https://github.com/ecell/ecell3-python2cpp

Python to C++ model translator for E-Cell 3
https://github.com/ecell/ecell3-python2cpp

Last synced: about 2 months ago
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Python to C++ model translator for E-Cell 3

• Host: GitHub
• URL: https://github.com/ecell/ecell3-python2cpp
• Owner: ecell
• License: other
• Created: 2013-09-09T13:43:12.000Z (over 11 years ago)
• Default Branch: master
• Last Pushed: 2013-09-10T02:13:53.000Z (over 11 years ago)
• Last Synced: 2024-03-26T07:44:15.890Z (9 months ago)
• Language: Python
• Homepage:
• Size: 125 KB
• Stars: 0
• Watchers: 7
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst
  • License: COPYING

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README

        
=================

ecell3-python2cpp

=================

What's this?

------------

This small program translates an E-Cell 3 model written in Python to the equivalent C++ code.

The source python code::

    def buildModel( theSimulator ): 

        stepper_DE1 = theSimulator.createStepper("FixedODE1Stepper", "DE1")

        theSimulator.rootSystem.StepperID = "DE1"

        Variable___SIZE = theSimulator.createEntity("Variable", "Variable:/:SIZE")

        Variable___SIZE.Value = 1e-18

        Variable___S = theSimulator.createEntity("Variable", "Variable:/:S")

        Variable___S.Value = 1000000.0

        Variable___P = theSimulator.createEntity("Variable", "Variable:/:P")

        Variable___P.Value = 0.0

        Variable___E = theSimulator.createEntity("Variable", "Variable:/:E")

        Variable___E.Value = 1000.0

        Process___E = theSimulator.createEntity("MichaelisUniUniFluxProcess", "Process:/:E")

        Process___E.VariableReferenceList = [["S0", ":.:S", "-1"], ["P0", ":.:P", "1"], ["C0", ":.:E", "0"]]

        Process___E.KmS = "1"

        Process___E.KcF = "10"

    

    buildModel( theSimulator )

    

The resulting C++ code::

    #include 

    #include 

    #include 

    #include 

    #include 

    #include 

    #include 

    #include 

    

    void buildModel(libecs::Model& model)

    {

        libecs::Stepper* stepper_DE1 = model.createStepper("FixedODE1Stepper", "DE1");

        {

        }

        libecs::System* root = model.getRootSystem();

        {

            root->loadProperty("StepperID", libecs::Polymorph("DE1"));

        }

        libecs::Variable* P = reinterpret_cast(model.createEntity("Variable", libecs::FullID("Variable:/:P")));

        {

            P->loadProperty("Value", libecs::Polymorph(static_cast(0.0)));

        }

        libecs::Variable* S = reinterpret_cast(model.createEntity("Variable", libecs::FullID("Variable:/:S")));

        {

            S->loadProperty("Value", libecs::Polymorph(static_cast(1000000.0)));

        }

        libecs::Variable* v_E = reinterpret_cast(model.createEntity("Variable", libecs::FullID("Variable:/:E")));

        {

            v_E->loadProperty("Value", libecs::Polymorph(static_cast(1000.0)));

        }

        libecs::Variable* SIZE = reinterpret_cast(model.createEntity("Variable", libecs::FullID("Variable:/:SIZE")));

        {

            SIZE->loadProperty("Value", libecs::Polymorph(static_cast(1e-18)));

        }

        libecs::Process* p_E = reinterpret_cast(model.createEntity("MichaelisUniUniFluxProcess", libecs::FullID("Process:/:E")));

        {

            p_E->loadProperty("KcF", libecs::Polymorph("10"));

            p_E->loadProperty("KmS", libecs::Polymorph("1"));

            p_E->registerVariableReference("S0", libecs::FullID(":.:S"), -1, false);

            p_E->registerVariableReference("P0", libecs::FullID(":.:P"), 1, false);

            p_E->registerVariableReference("C0", libecs::FullID(":.:E"), 0, false);

        }

    }

    

    int main()

    {

        typedef ModuleMaker PropertiedObjectMaker;

        struct RAII

        {

            RAII() { libecs::initialize(); }

            ~RAII() { libecs::finalize(); }

        } _;

        boost::scoped_ptr propertiedObjectMaker(libecs::createDefaultModuleMaker());

        libecs::Model model(*propertiedObjectMaker);

        

        // initialize the model

        {

            const char* dmpath = getenv("ECELL3_DM_PATH");

            if ( dmpath )

                model.setDMSearchPath(dmpath);

        }

        model.setup();

        

        // build the model

        buildModel(model);

        

        // initialize the simulation state

        model.initialize();

        

        // advance the simulation

        {

            libecs::Variable* const SIZE = reinterpret_cast(model.getEntity(libecs::FullID("Variable:/:SIZE")));

            libecs::Variable* const S = reinterpret_cast(model.getEntity(libecs::FullID("Variable:/:S")));

            libecs::Variable* const P = reinterpret_cast(model.getEntity(libecs::FullID("Variable:/:P")));

            libecs::Variable* const v_E = reinterpret_cast(model.getEntity(libecs::FullID("Variable:/:E")));

            for (int i = 0; i < 10; ++i)

            {

                std::cout << "<>" << std::endl;

                std::cout << "Variable:/:SIZE" << "=" << SIZE->getValue() << std::endl;

                std::cout << "Variable:/:S" << "=" << S->getValue() << std::endl;

                std::cout << "Variable:/:P" << "=" << P->getValue() << std::endl;

                std::cout << "Variable:/:E" << "=" << v_E->getValue() << std::endl;

                model.step();

            }

        }

    }

Usage

-----

::

    $ ecell3-python ecell3-python2cpp simple.py