freeflux.analysis.inst_simulate
===============================

.. py:module:: freeflux.analysis.inst_simulate

.. autoapi-nested-parse::

   Define the InstSimulator class.



Attributes
----------

.. autoapisummary::

   freeflux.analysis.inst_simulate.__author__


Classes
-------

.. autoapisummary::

   freeflux.analysis.inst_simulate.InstSimulator


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

.. py:data:: __author__
   :value: 'Chao Wu'


.. py:class:: InstSimulator(model)

   Bases: :py:obj:`freeflux.analysis.simulate.Simulator`


   Provided fluxes should be in the unit of umol/gCDW/s if concentrations in the unit of
   umol/gCDW and timepoints in the unit of s.


   .. py:method:: set_concentration(metabid, value)

      Set metabolite concentration in unit of umol/gCDW.

      :param metabid: Metabolite ID.
      :type metabid: str
      :param value: Intracellular concentration.
      :type value: float



   .. py:method:: set_concentrations_from_file(file)

      Read metabolite concentrations (umol/gCDW) from file.

      :param file: tsv or excel file with fields "metabolite_ID" and "value".
      :type file: file path



   .. py:method:: _unset_concentrations(metabids)

      :param metabids: Metabolite ID(s).
      :type metabids: str or list of str



   .. py:method:: set_timepoints(timepoints)

      Set timepoints in unit of s.

      Parameters
      timepoints: list of float
          Timepoints when MDVs are simulated.



   .. py:method:: _unset_timepoints()


   .. py:method:: _lambdify_matrix_Ms()


   .. py:method:: _unset_matrix_Ms()


   .. py:method:: _calculate_initial_matrix_Xs()


   .. py:method:: _unset_initial_matrix_Xs()


   .. py:method:: _calculate_initial_matrix_Ys()


   .. py:method:: _unset_initial_matrix_Ys()


   .. py:method:: _build_initial_sim_MDVs()


   .. py:method:: _unset_initial_sim_MDVs()


   .. py:method:: prepare(n_jobs=1)

      :param n_jobs: If n_jobs > 1, decomposition job will run in parallel.
      :type n_jobs: int



   .. py:method:: _check_dependencies()


   .. py:method:: simulate()

      :returns: **instTargetMDVs** -- EMU IDs => {measurement timepoints => simulated MDVs}
      :rtype: dict of dict