freeflux.analysis.simulate
==========================

.. py:module:: freeflux.analysis.simulate

.. autoapi-nested-parse::

   Define the Simulator class.



Attributes
----------

.. autoapisummary::

   freeflux.analysis.simulate.__author__


Classes
-------

.. autoapisummary::

   freeflux.analysis.simulate.Simulator


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

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


.. py:class:: Simulator(model)

   :param model: Freeflux Model.
   :type model: Model


   .. py:attribute:: model


   .. py:attribute:: calculator


   .. py:attribute:: contexts
      :value: []



   .. py:method:: __enter__()


   .. py:method:: __exit__(type, value, traceback)


   .. py:method:: set_target_EMUs(target_emus)

      :param target_emus: Metabolite ID => atom NOs or list of atom NOs. Atom NOs can be int list or str,
                          e.g.,, {'Ala': [[1,2,3], [2,3]], 'Ser': '123'}.
      :type target_emus: dict



   .. py:method:: _unset_target_EMUs(emuids)


   .. py:method:: set_labeling_strategy(labeled_substrate, labeling_pattern, percentage, purity, label_atom='C')

      Use this method for every substrate tracer.

      :param labeled_substrate: Metabolite ID.
      :type labeled_substrate: str
      :param labeling_pattern: Labeling pattern of substrate, '0' for unlabeled atom, '1' for labeled atom,
                               e.g., '100000' for 1-13C glucose.

                               List if tracer with multiple labeling patterns are used.

                               Natural substrate (with all '0's) don't need to be explicitly set.

                               If str, labeling_pattern should not be natural substrate.
      :type labeling_pattern: str or list of str
      :param percentage: Molar percentage (in range of [0,1]) of corresponding tracer.
                         Sum of percentage should be <= 1, and the rest will be considered as
                         natural substrate.

                         List if tracer with multiple labeling patterns are used.

                         * If list, len(percentage) should be equal to len(labeling_pattern).
                         * If float, labeling_pattern should not be natural substrate.
      :type percentage: float or list of float
      :param purity: Labeled atom purity (in range of [0,1]) of corresponding tracer.

                     List if tracer with multiple labeling patterns are used.

                     * If list, len(purity) should be equal to len(labeling_pattern).
                     * If float, labeling_pattern should not be natural substrate.
      :type purity: float or list of float
      :param label_atom: Labeled atom, i.e., base atom in the MDV. Currently supports only "H",
                         "C" and "N".
      :type label_atom: str



   .. py:method:: _unset_labeling_strategy(labeled_substrate)

      :param labeled_substrate: Metabolite ID.
      :type labeled_substrate: str



   .. py:method:: set_flux(fluxid, value)

      Set metabolic flux value.

      :param fluxid: Flux IDs, i.e., reaction ID + '_f' or '_b' for reversible reaction,
                     and reaction ID for irreversible reaction.
      :type fluxid: str
      :param value: Flux value.
      :type value: float



   .. py:method:: set_fluxes_from_file(file)

      Read metabolic flux values from file.

      :param file: tsv or excel file, fields are flux ID and value,
                   flux ID is reaction ID + '_f' or '_b' for reversible reaction,
                   and reaction ID for irreversible reaction.
      :type file: file path



   .. py:method:: _unset_fluxes(fluxids)

      :param fluxids: Flux ID(s).
      :type fluxids: str or list of str



   .. py:method:: _decompose_network(n_jobs, lump=True)

      :param n_jobs: # of jobs to run in parallel.
      :type n_jobs: int
      :param lump: Whether to lump linear EMUs.
      :type lump: bool



   .. py:method:: _unset_decomposition()


   .. py:method:: _lambdify_matrix_As_and_Bs()


   .. py:method:: _unset_matrix_As_and_Bs()


   .. py:method:: _calculate_substrate_MDVs(extra_subs=None)

      :param extra_subs: Metabolite ID(s). Additional metabolites that are considered as substrates.
      :type extra_subs: str or list of str



   .. py:method:: _unset_substrate_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()