syndirella.route.CobblerBench

syndirella.CobblerBench.py

This module contains the CobblerBench class. One instance is made for each step.

Classes

CobblerBench

This class is used to perform the whole process of finding analogues of reactants. Since the final elaborated products

Module Contents

class syndirella.route.CobblerBench.CobblerBench(product: str, reactants: Tuple[str] | str, reaction_name: str, output_dir: str, id: str, num_steps: int, current_step: int, filter: bool, route_uuid: str, atom_diff_min: int, atom_diff_max: int)

This class is used to perform the whole process of finding analogues of reactants. Since the final elaborated products are ‘slippers’ in this analogy, the CobblerBench is where these slippers are made.

It is given a step of a full route.

product: rdkit.Chem.Mol

reactant_smiles: Tuple[str] | str

reactants: Tuple[rdkit.Chem.Mol]

reaction_name: str

output_dir: str

smarts_handler: syndirella.SMARTSHandler.SMARTSHandler

id: str

num_steps: int

current_step: int

filter: bool

route_uuid: str

atom_diff_min: int

atom_diff_max: int

reaction: syndirella.route.Reaction.Reaction = None

library = None

additional_reactions: List[Tuple[str, Tuple[str, str]]] = ()

logger

_make_reactant_mols(reactants) → Tuple[rdkit.Chem.Mol]

This function is used to make reactant molecules from the input SMILES.

check_reaction()

This function is used to check the reaction is valid.

define_reaction()

This function is used to define the reaction and finding ids and attachment atoms.

get_additional_reactions() → bool

Gets the additional reaction by outputting edited reactants via SMARTS and new reaction names all controlled by the Reaction class.

find_analogues()

This function is used to find analogues of any step along the route.