rxnutils package

Subpackages

• rxnutils.chem package
  • Subpackages
    • rxnutils.chem.features package
      • Submodules
      • rxnutils.chem.features.reaction_centre_fp module
      • rxnutils.chem.features.rxnfp_runner module
      • rxnutils.chem.features.sc_score module
      • rxnutils.chem.features.simple_rdkit module
      • Module contents
    • rxnutils.chem.protection package
      • Submodules
      • rxnutils.chem.protection.amino_acids module
      • Module contents
    • rxnutils.chem.rinchi package
      • Submodules
      • rxnutils.chem.rinchi.download_rinchi module
      • rxnutils.chem.rinchi.rinchi_api module
      • Module contents
  • Submodules
  • rxnutils.chem.augmentation module
    • single_reactant_augmentation()
  • rxnutils.chem.cgr module
    • CondensedGraphReaction
      • CondensedGraphReaction.bonds_broken
      • CondensedGraphReaction.bonds_changed
      • CondensedGraphReaction.bonds_formed
      • CondensedGraphReaction.total_centers
      • CondensedGraphReaction.distance_to()
  • rxnutils.chem.reaction module
    • ReactionException
    • ChemicalReaction
      • ChemicalReaction.agents_list
      • ChemicalReaction.canonical_template
      • ChemicalReaction.products_list
      • ChemicalReaction.pseudo_rinchi
      • ChemicalReaction.pseudo_rinchi_key
      • ChemicalReaction.hashed_rid
      • ChemicalReaction.reactants_list
      • ChemicalReaction.retro_template
      • ChemicalReaction.rinchi
      • ChemicalReaction.rinchi_key_long
      • ChemicalReaction.rinchi_key_short
      • ChemicalReaction.generate_coreagent()
      • ChemicalReaction.generate_reaction_template()
      • ChemicalReaction.has_partial_mapping()
      • ChemicalReaction.is_complete()
      • ChemicalReaction.no_change()
      • ChemicalReaction.is_fuzzy()
      • ChemicalReaction.sanitization_check()
      • ChemicalReaction.canonical_template_generate_outcome()
      • ChemicalReaction.retro_template_generate_outcome()
      • ChemicalReaction.retro_template_selectivity()
  • rxnutils.chem.smartslib module
    • SmartsHit
      • SmartsHit.number_of_hits
      • SmartsHit.match
      • SmartsHit.atoms
      • SmartsHit.smarts_mol
    • SmartsLibrary
      • SmartsLibrary.load()
      • SmartsLibrary.detect_reactive_functions()
      • SmartsLibrary.match_smarts()
  • rxnutils.chem.template module
    • TemplateMolecule
      • TemplateMolecule.atoms()
      • TemplateMolecule.atom_invariants()
      • TemplateMolecule.atom_properties()
      • TemplateMolecule.fingerprint_bits()
      • TemplateMolecule.fingerprint_vector()
      • TemplateMolecule.fix_atom_properties()
      • TemplateMolecule.hash_from_smiles()
      • TemplateMolecule.hash_from_smarts()
      • TemplateMolecule.remove_atom_mapping()
      • TemplateMolecule.sanitize()
    • ReactionTemplate
      • ReactionTemplate.apply()
      • ReactionTemplate.fingerprint_bits()
      • ReactionTemplate.fingerprint_vector()
      • ReactionTemplate.hash_from_bits()
      • ReactionTemplate.hash_from_smiles()
      • ReactionTemplate.hash_from_smarts()
      • ReactionTemplate.rdkit_validation()
  • rxnutils.chem.utils module
    • get_symmetric_sites()
    • get_mol_weight()
    • get_special_groups()
    • has_atom_mapping()
    • canonicalize_tautomer()
    • enumerate_tautomers()
    • is_valid_mol()
    • remove_stereochemistry()
    • remove_atom_mapping()
    • remove_atom_mapping_template()
    • neutralize_molecules()
    • desalt_molecules()
    • same_molecule()
    • atom_mapping_numbers()
    • reassign_rsmi_atom_mapping()
    • split_rsmi()
    • join_smiles_from_reaction()
    • split_smiles_from_reaction()
    • recreate_rsmi()
    • reaction_centres()
  • Module contents
• rxnutils.data package
  • Subpackages
    • rxnutils.data.ord package
      • Submodules
      • rxnutils.data.ord.import_ord_dataset module
      • rxnutils.data.ord.preparation_pipeline module
      • Module contents
    • rxnutils.data.uspto package
      • Submodules
      • rxnutils.data.uspto.combine module
      • rxnutils.data.uspto.download module
      • rxnutils.data.uspto.preparation_pipeline module
      • rxnutils.data.uspto.uspto_yield module
      • Module contents
  • Submodules
  • rxnutils.data.base_pipeline module
    • DataBaseFlow
      • DataBaseFlow.nbatches
      • DataBaseFlow.folder
    • DataPreparationBaseFlow
      • DataPreparationBaseFlow.data_prefix
  • rxnutils.data.batch_utils module
    • nlines()
    • combine_batches()
    • combine_csv_batches()
    • combine_numpy_array_batches()
    • combine_sparse_matrix_batches()
    • create_csv_batches()
    • read_csv_batch()
  • rxnutils.data.mapping module
    • main()
  • rxnutils.data.mapping_pipeline module
    • RxnMappingFlow
      • RxnMappingFlow.data_prefix
      • RxnMappingFlow.start()
      • RxnMappingFlow.do_mapping()
      • RxnMappingFlow.join_mapping()
      • RxnMappingFlow.end()
  • Module contents
• rxnutils.pipeline package
  • Subpackages
    • rxnutils.pipeline.actions package
      • Submodules
      • rxnutils.pipeline.actions.dataframe_mod module
      • rxnutils.pipeline.actions.reaction_mod module
      • rxnutils.pipeline.actions.reaction_props module
      • rxnutils.pipeline.actions.templates module
      • Module contents
  • Submodules
  • rxnutils.pipeline.base module
    • action()
    • list_actions()
    • create_action()
    • ReactionActionMixIn
      • ReactionActionMixIn.join_lists()
      • ReactionActionMixIn.join_smiles()
      • ReactionActionMixIn.split_lists()
      • ReactionActionMixIn.split_smiles()
  • rxnutils.pipeline.runner module
    • run_pipeline()
    • main()
  • Module contents
• rxnutils.routes package
  • Subpackages
    • rxnutils.routes.chemformer_feasibility package
      • Submodules
      • rxnutils.routes.chemformer_feasibility.model_interface module
      • rxnutils.routes.chemformer_feasibility.scoring module
      • Module contents
    • rxnutils.routes.deepset package
      • Submodules
      • rxnutils.routes.deepset.featurizers module
      • rxnutils.routes.deepset.scoring module
      • Module contents
    • rxnutils.routes.retro_bleu package
      • Submodules
      • rxnutils.routes.retro_bleu.ngram_collection module
      • rxnutils.routes.retro_bleu.scoring module
      • Module contents
    • rxnutils.routes.ted package
      • Submodules
      • rxnutils.routes.ted.distances_calculator module
      • rxnutils.routes.ted.reactiontree module
      • rxnutils.routes.ted.utils module
      • Module contents
    • rxnutils.routes.utils package
      • Submodules
      • rxnutils.routes.utils.validation module
      • Module contents
  • Submodules
  • rxnutils.routes.base module
    • SynthesisRoute
      • SynthesisRoute.mapped_root_smiles
      • SynthesisRoute.nsteps
      • SynthesisRoute.atom_mapped_reaction_smiles()
      • SynthesisRoute.assign_atom_mapping()
      • SynthesisRoute.chains()
      • SynthesisRoute.image()
      • SynthesisRoute.intermediate_counts()
      • SynthesisRoute.intermediates()
      • SynthesisRoute.is_solved()
      • SynthesisRoute.leaf_counts()
      • SynthesisRoute.leaves()
      • SynthesisRoute.reaction_data()
      • SynthesisRoute.reaction_ngrams()
      • SynthesisRoute.reaction_smiles()
      • SynthesisRoute.remap()
      • SynthesisRoute.update_stock()
    • smiles2inchikey()
  • rxnutils.routes.comparison module
    • simple_route_similarity()
    • atom_matching_bonanza_similarity()
    • simple_bond_forming_similarity()
    • route_distances_calculator()
  • rxnutils.routes.image module
    • molecule_to_image()
    • molecules_to_images()
    • crop_image()
    • draw_rounded_rectangle()
    • RouteImageFactory
  • rxnutils.routes.readers module
    • read_reaction_lists()
    • read_aizynthcli_dataframe()
    • read_aizynthfinder_dict()
    • read_reactions_dataframe()
    • reactions2route()
    • read_rdf_file()
  • rxnutils.routes.scoring module
    • route_sorter()
    • route_ranks()
    • badowski_route_score()
    • reaction_class_rank_score()
  • Module contents

Module contents