syndirella.fairy
================

.. py:module:: syndirella.fairy

.. autoapi-nested-parse::

   syndirella.fairy.py

   This module provides functions to find similar cheaper reactants, filter out
   reactants based on simple filters, fingerprint generation, and others...



Attributes
----------

.. autoapisummary::

   syndirella.fairy.logger


Functions
---------

.. autoapisummary::

   syndirella.fairy.load_reactant_filters
   syndirella.fairy.load_additional_rxn_options
   syndirella.fairy.do_i_need_alternative_route
   syndirella.fairy.find_similar_reactants
   syndirella.fairy.get_similar_reactant
   syndirella.fairy.make_similar_reactant
   syndirella.fairy.filter_molecules
   syndirella.fairy.simple_filters
   syndirella.fairy.remove_hydrogen_ions
   syndirella.fairy.remove_repeat_mols
   syndirella.fairy.remove_non_abundant_isotopes
   syndirella.fairy.remove_chirality
   syndirella.fairy.remove_chirality_from_mol
   syndirella.fairy.print_diff
   syndirella.fairy.calculate_tanimoto
   syndirella.fairy.find_reaction_by_name
   syndirella.fairy.get_morgan_fingerprint
   syndirella.fairy.generate_inchi_ID
   syndirella.fairy.check_mol_sanity


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

.. py:data:: logger

.. py:function:: load_reactant_filters() -> Dict[str, Dict[str, Any]]

.. py:function:: load_additional_rxn_options() -> List[Dict[str, str]]

.. py:function:: do_i_need_alternative_route(reaction_names: List[str], additional_rxn_options: List[Dict[str, str]]) -> bool

   Check if the reaction names need an alternative route.


.. py:function:: find_similar_reactants(reactant: syndirella.error.Chem.Mol, reaction_name: str, reactant_filters: Dict[str, Dict[str, Any]]) -> List[str] | None

   Find additional similar reactants that are cheaper as defined in the reactant_filters.


.. py:function:: get_similar_reactant(reactant: syndirella.error.Chem.Mol, reactant_filters: Dict[str, str]) -> Optional[str]

   Make similar reactant to query reactant from the reactant_filters.


.. py:function:: make_similar_reactant(reactant: syndirella.error.Chem.Mol, to_replace: str, matched_details: Dict[str, Any]) -> str

   Create a similar reactant by modifying the original reactant according to matched_details.


.. py:function:: filter_molecules(hits: List[Tuple[str, float]]) -> List[str]

   Filter out reactants and return a dictionary with SMILES strings as keys and their associated scores as values.


.. py:function:: simple_filters(mols: List[syndirella.error.Chem.Mol]) -> List[syndirella.error.Chem.Mol]

   Filter out molecules based on repeats, and non-abundant isotopes.


.. py:function:: remove_hydrogen_ions(mols: List[syndirella.error.Chem.Mol]) -> List[syndirella.error.Chem.Mol]

   Remove molecules with only hydrogen ions.


.. py:function:: remove_repeat_mols(mols: List[syndirella.error.Chem.Mol]) -> List[syndirella.error.Chem.Mol]

   Remove repeated molecules by checking for Tanimoto similarity of 1.


.. py:function:: remove_non_abundant_isotopes(mols: List[syndirella.error.Chem.Mol]) -> List[syndirella.error.Chem.Mol]

   Remove molecules with non-abundant isotopes.


.. py:function:: remove_chirality(mols: List[syndirella.error.Chem.Mol]) -> List[syndirella.error.Chem.Mol]

   Remove chirality from all molecules in the list.


.. py:function:: remove_chirality_from_mol(mol: syndirella.error.Chem.Mol) -> syndirella.error.Chem.Mol

   Remove chirality from a single molecule.


.. py:function:: print_diff(hits: List[Tuple[str, float]], valid_mols: List[syndirella.error.Chem.Mol], desc: str) -> None

   Print the difference between the original number of molecules and the number of valid molecules.


.. py:function:: calculate_tanimoto(mol1: syndirella.error.Chem.Mol, mol2: syndirella.error.Chem.Mol) -> float

.. py:function:: find_reaction_by_name(reaction_name: str, additional_rxn_options: List[Dict[str, str]]) -> Optional[Dict[str, Any]]

   Find a reaction by name in the additional_rxn_options.


.. py:function:: get_morgan_fingerprint(mol: syndirella.error.Chem.Mol) -> rdkit.Chem.rdFingerprintGenerator.MorganFP

   Get the fingerprint of a molecule.


.. py:function:: generate_inchi_ID(smiles: str | None = None, mol: syndirella.error.Chem.Mol | None = None, isomeric: bool = False) -> str | syndirella.error.MolError

   This function is used to generate a unique id for the route just using the scaffold.


.. py:function:: check_mol_sanity(mol: syndirella.error.Chem.Mol) -> syndirella.error.Chem.Mol | None

   Check if the molecule can be sanitized.