Detect

This module provides functionality to detect protonation sites in molecules using substructure matching with comprehensive error handling and validation.

ProtonationSiteDetectionError

Bases: Exception

Raised when protonation site detection encounters an error.

ProtonationSiteDetector(validate_sites=True, max_sites_per_molecule=50)

Robust detector for finding protonation sites in molecules.

Uses substructure matching to identify potential protonation sites based on known pKa patterns. Handles atom protection to prevent overlapping matches.

Initialize the detector with explicit configuration.

PARAMETER	DESCRIPTION
validate_sites	Whether to validate detected sites (explicit, not default) TYPE: bool DEFAULT: True
max_sites_per_molecule	Maximum sites to detect per molecule (bounded) TYPE: int DEFAULT: 50

max_sites_per_molecule = max_sites_per_molecule

pka_data = PKaData()

validate_sites = validate_sites

find_sites(mol_record)

Find protonation sites in a molecule. This is the main entry point.

PARAMETER	DESCRIPTION
mol_record	MoleculeRecord to analyze TYPE: MoleculeRecord

RETURNS	DESCRIPTION
tuple[MoleculeRecord, list[ProtonationSite]]	Tuple of (updated_mol_record, list_of_protonation_sites)

RAISES	DESCRIPTION
ProtonationSiteDetectionError	If detection fails critically

get_stats()

Get detection statistics.

RETURNS	DESCRIPTION
dict[str, int]	Dictionary of detection statistics

reset_stats()

Reset all detection statistics to zero.

canonicalize_smiles_list(mols, original_smiles='')

Generate canonical SMILES from molecule objects.

PARAMETER	DESCRIPTION
mols	List of RDKit mol objects to convert TYPE: list[Mol]
original_smiles	Original SMILES for logging context TYPE: str DEFAULT: ''

RETURNS	DESCRIPTION
list[str]	List of unique canonical SMILES strings

find(mol_record, validate_sites=True, max_sites_per_molecule=50)

Convenience function for finding protonation sites with default settings.

PARAMETER	DESCRIPTION
mol_record	MoleculeRecord to analyze TYPE: MoleculeRecord

RETURNS	DESCRIPTION
tuple[MoleculeRecord, list[ProtonationSite]]	Tuple of (updated_mol_record, list_of_protonation_sites)