syndirella.Cobbler

syndirella.cobbler.Cobbler.py

This module contains the Cobbler class. It is used to perform retrosynthetic analysis of the scaffold compound. It handles Postera searches, including multiple elaboration searches.

Classes

Cobbler

A single cobbler represents 1 scaffold compound design. It can contain multiple routes (CobblerWorkshop objects).

Module Contents

class syndirella.Cobbler.Cobbler(scaffold_compound: str, output_dir: str, atom_diff_min: int, atom_diff_max: int)

A single cobbler represents 1 scaffold compound design. It can contain multiple routes (CobblerWorkshop objects).

scaffold_compound: str

id: str

atom_diff_min: int

atom_diff_max: int

url = 'https://api.postera.ai'

api_key

reaction_names

n_reactants_per_reaction

output_dir

logger

get_routes() → List[syndirella.route.CobblersWorkshop.CobblersWorkshop]

This function is used to get the routes for the scaffold compound. Main function that is called.

get_route(routes: List[Dict[str, List[Dict[str, str]]]]) → syndirella.route.CobblersWorkshop.CobblersWorkshop

From Postera routes, choose the route, then create the cobblers workshop.

create_cobblers_workshop_from_Postera(route: List[Dict]) → syndirella.route.CobblersWorkshop.CobblersWorkshop

Creates a cobblers workshop from a route.

get_passing_routes(routes: List[Dict[str, List[Dict[str, str]]]]) → List[List[Dict]]

Gets the passing routes from the routes based on their reaction names are in the allowed list.

filter_routes(routes: List[List[Dict]]) → List[List[Dict]]

Filters routes that contain reactants with a single atom, or an intramolecular reaction that is coded as two reactants.

choose_route(routes: List[Dict[str, List[Dict[str, str]]]]) → List[Dict]

Gets first route from List if all the reaction names are allowed and if doesn’t contain a single atom as reactant.

_print_route(reaction_names: List[str], reactants: List[str], product: str)

This function is used to print the route.

save()

Pickle cobbler object, so it can be read later.