ml subpackages
- mlchem.chem package
- Subpackages
- mlchem.chem.calculator package
- mlchem.chem.visualise package
- Submodules
- mlchem.chem.visualise.drawing module
MolDrawerMolDrawer.molMolDrawer.highlightAtomsMolDrawer.sizeMolDrawer.legendMolDrawer.colour_dictionaryMolDrawer.drawing_optionsMolDrawer.__init__()MolDrawer.show_palette()MolDrawer.update_drawing_options()MolDrawer.reset_drawing_options()MolDrawer.draw_mol()MolDrawer.load_images()MolDrawer.load_mols()MolDrawer.show_images_grid()MolDrawer.__init__()MolDrawer.draw_mol()MolDrawer.load_images()MolDrawer.load_mols()MolDrawer.reset_drawing_options()MolDrawer.show_images_grid()MolDrawer.show_palette()MolDrawer.update_drawing_options()
- mlchem.chem.visualise.simmaps module
- mlchem.chem.visualise.space module
- mlchem.chem.visualise.drawing module
- Submodules
- Submodules
- mlchem.chem.manipulation module
MolCleanerMolCleaner.input_smiles_listMolCleaner.input_id_listMolCleaner.df_inputMolCleaner.n_stepsMolCleaner.smilesMolCleaner.idsMolCleaner.IsIsomericMolCleaner.IsCanonicalMolCleaner.IsKekulisedMolCleaner.df_acceptedMolCleaner.df_rejectedMolCleaner.__init__()MolCleaner.desalt_smiles()MolCleaner.full_clean()MolCleaner.initialise_smiles()MolCleaner.neutralise_smiles()MolCleaner.quality_checker()MolCleaner.remove_carbon_ions()MolCleaner.remove_inorganics()MolCleaner.remove_mixtures()MolCleaner.remove_organometallics()
MolGeneratorPatternRecognitionPatternRecognition.AtomsPatternRecognition.BasePatternRecognition.Base.check_smarts_pattern()PatternRecognition.Base.check_smiles_pattern()PatternRecognition.Base.count_atoms()PatternRecognition.Base.count_bonds()PatternRecognition.Base.get_MCS()PatternRecognition.Base.get_atoms()PatternRecognition.Base.get_bonds()PatternRecognition.Base.get_stereoisomers()PatternRecognition.Base.get_tautomers()PatternRecognition.Base.has_carbon_ion()PatternRecognition.Base.has_metal_salt()PatternRecognition.Base.is_organic()PatternRecognition.Base.pattern_abs_fraction_greater_than()PatternRecognition.Base.pattern_rel_fraction_greater_than()
PatternRecognition.BondsPatternRecognition.Bonds.check_aromatic_bonds()PatternRecognition.Bonds.check_bonds()PatternRecognition.Bonds.check_cyclic_bonds()PatternRecognition.Bonds.check_double_bonds()PatternRecognition.Bonds.check_rotatable_bonds()PatternRecognition.Bonds.check_single_bonds()PatternRecognition.Bonds.check_triple_bonds()PatternRecognition.Bonds.is_dative_bond()PatternRecognition.Bonds.is_double_bond()PatternRecognition.Bonds.is_single_bond()PatternRecognition.Bonds.is_triple_bond()
PatternRecognition.MolPatternsPatternRecognition.MolPatterns.alpha_nitroalkane()PatternRecognition.MolPatterns.check_acetylenic_carbon()PatternRecognition.MolPatterns.check_acyl_halide()PatternRecognition.MolPatterns.check_alanine()PatternRecognition.MolPatterns.check_alcohol()PatternRecognition.MolPatterns.check_aldehyde()PatternRecognition.MolPatterns.check_alkali_metals()PatternRecognition.MolPatterns.check_alkaline_earth_metals()PatternRecognition.MolPatterns.check_alkyl_carbon()PatternRecognition.MolPatterns.check_allenic_carbon()PatternRecognition.MolPatterns.check_alpha_dicarbonyl()PatternRecognition.MolPatterns.check_alpha_diketone()PatternRecognition.MolPatterns.check_amide()PatternRecognition.MolPatterns.check_amine()PatternRecognition.MolPatterns.check_amine_primary()PatternRecognition.MolPatterns.check_amine_quaternary()PatternRecognition.MolPatterns.check_amine_secondary()PatternRecognition.MolPatterns.check_amine_tertiary()PatternRecognition.MolPatterns.check_aminoacid()PatternRecognition.MolPatterns.check_anhydride()PatternRecognition.MolPatterns.check_arginine()PatternRecognition.MolPatterns.check_asparagine()PatternRecognition.MolPatterns.check_aspartate()PatternRecognition.MolPatterns.check_azide()PatternRecognition.MolPatterns.check_azo()PatternRecognition.MolPatterns.check_azoxy()PatternRecognition.MolPatterns.check_beta_dicarbonyl()PatternRecognition.MolPatterns.check_beta_diketone()PatternRecognition.MolPatterns.check_boron_group_elements()PatternRecognition.MolPatterns.check_bromine()PatternRecognition.MolPatterns.check_carbamate()PatternRecognition.MolPatterns.check_carbanion()PatternRecognition.MolPatterns.check_carbocation()PatternRecognition.MolPatterns.check_carbon()PatternRecognition.MolPatterns.check_carbon_group_elements()PatternRecognition.MolPatterns.check_carbonate_ester()PatternRecognition.MolPatterns.check_carbonic_acid()PatternRecognition.MolPatterns.check_carbonyl()PatternRecognition.MolPatterns.check_carbosulphone()PatternRecognition.MolPatterns.check_carbosulphoxide()PatternRecognition.MolPatterns.check_carboxyl()PatternRecognition.MolPatterns.check_chalcogens()PatternRecognition.MolPatterns.check_chlorine()PatternRecognition.MolPatterns.check_cyanamide()PatternRecognition.MolPatterns.check_cyanate()PatternRecognition.MolPatterns.check_cysteine()PatternRecognition.MolPatterns.check_delta_dicarbonyl()PatternRecognition.MolPatterns.check_diazo()PatternRecognition.MolPatterns.check_disulphide()PatternRecognition.MolPatterns.check_enamine()PatternRecognition.MolPatterns.check_enol()PatternRecognition.MolPatterns.check_ester()PatternRecognition.MolPatterns.check_ether()PatternRecognition.MolPatterns.check_fluorine()PatternRecognition.MolPatterns.check_gamma_dicarbonyl()PatternRecognition.MolPatterns.check_gamma_diketone()PatternRecognition.MolPatterns.check_glutamate()PatternRecognition.MolPatterns.check_glycine()PatternRecognition.MolPatterns.check_haloalkane()PatternRecognition.MolPatterns.check_haloalkane_primary()PatternRecognition.MolPatterns.check_haloalkane_secondary()PatternRecognition.MolPatterns.check_haloalkane_tertiary()PatternRecognition.MolPatterns.check_haloalkene()PatternRecognition.MolPatterns.check_halogen()PatternRecognition.MolPatterns.check_halogen_carbon()PatternRecognition.MolPatterns.check_halogen_nitrogen()PatternRecognition.MolPatterns.check_halogen_oxygen()PatternRecognition.MolPatterns.check_hbond_acceptors()PatternRecognition.MolPatterns.check_hbond_acceptors_higher_than()PatternRecognition.MolPatterns.check_hbond_acceptors_lower_than()PatternRecognition.MolPatterns.check_hbond_donors()PatternRecognition.MolPatterns.check_hbond_donors_higher_than()PatternRecognition.MolPatterns.check_hbond_donors_lower_than()PatternRecognition.MolPatterns.check_histidine()PatternRecognition.MolPatterns.check_hydrazine()PatternRecognition.MolPatterns.check_hydrazone()PatternRecognition.MolPatterns.check_imide()PatternRecognition.MolPatterns.check_imine()PatternRecognition.MolPatterns.check_iminium()PatternRecognition.MolPatterns.check_iodine()PatternRecognition.MolPatterns.check_isocyanate()PatternRecognition.MolPatterns.check_isoleucine()PatternRecognition.MolPatterns.check_isonitrile()PatternRecognition.MolPatterns.check_isothiocyanate()PatternRecognition.MolPatterns.check_ketone()PatternRecognition.MolPatterns.check_leucine()PatternRecognition.MolPatterns.check_lysine()PatternRecognition.MolPatterns.check_methionine()PatternRecognition.MolPatterns.check_n_oxide()PatternRecognition.MolPatterns.check_neg_charge_1()PatternRecognition.MolPatterns.check_neg_charge_2()PatternRecognition.MolPatterns.check_neg_charge_3()PatternRecognition.MolPatterns.check_nitrate()PatternRecognition.MolPatterns.check_nitrile()PatternRecognition.MolPatterns.check_nitro()PatternRecognition.MolPatterns.check_nitrogen()PatternRecognition.MolPatterns.check_nitrogen_group_elements()PatternRecognition.MolPatterns.check_nitroso()PatternRecognition.MolPatterns.check_noble_gases()PatternRecognition.MolPatterns.check_oxohalide()PatternRecognition.MolPatterns.check_oxygen()PatternRecognition.MolPatterns.check_pattern_aliphatic()PatternRecognition.MolPatterns.check_pattern_aromatic()PatternRecognition.MolPatterns.check_pattern_aromatic_substituent()PatternRecognition.MolPatterns.check_phenylalanine()PatternRecognition.MolPatterns.check_phosphoric_acid()PatternRecognition.MolPatterns.check_phosphoric_ester()PatternRecognition.MolPatterns.check_phosphorus()PatternRecognition.MolPatterns.check_pos_charge_1()PatternRecognition.MolPatterns.check_pos_charge_2()PatternRecognition.MolPatterns.check_pos_charge_3()PatternRecognition.MolPatterns.check_proline()PatternRecognition.MolPatterns.check_serine()PatternRecognition.MolPatterns.check_sulphamic_acid()PatternRecognition.MolPatterns.check_sulphamic_ester()PatternRecognition.MolPatterns.check_sulphenic_acid()PatternRecognition.MolPatterns.check_sulphenic_ester()PatternRecognition.MolPatterns.check_sulphide()PatternRecognition.MolPatterns.check_sulphinic_acid()PatternRecognition.MolPatterns.check_sulphinic_ester()PatternRecognition.MolPatterns.check_sulphonamide()PatternRecognition.MolPatterns.check_sulphone()PatternRecognition.MolPatterns.check_sulphonic_acid()PatternRecognition.MolPatterns.check_sulphonic_ester()PatternRecognition.MolPatterns.check_sulphoxide()PatternRecognition.MolPatterns.check_sulphur()PatternRecognition.MolPatterns.check_sulphuric_acid()PatternRecognition.MolPatterns.check_sulphuric_ester()PatternRecognition.MolPatterns.check_thioaldehyde()PatternRecognition.MolPatterns.check_thioanhydride()PatternRecognition.MolPatterns.check_thiocarbamate()PatternRecognition.MolPatterns.check_thiocarbonyl()PatternRecognition.MolPatterns.check_thiocarboxylic()PatternRecognition.MolPatterns.check_thiocyanate()PatternRecognition.MolPatterns.check_thioester()PatternRecognition.MolPatterns.check_thioketone()PatternRecognition.MolPatterns.check_thiol()PatternRecognition.MolPatterns.check_threonine()PatternRecognition.MolPatterns.check_transition_metals()PatternRecognition.MolPatterns.check_tryptophan()PatternRecognition.MolPatterns.check_tyrosine()PatternRecognition.MolPatterns.check_unbranched_rotatable_carbons()PatternRecognition.MolPatterns.check_unbranched_rotatable_chain()PatternRecognition.MolPatterns.check_unbranched_structure()PatternRecognition.MolPatterns.check_valine()PatternRecognition.MolPatterns.check_vinylic_carbon()PatternRecognition.MolPatterns.check_zwitterion()
PatternRecognition.RingsPatternRecognition.Rings.check_heterocycle()PatternRecognition.Rings.check_heterocycle_N()PatternRecognition.Rings.check_heterocycle_O()PatternRecognition.Rings.check_heterocycle_S()PatternRecognition.Rings.check_macrocycle()PatternRecognition.Rings.check_meta_substituted_aromatic_r6()PatternRecognition.Rings.check_ortho_substituted_aromatic_r6()PatternRecognition.Rings.check_para_substituted_aromatic_r6()PatternRecognition.Rings.check_pattern_cyclic()PatternRecognition.Rings.check_pattern_cyclic_substituent()PatternRecognition.Rings.check_ring()PatternRecognition.Rings.check_ring_fusion()PatternRecognition.Rings.check_ring_size()
PropManagerPropManager.AtomPropManager.Atom.clear_atomprops()PropManager.Atom.get_atomic_num()PropManager.Atom.get_bonds()PropManager.Atom.get_degree()PropManager.Atom.get_explicit_valence()PropManager.Atom.get_formal_charge()PropManager.Atom.get_hybridisation()PropManager.Atom.get_idx()PropManager.Atom.get_implicit_valence()PropManager.Atom.get_mass()PropManager.Atom.get_neighbours()PropManager.Atom.get_num_explicit_h()PropManager.Atom.get_num_implicit_h()PropManager.Atom.get_num_radical_electrons()PropManager.Atom.get_tot_h()PropManager.Atom.get_total_degree()PropManager.Atom.get_total_valence()PropManager.Atom.has_valence_violation()PropManager.Atom.is_aromatic()PropManager.Atom.is_in_ring()PropManager.Atom.is_in_ring_size()PropManager.Atom.set_atom_map_num()PropManager.Atom.set_formal_charge()PropManager.Atom.set_is_aromatic()PropManager.Atom.set_num_explicit_h()PropManager.Atom.set_num_radical_electrons()
PropManager.BasePropManager.Base.assign_atom_labels()PropManager.Base.assign_atom_mapnumbers()PropManager.Base.assign_atom_notes()PropManager.Base.assign_bond_notes()PropManager.Base.clear_all_atomprops()PropManager.Base.clear_prop()PropManager.Base.get_owning_mol()PropManager.Base.get_prop()PropManager.Base.get_prop_names()PropManager.Base.get_props_dict()PropManager.Base.set_prop()
PropManager.BondPropManager.Bond.get_begin_atom()PropManager.Bond.get_begin_atom_idx()PropManager.Bond.get_bond_type()PropManager.Bond.get_end_atom()PropManager.Bond.get_end_atom_idx()PropManager.Bond.get_idx()PropManager.Bond.get_other_atom()PropManager.Bond.get_other_atom_idx()PropManager.Bond.get_valence_contribution()PropManager.Bond.is_aromatic()PropManager.Bond.is_conjugated()PropManager.Bond.is_in_ring()PropManager.Bond.is_in_ring_size()PropManager.Bond.set_is_aromatic()
PropManager.ConformationPropManager.Conformation.add_conformer()PropManager.Conformation.calculate_conformer_energy_from_mol()PropManager.Conformation.canonicalise_conformer()PropManager.Conformation.canonicalise_mol_conformers()PropManager.Conformation.display_3dmols_overlapped()PropManager.Conformation.display_conformers()PropManager.Conformation.generate_conformers()PropManager.Conformation.get_shape_descriptors()PropManager.Conformation.optimise_conformers()PropManager.Conformation.optimise_molecule()PropManager.Conformation.straighten_mol_2d()
PropManager.MolPropManager.Mol.get_atoms()PropManager.Mol.get_atoms_from_idx()PropManager.Mol.get_bond_between_atoms()PropManager.Mol.get_bonds()PropManager.Mol.get_bonds_from_idx()PropManager.Mol.get_conf_ids()PropManager.Mol.get_conformer()PropManager.Mol.get_conformers()PropManager.Mol.get_coordinates()PropManager.Mol.get_distance_matrix()PropManager.Mol.get_gasteiger_charges()PropManager.Mol.get_stereogroups()PropManager.Mol.remove_all_conformers()PropManager.Mol.remove_conformer()
create_molecule()generate_resonance()kekulise_smiles()mol_from_string()mol_to_binary()neutralise_mol()remove_smarts_pattern()smarts_from_string()smiles_to_inchi()unkekulise_smiles()
- mlchem.chem.manipulation module
- Subpackages
- mlchem.ml package
- Subpackages
- mlchem.ml.feature_selection package
- Submodules
- mlchem.ml.feature_selection.filters module
- mlchem.ml.feature_selection.wrappers module
CombinatorialSelectionSequentialForwardSelectionSequentialForwardSelection.estimatorSequentialForwardSelection.estimator_stringSequentialForwardSelection.metricSequentialForwardSelection.max_featuresSequentialForwardSelection.cv_iterSequentialForwardSelection.logicSequentialForwardSelection.task_typeSequentialForwardSelection.__init__()SequentialForwardSelection.find_best()SequentialForwardSelection.fit()SequentialForwardSelection.plot()
- Submodules
- mlchem.ml.modelling package
- Submodules
- mlchem.ml.modelling.model_evaluation module
- mlchem.ml.modelling.model_interpretation module
DescriptorExplainerDescriptorExplainer.df_trainDescriptorExplainer.df_testDescriptorExplainer.target_trainDescriptorExplainer.target_testDescriptorExplainer.target_nameDescriptorExplainer.estimatorDescriptorExplainer.metricDescriptorExplainer.logicDescriptorExplainer.task_typeDescriptorExplainer.__init__()DescriptorExplainer.display()DescriptorExplainer.fit_stage_1()DescriptorExplainer.fit_stage_2()
ShapExplainerShapExplainer.model_typeShapExplainer.dataShapExplainer.yShapExplainer.estimatorShapExplainer.explain()ShapExplainer.load()ShapExplainer.save()ShapExplainer.force_plot()ShapExplainer.force_plot_single()ShapExplainer.dependence_plot()ShapExplainer.dependence_plot_all()ShapExplainer.summary_plot()ShapExplainer.waterfall_plot()ShapExplainer.bar_plot()ShapExplainer.feature_importance()ShapExplainer.decision_plot()ShapExplainer.__init__()ShapExplainer.bar_plot()ShapExplainer.decision_plot()ShapExplainer.dependence_plot()ShapExplainer.dependence_plot_all()ShapExplainer.explain()ShapExplainer.feature_importance()ShapExplainer.force_plot()ShapExplainer.force_plot_single()ShapExplainer.heatmap()ShapExplainer.load()ShapExplainer.save()ShapExplainer.summary_plot()ShapExplainer.waterfall_plot()
- Submodules
- mlchem.ml.preprocessing package
- Submodules
- mlchem.ml.preprocessing.dimensional_reduction module
CompressorCompressor.dataframeCompressor.initial_columns_to_ignoreCompressor.algorithmCompressor.params_Compressor.X_compressedCompressor.dataframe_compressedCompressor.compress_PCA()Compressor.compress_TSNE()Compressor.compress_SE()Compressor.compress_UMAP()Compressor.compress_MDS()Compressor.compress_LLE()Compressor.compress_ISOMAP()Compressor.__init__()Compressor.compress_ISOMAP()Compressor.compress_LLE()Compressor.compress_MDS()Compressor.compress_PCA()Compressor.compress_SE()Compressor.compress_TSNE()Compressor.compress_UMAP()
- mlchem.ml.preprocessing.feature_transformation module
- mlchem.ml.preprocessing.scaling module
- mlchem.ml.preprocessing.undersampling module
- mlchem.ml.preprocessing.dimensional_reduction module
- Submodules
- mlchem.ml.feature_selection package
- Subpackages
- mlchem.helper module
add_inchi_to_dataframe()assign_sign()bokeh_plot()compute_alpha()convert_rgb()convert_size()count_features()create_mask()create_progressive_column_names()create_smooth_gradient_circle()create_structure_files()dfs_to_excel()find_all_occurrences()flatten()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()show_png()size_ratio()sort_list_by_other_list()standardise_path()suppress_warnings()try_except()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()get_geometric_S()get_mcc()get_r2()get_rmse()get_sensitivity()get_specificity()rmse_to_std_ratio()
- mlchem.chem package
- chem and ml subpackages