Index

_

__init__() (ChemicalSpace method) (CombinatorialSelection method) (Compressor method) (DescriptorExplainer method) (MajorityVote method) (MolCleaner method) (MolDrawer method), [1] (MolGenerator method) (SequentialForwardSelection method) (ShapExplainer method)

A

add_conformer() (PropManager.Conformation static method) add_inchi_to_dataframe() (in module mlchem.helper) algorithm (Compressor attribute) AllBitSimilarity() (in module mlchem.metrics) alpha_nitroalkane() (PatternRecognition.MolPatterns static method) ApplicabilityDomain (class in mlchem.ml.modelling.model_evaluation)

assign_atom_labels() (PropManager.Base static method) assign_atom_mapnumbers() (PropManager.Base static method) assign_atom_notes() (PropManager.Base static method) assign_bond_notes() (PropManager.Base static method) assign_sign() (in module mlchem.helper) AsymmetricSimilarity() (in module mlchem.metrics)

B

bar_plot() (ShapExplainer method), [1] bernoulli() (in module mlchem.chem.calculator.tools), [1]

bokeh_plot() (in module mlchem.helper) boltzmann_probability() (in module mlchem.chem.calculator.tools), [1] BraunBlanquetSimilarity() (in module mlchem.metrics)

C

calc_centroid() (in module mlchem.chem.calculator.tools), [1] calc_gyration_tensor() (in module mlchem.chem.calculator.tools), [1] calc_logD_HH() (in module mlchem.chem.calculator.tools), [1] calc_shape_descriptors_from_gyration_tensor() (in module mlchem.chem.calculator.tools), [1] calculate_conformer_energy_from_mol() (PropManager.Conformation static method) canonicalise_conformer() (PropManager.Conformation static method) canonicalise_mol_conformers() (PropManager.Conformation static method) check_acetylenic_carbon() (PatternRecognition.MolPatterns static method) check_acyl_halide() (PatternRecognition.MolPatterns static method) check_alanine() (PatternRecognition.MolPatterns static method) check_alcohol() (PatternRecognition.MolPatterns static method) check_aldehyde() (PatternRecognition.MolPatterns static method) check_alkali_metals() (PatternRecognition.MolPatterns static method) check_alkaline_earth_metals() (PatternRecognition.MolPatterns static method) check_alkyl_carbon() (PatternRecognition.MolPatterns static method) check_allenic_carbon() (PatternRecognition.MolPatterns static method) check_alpha_dicarbonyl() (PatternRecognition.MolPatterns static method) check_alpha_diketone() (PatternRecognition.MolPatterns static method) check_amide() (PatternRecognition.MolPatterns static method) check_amine() (PatternRecognition.MolPatterns static method) check_amine_primary() (PatternRecognition.MolPatterns static method) check_amine_quaternary() (PatternRecognition.MolPatterns static method) check_amine_secondary() (PatternRecognition.MolPatterns static method) check_amine_tertiary() (PatternRecognition.MolPatterns static method) check_aminoacid() (PatternRecognition.MolPatterns static method) check_anhydride() (PatternRecognition.MolPatterns static method) check_arginine() (PatternRecognition.MolPatterns static method) check_aromatic_bonds() (PatternRecognition.Bonds static method) check_asparagine() (PatternRecognition.MolPatterns static method) check_aspartate() (PatternRecognition.MolPatterns static method) check_azide() (PatternRecognition.MolPatterns static method) check_azo() (PatternRecognition.MolPatterns static method) check_azoxy() (PatternRecognition.MolPatterns static method) check_beta_dicarbonyl() (PatternRecognition.MolPatterns static method) check_beta_diketone() (PatternRecognition.MolPatterns static method) check_bonds() (PatternRecognition.Bonds static method) check_boron_group_elements() (PatternRecognition.MolPatterns static method) check_bromine() (PatternRecognition.MolPatterns static method) check_carbamate() (PatternRecognition.MolPatterns static method) check_carbanion() (PatternRecognition.MolPatterns static method) check_carbocation() (PatternRecognition.MolPatterns static method) check_carbon() (PatternRecognition.MolPatterns static method) check_carbon_group_elements() (PatternRecognition.MolPatterns static method) check_carbonate_ester() (PatternRecognition.MolPatterns static method) check_carbonic_acid() (PatternRecognition.MolPatterns static method) check_carbonyl() (PatternRecognition.MolPatterns static method) check_carbosulphone() (PatternRecognition.MolPatterns static method) check_carbosulphoxide() (PatternRecognition.MolPatterns static method) check_carboxyl() (PatternRecognition.MolPatterns static method) check_chalcogens() (PatternRecognition.MolPatterns static method) check_chlorine() (PatternRecognition.MolPatterns static method) check_class_balance() (in module mlchem.ml.preprocessing.undersampling), [1] check_cyanamide() (PatternRecognition.MolPatterns static method) check_cyanate() (PatternRecognition.MolPatterns static method) check_cyclic_bonds() (PatternRecognition.Bonds static method) check_cysteine() (PatternRecognition.MolPatterns static method) check_delta_dicarbonyl() (PatternRecognition.MolPatterns static method) check_diazo() (PatternRecognition.MolPatterns static method) check_disulphide() (PatternRecognition.MolPatterns static method) check_double_bonds() (PatternRecognition.Bonds static method) check_enamine() (PatternRecognition.MolPatterns static method) check_enol() (PatternRecognition.MolPatterns static method) check_ester() (PatternRecognition.MolPatterns static method) check_ether() (PatternRecognition.MolPatterns static method) check_fluorine() (PatternRecognition.MolPatterns static method) check_gamma_dicarbonyl() (PatternRecognition.MolPatterns static method) check_gamma_diketone() (PatternRecognition.MolPatterns static method) check_glutamate() (PatternRecognition.MolPatterns static method) check_glycine() (PatternRecognition.MolPatterns static method) check_haloalkane() (PatternRecognition.MolPatterns static method) check_haloalkane_primary() (PatternRecognition.MolPatterns static method) check_haloalkane_secondary() (PatternRecognition.MolPatterns static method) check_haloalkane_tertiary() (PatternRecognition.MolPatterns static method) check_haloalkene() (PatternRecognition.MolPatterns static method) check_halogen() (PatternRecognition.MolPatterns static method) check_halogen_carbon() (PatternRecognition.MolPatterns static method) check_halogen_nitrogen() (PatternRecognition.MolPatterns static method) check_halogen_oxygen() (PatternRecognition.MolPatterns static method) check_hbond_acceptors() (PatternRecognition.MolPatterns static method) check_hbond_acceptors_higher_than() (PatternRecognition.MolPatterns static method) check_hbond_acceptors_lower_than() (PatternRecognition.MolPatterns static method) check_hbond_donors() (PatternRecognition.MolPatterns static method) check_hbond_donors_higher_than() (PatternRecognition.MolPatterns static method) check_hbond_donors_lower_than() (PatternRecognition.MolPatterns static method) check_heterocycle() (PatternRecognition.Rings static method) check_heterocycle_N() (PatternRecognition.Rings static method) check_heterocycle_O() (PatternRecognition.Rings static method) check_heterocycle_S() (PatternRecognition.Rings static method) check_histidine() (PatternRecognition.MolPatterns static method) check_hydrazine() (PatternRecognition.MolPatterns static method) check_hydrazone() (PatternRecognition.MolPatterns static method) check_imide() (PatternRecognition.MolPatterns static method) check_imine() (PatternRecognition.MolPatterns static method) check_iminium() (PatternRecognition.MolPatterns static method) check_iodine() (PatternRecognition.MolPatterns static method) check_isocyanate() (PatternRecognition.MolPatterns static method) check_isoleucine() (PatternRecognition.MolPatterns static method) check_isonitrile() (PatternRecognition.MolPatterns static method) check_isothiocyanate() (PatternRecognition.MolPatterns static method) check_ketone() (PatternRecognition.MolPatterns static method) check_leucine() (PatternRecognition.MolPatterns static method) check_lysine() (PatternRecognition.MolPatterns static method) check_macrocycle() (PatternRecognition.Rings static method)

check_meta_substituted_aromatic_r6() (PatternRecognition.Rings static method) check_methionine() (PatternRecognition.MolPatterns static method) check_n_oxide() (PatternRecognition.MolPatterns static method) check_neg_charge_1() (PatternRecognition.MolPatterns static method) check_neg_charge_2() (PatternRecognition.MolPatterns static method) check_neg_charge_3() (PatternRecognition.MolPatterns static method) check_nitrate() (PatternRecognition.MolPatterns static method) check_nitrile() (PatternRecognition.MolPatterns static method) check_nitro() (PatternRecognition.MolPatterns static method) check_nitrogen() (PatternRecognition.MolPatterns static method) check_nitrogen_group_elements() (PatternRecognition.MolPatterns static method) check_nitroso() (PatternRecognition.MolPatterns static method) check_noble_gases() (PatternRecognition.MolPatterns static method) check_ortho_substituted_aromatic_r6() (PatternRecognition.Rings static method) check_oxohalide() (PatternRecognition.MolPatterns static method) check_oxygen() (PatternRecognition.MolPatterns static method) check_para_substituted_aromatic_r6() (PatternRecognition.Rings static method) check_pattern_aliphatic() (PatternRecognition.MolPatterns static method) check_pattern_aromatic() (PatternRecognition.MolPatterns static method) check_pattern_aromatic_substituent() (PatternRecognition.MolPatterns static method) check_pattern_cyclic() (PatternRecognition.Rings static method) check_pattern_cyclic_substituent() (PatternRecognition.Rings static method) check_phenylalanine() (PatternRecognition.MolPatterns static method) check_phosphoric_acid() (PatternRecognition.MolPatterns static method) check_phosphoric_ester() (PatternRecognition.MolPatterns static method) check_phosphorus() (PatternRecognition.MolPatterns static method) check_pos_charge_1() (PatternRecognition.MolPatterns static method) check_pos_charge_2() (PatternRecognition.MolPatterns static method) check_pos_charge_3() (PatternRecognition.MolPatterns static method) check_proline() (PatternRecognition.MolPatterns static method) check_ring() (PatternRecognition.Rings static method) check_ring_fusion() (PatternRecognition.Rings static method) check_ring_size() (PatternRecognition.Rings static method) check_rotatable_bonds() (PatternRecognition.Bonds static method) check_serine() (PatternRecognition.MolPatterns static method) check_single_bonds() (PatternRecognition.Bonds static method) check_smarts_pattern() (PatternRecognition.Base static method) check_smiles_pattern() (PatternRecognition.Base static method) check_sulphamic_acid() (PatternRecognition.MolPatterns static method) check_sulphamic_ester() (PatternRecognition.MolPatterns static method) check_sulphenic_acid() (PatternRecognition.MolPatterns static method) check_sulphenic_ester() (PatternRecognition.MolPatterns static method) check_sulphide() (PatternRecognition.MolPatterns static method) check_sulphinic_acid() (PatternRecognition.MolPatterns static method) check_sulphinic_ester() (PatternRecognition.MolPatterns static method) check_sulphonamide() (PatternRecognition.MolPatterns static method) check_sulphone() (PatternRecognition.MolPatterns static method) check_sulphonic_acid() (PatternRecognition.MolPatterns static method) check_sulphonic_ester() (PatternRecognition.MolPatterns static method) check_sulphoxide() (PatternRecognition.MolPatterns static method) check_sulphur() (PatternRecognition.MolPatterns static method) check_sulphuric_acid() (PatternRecognition.MolPatterns static method) check_sulphuric_ester() (PatternRecognition.MolPatterns static method) check_thioaldehyde() (PatternRecognition.MolPatterns static method) check_thioanhydride() (PatternRecognition.MolPatterns static method) check_thiocarbamate() (PatternRecognition.MolPatterns static method) check_thiocarbonyl() (PatternRecognition.MolPatterns static method) check_thiocarboxylic() (PatternRecognition.MolPatterns static method) check_thiocyanate() (PatternRecognition.MolPatterns static method) check_thioester() (PatternRecognition.MolPatterns static method) check_thioketone() (PatternRecognition.MolPatterns static method) check_thiol() (PatternRecognition.MolPatterns static method) check_threonine() (PatternRecognition.MolPatterns static method) check_transition_metals() (PatternRecognition.MolPatterns static method) check_triple_bonds() (PatternRecognition.Bonds static method) check_tryptophan() (PatternRecognition.MolPatterns static method) check_tyrosine() (PatternRecognition.MolPatterns static method) check_unbranched_rotatable_carbons() (PatternRecognition.MolPatterns static method) check_unbranched_rotatable_chain() (PatternRecognition.MolPatterns static method) check_unbranched_structure() (PatternRecognition.MolPatterns static method) check_valine() (PatternRecognition.MolPatterns static method) check_vinylic_carbon() (PatternRecognition.MolPatterns static method) check_zwitterion() (PatternRecognition.MolPatterns static method) ChemicalSpace (class in mlchem.chem.visualise.space) clear_all_atomprops() (PropManager.Base static method) clear_atomprops() (PropManager.Atom static method) clear_prop() (PropManager.Base static method) collinearity_filter() (in module mlchem.ml.feature_selection.filters), [1] colour_dictionary (MolDrawer attribute) CombinatorialSelection (class in mlchem.ml.feature_selection.wrappers) compress_ISOMAP() (Compressor method), [1] compress_LLE() (Compressor method), [1] compress_MDS() (Compressor method), [1] compress_PCA() (Compressor method), [1] compress_SE() (Compressor method), [1] compress_TSNE() (Compressor method), [1] compress_UMAP() (Compressor method), [1] Compressor (class in mlchem.ml.preprocessing.dimensional_reduction) compute_alpha() (in module mlchem.helper) convert_rgb() (in module mlchem.helper) convert_size() (in module mlchem.helper) CosineSimilarity() (in module mlchem.metrics) count_atoms() (PatternRecognition.Base static method) count_bonds() (PatternRecognition.Base static method) count_features() (in module mlchem.helper) create_mask() (in module mlchem.helper) create_molecule() (in module mlchem.chem.manipulation), [1] create_progressive_column_names() (in module mlchem.helper) create_smooth_gradient_circle() (in module mlchem.helper) create_structure_files() (in module mlchem.helper) crossval() (in module mlchem.ml.feature_selection.wrappers) (in module mlchem.ml.modelling.model_evaluation), [1] cv_iter (SequentialForwardSelection attribute)

D

data (ShapExplainer attribute) dataframe (Compressor attribute) dataframe_compressed (Compressor attribute) decision_plot() (ShapExplainer method), [1] dependence_plot() (ShapExplainer method), [1] dependence_plot_all() (ShapExplainer method), [1] desalt_smiles() (MolCleaner method) DescriptorExplainer (class in mlchem.ml.modelling.model_interpretation) df_accepted (MolCleaner attribute) df_input (MolCleaner attribute) df_rejected (MolCleaner attribute)

df_test (DescriptorExplainer attribute) df_train (DescriptorExplainer attribute) dfs_to_excel() (in module mlchem.helper) DiceSimilarity() (in module mlchem.metrics) display() (DescriptorExplainer method) (in module mlchem.chem.manipulation) display_3dmols_overlapped() (PropManager.Conformation static method) display_best() (CombinatorialSelection method) display_conformers() (PropManager.Conformation static method) diversity_filter() (in module mlchem.ml.feature_selection.filters), [1] draw_mol() (MolDrawer method), [1] drawing_options (MolDrawer attribute)

E

estimator (CombinatorialSelection attribute) (DescriptorExplainer attribute) (SequentialForwardSelection attribute) (ShapExplainer attribute)

estimator_string (SequentialForwardSelection attribute) explain() (ShapExplainer method), [1]

F

feature_importance() (ShapExplainer method), [1] find_all_occurrences() (in module mlchem.helper) find_best() (SequentialForwardSelection method) FingerprintSimilarity() (in module mlchem.metrics) fit() (MajorityVote method) (SequentialForwardSelection method) fit_stage_1() (CombinatorialSelection method) (DescriptorExplainer method)

fit_stage_2() (CombinatorialSelection method) (DescriptorExplainer method) flatten() (in module mlchem.helper) force_plot() (ShapExplainer method), [1] force_plot_single() (ShapExplainer method), [1] full_clean() (MolCleaner method)

G

generate_combination_cascade() (in module mlchem.helper) (in module mlchem.ml.feature_selection.wrappers) generate_conformers() (PropManager.Conformation static method) generate_random_rgb() (in module mlchem.helper) generate_resonance() (in module mlchem.chem.manipulation), [1] generate_smiles() (MolGenerator method) get_allDesc() (in module mlchem.chem.calculator.descriptors), [1] get_atomic_num() (PropManager.Atom static method) get_atomicDesc() (in module mlchem.chem.calculator.descriptors), [1] get_atoms() (PatternRecognition.Base static method) (PropManager.Mol static method) get_atoms_from_idx() (PropManager.Mol static method) get_begin_atom() (PropManager.Bond static method) get_begin_atom_idx() (PropManager.Bond static method) get_bond_between_atoms() (PropManager.Mol static method) get_bond_type() (PropManager.Bond static method) get_bonds() (PatternRecognition.Base static method) (PropManager.Atom static method) (PropManager.Mol static method) get_bonds_from_idx() (PropManager.Mol static method) get_chemotypes() (in module mlchem.chem.calculator.descriptors), [1] get_conf_ids() (PropManager.Mol static method) get_conformer() (PropManager.Mol static method) get_conformers() (PropManager.Mol static method) get_coordinates() (PropManager.Mol static method) get_degree() (PropManager.Atom static method) get_distance_matrix() (PropManager.Mol static method) get_EHT_descriptors() (in module mlchem.chem.calculator.descriptors), [1] get_end_atom() (PropManager.Bond static method) get_end_atom_idx() (PropManager.Bond static method) get_explicit_valence() (PropManager.Atom static method) get_fingerprint() (in module mlchem.chem.calculator.descriptors), [1] get_fingerprint_df() (in module mlchem.chem.calculator.descriptors), [1] get_formal_charge() (PropManager.Atom static method) get_gasteiger_charges() (PropManager.Mol static method)

get_geometric_S() (in module mlchem.metrics) get_hybridisation() (PropManager.Atom static method) get_idx() (PropManager.Atom static method) (PropManager.Bond static method) get_implicit_valence() (PropManager.Atom static method) get_mass() (PropManager.Atom static method) get_mcc() (in module mlchem.metrics) get_MCS() (PatternRecognition.Base static method) get_mordredDesc() (in module mlchem.chem.calculator.descriptors), [1] get_neighbours() (PropManager.Atom static method) get_num_explicit_h() (PropManager.Atom static method) get_num_implicit_h() (PropManager.Atom static method) get_num_radical_electrons() (PropManager.Atom static method) get_other_atom() (PropManager.Bond static method) get_other_atom_idx() (PropManager.Bond static method) get_owning_mol() (PropManager.Base static method) get_prop() (PropManager.Base static method) get_prop_names() (PropManager.Base static method) get_props_dict() (PropManager.Base static method) get_r2() (in module mlchem.metrics) get_rdkitDesc() (in module mlchem.chem.calculator.descriptors), [1] get_ring_size() (PatternRecognition.Atoms static method) get_rmse() (in module mlchem.metrics) get_sensitivity() (in module mlchem.metrics) get_shape_descriptors() (PropManager.Conformation static method) get_similarity_map_from_weights() (SimMaps static method) get_specificity() (in module mlchem.metrics) get_stereogroups() (PropManager.Mol static method) get_stereoisomers() (PatternRecognition.Base static method) get_tautomers() (PatternRecognition.Base static method) get_tot_h() (PropManager.Atom static method) get_total_degree() (PropManager.Atom static method) get_total_valence() (PropManager.Atom static method) get_valence_contribution() (PropManager.Bond static method) get_weights_from_fingerprint() (SimMaps static method) get_weights_from_model() (SimMaps static method)

H

has_carbon_ion() (PatternRecognition.Base static method) has_metal_salt() (PatternRecognition.Base static method)

has_valence_violation() (PropManager.Atom static method) heatmap() (ShapExplainer method) highlightAtoms (MolDrawer attribute)

I

identify_df_duplicates() (in module mlchem.helper) ids (MolCleaner attribute) initial_columns_to_ignore (Compressor attribute) initialise_smiles() (MolCleaner method) input_id_list (MolCleaner attribute) input_smiles_list (MolCleaner attribute) insert_string_piece() (in module mlchem.helper) is_aromatic() (PropManager.Atom static method) (PropManager.Bond static method) is_conjugated() (PropManager.Bond static method) is_dative_bond() (PatternRecognition.Bonds static method) is_double_bond() (PatternRecognition.Bonds static method)

is_in_ring() (PropManager.Atom static method) (PropManager.Bond static method) is_in_ring_size() (PropManager.Atom static method) (PropManager.Bond static method) is_organic() (PatternRecognition.Base static method) is_single_bond() (PatternRecognition.Bonds static method) is_SP() (PatternRecognition.Atoms static method) is_SP2() (PatternRecognition.Atoms static method) is_SP3() (PatternRecognition.Atoms static method) is_triple_bond() (PatternRecognition.Bonds static method) IsCanonical (MolCleaner attribute) IsIsomeric (MolCleaner attribute) IsKekulised (MolCleaner attribute)

K

kekulise_smiles() (in module mlchem.chem.manipulation), [1]

KulczynskiSimilarity() (in module mlchem.metrics)

L

legend (MolDrawer attribute) leverage() (ApplicabilityDomain static method) load() (ShapExplainer method), [1] load_images() (MolDrawer method), [1] load_mols() (MolDrawer method), [1]

loadingbar() (in module mlchem.helper) (in module mlchem.ml.feature_selection.wrappers) logic (CombinatorialSelection attribute) (DescriptorExplainer attribute) (SequentialForwardSelection attribute) logit_to_proba() (in module mlchem.chem.calculator.tools), [1]

M

MajorityVote (class in mlchem.ml.modelling.model_evaluation) make_rgb_transparent() (in module mlchem.helper) max_features (SequentialForwardSelection attribute) McConnaugheySimilarity() (in module mlchem.metrics) merge_dicts_with_duplicates() (in module mlchem.helper) metric (CombinatorialSelection attribute) (DescriptorExplainer attribute) (SequentialForwardSelection attribute) mlchem.chem.calculator.descriptors module mlchem.chem.calculator.tools module mlchem.chem.manipulation module mlchem.chem.visualise.drawing module mlchem.chem.visualise.simmaps module mlchem.chem.visualise.space module mlchem.helper module mlchem.importables module mlchem.metrics module mlchem.ml.feature_selection.filters module mlchem.ml.feature_selection.wrappers module mlchem.ml.modelling.model_evaluation module mlchem.ml.modelling.model_interpretation module

mlchem.ml.preprocessing.dimensional_reduction module mlchem.ml.preprocessing.feature_transformation module mlchem.ml.preprocessing.scaling module mlchem.ml.preprocessing.undersampling module model_type (ShapExplainer attribute) module mlchem.chem.calculator.descriptors mlchem.chem.calculator.tools mlchem.chem.manipulation mlchem.chem.visualise.drawing mlchem.chem.visualise.simmaps mlchem.chem.visualise.space mlchem.helper mlchem.importables mlchem.metrics mlchem.ml.feature_selection.filters mlchem.ml.feature_selection.wrappers mlchem.ml.modelling.model_evaluation mlchem.ml.modelling.model_interpretation mlchem.ml.preprocessing.dimensional_reduction mlchem.ml.preprocessing.feature_transformation mlchem.ml.preprocessing.scaling mlchem.ml.preprocessing.undersampling mol (MolDrawer attribute) mol_from_string() (in module mlchem.chem.manipulation), [1] mol_to_binary() (in module mlchem.chem.manipulation), [1] MolCleaner (class in mlchem.chem.manipulation) MolDrawer (class in mlchem.chem.visualise.drawing) MolGenerator (class in mlchem.chem.manipulation)

N

n_steps (MolCleaner attribute) neutralise_mol() (in module mlchem.chem.manipulation), [1]

neutralise_smiles() (MolCleaner method) normalise_iterable() (in module mlchem.helper)

O

OffBitProjSimilarity() (in module mlchem.metrics) OnBitSimilarity() (in module mlchem.metrics)

optimise_conformers() (PropManager.Conformation static method) optimise_molecule() (PropManager.Conformation static method)

P

pairwise_euclidean_distance() (in module mlchem.chem.calculator.tools), [1] params_ (Compressor attribute) pattern_abs_fraction_greater_than() (PatternRecognition.Base static method) pattern_rel_fraction_greater_than() (PatternRecognition.Base static method) PatternRecognition (class in mlchem.chem.manipulation) PatternRecognition.Atoms (class in mlchem.chem.manipulation) PatternRecognition.Base (class in mlchem.chem.manipulation) PatternRecognition.Bonds (class in mlchem.chem.manipulation) PatternRecognition.MolPatterns (class in mlchem.chem.manipulation) PatternRecognition.Rings (class in mlchem.chem.manipulation) plot() (ChemicalSpace method) (SequentialForwardSelection method)

polynomial_expansion() (in module mlchem.ml.preprocessing.feature_transformation), [1] predict() (MajorityVote method) prepare() (ChemicalSpace method) prepare_dataframe() (in module mlchem.helper) prepare_datatable() (in module mlchem.helper) process() (ChemicalSpace method) process_custom_string() (in module mlchem.helper) PropManager (class in mlchem.chem.manipulation) PropManager.Atom (class in mlchem.chem.manipulation) PropManager.Base (class in mlchem.chem.manipulation) PropManager.Bond (class in mlchem.chem.manipulation) PropManager.Conformation (class in mlchem.chem.manipulation) PropManager.Mol (class in mlchem.chem.manipulation)

Q

quality_checker() (MolCleaner method)

R

remove_all_conformers() (PropManager.Mol static method) remove_carbon_ions() (MolCleaner method) remove_conformer() (PropManager.Mol static method) remove_inorganics() (MolCleaner method) remove_mixtures() (MolCleaner method) remove_organometallics() (MolCleaner method) remove_smarts_pattern() (in module mlchem.chem.manipulation), [1]

reset_bokeh_options() (ChemicalSpace method) reset_bokeh_tooltips() (ChemicalSpace method) reset_drawing_options() (MolDrawer method), [1] reset_string() (in module mlchem.helper) rmse_to_std_ratio() (in module mlchem.metrics) RogotGoldbergSimilarity() (in module mlchem.metrics) RusselSimilarity() (in module mlchem.metrics)

S

save() (ShapExplainer method), [1] scale_df_minmax() (in module mlchem.ml.preprocessing.scaling), [1] scale_df_robust() (in module mlchem.ml.preprocessing.scaling), [1] scale_df_standard() (in module mlchem.ml.preprocessing.scaling), [1] SequentialForwardSelection (class in mlchem.ml.feature_selection.wrappers) set_atom_map_num() (PropManager.Atom static method) set_formal_charge() (PropManager.Atom static method) set_is_aromatic() (PropManager.Atom static method) (PropManager.Bond static method) set_num_explicit_h() (PropManager.Atom static method) set_num_radical_electrons() (PropManager.Atom static method) set_prop() (PropManager.Base static method) shannon_entropy() (in module mlchem.chem.calculator.tools), [1] (in module mlchem.ml.feature_selection.filters) ShapExplainer (class in mlchem.ml.modelling.model_interpretation)

show_images_grid() (MolDrawer method), [1] show_palette() (MolDrawer method), [1] show_png() (in module mlchem.helper) SimMaps (class in mlchem.chem.visualise.simmaps) size (MolDrawer attribute) size_ratio() (in module mlchem.helper) smarts_from_string() (in module mlchem.chem.manipulation), [1] smiles (MolCleaner attribute) smiles_to_inchi() (in module mlchem.chem.manipulation), [1] SokalSimilarity() (in module mlchem.metrics) sort_list_by_other_list() (in module mlchem.helper) standardise_path() (in module mlchem.helper) straighten_mol_2d() (PropManager.Conformation static method) summary_plot() (ShapExplainer method), [1] suppress_warnings() (in module mlchem.helper) (in module mlchem.ml.feature_selection.filters)

T

TanimotoSimilarity() (in module mlchem.metrics) target_name (DescriptorExplainer attribute) target_test (DescriptorExplainer attribute) target_train (DescriptorExplainer attribute) task_type (CombinatorialSelection attribute) (DescriptorExplainer attribute) (SequentialForwardSelection attribute)

transform_df() (in module mlchem.ml.preprocessing.scaling), [1] try_except() (in module mlchem.helper) TverskySimilarity() (in module mlchem.metrics)

U

undersample() (in module mlchem.ml.preprocessing.undersampling), [1] unkekulise_smiles() (in module mlchem.chem.manipulation), [1]

update_bokeh_options() (ChemicalSpace method) update_drawing_options() (MolDrawer method), [1]

V

visualise_colour() (in module mlchem.helper)

visualise_colour_grid() (in module mlchem.helper)

W

waterfall_plot() (ShapExplainer method), [1]

X

X_compressed (Compressor attribute)

Y

y (ShapExplainer attribute)

y_scrambling() (in module mlchem.ml.modelling.model_evaluation), [1]