Mol

Class for handling SMILES strings and RDKit mol objects.

MoleculeRecord(smiles, identifier='')

Enhanced class for managing SMILES strings and RDKit mol objects.

Handles all molecule-related operations including validation, conversion, neutralization, and hydrogen management.

Initialize a MoleculeRecord.

PARAMETER	DESCRIPTION
smiles	SMILES string representation of the molecule TYPE: str
identifier	Optional unique identifier for the molecule TYPE: str DEFAULT: ''

RAISES	DESCRIPTION
ValueError	If smiles is not a valid string

identifier = identifier

Unique identifier for molecule

mol

Get the RDKit mol object, creating it if necessary.

smiles = smiles

Current SMILES after any processing

smiles_original = smiles

Original SMILES used to initialize this MoleculeRecord

__eq__(other)

Check equality based on canonical SMILES.

__hash__()

Hash based on canonical SMILES.

__repr__()

Detailed string representation of the molecule.

__str__()

String representation of the molecule.

add_hydrogens(mol)

Add explicit hydrogens to a molecule.

PARAMETER	DESCRIPTION
mol	RDKit mol object TYPE: Mol

RETURNS	DESCRIPTION
Mol | None	Mol object with explicit hydrogens or None if failed

copy()

Create a deep copy of this MoleculeRecord.

RETURNS	DESCRIPTION
MoleculeRecord	New MoleculeRecord instance

get_atom_count()

Get the number of atoms in the molecule.

RETURNS	DESCRIPTION
int	Number of atoms, or 0 if mol is invalid

get_canonical_smiles(isomeric=True)

Get canonical SMILES representation.

PARAMETER	DESCRIPTION
isomeric	Whether to include stereochemistry information TYPE: bool DEFAULT: True

RETURNS	DESCRIPTION
str | None	Canonical SMILES string or None if conversion fails

get_heavy_atom_count()

Get the number of heavy (non-hydrogen) atoms in the molecule.

RETURNS	DESCRIPTION
int	Number of heavy atoms, or 0 if mol is invalid

get_neutralized(smiles)

get_substructure_matches(pattern)

Get all matches of a substructure pattern.

PARAMETER	DESCRIPTION
pattern	SMARTS string or RDKit mol object to search for TYPE: str | Mol

RETURNS	DESCRIPTION
list[tuple[int, ...]]	List of tuples containing atom indices for each match

has_substructure(pattern)

Check if molecule contains a specific substructure.

PARAMETER	DESCRIPTION
pattern	SMARTS string or RDKit mol object to search for TYPE: str | Mol

RETURNS	DESCRIPTION
bool	True if substructure is found, False otherwise

is_atom_protected(mol, atom_idx)

Check if an atom is protected.

PARAMETER	DESCRIPTION
mol	RDKit mol object TYPE: Mol
atom_idx	Atom index to check TYPE: int

RETURNS	DESCRIPTION
bool	True if atom is protected, False otherwise

is_valid()

Check if the current SMILES represents a valid molecule.

RETURNS	DESCRIPTION
bool	True if valid, False otherwise

make_canonical(isomeric=True)

neutralize()

Neutralize the molecule using the neutralizer.

RETURNS	DESCRIPTION
	True if neutralization was successful, False otherwise

prepare_for_protonation()

Prepare molecule for protonation site detection.

RETURNS	DESCRIPTION
Mol	Prepared RDKit mol object or None if preparation fails

process_azides()

Process azide patterns in SMILES string.

PARAMETER	DESCRIPTION
smiles	Input SMILES string

RETURNS	DESCRIPTION
None	SMILES string with processed azides

protect_atoms(mol, atom_indices)

Set the protected property on specified atoms to 1.

PARAMETER	DESCRIPTION
mol	RDKit mol object TYPE: Mol
atom_indices	List of atom indices to protect TYPE: list[int]

RETURNS	DESCRIPTION
Mol	The same mol object (modified in place)

refresh_mol_from_smiles()

Refresh the mol object from current SMILES string.

RETURNS	DESCRIPTION
bool	True if successful, False otherwise

remove_hydrogens(mol)

Remove explicit hydrogens from a molecule.

PARAMETER	DESCRIPTION
mol	RDKit mol object TYPE: Mol

RETURNS	DESCRIPTION
Mol | None	Mol object without explicit hydrogens or None if failed

to_mol()

Convert current SMILES to a RDKit Mol object.

RETURNS	DESCRIPTION
Mol | None	RDKit Mol object or None if conversion fails

to_mol_silenced(smiles)

Capture RDKit stderr output and return mol object with error messages.

PARAMETER	DESCRIPTION
smiles	SMILES string to convert TYPE: str

RETURNS	DESCRIPTION
dict[str, Any]	Dictionary with 'mol' (RDKit Mol or None)

to_mol_with_hs()

Get RDKit mol object with explicit hydrogens.

RETURNS	DESCRIPTION
Mol | None	RDKit Mol object with explicit hydrogens or None if conversion fails

unprotect_atoms(mol)

Set the protected property on all atoms to 0.

PARAMETER	DESCRIPTION
mol	RDKit mol object to unprotect TYPE: Mol

RETURNS	DESCRIPTION
Mol	The same mol object (modified in place)

update_smiles_from_mol(mol=None)

Update SMILES string from RDKit mol object.

PARAMETER	DESCRIPTION
mol	Optional mol object to use. If None, uses self.mol TYPE: Mol | None DEFAULT: None

RETURNS	DESCRIPTION
bool	True if successful, False otherwise