polymerist.polymers.monographs
==============================

.. py:module:: polymerist.polymers.monographs

.. autoapi-nested-parse::

   Tools for generating and manipulating monomer connectivity graphs



Attributes
----------

.. autoapisummary::

   polymerist.polymers.monographs.MonoGraph


Classes
-------

.. autoapisummary::

   polymerist.polymers.monographs.MonomerGraph
   polymerist.polymers.monographs.MonomerGraphSerializer


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

.. py:class:: MonomerGraph(incoming_graph_data=None, **attr)

   Bases: :py:obj:`networkx.Graph`


   A graph representation of the connectivity of monomer fragments in a polymer topology


   .. py:attribute:: MONOMER_NAME_ATTR
      :type:  ClassVar[str]
      :value: 'monomer_name'



   .. py:attribute:: FLAVOR_DICT_ATTR
      :type:  ClassVar[dict[int, int]]
      :value: 'neighbor_flavors'



   .. py:attribute:: BONDTYPE_ATTR
      :type:  ClassVar[str]
      :value: 'bondtype'



   .. py:method:: get_monomer_name_at_node_index(node_idx: int) -> Optional[str]

      Recover the assigned monomer name for the node at the given index



   .. py:method:: get_flavor_dict_at_node_index(node_idx: int) -> Optional[dict[int, int]]

      Recover the assigned dictionary of neighbor flavors for the node at the given index



   .. py:property:: num_monomers
      :type: int


      Number of monomer units represented in the current polymer


   .. py:property:: is_unbranched
      :type: bool


      Whether the monomer graph represents straight chain(s) without branching


   .. py:attribute:: is_linear


   .. py:property:: terminal_monomers
      :type: Generator[int, None, None]


      Generates the indices of all nodes corresponding to terminal monomers (i.e. those wiht only one outgoing bond)


   .. py:property:: num_chains
      :type: int


      The number of disconnected chains represented by the MonoGraph


   .. py:property:: chains
      :type: Generator[MonomerGraph, None, None]


      Generates all disconnected polymers chains in the graph sequentially


   .. py:property:: unique_monomer_names
      :type: set[str]


      The collection of unique monomer names embedded in the graph nodes


   .. py:method:: draw(label_monomers: bool = True, label_bonds: bool = True, **kwargs) -> None

      Visualize graph structure with NetworkX



   .. py:attribute:: visualize


   .. py:method:: insert_chemical_info(chemical_info: dict[str, dict]) -> None

      Insert SMILES, SMARTS, and atom/linker count info into nodes from minimal set of monomer info templates



   .. py:method:: from_smidge_string(smidge_string: str, start_node_idx: int = 0) -> MonomerGraph
      :classmethod:


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



   .. py:method:: to_smidge_string(start_node_idxs: Optional[Union[int, Sequence[int]]] = None) -> str

      Convert a monomer graph into a SMIDGE ("SMILES-like Monomer Interconnectivity & Degree Graph Encoding") string



.. py:data:: MonoGraph

.. py:class:: MonomerGraphSerializer

   Bases: :py:obj:`polymerist.genutils.fileutils.jsonio.serialize.TypeSerializer`


   JSON serializer for storing MonomerGraphs as SMIDGE strings


   .. py:method:: encode(python_obj: MonomerGraph) -> str
      :staticmethod:



   .. py:method:: decode(json_obj: str) -> MonomerGraph
      :staticmethod: