biggr_models.queries.metabolite_queries
=======================================

.. py:module:: biggr_models.queries.metabolite_queries


Attributes
----------

.. autoapisummary::

   biggr_models.queries.metabolite_queries.LINKOUT_PROPERTY_KEYS
   biggr_models.queries.metabolite_queries.ANNOTATION_TYPES
   biggr_models.queries.metabolite_queries.REFERENCE_COMPOUND_TYPES
   biggr_models.queries.metabolite_queries.REF_ANNOTATIONS_SUBQ
   biggr_models.queries.metabolite_queries.COMP_ANNOTATIONS_SUBQ


Functions
---------

.. autoapisummary::

   biggr_models.queries.metabolite_queries.get_universal_metabolites_count
   biggr_models.queries.metabolite_queries.get_universal_metabolites
   biggr_models.queries.metabolite_queries.get_model_metabolites_count
   biggr_models.queries.metabolite_queries.get_model_metabolites
   biggr_models.queries.metabolite_queries.process_annotation_for_template
   biggr_models.queries.metabolite_queries.get_metabolite
   biggr_models.queries.metabolite_queries.get_model_list_for_metabolite
   biggr_models.queries.metabolite_queries.get_model_comp_metabolite
   biggr_models.queries.metabolite_queries.get_component_object
   biggr_models.queries.metabolite_queries.get_universal_component_object
   biggr_models.queries.metabolite_queries.get_compartmentalized_component_object
   biggr_models.queries.metabolite_queries.get_model_compartmentalized_component_object
   biggr_models.queries.metabolite_queries.get_any_components_by_identifiers


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

.. py:data:: LINKOUT_PROPERTY_KEYS

.. py:data:: ANNOTATION_TYPES

.. py:data:: REFERENCE_COMPOUND_TYPES

.. py:function:: get_universal_metabolites_count(session)

.. py:function:: get_universal_metabolites(session, page=None, size=None, sort_column=None, sort_direction='ascending', **kwargs)

   Get universal metabolites.

   :param session:
   :type session: An ome session object.
   :param page:
   :type page: The page, or None for all pages.
   :param size:
   :type size: The page length, or None for all pages.
   :param sort_column:
   :type sort_column: The name of the column to sort. Must be one of 'bigg_id', 'name'.
   :param sort_direction:
   :type sort_direction: Either 'ascending' or 'descending'.

   :rtype: A list of objects with keys 'bigg_id', 'name'.


.. py:function:: get_model_metabolites_count(model_bigg_id, session)

   Count the model metabolites.


.. py:function:: get_model_metabolites(model_bigg_id, session, page=None, size=None, sort_column=None, sort_direction='ascending', **kwargs)

   Get model metabolites.

   :param model_bigg_id:
   :type model_bigg_id: The bigg id of the model to retrieve metabolites.
   :param session:
   :type session: An ome session object.
   :param page:
   :type page: The page, or None for all pages.
   :param size:
   :type size: The page length, or None for all pages.
   :param sort_column:
   :type sort_column: The name of the column to sort. Must be one of 'bigg_id',
   :param 'name':
   :param 'model_bigg_id':
   :param and 'organism'.:
   :param sort_direction:
   :type sort_direction: Either 'ascending' or 'descending'.

   :returns: * *A list of objects with keys 'bigg_id', 'name', 'compartment_bigg_id',*
             * *'model_bigg_id', and 'organism'.*


.. py:function:: process_annotation_for_template(ann: cobradb.models.Annotation)

.. py:function:: get_metabolite(met_bigg_id, session)

.. py:function:: get_model_list_for_metabolite(metabolite_bigg_id, session)

.. py:function:: get_model_comp_metabolite(comp_met_id, model_bigg_id, session)

.. py:data:: REF_ANNOTATIONS_SUBQ

.. py:data:: COMP_ANNOTATIONS_SUBQ

.. py:function:: get_component_object(session: sqlalchemy.orm.Session, id: biggr_models.queries.utils.IDType, load_annotations: bool = True) -> Dict[str, Any]

.. py:function:: get_universal_component_object(session, id: biggr_models.queries.utils.IDType, load_annotations: bool = True)

.. py:function:: get_compartmentalized_component_object(session, id: biggr_models.queries.utils.IDType, load_annotations: bool = True)

.. py:function:: get_model_compartmentalized_component_object(session, id: biggr_models.queries.utils.IDType, model_id: biggr_models.queries.utils.IDType, load_annotations: bool = True)

.. py:function:: get_any_components_by_identifiers(session: sqlalchemy.orm.Session, identifiers: biggr_models.queries.utils.StrList, model_bigg_id: biggr_models.queries.utils.OptStr = None)