syndirella.SMARTSHandler
========================

.. py:module:: syndirella.SMARTSHandler

.. autoapi-nested-parse::

   SMARTSHandler.py

   This module contains the SMARTSHandler class. This class contains information about the reaction SMARTS.



Classes
-------

.. autoapisummary::

   syndirella.SMARTSHandler.SMARTSHandler


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

.. py:class:: SMARTSHandler(rxn_smirks_path: str = None)

   .. py:attribute:: reaction_smarts


   .. py:attribute:: reactant1_dict


   .. py:attribute:: reactant2_dict


   .. py:attribute:: product_smarts


   .. py:attribute:: n_reactants_per_reaction


   .. py:attribute:: pattern_products


   .. py:attribute:: pattern_reactant1


   .. py:attribute:: pattern_reactant2


   .. py:attribute:: matched_reactants
      :value: None



   .. py:attribute:: found_1
      :value: None



   .. py:attribute:: found_2
      :value: None



   .. py:attribute:: logger


   .. py:method:: fromReactionFullNameToReactantName(reactionName, reactantNum)


   .. py:method:: fromReactantNameToReactionFullName(reactantName)


   .. py:method:: from_SMARTS_to_patterns(smarts_dict)


   .. py:method:: assign_reactants_w_rxn_smarts(product: rdkit.Chem.Mol, reactant_attach_ids: Dict[rdkit.Chem.Mol, List[Tuple[int, int]]], reaction_name: str) -> dict[str, tuple[rdkit.Chem.Mol, list[int], str]] | None | dict[Any | None, None]

      This function is used to assign the reactant number to input reactants using the reaction SMARTS. For now it
      only supports bimolecular reactions.



   .. py:method:: seperate_matching_reactants(r1: rdkit.Chem.Mol, r2: rdkit.Chem.Mol, found_1: Dict[str, bool], found_2: Dict[str, bool], patt1: str, patt2: str) -> Dict[str, Tuple[rdkit.Chem.Mol, List[int], str]]

      This function is used to fix edge cases:
      - to separate reactants that match both reactant SMARTS.
      - one reactant matches both reactant SMARTS.

      These found_1 and found_2 dictionaries are a bit confusing:
      Key: 'r1' or 'r2'
      Value: False if no match, List of atom indices within reactant that match the SMARTS of that reactant.



   .. py:method:: check_found_reactants(product: rdkit.Chem.Mol, found_1: Dict[str, bool], found_2: Dict[str, bool], reaction_name: str, r1: rdkit.Chem.Mol, r2: rdkit.Chem.Mol) -> bool

      This function checks that both reactants have been found. It raises a warning if both reactants are matched
      to the same reactant SMARTS.

      Returns False when both reactants match both reactant SMARTS.



   .. py:method:: find_matching_atoms(reactant: rdkit.Chem.Mol, patt1: str, patt2: str, attachment_idx: set) -> Dict[str, Tuple[int] | bool]

      This function finds the matched atoms in a reactant against both reactant SMARTS.



   .. py:method:: format_matched_reactant_for_one(reactant_mol: rdkit.Chem.Mol, attach_ids: List[Tuple[int, int]], patt: str) -> Dict[str, Tuple[rdkit.Chem.Mol, List[int], str]]

      Formats matched reactants for one reactant.