polymerist.polymers.smidgelib.smidgeread
========================================

.. py:module:: polymerist.polymers.smidgelib.smidgeread

.. autoapi-nested-parse::

   Automata for reading SMIDGE strings into their graph representations



Attributes
----------

.. autoapisummary::

   polymerist.polymers.smidgelib.smidgeread.LOGGER


Classes
-------

.. autoapisummary::

   polymerist.polymers.smidgelib.smidgeread.SMIDGEReaderRegister
   polymerist.polymers.smidgelib.smidgeread.SMIDGEReadState
   polymerist.polymers.smidgelib.smidgeread.Accumulate
   polymerist.polymers.smidgelib.smidgeread.ChainNew
   polymerist.polymers.smidgelib.smidgeread.MonomerStart
   polymerist.polymers.smidgelib.smidgeread.MonomerEnd
   polymerist.polymers.smidgelib.smidgeread.BondStart
   polymerist.polymers.smidgelib.smidgeread.BondEnd
   polymerist.polymers.smidgelib.smidgeread.BranchStart
   polymerist.polymers.smidgelib.smidgeread.BranchEnd
   polymerist.polymers.smidgelib.smidgeread.SMIDGEReader


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

.. py:data:: LOGGER

.. py:class:: SMIDGEReaderRegister

   Information accessed by machine states during the SMIDGE writing process


   .. py:attribute:: monograph
      :type:  Optional[polymerist.polymers.monographs.MonomerGraph]


   .. py:attribute:: bond_info
      :type:  polymerist.polymers.smidgelib.MonomerGraphBondInfo


   .. py:attribute:: curr_token
      :type:  str
      :value: ''



   .. py:attribute:: node_idx
      :type:  int
      :value: 0



   .. py:attribute:: str_buffer
      :type:  str
      :value: ''



   .. py:attribute:: node_stack
      :type:  list[int]
      :value: []



.. py:class:: SMIDGEReadState

   Bases: :py:obj:`abc.ABC`


   Abstract based for reading MID graphs from SMIDGE strings


   .. py:method:: state_action(register: SMIDGEReaderRegister) -> None
      :abstractmethod:



   .. py:method:: transition(register: SMIDGEReaderRegister) -> SMIDGEReadState

      Define which states should follow the current one based on input



.. py:class:: Accumulate

   Bases: :py:obj:`SMIDGEReadState`


   Collect characters into a buffer


   .. py:method:: state_action(register: SMIDGEReaderRegister) -> None


.. py:class:: ChainNew

   Bases: :py:obj:`SMIDGEReadState`


   Reset actions when beginning a new chain


   .. py:method:: state_action(register: SMIDGEReaderRegister) -> None


.. py:class:: MonomerStart

   Bases: :py:obj:`SMIDGEReadState`


   Begin reading in a new monomer


   .. py:method:: state_action(register: SMIDGEReaderRegister) -> None


.. py:class:: MonomerEnd

   Bases: :py:obj:`SMIDGEReadState`


   Finish reading a monomer and add it to the graph


   .. py:method:: state_action(register: SMIDGEReaderRegister) -> None


.. py:class:: BondStart

   Bases: :py:obj:`SMIDGEReadState`


   Initialize reading of a bond token


   .. py:method:: state_action(register: SMIDGEReaderRegister) -> None


.. py:class:: BondEnd

   Bases: :py:obj:`SMIDGEReadState`


   Abstract based for reading MID graphs from SMIDGE strings


   .. py:method:: state_action(register: SMIDGEReaderRegister) -> None


.. py:class:: BranchStart

   Bases: :py:obj:`SMIDGEReadState`


   Mark position of branch point in stack for backtrack


   .. py:method:: state_action(register: SMIDGEReaderRegister) -> None


.. py:class:: BranchEnd

   Bases: :py:obj:`SMIDGEReadState`


   Return to previous branch point


   .. py:method:: state_action(register: SMIDGEReaderRegister) -> None


.. py:class:: SMIDGEReader

   Pushdown automaton for translating SMIDGE strings to and from monomer graphs


   .. py:attribute:: state
      :type:  SMIDGEReadState


   .. py:method:: read_smidge(smidge_string: str, start_node_idx: int = 0) -> polymerist.polymers.monographs.MonomerGraph

      Parse a SMIDGE ("SMILES-like Monomer Interconnectivity & Degree Graph Encoding") string and read it into a networkX Graph