Index

_

__init__() (rxn.reaction_preprocessing.annotations.annotation_criterion.AnnotationCriterion method) (rxn.reaction_preprocessing.annotations.annotation_info.AnnotationInfo method) (rxn.reaction_preprocessing.annotations.missing_annotation_detector.MissingAnnotationDetector method) (rxn.reaction_preprocessing.annotations.molecule_annotation.AnnotationDecision method) (rxn.reaction_preprocessing.annotations.molecule_annotation.MoleculeAnnotation method) (rxn.reaction_preprocessing.annotations.molecule_replacer.MoleculeReplacer method) (rxn.reaction_preprocessing.annotations.rejected_molecules_filter.RejectedMoleculesFilter method) (rxn.reaction_preprocessing.augmenter.Augmenter method) (rxn.reaction_preprocessing.config.AugmentConfig method) (rxn.reaction_preprocessing.config.CommonConfig method) (rxn.reaction_preprocessing.config.Config method) (rxn.reaction_preprocessing.config.DataConfig method) (rxn.reaction_preprocessing.config.FragmentBond method) (rxn.reaction_preprocessing.config.InitialDataFormat method) (rxn.reaction_preprocessing.config.InputOutputTuple method) (rxn.reaction_preprocessing.config.InputOutputTupleWithColumnName method) (rxn.reaction_preprocessing.config.PreprocessConfig method) (rxn.reaction_preprocessing.config.RxnImportConfig method) (rxn.reaction_preprocessing.config.SplitConfig method) (rxn.reaction_preprocessing.config.StandardizeConfig method) (rxn.reaction_preprocessing.config.Step method) (rxn.reaction_preprocessing.config.TokenizeConfig method) (rxn.reaction_preprocessing.importer.RxnImporter method) (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method) (rxn.reaction_preprocessing.molecule_standardizer.MoleculeStandardizer method) (rxn.reaction_preprocessing.pistachio_record_standardizer.PistachioRecordStandardizer method) (rxn.reaction_preprocessing.preprocessor.Preprocessor method) (rxn.reaction_preprocessing.reaction_standardizer.ReactionStandardizer method) (rxn.reaction_preprocessing.smiles_tokenizer.SmilesTokenizer method) (rxn.reaction_preprocessing.stable_data_splitter.StableDataSplitter method) (rxn.reaction_preprocessing.stable_data_splitter.StableSplitter method) (rxn.reaction_preprocessing.standardizer.StandardizationOutput method) (rxn.reaction_preprocessing.standardizer.Standardizer method) (rxn.reaction_preprocessing.utils.DataSplit method) (rxn.reaction_preprocessing.utils.MolEquation method) (rxn.reaction_preprocessing.utils.RandomType method) (rxn.reaction_preprocessing.utils.ReactionSection method)

A

add_custom_logger_to_file() (in module rxn.reaction_preprocessing.utils) add_heat_token() (in module rxn.reaction_preprocessing.special_tokens) add_light_token() (in module rxn.reaction_preprocessing.special_tokens) AnnotationCriterion (class in rxn.reaction_preprocessing.annotations.annotation_criterion) AnnotationDecision (class in rxn.reaction_preprocessing.annotations.molecule_annotation)

AnnotationInfo (class in rxn.reaction_preprocessing.annotations.annotation_info) augment() (in module rxn.reaction_preprocessing.augmenter) (rxn.reaction_preprocessing.augmenter.Augmenter method) AugmentConfig (class in rxn.reaction_preprocessing.config) Augmenter (class in rxn.reaction_preprocessing.augmenter)

C

CommonConfig (class in rxn.reaction_preprocessing.config) Config (class in rxn.reaction_preprocessing.config)

contains_heat_token() (in module rxn.reaction_preprocessing.special_tokens) contains_light_token() (in module rxn.reaction_preprocessing.special_tokens)

D

data_directory() (in module rxn.reaction_preprocessing.utils) data_pipeline() (in module rxn.reaction_preprocessing.main)

DataConfig (class in rxn.reaction_preprocessing.config) DataSplit (class in rxn.reaction_preprocessing.utils) different_atom_types() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method)

E

extended_transition_metal_numbers() (rxn.reaction_preprocessing.annotations.annotation_criterion.AnnotationCriterion static method)

extended_transition_metals() (rxn.reaction_preprocessing.annotations.annotation_criterion.AnnotationCriterion static method)

F

formal_charge_exceeded() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method) FragmentBond (class in rxn.reaction_preprocessing.config)

from_molecule_annotations() (rxn.reaction_preprocessing.annotations.missing_annotation_detector.MissingAnnotationDetector class method) (rxn.reaction_preprocessing.annotations.molecule_replacer.MoleculeReplacer class method) (rxn.reaction_preprocessing.annotations.rejected_molecules_filter.RejectedMoleculesFilter class method)

G

get_atoms_for_mols() (in module rxn.reaction_preprocessing.utils)

get_formal_charge_for_mols() (in module rxn.reaction_preprocessing.utils)

I

import_from_file() (rxn.reaction_preprocessing.importer.RxnImporter method) import_from_iterator() (rxn.reaction_preprocessing.importer.RxnImporter method) InitialDataFormat (class in rxn.reaction_preprocessing.config) InputOutputTuple (class in rxn.reaction_preprocessing.config) InputOutputTupleWithColumnName (class in rxn.reaction_preprocessing.config) invalid_atom_type() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method) InvalidColumn

is_accepted() (rxn.reaction_preprocessing.annotations.annotation_info.AnnotationInfo method) is_annotated() (rxn.reaction_preprocessing.annotations.annotation_info.AnnotationInfo method) is_rejected() (rxn.reaction_preprocessing.annotations.annotation_info.AnnotationInfo method) is_valid() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method) is_valid_molecule_smiles() (rxn.reaction_preprocessing.annotations.rejected_molecules_filter.RejectedMoleculesFilter method) is_valid_reaction_equation() (rxn.reaction_preprocessing.annotations.rejected_molecules_filter.RejectedMoleculesFilter method) is_valid_reaction_smiles() (rxn.reaction_preprocessing.annotations.rejected_molecules_filter.RejectedMoleculesFilter method) iterate_rxn_smiles() (in module rxn.reaction_preprocessing.scripts.annotation_check)

K

keys() (rxn.reaction_preprocessing.standardizer.StandardizationOutput static method)

L

load_annotations() (in module rxn.reaction_preprocessing.annotations.molecule_annotation)

load_annotations_multiple() (in module rxn.reaction_preprocessing.annotations.molecule_annotation)

M

main() (in module rxn.reaction_preprocessing.scripts.standardize_pistachio_records) max_agent_tokens_exceeded() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method) max_agents_exceeded() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method) max_product_tokens_exceeded() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method) max_products_exceeded() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method) max_reactant_tokens_exceeded() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method) max_reactants_exceeded() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method) min_agents_subceeded() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method) min_products_subceeded() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method) min_reactants_subceeded() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method) missing_in_reaction_equation() (rxn.reaction_preprocessing.annotations.missing_annotation_detector.MissingAnnotationDetector method) missing_in_reaction_equations() (rxn.reaction_preprocessing.annotations.missing_annotation_detector.MissingAnnotationDetector method) missing_in_reaction_smiles() (rxn.reaction_preprocessing.annotations.missing_annotation_detector.MissingAnnotationDetector method) MissingAnnotation MissingAnnotationDetector (class in rxn.reaction_preprocessing.annotations.missing_annotation_detector) MixedReactionFilter (class in rxn.reaction_preprocessing.mixed_reaction_filter) module rxn.reaction_preprocessing rxn.reaction_preprocessing.annotations rxn.reaction_preprocessing.annotations.annotation_criterion rxn.reaction_preprocessing.annotations.annotation_info rxn.reaction_preprocessing.annotations.missing_annotation_detector rxn.reaction_preprocessing.annotations.molecule_annotation rxn.reaction_preprocessing.annotations.molecule_replacer rxn.reaction_preprocessing.annotations.rejected_molecules_filter rxn.reaction_preprocessing.augmenter rxn.reaction_preprocessing.cleaner rxn.reaction_preprocessing.config rxn.reaction_preprocessing.importer rxn.reaction_preprocessing.main rxn.reaction_preprocessing.mixed_reaction_filter rxn.reaction_preprocessing.molecule_standardizer rxn.reaction_preprocessing.pistachio_record_standardizer rxn.reaction_preprocessing.preprocessor rxn.reaction_preprocessing.reaction_standardizer rxn.reaction_preprocessing.scripts rxn.reaction_preprocessing.scripts.annotation_check rxn.reaction_preprocessing.scripts.combine_class_token rxn.reaction_preprocessing.scripts.find_missing_annotations rxn.reaction_preprocessing.scripts.standardize_pistachio_records rxn.reaction_preprocessing.smiles_tokenizer rxn.reaction_preprocessing.special_tokens rxn.reaction_preprocessing.stable_data_splitter rxn.reaction_preprocessing.standardizer rxn.reaction_preprocessing.utils

molecule_needs_annotation() (rxn.reaction_preprocessing.annotations.missing_annotation_detector.MissingAnnotationDetector method) MoleculeAnnotation (class in rxn.reaction_preprocessing.annotations.molecule_annotation) MoleculeNotAnnotated MoleculeReplacer (class in rxn.reaction_preprocessing.annotations.molecule_replacer) molecules_permutation_given_index() (in module rxn.reaction_preprocessing.augmenter) MoleculeStandardizationError MoleculeStandardizer (class in rxn.reaction_preprocessing.molecule_standardizer) MolEquation (class in rxn.reaction_preprocessing.utils)

O

original_without_fragment_bond (rxn.reaction_preprocessing.annotations.molecule_annotation.MoleculeAnnotation property)

overwrite_logging_format() (in module rxn.reaction_preprocessing.utils)

P

PistachioRecordStandardizer (class in rxn.reaction_preprocessing.pistachio_record_standardizer) preprocess() (in module rxn.reaction_preprocessing.preprocessor) preprocess_data() (in module rxn.reaction_preprocessing.main) PreprocessConfig (class in rxn.reaction_preprocessing.config) Preprocessor (class in rxn.reaction_preprocessing.preprocessor)

print_stats() (rxn.reaction_preprocessing.preprocessor.Preprocessor method) process_file() (rxn.reaction_preprocessing.preprocessor.Preprocessor method) process_iterator() (rxn.reaction_preprocessing.preprocessor.Preprocessor method) products_single_atoms() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method) products_subset_of_reactants() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method)

R

RandomType (class in rxn.reaction_preprocessing.utils) ReactionFilterError ReactionSection (class in rxn.reaction_preprocessing.utils) ReactionStandardizer (class in rxn.reaction_preprocessing.reaction_standardizer) read_csv() (rxn.reaction_preprocessing.augmenter.Augmenter static method) RejectedMolecule RejectedMoleculesFilter (class in rxn.reaction_preprocessing.annotations.rejected_molecules_filter) remove_isotope_information() (in module rxn.reaction_preprocessing.cleaner) replace_in_reaction_equation() (rxn.reaction_preprocessing.annotations.molecule_replacer.MoleculeReplacer method) replace_in_reaction_smiles() (rxn.reaction_preprocessing.annotations.molecule_replacer.MoleculeReplacer method) replace_molecule_smiles() (rxn.reaction_preprocessing.annotations.molecule_replacer.MoleculeReplacer method) requires_annotation() (rxn.reaction_preprocessing.annotations.annotation_criterion.AnnotationCriterion method) reset_random_seed() (in module rxn.reaction_preprocessing.utils) root_directory() (in module rxn.reaction_preprocessing.utils) rxn.reaction_preprocessing module rxn.reaction_preprocessing.annotations module rxn.reaction_preprocessing.annotations.annotation_criterion module rxn.reaction_preprocessing.annotations.annotation_info module rxn.reaction_preprocessing.annotations.missing_annotation_detector module rxn.reaction_preprocessing.annotations.molecule_annotation module rxn.reaction_preprocessing.annotations.molecule_replacer module rxn.reaction_preprocessing.annotations.rejected_molecules_filter module rxn.reaction_preprocessing.augmenter module rxn.reaction_preprocessing.cleaner module rxn.reaction_preprocessing.config module rxn.reaction_preprocessing.importer module

rxn.reaction_preprocessing.main module rxn.reaction_preprocessing.mixed_reaction_filter module rxn.reaction_preprocessing.molecule_standardizer module rxn.reaction_preprocessing.pistachio_record_standardizer module rxn.reaction_preprocessing.preprocessor module rxn.reaction_preprocessing.reaction_standardizer module rxn.reaction_preprocessing.scripts module rxn.reaction_preprocessing.scripts.annotation_check module rxn.reaction_preprocessing.scripts.combine_class_token module rxn.reaction_preprocessing.scripts.find_missing_annotations module rxn.reaction_preprocessing.scripts.standardize_pistachio_records module rxn.reaction_preprocessing.smiles_tokenizer module rxn.reaction_preprocessing.special_tokens module rxn.reaction_preprocessing.stable_data_splitter module rxn.reaction_preprocessing.standardizer module rxn.reaction_preprocessing.utils module rxn_import() (in module rxn.reaction_preprocessing.importer) RxnImportConfig (class in rxn.reaction_preprocessing.config) RxnImporter (class in rxn.reaction_preprocessing.importer) RxnImportError

S

SmilesTokenizer (class in rxn.reaction_preprocessing.smiles_tokenizer) split() (in module rxn.reaction_preprocessing.stable_data_splitter) split_file() (rxn.reaction_preprocessing.stable_data_splitter.StableDataSplitter method) SplitConfig (class in rxn.reaction_preprocessing.config) StableDataSplitter (class in rxn.reaction_preprocessing.stable_data_splitter) StableSplitter (class in rxn.reaction_preprocessing.stable_data_splitter) standardization_files_directory() (in module rxn.reaction_preprocessing.utils) StandardizationOutput (class in rxn.reaction_preprocessing.standardizer) standardize() (in module rxn.reaction_preprocessing.standardizer) (rxn.reaction_preprocessing.molecule_standardizer.MoleculeStandardizer method) (rxn.reaction_preprocessing.pistachio_record_standardizer.PistachioRecordStandardizer method) (rxn.reaction_preprocessing.reaction_standardizer.ReactionStandardizer method)

standardize_file() (rxn.reaction_preprocessing.standardizer.Standardizer method) standardize_in_equation() (rxn.reaction_preprocessing.molecule_standardizer.MoleculeStandardizer method) standardize_in_equation_with_errors() (rxn.reaction_preprocessing.molecule_standardizer.MoleculeStandardizer method) standardize_iterator() (rxn.reaction_preprocessing.standardizer.Standardizer method) StandardizeConfig (class in rxn.reaction_preprocessing.config) Standardizer (class in rxn.reaction_preprocessing.standardizer) Step (class in rxn.reaction_preprocessing.config) strip_all_special_tokens() (in module rxn.reaction_preprocessing.special_tokens) strip_heat_token() (in module rxn.reaction_preprocessing.special_tokens) strip_light_token() (in module rxn.reaction_preprocessing.special_tokens)

T

tokenize() (in module rxn.reaction_preprocessing.smiles_tokenizer) (rxn.reaction_preprocessing.smiles_tokenizer.SmilesTokenizer method)

TokenizeConfig (class in rxn.reaction_preprocessing.config)

U

updated_without_fragment_bond (rxn.reaction_preprocessing.annotations.molecule_annotation.MoleculeAnnotation property)

V

validate() (rxn.reaction_preprocessing.mixed_reaction_filter.MixedReactionFilter method)

values() (rxn.reaction_preprocessing.standardizer.StandardizationOutput method)