skimpy.io.yaml
==============

.. py:module:: skimpy.io.yaml

.. autoapi-nested-parse::

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

   .. moduleauthor:: SKiMPy team

   [---------]

   Copyright 2017 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.yaml.ALL_GENERIC_MECHANISM_SUBCLASSES
   skimpy.io.yaml.FIELDS_TO_SERIALIZE


Functions
---------

.. autoapisummary::

   skimpy.io.yaml.get_mechanism_subclasses
   skimpy.io.yaml.get_boundary_subclasses
   skimpy.io.yaml.get_modifier_subclasses
   skimpy.io.yaml.parameter_representer
   skimpy.io.yaml.reactant_representer
   skimpy.io.yaml.compartment_representer
   skimpy.io.yaml.mechanism_representer
   skimpy.io.yaml.reaction_representer
   skimpy.io.yaml.boundary_condition_representer
   skimpy.io.yaml.refresh_representers
   skimpy.io.yaml.export_to_yaml
   skimpy.io.yaml.get_mechanism
   skimpy.io.yaml.get_generic_constructor
   skimpy.io.yaml.get_stoich
   skimpy.io.yaml.load_yaml_model
   skimpy.io.yaml.rebuild_dependent_mets


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

.. py:function:: get_mechanism_subclasses()

.. py:function:: get_boundary_subclasses()

.. py:function:: get_modifier_subclasses()

.. py:data:: ALL_GENERIC_MECHANISM_SUBCLASSES

.. py:data:: FIELDS_TO_SERIALIZE
   :value: ['boundary_conditions', 'parameters', 'constraints', 'reactions', 'name', 'initial_conditions',...


.. py:function:: parameter_representer(dumper, data)

.. py:function:: reactant_representer(dumper, data)

.. py:function:: compartment_representer(dumper, data)

.. py:function:: mechanism_representer(dumper, data)

.. py:function:: reaction_representer(dumper, data)

.. py:function:: boundary_condition_representer(dumper, data)

.. py:function:: refresh_representers()

   This function refreshes the representers of custom-made reaction mechanisms 
   (n-to-m Convenience Kinetics for example)


.. py:function:: export_to_yaml(model, path=None, **kwargs)

.. py:function:: get_mechanism(classdict)

   This function should construct mechanism for the generic types
   and get the mechanism for modifiers and the defined types

   :param classdict: Looks like {'class':'MichaelisMenten',
                                 'substrate1':'atp_c',
                                 'product1'  :'gtp_c',
                                 }

   :return:


.. py:function:: get_generic_constructor(s)

.. py:function:: get_stoich(s)

.. py:function:: load_yaml_model(path)

.. py:function:: rebuild_dependent_mets(new, the_dict)