skimpy.io.sbml
==============

.. py:module:: skimpy.io.sbml

.. autoapi-nested-parse::

   .. module:: skimpy
      :platform: Unix, Windows
      :synopsis: Simple Kinetic Models in Python

   .. moduleauthor:: SKiMPy team

   [---------]

   Copyright 2022 Laboratory of Computational Systems Biotechnology (LCSB),
   Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

   http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.



Attributes
----------

.. autoapisummary::

   skimpy.io.sbml.TIME
   skimpy.io.sbml.SUBSTANCE
   skimpy.io.sbml.VOLUME


Functions
---------

.. autoapisummary::

   skimpy.io.sbml.check
   skimpy.io.sbml.export_sbml
   skimpy.io.sbml.import_sbml
   skimpy.io.sbml.get_reversiblity
   skimpy.io.sbml.get_unit
   skimpy.io.sbml.add_units


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

.. py:data:: TIME
   :value: 'hour'


.. py:data:: SUBSTANCE
   :value: 'micromole'


.. py:data:: VOLUME
   :value: 'litre'


   Check function adapted as recommended from SBML-examples:
   See: https://synonym.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/create_simple_model_8py-example.html


.. py:function:: check(value, message)

   If 'value' is None, prints an error message constructed using
   'message' and then exits with status code 1.  If 'value' is an integer,
   it assumes it is a libSBML return status code.  If the code value is
   LIBSBML_OPERATION_SUCCESS, returns without further action; if it is not,
   prints an error message constructed using 'message' along with text from
   libSBML explaining the meaning of the code, and exits with status code 1.


.. py:function:: export_sbml(kmodel, filename, time_unit=TIME, substance_unit=SUBSTANCE, volume_unit=VOLUME)

.. py:function:: import_sbml(filename)

.. py:function:: get_reversiblity(reaction)

.. py:function:: get_unit(parameter_name, substance_unit=SUBSTANCE)

.. py:function:: add_units(model, time_unit=TIME, substance_unit=SUBSTANCE, volume_unit=VOLUME)