:mod:`dfba.library`
===================

.. py:module:: dfba.library

.. autoapi-nested-parse::

   Functions to add a given `DfbaModel` to the dynamic library.



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


Functions
~~~~~~~~~

.. autoapisummary::

   dfba.library.WriteIndent
   dfba.library.indices
   dfba.library.col_indices
   dfba.library.ctrl_parm_expression
   dfba.library.create
   dfba.library.write_model_to_file



.. function:: WriteIndent(theFile: TextIO, indentCount: int, text: str) -> None

   Write indent.

   :param theFile: Open cpp file.
   :type theFile: file
   :param indentCount: Number of tabs to indent.
   :type indentCount: int
   :param text: The line of text to write to file.
   :type text: string


.. function:: indices(nrow: int, reactions: cobra.DictList, reaction_id: str) -> List[int]

   Write indices.

   :param nrow: Number of rows in LP problem.
   :type nrow: int
   :param reactions: A DictList where the key is the reaction identifier and the value a
                     `cobra.Reaction` object.
   :type reactions: DictList
   :param reaction_id: Identifier of the reaction to return indices for.
   :type reaction_id: string

   :returns: **indices** -- lpindices of forward and reverse reaction.
   :rtype: list


.. function:: col_indices(reactions: cobra.DictList, reaction_id: str) -> List[int]

   Write column indices.

   :param reactions: A `DictList` object where the key is the reaction identifier
                     and the value a `cobra.Reaction` object.
   :type reactions: DictList
   :param reaction_id: Identifier of the reaction to return column indices for.
   :type reaction_id: string

   :returns: **indices** -- Column indices of forward and reverse reaction.
   :rtype: list


.. function:: ctrl_parm_expression(ctrl_parms: Dict, change_pnts: List) -> str

   Control paramter expression.

   :param ctrl_parms: A dict of control parameters to be included in expression.
   :type ctrl_parms: dict
   :param change_pnts: Ordered list of change points from control parameters in model.
   :type change_pnts: list

   :returns: **control_expression** -- The control parameter expression.
   :rtype: string


.. function:: create(directory: str) -> None

   Create library.

   :param directory: Path to temporary directory containing library.
   :type directory: string


.. function:: write_model_to_file(name: str, kinetic_variables: cobra.DictList, exchange_fluxes: cobra.DictList, nexc: int, nreq: int, exchange_indices: List[int], change_pnts: List, directory: str) -> None

   Write `DfbaModel` to file.

   :param name: str of `DfbaModel` id
   :type name: string
   :param kinetic_variables: A `DictList` object where the key is the kinetic variable
                             identifier and the value a `KineticValue` object.
   :type kinetic_variables: DictList
   :param exchange_fluxes: A `DictList` object where the key is the exchange flux
                           identifier and the value an `ExchangeFLux` object.
   :type exchange_fluxes: DictList
   :param nexc: Number of exchange fluxes.
   :type nexc: int
   :param nreq: Number of fluxes required to define ODE right-hand side.
   :type nreq: int
   :param exchange_indics: Indices of exchange fluxes.
   :type exchange_indics: list
   :param change_pnts: Ordered list of change points from control parameters in model.
   :type change_pnts: list
   :param directory: Path to temporary directory containing library.
   :type directory: string