inc

Model

class Model

High-level wrapper around SBML model, geometry, and simulation data.

Public Functions

bool getIsValid() const

Returns true if model loaded/constructed successfully.

Returns:

true if model state is valid.

const QString &getErrorMessage() const

Error message from last load/parse failure.

Returns:

Error message string.

bool getHasUnsavedChanges() const

Returns true if any contained model data is unsaved.

Returns:

true if model has unsaved changes.

const QString &getCurrentFilename() const

Current file path associated with model.

Returns:

Current filename/path.

void setName(const QString &name)

Set model name.

Parameters:

name – New model name.

QString getName() const

Get model name.

Returns:

Model name.

ModelCompartments &getCompartments()

Mutable access to compartment manager.

const ModelCompartments &getCompartments() const

Immutable access to compartment manager.

ModelGeometry &getGeometry()

Mutable access to geometry manager.

const ModelGeometry &getGeometry() const

Immutable access to geometry manager.

ModelMembranes &getMembranes()

Mutable access to membrane manager.

const ModelMembranes &getMembranes() const

Immutable access to membrane manager.

ModelSpecies &getSpecies()

Mutable access to species manager.

const ModelSpecies &getSpecies() const

Immutable access to species manager.

ModelReactions &getReactions()

Mutable access to reaction manager.

const ModelReactions &getReactions() const

Immutable access to reaction manager.

ModelFunctions &getFunctions()

Mutable access to function-definition manager.

const ModelFunctions &getFunctions() const

Immutable access to function-definition manager.

ModelParameters &getParameters()

Mutable access to parameter manager.

const ModelParameters &getParameters() const

Immutable access to parameter manager.

ModelEvents &getEvents()

Mutable access to event manager.

const ModelEvents &getEvents() const

Immutable access to event manager.

ModelUnits &getUnits()

Mutable access to units manager.

const ModelUnits &getUnits() const

Immutable access to units manager.

ModelMath &getMath()

Mutable access to math parser/evaluator.

const ModelMath &getMath() const

Immutable access to math parser/evaluator.

simulate::SimulationData &getSimulationData()

Mutable simulation results storage.

const simulate::SimulationData &getSimulationData() const

Immutable simulation results storage.

SimulationSettings &getSimulationSettings()

Mutable simulation settings.

const SimulationSettings &getSimulationSettings() const

Immutable simulation settings.

MeshParameters &getMeshParameters()

Mutable mesh settings.

const MeshParameters &getMeshParameters() const

Immutable mesh settings.

simulate::OptimizeOptions &getOptimizeOptions()

Mutable optimization settings.

const simulate::OptimizeOptions &getOptimizeOptions() const

Immutable optimization settings.

const std::vector<QRgb> &getSampledFieldColors() const

Imported sampled-field colors.

Returns:

Vector of sampled-field colors.

ModelFeatures &getFeatures()

Mutable access to feature manager.

const ModelFeatures &getFeatures() const

Immutable access to feature manager.

explicit Model()

Construct empty model wrapper.

Model(Model&&) noexcept = default

Model &operator=(Model&&) noexcept = default

Model &operator=(const Model&) = delete

Model(const Model&) = delete

~Model()

Destructor.

void createSBMLFile(const std::string &name)

Create a new spatial SBML model.

Parameters:

name – Model name.

void importSBMLFile(const std::string &filename)

Import SBML from file.

Parameters:

filename – Path to SBML file.

void importSBMLString(const std::string &xml, const std::string &filename = {})

Import SBML from XML string.

Parameters:

• xml – SBML XML text.

• filename – Optional source filename.

void exportSBMLFile(const std::string &filename)

Export SBML to file.

Parameters:

filename – Output SBML filename.

void importFile(const std::string &filename)

Import SBML/SME file by extension/probing.

Parameters:

filename – Input filename.

void exportSMEFile(const std::string &filename)

Export SME project file.

Parameters:

filename – Output SME filename.

QString getXml()

Serialize current SBML XML.

Returns:

SBML XML as text.

void clear()

Clear model state.

SpeciesGeometry getSpeciesGeometry(const QString &speciesID) const

Geometry context for given species id.

Parameters:

speciesID – Species id.

Returns:

Geometry context for species.

std::string inlineExpr(const std::string &mathExpression) const

Inline functions/assignments in a math expression.

Parameters:

mathExpression – Expression to inline.

Returns:

Inlined expression string.

DisplayOptions getDisplayOptions() const

Current display options.

Returns:

Display options.

void setDisplayOptions(const DisplayOptions &displayOptions)

Set display options.

Parameters:

displayOptions – New display options.

ModelCompartments

class ModelCompartments

SBML compartment manager plus geometry-backed compartment objects.

Public Functions

ModelCompartments()

Construct empty compartment model.

ModelCompartments(libsbml::Model *model, ModelMembranes *membranes, const ModelUnits *units, simulate::SimulationData *data)

Construct compartment model from SBML model.

void setGeometryPtr(ModelGeometry *geometry)

Set geometry dependency pointer.

void setSpeciesPtr(ModelSpecies *species)

Set species dependency pointer.

void setReactionsPtr(ModelReactions *reactions)

Set reactions dependency pointer.

void setSimulationDataPtr(simulate::SimulationData *data)

Set simulation-data dependency pointer.

const QStringList &getIds() const

Compartment ids.

const QStringList &getNames() const

Compartment names.

const QVector<QRgb> &getColors() const

Compartment display colors.

QString add(const QString &name)

Add compartment.

bool remove(const QString &id)

Remove compartment.

QString getName(const QString &id) const

Get compartment name.

QString setName(const QString &id, const QString &name)

Set compartment name.

std::optional<std::vector<QPointF>> getInteriorPoints(const QString &id) const

Get interior points used for meshing.

void setInteriorPoints(const QString &id, const std::vector<QPointF> &points)

Set interior points used for meshing.

void setColor(const QString &id, QRgb color)

Set compartment display color.

QRgb getColor(const QString &id) const

Get compartment display color.

QString getIdFromColor(QRgb color) const

Find compartment id from display color.

const std::vector<std::unique_ptr<geometry::Compartment>> &getCompartments() const

Geometry-backed compartment objects.

geometry::Compartment *getCompartment(const QString &id)

Mutable geometry-backed compartment object.

const geometry::Compartment *getCompartment(const QString &id) const

Immutable geometry-backed compartment object.

double getSize(const QString &id) const

Compartment size in model units.

const std::map<std::string, double, std::less<>> &getInitialCompartmentSizes() const

Initial compartment sizes captured on import.

void clear()

Clear all compartments.

bool getHasUnsavedChanges() const

Unsaved state flag.

void setHasUnsavedChanges(bool unsavedChanges)

Set unsaved state flag.

ModelEvents

class ModelEvents

Public Functions

ModelEvents()

Construct empty event model.

explicit ModelEvents(libsbml::Model *model, ModelParameters *parameters = nullptr, ModelSpecies *species = nullptr)

Construct event model from SBML model.

const QStringList &getIds() const

Event ids.

const QStringList &getNames() const

Event names.

QString setName(const QString &id, const QString &name)

Set display name.

QString getName(const QString &id) const

Get display name.

void setVariable(const QString &id, const QString &variable)

Set target variable id modified by event.

QString getVariable(const QString &id) const

Get target variable id.

void setTime(const QString &id, double time)

Set trigger time for event.

double getTime(const QString &id) const

Get trigger time for event.

void setExpression(const QString &id, const QString &expr)

Set assignment expression.

QString getExpression(const QString &id) const

Get assignment expression.

QString add(const QString &name, const QString &variable)

Add new event.

bool isParameter(const QString &id) const

Returns true if id refers to a parameter.

double getValue(const QString &id) const

Get current value of event target variable.

void remove(const QString &id)

Remove event.

void removeAnyUsingVariable(const QString &variable)

Remove events targeting the supplied variable.

void applyEvent(const QString &id)

Apply event assignment immediately.

bool getHasUnsavedChanges() const

Unsaved state flag.

void setHasUnsavedChanges(bool unsavedChanges)

Set unsaved state flag.

ModelFunctions

class ModelFunctions

SBML function-definition manager.

Public Functions

ModelFunctions()

Construct empty function model.

explicit ModelFunctions(libsbml::Model *model)

Construct function model from SBML model.

const QStringList &getIds() const

Function ids.

const QStringList &getNames() const

Function names.

QString setName(const QString &id, const QString &name)

Set function display name.

QString getName(const QString &id) const

Get function display name.

void setExpression(const QString &id, const QString &expression)

Set function expression/body.

QString getExpression(const QString &id) const

Get function expression/body.

QStringList getArguments(const QString &id) const

Get function argument ids.

QString addArgument(const QString &functionId, const QString &argumentId)

Add argument to function.

void removeArgument(const QString &functionId, const QString &argumentId)

Remove argument from function.

QString add(const QString &name)

Add new function with default expression.

void remove(const QString &id)

Remove function.

std::vector<common::SymbolicFunction> getSymbolicFunctions() const

Convert to symbolic-function objects for expression processing.

bool getHasUnsavedChanges() const

Unsaved state flag.

void setHasUnsavedChanges(bool unsavedChanges)

Set unsaved state flag.

ModelGeometry

class ModelGeometry

SBML geometry manager and mesh owner.

Public Functions

ModelGeometry()

Construct empty geometry model.

explicit ModelGeometry(libsbml::Model *model, ModelCompartments *compartments, ModelMembranes *membranes, const ModelUnits *units, Settings *annotation)

Construct geometry model from SBML model and dependencies.

Parameters:

• model – SBML model pointer.

• compartments – Compartment manager.

• membranes – Membrane manager.

• units – Units manager.

• annotation – Settings annotation.

void importSampledFieldGeometry(const libsbml::Model *model, const std::optional<common::Volume> &analyticImageSize = std::nullopt)

Import sampled-field geometry from SBML model.

Parameters:

• model – Source SBML model.

• analyticImageSize – Optional raster size for analytic fallback.

void importSampledFieldGeometry(const QString &filename, const std::optional<common::Volume> &analyticImageSize = std::nullopt)

Import sampled-field/analytic geometry from file.

Parameters:

• filename – Source filename.

• analyticImageSize – Optional raster size for analytic fallback.

void importGeometryFromImages(const common::ImageStack &imgs, bool keepColorAssignments)

Replace geometry from image stack.

Parameters:

• imgs – Geometry images.

• keepColorAssignments – Keep previous compartment-color mapping.

void importGeometryFromGmsh(const common::ImageStack &imgs, const mesh::GMSHMesh &gmshMesh, bool importAsFixedTopology)

Import geometry rasterized from a Gmsh mesh and align physical coordinates with the mesh bounds.

Parameters:

• imgs – Voxelized geometry image stack.

• gmshMesh – Source Gmsh mesh used for voxelization.

• importAsFixedTopology – Store mesh as fixed topology if true.

void setImportedGmshMesh(const mesh::GMSHMesh &gmshMesh, const std::optional<std::vector<std::pair<QRgb, int>>> &colorTagPairs = std::nullopt)

Store imported Gmsh mesh for fixed-topology meshing.

Parameters:

• gmshMesh – Imported Gmsh mesh (tetrahedra for 3D or triangles for 2D).

• colorTagPairs – Optional explicit mapping from compartment color to Gmsh physical tag.

void setImportedMesh2d(const mesh::FixedTopology2d &fixedMesh2d)

Store imported fixed 2d mesh topology for fixed-topology meshing.

Parameters:

fixedMesh2d – Imported 2d fixed mesh.

void captureCurrentMeshAsFixedTopology()

Capture current active mesh as fixed-topology mesh.

Captures current 2D or 3D mesh (if valid) and stores it as the fixed mesh topology source for subsequent remeshing.

void clearImportedMesh()

Clear any stored imported mesh topology.

bool hasImportedMesh() const

Returns true if imported mesh topology is available.

Returns:

true if imported mesh exists.

const QString &getFixedMeshImportDiagnostic() const

Diagnostic message from ParametricGeometry fixed-mesh import.

Returns:

Empty string if no import diagnostic is available.

const QString &getFixedMeshExportDiagnostic() const

Diagnostic message from ParametricGeometry fixed-mesh export.

Returns:

Empty string if no export diagnostic is available.

void updateMesh()

Rebuild mesh objects from current geometry.

void clear()

Clear geometry and mesh state.

int getNumDimensions() const

Number of spatial dimensions.

Returns:

Number of spatial dimensions.

const common::VolumeF &getVoxelSize() const

Physical voxel size.

Returns:

Physical voxel size.

void setVoxelSize(const common::VolumeF &newVoxelSize, bool updateSBML = true)

Set physical voxel size and optionally write to SBML.

Parameters:

• newVoxelSize – New voxel size.

• updateSBML – If true, write updates back to SBML.

void setPhysicalOrigin(const common::VoxelF &newPhysicalOrigin, bool updateSBML = true)

Set physical origin and optionally write to SBML.

Parameters:

• newPhysicalOrigin – New physical origin.

• updateSBML – If true, write updates back to SBML.

const common::VoxelF &getPhysicalOrigin() const

Physical origin of voxel (0,0,0).

Returns:

Physical origin.

const common::VolumeF &getPhysicalSize() const

Physical total geometry size.

Returns:

Physical geometry size.

common::VoxelF getPhysicalPoint(const common::Voxel &voxel) const

Convert voxel index to physical coordinate.

Parameters:

voxel – Voxel index.

Returns:

Physical coordinate of voxel center.

QString getPhysicalPointAsString(const common::Voxel &voxel) const

Convert voxel index to formatted physical coordinate string.

Parameters:

voxel – Voxel index.

Returns:

Formatted coordinate string.

const common::ImageStack &getImages() const

Geometry images.

Returns:

Geometry image stack.

mesh::Mesh2d *getMesh2d() const

2D mesh object (nullable).

Returns:

2D mesh pointer or nullptr.

mesh::Mesh3d *getMesh3d() const

3D mesh object (nullable).

Returns:

3D mesh pointer or nullptr.

bool getIsValid() const

Returns true if geometry is valid.

Returns:

Geometry validity.

bool getIsMeshValid() const

Returns true if mesh is valid.

Returns:

Mesh validity.

bool getHasImage() const

Returns true if geometry image data is available.

Returns:

true if geometry images exist.

void updateGeometryImageColor(QRgb oldColor, QRgb newColor)

Replace one geometry color with another.

Parameters:

• oldColor – Existing color.

• newColor – Replacement color.

void writeGeometryToSBML() const

Write current geometry representation to SBML.

bool getHasUnsavedChanges() const

Unsaved state flag.

Returns:

Unsaved state flag.

void setHasUnsavedChanges(bool unsavedChanges)

Set unsaved state flag.

Parameters:

unsavedChanges – New unsaved state.

Public Static Functions

static std::optional<int> getAnalyticGeometryNumDimensions(const QString &filename)

Number of spatial dimensions in analytic geometry file.

Parameters:

filename – Analytic-geometry file.

Returns:

Number of dimensions if file contains analytic geometry.

static std::optional<common::Volume> getDefaultAnalyticGeometryImageSize(const QString &filename)

Default raster size for analytic geometry import.

Parameters:

filename – Analytic-geometry file.

Returns:

Suggested image size if available.

static common::ImageStack getAnalyticGeometryPreview(const QString &filename, const common::Volume &imageSize)

Preview rasterized analytic geometry.

Parameters:

• filename – Analytic-geometry file.

• imageSize – Requested preview image size.

Returns:

Preview image stack.

ModelMath

class ModelMath

Parser/evaluator for SBML math expressions.

Public Functions

ModelMath()

Construct invalid empty math object.

explicit ModelMath(const libsbml::Model *model)

Construct math parser bound to an SBML model.

void parse(const std::string &expr)

Parse expression and update validity state.

double eval(const std::map<const std::string, std::pair<double, bool>> &vars = {}) const

Evaluate parsed expression.

bool isValid() const

Returns true if parsed expression is valid.

const std::string &getErrorMessage() const

Parse/evaluation error message.

ModelMembranes

class ModelMembranes

SBML membrane manager.

Public Functions

const QStringList &getIds() const

Membrane ids.

const QStringList &getNames() const

Membrane names.

QString setName(const QString &id, const QString &name)

Set membrane display name.

QString getName(const QString &id) const

Get membrane display name.

const std::vector<geometry::Membrane> &getMembranes() const

Geometry membrane objects.

const geometry::Membrane *getMembrane(const QString &id) const

Get membrane by id.

const std::vector<std::pair<std::string, std::pair<QRgb, QRgb>>> &getIdColorPairs() const

Membrane id and adjacent compartment color pairs.

double getSize(const QString &id) const

Membrane size in model units.

void updateCompartmentNames(const QStringList &compartmentNames)

Update cached compartment-name text.

void updateCompartments(const std::vector<std::unique_ptr<geometry::Compartment>> &compartments)

Recompute membranes from compartment geometry.

void updateCompartmentImages(const common::ImageStack &imgs)

Recompute membrane pixels from geometry images.

void updateGeometryImageColor(QRgb oldColor, QRgb newColor)

Replace a compartment color in membrane definitions.

void importMembraneIdsAndNames()

Import membrane ids/names from SBML annotations.

void exportToSBML(const common::VolumeF &voxelSize)

Export membrane data to SBML.

explicit ModelMembranes(libsbml::Model *model = nullptr)

Construct membrane model.

~ModelMembranes()

Destructor.

bool getHasUnsavedChanges() const

Unsaved state flag.

void setHasUnsavedChanges(bool unsavedChanges)

Set unsaved state flag.

ModelParameters

class ModelParameters

SBML parameter manager.

Public Functions

ModelParameters()

Construct empty parameter model.

explicit ModelParameters(libsbml::Model *model)

Construct parameter model from SBML model.

void setEventsPtr(ModelEvents *events)

Set events dependency pointer.

void setSpeciesPtr(ModelSpecies *species)

Set species dependency pointer.

const QStringList &getIds() const

Parameter ids.

const QStringList &getNames() const

Parameter names.

QString setName(const QString &id, const QString &name)

Set display name.

QString getName(const QString &id) const

Get display name.

void setExpression(const QString &id, const QString &expr)

Set parameter expression/value.

QString getExpression(const QString &id) const

Get parameter expression/value.

QString add(const QString &name)

Add new parameter.

void remove(const QString &id)

Remove parameter.

const SpatialCoordinates &getSpatialCoordinates() const

Spatial coordinate parameters.

void setSpatialCoordinates(SpatialCoordinates coords)

Set spatial coordinate parameter ids.

std::vector<IdName> getSymbols(const QStringList &compartments = {}) const

Symbols available for expression substitution.

std::vector<IdNameValue> getGlobalConstants() const

Constant parameters.

std::vector<IdNameExpr> getNonConstantParameters() const

Non-constant parameters.

bool getHasUnsavedChanges() const

Unsaved state flag.

void setHasUnsavedChanges(bool unsavedChanges)

Set unsaved state flag.

ModelReactions

class ModelReactions

SBML reaction manager.

Public Functions

ModelReactions()

Construct empty reaction model.

explicit ModelReactions(libsbml::Model *model, const ModelCompartments *compartments, const ModelMembranes *membranes, bool isNonSpatialModel)

Construct reaction model from SBML model.

void makeReactionLocationsValid()

Ensure all reactions reference valid locations.

void applySpatialReactionRescalings(const std::vector<ReactionRescaling> &reactionRescalings)

Apply precomputed reaction expression rescalings.

std::vector<ReactionRescaling> getSpatialReactionRescalings() const

Compute expression rescalings for spatial unit consistency.

bool getIsIncompleteODEImport() const

Returns true if imported ODE reactions were incomplete.

QStringList getIds(const QString &locationId) const

Reaction ids for a location id.

QStringList getIds(const ReactionLocation &reactionLocation) const

Reaction ids for a location descriptor.

std::vector<ReactionLocation> getReactionLocations() const

All available reaction locations.

QString add(const QString &name, const QString &locationId, const QString &rateExpression = "1")

Add reaction.

void remove(const QString &id)

Remove reaction.

void removeAllInvolvingSpecies(const QString &speciesId)

Remove all reactions involving species.

QString setName(const QString &id, const QString &name)

Set reaction name.

QString getName(const QString &id) const

Get reaction name.

QString getScheme(const QString &id) const

Get stoichiometric scheme string.

void setLocation(const QString &id, const QString &locationId)

Set reaction location id.

QString getLocation(const QString &id) const

Get reaction location id.

double getSpeciesStoichiometry(const QString &id, const QString &speciesId) const

Stoichiometry of a species in a reaction.

void setSpeciesStoichiometry(const QString &id, const QString &speciesId, double stoichiometry)

Set stoichiometry for species in reaction.

QString getRateExpression(const QString &id) const

Get kinetic rate expression.

void setRateExpression(const QString &id, const QString &expression)

Set kinetic rate expression.

QStringList getParameterIds(const QString &id) const

Local parameter ids for reaction.

QString setParameterName(const QString &reactionId, const QString &parameterId, const QString &name)

Set local parameter name.

QString getParameterName(const QString &reactionId, const QString &parameterId) const

Get local parameter name.

void setParameterValue(const QString &reactionId, const QString &parameterId, double value)

Set local parameter value.

double getParameterValue(const QString &reactionId, const QString &parameterId) const

Get local parameter value.

QString addParameter(const QString &reactionId, const QString &name, double value)

Add local parameter to reaction.

void removeParameter(const QString &reactionId, const QString &id)

Remove local parameter from reaction.

bool dependOnVariable(const QString &variableId) const

Returns true if any reaction depends on variable id.

bool getHasUnsavedChanges() const

Unsaved state flag.

void setHasUnsavedChanges(bool unsavedChanges)

Set unsaved state flag.

ModelSpecies

class ModelSpecies

SBML species manager with spatial field data.

Public Functions

ModelSpecies()

Construct empty species model.

ModelSpecies(libsbml::Model *model, const ModelCompartments *compartments, const ModelGeometry *geometry, const ModelParameters *parameters, const ModelFunctions *functions, simulate::SimulationData *data, Settings *annotation)

Construct species model from SBML model and dependencies.

Parameters:

• model – SBML model pointer.

• compartments – Compartment manager.

• geometry – Geometry manager.

• parameters – Parameter manager.

• functions – Function manager.

• data – Simulation data storage.

• annotation – Settings annotation.

void setReactionsPtr(ModelReactions *reactions)

Set reactions dependency pointer.

Parameters:

reactions – Reaction manager.

void setSimulationDataPtr(simulate::SimulationData *data)

Set simulation-data dependency pointer.

Parameters:

data – Simulation data storage.

bool containsNonSpatialReactiveSpecies() const

Returns true if any reactive species is non-spatial.

Returns:

true if non-spatial reactive species exist.

QString add(const QString &name, const QString &compartmentId)

Add species to compartment.

Parameters:

• name – Species display name.

• compartmentId – Target compartment id.

Returns:

New species id.

void remove(const QString &id)

Remove species.

Parameters:

id – Species id.

QString setName(const QString &id, const QString &name)

Set species name.

Parameters:

• id – Species id.

• name – New species name.

Returns:

Final (possibly uniquified) name.

QString getName(const QString &id) const

Get species name.

Parameters:

id – Species id.

Returns:

Species name.

void updateCompartmentGeometry(const QString &compartmentId)

Rebuild field geometry after compartment geometry changes.

Parameters:

compartmentId – Compartment id.

void setCompartment(const QString &id, const QString &compartmentId)

Move species to another compartment.

Parameters:

• id – Species id.

• compartmentId – Target compartment id.

QString getCompartment(const QString &id) const

Get species compartment id.

Parameters:

id – Species id.

Returns:

Compartment id.

QStringList getIds(const QString &compartmentId) const

Species ids in a compartment.

Parameters:

compartmentId – Compartment id.

Returns:

Species ids in compartment.

QStringList getNames(const QString &compartmentId) const

Species names in a compartment.

Parameters:

compartmentId – Compartment id.

Returns:

Species names in compartment.

void setIsSpatial(const QString &id, bool isSpatial)

Set whether species is spatial.

Parameters:

• id – Species id.

• isSpatial – Spatial flag.

bool getIsSpatial(const QString &id) const

Returns whether species is spatial.

Parameters:

id – Species id.

Returns:

Spatial flag.

void setDiffusionConstant(const QString &id, double diffusionConstant)

Set uniform diffusion constant.

Parameters:

• id – Species id.

• diffusionConstant – Diffusion constant value.

double getDiffusionConstant(const QString &id) const

Get uniform diffusion constant.

Parameters:

id – Species id.

Returns:

Diffusion constant.

void setStorage(const QString &id, double storageValue)

Set species storage coefficient.

Parameters:

• id – Species id.

• storageValue – Storage value.

double getStorage(const QString &id) const

Get species storage coefficient.

Parameters:

id – Species id.

Returns:

Storage value.

SpatialDataType getDiffusionConstantType(const QString &id) const

Representation type of diffusion constant data.

Parameters:

id – Species id.

Returns:

Diffusion data representation type.

SpatialDataType getInitialConcentrationType(const QString &id) const

Representation type of initial concentration data.

Parameters:

id – Species id.

Returns:

Initial concentration representation type.

void setInitialConcentration(const QString &id, double concentration)

Set uniform initial concentration.

Parameters:

• id – Species id.

• concentration – Initial concentration value.

double getInitialConcentration(const QString &id) const

Get uniform initial concentration.

Parameters:

id – Species id.

Returns:

Initial concentration value.

void setAnalyticConcentration(const QString &id, const QString &analyticExpression)

Set analytic initial concentration expression.

Parameters:

• id – Species id.

• analyticExpression – Analytic concentration expression.

void setFieldConcAnalytic(geometry::Field &field, const std::string &expr, const std::map<std::string, double, std::less<>> &substitutions = {})

Apply analytic concentration expression to a field.

Parameters:

• field – Field to update.

• expr – Analytic expression.

• substitutions – Constant substitutions.

QString getAnalyticConcentration(const QString &id) const

Get analytic concentration expression.

Parameters:

id – Species id.

Returns:

Analytic concentration expression.

void updateAllAnalyticConcentrations()

Recompute all analytic concentrations.

void setSampledFieldConcentration(const QString &id, const std::vector<double> &concentrationArray)

Set sampled-field concentration array.

Parameters:

• id – Species id.

• concentrationArray – Concentration values in image order.

std::vector<double> getSampledFieldConcentration(const QString &id, bool maskAndInvertY = false) const

Get sampled-field concentration array.

Parameters:

• id – Species id.

• maskAndInvertY – If true, apply mask and Y inversion.

Returns:

Concentration values in image order.

void setSampledFieldDiffusionConstant(const QString &id, const std::vector<double> &diffusionConstantArray)

Set sampled-field diffusion constant array.

Parameters:

• id – Species id.

• diffusionConstantArray – Diffusion values in image order.

std::vector<double> getSampledFieldDiffusionConstant(const QString &id, bool maskAndInvertY = false) const

Get sampled-field diffusion constant array.

Parameters:

• id – Species id.

• maskAndInvertY – If true, apply mask and Y inversion.

Returns:

Diffusion values in image order.

bool isValidAnalyticDiffusionExpression(const QString &analyticExpression) const

Validate analytic diffusion expression.

Parameters:

analyticExpression – Expression to validate.

Returns:

true if expression is valid.

void setAnalyticDiffusionConstant(const QString &id, const QString &analyticExpression)

Set analytic diffusion constant expression.

Parameters:

• id – Species id.

• analyticExpression – Analytic diffusion expression.

QString getAnalyticDiffusionConstant(const QString &id) const

Get analytic diffusion constant expression.

Parameters:

id – Species id.

Returns:

Analytic diffusion expression.

bool isValidCrossDiffusionExpression(const QString &id, const QString &expression) const

Validate cross-diffusion expression for species pair.

Parameters:

• id – Primary species id.

• expression – Cross-diffusion expression.

Returns:

true if expression is valid.

void setCrossDiffusionConstant(const QString &id, const QString &otherId, const QString &expression)

Set cross-diffusion expression for species pair.

Parameters:

• id – Primary species id.

• otherId – Coupled species id.

• expression – Cross-diffusion expression.

void removeCrossDiffusionConstant(const QString &id, const QString &otherId)

Remove cross-diffusion expression for species pair.

Parameters:

• id – Primary species id.

• otherId – Coupled species id.

QString getCrossDiffusionConstant(const QString &id, const QString &otherId) const

Get cross-diffusion expression for species pair.

Parameters:

• id – Primary species id.

• otherId – Coupled species id.

Returns:

Cross-diffusion expression.

std::map<std::string, std::string> getCrossDiffusionConstants(const QString &id) const

Get all cross-diffusion expressions for a species.

Parameters:

id – Species id.

Returns:

Mapping from coupled species id to expression.

common::ImageStack getConcentrationImages(const QString &id) const

Concentration images for species.

Parameters:

id – Species id.

Returns:

Concentration image stack.

void setColor(const QString &id, QRgb color)

Set species display color.

Parameters:

• id – Species id.

• color – New display color.

QRgb getColor(const QString &id) const

Get species display color.

Parameters:

id – Species id.

Returns:

Species display color.

void setIsConstant(const QString &id, bool constant)

Set constant/non-constant species flag.

Parameters:

• id – Species id.

• constant – Constant flag.

bool getIsConstant(const QString &id) const

Get constant/non-constant species flag.

Parameters:

id – Species id.

Returns:

Constant flag.

bool isScalarConstantSpecies(const QString &id) const

Returns whether species is a scalar constant.

Parameters:

id – Species id.

Returns:

true if species is constant and non-spatial.

bool isSimulatedSpecies(const QString &id) const

Returns whether species should be present in simulation fields.

Parameters:

id – Species id.

Returns:

true if species should appear in simulation state/results.

bool isReactive(const QString &id) const

Returns whether species participates in any reaction.

Parameters:

id – Species id.

Returns:

true if species is reactive.

void removeInitialAssignments()

Remove all species initial assignments.

QString getSampledFieldInitialAssignment(const QString &id) const

Get sampled-field initial-assignment expression.

Parameters:

id – Species id.

Returns:

Initial-assignment expression.

geometry::Field *getField(const QString &id)

Mutable field object for species id.

Parameters:

id – Species id.

Returns:

Mutable field pointer or nullptr.

const geometry::Field *getField(const QString &id) const

Immutable field object for species id.

Parameters:

id – Species id.

Returns:

Immutable field pointer or nullptr.

bool getHasUnsavedChanges() const

Unsaved state flag.

Returns:

Unsaved state flag.

void setHasUnsavedChanges(bool unsavedChanges)

Set unsaved state flag.

Parameters:

unsavedChanges – New unsaved state.

ModelUnits

class ModelUnits

Model unit system and derived display strings.

Public Functions

explicit ModelUnits(libsbml::Model *model = nullptr)

Construct units manager from SBML model.

const Unit &getTime() const

Selected time unit.

int getTimeIndex() const

Selected time unit index.

const QVector<Unit> &getTimeUnits() const

Available time units.

QVector<Unit> &getTimeUnits()

Mutable time unit list.

void setTimeIndex(int index)

Set selected time unit index.

const Unit &getLength() const

Selected length unit.

int getLengthIndex() const

Selected length unit index.

const QVector<Unit> &getLengthUnits() const

Available length units.

QVector<Unit> &getLengthUnits()

Mutable length unit list.

void setLengthIndex(int index)

Set selected length unit index.

const Unit &getVolume() const

Selected volume unit.

int getVolumeIndex() const

Selected volume unit index.

const QVector<Unit> &getVolumeUnits() const

Available volume units.

QVector<Unit> &getVolumeUnits()

Mutable volume unit list.

void setVolumeIndex(int index)

Set selected volume unit index.

const Unit &getAmount() const

Selected amount unit.

int getAmountIndex() const

Selected amount unit index.

const QVector<Unit> &getAmountUnits() const

Available amount units.

QVector<Unit> &getAmountUnits()

Mutable amount unit list.

void setAmountIndex(int index)

Set selected amount unit index.

const QString &getConcentration() const

Derived concentration unit string.

const QString &getDiffusion() const

Derived diffusion unit string.

const QString &getCompartmentReaction() const

Derived compartment reaction-rate unit string.

const QString &getMembraneReaction() const

Derived membrane reaction-rate unit string.

bool getHasUnsavedChanges() const

Unsaved state flag.

void setHasUnsavedChanges(bool unsavedChanges)

Set unsaved state flag.

Settings

struct Settings

Complete SME model annotation payload.

Public Functions

template<class Archive>
inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

SimulationSettings simulationSettings = {}

Simulation settings.

DisplayOptions displayOptions = {}

Display settings.

MeshParameters meshParameters = {}

Mesh settings.

std::map<std::string, QRgb> speciesColors = {}

Species id to display color mapping.

sme::simulate::OptimizeOptions optimizeOptions = {}

Parameter optimization settings.

std::vector<QRgb> sampledFieldColors = {}

Imported sampled-field compartment colors.

std::map<std::string, std::vector<double>> speciesDiffusionConstantArrays = {}

Species diffusion constants for image-based definitions.

std::map<std::string, std::string> speciesAnalyticDiffusionConstants = {}

Species diffusion constants as analytic expressions.

std::map<std::string, std::map<std::string, std::string>> speciesCrossDiffusionConstants = {}

Cross-diffusion expressions by species pair.

std::map<std::string, double> speciesStorageValues = {}

Optional species storage coefficients.

std::vector<simulate::FeatureDefinition> features = {}

Feature definitions for extracting scalar time-series from ROIs.

struct SimulationSettings

Simulation settings persisted with model annotation.

Public Functions

template<class Archive>
inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

std::vector<std::pair<std::size_t, double>> times = {}

Sequence of simulation segments: (nSteps, dt).

simulate::Options options = {}

Solver runtime options.

sme::simulate::SimulatorType simulatorType = {}

Selected simulator backend.

struct DisplayOptions

UI display preferences persisted with the model.

Public Functions

template<class Archive>
inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

std::vector<bool> showSpecies = {}

Per-species visibility flags.

bool showMinMax = {true}

Display min/max concentration overlays.

bool normaliseOverAllTimepoints = {true}

Normalize colormap over all simulated timepoints.

bool normaliseOverAllSpecies = {true}

Normalize colormap over all species.

bool showGeometryGrid = {false}

Show geometry grid overlay.

bool showGeometryScale = {false}

Show geometry scale annotation.

bool invertYAxis = {false}

Invert vertical image axis in views/export.

std::vector<bool> showFeatures = {}

Per-feature visibility flags.

struct MeshParameters

Mesh generation options stored in model annotation.

Public Functions

template<class Archive>
inline void serialize(Archive &ar, std::uint32_t const version)

Public Members

std::vector<std::size_t> maxPoints = {}

Maximum boundary points per boundary or global total (mode dependent).

std::vector<std::size_t> maxAreas = {}

Maximum triangle area per compartment.

std::size_t boundarySimplifierType = {0}

Boundary simplification algorithm selection.

std::vector<std::size_t> maxCellVolumes = {}

Maximum tetrahedron cell volume per compartment (3D voxel mesh).

MeshSourceType meshSourceType = {MeshSourceType::VoxelGeometry}

Mesh source mode.