rxn.reaction_preprocessing.annotations.molecule_replacer.MoleculeReplacer

class rxn.reaction_preprocessing.annotations.molecule_replacer.MoleculeReplacer(replacements)[source]

Bases: object

Class to replace SMILES strings by their improved alternatives (for instance from the catalyst annotations).

Parameters: replacements (Mapping[str, Union[str, List[str]]]) –

__init__(replacements)[source]

Parameters: replacements (Mapping[str, Union[str, List[str]]]) – mapping between SMILES strings to replace, and what to replace them with (given as a string or list of strings). Use dots for fragment bonds!

Methods

`__init__`(replacements)	type replacements `Mapping`[`str`, `Union`[`str`, `List`[`str`]]]
`from_molecule_annotations`(molecule_annotations)	Instantiate from a list of molecule annotations.
`replace_in_reaction_equation`(reaction_equation)	Do the molecule replacements in a ReactionEquation instance.
`replace_in_reaction_smiles`(smiles[, ...])	Do the molecule replacements in a reaction SMILES.
`replace_molecule_smiles`(smiles)	Do the molecule replacements in a molecule SMILES.

classmethod from_molecule_annotations(molecule_annotations)[source]

Instantiate from a list of molecule annotations.

replace_in_reaction_equation(reaction_equation)[source]

Do the molecule replacements in a ReactionEquation instance.

replace_in_reaction_smiles(smiles, fragment_bond=None)[source]

Do the molecule replacements in a reaction SMILES.

Parameters

smiles (str) – reaction SMILES.
fragment_bond (Optional[str], default: None) – fragment bond used in the reaction SMILES.

Return type

str

replace_molecule_smiles(smiles)[source]

Do the molecule replacements in a molecule SMILES.