Reactions and SOMs

gloryxr.reactions

Core chemical reaction processing engine for GLORYxR.

This module handles both abstract reaction management and concrete reaction generation.

class gloryxr.reactions.Reactor(strict_soms: bool = False)

Core chemical reaction processing engine for GLORYxR.

This class manages abstract reactions and provides methods to generate concrete reactions from input molecules.

Parameters:

strict_soms – Whether to use strict SOM validation

react_one(mol: Mol) → list[ChemicalReaction]

Applies abstract reactions to a molecule to generate concrete reactions.

Parameters:

mol – RDKit molecule object

Returns:

List of concrete reactions with SOM annotations

gloryxr.som

Functions to annotate the educt molecule with SOM indices.

gloryxr.som.annotate_educt_and_product_inplace(educt: Mol, product: Mol, strict_soms: bool = False) → None

Annotate the educt and product molecules with SOM indices.