Using generated code¶

The generated classes are ordinary Chaste C++, designed to live in a Chaste user project. This page shows a typical user project layout.

Project layout¶

A Chaste user project sits under projects/ in your Chaste source tree and has a src/ directory for code and a test/ directory for tests:

Chaste/projects/MyProject/
├── CMakeLists.txt
├── src/
│   ├── AbstractSbmlOdeSystem.hpp/.cpp     # copied base classes
│   ├── AbstractSbmlSrnModel.hpp/.cpp
│   ├── SbmlMath.hpp
│   ├── ...
│   ├── MyModelSbmlOdeSystem.hpp/.cpp      # generated
│   └── MyModelSbmlSrnModel.hpp/.cpp       # generated
└── test/
    ├── CMakeLists.txt
    ├── ContinuousTestPack.txt
    └── TestMyModelSbml.hpp                # generated placeholder test

CMakeLists.txt configures the user project:

find_package(Chaste COMPONENTS cell_based)
chaste_do_project(MyProject)

test/CMakeLists.txt configures the tests:

chaste_do_test_project(MyProject)

Project setup¶

Copy the base classes into your project’s src/:

chaste-sbml --copy-base-classes --output-dir Chaste/projects/MyProject/src

Note

Do this once per project, and again whenever you upgrade chaste-sbml. See the base classes for what gets copied.

Generate the model into src/, and the placeholder test into test/ (--test-output-dir asks for the placeholder as well as placing it):

chaste-sbml my_model.xml \
  --model-type srn \
  --output-dir Chaste/projects/MyProject/src \
  --test-output-dir Chaste/projects/MyProject/test

Chaste discovers tests through test packs, which are text files in test/ listing the test headers to build. Add the generated placeholder to one:

# test/ContinuousTestPack.txt
TestMyModelSbml.hpp

Configure and build from your Chaste build directory as usual:

cd Chaste/build
cmake ..
cmake --build . --target project_MyProject

Run the user-project tests:

ctest -R MyProject

Using the classes in a simulation¶

Once compiled, the generated classes are used like any other Chaste ODE system, SRN model, or cell-cycle model.

For a generic model, construct the ODE system and hand it to a Chaste ODE solver:

#include "MyModelSbmlOdeSystem.hpp"

MyModelSbmlOdeSystem ode_system;
// solve with any AbstractIvpOdeSolver, then read state / derived quantities

For an SRN model, attach it to a cell so it runs as that cell’s subcellular reaction network:

#include "MyModelSbmlSrnModel.hpp"
#include "UniformCellCycleModel.hpp"

MAKE_PTR(WildTypeCellMutationState, p_state);
MAKE_PTR(StemCellProliferativeType, p_type);
CellPtr p_cell(new Cell(p_state, new UniformCellCycleModel(), new MyModelSbmlSrnModel()));
p_cell->SetCellProliferativeType(p_type);
p_cell->InitialiseCellCycleModel();
p_cell->InitialiseSrnModel();

For a cell-cycle model, pass it as the cell’s cell-cycle model; division is driven by the SBML cell-division event:

#include "MyModelSbmlCellCycleModel.hpp"

CellPtr p_cell(new Cell(p_state, new MyModelSbmlCellCycleModel()));
p_cell->InitialiseCellCycleModel();