syndirella.Cobbler
==================

.. py:module:: syndirella.Cobbler

.. autoapi-nested-parse::

   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
-------

.. autoapisummary::

   syndirella.Cobbler.Cobbler


Module Contents
---------------

.. py:class:: 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).


   .. py:attribute:: scaffold_compound
      :type:  str


   .. py:attribute:: id
      :type:  str


   .. py:attribute:: atom_diff_min
      :type:  int


   .. py:attribute:: atom_diff_max
      :type:  int


   .. py:attribute:: url
      :value: 'https://api.postera.ai'



   .. py:attribute:: api_key


   .. py:attribute:: reaction_names


   .. py:attribute:: n_reactants_per_reaction


   .. py:attribute:: output_dir


   .. py:attribute:: logger


   .. py:method:: get_routes() -> List[syndirella.route.CobblersWorkshop.CobblersWorkshop]

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



   .. py:method:: 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.



   .. py:method:: create_cobblers_workshop_from_Postera(route: List[Dict]) -> syndirella.route.CobblersWorkshop.CobblersWorkshop

      Creates a cobblers workshop from a route.



   .. py:method:: 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.



   .. py:method:: 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.



   .. py:method:: 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.



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

      This function is used to print the route.



   .. py:method:: save()

      Pickle cobbler object, so it can be read later.