Index

_

__author__ (in module syndirella) __citation__ (in module syndirella) __date__ (in module syndirella) __doc__ (in module syndirella) __email__ (in module syndirella) __license__ (in module syndirella) __version__ (in module syndirella) (in module syndirella.version) _angle_check() (in module syndirella.slipper.intra_geometry) _bond_check() (in module syndirella.slipper.intra_geometry) _check_intra_geom_flatness_results() (syndirella.slipper.SlipperFitter.SlipperFitter method) _clash_check() (in module syndirella.slipper.intra_geometry) _delete_file_or_directory() (syndirella.slipper.Slipper.Slipper method) _empty_results (in module syndirella.slipper.flatness) (in module syndirella.slipper.intra_geometry) _find_analogues_pkl_name() (syndirella.route.Library.Library method) _find_attachment_id_from_dummy() (syndirella.route.Reaction.Reaction method) _find_products_pkl_name() (syndirella.route.Library.Library method) _flat (in module syndirella.slipper.flatness) _get_angle_atom_indices() (in module syndirella.slipper.intra_geometry) _get_bond_atom_indices() (in module syndirella.slipper.intra_geometry) _get_coords() (in module syndirella.slipper.flatness)

_get_distances_to_plane() (in module syndirella.slipper.flatness) _get_scaffold() (syndirella.slipper.SlipperFitter.SlipperFitter method) _has_hydrogen() (in module syndirella.slipper.intra_geometry) _has_non_mcs_bond() (syndirella.slipper.slipper_synthesizer.Labeler.Labeler method) _is_hydrogen() (in module syndirella.slipper.intra_geometry) _label_product_with_atom_ids() (syndirella.slipper.slipper_synthesizer.Labeler.Labeler method) _load_products_dfs() (syndirella.slipper.Slipper.Slipper method) _make_reactant_mols() (syndirella.route.CobblerBench.CobblerBench method) _pairwise_distance() (in module syndirella.slipper.intra_geometry) _place_scaffold() (syndirella.slipper.SlipperFitter.SlipperFitter method) _prep_scaffold_input_df() (syndirella.slipper.SlipperFitter.SlipperFitter method) _prepare_input_df() (syndirella.slipper.SlipperFitter.SlipperFitter method) _print_diff() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) (syndirella.slipper.SlipperFitter.SlipperFitter method) _print_route() (syndirella.Cobbler.Cobbler method) _put_hippo_dfs_together() (syndirella.slipper.Slipper.Slipper method) _replace_carboxylic_acid_hydroxy_with_dummy() (syndirella.route.Reaction.Reaction method) _replace_halide_with_dummy() (syndirella.route.Reaction.Reaction method) _should_delete_file() (syndirella.slipper.Slipper.Slipper method) _sort_bond() (in module syndirella.slipper.intra_geometry) _structure_products_for_hippo() (syndirella.slipper.Slipper.Slipper method) _structure_step_for_hippo() (syndirella.slipper.Slipper.Slipper method) _two_bonds_to_angle() (in module syndirella.slipper.intra_geometry)

A

add_hits() (syndirella.slipper.SlipperFitter.SlipperFitter method) add_metadata() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) add_new_route_to_output_df() (in module syndirella.structure_outputs) add_outcome_info() (in module syndirella.structure_outputs) add_paths_to_placements() (syndirella.slipper.SlipperFitter.SlipperFitter method) add_route_info() (in module syndirella.structure_outputs) additional_info (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) additional_reactions (syndirella.route.CobblerBench.CobblerBench attribute) additional_rxn_options (syndirella.route.Reaction.Reaction attribute) additional_rxn_options_path (in module syndirella.cli_defaults) ae() (in module syndirella.slipper.stats) all_attach_ids (syndirella.route.Reaction.Reaction attribute) alt_reaction() (syndirella.route.Reaction.Reaction method) alt_reactions (syndirella.route.Reaction.Reaction attribute) analogue_columns (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) analogues_dataframes (syndirella.route.Library.Library attribute) analogues_dataframes_to_react (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) ape() (in module syndirella.slipper.stats) api_key (syndirella.Cobbler.Cobbler attribute) (syndirella.DatabaseSearch.DatabaseSearch attribute) (syndirella.Postera.Postera attribute)

APIQueryError apply_reaction() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) apply_reaction_single() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) assert_scaffold_placement() (in module syndirella.pipeline) assign_names_based_on_groups() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) assign_reactants_w_rxn_smarts() (syndirella.SMARTSHandler.SMARTSHandler method) atom_diff_max (syndirella.Cobbler.Cobbler attribute) (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) (syndirella.route.Library.Library attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute) atom_diff_min (syndirella.Cobbler.Cobbler attribute) (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) (syndirella.route.Library.Library attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute) atom_ids_expansion (syndirella.slipper.slipper_synthesizer.Labeler.Labeler attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) atoms_ids_expansion (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) (syndirella.slipper.Slipper.Slipper attribute)

B

bae() (in module syndirella.slipper.stats) bape() (in module syndirella.slipper.stats) batch_num (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute)

bound_matrix_params (in module syndirella.slipper.intra_geometry) bpe() (in module syndirella.slipper.stats)

C

calc_num_atom_diff_absolute() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) calc_num_atom_diff_mcs() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) calculate_fingerprints() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) calculate_inchi_similarity() (syndirella.slipper.Slipper.Slipper method) calculate_tanimoto() (in module syndirella.fairy) can_be_sanitized() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) CAR check_additional_columns() (in module syndirella.check_inputs) check_additional_info_to_add() (in module syndirella.structure_outputs) check_analogue_contains_all_smarts_patterns() (syndirella.route.Library.Library method) check_analogue_contains_other_reactant_smarts_pattern() (syndirella.route.Library.Library method) check_analogue_contains_smarts_pattern() (syndirella.route.Library.Library method) check_analogues_pkl_exists() (syndirella.route.Library.Library method) check_apo_template() (in module syndirella.check_inputs) check_csv() (in module syndirella.check_inputs) check_flatness() (in module syndirella.slipper.flatness) check_found_reactants() (syndirella.SMARTSHandler.SMARTSHandler method) check_geometry() (in module syndirella.slipper.intra_geometry) check_hit_names() (in module syndirella.check_inputs) check_intra_geometry() (syndirella.slipper.SlipperFitter.SlipperFitter method) check_manual() (in module syndirella.check_inputs) check_mol_sanity() (in module syndirella.fairy) check_pipeline_inputs() (in module syndirella.check_inputs) check_placement_to_add() (in module syndirella.structure_outputs) check_product() (syndirella.route.CobblersWorkshop.CobblersWorkshop method) check_product_pkl_exists() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) check_reactants() (syndirella.route.CobblersWorkshop.CobblersWorkshop method) check_reaction() (syndirella.route.CobblerBench.CobblerBench method) check_reaction_can_produce_product() (syndirella.route.Reaction.Reaction method) check_reaction_names() (syndirella.route.CobblersWorkshop.CobblersWorkshop method) check_route() (in module syndirella.check_inputs) check_route_to_add() (in module syndirella.structure_outputs) check_scaffold() (syndirella.slipper.SlipperFitter.SlipperFitter method) check_scaffold_in_hippo() (syndirella.slipper.Slipper.Slipper method) check_template_paths() (in module syndirella.check_inputs) ChemicalErrorBase choose_route() (syndirella.Cobbler.Cobbler method) clean_up_placements() (syndirella.slipper.Slipper.Slipper method) cli_default_settings (in module syndirella.cli_defaults)

cluster_analogues() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) Cobbler (class in syndirella.Cobbler) cobbler_benches (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) CobblerBench (class in syndirella.route.CobblerBench) CobblersWorkshop (class in syndirella.route.CobblersWorkshop) col_angles_result (in module syndirella.slipper.intra_geometry) col_bape (in module syndirella.slipper.intra_geometry) col_bonds_result (in module syndirella.slipper.intra_geometry) col_bpe (in module syndirella.slipper.intra_geometry) col_clash_result (in module syndirella.slipper.intra_geometry) col_closest_noncov (in module syndirella.slipper.intra_geometry) col_extremest_angle (in module syndirella.slipper.intra_geometry) col_lb (in module syndirella.slipper.intra_geometry) col_longest_bond (in module syndirella.slipper.intra_geometry) col_n_angles (in module syndirella.slipper.intra_geometry) col_n_bad_angles (in module syndirella.slipper.intra_geometry) col_n_bonds (in module syndirella.slipper.intra_geometry) col_n_clashes (in module syndirella.slipper.intra_geometry) col_n_good_angles (in module syndirella.slipper.intra_geometry) col_n_good_bonds (in module syndirella.slipper.intra_geometry) col_n_good_noncov (in module syndirella.slipper.intra_geometry) col_n_long_bonds (in module syndirella.slipper.intra_geometry) col_n_noncov (in module syndirella.slipper.intra_geometry) col_n_short_bonds (in module syndirella.slipper.intra_geometry) col_pe (in module syndirella.slipper.intra_geometry) col_shortest_bond (in module syndirella.slipper.intra_geometry) col_ub (in module syndirella.slipper.intra_geometry) combine_analogues() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) combine_flags() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) config_parser() (in module syndirella.cli) configure_additional_routes() (syndirella.route.CobblersWorkshop.CobblersWorkshop method) create_cobblers_workshop_from_Postera() (syndirella.Cobbler.Cobbler method) create_library() (syndirella.route.Library.Library method) current_step (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.route.Library.Library attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) cut_analogues() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method)

D

DatabaseSearch (class in syndirella.DatabaseSearch) define_reaction() (syndirella.route.CobblerBench.CobblerBench method) (syndirella.route.CobblersWorkshop.CobblersWorkshop method)

do_i_need_alternative_route() (in module syndirella.fairy)

E

edit_reactant() (syndirella.route.Reaction.Reaction method) elaborate_compound_full_auto() (in module syndirella.pipeline) elaborate_compound_with_manual_routes() (in module syndirella.pipeline)

elaborate_from_cobbler_workshops() (in module syndirella.pipeline) enumerate_stereoisomers() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) extra_dir_path (syndirella.route.Library.Library attribute)

F

Fairy fill_in_product() (in module syndirella.check_inputs) filter (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) (syndirella.route.Library.Library attribute) filter_analogues() (syndirella.route.Library.Library method) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) filter_analogues_by_size() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) filter_analogues_on_smarts() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) filter_molecules() (in module syndirella.fairy) filter_on_substructure_filters() (syndirella.route.Library.Library method) filter_products() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) filter_routes() (syndirella.Cobbler.Cobbler method) final_library (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) final_products (syndirella.slipper.SlipperFitter.SlipperFitter attribute) final_products_csv_path (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute) final_products_pkl_path (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute) find_analogues() (syndirella.route.CobblerBench.CobblerBench method) find_attachment_id_for_reactant() (syndirella.route.Reaction.Reaction method) find_attachment_ids_for_all_reactants() (syndirella.route.Reaction.Reaction method)

find_matches() (syndirella.slipper.Slipper.Slipper method) find_matching_atoms() (syndirella.SMARTSHandler.SMARTSHandler method) find_products_csv() (in module syndirella.slipper._placement_data) find_products_from_reactants() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) find_reaction_atoms_for_all_reactants() (syndirella.route.Reaction.Reaction method) find_reaction_by_name() (in module syndirella.fairy) find_similar_reactants() (in module syndirella.fairy) find_similarity_groups() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) find_stereoisomers() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) first_library (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) fit_products() (syndirella.slipper.SlipperFitter.SlipperFitter method) fix_intxns() (syndirella.slipper.SlipperFitter.SlipperFitter method) format_additional_info() (in module syndirella.check_inputs) format_manual_route() (in module syndirella.check_inputs) format_matched_reactant_for_one() (syndirella.SMARTSHandler.SMARTSHandler method) format_matched_smarts_to_index() (syndirella.route.Reaction.Reaction method) format_placements() (syndirella.slipper.SlipperFitter.SlipperFitter method) format_routes() (in module syndirella.justretroquery) format_scaffold_placements() (syndirella.slipper.SlipperFitter.SlipperFitter method) format_workshops_from_routes() (syndirella.route.CobblersWorkshop.CobblersWorkshop method) found_1 (syndirella.SMARTSHandler.SMARTSHandler attribute) found_2 (syndirella.SMARTSHandler.SMARTSHandler attribute) from_SMARTS_to_patterns() (syndirella.SMARTSHandler.SMARTSHandler method) fromReactantNameToReactionFullName() (syndirella.SMARTSHandler.SMARTSHandler method) fromReactionFullNameToReactantName() (syndirella.SMARTSHandler.SMARTSHandler method)

G

generate_inchi_ID() (in module syndirella.fairy) get_additional_reactions() (syndirella.route.CobblerBench.CobblerBench method) (syndirella.route.Reaction.Reaction method) get_additional_routes() (syndirella.route.CobblersWorkshop.CobblersWorkshop method) get_bound_unbound() (in module syndirella.slipper._placement_data) get_cobbler_bench() (syndirella.route.CobblersWorkshop.CobblersWorkshop method) get_delta_delta_G() (in module syndirella.slipper._placement_data) get_error_info() (in module syndirella.structure_outputs) get_exact_hit_names() (in module syndirella.check_inputs) get_final_library() (syndirella.route.CobblersWorkshop.CobblersWorkshop method) get_inchi() (in module syndirella.structure_outputs) get_morgan_fingerprint() (in module syndirella.fairy) get_output_df() (in module syndirella.structure_outputs) get_passing_routes() (syndirella.Cobbler.Cobbler method)

get_placement_data() (in module syndirella.slipper._placement_data) get_placements_df() (syndirella.slipper.Slipper.Slipper method) get_products() (syndirella.slipper.Slipper.Slipper method) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) get_products_from_single_reactant() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) get_resp_json() (syndirella.DatabaseSearch.DatabaseSearch method) (syndirella.Postera.Postera static method) get_route() (syndirella.Cobbler.Cobbler method) get_routes() (syndirella.Cobbler.Cobbler method) get_scaffold_check_values() (syndirella.slipper.SlipperFitter.SlipperFitter method) get_scaffold_smiles() (in module syndirella.structure_outputs) get_search_results() (syndirella.Postera.Postera static method) get_similar_reactant() (in module syndirella.fairy) get_template_path() (in module syndirella.check_inputs) get_versions() (in module syndirella.version)

H

hits_names (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute)

hits_path (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute)

I

id (syndirella.Cobbler.Cobbler attribute) (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) (syndirella.route.Library.Library attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute)

inchi (syndirella.error.ChemicalErrorBase attribute)

L

label_products() (syndirella.slipper.slipper_synthesizer.Labeler.Labeler method) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) label_products_with_atom_ids() (syndirella.slipper.slipper_synthesizer.Labeler.Labeler method) Labeler (class in syndirella.slipper.slipper_synthesizer.Labeler) Library (class in syndirella.route.Library) library (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.slipper_synthesizer.Labeler.Labeler attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) load() (syndirella.route.Library.Library static method) load_additional_rxn_options() (in module syndirella.fairy) load_database_search() (syndirella.DatabaseSearch.DatabaseSearch method) (syndirella.Postera.Postera method) load_library() (syndirella.route.Library.Library method) load_pipeline_module() (in module syndirella.cli) load_products() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method)

load_reactant_filters() (in module syndirella.fairy) log_route() (syndirella.route.CobblersWorkshop.CobblersWorkshop method) logger (in module syndirella.check_inputs) (in module syndirella.fairy) (in module syndirella.justretroquery) (in module syndirella.pipeline) (in module syndirella.slipper.intra_geometry) (in module syndirella.structure_outputs) (syndirella.Cobbler.Cobbler attribute) (syndirella.Postera.Postera attribute) (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) (syndirella.route.Library.Library attribute) (syndirella.route.Reaction.Reaction attribute) (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute) (syndirella.SMARTSHandler.SMARTSHandler attribute)

M

main() (in module syndirella.cli) make_fragmenstein_placements_csv() (in module syndirella.slipper._placement_data) make_query() (syndirella.Postera.Postera method) make_similar_reactant() (in module syndirella.fairy) make_success_csv_row() (in module syndirella.slipper._placement_data) matched_reactants (syndirella.SMARTSHandler.SMARTSHandler attribute) merge_placements() (syndirella.slipper.SlipperFitter.SlipperFitter method) merged_placements (syndirella.slipper.SlipperFitter.SlipperFitter attribute) message (syndirella.error.ChemicalErrorBase attribute) metadata_dict() (in module syndirella.check_inputs) module setup syndirella syndirella.__main__ syndirella.check_inputs syndirella.cli syndirella.cli_defaults syndirella.Cobbler syndirella.constants syndirella.DatabaseSearch syndirella.error syndirella.fairy syndirella.justretroquery syndirella.pipeline syndirella.Postera syndirella.route syndirella.route.CobblerBench syndirella.route.CobblersWorkshop syndirella.route.Library syndirella.route.Reaction syndirella.slipper syndirella.slipper._placement_data syndirella.slipper.flatness syndirella.slipper.intra_geometry syndirella.slipper.Slipper syndirella.slipper.slipper_synthesizer syndirella.slipper.slipper_synthesizer.Labeler syndirella.slipper.slipper_synthesizer.SlipperSynthesizer syndirella.slipper.SlipperFitter syndirella.slipper.stats syndirella.SMARTSHandler syndirella.structure_outputs syndirella.version

mol (syndirella.error.ChemicalErrorBase attribute) MolError

N

n_cores (syndirella.slipper.SlipperFitter.SlipperFitter attribute) n_reactants_per_reaction (syndirella.Cobbler.Cobbler attribute) (syndirella.SMARTSHandler.SMARTSHandler attribute) NoReactants NoScaffold NoSynthesisRoute NoToHippo num_placed (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute)

num_products_enumstereo (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) num_steps (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) (syndirella.route.Library.Library attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) num_successful (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute) num_unique_products (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute)

O

order_analogues() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) output_dir (syndirella.Cobbler.Cobbler attribute) (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) (syndirella.route.Library.Library attribute) (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.slipper_synthesizer.Labeler.Labeler attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute)

output_path (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute)

P

pattern_products (syndirella.SMARTSHandler.SMARTSHandler attribute) pattern_reactant1 (syndirella.SMARTSHandler.SMARTSHandler attribute) pattern_reactant2 (syndirella.SMARTSHandler.SMARTSHandler attribute) pe() (in module syndirella.slipper.stats) perform_database_search() (syndirella.DatabaseSearch.DatabaseSearch method) (syndirella.Postera.Postera method) perform_exact_batch_search() (syndirella.Postera.Postera method) perform_exact_search() (syndirella.Postera.Postera method) perform_route_search() (syndirella.Postera.Postera method) perform_superstructure_search() (syndirella.Postera.Postera method) place_products() (syndirella.slipper.Slipper.Slipper method) (syndirella.slipper.SlipperFitter.SlipperFitter method) Placement PlacementError placements (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute)

Postera (class in syndirella.Postera) prep_products() (syndirella.slipper.SlipperFitter.SlipperFitter method) print_diff() (in module syndirella.fairy) (syndirella.route.Library.Library method) process_analogues() (syndirella.route.Library.Library method) process_df() (in module syndirella.justretroquery) process_reactant() (syndirella.route.Library.Library method) product (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) product_smarts (syndirella.SMARTSHandler.SMARTSHandler attribute) ProductFormationError products (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.slipper_synthesizer.Labeler.Labeler attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute)

R

r1 (syndirella.route.Library.Library attribute) r2 (syndirella.route.Library.Library attribute) reactant1_dict (syndirella.SMARTSHandler.SMARTSHandler attribute) reactant2_dict (syndirella.SMARTSHandler.SMARTSHandler attribute) reactant_combinations (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) reactant_filters_path (in module syndirella.cli_defaults) reactant_smiles (syndirella.route.CobblerBench.CobblerBench attribute) reactants (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) (syndirella.route.Reaction.Reaction attribute) Reaction (class in syndirella.route.Reaction) reaction (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.route.Library.Library attribute) reaction_name (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.route.Reaction.Reaction attribute) reaction_names (syndirella.Cobbler.Cobbler attribute) (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) reaction_pattern (syndirella.route.Reaction.Reaction attribute) reaction_smarts (in module syndirella.justretroquery) (syndirella.SMARTSHandler.SMARTSHandler attribute) reaction_smarts_names (in module syndirella.justretroquery) ReactionError readme() (in module setup) remove_chirality() (in module syndirella.fairy) remove_chirality_from_mol() (in module syndirella.fairy)

remove_hydrogen_ions() (in module syndirella.fairy) remove_non_abundant_isotopes() (in module syndirella.fairy) remove_repeat_mols() (in module syndirella.fairy) requirements (in module setup) retro_search() (in module syndirella.justretroquery) route_uuid (syndirella.error.APIQueryError attribute) (syndirella.error.MolError attribute) (syndirella.error.NoReactants attribute) (syndirella.error.NoScaffold attribute) (syndirella.error.NoToHippo attribute) (syndirella.error.PlacementError attribute) (syndirella.error.ProductFormationError attribute) (syndirella.error.ReactionError attribute) (syndirella.error.ScaffoldPlacementError attribute) (syndirella.error.SMARTSError attribute) (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.route.CobblersWorkshop.CobblersWorkshop attribute) (syndirella.route.Library.Library attribute) (syndirella.route.Reaction.Reaction attribute) (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute) run_justretroquery() (in module syndirella.cli) (in module syndirella.justretroquery) run_pipeline() (in module syndirella.cli) (in module syndirella.pipeline) rxn_smarts_path (in module syndirella.cli_defaults)

S

save() (syndirella.Cobbler.Cobbler method) (syndirella.route.Library.Library method) save_database_search() (syndirella.DatabaseSearch.DatabaseSearch method) (syndirella.Postera.Postera method) save_df() (in module syndirella.justretroquery) save_library() (syndirella.route.Library.Library method) save_output_df() (in module syndirella.structure_outputs) save_placements() (syndirella.slipper.SlipperFitter.SlipperFitter method) save_products() (syndirella.slipper.slipper_synthesizer.SlipperSynthesizer.SlipperSynthesizer method) Scaffold scaffold (syndirella.route.Reaction.Reaction attribute) scaffold_compound (syndirella.Cobbler.Cobbler attribute) scaffold_placements (syndirella.slipper.Slipper.Slipper attribute) (syndirella.slipper.SlipperFitter.SlipperFitter attribute) ScaffoldPlacementError seperate_matching_reactants() (syndirella.SMARTSHandler.SMARTSHandler method) setup module setup_Fragmenstein() (syndirella.slipper.SlipperFitter.SlipperFitter method) setup_logging() (in module syndirella.cli) show_atoms_to_expand_and_not_expand() (syndirella.slipper.slipper_synthesizer.Labeler.Labeler method) show_mcs_on_products() (syndirella.slipper.slipper_synthesizer.Labeler.Labeler method) simple_filters() (in module syndirella.fairy) Slipper (class in syndirella.slipper.Slipper) SlipperFitter (class in syndirella.slipper.SlipperFitter) SlipperSynthesizer (class in syndirella.slipper.slipper_synthesizer.SlipperSynthesizer) smarts_handler (syndirella.route.CobblerBench.CobblerBench attribute) (syndirella.route.Reaction.Reaction attribute) SMARTSError SMARTSHandler (class in syndirella.SMARTSHandler) smiles (syndirella.error.ChemicalErrorBase attribute) start_elaboration() (in module syndirella.pipeline) structure_output() (syndirella.Postera.Postera method) structure_pipeline_outputs() (in module syndirella.structure_outputs) structure_route_outputs() (in module syndirella.structure_outputs) syndirella module syndirella.__main__ module syndirella.check_inputs module syndirella.cli module syndirella.cli_defaults module syndirella.Cobbler module

syndirella.constants module syndirella.DatabaseSearch module syndirella.error module syndirella.fairy module syndirella.justretroquery module syndirella.pipeline module syndirella.Postera module syndirella.route module syndirella.route.CobblerBench module syndirella.route.CobblersWorkshop module syndirella.route.Library module syndirella.route.Reaction module syndirella.slipper module syndirella.slipper._placement_data module syndirella.slipper.flatness module syndirella.slipper.intra_geometry module syndirella.slipper.Slipper module syndirella.slipper.slipper_synthesizer module syndirella.slipper.slipper_synthesizer.Labeler module syndirella.slipper.slipper_synthesizer.SlipperSynthesizer module syndirella.slipper.SlipperFitter module syndirella.slipper.stats module syndirella.SMARTSHandler module syndirella.structure_outputs module syndirella.version module syndirella_base_path (in module syndirella.cli_defaults)

T

template (syndirella.slipper.Slipper.Slipper attribute) template_path (syndirella.slipper.SlipperFitter.SlipperFitter attribute)

this_directory (in module setup) timeout (syndirella.slipper.SlipperFitter.SlipperFitter attribute) to_hippo_path (syndirella.slipper.Slipper.Slipper attribute)

U

url (syndirella.Cobbler.Cobbler attribute) (syndirella.DatabaseSearch.DatabaseSearch attribute) (syndirella.Postera.Postera attribute)

use_fmcs() (syndirella.route.Reaction.Reaction method)

W

which_reactant_was_previous_product() (syndirella.slipper.Slipper.Slipper method)

write_products_to_hippo() (syndirella.slipper.Slipper.Slipper method)