Index

_

__init__() (rxn.chemutils.rdf.property_parser.PropertyParser method) (rxn.chemutils.rdf.property_parser.PropertySerializer method) (rxn.chemutils.rdf.rdf_parser.ParsedReaction method) (rxn.chemutils.rdf.rdf_parser.RdfParser method) (rxn.chemutils.rdf.rdf_reaction.RdfReaction method) (rxn.chemutils.rdf.reaction_properties.Compound method) (rxn.chemutils.rdf.reaction_properties.ReactionProperties method) (rxn.chemutils.rdf.reaction_smiles_extractor.ReactionSmilesExtractor method) (rxn.chemutils.reaction_combiner.ReactionCombiner method) (rxn.chemutils.reaction_equation.ReactionEquation method) (rxn.chemutils.reaction_smiles.ReactionFormat method) (rxn.chemutils.smiles_augmenter.SmilesAugmenter method)

A

additional_reagents_from_meta() (rxn.chemutils.rdf.rdf_reaction.RdfReaction method) agents (rxn.chemutils.reaction_equation.ReactionEquation attribute) all_reagents() (rxn.chemutils.rdf.rdf_reaction.RdfReaction method) apply_to_any_smiles() (in module rxn.chemutils.miscellaneous) apply_to_compound_groups() (in module rxn.chemutils.reaction_equation)

apply_to_compounds() (in module rxn.chemutils.reaction_equation) apply_to_multicomponent_smiles() (in module rxn.chemutils.multicomponent_smiles) apply_to_smiles_groups() (in module rxn.chemutils.miscellaneous) atom_type_counter() (in module rxn.chemutils.miscellaneous) augment() (rxn.chemutils.smiles_augmenter.SmilesAugmenter method)

B

block_type() (rxn.chemutils.rdf.rdf_parser.ParsedReaction method)

C

canonicalize_any() (in module rxn.chemutils.miscellaneous) canonicalize_compounds() (in module rxn.chemutils.reaction_equation) canonicalize_file() (in module rxn.chemutils.miscellaneous) canonicalize_multicomponent_smiles() (in module rxn.chemutils.multicomponent_smiles) canonicalize_smiles() (in module rxn.chemutils.conversion) cleanup_compounds() (in module rxn.chemutils.reaction_equation)

cleanup_smiles() (in module rxn.chemutils.conversion) combine() (rxn.chemutils.reaction_combiner.ReactionCombiner method) combine_iterators() (rxn.chemutils.reaction_combiner.ReactionCombiner method) combine_mols() (in module rxn.chemutils.rdkit_utils) combine_sequences() (rxn.chemutils.reaction_combiner.ReactionCombiner method) Compound (class in rxn.chemutils.rdf.reaction_properties) copy_as_detokenized() (in module rxn.chemutils.tokenization)

D

determine_format() (in module rxn.chemutils.reaction_smiles) determine_fragment_groups() (in module rxn.chemutils.extended_reaction_smiles)

detokenize_file() (in module rxn.chemutils.tokenization) detokenize_smiles() (in module rxn.chemutils.tokenization)

E

ensure_tokenized_file() (in module rxn.chemutils.tokenization)

equivalent_smiles() (in module rxn.chemutils.miscellaneous) EXTENDED (rxn.chemutils.reaction_smiles.ReactionFormat attribute)

F

file_is_tokenized() (in module rxn.chemutils.tokenization) find_compounds() (in module rxn.chemutils.rdf.reaction_properties)

find_compounds_with_category() (in module rxn.chemutils.rdf.reaction_properties) from_string() (rxn.chemutils.reaction_equation.ReactionEquation class method)

G

get_compound_dicts() (rxn.chemutils.rdf.reaction_properties.ReactionProperties method) get_compounds() (rxn.chemutils.rdf.reaction_properties.ReactionProperties method)

get_individual_compounds() (in module rxn.chemutils.miscellaneous) get_mol_structure() (rxn.chemutils.rdf.rdf_reaction.RdfReaction method) get_name() (rxn.chemutils.rdf.reaction_properties.Compound method)

H

has_repeated_molecules() (in module rxn.chemutils.reaction_equation)

I

inchi_to_mol() (in module rxn.chemutils.conversion) IncompleteReaction InvalidBlock InvalidInchi InvalidMdl

InvalidReactionSmiles InvalidSmiles is_valid_smiles() (in module rxn.chemutils.miscellaneous) iter_all_smiles() (rxn.chemutils.reaction_equation.ReactionEquation method) iterate_reactions_from_file() (in module rxn.chemutils.rdf.rdf_parser)

L

list_to_multicomponent_smiles() (in module rxn.chemutils.multicomponent_smiles)

M

maybe_canonicalize() (in module rxn.chemutils.conversion) mdl_to_mol() (in module rxn.chemutils.conversion) mdl_to_smiles() (in module rxn.chemutils.conversion) merge_molecules_from_fragment_groups() (in module rxn.chemutils.extended_reaction_smiles) merge_reactants_and_agents() (in module rxn.chemutils.reaction_equation) merge_reactions() (in module rxn.chemutils.miscellaneous) meta (rxn.chemutils.rdf.rdf_reaction.RdfReaction attribute) module rxn.chemutils rxn.chemutils.conversion rxn.chemutils.exceptions rxn.chemutils.extended_reaction_smiles rxn.chemutils.miscellaneous rxn.chemutils.multicomponent_smiles rxn.chemutils.rdf rxn.chemutils.rdf.property_parser rxn.chemutils.rdf.rdf_parser rxn.chemutils.rdf.rdf_reaction rxn.chemutils.rdf.reaction_properties rxn.chemutils.rdf.reaction_smiles_extractor rxn.chemutils.rdkit_utils rxn.chemutils.reaction_combiner rxn.chemutils.reaction_equation rxn.chemutils.reaction_smiles rxn.chemutils.scripts rxn.chemutils.scripts.canonicalize rxn.chemutils.scripts.combine_reaction rxn.chemutils.scripts.detokenize rxn.chemutils.scripts.rdf_to_smiles rxn.chemutils.scripts.tokenize rxn.chemutils.smiles_augmenter rxn.chemutils.smiles_randomization rxn.chemutils.smiles_standardization rxn.chemutils.tokenization rxn.chemutils.utils

mol_has_atom_mapping() (in module rxn.chemutils.miscellaneous) mol_to_inchi() (in module rxn.chemutils.conversion) mol_to_mdl() (in module rxn.chemutils.conversion) mol_to_smiles() (in module rxn.chemutils.conversion) multicomponent_smiles_to_list() (in module rxn.chemutils.multicomponent_smiles)

P

parse_any_reaction_smiles() (in module rxn.chemutils.reaction_smiles) parse_extended_reaction_smiles() (in module rxn.chemutils.extended_reaction_smiles) parse_properties() (in module rxn.chemutils.rdf.property_parser) parse_reaction_smiles() (in module rxn.chemutils.reaction_smiles)

ParsedReaction (class in rxn.chemutils.rdf.rdf_parser) products (rxn.chemutils.rdf.rdf_reaction.RdfReaction attribute) (rxn.chemutils.reaction_equation.ReactionEquation attribute) PropertyParser (class in rxn.chemutils.rdf.property_parser) PropertySerializer (class in rxn.chemutils.rdf.property_parser)

R

randomize_smiles_restricted() (in module rxn.chemutils.smiles_randomization) randomize_smiles_rotated() (in module rxn.chemutils.smiles_randomization) randomize_smiles_unrestricted() (in module rxn.chemutils.smiles_randomization) RdfParser (class in rxn.chemutils.rdf.rdf_parser) RdfParsingError RdfReaction (class in rxn.chemutils.rdf.rdf_reaction) reactants (rxn.chemutils.rdf.rdf_reaction.RdfReaction attribute) (rxn.chemutils.reaction_equation.ReactionEquation attribute) reaction_index (rxn.chemutils.rdf.rdf_reaction.RdfReaction attribute) ReactionCombiner (class in rxn.chemutils.reaction_combiner) ReactionEquation (class in rxn.chemutils.reaction_equation) ReactionFormat (class in rxn.chemutils.reaction_smiles) ReactionProperties (class in rxn.chemutils.rdf.reaction_properties) ReactionSmilesExtractor (class in rxn.chemutils.rdf.reaction_smiles_extractor) reagents (rxn.chemutils.rdf.rdf_reaction.RdfReaction attribute) remove_atom_mapping() (in module rxn.chemutils.utils) remove_chiral_centers() (in module rxn.chemutils.miscellaneous) remove_double_bond_stereochemistry() (in module rxn.chemutils.miscellaneous) remove_duplicate_compounds() (in module rxn.chemutils.reaction_equation) remove_duplicates_in_multicomponent_smiles() (in module rxn.chemutils.multicomponent_smiles) remove_hydrogens() (in module rxn.chemutils.conversion) remove_precursors_from_products() (in module rxn.chemutils.reaction_equation) rxn.chemutils module rxn.chemutils.conversion module rxn.chemutils.exceptions module rxn.chemutils.extended_reaction_smiles module rxn.chemutils.miscellaneous module rxn.chemutils.multicomponent_smiles module rxn.chemutils.rdf module rxn.chemutils.rdf.property_parser module

rxn.chemutils.rdf.rdf_parser module rxn.chemutils.rdf.rdf_reaction module rxn.chemutils.rdf.reaction_properties module rxn.chemutils.rdf.reaction_smiles_extractor module rxn.chemutils.rdkit_utils module rxn.chemutils.reaction_combiner module rxn.chemutils.reaction_equation module rxn.chemutils.reaction_smiles module rxn.chemutils.scripts module rxn.chemutils.scripts.canonicalize module rxn.chemutils.scripts.combine_reaction module rxn.chemutils.scripts.detokenize module rxn.chemutils.scripts.rdf_to_smiles module rxn.chemutils.scripts.tokenize module rxn.chemutils.smiles_augmenter module rxn.chemutils.smiles_randomization module rxn.chemutils.smiles_standardization module rxn.chemutils.tokenization module rxn.chemutils.utils module rxn_standardization() (in module rxn.chemutils.reaction_equation)

S

SanitizationError sanitize_mol() (in module rxn.chemutils.conversion) serialize_properties() (in module rxn.chemutils.rdf.property_parser) smiles_has_atom_mapping() (in module rxn.chemutils.miscellaneous) smiles_to_inchi() (in module rxn.chemutils.conversion) smiles_to_mol() (in module rxn.chemutils.conversion) SmilesAugmenter (class in rxn.chemutils.smiles_augmenter) sort_any() (in module rxn.chemutils.miscellaneous)

sort_compounds() (in module rxn.chemutils.reaction_equation) sort_multicomponent_smiles() (in module rxn.chemutils.multicomponent_smiles) split_smiles_and_fragment_info() (in module rxn.chemutils.conversion) STANDARD (rxn.chemutils.reaction_smiles.ReactionFormat attribute) STANDARD_WITH_TILDE (rxn.chemutils.reaction_smiles.ReactionFormat attribute) standardize_molecules() (in module rxn.chemutils.smiles_standardization) standardize_smiles() (in module rxn.chemutils.smiles_standardization) string_is_tokenized() (in module rxn.chemutils.tokenization)

T

to_dict() (rxn.chemutils.rdf.reaction_properties.Compound method) to_extended_reaction_smiles() (in module rxn.chemutils.extended_reaction_smiles) to_reaction_equation() (rxn.chemutils.rdf.reaction_smiles_extractor.ReactionSmilesExtractor method) to_reaction_smiles() (in module rxn.chemutils.reaction_smiles) (rxn.chemutils.rdf.reaction_smiles_extractor.ReactionSmilesExtractor method)

to_string() (rxn.chemutils.rdf.reaction_smiles_extractor.ReactionSmilesExtractor method) (rxn.chemutils.reaction_equation.ReactionEquation method) to_tokens() (in module rxn.chemutils.tokenization) TokenizationError tokenize_file() (in module rxn.chemutils.tokenization) tokenize_smiles() (in module rxn.chemutils.tokenization)

U

UnclearWhetherTokenized

UnsupportedExtendedReactionSmiles