Convert Goldbeter 1991 Srn Model

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2023, Chaste - Cancer Heart and Soft Tissue Environment
+Copyright (c) 2025, Chaste - Cancer Heart and Soft Tissue Environment
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

README.md

@@ -1,34 +1,44 @@
-# Chaste code generation from SBML
+# SBML → Chaste
 
-The `chaste_codegen_sbml` module takes [SBML](https://synonym.caltech.edu/) models as input and uses [libSBML](https://synonym.caltech.edu/software/libsbml/) to parse the models and output C++ code for Chaste.
+`chaste_codegen_sbml` converts [SBML](https://synonym.caltech.edu/) models to C++ Chaste code. It relies on [libSBML](https://synonym.caltech.edu/software/libsbml/) for parsing SBML.
 
 ## Installation
-### User install
 Installation via [`pipx`](https://pipx.pypa.io/) is recommended
 ```
 pipx install git+https://github.com/Chaste/chaste-codegen-sbml@develop
 ```
 
-Alternatively, install via `pip` (optionally in a virtual environment)
+Alternatively, install via `pip`
 ```
-# Create and activate a virtual environment
+# Create and activate a virtual environment (optional)
 python -m venv sbml-venv
+source sbml-venv/bin/activate
 
 # Install
 pip install git+https://github.com/Chaste/chaste-codegen-sbml@develop
 ```
 
-### Developer install
-Clone the repository and install the package in editable mode along with the `dev` dependencies:
+## Usage
+```
+chaste_codegen_sbml [-h]
+```
+
+## Development
+### Getting the code
 ```
+# Clone the repository
 git clone https://github.com/Chaste/chaste-codegen-sbml
 cd chaste-codegen-sbml
-pip install -e .[dev]
+
+# Create and activate a virtual environment
+python -m venv venv
+source venv/bin/activate
+
+# Install in editable mode along with dev dependencies
+pip install -e ."[dev]"
 ```
 
-## Usage
+### Running tests
 ```
-chaste_codegen_sbml [-h]
+python -m pytest
 ```
-
-## Testing

chaste_codegen_sbml/filewriters.py

@@ -1,6 +1,3 @@
-import sys
-import os.path
-from libsbml import *
 from . import translator
 
 # Script with functions that will write all the necessary SBML info into Chaste .cpp 
@@ -259,13 +256,11 @@ def GetClassDefinition(filename, model):
   ode_name = GetOdeSystemName(filename)
 
   ##### EDITED ###################### - in this case, the rules are also variables (as totals of other variables)
-  odes_dict = translator.GetOdesDictionary(model)
-  rules_dict = translator.GetRulesDictionary(model)
-  num_species = len(odes_dict) + len(rules_dict)
+  num_state_vars = len(translator.GetOdesDictionary(model))
 
   class_defn_str = (translator.GetBlockCommentDefinition(0, "SBML ODE System", True) + 
                     ode_name + "::" + ode_name + " (std::vector<double> stateVariables)\n" +
-                    translator.AddTabs(1) + ": AbstractOdeSystem(" + str(num_species) + ")\n" 
+                    translator.AddTabs(1) + ": AbstractOdeSystem(" + str(num_state_vars) + ")\n"
                     "{\n" + 
                     translator.AddTabs(1) + "mpSystemInfo.reset(new CellwiseOdeSystemInformation<" + ode_name + ">);\n"
                     "\n" + 

chaste_codegen_sbml/generator.py

@@ -1,7 +1,5 @@
-import sys
 import os
-from os.path import basename
-from libsbml import *
+from libsbml import SBMLReader
 from . import translator
 from . import filewriters
 
@@ -46,42 +44,30 @@ def MoveFilesToDirectory(files, new_path):
     for i in range(len(files)):
         os.rename(current_path + "/" + files[i], new_path + "/" + files[i])
 
-def Generate(path_to_file):
+def Generate(sbml_file, output_filename=None, output_directory=None):
     """ Main function. Arguments are:
     Input, Output Filename, Output Directory. """
 
-    # path_to_file = args[1]
-
     #Get the model from the file
     reader = SBMLReader()
-    document = reader.readSBMLFromFile(path_to_file)
+    document = reader.readSBMLFromFile(sbml_file)
     model = document.getModel()
 
     #Get Name of file
-    # if(len(args) > 2):
-    #     model_name = args[2]
-    # else:
-    #     filename = basename(path_to_file)
-    #     split_fname = filename.split('.')
-    #     model_name = split_fname[0]
-
-    filename = basename(path_to_file)
-    model_name = filename.split('.')[0]
+    if not output_filename:
+        output_filename = os.path.basename(sbml_file).split('.')[0]
 
     # If there are events in the model, we define the class as a cell cycle model.
     # Otherwise, the model is assumed to be a subcellular reaction network model.
-    if( translator.IsSrnModel(model) ):
-        filewriters.WriteSrnModelToFile(model_name, model)
+    if translator.IsSrnModel(model):
+        filewriters.WriteSrnModelToFile(output_filename, model)
     else:
-        filewriters.WriteCcmModelToFile(model_name, model)
+        filewriters.WriteCcmModelToFile(output_filename, model)
 
-    # if(len(args) > 3):
-    #     output_directory = args[3]
-    # else:
-    #     output_directory = "."
-    output_directory = "."
+    if not output_directory:
+        output_directory = "."
 
-    output_files = GetOutputFilenames(path_to_file, model_name)
+    output_files = GetOutputFilenames(sbml_file, output_filename)
 
     #Move created files if output directory has been specified.
     MoveFilesToDirectory(output_files, output_directory)

chaste_codegen_sbml/templates/SbmlSrnWrapperModel.cpp

@@ -0,0 +1,190 @@
+/*
+
+Copyright (c) 2005-2013, University of Oxford.
+All rights reserved.
+
+University of Oxford means the Chancellor, Masters and Scholars of the
+University of Oxford, having an administrative office at Wellington
+Square, Oxford OX1 2JD, UK.
+
+This file is part of Chaste.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+ * Neither the name of the University of Oxford nor the names of its
+   contributors may be used to endorse or promote products derived from this
+   software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+*/
+
+#ifndef SBMLSRNWRAPPERMODEL_CPP_
+#define SBMLSRNWRAPPERMODEL_CPP_
+
+//#include "UblasIncludes.hpp"
+#include "SbmlSrnWrapperModel.hpp"
+#include "CellCycleModelOdeSolver.hpp"
+#include "RungeKutta4IvpOdeSolver.hpp"
+#include "AbstractOdeSrnModel.hpp"
+#include "CvodeAdaptor.hpp"
+//#include "Exception.hpp"
+#include "Debug.hpp"
+
+
+template<typename SBMLODE, unsigned SIZE>
+SbmlSrnWrapperModel<SBMLODE, SIZE>::SbmlSrnWrapperModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
+    : AbstractOdeSrnModel(SIZE, pOdeSolver)
+{
+
+	// TODO add CVODE solver. See VanLeeuwen CCM in trunk
+
+    if (mpOdeSolver == boost::shared_ptr<AbstractCellCycleModelOdeSolver>())
+    {
+
+    	#ifdef CHASTE_CVODE
+        mpOdeSolver = CellCycleModelOdeSolver<SbmlSrnWrapperModel<SBMLODE, SIZE>, CvodeAdaptor>::Instance();
+        mpOdeSolver->Initialise();
+        // Chaste solvers always check for stopping events, CVODE needs to be instructed to do so
+        mpOdeSolver->CheckForStoppingEvents();
+        mpOdeSolver->SetMaxSteps(10000);
+		#else
+        mpOdeSolver = CellCycleModelOdeSolver<SbmlSrnWrapperModel<SBMLODE, SIZE>, RungeKutta4IvpOdeSolver>::Instance();
+        mpOdeSolver->Initialise();
+        SetDt(0.0001); // This is small enough for both examples to converge
+		#endif //CHASTE_CVODE
+    }
+
+    assert(mpOdeSolver->IsSetUp());
+}
+
+//New method for copy constructor
+template<typename SBMLODE, unsigned SIZE>
+SbmlSrnWrapperModel<SBMLODE, SIZE>::SbmlSrnWrapperModel(const SbmlSrnWrapperModel& rModel)
+    : AbstractOdeSrnModel(rModel)
+{
+    /*
+     * Set each member variable of the new SRN model that inherits
+     * its value from the parent.
+     *
+     * Note 1: some of the new SRN model's member variables
+     * will already have been correctly initialized in its constructor.
+     *
+     * Note 2: one or more of the new SRN model's member variables
+     * may be set/overwritten as soon as InitialiseDaughterCell() is called on
+     * the new SRN model.
+     *
+     * Note 3: Only set the variables defined in this class. Variables defined
+     * in parent classes will be defined there.
+     */
+
+    assert(rModel.GetOdeSystem());
+    SetOdeSystem(new SBMLODE(rModel.GetOdeSystem()->rGetStateVariables()));
+}
+
+template<typename SBMLODE, unsigned SIZE>
+AbstractSrnModel* SbmlSrnWrapperModel<SBMLODE, SIZE>::CreateSrnModel()
+{
+	return new SbmlSrnWrapperModel(*this);
+}
+
+
+template<typename SBMLODE, unsigned SIZE>
+void SbmlSrnWrapperModel<SBMLODE, SIZE>::SimulateToCurrentTime()
+{
+
+	assert(mpOdeSystem != NULL);
+	assert(mpCell != NULL);
+
+	/* Custom behaviour: store the state variables as cell data and set any parameters
+	 * using cell data, so that we can visualise different concentrations in Paraview.
+	 */
+
+	std::vector<std::string> parameterNames = mpOdeSystem->rGetParameterNames();
+	//Set parameters that need to be set
+	for (unsigned i = 0; i < parameterNames.size(); i++)
+	{
+		std::string parameterName = parameterNames[i];
+
+		//Get the value from cell data
+		double parameterValue = mpCell->GetCellData()->GetItem(parameterName);
+
+		mpOdeSystem->SetParameter(parameterName, parameterValue);
+	}
+
+	std::vector<std::string> stateVariableNames = mpOdeSystem->rGetStateVariableNames();
+
+	for (unsigned i = 0; i < stateVariableNames.size(); i++)
+	{
+		std::string stateName = stateVariableNames[i];
+		double stateValue = mpOdeSystem->rGetStateVariables()[i];
+
+		//Set current state variable value as cell data
+		mpCell->GetCellData()->SetItem(stateName, stateValue);
+	}
+
+
+    // run the ODE simulation as needed
+    AbstractOdeSrnModel::SimulateToCurrentTime();
+
+
+}
+
+template<typename SBMLODE, unsigned SIZE>
+void SbmlSrnWrapperModel<SBMLODE, SIZE>::Initialise()
+{
+	AbstractOdeSrnModel::Initialise(new SBMLODE);
+
+	//Initialise cell data
+	assert(mpOdeSystem != NULL);
+	assert(mpCell != NULL);
+
+	/* Custom behaviour: store the state variables as cell data and set any parameters
+	 * using cell data, so that we can visualise different concentrations in Paraview.
+	 */
+
+	std::vector<std::string> stateVariableNames = mpOdeSystem->rGetStateVariableNames();
+
+	for (unsigned i = 0; i < stateVariableNames.size(); i++)
+	{
+		std::string stateName = stateVariableNames[i];
+		double stateValue = mpOdeSystem->rGetStateVariables()[i];
+
+		//Set current state variable value as cell data
+		mpCell->GetCellData()->SetItem(stateName, stateValue);
+	}
+
+}
+
+
+template<typename SBMLODE, unsigned SIZE>
+void SbmlSrnWrapperModel<SBMLODE, SIZE>::OutputSrnModelParameters(out_stream& rParamsFile)
+{
+    // No new parameters to output.
+
+    // Call direct parent class
+    AbstractOdeSrnModel::OutputSrnModelParameters(rParamsFile);
+}
+
+template<typename SBMLODE, unsigned SIZE>
+double SbmlSrnWrapperModel<SBMLODE, SIZE>::GetStateVariable(const std::string& rName)
+{
+    assert(mpOdeSystem != nullptr);
+    return mpOdeSystem->GetStateVariable(rName);
+}
+
+#endif /* SBMLSRNWRAPPERMODEL_CPP_ */