polymerist.smileslib.cleanup

Utilities for validating, cleaning, and adding information into up SMILES and SMARTS strings

Attributes

`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

`suppress_rdkit_errors`(→ Callable[Ellipsis, T])	Decorator to suppress RDKit error messages during function execution
`is_valid_SMARTS`(→ bool)	Check if SMARTS string is valid (according to RDKit)
`is_valid_SMILES`(→ 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

polymerist.smileslib.cleanup.suppress_rdkit_errors(func: Callable[Ellipsis, T]) → Callable[Ellipsis, T][source]: Decorator to suppress RDKit error messages during function execution

polymerist.smileslib.cleanup.is_valid_SMARTS(smarts: Smarts) → bool[source]: Check if SMARTS string is valid (according to RDKit)

polymerist.smileslib.cleanup.is_valid_SMILES(smiles: Smiles) → bool[source]: Check if SMARTS string is valid (according to RDKit)

exception polymerist.smileslib.cleanup.InvalidChemicalLineNotation[source]

Bases: ValueError

Exception raised when a malformed chemical notation string is passed somewhere

exception polymerist.smileslib.cleanup.InvalidSMILES[source]

Exception raised when a malformed SMILES string is passed somewhere

exception polymerist.smileslib.cleanup.InvalidSMARTS[source]

Exception raised when a malformed SMARTS string is passed somewhere

exception polymerist.smileslib.cleanup.InvalidInChI[source]

Exception raised when a malformed InChI string is passed somewhere

polymerist.smileslib.cleanup.canonical_SMILES_from_mol(mol: rdkit.Chem.Mol) → str[source]: Cast Mol to a “canonical” SMILES format Mols with identical chemical structure should produce identical strings

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