syndirella.route.Reaction

syndirella.route.Reaction.py

This module contains the Reaction class. One instance of this object is used to describe a single reaction.

Classes

Reaction

This class contains information about the reaction. It is used to find the atoms on the reactants involved in

Module Contents

class syndirella.route.Reaction.Reaction(product: rdkit.Chem.Mol, reactants: List[rdkit.Chem.Mol], reaction_name: str, smarts_handler: syndirella.SMARTSHandler.SMARTSHandler, route_uuid: str)

This class contains information about the reaction. It is used to find the atoms on the reactants involved in the reaction, check the reaction atoms are the ones that are supposed to be connected.

route_uuid: str

logger

scaffold: rdkit.Chem.Mol

reactants: List[rdkit.Chem.Mol]

reaction_name: str

smarts_handler: syndirella.SMARTSHandler.SMARTSHandler

reaction_pattern: rdkit.Chem.rdChemReactions

all_attach_ids: Dict[rdkit.Chem.Mol, List[int]] | None

additional_rxn_options: List[Dict[str, str]]

alt_reactions: List[Dict[str, str]] | None = []

alt_reaction() → List[Dict[str, str]] | None

This function is used to determine if an additional reaction is specified.

get_additional_reactions() → List[Tuple[str, Tuple[str, str]]] | None

This function edits the reactants to make an additional reaction.

check_reaction_can_produce_product(new_reactant: rdkit.Chem.Mol, other_reactant: rdkit.Chem.Mol, reaction_name: str) → bool

This function is used to check if the new reactants can simply produce a scaffold from the labeled reaction.

edit_reactant(reactant: Tuple[rdkit.Chem.Mol, Tuple[int], str], new_reactant_smarts: str, to_replace_smarts: str, replacement_connecting_atom_id: int) → rdkit.Chem.Mol | None

Directly edits the reactant to replace SMARTS matched atoms to new SMARTS.

_replace_carboxylic_acid_hydroxy_with_dummy(mol: rdkit.Chem.Mol) → rdkit.Chem.Mol

_replace_halide_with_dummy(mol: rdkit.Chem.Mol, atom_to_check_by_symbol=None) → rdkit.Chem.Mol

_find_attachment_id_from_dummy(reactant: rdkit.Chem.Mol, dummy_symbol='*') → Tuple[List[int], List[List[int]]]

use_fmcs(reactant: rdkit.Chem.Mol) → Dict[int, int]

find_attachment_id_for_reactant(reactant: rdkit.Chem.Mol) → List[int] | None

This function is used to find the attachment indices of a single reactant in the reaction. :param reactant: a single reactant molecule :returns a list of tuples (attachmentIdx_whole, attachmentIdx_subMol)

find_attachment_ids_for_all_reactants() → Dict[rdkit.Chem.Mol, List[int]] | None

This function is used to find the attachment indices of all reactants in the reaction. :returns a list of lists, each containing tuples of attachment indices for each reactant

format_matched_smarts_to_index(matched_reactants: Dict[str, Tuple[rdkit.Chem.Mol, List[int], str]]) → Dict[int, Tuple[rdkit.Chem.Mol, List[int], str]] | None

Formats matched smarts to reactant by using reactant index in smarts as the key.

find_reaction_atoms_for_all_reactants() → Tuple[Dict[str, Tuple[rdkit.Chem.Mol, List[int], str]] | None, Dict[int, Tuple[rdkit.Chem.Mol, List[int], str]]]

This function is used to find the reaction atoms of both reactants. And how those atoms correspond to the SMARTS pattern associated with the reaction.