Index

A

add_dataset() (in module ord_schema.orm.database) add_parquet_dataset() (in module ord_schema.orm.database) add_solution() (in module ord_schema.macros.workups) allow_reaction_smiles_only (ord_schema.validations.ValidationOptions attribute)

apply_cross_reference_substitutions() (in module ord_schema.updates) apply_reaction_updates() (in module ord_schema.updates) assign_dataset_id() (in module ord_schema.updates) assign_id_substitutions() (in module ord_schema.updates)

B

BINARY (ord_schema.message_helpers.MessageFormat attribute) BINPB (ord_schema.message_helpers.MessageFormat attribute) brine() (in module ord_schema.macros.solutions)

build_compound() (in module ord_schema.message_helpers) build_data() (in module ord_schema.message_helpers) build_mapper() (in module ord_schema.orm.mappers) build_mappers() (in module ord_schema.orm.mappers)

C

cache_ok (ord_schema.orm.rdkit_mappers.CString attribute) (ord_schema.orm.rdkit_mappers.RDKitBfp attribute) (ord_schema.orm.rdkit_mappers.RDKitMol attribute) (ord_schema.orm.rdkit_mappers.RDKitReaction attribute) (ord_schema.orm.rdkit_mappers.RDKitSfp attribute) canonicalize_smiles() (in module ord_schema.resolvers) check_compound_identifiers() (in module ord_schema.message_helpers)

check_type_and_details() (in module ord_schema.validations) check_value_and_units() (in module ord_schema.validations) compute_solute_quantity() (in module ord_schema.units) contains_substructure() (ord_schema.orm.rdkit_mappers.RDKitMols class method) convert() (ord_schema.units.UnitResolver method) create_message() (in module ord_schema.message_helpers) CString (class in ord_schema.orm.rdkit_mappers)

D

DatasetCrossRefState (class in ord_schema.validations) defined_ids (ord_schema.validations.DatasetCrossRefState attribute)

delete_dataset() (in module ord_schema.orm.database) drying_agent() (in module ord_schema.macros.workups) duplicate_count (ord_schema.validations.DatasetCrossRefState attribute)

E

emit_warnings() (ord_schema.validations.DatasetCrossRefState method) ensure_float_nonnegative() (in module ord_schema.validations)

ensure_float_range() (in module ord_schema.validations) errors (ord_schema.validations.ValidationOutput attribute) extend() (ord_schema.validations.ValidationOutput method)

F

fetch_dataset() (in module ord_schema.message_helpers) filtration() (in module ord_schema.macros.workups) find_submessages() (in module ord_schema.message_helpers)

FingerprintType (class in ord_schema.orm.rdkit_mappers) format_message() (in module ord_schema.units) from_proto() (in module ord_schema.orm.mappers) FrozenMessage (class in ord_schema.frozen_message)

G

generate_dataset() (in module ord_schema.templating) get_col_spec() (ord_schema.orm.rdkit_mappers.CString method) (ord_schema.orm.rdkit_mappers.RDKitBfp method) (ord_schema.orm.rdkit_mappers.RDKitMol method) (ord_schema.orm.rdkit_mappers.RDKitReaction method) (ord_schema.orm.rdkit_mappers.RDKitSfp method) get_compound_identifier() (in module ord_schema.message_helpers) get_compound_molblock() (in module ord_schema.message_helpers) get_compound_name() (in module ord_schema.message_helpers)

get_compound_smiles() (in module ord_schema.message_helpers) get_connection_string() (in module ord_schema.orm.database) get_dataset_md5() (in module ord_schema.orm.database) get_dataset_size() (in module ord_schema.orm.database) get_logger() (in module ord_schema.logging) get_message_type() (in module ord_schema.orm.mappers) get_parents() (in module ord_schema.orm.mappers) get_product_yield() (in module ord_schema.message_helpers) get_reaction_smiles() (in module ord_schema.message_helpers) get_referenced_reaction_ids() (in module ord_schema.validations)

H

has_atom_mapping() (in module ord_schema.validations)

has_transition_metal() (in module ord_schema.message_helpers)

I

id (ord_schema.orm.rdkit_mappers.RDKitMols attribute) (ord_schema.orm.rdkit_mappers.RDKitReactions attribute) id_filename() (in module ord_schema.message_helpers) is_empty() (in module ord_schema.validations)

is_transition_metal() (in module ord_schema.message_helpers) is_url() (in module ord_schema.validations) is_valid_dataset_id() (in module ord_schema.validations) is_valid_orcid() (in module ord_schema.validations) is_valid_reaction_id() (in module ord_schema.validations)

J

JSON (ord_schema.message_helpers.MessageFormat attribute)

L

load_message() (in module ord_schema.message_helpers)

M

matches_smarts() (ord_schema.orm.rdkit_mappers.RDKitMols class method) (ord_schema.orm.rdkit_mappers.RDKitReactions class method) merge() (ord_schema.validations.DatasetCrossRefState method) message_to_row() (in module ord_schema.message_helpers) MessageFormat (class in ord_schema.message_helpers) messages_to_dataframe() (in module ord_schema.message_helpers) module ord_schema ord_schema.frozen_message ord_schema.logging ord_schema.macros ord_schema.macros.solutions ord_schema.macros.workups ord_schema.message_helpers ord_schema.orm ord_schema.orm.database ord_schema.orm.mappers ord_schema.orm.rdkit_mappers ord_schema.resolvers ord_schema.templating ord_schema.units ord_schema.updates ord_schema.validations

mol (ord_schema.orm.rdkit_mappers.RDKitMols attribute) mol_from_compound() (in module ord_schema.message_helpers) molblock_from_compound() (in module ord_schema.message_helpers) MORGAN_BFP (ord_schema.orm.rdkit_mappers.FingerprintType attribute) morgan_bfp (ord_schema.orm.rdkit_mappers.RDKitMols attribute) MORGAN_SFP (ord_schema.orm.rdkit_mappers.FingerprintType attribute) morgan_sfp (ord_schema.orm.rdkit_mappers.RDKitMols attribute)

N

name_resolve() (in module ord_schema.resolvers)

O

observe() (ord_schema.validations.DatasetCrossRefState method) ord_schema module ord_schema.frozen_message module ord_schema.logging module ord_schema.macros module ord_schema.macros.solutions module ord_schema.macros.workups module ord_schema.message_helpers module ord_schema.orm module

ord_schema.orm.database module ord_schema.orm.mappers module ord_schema.orm.rdkit_mappers module ord_schema.resolvers module ord_schema.templating module ord_schema.units module ord_schema.updates module ord_schema.validations module

P

parse_doi() (in module ord_schema.message_helpers) PBTXT (ord_schema.message_helpers.MessageFormat attribute) prepare_database() (in module ord_schema.orm.database) python_type (ord_schema.orm.rdkit_mappers.CString property) (ord_schema.orm.rdkit_mappers.RDKitBfp property) (ord_schema.orm.rdkit_mappers.RDKitMol property) (ord_schema.orm.rdkit_mappers.RDKitReaction property) (ord_schema.orm.rdkit_mappers.RDKitSfp property)

R

rdkit_cartridge() (in module ord_schema.orm.rdkit_mappers) RDKitBfp (class in ord_schema.orm.rdkit_mappers) RDKitMol (class in ord_schema.orm.rdkit_mappers) RDKitMols (class in ord_schema.orm.rdkit_mappers) RDKitReaction (class in ord_schema.orm.rdkit_mappers) RDKitReactions (class in ord_schema.orm.rdkit_mappers) RDKitSfp (class in ord_schema.orm.rdkit_mappers) reaction (ord_schema.orm.rdkit_mappers.RDKitReactions attribute) reaction_from_smiles() (in module ord_schema.message_helpers) reaction_has_internal_standard() (in module ord_schema.validations)

reaction_has_limiting_component() (in module ord_schema.validations) reaction_needs_internal_standard() (in module ord_schema.validations) reaction_smiles (ord_schema.orm.rdkit_mappers.RDKitReactions attribute) read_spreadsheet() (in module ord_schema.templating) referenced_ids (ord_schema.validations.DatasetCrossRefState attribute) require_provenance (ord_schema.validations.ValidationOptions attribute) resolve() (ord_schema.units.UnitResolver method) resolve_input() (in module ord_schema.resolvers) resolve_names() (in module ord_schema.resolvers) resolve_unit() (ord_schema.units.UnitResolver method) rotovap() (in module ord_schema.macros.workups)

S

safe_update() (in module ord_schema.message_helpers) self_reference_count (ord_schema.validations.DatasetCrossRefState attribute) separate_phases() (in module ord_schema.macros.workups) set_compound_identifier() (in module ord_schema.message_helpers) set_compound_molblock() (in module ord_schema.message_helpers) set_compound_name() (in module ord_schema.message_helpers)

set_compound_smiles() (in module ord_schema.message_helpers) set_dative_bonds() (in module ord_schema.message_helpers) set_solute_moles() (in module ord_schema.message_helpers) silence_rdkit_logs() (in module ord_schema.logging) simple_solution() (in module ord_schema.macros.solutions) smiles (ord_schema.orm.rdkit_mappers.RDKitMols attribute) smiles_from_compound() (in module ord_schema.message_helpers)

T

tanimoto() (ord_schema.orm.rdkit_mappers.RDKitMols class method)

to_proto() (in module ord_schema.orm.mappers) TXTPB (ord_schema.message_helpers.MessageFormat attribute)

U

UnitResolver (class in ord_schema.units) update_dataset() (in module ord_schema.updates)

update_parquet_dataset() (in module ord_schema.updates) update_rdkit_ids() (in module ord_schema.orm.database) update_rdkit_tables() (in module ord_schema.orm.database)

V

validate_addition_device() (in module ord_schema.validations) validate_addition_speed() (in module ord_schema.validations) validate_amount() (in module ord_schema.validations) validate_analysis() (in module ord_schema.validations) validate_atmosphere() (in module ord_schema.validations) validate_compound() (in module ord_schema.validations) validate_compound_identifier() (in module ord_schema.validations) validate_compound_preparation() (in module ord_schema.validations) validate_concentration() (in module ord_schema.validations) validate_crude_component() (in module ord_schema.validations) validate_current() (in module ord_schema.validations) validate_data() (in module ord_schema.validations) validate_dataset() (in module ord_schema.validations) validate_dataset_example() (in module ord_schema.validations) validate_dataset_streaming() (in module ord_schema.validations) validate_datasets() (in module ord_schema.validations) validate_date_time() (in module ord_schema.validations) validate_electrochemistry_cell() (in module ord_schema.validations) validate_electrochemistry_conditions() (in module ord_schema.validations) validate_electrochemistry_measurement() (in module ord_schema.validations) validate_float_value() (in module ord_schema.validations) validate_flow_conditions() (in module ord_schema.validations) validate_flow_rate() (in module ord_schema.validations) validate_ids (ord_schema.validations.ValidationOptions attribute) validate_illumination_conditions() (in module ord_schema.validations) validate_length() (in module ord_schema.validations) validate_mass() (in module ord_schema.validations) validate_mass_spec_measurement_type() (in module ord_schema.validations) validate_message() (in module ord_schema.validations) validate_moles() (in module ord_schema.validations) validate_percentage() (in module ord_schema.validations) validate_person() (in module ord_schema.validations) validate_pressure() (in module ord_schema.validations) validate_pressure_conditions() (in module ord_schema.validations) validate_pressure_control() (in module ord_schema.validations) validate_pressure_measurement() (in module ord_schema.validations) validate_product_compound() (in module ord_schema.validations)

validate_product_measurement() (in module ord_schema.validations) validate_reaction() (in module ord_schema.validations) validate_reaction_conditions() (in module ord_schema.validations) validate_reaction_environment() (in module ord_schema.validations) validate_reaction_identifier() (in module ord_schema.validations) validate_reaction_input() (in module ord_schema.validations) validate_reaction_notes() (in module ord_schema.validations) validate_reaction_observation() (in module ord_schema.validations) validate_reaction_outcome() (in module ord_schema.validations) validate_reaction_provenance() (in module ord_schema.validations) validate_reaction_setup() (in module ord_schema.validations) validate_reaction_smiles() (in module ord_schema.message_helpers) validate_reaction_workup() (in module ord_schema.validations) validate_record_event() (in module ord_schema.validations) validate_selectivity() (in module ord_schema.validations) validate_source() (in module ord_schema.validations) validate_stirring_conditions() (in module ord_schema.validations) validate_stirring_rate() (in module ord_schema.validations) validate_temperature() (in module ord_schema.validations) validate_temperature_conditions() (in module ord_schema.validations) validate_temperature_control() (in module ord_schema.validations) validate_temperature_measurement() (in module ord_schema.validations) validate_texture() (in module ord_schema.validations) validate_time() (in module ord_schema.validations) validate_tubing() (in module ord_schema.validations) validate_unmeasured_amount() (in module ord_schema.validations) validate_vessel() (in module ord_schema.validations) validate_vessel_attachment() (in module ord_schema.validations) validate_vessel_material() (in module ord_schema.validations) validate_vessel_preparation() (in module ord_schema.validations) validate_voltage() (in module ord_schema.validations) validate_volume() (in module ord_schema.validations) validate_wavelength() (in module ord_schema.validations) ValidationError ValidationOptions (class in ord_schema.validations) ValidationOutput (class in ord_schema.validations) ValidationWarning

W

warnings (ord_schema.validations.ValidationOutput attribute)

write_dataset() (in module ord_schema.message_helpers) write_message() (in module ord_schema.message_helpers)