Core
The core library implements all the functionality, which is then exposed to the user via the GUI, Python library, or CLI.
It is split into four (somewhat interdependent) parts: sme::model, sme::mesh, sme::simulate and sme::common.
The public headers for each part are in /include/sme
, and the private implementation details are in /src
.
For each component X there is
X.hpp
the public interfaceX.cpp
the private implementationX_t.cpp
the testsX_bench.cpp
the benchmarks (optional)
sme::model
Importing, exporting and editing spatial models.
- inc
- Model
Model
Model::getIsValid()
Model::getErrorMessage()
Model::getHasUnsavedChanges()
Model::getCurrentFilename()
Model::setName()
Model::getName()
Model::getCompartments()
Model::getCompartments()
Model::getGeometry()
Model::getGeometry()
Model::getMembranes()
Model::getMembranes()
Model::getSpecies()
Model::getSpecies()
Model::getReactions()
Model::getReactions()
Model::getFunctions()
Model::getFunctions()
Model::getParameters()
Model::getParameters()
Model::getEvents()
Model::getEvents()
Model::getUnits()
Model::getUnits()
Model::getMath()
Model::getMath()
Model::getSimulationData()
Model::getSimulationData()
Model::getSimulationSettings()
Model::getSimulationSettings()
Model::getMeshParameters()
Model::getMeshParameters()
Model::getOptimizeOptions()
Model::getOptimizeOptions()
Model::getSampledFieldColours()
Model::Model()
Model::Model()
Model::operator=()
Model::operator=()
Model::Model()
Model::~Model()
Model::createSBMLFile()
Model::importSBMLFile()
Model::importSBMLString()
Model::exportSBMLFile()
Model::importFile()
Model::exportSMEFile()
Model::getXml()
Model::clear()
Model::getSpeciesGeometry()
Model::inlineExpr()
Model::getDisplayOptions()
Model::setDisplayOptions()
- ModelCompartments
ModelCompartments
ModelCompartments::ModelCompartments()
ModelCompartments::ModelCompartments()
ModelCompartments::setGeometryPtr()
ModelCompartments::setSpeciesPtr()
ModelCompartments::setReactionsPtr()
ModelCompartments::setSimulationDataPtr()
ModelCompartments::getIds()
ModelCompartments::getNames()
ModelCompartments::getColours()
ModelCompartments::add()
ModelCompartments::remove()
ModelCompartments::getName()
ModelCompartments::setName()
ModelCompartments::getInteriorPoints()
ModelCompartments::setInteriorPoints()
ModelCompartments::setColour()
ModelCompartments::getColour()
ModelCompartments::getIdFromColour()
ModelCompartments::getCompartments()
ModelCompartments::getCompartment()
ModelCompartments::getCompartment()
ModelCompartments::getSize()
ModelCompartments::getInitialCompartmentSizes()
ModelCompartments::clear()
ModelCompartments::getHasUnsavedChanges()
ModelCompartments::setHasUnsavedChanges()
- ModelEvents
ModelEvents
ModelEvents::ModelEvents()
ModelEvents::ModelEvents()
ModelEvents::getIds()
ModelEvents::getNames()
ModelEvents::setName()
ModelEvents::getName()
ModelEvents::setVariable()
ModelEvents::getVariable()
ModelEvents::setTime()
ModelEvents::getTime()
ModelEvents::setExpression()
ModelEvents::getExpression()
ModelEvents::add()
ModelEvents::isParameter()
ModelEvents::getValue()
ModelEvents::remove()
ModelEvents::removeAnyUsingVariable()
ModelEvents::applyEvent()
ModelEvents::getHasUnsavedChanges()
ModelEvents::setHasUnsavedChanges()
- ModelFunctions
ModelFunctions
ModelFunctions::ModelFunctions()
ModelFunctions::ModelFunctions()
ModelFunctions::getIds()
ModelFunctions::getNames()
ModelFunctions::setName()
ModelFunctions::getName()
ModelFunctions::setExpression()
ModelFunctions::getExpression()
ModelFunctions::getArguments()
ModelFunctions::addArgument()
ModelFunctions::removeArgument()
ModelFunctions::add()
ModelFunctions::remove()
ModelFunctions::getSymbolicFunctions()
ModelFunctions::getHasUnsavedChanges()
ModelFunctions::setHasUnsavedChanges()
- ModelGeometry
ModelGeometry
ModelGeometry::ModelGeometry()
ModelGeometry::ModelGeometry()
ModelGeometry::importSampledFieldGeometry()
ModelGeometry::importSampledFieldGeometry()
ModelGeometry::importGeometryFromImages()
ModelGeometry::updateMesh()
ModelGeometry::clear()
ModelGeometry::getNumDimensions()
ModelGeometry::getVoxelSize()
ModelGeometry::setVoxelSize()
ModelGeometry::getPhysicalOrigin()
ModelGeometry::getPhysicalSize()
ModelGeometry::getPhysicalPoint()
ModelGeometry::getPhysicalPointAsString()
ModelGeometry::getImages()
ModelGeometry::getMesh2d()
ModelGeometry::getMesh3d()
ModelGeometry::getIsValid()
ModelGeometry::getIsMeshValid()
ModelGeometry::getHasImage()
ModelGeometry::updateGeometryImageColor()
ModelGeometry::writeGeometryToSBML()
ModelGeometry::getHasUnsavedChanges()
ModelGeometry::setHasUnsavedChanges()
- ModelMath
- ModelMembranes
ModelMembranes
ModelMembranes::getIds()
ModelMembranes::getNames()
ModelMembranes::setName()
ModelMembranes::getName()
ModelMembranes::getMembranes()
ModelMembranes::getMembrane()
ModelMembranes::getIdColourPairs()
ModelMembranes::getSize()
ModelMembranes::updateCompartmentNames()
ModelMembranes::updateCompartments()
ModelMembranes::updateCompartmentImages()
ModelMembranes::importMembraneIdsAndNames()
ModelMembranes::exportToSBML()
ModelMembranes::ModelMembranes()
ModelMembranes::~ModelMembranes()
ModelMembranes::getHasUnsavedChanges()
ModelMembranes::setHasUnsavedChanges()
- ModelParameters
ModelParameters
ModelParameters::ModelParameters()
ModelParameters::ModelParameters()
ModelParameters::setEventsPtr()
ModelParameters::setSpeciesPtr()
ModelParameters::getIds()
ModelParameters::getNames()
ModelParameters::setName()
ModelParameters::getName()
ModelParameters::setExpression()
ModelParameters::getExpression()
ModelParameters::add()
ModelParameters::remove()
ModelParameters::getSpatialCoordinates()
ModelParameters::setSpatialCoordinates()
ModelParameters::getSymbols()
ModelParameters::getGlobalConstants()
ModelParameters::getNonConstantParameters()
ModelParameters::getHasUnsavedChanges()
ModelParameters::setHasUnsavedChanges()
- ModelReactions
ModelReactions
ModelReactions::ModelReactions()
ModelReactions::ModelReactions()
ModelReactions::makeReactionLocationsValid()
ModelReactions::applySpatialReactionRescalings()
ModelReactions::getSpatialReactionRescalings()
ModelReactions::getIsIncompleteODEImport()
ModelReactions::getIds()
ModelReactions::getIds()
ModelReactions::getReactionLocations()
ModelReactions::add()
ModelReactions::remove()
ModelReactions::removeAllInvolvingSpecies()
ModelReactions::setName()
ModelReactions::getName()
ModelReactions::getScheme()
ModelReactions::setLocation()
ModelReactions::getLocation()
ModelReactions::getSpeciesStoichiometry()
ModelReactions::setSpeciesStoichiometry()
ModelReactions::getRateExpression()
ModelReactions::setRateExpression()
ModelReactions::getParameterIds()
ModelReactions::setParameterName()
ModelReactions::getParameterName()
ModelReactions::setParameterValue()
ModelReactions::getParameterValue()
ModelReactions::addParameter()
ModelReactions::removeParameter()
ModelReactions::dependOnVariable()
ModelReactions::getHasUnsavedChanges()
ModelReactions::setHasUnsavedChanges()
- ModelSpecies
ModelSpecies
ModelSpecies::ModelSpecies()
ModelSpecies::ModelSpecies()
ModelSpecies::setReactionsPtr()
ModelSpecies::setSimulationDataPtr()
ModelSpecies::containsNonSpatialReactiveSpecies()
ModelSpecies::add()
ModelSpecies::remove()
ModelSpecies::setName()
ModelSpecies::getName()
ModelSpecies::updateCompartmentGeometry()
ModelSpecies::setCompartment()
ModelSpecies::getCompartment()
ModelSpecies::getIds()
ModelSpecies::getNames()
ModelSpecies::setIsSpatial()
ModelSpecies::getIsSpatial()
ModelSpecies::setDiffusionConstant()
ModelSpecies::getDiffusionConstant()
ModelSpecies::getInitialConcentrationType()
ModelSpecies::setInitialConcentration()
ModelSpecies::getInitialConcentration()
ModelSpecies::setAnalyticConcentration()
ModelSpecies::setFieldConcAnalytic()
ModelSpecies::getAnalyticConcentration()
ModelSpecies::updateAllAnalyticConcentrations()
ModelSpecies::setSampledFieldConcentration()
ModelSpecies::getSampledFieldConcentration()
ModelSpecies::getConcentrationImages()
ModelSpecies::setColour()
ModelSpecies::getColour()
ModelSpecies::setIsConstant()
ModelSpecies::getIsConstant()
ModelSpecies::isReactive()
ModelSpecies::removeInitialAssignments()
ModelSpecies::getSampledFieldInitialAssignment()
ModelSpecies::getField()
ModelSpecies::getField()
ModelSpecies::getHasUnsavedChanges()
ModelSpecies::setHasUnsavedChanges()
- ModelUnits
ModelUnits
ModelUnits::ModelUnits()
ModelUnits::getTime()
ModelUnits::getTimeIndex()
ModelUnits::getTimeUnits()
ModelUnits::getTimeUnits()
ModelUnits::setTimeIndex()
ModelUnits::getLength()
ModelUnits::getLengthIndex()
ModelUnits::getLengthUnits()
ModelUnits::getLengthUnits()
ModelUnits::setLengthIndex()
ModelUnits::getVolume()
ModelUnits::getVolumeIndex()
ModelUnits::getVolumeUnits()
ModelUnits::getVolumeUnits()
ModelUnits::setVolumeIndex()
ModelUnits::getAmount()
ModelUnits::getAmountIndex()
ModelUnits::getAmountUnits()
ModelUnits::getAmountUnits()
ModelUnits::setAmountIndex()
ModelUnits::getConcentration()
ModelUnits::getDiffusion()
ModelUnits::getCompartmentReaction()
ModelUnits::getMembraneReaction()
ModelUnits::getHasUnsavedChanges()
ModelUnits::setHasUnsavedChanges()
- Settings
- Model
- src
sme::mesh
Constructing the simplified boundary lines and triangular mesh approximation to the geometry.
- inc
- Mesh
Mesh2d
Mesh2d::Mesh2d()
Mesh2d::Mesh2d()
Mesh2d::~Mesh2d()
Mesh2d::constructMesh()
Mesh2d::isValid()
Mesh2d::getErrorMessage()
Mesh2d::getNumBoundaries()
Mesh2d::getBoundarySimplificationType()
Mesh2d::setBoundarySimplificationType()
Mesh2d::setBoundaryMaxPoints()
Mesh2d::getBoundaryMaxPoints()
Mesh2d::getBoundaryMaxPoints()
Mesh2d::setCompartmentMaxTriangleArea()
Mesh2d::getCompartmentMaxTriangleArea()
Mesh2d::getCompartmentMaxTriangleArea()
Mesh2d::getCompartmentInteriorPoints()
Mesh2d::setPhysicalGeometry()
Mesh2d::getVerticesAsFlatArray()
Mesh2d::getTriangleIndicesAsFlatArray()
Mesh2d::getTriangleIndices()
Mesh2d::getBoundariesImages()
Mesh2d::getMeshImages()
Mesh2d::getGMSH()
Mesh2d::dim
Mesh3d
Mesh3d::Mesh3d()
Mesh3d::Mesh3d()
Mesh3d::~Mesh3d()
Mesh3d::isValid()
Mesh3d::getErrorMessage()
Mesh3d::setCompartmentMaxCellVolume()
Mesh3d::getCompartmentMaxCellVolume()
Mesh3d::getCompartmentMaxCellVolume()
Mesh3d::setPhysicalGeometry()
Mesh3d::getVertices()
Mesh3d::getVerticesAsFlatArray()
Mesh3d::getNumberOfCompartments()
Mesh3d::getTetrahedronIndicesAsFlatArray()
Mesh3d::getTetrahedronIndices()
Mesh3d::getGMSH()
Mesh3d::getColors()
Mesh3d::setColors()
Mesh3d::dim
- Mesh
- src
sme::simulate
Simulating the model, either with Pixel or dune-copasi.
- inc
- DuneConverter
DuneConverter
DuneConverter::DuneConverter()
DuneConverter::getIniFile()
DuneConverter::getMesh()
DuneConverter::getMesh3d()
DuneConverter::getConcentrations()
DuneConverter::getSpeciesNames()
DuneConverter::getCompartmentNames()
DuneConverter::getOrigin()
DuneConverter::getVoxelSize()
DuneConverter::getImageSize()
- Pde
- Simulation
Simulation
Simulation::Simulation()
Simulation::~Simulation()
Simulation::doTimesteps()
Simulation::doMultipleTimesteps()
Simulation::errorMessage()
Simulation::errorImages()
Simulation::getCompartmentIds()
Simulation::getSpeciesIds()
Simulation::getSpeciesColors()
Simulation::getTimePoints()
Simulation::getAvgMinMax()
Simulation::getConc()
Simulation::getConcArray()
Simulation::applyConcsToModel()
Simulation::getDcdt()
Simulation::getDcdtArray()
Simulation::getLowerOrderConc()
Simulation::getConcImage()
Simulation::getPyNames()
Simulation::getPyConcs()
Simulation::getPyDcdts()
Simulation::getNCompletedTimesteps()
Simulation::getSimulationData()
Simulation::getIsRunning()
Simulation::getIsStopping()
Simulation::requestStop()
- SimulationData
- SimulationOptions
- Optimization
Optimization
Optimization::Optimization()
Optimization::evolve()
Optimization::applyParametersToModel()
Optimization::getParams()
Optimization::getParamNames()
Optimization::getFitness()
Optimization::setBestResults()
Optimization::getTargetImage()
Optimization::getUpdatedBestResultImage()
Optimization::getIterations()
Optimization::getIsRunning()
Optimization::getIsStopping()
Optimization::requestStop()
Optimization::getErrorMessage()
- OptimizationOptions
- DuneConverter
- src
sme::common
Symbolic math, TIFF import/export, other utility functions.
- inc
- Symbolic
Symbolic
Symbolic::Symbolic()
Symbolic::Symbolic()
Symbolic::Symbolic()
Symbolic::parse()
Symbolic::parse()
Symbolic::compile()
Symbolic::expr()
Symbolic::inlinedExpr()
Symbolic::diff()
Symbolic::relabel()
Symbolic::rescale()
Symbolic::eval()
Symbolic::eval()
Symbolic::isValid()
Symbolic::isCompiled()
Symbolic::getErrorMessage()
Symbolic::clear()
- TiffReader
- serialization.hpp
- utils.hpp
sme::common::unique_C_ptr
sme::common::sum()
sme::common::average()
sme::common::min()
sme::common::max()
sme::common::get_unique_values()
sme::common::isItIndexes()
sme::common::minmax()
sme::common::element_index()
sme::common::decltypeStr()
sme::common::stringToVector()
sme::common::vectorToString()
sme::common::cyclicErase()
sme::common::isCyclicPermutation()
sme::common::isalpha()
sme::common::isalnum()
sme::common::isdigit()
sme::common::indexedColours
sme::common::free_deleter
- Symbolic
- src