pySTDLM.SBMLReader#

Functions

getRate(rxn, rcts, prds, sim, globalP, globalPV)

importSBMLModel(filename)

importSBMLModelL3V1(model, sim[, region])

readSBMLtoCME(sim, filename)

Read an SBML file for the reaction model for a CME simulation

readSBMLtoRDME(sim, filename)

Read an SBML file for the reaction model for a RDME simulation

readSBMLtoRegion(sim, region, filename)

Read an SBML file for the reaction model into a specific region of the RDME simulation

setLMLogConsole([level])

Set the logger to write to the console as the code is working

setLMLogFile(filename[, level])

Set up file handler to print log to file

setLMLoggerLevel(level)

Set the level of the logger for the application
pySTDLM.SBMLReader.getRate(rxn, rcts, prds, sim, globalP, globalPV)[source]#
pySTDLM.SBMLReader.importSBMLModel(filename)[source]#
pySTDLM.SBMLReader.importSBMLModelL3V1(model, sim, region=None)[source]#
pySTDLM.SBMLReader.readSBMLtoCME(sim, filename)[source]#

Read an SBML file for the reaction model for a CME simulation

Parameters:

  • sim – A CMESimulation object

  • filename – A SBML filename/filepath

Returns:

The simulation object

pySTDLM.SBMLReader.readSBMLtoRDME(sim, filename)[source]#

Read an SBML file for the reaction model for a RDME simulation

Parameters:

  • sim – A RDMESimulation object

  • filename – A SBML filename/filepath

Returns:

The simulation object

pySTDLM.SBMLReader.readSBMLtoRegion(sim, region, filename)[source]#

Read an SBML file for the reaction model into a specific region of the RDME simulation

Parameters:

  • sim – A RDMESimulation object

  • region – A region name that already exists in the RDMESimulation

  • filename – A SBML filename/filepath

Returns:

The simulation object