=================== Tellurium Methods =================== ------------------- Installing Packages ------------------- Tellurium provides utility methods for installing Python packages from `PyPI `_. These methods simply delegate to ``pip``, and are usually more reliable than running ``!pip install xyz``. .. autofunction:: tellurium.installPackage .. autofunction:: tellurium.upgradePackage .. autofunction:: tellurium.uninstallPackage .. autofunction:: tellurium.searchPackage .. include:: _notebooks/core/methods_installing_packages.rst ---------------- Utility Methods ---------------- The most useful methods here are the notices routines. Roadrunner will offen issue warning or informational messages. For repeated simulation such messages will clutter up the outputs. noticesOff and noticesOn can be used to turn on an off the messages. .. autofunction:: tellurium.getVersionInfo .. autofunction:: tellurium.printVersionInfo .. autofunction:: tellurium.getTelluriumVersion .. autofunction:: tellurium.noticesOff .. autofunction:: tellurium.noticesOn .. autofunction:: tellurium.saveToFile .. autofunction:: tellurium.readFromFile .. include:: _notebooks/core/tellurium_utility.rst ------------------------- Model Loading ------------------------- There are a variety of methods to load models into libRoadrunner. .. autofunction:: tellurium.loada .. autofunction:: tellurium.loadAntimonyModel .. autofunction:: tellurium.loadSBMLModel .. autofunction:: tellurium.loadCellMLModel .. include:: _notebooks/core/tellurium_model_loading.rst ---------------------------------------- Interconversion Utilities ---------------------------------------- Use these routines to interconvert verious standard formats .. autofunction:: tellurium.antimonyToSBML .. autofunction:: tellurium.antimonyToCellML .. autofunction:: tellurium.sbmlToAntimony .. autofunction:: tellurium.sbmlToCellML .. autofunction:: tellurium.cellmlToAntimony .. autofunction:: tellurium.cellmlToSBML .. include:: _notebooks/core/tellurium_interconversion.rst ---------------------------------------- Export Utilities ---------------------------------------- Use these routines to convert the current model state into other formats, like Matlab, CellML, Antimony and SBML. .. autoclass:: tellurium.tellurium.ExtendedRoadRunner :members: exportToSBML, exportToAntimony, exportToCellML, exportToMatlab, getAntimony, getCurrentAntimony, getCellML, getCurrentCellML, getMatlab, getCurrentMatlab .. include:: _notebooks/core/tellurium_export.rst ---------------------------------------- Stochastic Simulation ---------------------------------------- Use these routines to carry out Gillespie style stochastic simulations. .. autoclass:: tellurium.tellurium.ExtendedRoadRunner :members: getSeed, setSeed, gillespie .. include:: _notebooks/core/tellurium_stochastic.rst ---------------------------------------- Math ---------------------------------------- Use these routines to perform various calculations. .. autofunction:: tellurium.getEigenvalues .. autofunction:: tellurium.rank .. autofunction:: tellurium.nullspace .. autofunction:: tellurium.rref ---------------------------------------- ODE Extraction Methods ---------------------------------------- Routines to extract ODEs. .. autofunction:: tellurium.getODEsFromSBMLFile .. autofunction:: tellurium.getODEsFromSBMLString .. autofunction:: tellurium.getODEsFromModel ---------------------------------------- Plotting ---------------------------------------- Tellurium has a plotting engine which can target either Plotly (when used in a notebook environment) or Matplotlib. To specify which engine to use, use ``te.setDefaultPlottingEngine()``. .. autofunction:: tellurium.plot **NOTE: When loading a model with r = te.loada('antimony_string') and calling r.plot(), it is the below tellerium.ExtendedRoadRunner.plot() method below that is called not te.plot().** .. autofunction:: tellurium.plotArray The function tellurium.plotArray assumes that the first column in the array is the x-axis and the second and subsequent columns represent curves on the y-axis. .. autoclass:: tellurium.tellurium.ExtendedRoadRunner :members: draw, plot **NOTE: When loading a model with r = te.loada('antimony_string') and calling r.plot(), it is the above tellerium.ExtendedRoadRunner.plot() method below that is called not te.plot().** .. include:: _notebooks/core/tellurium_plotting.rst ---------------------------------------- Model Reset ---------------------------------------- .. include:: _notebooks/core/tellurium_reset.rst ---------------------------------------- jarnac Short-cuts ---------------------------------------- Routines to support the Jarnac compatibility layer .. autoclass:: tellurium.tellurium.ExtendedRoadRunner :members: fjac, sm, rs, fs, bs, ps, vs, dv, rv, sv ---------------------------------------- Test Models ---------------------------------------- RoadRunner has built into it a number of predefined models that can be use to easily try and test tellurium. .. autofunction:: tellurium.loadTestModel .. autofunction:: tellurium.getTestModel .. autofunction:: tellurium.listTestModels .. include:: _notebooks/core/tellurium_test.rst ---------------------------------------- Running external tools ---------------------------------------- Routines to run external tools. .. autofunction:: tellurium.runTool ---------------------------------------- Model Methods ---------------------------------------- Routines flattened from model, saves typing and easier for finding the methods .. autoclass:: tellurium.tellurium.ExtendedRoadRunner :members: getRatesOfChange, getBoundarySpeciesConcentrations, getBoundarySpeciesIds, getNumBoundarySpecies, getFloatingSpeciesConcentrations, getFloatingSpeciesIds, getNumFloatingSpecies, getGlobalParameterIds, getGlobalParameterValues, getNumGlobalParameters, getCompartmentIds, getCompartmentVolumes, getNumCompartments, getConservedMoietyValues, getNumConservedMoieties, getNumDepFloatingSpecies, getNumIndFloatingSpecies, getNumReactions, getReactionIds, getReactionRates, getNumEvents, setStartTime, setEndTime, getStartTime, getEndTime, getNumberOfPoints, setNumberOfPoints, getNumRateRules