polymerist.smileslib

General-purpose utilities related to SMILES and SMARTS string manipulations

Submodules

• polymerist.smileslib.chemdbqueries
• polymerist.smileslib.cleanup
• polymerist.smileslib.functgroups
• polymerist.smileslib.primitives
• polymerist.smileslib.special

Attributes

Smiles
Smarts

Exceptions

InvalidChemicalLineNotation	Exception raised when a malformed chemical notation string is passed somewhere
InvalidSMILES	Exception raised when a malformed SMILES string is passed somewhere
InvalidSMARTS	Exception raised when a malformed SMARTS string is passed somewhere
InvalidInChI	Exception raised when a malformed InChI string is passed somewhere

Functions

is_valid_SMILES(→ bool)	Check if SMARTS string is valid (according to RDKit)
is_valid_SMARTS(→ bool)	Check if SMARTS string is valid (according to RDKit)
canonical_SMILES_from_mol(→ str)	Cast Mol to a "canonical" SMILES format
expanded_SMILES(→ str)	Expands and clarifies the chemical information contained within a passed SMILES string

Package Contents

type polymerist.smileslib.Smiles = str

polymerist.smileslib.is_valid_SMILES(smiles: Smiles) → bool

Check if SMARTS string is valid (according to RDKit)

type polymerist.smileslib.Smarts = str

polymerist.smileslib.is_valid_SMARTS(smarts: Smarts) → bool

Check if SMARTS string is valid (according to RDKit)

exception polymerist.smileslib.InvalidChemicalLineNotation

Bases: ValueError

Exception raised when a malformed chemical notation string is passed somewhere

exception polymerist.smileslib.InvalidSMILES

Bases: InvalidChemicalLineNotation

Exception raised when a malformed SMILES string is passed somewhere

exception polymerist.smileslib.InvalidSMARTS

Bases: InvalidChemicalLineNotation

Exception raised when a malformed SMARTS string is passed somewhere

exception polymerist.smileslib.InvalidInChI

Bases: InvalidChemicalLineNotation

Exception raised when a malformed InChI string is passed somewhere

polymerist.smileslib.canonical_SMILES_from_mol(mol: rdkit.Chem.Mol) → str

Cast Mol to a “canonical” SMILES format Mols with identical chemical structure should produce identical strings

polymerist.smileslib.expanded_SMILES(smiles: str, assign_map_nums: bool = True, start_from: int = 1, kekulize: bool = True, canonicalize: bool = True) → str

Expands and clarifies the chemical information contained within a passed SMILES string namely explicit hydrogens and bond orders, and (optionally) kekulized aromatic bonds and atom map numbers