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

.. py:module:: polymerist.smileslib

.. autoapi-nested-parse::

   General-purpose utilities related to SMILES and SMARTS string manipulations



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/polymerist/smileslib/chemdbqueries/index
   /autoapi/polymerist/smileslib/cleanup/index
   /autoapi/polymerist/smileslib/functgroups/index
   /autoapi/polymerist/smileslib/primitives/index
   /autoapi/polymerist/smileslib/special/index


Attributes
----------

.. autoapisummary::

   polymerist.smileslib.Smiles
   polymerist.smileslib.Smarts


Exceptions
----------

.. autoapisummary::

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


Functions
---------

.. autoapisummary::

   polymerist.smileslib.is_valid_SMILES
   polymerist.smileslib.is_valid_SMARTS
   polymerist.smileslib.canonical_SMILES_from_mol
   polymerist.smileslib.expanded_SMILES


Package Contents
----------------

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


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

   Check if SMARTS string is valid (according to RDKit)


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


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