syndirella.route.CobblersWorkshop

syndirella.route.CobblersWorkshop.py

This module contains the CobblersWorkshop class. One instance of this object is used to describe a full route.

Classes

CobblersWorkshop

This is the CobblersWorkshop class. It represents a full route.

Module Contents

class syndirella.route.CobblersWorkshop.CobblersWorkshop(product: str, reactants: List[Tuple[str]], reaction_names: List[str], num_steps: int, output_dir: str, filter: bool, id: str, atom_diff_min: int, atom_diff_max: int, atoms_ids_expansion: dict = None)

This is the CobblersWorkshop class. It represents a full route.

logger

route_uuid: str

product: str

id: str

reactants: List[Tuple[str]]

reaction_names: List[str]

atom_diff_min: int

atom_diff_max: int

num_steps: int

output_dir: str

filter: bool

atoms_ids_expansion: dict = None

cobbler_benches: List[syndirella.route.CobblerBench.CobblerBench] = []

first_library: syndirella.route.Library.Library = None

final_library: syndirella.route.Library.Library = None

check_product(product: str) → str

Checks scaffold can be converted to a molecule and can be sanitized. If not, logs an error.

check_reactants(reactants: List[Tuple[str]]) → List[Tuple[str]]

Checks reactants can be converted to molecules and can be sanitized. If not, logs an error.

check_reaction_names(reaction_names: List[str]) → List[str]

Checks reaction names are valid. If not, logs an error.

get_cobbler_bench(step: int) → syndirella.route.CobblerBench.CobblerBench

This function is used to get the cobbler bench for a specific step.

define_reaction()

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

format_workshops_from_routes(routes: List[Tuple[Tuple[str, Tuple[str]], Ellipsis]])

This function is used to format workshops from the combinations of reaction names and reactants. Combinations is structured like: [((‘reaction1_name’, (‘reactant1_smiles’,’reactant2_smiles)), (‘reaction2_name’, (‘reactant2_smiles’,)), …), # first route ((‘reaction1_name’, (‘reactant1_smiles’,’reactant2_smiles)), (‘reaction2_name’, (‘reactant2_smiles’,)), …),…]

configure_additional_routes(reaction_names_to_replace: List[str]) → List

This function is used to configure the additional routes from the combination of all the cobbler benches.

get_additional_routes(edit_route: bool = True) → List | None

This function is used to get an alternative route (as a CobblersWorkshop object) if it is needed.

Args: edit_route: bool

If True, the reactants in the route will be directly edited via SMARTS. If False, an additional route containing the additional reactions specified from a Postera search will be

returned.

log_route()

This function is used to log the route.

get_final_library()

This function is used to get the final library of products. It dynamically handles any number of steps.