polymerist.polymers.smidgelib.smidgewrite
=========================================

.. py:module:: polymerist.polymers.smidgelib.smidgewrite

.. autoapi-nested-parse::

   Automata for reading SMIDGE strings into their graph representations



Attributes
----------

.. autoapisummary::

   polymerist.polymers.smidgelib.smidgewrite.LOGGER


Classes
-------

.. autoapisummary::

   polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterRegister
   polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriterState
   polymerist.polymers.smidgelib.smidgewrite.CheckIsVisitedNode
   polymerist.polymers.smidgelib.smidgewrite.VisitNode
   polymerist.polymers.smidgelib.smidgewrite.WriteNode
   polymerist.polymers.smidgelib.smidgewrite.WriteEdge
   polymerist.polymers.smidgelib.smidgewrite.DetermineNodeSuccessors
   polymerist.polymers.smidgelib.smidgewrite.PushNodeSuccessor
   polymerist.polymers.smidgelib.smidgewrite.UpdateNodeSuccessors
   polymerist.polymers.smidgelib.smidgewrite.BranchStart
   polymerist.polymers.smidgelib.smidgewrite.BranchEnd
   polymerist.polymers.smidgelib.smidgewrite.SMIDGEWriter


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

.. py:data:: LOGGER

.. py:class:: SMIDGEWriterRegister

   Information accessed by machine states during the SMIDGE writing process


   .. py:attribute:: monograph
      :type:  polymerist.polymers.monographs.MonomerGraph


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


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



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



   .. py:attribute:: visited
      :type:  set


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



   .. py:attribute:: successors
      :type:  dict[int, list[int]]


   .. py:attribute:: predecessors
      :type:  dict[int, int]


   .. py:attribute:: finished
      :type:  bool
      :value: False



   .. py:property:: prev_idx
      :type: Optional[int]


      The index of the precursor to the currently active node


   .. py:property:: node_successors
      :type: list[int]


      The nodes which follow the current node in the DFS traversal (could be empty)


.. py:class:: SMIDGEWriterState

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


   Abstract base for automaton states used in writing MID graphs to SMIDGE strings


   .. py:method:: state_action(register: SMIDGEWriterRegister) -> SMIDGEWriterState


   .. py:method:: transition(register: SMIDGEWriterRegister) -> SMIDGEWriterState
      :abstractmethod:


      Define which states should follow the current one based on input



.. py:class:: CheckIsVisitedNode

   Bases: :py:obj:`SMIDGEWriterState`


   Read a node index off the stack and check if it has already been visited


   .. py:method:: state_action(register: SMIDGEWriterRegister) -> SMIDGEWriterState


   .. py:method:: transition(register: SMIDGEWriterRegister) -> SMIDGEWriterState

      Define which states should follow the current one based on input



.. py:class:: VisitNode

   Bases: :py:obj:`SMIDGEWriterState`


   Visit a node, check if it has predecessors, and mark it as visited


   .. py:method:: state_action(register: SMIDGEWriterRegister) -> SMIDGEWriterState


   .. py:method:: transition(register: SMIDGEWriterRegister) -> SMIDGEWriterState

      Define which states should follow the current one based on input



.. py:class:: WriteNode

   Bases: :py:obj:`SMIDGEWriterState`


   Add an entry for the current node to the output tokens


   .. py:method:: state_action(register: SMIDGEWriterRegister) -> SMIDGEWriterState


   .. py:method:: transition(register: SMIDGEWriterRegister) -> SMIDGEWriterState

      Define which states should follow the current one based on input



.. py:class:: WriteEdge

   Bases: :py:obj:`SMIDGEWriterState`


   Add an entry for the current edge to the output tokens


   .. py:method:: state_action(register: SMIDGEWriterRegister) -> SMIDGEWriterState


   .. py:method:: transition(register: SMIDGEWriterRegister) -> SMIDGEWriterState

      Define which states should follow the current one based on input



.. py:class:: DetermineNodeSuccessors

   Bases: :py:obj:`SMIDGEWriterState`


   Determine branching and next-node behavior


   .. py:method:: transition(register: SMIDGEWriterRegister) -> SMIDGEWriterState

      Define which states should follow the current one based on input



.. py:class:: PushNodeSuccessor

   Bases: :py:obj:`SMIDGEWriterState`


   Add a nodes DFS successor to the traversal stack


   .. py:method:: state_action(register: SMIDGEWriterRegister) -> SMIDGEWriterState


   .. py:method:: transition(register: SMIDGEWriterRegister) -> SMIDGEWriterState

      Define which states should follow the current one based on input



.. py:class:: UpdateNodeSuccessors

   Bases: :py:obj:`SMIDGEWriterState`


   Remove any node with no successors from the DFS traversal map


   .. py:method:: state_action(register: SMIDGEWriterRegister) -> SMIDGEWriterState


   .. py:method:: transition(register: SMIDGEWriterRegister) -> SMIDGEWriterState

      Define which states should follow the current one based on input



.. py:class:: BranchStart

   Bases: :py:obj:`SMIDGEWriterState`


   Mark position of branch point in stack for backtrack


   .. py:method:: state_action(register: SMIDGEWriterRegister) -> SMIDGEWriterState


   .. py:method:: transition(register: SMIDGEWriterRegister) -> SMIDGEWriterState

      Define which states should follow the current one based on input



.. py:class:: BranchEnd

   Bases: :py:obj:`SMIDGEWriterState`


   Mark the end of a branch


   .. py:method:: state_action(register: SMIDGEWriterRegister) -> SMIDGEWriterState


   .. py:method:: transition(register: SMIDGEWriterRegister) -> SMIDGEWriterState

      Define which states should follow the current one based on input



.. py:class:: SMIDGEWriter

   Register machine for translating SMIDGE strings to and from monomer graphs


   .. py:attribute:: state
      :type:  SMIDGEWriterState


   .. py:method:: write_smidge_connected_component(monograph: polymerist.polymers.monographs.MonomerGraph, start_node_idx: Optional[int] = None) -> polymerist.polymers.monographs.MonomerGraph

      Parse a single connected component of a monomer graph into a SMIDGE string



   .. py:method:: write_smidge(monograph: polymerist.polymers.monographs.MonomerGraph, start_node_idxs: Optional[Union[int, Sequence[int]]] = None) -> str

      Parse all connected components of a monograph into a complete SMIDGE string