dfba.library

Functions to add a given DfbaModel to the dynamic library.

Module Contents

Functions

WriteIndent(theFile: TextIO, indentCount: int, text: str) Write indent.
indices(nrow: int, reactions: DictList, reaction_id: str) Write indices.
col_indices(reactions: DictList, reaction_id: str) Write column indices.
ctrl_parm_expression(ctrl_parms: Dict, change_pnts: List) Control paramter expression.
create(directory: str) Create library.
write_model_to_file(name: str, kinetic_variables: DictList, exchange_fluxes: DictList, nexc: int, nreq: int, exchange_indices: List[int], change_pnts: List, directory: str) Write DfbaModel to file.
dfba.library.WriteIndent(theFile: TextIO, indentCount: int, text: str) → None[source]

Write indent.

Parameters:
  • theFile (file) – Open cpp file.
  • indentCount (int) – Number of tabs to indent.
  • text (string) – The line of text to write to file.
dfba.library.indices(nrow: int, reactions: DictList, reaction_id: str) → List[int][source]

Write indices.

Parameters:
  • nrow (int) – Number of rows in LP problem.
  • reactions (DictList) – A DictList where the key is the reaction identifier and the value a cobra.Reaction object.
  • reaction_id (string) – Identifier of the reaction to return indices for.
Returns:

indices – lpindices of forward and reverse reaction.
Return type:

list
dfba.library.col_indices(reactions: DictList, reaction_id: str) → List[int][source]

Write column indices.

Parameters:
  • reactions (DictList) – A DictList object where the key is the reaction identifier and the value a cobra.Reaction object.
  • reaction_id (string) – Identifier of the reaction to return column indices for.
Returns:

indices – Column indices of forward and reverse reaction.
Return type:

list
dfba.library.ctrl_parm_expression(ctrl_parms: Dict, change_pnts: List) → str[source]

Control paramter expression.

Parameters:
  • ctrl_parms (dict) – A dict of control parameters to be included in expression.
  • change_pnts (list) – Ordered list of change points from control parameters in model.
Returns:

control_expression – The control parameter expression.
Return type:

string
dfba.library.create(directory: str) → None[source]

Create library.

Parameters:directory (string) – Path to temporary directory containing library.
dfba.library.write_model_to_file(name: str, kinetic_variables: DictList, exchange_fluxes: DictList, nexc: int, nreq: int, exchange_indices: List[int], change_pnts: List, directory: str) → None[source]

Write DfbaModel to file.

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