spatial-model-editor
stable
Getting started
Getting Started
Importing a Model
Importing Geometry
Assign Compartments
Rescale Reactions
Mesh generation
Species properties
Reactions
Running a Simulation
Python interface
Python Interface
Example Notebooks
API Reference
Reference documentation
dune-copasi simulator
Pixel simulator
Parameter optimization
Mesh generation
Command Line Interface
Maths
Units
Changelog
Source Code
License
Developer documentation
Core
Tests
spatial-model-editor
Index
Edit on GitHub
Index
_
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A
|
C
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D
|
E
|
G
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I
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M
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N
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O
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P
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R
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S
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T
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U
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V
_
__init__() (sme.Compartment method)
(sme.CompartmentList method)
(sme.ConcentrationType method)
(sme.Membrane method)
(sme.MembraneList method)
(sme.Model method)
(sme.Parameter method)
(sme.ParameterList method)
(sme.Reaction method)
(sme.ReactionList method)
(sme.ReactionParameter method)
(sme.ReactionParameterList method)
(sme.SimulationResult method)
(sme.SimulationResultList method)
(sme.SimulatorType method)
(sme.Species method)
(sme.SpeciesList method)
A
Analytic (sme.ConcentrationType attribute)
analytic_concentration (sme.Species property)
C
Compartment (class in sme)
compartment_image (sme.Model property)
CompartmentList (class in sme)
compartments (sme.Model property)
concentration_image (sme.SimulationResult property)
(sme.Species property)
concentration_type (sme.Species property)
ConcentrationType (class in sme)
D
diffusion_constant (sme.Species property)
DUNE (sme.SimulatorType attribute)
E
export_sbml_file() (sme.Model method)
export_sme_file() (sme.Model method)
G
geometry_mask (sme.Compartment property)
I
Image (sme.ConcentrationType attribute)
import_geometry_from_image() (sme.Model method)
InvalidArgument
M
Membrane (class in sme)
MembraneList (class in sme)
membranes (sme.Model property)
Model (class in sme)
module
sme
N
name (sme.Compartment property)
(sme.ConcentrationType property)
(sme.Membrane property)
(sme.Model property)
(sme.Parameter property)
(sme.Reaction property)
(sme.ReactionParameter property)
(sme.SimulatorType property)
(sme.Species property)
O
open_example_model() (in module sme)
open_file() (in module sme)
open_sbml_file() (in module sme)
P
Parameter (class in sme)
ParameterList (class in sme)
parameters (sme.Model property)
(sme.Reaction property)
Pixel (sme.SimulatorType attribute)
R
Reaction (class in sme)
ReactionList (class in sme)
ReactionParameter (class in sme)
ReactionParameterList (class in sme)
reactions (sme.Compartment property)
(sme.Membrane property)
RuntimeError
S
simulate() (sme.Model method)
simulation_results() (sme.Model method)
SimulationResult (class in sme)
SimulationResultList (class in sme)
SimulatorType (class in sme)
sme
module
sme (C++ type)
,
[1]
sme::common (C++ type)
,
[1]
sme::common::average (C++ function)
sme::common::cyclicErase (C++ function)
sme::common::decltypeStr (C++ function)
sme::common::element_index (C++ function)
sme::common::free_deleter (C++ struct)
sme::common::free_deleter::operator() (C++ function)
sme::common::get_unique_values (C++ function)
sme::common::indexedColours (C++ class)
sme::common::indexedColours::colours (C++ member)
sme::common::indexedColours::operator[] (C++ function)
sme::common::isCyclicPermutation (C++ function)
sme::common::isItIndexes (C++ function)
sme::common::max (C++ function)
sme::common::min (C++ function)
sme::common::minmax (C++ function)
sme::common::SmeFileContents (C++ struct)
sme::common::SmeFileContents::simulationData (C++ member)
sme::common::SmeFileContents::xmlModel (C++ member)
sme::common::stringToVector (C++ function)
sme::common::sum (C++ function)
sme::common::Symbolic (C++ class)
sme::common::Symbolic::clear (C++ function)
sme::common::Symbolic::compile (C++ function)
sme::common::Symbolic::diff (C++ function)
sme::common::Symbolic::eval (C++ function)
,
[1]
sme::common::Symbolic::expr (C++ function)
sme::common::Symbolic::getErrorMessage (C++ function)
sme::common::Symbolic::inlinedExpr (C++ function)
sme::common::Symbolic::isCompiled (C++ function)
sme::common::Symbolic::isValid (C++ function)
sme::common::Symbolic::parse (C++ function)
,
[1]
sme::common::Symbolic::relabel (C++ function)
sme::common::Symbolic::rescale (C++ function)
sme::common::Symbolic::Symbolic (C++ function)
,
[1]
,
[2]
sme::common::TiffReader (C++ class)
sme::common::TiffReader::empty (C++ function)
sme::common::TiffReader::getErrorMessage (C++ function)
sme::common::TiffReader::getImages (C++ function)
sme::common::TiffReader::TiffReader (C++ function)
sme::common::unique_C_ptr (C++ type)
sme::common::vectorToString (C++ function)
sme::mesh::Boundary (C++ class)
sme::mesh::Boundary::Boundary (C++ function)
sme::mesh::Boundary::getAllPoints (C++ function)
sme::mesh::Boundary::getMaxPoints (C++ function)
sme::mesh::Boundary::getPoints (C++ function)
sme::mesh::Boundary::isLoop (C++ function)
sme::mesh::Boundary::isValid (C++ function)
sme::mesh::Boundary::setMaxPoints (C++ function)
,
[1]
sme::mesh::Boundary::setPoints (C++ function)
sme::mesh::ContourMap (C++ class)
sme::mesh::ContourMap::ContourMap (C++ function)
sme::mesh::ContourMap::getContourIndices (C++ function)
sme::mesh::ContourMap::isFixedPoint (C++ function)
sme::mesh::Contours (C++ struct)
sme::mesh::Contours::compartmentEdges (C++ member)
sme::mesh::Contours::domainEdges (C++ member)
sme::mesh::getInteriorPoints (C++ function)
sme::mesh::LineError (C++ struct)
sme::mesh::LineError::average (C++ member)
sme::mesh::LineError::total (C++ member)
sme::mesh::LineSimplifier (C++ class)
sme::mesh::LineSimplifier::getAllVertices (C++ function)
sme::mesh::LineSimplifier::getSimplifiedLine (C++ function)
,
[1]
sme::mesh::LineSimplifier::isLoop (C++ function)
sme::mesh::LineSimplifier::isValid (C++ function)
sme::mesh::LineSimplifier::LineSimplifier (C++ function)
sme::mesh::LineSimplifier::maxPoints (C++ function)
sme::mesh::Mesh2d (C++ class)
sme::mesh::Mesh2d::dim (C++ member)
sme::mesh::Mesh2d::getBoundariesImages (C++ function)
sme::mesh::Mesh2d::getBoundaryMaxPoints (C++ function)
,
[1]
sme::mesh::Mesh2d::getBoundarySimplificationType (C++ function)
sme::mesh::Mesh2d::getCompartmentInteriorPoints (C++ function)
sme::mesh::Mesh2d::getCompartmentMaxTriangleArea (C++ function)
,
[1]
sme::mesh::Mesh2d::getErrorMessage (C++ function)
sme::mesh::Mesh2d::getGMSH (C++ function)
sme::mesh::Mesh2d::getMeshImages (C++ function)
sme::mesh::Mesh2d::getNumBoundaries (C++ function)
sme::mesh::Mesh2d::getTriangleIndices (C++ function)
sme::mesh::Mesh2d::getTriangleIndicesAsFlatArray (C++ function)
sme::mesh::Mesh2d::getVerticesAsFlatArray (C++ function)
sme::mesh::Mesh2d::isValid (C++ function)
sme::mesh::Mesh2d::Mesh2d (C++ function)
,
[1]
sme::mesh::Mesh2d::setBoundaryMaxPoints (C++ function)
sme::mesh::Mesh2d::setBoundarySimplificationType (C++ function)
sme::mesh::Mesh2d::setCompartmentMaxTriangleArea (C++ function)
sme::mesh::Mesh2d::setPhysicalGeometry (C++ function)
sme::mesh::Mesh2d::~Mesh2d (C++ function)
sme::mesh::Mesh3d (C++ class)
sme::mesh::Mesh3d::dim (C++ member)
sme::mesh::Mesh3d::getColors (C++ function)
sme::mesh::Mesh3d::getCompartmentMaxCellVolume (C++ function)
,
[1]
sme::mesh::Mesh3d::getErrorMessage (C++ function)
sme::mesh::Mesh3d::getGMSH (C++ function)
sme::mesh::Mesh3d::getMeshTrianglesIndicesAsFlatArray (C++ function)
sme::mesh::Mesh3d::getNumberOfCompartment (C++ function)
sme::mesh::Mesh3d::getOffset (C++ function)
sme::mesh::Mesh3d::getTetrahedronIndices (C++ function)
sme::mesh::Mesh3d::getTetrahedronIndicesAsFlatArray (C++ function)
sme::mesh::Mesh3d::getVerticesAsFlatArray (C++ function)
sme::mesh::Mesh3d::getVerticesAsQVector4DArrayInHomogeneousCoord (C++ function)
sme::mesh::Mesh3d::isValid (C++ function)
sme::mesh::Mesh3d::Mesh3d (C++ function)
,
[1]
sme::mesh::Mesh3d::setCompartmentMaxCellVolume (C++ function)
sme::mesh::Mesh3d::setPhysicalGeometry (C++ function)
sme::mesh::Mesh3d::~Mesh3d (C++ function)
sme::mesh::PixelCornerIterator (C++ class)
sme::mesh::PixelCornerIterator::done (C++ function)
sme::mesh::PixelCornerIterator::operator++ (C++ function)
sme::mesh::PixelCornerIterator::PixelCornerIterator (C++ function)
sme::mesh::PixelCornerIterator::vertex (C++ function)
sme::mesh::Triangulate (C++ class)
sme::mesh::Triangulate::getPoints (C++ function)
sme::mesh::Triangulate::getTriangleIndices (C++ function)
sme::mesh::Triangulate::Triangulate (C++ function)
sme::model::DisplayOptions (C++ struct)
sme::model::DisplayOptions::invertYAxis (C++ member)
sme::model::DisplayOptions::normaliseOverAllSpecies (C++ member)
sme::model::DisplayOptions::normaliseOverAllTimepoints (C++ member)
sme::model::DisplayOptions::serialize (C++ function)
sme::model::DisplayOptions::showGeometryGrid (C++ member)
sme::model::DisplayOptions::showGeometryScale (C++ member)
sme::model::DisplayOptions::showMinMax (C++ member)
sme::model::DisplayOptions::showSpecies (C++ member)
sme::model::MeshParameters (C++ struct)
sme::model::MeshParameters::boundarySimplifierType (C++ member)
sme::model::MeshParameters::maxAreas (C++ member)
sme::model::MeshParameters::maxPoints (C++ member)
sme::model::MeshParameters::serialize (C++ function)
sme::model::Model (C++ class)
sme::model::Model::clear (C++ function)
sme::model::Model::createSBMLFile (C++ function)
sme::model::Model::exportSBMLFile (C++ function)
sme::model::Model::exportSMEFile (C++ function)
sme::model::Model::getCompartments (C++ function)
,
[1]
sme::model::Model::getCurrentFilename (C++ function)
sme::model::Model::getDisplayOptions (C++ function)
sme::model::Model::getErrorMessage (C++ function)
sme::model::Model::getEvents (C++ function)
,
[1]
sme::model::Model::getFunctions (C++ function)
,
[1]
sme::model::Model::getGeometry (C++ function)
,
[1]
sme::model::Model::getHasUnsavedChanges (C++ function)
sme::model::Model::getIsValid (C++ function)
sme::model::Model::getMath (C++ function)
,
[1]
sme::model::Model::getMembranes (C++ function)
,
[1]
sme::model::Model::getMeshParameters (C++ function)
,
[1]
sme::model::Model::getName (C++ function)
sme::model::Model::getOptimizeOptions (C++ function)
,
[1]
sme::model::Model::getParameters (C++ function)
,
[1]
sme::model::Model::getReactions (C++ function)
,
[1]
sme::model::Model::getSampledFieldColours (C++ function)
sme::model::Model::getSimulationData (C++ function)
,
[1]
sme::model::Model::getSimulationSettings (C++ function)
,
[1]
sme::model::Model::getSpecies (C++ function)
,
[1]
sme::model::Model::getSpeciesGeometry (C++ function)
sme::model::Model::getUnits (C++ function)
,
[1]
sme::model::Model::getXml (C++ function)
sme::model::Model::importFile (C++ function)
sme::model::Model::importSBMLFile (C++ function)
sme::model::Model::importSBMLString (C++ function)
sme::model::Model::inlineExpr (C++ function)
sme::model::Model::Model (C++ function)
,
[1]
,
[2]
sme::model::Model::operator= (C++ function)
,
[1]
sme::model::Model::setDisplayOptions (C++ function)
sme::model::Model::setName (C++ function)
sme::model::Model::~Model (C++ function)
sme::model::ModelCompartments (C++ class)
sme::model::ModelCompartments::add (C++ function)
sme::model::ModelCompartments::clear (C++ function)
sme::model::ModelCompartments::getColour (C++ function)
sme::model::ModelCompartments::getColours (C++ function)
sme::model::ModelCompartments::getCompartment (C++ function)
,
[1]
sme::model::ModelCompartments::getCompartments (C++ function)
sme::model::ModelCompartments::getHasUnsavedChanges (C++ function)
sme::model::ModelCompartments::getIdFromColour (C++ function)
sme::model::ModelCompartments::getIds (C++ function)
sme::model::ModelCompartments::getInitialCompartmentSizes (C++ function)
sme::model::ModelCompartments::getInteriorPoints (C++ function)
sme::model::ModelCompartments::getName (C++ function)
sme::model::ModelCompartments::getNames (C++ function)
sme::model::ModelCompartments::getSize (C++ function)
sme::model::ModelCompartments::ModelCompartments (C++ function)
,
[1]
sme::model::ModelCompartments::remove (C++ function)
sme::model::ModelCompartments::setColour (C++ function)
sme::model::ModelCompartments::setGeometryPtr (C++ function)
sme::model::ModelCompartments::setHasUnsavedChanges (C++ function)
sme::model::ModelCompartments::setInteriorPoints (C++ function)
sme::model::ModelCompartments::setName (C++ function)
sme::model::ModelCompartments::setReactionsPtr (C++ function)
sme::model::ModelCompartments::setSimulationDataPtr (C++ function)
sme::model::ModelCompartments::setSpeciesPtr (C++ function)
sme::model::ModelEvents (C++ class)
sme::model::ModelEvents::add (C++ function)
sme::model::ModelEvents::applyEvent (C++ function)
sme::model::ModelEvents::getExpression (C++ function)
sme::model::ModelEvents::getHasUnsavedChanges (C++ function)
sme::model::ModelEvents::getIds (C++ function)
sme::model::ModelEvents::getName (C++ function)
sme::model::ModelEvents::getNames (C++ function)
sme::model::ModelEvents::getTime (C++ function)
sme::model::ModelEvents::getValue (C++ function)
sme::model::ModelEvents::getVariable (C++ function)
sme::model::ModelEvents::isParameter (C++ function)
sme::model::ModelEvents::ModelEvents (C++ function)
,
[1]
sme::model::ModelEvents::remove (C++ function)
sme::model::ModelEvents::removeAnyUsingVariable (C++ function)
sme::model::ModelEvents::setExpression (C++ function)
sme::model::ModelEvents::setHasUnsavedChanges (C++ function)
sme::model::ModelEvents::setName (C++ function)
sme::model::ModelEvents::setTime (C++ function)
sme::model::ModelEvents::setVariable (C++ function)
sme::model::ModelFunctions (C++ class)
sme::model::ModelFunctions::add (C++ function)
sme::model::ModelFunctions::addArgument (C++ function)
sme::model::ModelFunctions::getArguments (C++ function)
sme::model::ModelFunctions::getExpression (C++ function)
sme::model::ModelFunctions::getHasUnsavedChanges (C++ function)
sme::model::ModelFunctions::getIds (C++ function)
sme::model::ModelFunctions::getName (C++ function)
sme::model::ModelFunctions::getNames (C++ function)
sme::model::ModelFunctions::getSymbolicFunctions (C++ function)
sme::model::ModelFunctions::ModelFunctions (C++ function)
,
[1]
sme::model::ModelFunctions::remove (C++ function)
sme::model::ModelFunctions::removeArgument (C++ function)
sme::model::ModelFunctions::setExpression (C++ function)
sme::model::ModelFunctions::setHasUnsavedChanges (C++ function)
sme::model::ModelFunctions::setName (C++ function)
sme::model::ModelGeometry (C++ class)
sme::model::ModelGeometry::clear (C++ function)
sme::model::ModelGeometry::getHasImage (C++ function)
sme::model::ModelGeometry::getHasUnsavedChanges (C++ function)
sme::model::ModelGeometry::getImages (C++ function)
sme::model::ModelGeometry::getIsMeshValid (C++ function)
sme::model::ModelGeometry::getIsValid (C++ function)
sme::model::ModelGeometry::getMesh2d (C++ function)
sme::model::ModelGeometry::getMesh3d (C++ function)
sme::model::ModelGeometry::getNumDimensions (C++ function)
sme::model::ModelGeometry::getPhysicalOrigin (C++ function)
sme::model::ModelGeometry::getPhysicalPoint (C++ function)
sme::model::ModelGeometry::getPhysicalPointAsString (C++ function)
sme::model::ModelGeometry::getPhysicalSize (C++ function)
sme::model::ModelGeometry::getVoxelSize (C++ function)
sme::model::ModelGeometry::importGeometryFromImages (C++ function)
sme::model::ModelGeometry::importSampledFieldGeometry (C++ function)
,
[1]
sme::model::ModelGeometry::ModelGeometry (C++ function)
,
[1]
sme::model::ModelGeometry::setHasUnsavedChanges (C++ function)
sme::model::ModelGeometry::setVoxelSize (C++ function)
sme::model::ModelGeometry::updateMesh (C++ function)
sme::model::ModelGeometry::writeGeometryToSBML (C++ function)
sme::model::ModelMath (C++ class)
sme::model::ModelMath::eval (C++ function)
sme::model::ModelMath::getErrorMessage (C++ function)
sme::model::ModelMath::isValid (C++ function)
sme::model::ModelMath::ModelMath (C++ function)
,
[1]
sme::model::ModelMath::parse (C++ function)
sme::model::ModelMembranes (C++ class)
sme::model::ModelMembranes::exportToSBML (C++ function)
sme::model::ModelMembranes::getHasUnsavedChanges (C++ function)
sme::model::ModelMembranes::getIdColourPairs (C++ function)
sme::model::ModelMembranes::getIds (C++ function)
sme::model::ModelMembranes::getMembrane (C++ function)
sme::model::ModelMembranes::getMembranes (C++ function)
sme::model::ModelMembranes::getName (C++ function)
sme::model::ModelMembranes::getNames (C++ function)
sme::model::ModelMembranes::getSize (C++ function)
sme::model::ModelMembranes::importMembraneIdsAndNames (C++ function)
sme::model::ModelMembranes::ModelMembranes (C++ function)
sme::model::ModelMembranes::setHasUnsavedChanges (C++ function)
sme::model::ModelMembranes::setName (C++ function)
sme::model::ModelMembranes::updateCompartmentImages (C++ function)
sme::model::ModelMembranes::updateCompartmentNames (C++ function)
sme::model::ModelMembranes::updateCompartments (C++ function)
sme::model::ModelMembranes::~ModelMembranes (C++ function)
sme::model::ModelParameters (C++ class)
sme::model::ModelParameters::add (C++ function)
sme::model::ModelParameters::getExpression (C++ function)
sme::model::ModelParameters::getGlobalConstants (C++ function)
sme::model::ModelParameters::getHasUnsavedChanges (C++ function)
sme::model::ModelParameters::getIds (C++ function)
sme::model::ModelParameters::getName (C++ function)
sme::model::ModelParameters::getNames (C++ function)
sme::model::ModelParameters::getNonConstantParameters (C++ function)
sme::model::ModelParameters::getSpatialCoordinates (C++ function)
sme::model::ModelParameters::getSymbols (C++ function)
sme::model::ModelParameters::ModelParameters (C++ function)
,
[1]
sme::model::ModelParameters::remove (C++ function)
sme::model::ModelParameters::setEventsPtr (C++ function)
sme::model::ModelParameters::setExpression (C++ function)
sme::model::ModelParameters::setHasUnsavedChanges (C++ function)
sme::model::ModelParameters::setName (C++ function)
sme::model::ModelParameters::setSpatialCoordinates (C++ function)
sme::model::ModelParameters::setSpeciesPtr (C++ function)
sme::model::ModelReactions (C++ class)
sme::model::ModelReactions::add (C++ function)
sme::model::ModelReactions::addParameter (C++ function)
sme::model::ModelReactions::applySpatialReactionRescalings (C++ function)
sme::model::ModelReactions::dependOnVariable (C++ function)
sme::model::ModelReactions::getHasUnsavedChanges (C++ function)
sme::model::ModelReactions::getIds (C++ function)
,
[1]
sme::model::ModelReactions::getIsIncompleteODEImport (C++ function)
sme::model::ModelReactions::getLocation (C++ function)
sme::model::ModelReactions::getName (C++ function)
sme::model::ModelReactions::getParameterIds (C++ function)
sme::model::ModelReactions::getParameterName (C++ function)
sme::model::ModelReactions::getParameterValue (C++ function)
sme::model::ModelReactions::getRateExpression (C++ function)
sme::model::ModelReactions::getReactionLocations (C++ function)
sme::model::ModelReactions::getScheme (C++ function)
sme::model::ModelReactions::getSpatialReactionRescalings (C++ function)
sme::model::ModelReactions::getSpeciesStoichiometry (C++ function)
sme::model::ModelReactions::makeReactionLocationsValid (C++ function)
sme::model::ModelReactions::ModelReactions (C++ function)
,
[1]
sme::model::ModelReactions::remove (C++ function)
sme::model::ModelReactions::removeAllInvolvingSpecies (C++ function)
sme::model::ModelReactions::removeParameter (C++ function)
sme::model::ModelReactions::setHasUnsavedChanges (C++ function)
sme::model::ModelReactions::setLocation (C++ function)
sme::model::ModelReactions::setName (C++ function)
sme::model::ModelReactions::setParameterName (C++ function)
sme::model::ModelReactions::setParameterValue (C++ function)
sme::model::ModelReactions::setRateExpression (C++ function)
sme::model::ModelReactions::setSpeciesStoichiometry (C++ function)
sme::model::ModelSpecies (C++ class)
sme::model::ModelSpecies::add (C++ function)
sme::model::ModelSpecies::containsNonSpatialReactiveSpecies (C++ function)
sme::model::ModelSpecies::getAnalyticConcentration (C++ function)
sme::model::ModelSpecies::getColour (C++ function)
sme::model::ModelSpecies::getCompartment (C++ function)
sme::model::ModelSpecies::getConcentrationImages (C++ function)
sme::model::ModelSpecies::getDiffusionConstant (C++ function)
sme::model::ModelSpecies::getField (C++ function)
,
[1]
sme::model::ModelSpecies::getHasUnsavedChanges (C++ function)
sme::model::ModelSpecies::getIds (C++ function)
sme::model::ModelSpecies::getInitialConcentration (C++ function)
sme::model::ModelSpecies::getInitialConcentrationType (C++ function)
sme::model::ModelSpecies::getIsConstant (C++ function)
sme::model::ModelSpecies::getIsSpatial (C++ function)
sme::model::ModelSpecies::getName (C++ function)
sme::model::ModelSpecies::getNames (C++ function)
sme::model::ModelSpecies::getSampledFieldConcentration (C++ function)
sme::model::ModelSpecies::getSampledFieldInitialAssignment (C++ function)
sme::model::ModelSpecies::isReactive (C++ function)
sme::model::ModelSpecies::ModelSpecies (C++ function)
,
[1]
sme::model::ModelSpecies::remove (C++ function)
sme::model::ModelSpecies::removeInitialAssignments (C++ function)
sme::model::ModelSpecies::setAnalyticConcentration (C++ function)
sme::model::ModelSpecies::setColour (C++ function)
sme::model::ModelSpecies::setCompartment (C++ function)
sme::model::ModelSpecies::setDiffusionConstant (C++ function)
sme::model::ModelSpecies::setFieldConcAnalytic (C++ function)
sme::model::ModelSpecies::setHasUnsavedChanges (C++ function)
sme::model::ModelSpecies::setInitialConcentration (C++ function)
sme::model::ModelSpecies::setIsConstant (C++ function)
sme::model::ModelSpecies::setIsSpatial (C++ function)
sme::model::ModelSpecies::setName (C++ function)
sme::model::ModelSpecies::setReactionsPtr (C++ function)
sme::model::ModelSpecies::setSampledFieldConcentration (C++ function)
sme::model::ModelSpecies::setSimulationDataPtr (C++ function)
sme::model::ModelSpecies::updateAllAnalyticConcentrations (C++ function)
sme::model::ModelSpecies::updateCompartmentGeometry (C++ function)
sme::model::ModelUnits (C++ class)
sme::model::ModelUnits::getAmount (C++ function)
sme::model::ModelUnits::getAmountIndex (C++ function)
sme::model::ModelUnits::getAmountUnits (C++ function)
,
[1]
sme::model::ModelUnits::getCompartmentReaction (C++ function)
sme::model::ModelUnits::getConcentration (C++ function)
sme::model::ModelUnits::getDiffusion (C++ function)
sme::model::ModelUnits::getHasUnsavedChanges (C++ function)
sme::model::ModelUnits::getLength (C++ function)
sme::model::ModelUnits::getLengthIndex (C++ function)
sme::model::ModelUnits::getLengthUnits (C++ function)
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[1]
sme::model::ModelUnits::getMembraneReaction (C++ function)
sme::model::ModelUnits::getTime (C++ function)
sme::model::ModelUnits::getTimeIndex (C++ function)
sme::model::ModelUnits::getTimeUnits (C++ function)
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[1]
sme::model::ModelUnits::getVolume (C++ function)
sme::model::ModelUnits::getVolumeIndex (C++ function)
sme::model::ModelUnits::getVolumeUnits (C++ function)
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[1]
sme::model::ModelUnits::ModelUnits (C++ function)
sme::model::ModelUnits::setAmountIndex (C++ function)
sme::model::ModelUnits::setHasUnsavedChanges (C++ function)
sme::model::ModelUnits::setLengthIndex (C++ function)
sme::model::ModelUnits::setTimeIndex (C++ function)
sme::model::ModelUnits::setVolumeIndex (C++ function)
sme::model::Settings (C++ struct)
sme::model::Settings::displayOptions (C++ member)
sme::model::Settings::meshParameters (C++ member)
sme::model::Settings::optimizeOptions (C++ member)
sme::model::Settings::sampledFieldColours (C++ member)
sme::model::Settings::serialize (C++ function)
sme::model::Settings::simulationSettings (C++ member)
sme::model::Settings::speciesColours (C++ member)
sme::model::SimulationSettings (C++ struct)
sme::model::SimulationSettings::options (C++ member)
sme::model::SimulationSettings::serialize (C++ function)
sme::model::SimulationSettings::simulatorType (C++ member)
sme::model::SimulationSettings::times (C++ member)
sme::simulate::AvgMinMax (C++ struct)
sme::simulate::AvgMinMax::avg (C++ member)
sme::simulate::AvgMinMax::max (C++ member)
sme::simulate::AvgMinMax::min (C++ member)
sme::simulate::AvgMinMax::serialize (C++ function)
sme::simulate::BaseSim (C++ class)
sme::simulate::BaseSim::errorImages (C++ function)
sme::simulate::BaseSim::errorMessage (C++ function)
sme::simulate::BaseSim::getConcentrationPadding (C++ function)
sme::simulate::BaseSim::getConcentrations (C++ function)
sme::simulate::BaseSim::run (C++ function)
sme::simulate::BaseSim::setStopRequested (C++ function)
sme::simulate::BaseSim::~BaseSim (C++ function)
sme::simulate::DuneConverter (C++ class)
sme::simulate::DuneConverter::DuneConverter (C++ function)
sme::simulate::DuneConverter::getCompartmentNames (C++ function)
sme::simulate::DuneConverter::getConcentrations (C++ function)
sme::simulate::DuneConverter::getImageSize (C++ function)
sme::simulate::DuneConverter::getIniFile (C++ function)
sme::simulate::DuneConverter::getMesh (C++ function)
sme::simulate::DuneConverter::getMesh3d (C++ function)
sme::simulate::DuneConverter::getOrigin (C++ function)
sme::simulate::DuneConverter::getSpeciesNames (C++ function)
sme::simulate::DuneConverter::getVoxelSize (C++ function)
sme::simulate::DuneDiscretizationType (C++ enum)
sme::simulate::DuneDiscretizationType::FEM1 (C++ enumerator)
sme::simulate::DuneImpl (C++ class)
sme::simulate::DuneImpl::DuneImpl (C++ function)
sme::simulate::DuneImpl::getConcentrations (C++ function)
sme::simulate::DuneImpl::run (C++ function)
sme::simulate::DuneImpl::~DuneImpl (C++ function)
sme::simulate::DuneOptions (C++ struct)
sme::simulate::DuneOptions::decrease (C++ member)
sme::simulate::DuneOptions::discretization (C++ member)
sme::simulate::DuneOptions::dt (C++ member)
sme::simulate::DuneOptions::increase (C++ member)
sme::simulate::DuneOptions::integrator (C++ member)
sme::simulate::DuneOptions::linearSolver (C++ member)
sme::simulate::DuneOptions::maxDt (C++ member)
sme::simulate::DuneOptions::minDt (C++ member)
sme::simulate::DuneOptions::newtonAbsErr (C++ member)
sme::simulate::DuneOptions::newtonRelErr (C++ member)
sme::simulate::DuneOptions::serialize (C++ function)
sme::simulate::DuneOptions::writeVTKfiles (C++ member)
sme::simulate::DuneSim (C++ class)
sme::simulate::DuneSim::DuneSim (C++ function)
sme::simulate::DuneSim::errorImages (C++ function)
sme::simulate::DuneSim::errorMessage (C++ function)
sme::simulate::DuneSim::getConcentrationPadding (C++ function)
sme::simulate::DuneSim::getConcentrations (C++ function)
sme::simulate::DuneSim::run (C++ function)
sme::simulate::DuneSim::setStopRequested (C++ function)
sme::simulate::DuneSim::~DuneSim (C++ function)
sme::simulate::IniFile (C++ class)
sme::simulate::IniFile::addSection (C++ function)
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[1]
,
[2]
,
[3]
,
[4]
,
[5]
sme::simulate::IniFile::addValue (C++ function)
,
[1]
,
[2]
sme::simulate::IniFile::clear (C++ function)
sme::simulate::IniFile::getText (C++ function)
sme::simulate::OptAlgorithm (C++ struct)
sme::simulate::OptAlgorithm::islands (C++ member)
sme::simulate::OptAlgorithm::optAlgorithmType (C++ member)
sme::simulate::OptAlgorithm::population (C++ member)
sme::simulate::OptAlgorithm::serialize (C++ function)
sme::simulate::OptAlgorithmType (C++ enum)
sme::simulate::OptAlgorithmType::ABC (C++ enumerator)
sme::simulate::OptAlgorithmType::DE (C++ enumerator)
sme::simulate::OptAlgorithmType::gaco (C++ enumerator)
sme::simulate::OptAlgorithmType::GPSO (C++ enumerator)
sme::simulate::OptAlgorithmType::iDE (C++ enumerator)
sme::simulate::OptAlgorithmType::jDE (C++ enumerator)
sme::simulate::OptAlgorithmType::pDE (C++ enumerator)
sme::simulate::OptAlgorithmType::PSO (C++ enumerator)
sme::simulate::OptCost (C++ struct)
sme::simulate::OptCost::compartmentIndex (C++ member)
sme::simulate::OptCost::epsilon (C++ member)
sme::simulate::OptCost::id (C++ member)
sme::simulate::OptCost::name (C++ member)
sme::simulate::OptCost::optCostDiffType (C++ member)
sme::simulate::OptCost::optCostType (C++ member)
sme::simulate::OptCost::serialize (C++ function)
sme::simulate::OptCost::simulationTime (C++ member)
sme::simulate::OptCost::speciesIndex (C++ member)
sme::simulate::OptCost::targetValues (C++ member)
sme::simulate::OptCost::weight (C++ member)
sme::simulate::OptCostDiffType (C++ enum)
sme::simulate::OptCostDiffType::Absolute (C++ enumerator)
sme::simulate::OptCostDiffType::Relative (C++ enumerator)
sme::simulate::OptCostType (C++ enum)
sme::simulate::OptCostType::Concentration (C++ enumerator)
sme::simulate::OptCostType::ConcentrationDcdt (C++ enumerator)
sme::simulate::Optimization (C++ class)
sme::simulate::Optimization::applyParametersToModel (C++ function)
sme::simulate::Optimization::evolve (C++ function)
sme::simulate::Optimization::getErrorMessage (C++ function)
sme::simulate::Optimization::getFitness (C++ function)
sme::simulate::Optimization::getIsRunning (C++ function)
sme::simulate::Optimization::getIsStopping (C++ function)
sme::simulate::Optimization::getIterations (C++ function)
sme::simulate::Optimization::getParamNames (C++ function)
sme::simulate::Optimization::getParams (C++ function)
sme::simulate::Optimization::getTargetImage (C++ function)
sme::simulate::Optimization::getUpdatedBestResultImage (C++ function)
sme::simulate::Optimization::Optimization (C++ function)
sme::simulate::Optimization::requestStop (C++ function)
sme::simulate::Optimization::setBestResults (C++ function)
sme::simulate::OptimizeOptions (C++ struct)
sme::simulate::OptimizeOptions::optAlgorithm (C++ member)
sme::simulate::OptimizeOptions::optCosts (C++ member)
sme::simulate::OptimizeOptions::optParams (C++ member)
sme::simulate::OptimizeOptions::serialize (C++ function)
sme::simulate::Options (C++ struct)
sme::simulate::Options::dune (C++ member)
sme::simulate::Options::pixel (C++ member)
sme::simulate::Options::serialize (C++ function)
sme::simulate::OptParam (C++ struct)
sme::simulate::OptParam::id (C++ member)
sme::simulate::OptParam::lowerBound (C++ member)
sme::simulate::OptParam::name (C++ member)
sme::simulate::OptParam::optParamType (C++ member)
sme::simulate::OptParam::parentId (C++ member)
sme::simulate::OptParam::serialize (C++ function)
sme::simulate::OptParam::upperBound (C++ member)
sme::simulate::OptParamType (C++ enum)
sme::simulate::OptParamType::ModelParameter (C++ enumerator)
sme::simulate::OptParamType::ReactionParameter (C++ enumerator)
sme::simulate::PagmoUDP (C++ class)
sme::simulate::PagmoUDP::fitness (C++ function)
sme::simulate::PagmoUDP::get_bounds (C++ function)
sme::simulate::PagmoUDP::PagmoUDP (C++ function)
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[1]
sme::simulate::Pde (C++ class)
sme::simulate::Pde::getJacobian (C++ function)
sme::simulate::Pde::getRHS (C++ function)
sme::simulate::Pde::Pde (C++ function)
sme::simulate::PixelIntegratorError (C++ struct)
sme::simulate::PixelIntegratorError::abs (C++ member)
sme::simulate::PixelIntegratorError::rel (C++ member)
sme::simulate::PixelIntegratorError::serialize (C++ function)
sme::simulate::PixelIntegratorType (C++ enum)
sme::simulate::PixelIntegratorType::RK101 (C++ enumerator)
sme::simulate::PixelIntegratorType::RK212 (C++ enumerator)
sme::simulate::PixelIntegratorType::RK323 (C++ enumerator)
sme::simulate::PixelIntegratorType::RK435 (C++ enumerator)
sme::simulate::PixelOptions (C++ struct)
sme::simulate::PixelOptions::doCSE (C++ member)
sme::simulate::PixelOptions::enableMultiThreading (C++ member)
sme::simulate::PixelOptions::integrator (C++ member)
sme::simulate::PixelOptions::maxErr (C++ member)
sme::simulate::PixelOptions::maxThreads (C++ member)
sme::simulate::PixelOptions::maxTimestep (C++ member)
sme::simulate::PixelOptions::optLevel (C++ member)
sme::simulate::PixelOptions::serialize (C++ function)
sme::simulate::PixelSim (C++ class)
sme::simulate::PixelSim::errorImages (C++ function)
sme::simulate::PixelSim::errorMessage (C++ function)
sme::simulate::PixelSim::getConcentrationPadding (C++ function)
sme::simulate::PixelSim::getConcentrations (C++ function)
sme::simulate::PixelSim::getDcdt (C++ function)
sme::simulate::PixelSim::getLowerOrderConcentration (C++ function)
sme::simulate::PixelSim::PixelSim (C++ function)
sme::simulate::PixelSim::run (C++ function)
sme::simulate::PixelSim::setStopRequested (C++ function)
sme::simulate::PixelSim::~PixelSim (C++ function)
sme::simulate::Simulation (C++ class)
sme::simulate::Simulation::applyConcsToModel (C++ function)
sme::simulate::Simulation::doMultipleTimesteps (C++ function)
sme::simulate::Simulation::doTimesteps (C++ function)
sme::simulate::Simulation::errorImages (C++ function)
sme::simulate::Simulation::errorMessage (C++ function)
sme::simulate::Simulation::getAvgMinMax (C++ function)
sme::simulate::Simulation::getCompartmentIds (C++ function)
sme::simulate::Simulation::getConc (C++ function)
sme::simulate::Simulation::getConcArray (C++ function)
sme::simulate::Simulation::getConcImage (C++ function)
sme::simulate::Simulation::getDcdt (C++ function)
sme::simulate::Simulation::getDcdtArray (C++ function)
sme::simulate::Simulation::getIsRunning (C++ function)
sme::simulate::Simulation::getIsStopping (C++ function)
sme::simulate::Simulation::getLowerOrderConc (C++ function)
sme::simulate::Simulation::getNCompletedTimesteps (C++ function)
sme::simulate::Simulation::getPyConcs (C++ function)
sme::simulate::Simulation::getPyDcdts (C++ function)
sme::simulate::Simulation::getPyNames (C++ function)
sme::simulate::Simulation::getSimulationData (C++ function)
sme::simulate::Simulation::getSpeciesColors (C++ function)
sme::simulate::Simulation::getSpeciesIds (C++ function)
sme::simulate::Simulation::getTimePoints (C++ function)
sme::simulate::Simulation::requestStop (C++ function)
sme::simulate::Simulation::Simulation (C++ function)
sme::simulate::Simulation::~Simulation (C++ function)
sme::simulate::SimulationData (C++ class)
sme::simulate::SimulationData::avgMinMax (C++ member)
sme::simulate::SimulationData::clear (C++ function)
sme::simulate::SimulationData::concentration (C++ member)
sme::simulate::SimulationData::concentrationMax (C++ member)
sme::simulate::SimulationData::concPadding (C++ member)
sme::simulate::SimulationData::pop_back (C++ function)
sme::simulate::SimulationData::reserve (C++ function)
sme::simulate::SimulationData::serialize (C++ function)
sme::simulate::SimulationData::size (C++ function)
sme::simulate::SimulationData::timePoints (C++ member)
sme::simulate::SimulationData::xmlModel (C++ member)
sme::simulate::SimulatorType (C++ enum)
sme::simulate::SimulatorType::DUNE (C++ enumerator)
sme::simulate::SimulatorType::Pixel (C++ enumerator)
Species (class in sme)
species (sme.Compartment property)
species_concentration (sme.SimulationResult property)
species_dcdt (sme.SimulationResult property)
SpeciesList (class in sme)
T
time_point (sme.SimulationResult property)
U
Uniform (sme.ConcentrationType attribute)
uniform_concentration (sme.Species property)
V
value (sme.ConcentrationType property)
(sme.Parameter property)
(sme.ReactionParameter property)
(sme.SimulatorType property)
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