polymerist.smileslib.cleanup
============================

.. py:module:: polymerist.smileslib.cleanup

.. autoapi-nested-parse::

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



Attributes
----------

.. autoapisummary::

   polymerist.smileslib.cleanup.T
   polymerist.smileslib.cleanup.Smiles
   polymerist.smileslib.cleanup.Smarts


Exceptions
----------

.. autoapisummary::

   polymerist.smileslib.cleanup.InvalidChemicalLineNotation
   polymerist.smileslib.cleanup.InvalidSMILES
   polymerist.smileslib.cleanup.InvalidSMARTS
   polymerist.smileslib.cleanup.InvalidInChI


Functions
---------

.. autoapisummary::

   polymerist.smileslib.cleanup.suppress_rdkit_errors
   polymerist.smileslib.cleanup.is_valid_SMARTS
   polymerist.smileslib.cleanup.is_valid_SMILES
   polymerist.smileslib.cleanup.canonical_SMILES_from_mol
   polymerist.smileslib.cleanup.expanded_SMILES


Module Contents
---------------

.. py:data:: T

.. py:function:: suppress_rdkit_errors(func: Callable[Ellipsis, T]) -> Callable[Ellipsis, T]

   Decorator to suppress RDKit error messages during function execution


.. py:type:: Smiles
   :canonical: str


.. py:type:: Smarts
   :canonical: str


.. py:function:: is_valid_SMARTS(smarts: Smarts) -> bool

   Check if SMARTS string is valid (according to RDKit)


.. py:function:: is_valid_SMILES(smiles: Smiles) -> bool

   Check if SMARTS string is valid (according to RDKit)


.. py:exception:: InvalidChemicalLineNotation

   Bases: :py:obj:`ValueError`


   Exception raised when a malformed chemical notation string is passed somewhere


.. py:exception:: InvalidSMILES

   Bases: :py:obj:`InvalidChemicalLineNotation`


   Exception raised when a malformed SMILES string is passed somewhere


.. py:exception:: InvalidSMARTS

   Bases: :py:obj:`InvalidChemicalLineNotation`


   Exception raised when a malformed SMARTS string is passed somewhere


.. py:exception:: InvalidInChI

   Bases: :py:obj:`InvalidChemicalLineNotation`


   Exception raised when a malformed InChI string is passed somewhere


.. py:function:: 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


.. py:function:: 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