syndirella.route.CobblerBench
=============================

.. py:module:: syndirella.route.CobblerBench

.. autoapi-nested-parse::

   syndirella.CobblerBench.py

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



Classes
-------

.. autoapisummary::

   syndirella.route.CobblerBench.CobblerBench


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

.. py:class:: 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.


   .. py:attribute:: product
      :type:  rdkit.Chem.Mol


   .. py:attribute:: reactant_smiles
      :type:  Tuple[str] | str


   .. py:attribute:: reactants
      :type:  Tuple[rdkit.Chem.Mol]


   .. py:attribute:: reaction_name
      :type:  str


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


   .. py:attribute:: smarts_handler
      :type:  syndirella.SMARTSHandler.SMARTSHandler


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


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


   .. py:attribute:: current_step
      :type:  int


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


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


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


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


   .. py:attribute:: reaction
      :type:  syndirella.route.Reaction.Reaction
      :value: None



   .. py:attribute:: library
      :value: None



   .. py:attribute:: additional_reactions
      :type:  List[Tuple[str, Tuple[str, str]]]
      :value: ()



   .. py:attribute:: logger


   .. py:method:: _make_reactant_mols(reactants) -> Tuple[rdkit.Chem.Mol]

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



   .. py:method:: check_reaction()

      This function is used to check the reaction is valid.



   .. py:method:: define_reaction()

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



   .. py:method:: get_additional_reactions() -> bool

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



   .. py:method:: find_analogues()

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