Index

A

action() (in module rxnutils.pipeline.base) agents_list (rxnutils.chem.reaction.ChemicalReaction property) apply() (rxnutils.chem.template.ReactionTemplate method) AptedConfig (class in rxnutils.routes.ted.utils) assign_atom_mapping() (rxnutils.routes.base.SynthesisRoute method) atom_invariants() (rxnutils.chem.template.TemplateMolecule method)

atom_mapped_reaction_smiles() (rxnutils.routes.base.SynthesisRoute method) atom_mapping_numbers() (in module rxnutils.chem.utils) atom_matching_bonanza_similarity() (in module rxnutils.routes.comparison) atom_properties() (rxnutils.chem.template.TemplateMolecule method) AtomMapTagDisconnectionSite (class in rxnutils.pipeline.actions.reaction_mod) atoms() (rxnutils.chem.template.TemplateMolecule method)

B

bad_column (rxnutils.pipeline.actions.reaction_mod.RemoveUnsanitizable attribute) bad_columns (rxnutils.pipeline.actions.reaction_props.HasUnsanitizableReactants attribute) badowski_route_score() (in module rxnutils.routes.scoring)

bonds_broken (rxnutils.chem.cgr.CondensedGraphReaction property) bonds_changed (rxnutils.chem.cgr.CondensedGraphReaction property) bonds_formed (rxnutils.chem.cgr.CondensedGraphReaction property) BOTH (rxnutils.routes.ted.utils.TreeContent attribute)

C

calc_yield_column (rxnutils.data.uspto.uspto_yield.UsptoYieldCuration attribute) canonical_template (rxnutils.chem.reaction.ChemicalReaction property) canonical_template_generate_outcome() (rxnutils.chem.reaction.ChemicalReaction method) canonicalize_tautomer() (in module rxnutils.chem.utils) CgrCreated (class in rxnutils.pipeline.actions.reaction_props) CgrNumberOfDynamicBonds (class in rxnutils.pipeline.actions.reaction_props) chains() (rxnutils.routes.base.SynthesisRoute method) ChemicalReaction (class in rxnutils.chem.reaction) children (rxnutils.routes.utils.validation.MoleculeNode attribute) (rxnutils.routes.utils.validation.ReactionNode attribute) children() (rxnutils.routes.ted.utils.AptedConfig method) collect_reaction_features() (in module rxnutils.routes.deepset.featurizers) columns (rxnutils.pipeline.actions.dataframe_mod.DropColumns attribute) (rxnutils.pipeline.actions.dataframe_mod.KeepColumns attribute)

combine_batches() (in module rxnutils.data.batch_utils) combine_csv_batches() (in module rxnutils.data.batch_utils) combine_files() (rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow method) combine_numpy_array_batches() (in module rxnutils.data.batch_utils) combine_sparse_matrix_batches() (in module rxnutils.data.batch_utils) CondensedGraphReaction (class in rxnutils.chem.cgr) ConvertAtomMapDisconnectionTag (class in rxnutils.pipeline.actions.reaction_mod) CountComponents (class in rxnutils.pipeline.actions.reaction_props) CountElements (class in rxnutils.pipeline.actions.reaction_props) CountTemplateComponents (class in rxnutils.pipeline.actions.templates) create_action() (in module rxnutils.pipeline.base) create_csv_batches() (in module rxnutils.data.batch_utils) crop_image() (in module rxnutils.routes.image)

D

data_prefix (rxnutils.data.base_pipeline.DataPreparationBaseFlow attribute) (rxnutils.data.mapping_pipeline.RxnMappingFlow attribute) (rxnutils.data.ord.preparation_pipeline.OrdDataPreparationFlow attribute) (rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow attribute) DataBaseFlow (class in rxnutils.data.base_pipeline) DataPreparationBaseFlow (class in rxnutils.data.base_pipeline) deepset_route_score() (in module rxnutils.routes.deepset.scoring) DeepsetModelClient (class in rxnutils.routes.deepset.scoring) default_reaction_featurizer() (in module rxnutils.routes.deepset.featurizers) desalt_molecules() (in module rxnutils.chem.utils) DesaltMolecules (class in rxnutils.pipeline.actions.reaction_mod)

distance_iter() (rxnutils.routes.ted.reactiontree.ReactionTreeWrapper method) distance_to() (rxnutils.chem.cgr.CondensedGraphReaction method) (rxnutils.routes.ted.reactiontree.ReactionTreeWrapper method) distance_to_with_sorting() (rxnutils.routes.ted.reactiontree.ReactionTreeWrapper method) do_cleaning() (rxnutils.data.ord.preparation_pipeline.OrdDataPreparationFlow method) (rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow method) do_mapping() (rxnutils.data.mapping_pipeline.RxnMappingFlow method) draw_rounded_rectangle() (in module rxnutils.routes.image) DropColumns (class in rxnutils.pipeline.actions.dataframe_mod) DropDuplicates (class in rxnutils.pipeline.actions.dataframe_mod) DropRows (class in rxnutils.pipeline.actions.dataframe_mod)

E

ecfp_fingerprint() (in module rxnutils.routes.deepset.featurizers) end() (rxnutils.data.mapping_pipeline.RxnMappingFlow method) (rxnutils.data.ord.preparation_pipeline.OrdDataPreparationFlow method) (rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow method)

enumerate_tautomers() (in module rxnutils.chem.utils) expected_reactants_column (rxnutils.pipeline.actions.templates.RetroTemplateReproduction attribute)

F

fingerprint_bits() (rxnutils.chem.template.ReactionTemplate method) (rxnutils.chem.template.TemplateMolecule method) fingerprint_vector() (rxnutils.chem.template.ReactionTemplate method) (rxnutils.chem.template.TemplateMolecule method)

first_tree (rxnutils.routes.ted.reactiontree.ReactionTreeWrapper property) fix_atom_properties() (rxnutils.chem.template.TemplateMolecule method) folder (rxnutils.data.base_pipeline.DataBaseFlow attribute) from_file() (rxnutils.routes.retro_bleu.ngram_collection.NgramCollection class method) from_tree_collection() (rxnutils.routes.retro_bleu.ngram_collection.NgramCollection class method)

G

generate_coreagent() (rxnutils.chem.reaction.ChemicalReaction method) generate_reaction_template() (rxnutils.chem.reaction.ChemicalReaction method) generate_rinchi() (in module rxnutils.chem.rinchi.rinchi_api)

get_mol_weight() (in module rxnutils.chem.utils) get_special_groups() (in module rxnutils.chem.utils) get_symmetric_sites() (in module rxnutils.chem.utils)

H

has_atom_mapping() (in module rxnutils.chem.utils) has_partial_mapping() (rxnutils.chem.reaction.ChemicalReaction method) hash_from_bits() (rxnutils.chem.template.ReactionTemplate method) hash_from_smarts() (rxnutils.chem.template.ReactionTemplate method) (rxnutils.chem.template.TemplateMolecule method)

hash_from_smiles() (rxnutils.chem.template.ReactionTemplate method) (rxnutils.chem.template.TemplateMolecule method) hashed_rid (rxnutils.chem.reaction.ChemicalReaction property) HasStereoInfo (class in rxnutils.pipeline.actions.reaction_props) HasUnmappedRadicalAtom (class in rxnutils.pipeline.actions.reaction_props) HasUnsanitizableReactants (class in rxnutils.pipeline.actions.reaction_props)

I

image() (rxnutils.routes.base.SynthesisRoute method) in_column (rxnutils.pipeline.actions.reaction_mod.AtomMapTagDisconnectionSite attribute) (rxnutils.pipeline.actions.reaction_mod.ConvertAtomMapDisconnectionTag attribute) (rxnutils.pipeline.actions.reaction_mod.DesaltMolecules attribute) (rxnutils.pipeline.actions.reaction_mod.InvertStereo attribute) (rxnutils.pipeline.actions.reaction_mod.IsotopeInfo attribute) (rxnutils.pipeline.actions.reaction_mod.NameRxn attribute) (rxnutils.pipeline.actions.reaction_mod.NeutralizeMolecules attribute) (rxnutils.pipeline.actions.reaction_mod.RDKitRxnRoles attribute) (rxnutils.pipeline.actions.reaction_mod.ReactantsToReagents attribute) (rxnutils.pipeline.actions.reaction_mod.ReagentsToReactants attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveAtomMapping attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveExtraAtomMapping attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveStereoInfo attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveUnchangedProducts attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveUnsanitizable attribute) (rxnutils.pipeline.actions.reaction_mod.RxnMapper attribute) (rxnutils.pipeline.actions.reaction_mod.SplitReaction attribute) (rxnutils.pipeline.actions.reaction_mod.TrimRxnSmiles attribute) (rxnutils.pipeline.actions.reaction_props.CgrCreated attribute) (rxnutils.pipeline.actions.reaction_props.CgrNumberOfDynamicBonds attribute) (rxnutils.pipeline.actions.reaction_props.CountComponents attribute) (rxnutils.pipeline.actions.reaction_props.CountElements attribute) (rxnutils.pipeline.actions.reaction_props.HasStereoInfo attribute) (rxnutils.pipeline.actions.reaction_props.HasUnmappedRadicalAtom attribute) (rxnutils.pipeline.actions.reaction_props.MaxRingNumber attribute) (rxnutils.pipeline.actions.reaction_props.ProductAtomMappingStats attribute) (rxnutils.pipeline.actions.reaction_props.ProductSize attribute) (rxnutils.pipeline.actions.reaction_props.PseudoReactionHash attribute) (rxnutils.pipeline.actions.reaction_props.PseudoSmilesHash attribute) (rxnutils.pipeline.actions.reaction_props.ReactantProductAtomBalance attribute) (rxnutils.pipeline.actions.reaction_props.ReactantSize attribute) (rxnutils.pipeline.actions.reaction_props.RingBondMade attribute) (rxnutils.pipeline.actions.reaction_props.RingMadeSize attribute) (rxnutils.pipeline.actions.reaction_props.RingNumberChange attribute) (rxnutils.pipeline.actions.reaction_props.SmilesLength attribute) (rxnutils.pipeline.actions.reaction_props.SmilesSanitizable attribute) (rxnutils.pipeline.actions.reaction_props.StereoCenterInReactantPotential attribute) (rxnutils.pipeline.actions.reaction_props.StereoCenterIsCreated attribute) (rxnutils.pipeline.actions.reaction_props.StereoCenterIsRemoved attribute) (rxnutils.pipeline.actions.reaction_props.StereoCenterOutsideReaction attribute) (rxnutils.pipeline.actions.reaction_props.StereoCentreChanges attribute) (rxnutils.pipeline.actions.reaction_props.StereoHasChiralReagent attribute) (rxnutils.pipeline.actions.reaction_props.StereoInvention attribute) (rxnutils.pipeline.actions.reaction_props.StereoMesoProduct attribute) (rxnutils.pipeline.actions.templates.CountTemplateComponents attribute)

in_columns (rxnutils.pipeline.actions.dataframe_mod.RenameColumns attribute) (rxnutils.pipeline.actions.dataframe_mod.StackColumns attribute) indicator_columns (rxnutils.pipeline.actions.dataframe_mod.DropRows attribute) info (rxnutils.routes.ted.reactiontree.ReactionTreeWrapper property) intermediate_counts() (rxnutils.routes.base.SynthesisRoute method) intermediates() (rxnutils.routes.base.SynthesisRoute method) InvertStereo (class in rxnutils.pipeline.actions.reaction_mod) is_complete() (rxnutils.chem.reaction.ChemicalReaction method) is_fuzzy() (rxnutils.chem.reaction.ChemicalReaction method) is_solved() (rxnutils.routes.base.SynthesisRoute method) is_valid_mol() (in module rxnutils.chem.utils) isotope_column (rxnutils.pipeline.actions.reaction_mod.IsotopeInfo attribute) IsotopeInfo (class in rxnutils.pipeline.actions.reaction_mod)

J

join_cleaning() (rxnutils.data.ord.preparation_pipeline.OrdDataPreparationFlow method) (rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow method) join_lists() (rxnutils.pipeline.base.ReactionActionMixIn method)

join_mapping() (rxnutils.data.mapping_pipeline.RxnMappingFlow method) join_smiles() (rxnutils.pipeline.base.ReactionActionMixIn method) join_smiles_from_reaction() (in module rxnutils.chem.utils)

K

keep_something (rxnutils.pipeline.actions.reaction_mod.DesaltMolecules attribute)

KeepColumns (class in rxnutils.pipeline.actions.dataframe_mod) key_columns (rxnutils.pipeline.actions.dataframe_mod.DropDuplicates attribute)

L

leaf_counts() (rxnutils.routes.base.SynthesisRoute method)

leaves() (rxnutils.routes.base.SynthesisRoute method) list_actions() (in module rxnutils.pipeline.base)

M

main() (in module rxnutils.chem.features.rxnfp_runner) (in module rxnutils.chem.rinchi.download_rinchi) (in module rxnutils.data.mapping) (in module rxnutils.data.ord.import_ord_dataset) (in module rxnutils.data.uspto.combine) (in module rxnutils.data.uspto.download) (in module rxnutils.pipeline.runner) mapped_root_smiles (rxnutils.routes.base.SynthesisRoute property) match_regex (rxnutils.pipeline.actions.reaction_mod.IsotopeInfo attribute) MaxRingNumber (class in rxnutils.pipeline.actions.reaction_props) metadata_key (rxnutils.routes.retro_bleu.ngram_collection.NgramCollection attribute) model_config (rxnutils.routes.utils.validation.MoleculeNode attribute) (rxnutils.routes.utils.validation.ReactionNode attribute) module rxnutils rxnutils.chem rxnutils.chem.augmentation rxnutils.chem.cgr rxnutils.chem.features rxnutils.chem.features.rxnfp_runner rxnutils.chem.features.sc_score rxnutils.chem.reaction rxnutils.chem.rinchi rxnutils.chem.rinchi.download_rinchi rxnutils.chem.rinchi.rinchi_api rxnutils.chem.template rxnutils.chem.utils rxnutils.data rxnutils.data.base_pipeline rxnutils.data.batch_utils rxnutils.data.mapping rxnutils.data.mapping_pipeline rxnutils.data.ord rxnutils.data.ord.import_ord_dataset rxnutils.data.ord.preparation_pipeline rxnutils.data.uspto rxnutils.data.uspto.combine rxnutils.data.uspto.download rxnutils.data.uspto.preparation_pipeline rxnutils.data.uspto.uspto_yield rxnutils.pipeline rxnutils.pipeline.actions rxnutils.pipeline.actions.dataframe_mod rxnutils.pipeline.actions.reaction_mod rxnutils.pipeline.actions.reaction_props rxnutils.pipeline.actions.templates rxnutils.pipeline.base rxnutils.pipeline.runner rxnutils.routes rxnutils.routes.base rxnutils.routes.comparison rxnutils.routes.deepset rxnutils.routes.deepset.featurizers rxnutils.routes.deepset.scoring rxnutils.routes.image rxnutils.routes.readers rxnutils.routes.retro_bleu rxnutils.routes.retro_bleu.ngram_collection rxnutils.routes.retro_bleu.scoring rxnutils.routes.scoring rxnutils.routes.ted rxnutils.routes.ted.distances_calculator rxnutils.routes.ted.reactiontree rxnutils.routes.ted.utils rxnutils.routes.utils rxnutils.routes.utils.validation

molecule_to_image() (in module rxnutils.routes.image) MoleculeNode (class in rxnutils.routes.utils.validation) MOLECULES (rxnutils.routes.ted.utils.TreeContent attribute) molecules_to_images() (in module rxnutils.routes.image)

N

NameRxn (class in rxnutils.pipeline.actions.reaction_mod) nbatches (rxnutils.data.base_pipeline.DataBaseFlow attribute) neutralize_molecules() (in module rxnutils.chem.utils) NeutralizeMolecules (class in rxnutils.pipeline.actions.reaction_mod) ngram_overlap_score() (in module rxnutils.routes.retro_bleu.scoring) NgramCollection (class in rxnutils.routes.retro_bleu.ngram_collection) ngrams (rxnutils.routes.retro_bleu.ngram_collection.NgramCollection attribute) nitems (rxnutils.routes.retro_bleu.ngram_collection.NgramCollection attribute) nlines() (in module rxnutils.data.batch_utils) nm_rxn_column (rxnutils.pipeline.actions.reaction_mod.NameRxn attribute) nmapped_products_column (rxnutils.pipeline.actions.reaction_props.CountComponents attribute) nmapped_reactants_column (rxnutils.pipeline.actions.reaction_props.CountComponents attribute)

nmapped_reagents_column (rxnutils.pipeline.actions.reaction_props.CountComponents attribute) nmc_column (rxnutils.pipeline.actions.reaction_mod.NameRxn attribute) no_change() (rxnutils.chem.reaction.ChemicalReaction method) no_reagents (rxnutils.pipeline.actions.reaction_props.PseudoReactionHash attribute) noutcomes_column (rxnutils.pipeline.actions.templates.RetroTemplateReproduction attribute) nproducts_column (rxnutils.pipeline.actions.reaction_props.CountComponents attribute) (rxnutils.pipeline.actions.templates.CountTemplateComponents attribute) nreactants_column (rxnutils.pipeline.actions.reaction_props.CountComponents attribute) (rxnutils.pipeline.actions.templates.CountTemplateComponents attribute) nreagents_column (rxnutils.pipeline.actions.reaction_props.CountComponents attribute) (rxnutils.pipeline.actions.templates.CountTemplateComponents attribute) nsteps (rxnutils.routes.base.SynthesisRoute property)

O

options (rxnutils.pipeline.actions.reaction_mod.NameRxn attribute) ord_data (rxnutils.data.ord.preparation_pipeline.OrdDataPreparationFlow attribute) OrdDataPreparationFlow (class in rxnutils.data.ord.preparation_pipeline) other_reactants_column (rxnutils.pipeline.actions.templates.RetroTemplateReproduction attribute) out_column (rxnutils.data.uspto.uspto_yield.UsptoYieldCuration attribute) (rxnutils.pipeline.actions.dataframe_mod.StackColumns attribute) (rxnutils.pipeline.actions.reaction_mod.AtomMapTagDisconnectionSite attribute) (rxnutils.pipeline.actions.reaction_mod.DesaltMolecules attribute) (rxnutils.pipeline.actions.reaction_mod.InvertStereo attribute) (rxnutils.pipeline.actions.reaction_mod.IsotopeInfo attribute) (rxnutils.pipeline.actions.reaction_mod.NeutralizeMolecules attribute) (rxnutils.pipeline.actions.reaction_mod.RDKitRxnRoles attribute) (rxnutils.pipeline.actions.reaction_mod.ReactantsToReagents attribute) (rxnutils.pipeline.actions.reaction_mod.ReagentsToReactants attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveAtomMapping attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveExtraAtomMapping attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveStereoInfo attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveUnchangedProducts attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveUnsanitizable attribute) (rxnutils.pipeline.actions.reaction_mod.RxnMapper attribute) (rxnutils.pipeline.actions.reaction_mod.TrimRxnSmiles attribute) (rxnutils.pipeline.actions.reaction_props.CgrCreated attribute) (rxnutils.pipeline.actions.reaction_props.CgrNumberOfDynamicBonds attribute) (rxnutils.pipeline.actions.reaction_props.CountElements attribute) (rxnutils.pipeline.actions.reaction_props.HasStereoInfo attribute) (rxnutils.pipeline.actions.reaction_props.HasUnmappedRadicalAtom attribute) (rxnutils.pipeline.actions.reaction_props.HasUnsanitizableReactants attribute) (rxnutils.pipeline.actions.reaction_props.MaxRingNumber attribute) (rxnutils.pipeline.actions.reaction_props.ProductSize attribute) (rxnutils.pipeline.actions.reaction_props.PseudoReactionHash attribute) (rxnutils.pipeline.actions.reaction_props.PseudoSmilesHash attribute) (rxnutils.pipeline.actions.reaction_props.ReactantProductAtomBalance attribute) (rxnutils.pipeline.actions.reaction_props.ReactantSize attribute) (rxnutils.pipeline.actions.reaction_props.RingBondMade attribute) (rxnutils.pipeline.actions.reaction_props.RingMadeSize attribute) (rxnutils.pipeline.actions.reaction_props.RingNumberChange attribute) (rxnutils.pipeline.actions.reaction_props.SmilesLength attribute) (rxnutils.pipeline.actions.reaction_props.SmilesSanitizable attribute) (rxnutils.pipeline.actions.reaction_props.StereoCenterInReactantPotential attribute) (rxnutils.pipeline.actions.reaction_props.StereoCenterIsCreated attribute) (rxnutils.pipeline.actions.reaction_props.StereoCenterIsRemoved attribute) (rxnutils.pipeline.actions.reaction_props.StereoCenterOutsideReaction attribute) (rxnutils.pipeline.actions.reaction_props.StereoCentreChanges attribute) (rxnutils.pipeline.actions.reaction_props.StereoHasChiralReagent attribute) (rxnutils.pipeline.actions.reaction_props.StereoInvention attribute) (rxnutils.pipeline.actions.reaction_props.StereoMesoProduct attribute)

out_column_reconstructed (rxnutils.pipeline.actions.reaction_mod.ConvertAtomMapDisconnectionTag attribute) out_column_tagged (rxnutils.pipeline.actions.reaction_mod.ConvertAtomMapDisconnectionTag attribute) out_columns (rxnutils.pipeline.actions.dataframe_mod.RenameColumns attribute) (rxnutils.pipeline.actions.reaction_mod.SplitReaction attribute)

P

pretty_name (rxnutils.pipeline.actions.dataframe_mod.DropColumns attribute) (rxnutils.pipeline.actions.dataframe_mod.DropDuplicates attribute) (rxnutils.pipeline.actions.dataframe_mod.DropRows attribute) (rxnutils.pipeline.actions.dataframe_mod.KeepColumns attribute) (rxnutils.pipeline.actions.dataframe_mod.QueryDataframe attribute) (rxnutils.pipeline.actions.dataframe_mod.RenameColumns attribute) (rxnutils.pipeline.actions.dataframe_mod.StackColumns attribute) (rxnutils.pipeline.actions.dataframe_mod.StackMultiColumns attribute) (rxnutils.pipeline.actions.reaction_mod.AtomMapTagDisconnectionSite attribute) (rxnutils.pipeline.actions.reaction_mod.ConvertAtomMapDisconnectionTag attribute) (rxnutils.pipeline.actions.reaction_mod.DesaltMolecules attribute) (rxnutils.pipeline.actions.reaction_mod.InvertStereo attribute) (rxnutils.pipeline.actions.reaction_mod.IsotopeInfo attribute) (rxnutils.pipeline.actions.reaction_mod.NameRxn attribute) (rxnutils.pipeline.actions.reaction_mod.NeutralizeMolecules attribute) (rxnutils.pipeline.actions.reaction_mod.RDKitRxnRoles attribute) (rxnutils.pipeline.actions.reaction_mod.ReactantsToReagents attribute) (rxnutils.pipeline.actions.reaction_mod.ReagentsToReactants attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveAtomMapping attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveExtraAtomMapping attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveStereoInfo attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveUnchangedProducts attribute) (rxnutils.pipeline.actions.reaction_mod.RemoveUnsanitizable attribute) (rxnutils.pipeline.actions.reaction_mod.RxnMapper attribute) (rxnutils.pipeline.actions.reaction_mod.SplitReaction attribute) (rxnutils.pipeline.actions.reaction_mod.TrimRxnSmiles attribute) (rxnutils.pipeline.actions.reaction_props.CgrCreated attribute) (rxnutils.pipeline.actions.reaction_props.CgrNumberOfDynamicBonds attribute) (rxnutils.pipeline.actions.reaction_props.CountComponents attribute) (rxnutils.pipeline.actions.reaction_props.CountElements attribute) (rxnutils.pipeline.actions.reaction_props.HasStereoInfo attribute) (rxnutils.pipeline.actions.reaction_props.HasUnmappedRadicalAtom attribute) (rxnutils.pipeline.actions.reaction_props.HasUnsanitizableReactants attribute) (rxnutils.pipeline.actions.reaction_props.MaxRingNumber attribute) (rxnutils.pipeline.actions.reaction_props.ProductAtomMappingStats attribute) (rxnutils.pipeline.actions.reaction_props.ProductSize attribute) (rxnutils.pipeline.actions.reaction_props.PseudoReactionHash attribute) (rxnutils.pipeline.actions.reaction_props.PseudoSmilesHash attribute) (rxnutils.pipeline.actions.reaction_props.ReactantProductAtomBalance attribute) (rxnutils.pipeline.actions.reaction_props.ReactantSize attribute) (rxnutils.pipeline.actions.reaction_props.RingBondMade attribute) (rxnutils.pipeline.actions.reaction_props.RingMadeSize attribute) (rxnutils.pipeline.actions.reaction_props.RingNumberChange attribute) (rxnutils.pipeline.actions.reaction_props.SmilesLength attribute) (rxnutils.pipeline.actions.reaction_props.SmilesSanitizable attribute) (rxnutils.pipeline.actions.reaction_props.StereoCenterInReactantPotential attribute) (rxnutils.pipeline.actions.reaction_props.StereoCenterIsCreated attribute) (rxnutils.pipeline.actions.reaction_props.StereoCenterIsRemoved attribute) (rxnutils.pipeline.actions.reaction_props.StereoCenterOutsideReaction attribute) (rxnutils.pipeline.actions.reaction_props.StereoCentreChanges attribute) (rxnutils.pipeline.actions.reaction_props.StereoHasChiralReagent attribute) (rxnutils.pipeline.actions.reaction_props.StereoInvention attribute) (rxnutils.pipeline.actions.reaction_props.StereoMesoProduct attribute) (rxnutils.pipeline.actions.templates.CountTemplateComponents attribute) (rxnutils.pipeline.actions.templates.RetroTemplateReproduction attribute)

ProductAtomMappingStats (class in rxnutils.pipeline.actions.reaction_props) products_list (rxnutils.chem.reaction.ChemicalReaction property) ProductSize (class in rxnutils.pipeline.actions.reaction_props) pseudo_rinchi (rxnutils.chem.reaction.ChemicalReaction property) pseudo_rinchi_key (rxnutils.chem.reaction.ChemicalReaction property) PseudoReactionHash (class in rxnutils.pipeline.actions.reaction_props) PseudoSmilesHash (class in rxnutils.pipeline.actions.reaction_props)

Q

query (rxnutils.pipeline.actions.dataframe_mod.QueryDataframe attribute)

QueryDataframe (class in rxnutils.pipeline.actions.dataframe_mod)

R

rdkit_validation() (rxnutils.chem.template.ReactionTemplate method) RDKitRxnRoles (class in rxnutils.pipeline.actions.reaction_mod) ReactantProductAtomBalance (class in rxnutils.pipeline.actions.reaction_props) reactants_list (rxnutils.chem.reaction.ChemicalReaction property) ReactantSize (class in rxnutils.pipeline.actions.reaction_props) ReactantsToReagents (class in rxnutils.pipeline.actions.reaction_mod) reaction_centres() (in module rxnutils.chem.utils) reaction_class_rank_score() (in module rxnutils.routes.scoring) reaction_data() (rxnutils.routes.base.SynthesisRoute method) reaction_difference_fingerprint() (in module rxnutils.routes.deepset.featurizers) reaction_ngrams() (rxnutils.routes.base.SynthesisRoute method) reaction_smiles() (rxnutils.routes.base.SynthesisRoute method) ReactionActionMixIn (class in rxnutils.pipeline.base) ReactionException ReactionNode (class in rxnutils.routes.utils.validation) REACTIONS (rxnutils.routes.ted.utils.TreeContent attribute) reactions2route() (in module rxnutils.routes.readers) ReactionTemplate (class in rxnutils.chem.template) ReactionTreeWrapper (class in rxnutils.routes.ted.reactiontree) read_aizynthcli_dataframe() (in module rxnutils.routes.readers) read_aizynthfinder_dict() (in module rxnutils.routes.readers) read_csv_batch() (in module rxnutils.data.batch_utils) read_rdf_file() (in module rxnutils.routes.readers) read_reaction_lists() (in module rxnutils.routes.readers) read_reactions_dataframe() (in module rxnutils.routes.readers) ReagentsToReactants (class in rxnutils.pipeline.actions.reaction_mod) reassign_rsmi_atom_mapping() (in module rxnutils.chem.utils) recreate_rsmi() (in module rxnutils.chem.utils) remap() (rxnutils.routes.base.SynthesisRoute method) remove_atom_mapping() (in module rxnutils.chem.utils) (rxnutils.chem.template.TemplateMolecule method) remove_atom_mapping_template() (in module rxnutils.chem.utils) remove_stereochemistry() (in module rxnutils.chem.utils) RemoveAtomMapping (class in rxnutils.pipeline.actions.reaction_mod) RemoveExtraAtomMapping (class in rxnutils.pipeline.actions.reaction_mod) RemoveStereoInfo (class in rxnutils.pipeline.actions.reaction_mod) RemoveUnchangedProducts (class in rxnutils.pipeline.actions.reaction_mod) RemoveUnsanitizable (class in rxnutils.pipeline.actions.reaction_mod) rename() (rxnutils.routes.ted.utils.AptedConfig method) RenameColumns (class in rxnutils.pipeline.actions.dataframe_mod) retro_bleu_score() (in module rxnutils.routes.retro_bleu.scoring) retro_template (rxnutils.chem.reaction.ChemicalReaction property) retro_template_generate_outcome() (rxnutils.chem.reaction.ChemicalReaction method) retro_template_selectivity() (rxnutils.chem.reaction.ChemicalReaction method) RetroTemplateReproduction (class in rxnutils.pipeline.actions.templates) rinchi (rxnutils.chem.reaction.ChemicalReaction property) rinchi_key_long (rxnutils.chem.reaction.ChemicalReaction property) rinchi_key_short (rxnutils.chem.reaction.ChemicalReaction property) RInChIError RInChIStructure (in module rxnutils.chem.rinchi.rinchi_api) RingBondMade (class in rxnutils.pipeline.actions.reaction_props) RingMadeSize (class in rxnutils.pipeline.actions.reaction_props) RingNumberChange (class in rxnutils.pipeline.actions.reaction_props) route_distances_calculator() (in module rxnutils.routes.comparison) route_ranks() (in module rxnutils.routes.scoring) route_sorter() (in module rxnutils.routes.scoring) RouteImageFactory (class in rxnutils.routes.image) rsmi_column (rxnutils.pipeline.actions.reaction_props.HasUnsanitizableReactants attribute) run_pipeline() (in module rxnutils.pipeline.runner) RxnMapper (class in rxnutils.pipeline.actions.reaction_mod) rxnmapper_command (rxnutils.pipeline.actions.reaction_mod.RxnMapper attribute) RxnMappingFlow (class in rxnutils.data.mapping_pipeline) rxnutils module rxnutils.chem module rxnutils.chem.augmentation module rxnutils.chem.cgr module rxnutils.chem.features module rxnutils.chem.features.rxnfp_runner module rxnutils.chem.features.sc_score module rxnutils.chem.reaction module rxnutils.chem.rinchi module rxnutils.chem.rinchi.download_rinchi module rxnutils.chem.rinchi.rinchi_api module

rxnutils.chem.template module rxnutils.chem.utils module rxnutils.data module rxnutils.data.base_pipeline module rxnutils.data.batch_utils module rxnutils.data.mapping module rxnutils.data.mapping_pipeline module rxnutils.data.ord module rxnutils.data.ord.import_ord_dataset module rxnutils.data.ord.preparation_pipeline module rxnutils.data.uspto module rxnutils.data.uspto.combine module rxnutils.data.uspto.download module rxnutils.data.uspto.preparation_pipeline module rxnutils.data.uspto.uspto_yield module rxnutils.pipeline module rxnutils.pipeline.actions module rxnutils.pipeline.actions.dataframe_mod module rxnutils.pipeline.actions.reaction_mod module rxnutils.pipeline.actions.reaction_props module rxnutils.pipeline.actions.templates module rxnutils.pipeline.base module rxnutils.pipeline.runner module rxnutils.routes module rxnutils.routes.base module rxnutils.routes.comparison module rxnutils.routes.deepset module rxnutils.routes.deepset.featurizers module rxnutils.routes.deepset.scoring module rxnutils.routes.image module rxnutils.routes.readers module rxnutils.routes.retro_bleu module rxnutils.routes.retro_bleu.ngram_collection module rxnutils.routes.retro_bleu.scoring module rxnutils.routes.scoring module rxnutils.routes.ted module rxnutils.routes.ted.distances_calculator module rxnutils.routes.ted.reactiontree module rxnutils.routes.ted.utils module rxnutils.routes.utils module rxnutils.routes.utils.validation module

S

same_molecule() (in module rxnutils.chem.utils) sanitization_check() (rxnutils.chem.reaction.ChemicalReaction method) sanitize() (rxnutils.chem.template.TemplateMolecule method) save_to_file() (rxnutils.routes.retro_bleu.ngram_collection.NgramCollection method) SCScore (class in rxnutils.chem.features.sc_score) setup_cleaning() (rxnutils.data.ord.preparation_pipeline.OrdDataPreparationFlow method) (rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow method) simple_bond_forming_similarity() (in module rxnutils.routes.comparison) simple_route_similarity() (in module rxnutils.routes.comparison) single_reactant_augmentation() (in module rxnutils.chem.augmentation) smiles (rxnutils.routes.utils.validation.MoleculeNode attribute) smiles2inchikey() (in module rxnutils.routes.base) smiles_column (rxnutils.pipeline.actions.templates.RetroTemplateReproduction attribute) smiles_column_index (rxnutils.pipeline.actions.reaction_mod.TrimRxnSmiles attribute) SmilesLength (class in rxnutils.pipeline.actions.reaction_props) SmilesSanitizable (class in rxnutils.pipeline.actions.reaction_props) split_lists() (rxnutils.pipeline.base.ReactionActionMixIn method) split_rsmi() (in module rxnutils.chem.utils) split_smiles() (rxnutils.pipeline.base.ReactionActionMixIn method)

split_smiles_from_reaction() (in module rxnutils.chem.utils) SplitReaction (class in rxnutils.pipeline.actions.reaction_mod) stack_columns (rxnutils.pipeline.actions.dataframe_mod.StackMultiColumns attribute) StackColumns (class in rxnutils.pipeline.actions.dataframe_mod) StackMultiColumns (class in rxnutils.pipeline.actions.dataframe_mod) StandardFingerprintFactory (class in rxnutils.routes.ted.utils) start() (rxnutils.data.mapping_pipeline.RxnMappingFlow method) (rxnutils.data.ord.preparation_pipeline.OrdDataPreparationFlow method) (rxnutils.data.uspto.preparation_pipeline.UsptoDataPreparationFlow method) stereo_changes_column (rxnutils.pipeline.actions.reaction_props.StereoCentreChanges attribute) StereoCenterInReactantPotential (class in rxnutils.pipeline.actions.reaction_props) StereoCenterIsCreated (class in rxnutils.pipeline.actions.reaction_props) StereoCenterIsRemoved (class in rxnutils.pipeline.actions.reaction_props) StereoCenterOutsideReaction (class in rxnutils.pipeline.actions.reaction_props) StereoCentreChanges (class in rxnutils.pipeline.actions.reaction_props) StereoHasChiralReagent (class in rxnutils.pipeline.actions.reaction_props) StereoInvention (class in rxnutils.pipeline.actions.reaction_props) StereoMesoProduct (class in rxnutils.pipeline.actions.reaction_props) sub_regex (rxnutils.pipeline.actions.reaction_mod.IsotopeInfo attribute) SynthesisRoute (class in rxnutils.routes.base)

T

target_columns (rxnutils.pipeline.actions.dataframe_mod.StackMultiColumns attribute) ted_distances_calculator() (in module rxnutils.routes.ted.distances_calculator) template_column (rxnutils.pipeline.actions.templates.RetroTemplateReproduction attribute) TemplateMolecule (class in rxnutils.chem.template) text_yield_column (rxnutils.data.uspto.uspto_yield.UsptoYieldCuration attribute)

total_centers (rxnutils.chem.cgr.CondensedGraphReaction property) TreeContent (class in rxnutils.routes.ted.utils) trees (rxnutils.routes.ted.reactiontree.ReactionTreeWrapper property) TrimRxnSmiles (class in rxnutils.pipeline.actions.reaction_mod) type (rxnutils.routes.utils.validation.MoleculeNode attribute) (rxnutils.routes.utils.validation.ReactionNode attribute)

U

unmapped_column (rxnutils.pipeline.actions.reaction_props.ProductAtomMappingStats attribute)

UsptoDataPreparationFlow (class in rxnutils.data.uspto.preparation_pipeline) UsptoYieldCuration (class in rxnutils.data.uspto.uspto_yield)

V

validate_dict() (in module rxnutils.routes.utils.validation)

W

widow_column (rxnutils.pipeline.actions.reaction_props.ProductAtomMappingStats attribute)