booldog.io.sbml
===============

.. py:module:: booldog.io.sbml

.. autoapi-nested-parse::

   Read-write SBML-qual files

   .. rubric:: Notes

   SBML-qual code is inspired by:

   * loadSBML.R of BoolNet (January 2024)
       https://github.com/cran/BoolNet/blob/af3a714c5bfa72ee7507db9c4eaf90ba2cd91809/R/loadSBML.R
   * sbmlqual.py of CellNOpt (January 2024)
       https://github.com/cellnopt/cellnopt/blob/319c956e890ed7ae88c8e6e540de7061acfaae00/cno/io/sbmlqual.py



Attributes
----------

.. autoapisummary::

   booldog.io.sbml._SBML_AVAILABLE
   booldog.io.sbml.logger
   booldog.io.sbml.SBML_INT_MAX
   booldog.io.sbml.TOKEN_REGEX


Exceptions
----------

.. autoapisummary::

   booldog.io.sbml.BoolDogSBMLException


Classes
-------

.. autoapisummary::

   booldog.io.sbml.SBMLQualReader
   booldog.io.sbml.TransitionParser
   booldog.io.sbml.MathMLParser
   booldog.io.sbml.SBMLQualWriter


Functions
---------

.. autoapisummary::

   booldog.io.sbml.read_sbmlqual
   booldog.io.sbml.write_sbmlqual


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

.. py:data:: _SBML_AVAILABLE
   :value: True


.. py:data:: logger

.. py:data:: SBML_INT_MAX
   :value: 2147483647


.. py:data:: TOKEN_REGEX

.. py:exception:: BoolDogSBMLException

   Bases: :py:obj:`Exception`


   Custom Exception for SBML parsing


.. py:class:: SBMLQualReader(file)

   .. py:attribute:: file


   .. py:attribute:: document


   .. py:attribute:: model


   .. py:attribute:: model_id


   .. py:attribute:: plugin


   .. py:attribute:: all_species


   .. py:attribute:: species_names


   .. py:attribute:: transitions


   .. py:attribute:: rules


   .. py:method:: _get_qual_plugin()


   .. py:method:: _get_all_species()


   .. py:method:: _get_all_transitions()


   .. py:method:: _get_all_rules()


   .. py:method:: to_bnet()

      Converts the SBML-qual file to a bnet format.

      :returns: **bnet** -- bnet representation of the Boolean network.
      :rtype: str



.. py:class:: TransitionParser

   Parse SBML transition to bnet format


   .. py:method:: parse_io(transition, all_species)
      :staticmethod:


      Extract transition inputs and outputs.

      :param transition: Transition specifying the logical rule associated with the
                         Transition outputs.
      :type transition: libsbml::Transition
      :param all_species: List ids of all species present in model
      :type all_species: list

      :returns: * **inputs** (*dict*) -- Dictionary of id: species information for this transition's inputs
                * **outputs** (*list*) -- List of this transition's outputs (dependents)



   .. py:method:: parse_function(transition, all_species, inputs)
      :staticmethod:


      Parse transition function to a logical rule.

      :param transition: Transition specifying the logical rule associated with the
                         Transition outputs.
      :type transition: libsbml::Transition
      :param all_species: List ids of all species present in model
      :type all_species: list
      :param inputs: Dictionary of id: species information for this transition's inputs
      :type inputs: dict

      :returns: **logic_rule** -- Logic rule of this transition (in bnet format)
      :rtype: str



.. py:class:: MathMLParser

   Parse MathML to bnet format


   .. py:method:: parse(node, all_species, inputs, level=0)
      :staticmethod:



   .. py:method:: _handle_operator(operator, children, level)
      :staticmethod:



   .. py:method:: _handle_xor(children)
      :staticmethod:


      Create disjunctive normal form (DNF) of an xor



   .. py:method:: _handle_comparison(operator, children)
      :staticmethod:


      Return bnet form of an (mathml) operator between two children.



.. py:class:: SBMLQualWriter(network, level=3, version=1, qual_version=1)

   .. py:attribute:: network


   .. py:attribute:: mplugin


   .. py:attribute:: node_dict


   .. py:attribute:: doc


   .. py:method:: write(outfile)


   .. py:method:: _add_species()


   .. py:method:: _add_transitions()


   .. py:method:: _rule_to_formula(rule, input_node_dict)

      Rule (as in bnet) to a formula as supported by parseL3Formula

      .. rubric:: Notes

      Replaces:

      * `&`  with `&&`
      * `|`  with `||`

      To support thresholds, we need to replace the bnet format with a
      format supported by libsbml's parseL3Formula:

      * `A`  to `(A >= theta_A)` f"({node_dict[node]} >= {input_node_dict[node]})"
      * `!A` to `(A < theta_A)`  f"({node_dict[node]} < {input_node_dict[node]})"

      This is currently NOT implemented.



.. py:function:: read_sbmlqual(file)

   Create Network from a SBML-qual file

   :param file: Path to SBML-qual file.
   :type file: str

   .. rubric:: Notes

   The SBML-qual file is converted to a Boolean network using libsbml, via
   the bnet format. To access the bnet format directly, you can use `py:booldog.io.sbmlqual2bnet`.


.. py:function:: write_sbmlqual(model, outfile, **kwargs)