Index

A

add_molecule_and_errors() (in module useful_rdkit_utils.pandas_utils)

align_mols_to_template() (in module useful_rdkit_utils.misc_utils)

B

bootstrap_confidence_interval() (in module useful_rdkit_utils.stat_utils)

boxplot_base64_image() (in module useful_rdkit_utils.misc_utils) build_ring_systems_dataframe() (in module useful_rdkit_utils.ring_systems)

C

calc_mol() (RDKitDescriptors method) (RDKitProperties method) (Ro5Calculator method) calc_smiles() (RDKitDescriptors method) (RDKitProperties method) (Ro5Calculator method) calculate_sali() (in module useful_rdkit_utils.sali) clean_and_scale_descriptors() (in module useful_rdkit_utils.descriptors)

clean_descriptors() (in module useful_rdkit_utils.descriptors) cleanup_fragment() (in module useful_rdkit_utils.scaffold_finder) cleanup_fragments() (RingSystemFinder method) cleave_linker_bonds() (RingSystemFinder static method) compare_datasets() (in module useful_rdkit_utils.descriptors) count_fragments() (in module useful_rdkit_utils.misc_utils) create_ring_dictionary() (in module useful_rdkit_utils.ring_systems) cross_validate() (in module useful_rdkit_utils.split_utils)

D

demo_block_logs() (in module useful_rdkit_utils.misc_utils)

drop_rule() (REOS method)

E

enumerate_library() (in module useful_rdkit_utils.reactions)

enumerate_library_sample() (in module useful_rdkit_utils.reactions)

F

find_ring_systems() (RingSystemFinder method)

find_scaffolds() (in module useful_rdkit_utils.scaffold_finder) fix_bond_stereo() (RingSystemFinder static method)

G

gen_3d() (in module useful_rdkit_utils.geometry) gen_conformers() (in module useful_rdkit_utils.geometry) generate_fragments() (in module useful_rdkit_utils.scaffold_finder) get_active_rule_sets() (REOS method) get_available_rule_sets() (REOS method) get_bemis_murcko_clusters() (in module useful_rdkit_utils.split_utils) get_butina_clusters() (in module useful_rdkit_utils.split_utils) get_center() (in module useful_rdkit_utils.geometry) get_conformer_energies() (in module useful_rdkit_utils.geometry) get_count_fp() (Smi2Fp method) get_fp() (Smi2Fp method) get_kmeans_clusters() (in module useful_rdkit_utils.split_utils)

get_largest_fragment() (in module useful_rdkit_utils.misc_utils) get_min_ring_frequency() (in module useful_rdkit_utils.ring_systems) get_molecules_with_scaffold() (in module useful_rdkit_utils.scaffold_finder) get_np() (Smi2Fp method) get_np_counts() (Smi2Fp method) get_random_clusters() (in module useful_rdkit_utils.split_utils) get_rule_file_location() (REOS method) get_rules_dict() (REOS method) get_scaffold() (in module useful_rdkit_utils.split_utils) get_shape_moments() (in module useful_rdkit_utils.geometry) get_spiro_atoms() (in module useful_rdkit_utils.ring_systems) get_unit_multiplier() (in module useful_rdkit_utils.units) GroupKFoldShuffle (class in useful_rdkit_utils.split_utils)

K

kcal_to_ki() (in module useful_rdkit_utils.units)

ki_to_kcal() (in module useful_rdkit_utils.units)

L

label_atoms() (in module useful_rdkit_utils.misc_utils)

M

main() (in module useful_rdkit_utils.scaffold_finder) max_possible_correlation() (in module useful_rdkit_utils.stat_utils) max_ring_size() (in module useful_rdkit_utils.ring_systems) mcs_align() (in module useful_rdkit_utils.misc_utils) mcs_rmsd() (in module useful_rdkit_utils.geometry) module useful_rdkit_utils.descriptors useful_rdkit_utils.geometry useful_rdkit_utils.jupyter_utils useful_rdkit_utils.misc_utils useful_rdkit_utils.pandas_utils useful_rdkit_utils.reactions useful_rdkit_utils.reos useful_rdkit_utils.ring_systems useful_rdkit_utils.sali useful_rdkit_utils.scaffold_finder useful_rdkit_utils.seaborn_utils useful_rdkit_utils.split_utils useful_rdkit_utils.stat_utils useful_rdkit_utils.units

mol2morgan_fp() (in module useful_rdkit_utils.descriptors) mol2numpy_fp() (in module useful_rdkit_utils.descriptors) mol_to_3D_view() (in module useful_rdkit_utils.geometry) mol_to_base64_image() (in module useful_rdkit_utils.misc_utils)

P

pandas_mols() (RDKitDescriptors method) (RDKitProperties method) (REOS method) (RingSystemLookup method) (Ro5Calculator method) pandas_smiles() (RDKitDescriptors method) (RDKitProperties method) (REOS method) (RingSystemLookup method) (Ro5Calculator method)

parse_smarts() (REOS method) pearson_confidence() (in module useful_rdkit_utils.stat_utils) plot_sali_pairs() (in module useful_rdkit_utils.sali) process_mol() (REOS method) (RingSystemLookup method) process_smiles() (REOS method) (RingSystemLookup method)

R

rd_enable_png() (in module useful_rdkit_utils.jupyter_utils) rd_enable_svg() (in module useful_rdkit_utils.jupyter_utils) rd_make_structures_pretty() (in module useful_rdkit_utils.jupyter_utils) rd_set_image_size() (in module useful_rdkit_utils.jupyter_utils) rd_setup_jupyter() (in module useful_rdkit_utils.jupyter_utils) rd_show_atom_indices() (in module useful_rdkit_utils.jupyter_utils) rd_show_cip_stereo() (in module useful_rdkit_utils.jupyter_utils) rd_shut_the_hell_up() (in module useful_rdkit_utils.misc_utils) RDKitDescriptors (class in useful_rdkit_utils.descriptors)

RDKitProperties (class in useful_rdkit_utils.descriptors) read_rules() (REOS method) refine_conformers() (in module useful_rdkit_utils.geometry) remove_dummy_atoms() (in module useful_rdkit_utils.misc_utils) REOS (class in useful_rdkit_utils.reos) ring_stats() (in module useful_rdkit_utils.ring_systems) RingSystemFinder (class in useful_rdkit_utils.ring_systems) RingSystemLookup (class in useful_rdkit_utils.ring_systems) Ro5Calculator (class in useful_rdkit_utils.descriptors)

S

scale_descriptors() (in module useful_rdkit_utils.descriptors) set_active_rule_sets() (REOS method) set_min_priority() (REOS method) set_output_smarts() (REOS method) set_sns_defaults() (in module useful_rdkit_utils.seaborn_utils) set_sns_size() (in module useful_rdkit_utils.seaborn_utils)

Smi2Fp (class in useful_rdkit_utils.descriptors) smi2mol_with_errors() (in module useful_rdkit_utils.misc_utils) smi2morgan_fp() (in module useful_rdkit_utils.descriptors) smi2numpy_fp() (in module useful_rdkit_utils.descriptors) smi_to_base64_image() (in module useful_rdkit_utils.misc_utils) split() (GroupKFoldShuffle method)

T

tag_atoms() (in module useful_rdkit_utils.misc_utils) tag_bonds_to_preserve() (RingSystemFinder method)

taylor_butina_clustering() (in module useful_rdkit_utils.misc_utils) test_ring_system_finder() (in module useful_rdkit_utils.ring_systems) test_ring_system_lookup() (in module useful_rdkit_utils.ring_systems)

U

ug_ml_to_uM() (in module useful_rdkit_utils.units) update_descriptors() (RDKitDescriptors method) useful_rdkit_utils.descriptors module useful_rdkit_utils.geometry module useful_rdkit_utils.jupyter_utils module useful_rdkit_utils.misc_utils module useful_rdkit_utils.pandas_utils module useful_rdkit_utils.reactions module useful_rdkit_utils.reos module

useful_rdkit_utils.ring_systems module useful_rdkit_utils.sali module useful_rdkit_utils.scaffold_finder module useful_rdkit_utils.seaborn_utils module useful_rdkit_utils.split_utils module useful_rdkit_utils.stat_utils module useful_rdkit_utils.units module

V

value_counts_df() (in module useful_rdkit_utils.pandas_utils)