Using RoadRunner from C++

Despite RoadRunner’s user interface being primarily in Python, RoadRunner is first and foremost a C++ library. It is therefore is possible to link roadrunner into an executable or library.

Note

You will need to have already installed RoadRunner into a directory on your system. See Installing RoadRunner section.

Note

You will also need to install cmake and add its “bin” directory to the PATH environment variable. You will know this is done if the command cmake –help works on the terminal/powershell.

The following is a very simple example of how to link roadrunner into an executable and run a simulation from C++. Create a new folder with whatever name seems appropriate and create the following files:

.
├── CMakeLists.txt
└── main.cpp

The CMakeLists.txt file should contain the following:

cmake_minimum_required(VERSION 3.22)
project(UseRoadRunnerFromC)

set(CMAKE_CXX_STANDARD 17)

# could be command line variables (-DROADRUNNER_INSTALL_PREFIX=...)
set(ROADRUNNER_INSTALL_PREFIX "D:/roadrunner/roadrunner/roadrunner-install-rel")
set(LLVM_INSTALL_PREFIX "D:/roadrunner/llvm-13.x/llvm-13.x-msvc2022-x64-rel")
set(CMAKE_PREFIX_PATH
        "${ROADRUNNER_INSTALL_PREFIX}/cmake" # needed because this is where poco installs config files to
        "${ROADRUNNER_INSTALL_PREFIX}/lib/cmake" # all other normal packages install config files to here
        )
# for registering location of ImportRoadRunnerAndDependencies
set(CMAKE_MODULE_PATH "${ROADRUNNER_INSTALL_PREFIX}/lib/cmake")

# Import roadrunner and all necessary dependencies for linking roadrunner.
# This command is a roadrunner convenience cmake script which does all of the
# calls to find_package(xxx, CONFIG) for us. If we didn't include this
# script, we would manually need to call find_package for roadrunner-static
# as well as roadrunner dependencies. Checkout The script
# under <rr_install_prefix>/lib/cmake.
include(ImportRoadRunnerAndDependencies)

# add an executable
add_executable(UseRoadRunnerFromCxx main.cpp)

# link roadrunner-static. Note that we have configured roadrunner-static target (which is imported
# under the alias roadrunner-static::roadrunner-static) with PUBLIC visibility, which means
# all includes and transitive linked libraries are automatically handled by cmake.
# without this, you would have to manually link roadrunner dependencies and manually
# include roadrunner include directories with something like:
#   - target_include_directories(UseRoadRunnerFromCxx PRIVATE "${ROADRUNNER_INSTALL_PREFIX}/include")
target_link_libraries(UseRoadRunnerFromCxx PRIVATE roadrunner-static::roadrunner-static)

Now you can use RoadRunner from C++.

#include <iostream>
#include "rr/rrRoadRunner.h"

using namespace rr;

static std::string getSBMLString(){
    return "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
           "<sbml xmlns=\"http://www.sbml.org/sbml/level3/version2/core\" level=\"3\" version=\"2\">\n"
           "  <model metaid=\"_case00001\" id=\"case00001\" name=\"case00001\" timeUnits=\"time\">\n"
           "    <listOfUnitDefinitions>\n"
           "      <unitDefinition id=\"volume\">\n"
           "        <listOfUnits>\n"
           "          <unit kind=\"litre\" exponent=\"1\" scale=\"0\" multiplier=\"1\"/>\n"
           "        </listOfUnits>\n"
           "      </unitDefinition>\n"
           "      <unitDefinition id=\"substance\">\n"
           "        <listOfUnits>\n"
           "          <unit kind=\"mole\" exponent=\"1\" scale=\"0\" multiplier=\"1\"/>\n"
           "        </listOfUnits>\n"
           "      </unitDefinition>\n"
           "      <unitDefinition id=\"time\">\n"
           "        <listOfUnits>\n"
           "          <unit kind=\"second\" exponent=\"1\" scale=\"0\" multiplier=\"1\"/>\n"
           "        </listOfUnits>\n"
           "      </unitDefinition>\n"
           "    </listOfUnitDefinitions>\n"
           "    <listOfCompartments>\n"
           "      <compartment id=\"compartment\" name=\"compartment\" spatialDimensions=\"3\" size=\"1\" units=\"volume\" constant=\"true\"/>\n"
           "    </listOfCompartments>\n"
           "    <listOfSpecies>\n"
           "      <species id=\"S1\" name=\"S1\" compartment=\"compartment\" initialAmount=\"0.00015\" substanceUnits=\"substance\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>\n"
           "      <species id=\"S2\" name=\"S2\" compartment=\"compartment\" initialAmount=\"0\" substanceUnits=\"substance\" hasOnlySubstanceUnits=\"false\" boundaryCondition=\"false\" constant=\"false\"/>\n"
           "    </listOfSpecies>\n"
           "    <listOfParameters>\n"
           "      <parameter id=\"k1\" name=\"k1\" value=\"1\" constant=\"true\"/>\n"
           "    </listOfParameters>\n"
           "    <listOfReactions>\n"
           "      <reaction id=\"reaction1\" name=\"reaction1\" reversible=\"false\">\n"
           "        <listOfReactants>\n"
           "          <speciesReference species=\"S1\" stoichiometry=\"1\" constant=\"true\"/>\n"
           "        </listOfReactants>\n"
           "        <listOfProducts>\n"
           "          <speciesReference species=\"S2\" stoichiometry=\"1\" constant=\"true\"/>\n"
           "        </listOfProducts>\n"
           "        <kineticLaw>\n"
           "          <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
           "            <apply>\n"
           "              <times/>\n"
           "              <ci> compartment </ci>\n"
           "              <ci> k1 </ci>\n"
           "              <ci> S1 </ci>\n"
           "            </apply>\n"
           "          </math>\n"
           "        </kineticLaw>\n"
           "      </reaction>\n"
           "    </listOfReactions>\n"
           "  </model>\n"
           "</sbml>";
}

int main() {
    RoadRunner roadRunner(getSBMLString());
    std::cout << *roadRunner.simulate(0, 1, 101) << std::endl;
    return 0;
}