syndirella.route.CobblersWorkshop
=================================

.. py:module:: syndirella.route.CobblersWorkshop

.. autoapi-nested-parse::

   syndirella.route.CobblersWorkshop.py

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



Classes
-------

.. autoapisummary::

   syndirella.route.CobblersWorkshop.CobblersWorkshop


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

.. py:class:: 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.


   .. py:attribute:: logger


   .. py:attribute:: route_uuid
      :type:  str


   .. py:attribute:: product
      :type:  str


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


   .. py:attribute:: reactants
      :type:  List[Tuple[str]]


   .. py:attribute:: reaction_names
      :type:  List[str]


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


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


   .. py:attribute:: num_steps
      :type:  int


   .. py:attribute:: output_dir
      :type:  str


   .. py:attribute:: filter
      :type:  bool


   .. py:attribute:: atoms_ids_expansion
      :type:  dict
      :value: None



   .. py:attribute:: cobbler_benches
      :type:  List[syndirella.route.CobblerBench.CobblerBench]
      :value: []



   .. py:attribute:: first_library
      :type:  syndirella.route.Library.Library
      :value: None



   .. py:attribute:: final_library
      :type:  syndirella.route.Library.Library
      :value: None



   .. py:method:: check_product(product: str) -> str

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



   .. py:method:: 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.



   .. py:method:: check_reaction_names(reaction_names: List[str]) -> List[str]

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



   .. py:method:: get_cobbler_bench(step: int) -> syndirella.route.CobblerBench.CobblerBench

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



   .. py:method:: define_reaction()

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



   .. py:method:: 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',)), ...),...]



   .. py:method:: 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.



   .. py:method:: 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.



   .. py:method:: log_route()

      This function is used to log the route.



   .. py:method:: get_final_library()

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