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libSBML Python API
5.18.0
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libSBML Python API
5.18.0
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| ▼C_object | |
| Clibsbml.ASTNode | Abstract Syntax Tree (AST) representation of a mathematical expression |
| Clibsbml.ASTNodeList | Class for managing lists of ASTNode objects |
| Clibsbml.ASTNodeValues_t | Proxy of C++ ASTNodeValues_t class |
| Clibsbml.Callback | Proxy of C++ Callback class |
| Clibsbml.ConversionOption | A single configuration setting for an SBML converter |
| Clibsbml.ConversionProperties | Set of configuration option values for a converter |
| Clibsbml.CVTerm | A MIRIAM-compliant controlled vocabulary term |
| Clibsbml.CVTermList | Class for managing lists of CVTerm objects |
| Clibsbml.Date | A MIRIAM-compliant date representation |
| Clibsbml.DateList | Class for managing lists of Date objects |
| Clibsbml.DefinitionURLRegistry | Registry of all libSBML SBML DefinitionURLs |
| Clibsbml.ElementFilter | Base class for filter functions |
| Clibsbml.float_array | Proxy of C++ float_array class |
| Clibsbml.int_array | Proxy of C++ int_array class |
| Clibsbml.L3ParserSettings | Controls the behavior of the Level 3 formula parser |
| Clibsbml.ModelCreator | MIRIAM-compliant data about a model's creator |
| Clibsbml.ModelCreatorList | Class for managing lists of ModelCreator objects |
| Clibsbml.ModelHistory | MIRIAM-compliant data about a model's history |
| ▼Clibsbml.ostream | Wrapper class for the C++ standard stream ostream |
| Clibsbml.ostringstream | Wrapper class for the C++ standard file stream ofstream |
| Clibsbml.RDFAnnotationParser | MIRIAM-compliant RDF annotation reader/writer |
| Clibsbml.RelAbsVector | render Vectors with an absolute value and a relative value |
| ▼Clibsbml.SBase | SBML's SBase class, base class of most SBML objects |
| Clibsbml.Association | fbc Annotation helper class for “fbc” Version 1 |
| Clibsbml.BoundingBox | layout A bounding box for an item in a diagram |
| Clibsbml.ColorDefinition | render Definition of an identifier for an RGBA color value |
| Clibsbml.Compartment | An SBML compartment, where species are located |
| Clibsbml.CompartmentReference | multi Child of a Compartment that references a different Compartment |
| Clibsbml.CompartmentType | A compartment type in SBML Level 2 |
| ▼Clibsbml.CompBase | comp Convenience class for SBase-derived classes |
| Clibsbml.ExternalModelDefinition | comp A reference to an externally-defined model |
| ▼Clibsbml.SBaseRef | comp Base class for references to objects |
| Clibsbml.Deletion | comp Deletion of an object from a submodel |
| Clibsbml.Port | comp An interface to be used in composition |
| ▼Clibsbml.Replacing | comp Convenience class |
| Clibsbml.ReplacedBy | comp Indicates an object replaced by another |
| Clibsbml.ReplacedElement | comp Indicates an object replaces another |
| Clibsbml.Submodel | comp A model instance inside another model |
| Clibsbml.Constraint | An SBML constraint, for stating validity assumptions |
| Clibsbml.Curve | layout A curve connecting elements in a diagram |
| Clibsbml.DefaultTerm | qual The default result of a Transition |
| Clibsbml.DefaultValues | render Encoding of default values |
| Clibsbml.Delay | A delay on the time of execution of an SBML event |
| Clibsbml.Dimensions | layout Spatial dimensions of a 2D or 3D shape |
| Clibsbml.Event | A discontinuous SBML event |
| Clibsbml.EventAssignment | An assignment to a variable by an SBML event |
| ▼Clibsbml.FbcAssociation | fbc Base class for FbcAnd, FbcOr, and GeneProductRef |
| Clibsbml.FbcAnd | fbc An “and” relationship for gene products |
| Clibsbml.FbcOr | fbc An “or” relationship for gene products |
| Clibsbml.GeneProductRef | fbc Reference to a gene product of a reaction |
| Clibsbml.FluxBound | fbc Max or min value for a reaction flux |
| Clibsbml.FluxObjective | fbc An objective function for a flux |
| Clibsbml.FunctionDefinition | A user-defined function in an SBML model |
| Clibsbml.FunctionTerm | qual A function term |
| Clibsbml.GeneAssociation | fbc Annotation helper class for “fbc” Version 1 |
| Clibsbml.GeneProduct | fbc Association of a gene product with a Reaction |
| Clibsbml.GeneProductAssociation | fbc Association between gene products and reactions |
| ▼Clibsbml.GradientBase | render Abstract base class for linear and radial gradients |
| Clibsbml.LinearGradient | render Representation of a linear gradient |
| Clibsbml.RadialGradient | render Representation of a radial gradient |
| Clibsbml.GradientStop | render A color at a certain location in a color gradient |
| ▼Clibsbml.GraphicalObject | layout Base class of objects that store layouts |
| Clibsbml.CompartmentGlyph | layout A glyph for an SBML compartment |
| Clibsbml.GeneralGlyph | layout A glyph for miscellaneous items |
| Clibsbml.ReactionGlyph | layout A glyph for an SBML reaction |
| Clibsbml.ReferenceGlyph | layout Connection between an object and a glyph |
| Clibsbml.SpeciesGlyph | layout A glyph for an SBML species |
| Clibsbml.SpeciesReferenceGlyph | layout A glyph for an SBML species reference |
| Clibsbml.TextGlyph | layout A glyph for a text label |
| Clibsbml.Group | groups Representation of a group of SBML components |
| Clibsbml.InitialAssignment | An SBML initial assignment, evaluated once only |
| Clibsbml.Input | qual The input to a QualitativeSpecies |
| Clibsbml.InSpeciesTypeBond | multi Defines a bond within a MultiSpeciesType |
| Clibsbml.KineticLaw | The rate expression for an SBML reaction |
| Clibsbml.Layout | layout The layout of a diagram of an SBML model |
| ▼Clibsbml.LineSegment | layout Representation of a line |
| Clibsbml.CubicBezier | layout A Cubic Bézier smooth curve |
| ▼Clibsbml.ListOf | Parent class for libSBML's 'ListOfXYZ' classes |
| Clibsbml.ListOfColorDefinitions | render A list of ColorDefinition objects |
| Clibsbml.ListOfCompartmentGlyphs | layout A list of CompartmentGlyph objects |
| Clibsbml.ListOfCompartmentReferences | multi A list of CompartmentReference objects |
| Clibsbml.ListOfCompartments | A list of Compartment objects |
| Clibsbml.ListOfCompartmentTypes | A list of CompartmentType objects |
| Clibsbml.ListOfConstraints | A list of Constraint objects |
| Clibsbml.ListOfCurveElements | render A list of curve elements |
| Clibsbml.ListOfDeletions | comp A list of Deletion objects |
| Clibsbml.ListOfDrawables | render A list of Transformation2D objects |
| Clibsbml.ListOfEventAssignments | A list of EventAssignment objects |
| Clibsbml.ListOfEvents | A list of Event objects |
| Clibsbml.ListOfExternalModelDefinitions | comp A list of ExternalModelDefinition objects |
| Clibsbml.ListOfFbcAssociations | fbc A list of FbcAssociation objects |
| Clibsbml.ListOfFluxBounds | fbc A list of FluxBound objects |
| Clibsbml.ListOfFluxObjectives | fbc A list of FluxObjective objects |
| Clibsbml.ListOfFunctionDefinitions | A list of FunctionDefinition objects |
| Clibsbml.ListOfFunctionTerms | qual A list of FunctionTerm objects |
| Clibsbml.ListOfGeneAssociations | fbc A list of GeneAssociation objects |
| Clibsbml.ListOfGeneProducts | fbc A list of GeneProduct objects |
| Clibsbml.ListOfGlobalRenderInformation | render A list of GlobalRenderInformation objects |
| Clibsbml.ListOfGlobalStyles | render A list of GlobalStyle objects |
| Clibsbml.ListOfGradientDefinitions | render A list of GradientBase objects |
| Clibsbml.ListOfGradientStops | render A list of one or more GradientStop objects |
| Clibsbml.ListOfGraphicalObjects | layout A list of GraphicalObject objects |
| Clibsbml.ListOfGroups | groups A list of Group objects |
| Clibsbml.ListOfInitialAssignments | A list of InitialAssignment objects |
| Clibsbml.ListOfInputs | qual A list of Input objects |
| Clibsbml.ListOfInSpeciesTypeBonds | multi A list of InSpeciesTypeBond objects |
| Clibsbml.ListOfLayouts | layout A list of Layout objects |
| Clibsbml.ListOfLineEndings | render A list of LineEnding objects |
| Clibsbml.ListOfLineSegments | layout A list of LineSegment objects |
| Clibsbml.ListOfLocalRenderInformation | render A list of LocalRenderInformation objects |
| Clibsbml.ListOfLocalStyles | render A list of LocalStyle objects |
| Clibsbml.ListOfMembers | groups A list of Member objects |
| Clibsbml.ListOfModelDefinitions | comp A list of ModelDefinition objects |
| Clibsbml.ListOfMultiSpeciesTypes | multi A list of MultiSpeciesType objects |
| Clibsbml.ListOfObjectives | fbc A list of Objective objects |
| Clibsbml.ListOfOutputs | qual A list of Output objects |
| Clibsbml.ListOfOutwardBindingSites | multi A list of OutwardBindingSite objects |
| ▼Clibsbml.ListOfParameters | A list of Parameter objects |
| Clibsbml.ListOfLocalParameters | A list of LocalParameter objects |
| Clibsbml.ListOfPorts | comp A list of Port objects |
| Clibsbml.ListOfPossibleSpeciesFeatureValues | multi A list of PossibleSpeciesFeatureValue objects |
| Clibsbml.ListOfQualitativeSpecies | qual A list of QualitativeSpecies objects |
| Clibsbml.ListOfReactionGlyphs | layout A list of ReactionGlyph objects |
| Clibsbml.ListOfReactions | A list of Reaction objects |
| Clibsbml.ListOfReferenceGlyphs | layout A list of ReferenceGlyph objects |
| Clibsbml.ListOfReplacedElements | comp A list of ReplacedElement objects |
| Clibsbml.ListOfRules | A list of Rule objects |
| Clibsbml.ListOfSpecies | A list of Species objects |
| Clibsbml.ListOfSpeciesFeatures | multi A list of SpeciesFeature objects |
| Clibsbml.ListOfSpeciesFeatureTypes | multi A list of SpeciesFeatureType objects |
| Clibsbml.ListOfSpeciesFeatureValues | multi A list of SpeciesFeatureValue objects |
| Clibsbml.ListOfSpeciesGlyphs | layout A list of SpeciesGlyph objects |
| Clibsbml.ListOfSpeciesReferenceGlyphs | layout A list of SpeciesReferenceGlyph objects |
| Clibsbml.ListOfSpeciesReferences | A list of SpeciesReference objects |
| Clibsbml.ListOfSpeciesTypeComponentIndexes | multi A list of SpeciesTypeComponentIndex objects |
| Clibsbml.ListOfSpeciesTypeComponentMapInProducts | multi A list of SpeciesTypeComponentMapInProduct objects |
| Clibsbml.ListOfSpeciesTypeInstances | multi A list of SpeciesTypeInstance objects |
| Clibsbml.ListOfSpeciesTypes | A list of SpeciesType objects |
| Clibsbml.ListOfSubmodels | comp A list of Submodel objects |
| Clibsbml.ListOfTextGlyphs | layout A list of TextGlyph objects |
| Clibsbml.ListOfTransitions | qual A list of Transition objects |
| Clibsbml.ListOfUnitDefinitions | A list of UnitDefinition objects |
| Clibsbml.ListOfUnits | A list of Unit objects |
| Clibsbml.SubListOfSpeciesFeatures | multi Defines a set of SpeciesFeature objects |
| Clibsbml.Member | groups The Member class defines what objects are parts of a Group |
| ▼Clibsbml.Model | An SBML model |
| Clibsbml.ModelDefinition | comp A model used in model composition |
| ▼Clibsbml.MultiSpeciesType | multi A type of Species in SBML Level 3 'multi' |
| Clibsbml.BindingSiteSpeciesType | multi Extension of MultiSpeciesType to define a binding site |
| Clibsbml.Objective | fbc An objective function |
| Clibsbml.Output | qual The output from a QualitativeSpecies |
| Clibsbml.OutwardBindingSite | multi Defines a outward-facing binding site for a MultiSpeciesType |
| ▼Clibsbml.Parameter | An SBML parameter: a named symbol with a value |
| Clibsbml.LocalParameter | A parameter inside an SBML reaction definition |
| Clibsbml.Point | layout Representation of a point |
| Clibsbml.PossibleSpeciesFeatureValue | multi Defines one value of a SpeciesFeature |
| Clibsbml.Priority | The priority of execution of an SBML event |
| Clibsbml.QualitativeSpecies | qual Extension of Species |
| ▼Clibsbml.Reaction | An SBML reaction between species in an SBML model |
| Clibsbml.IntraSpeciesReaction | multi A subclass of Reaction for changes of an internal species bond |
| ▼Clibsbml.RenderInformationBase | render Abstract base class for local and global rendering information |
| Clibsbml.GlobalRenderInformation | render Render information stored in a ListOfLayouts |
| Clibsbml.LocalRenderInformation | render Rendering information stored in Layouts |
| ▼Clibsbml.RenderPoint | render A point with both absolute and relative values |
| Clibsbml.RenderCubicBezier | render Representation of cubic Bezier curves |
| ▼Clibsbml.Rule | Parent class for SBML rules in libSBML |
| Clibsbml.AlgebraicRule | An SBML algebraic rule representing 0 = f(W) |
| Clibsbml.AssignmentRule | An SBML assignment rule representing x = f(Y) |
| Clibsbml.RateRule | An SBML rate rule representing dx/dt = f(Y) |
| Clibsbml.SBMLDocument | Overall SBML container object |
| ▼Clibsbml.SimpleSpeciesReference | Abstract class for references to species in reactions |
| Clibsbml.ModifierSpeciesReference | A reference to an SBML modifier species |
| Clibsbml.SpeciesReference | A reference to an SBML species in a reaction |
| Clibsbml.Species | An SBML species – a pool of entities |
| Clibsbml.SpeciesFeature | multi Defines a feature of a multi Species |
| Clibsbml.SpeciesFeatureType | multi Defines a template for referencing SpeciesFeature objects |
| Clibsbml.SpeciesFeatureValue | multi Defines a particular value for a SpeciesFeature |
| Clibsbml.SpeciesType | A species type in SBML Level 2 |
| Clibsbml.SpeciesTypeComponentIndex | multi Identifies a component within a MultiSpeciesType |
| Clibsbml.SpeciesTypeComponentMapInProduct | multi Distinguishes between components in reactants versus products |
| Clibsbml.SpeciesTypeInstance | multi Allows construction of structured MultiSpeciesType objects |
| Clibsbml.StoichiometryMath | Stochiometry expressions in SBML Level 2 reactions |
| ▼Clibsbml.Style | render Abstract base class for local and global styles |
| Clibsbml.GlobalStyle | render A style that can be associated with a layout |
| Clibsbml.LocalStyle | render Style information object used in LocalRenderInformation |
| ▼Clibsbml.Transformation | render Implementation of a 3D transformation matrix |
| ▼Clibsbml.Transformation2D | render Implementation of a 2D transformation matrix |
| ▼Clibsbml.GraphicalPrimitive1D | render Base class for graphical primitives implementing 1D attributes |
| ▼Clibsbml.GraphicalPrimitive2D | render Base class for graphical primitives implementing 2D attributes |
| Clibsbml.Ellipse | render Graphical representation of an ellipse |
| Clibsbml.LineEnding | render Decoration element for the start and/or end of curves |
| Clibsbml.Polygon | render Representation of a Polygon |
| Clibsbml.Rectangle | render Representation of a rectangle |
| Clibsbml.RenderGroup | render A group of graphical primitives creating a composite |
| Clibsbml.RenderCurve | render Representation of curves |
| Clibsbml.Text | render Representation of text elements |
| Clibsbml.Image | render Representation of images |
| Clibsbml.Transition | qual A transition of a QualitativeSpecies |
| Clibsbml.Trigger | The trigger expression for an SBML event |
| Clibsbml.Unit | A single unit referenced in an SBML unit definition |
| Clibsbml.UnitDefinition | A definition of a unit used in an SBML model |
| Clibsbml.SBaseList | Class for managing lists of SBase objects |
| ▼Clibsbml.SBasePlugin | Base class for extending SBML objects in packages |
| ▼Clibsbml.CompSBasePlugin | comp Extension of SBase |
| Clibsbml.CompModelPlugin | comp Extension of Model |
| Clibsbml.FbcModelPlugin | fbc Extension of Model |
| Clibsbml.FbcReactionPlugin | fbc Extension of Reaction by the “fbc” package |
| Clibsbml.FbcSpeciesPlugin | fbc Extension of Species |
| Clibsbml.GroupsModelPlugin | groups Extension of Model |
| Clibsbml.LayoutModelPlugin | layout Extension of Model |
| Clibsbml.LayoutSpeciesReferencePlugin | layout Extension of SpeciesReference |
| Clibsbml.MultiCompartmentPlugin | multi Extension of Compartment for the 'multi' package |
| Clibsbml.MultiListOfReactionsPlugin | multi Extension of ListOfReactions for the 'multi' package |
| Clibsbml.MultiModelPlugin | multi Extension of Model |
| ▼Clibsbml.MultiSimpleSpeciesReferencePlugin | multi Extension of SimpleSpeciesReference for the 'multi' package |
| Clibsbml.MultiSpeciesReferencePlugin | multi Extension of SpeciesReference for the 'multi' package |
| Clibsbml.MultiSpeciesPlugin | multi Extension of Species for the 'multi' package |
| Clibsbml.QualModelPlugin | qual Extension of Model |
| Clibsbml.RenderGraphicalObjectPlugin | render The Render extension of the layout GraphicalObject class |
| Clibsbml.RenderLayoutPlugin | render LibSBML implementation for the extension to the Layout class by the Render extension |
| Clibsbml.RenderListOfLayoutsPlugin | render A list of layout objects used by the 'render' extension |
| ▼Clibsbml.SBMLDocumentPlugin | Base class for extending SBMLDocument in packages |
| Clibsbml.CompSBMLDocumentPlugin | comp Extension of SBMLDocument |
| Clibsbml.FbcSBMLDocumentPlugin | fbc Extension of SBMLDocument for the “fbc” package |
| Clibsbml.MultiSBMLDocumentPlugin | multi Extension of SBMLDocument for the 'multi' package |
| ▼Clibsbml.SBMLConverter | Base class for SBML converters |
| Clibsbml.CobraToFbcConverter | fbc COBRA to SBML Level 3 “fbc” converter |
| Clibsbml.CompFlatteningConverter | comp 'Flattens' a model, removing composition |
| Clibsbml.FbcToCobraConverter | fbc SBML Level 3 “fbc” to COBRA converter |
| Clibsbml.FbcV1ToV2Converter | fbc Convert “fbc” Version 1 models to Version 2 |
| Clibsbml.FbcV2ToV1Converter | fbc Convert “fbc” Version 2 models to Version 1 |
| Clibsbml.SBMLFunctionDefinitionConverter | Converter to expand user-defined functions in-line |
| Clibsbml.SBMLIdConverter | Converter for replacing object identifiers |
| Clibsbml.SBMLInferUnitsConverter | Converter for inferring and setting parameter units |
| Clibsbml.SBMLInitialAssignmentConverter | Converter that removes SBML initial assignments |
| Clibsbml.SBMLLevel1Version1Converter | Whole-document SBML Level/Version converter |
| Clibsbml.SBMLLevelVersionConverter | Whole-document SBML Level/Version converter |
| Clibsbml.SBMLLocalParameterConverter | Converter to turn local parameters into global ones |
| Clibsbml.SBMLReactionConverter | Converter to replace reactions with SBML rate rules |
| Clibsbml.SBMLRuleConverter | Converter that sorts SBML rules and assignments |
| Clibsbml.SBMLStripPackageConverter | Converter that removes SBML Level 3 packages |
| Clibsbml.SBMLUnitsConverter | Converts a model's existing units to SI units |
| Clibsbml.SBMLConverterRegistry | Registry of all libSBML SBML converters |
| ▼Clibsbml.SBMLExtension | Base class for SBML Level 3 package plug-ins |
| Clibsbml.CompExtension | comp Base extension class for the package |
| Clibsbml.FbcExtension | fbc Base extension class for the “fbc” package |
| Clibsbml.GroupsExtension | groups Base extension class for the package |
| Clibsbml.LayoutExtension | layout Base extension class for the package |
| Clibsbml.MultiExtension | multi Base extension class for the package |
| Clibsbml.QualExtension | qual Base extension class for the package |
| Clibsbml.RenderExtension | render Base extension class for the package |
| Clibsbml.SBMLExtensionException | Exception used by package extensions |
| Clibsbml.SBMLExtensionRegistry | Registry where package extensions are registered |
| ▼Clibsbml.SBMLNamespaces | Set of SBML Level + Version + namespace triples |
| Clibsbml.CompPkgNamespaces | comp SBMLNamespaces extension for the package |
| Clibsbml.FbcPkgNamespaces | fbc SBMLNamespaces extension for the package |
| Clibsbml.GroupsPkgNamespaces | groups SBMLNamespaces extension for the package |
| Clibsbml.LayoutPkgNamespaces | layout SBMLNamespaces extension for the package |
| Clibsbml.MultiPkgNamespaces | multi SBMLNamespaces extension for the package |
| Clibsbml.QualPkgNamespaces | qual SBMLNamespaces extension for the package |
| Clibsbml.RenderPkgNamespaces | Set of SBML Level + Version + namespace triples |
| Clibsbml.SBMLNamespacesList | Class for managing lists of SBMLNamespaces objects |
| Clibsbml.SBMLReader | File and text-string SBML reader |
| ▼Clibsbml.SBMLResolver | comp Base class for SBML resolvers |
| Clibsbml.SBMLFileResolver | comp Resolves documents stored on a file system |
| Clibsbml.SBMLResolverRegistry | comp Registry of all SBML resolvers |
| Clibsbml.SBMLUri | comp Utility class for handling URIs |
| Clibsbml.SBMLValidator | Base class for SBML validators |
| Clibsbml.SBMLWriter | File and text-string SBML writer |
| Clibsbml.SBO | Facilities for using the Systems Biology Ontology |
| Clibsbml.StringSet | Proxy of C++ std::set<(std::string)> class |
| Clibsbml.SyntaxChecker | Methods for checking the validity of SBML identifiers |
| Clibsbml.XMLAttributes | A list of attributes on an XML element |
| ▼Clibsbml.XMLError | XML-level errors, warnings and other diagnostics |
| Clibsbml.SBMLError | An error, warning or other diagnostic |
| ▼Clibsbml.XMLErrorLog | Log of diagnostics reported during XML processing |
| Clibsbml.SBMLErrorLog | Log of diagnostics reported during processing |
| Clibsbml.XMLInputStream | An interface to an XML input stream |
| Clibsbml.XMLNamespaces | An XML Namespace |
| Clibsbml.XMLOutputStream | Interface to an XML output stream |
| Clibsbml.XMLOwningOutputFileStream | Proxy of C++ XMLOwningOutputFileStream class |
| Clibsbml.XMLOwningOutputStringStream | Proxy of C++ XMLOwningOutputStringStream class |
| ▼Clibsbml.XMLToken | A token in an XML stream |
| Clibsbml.XMLNode | A node in libSBML's XML document tree |
| Clibsbml.XMLTriple | A qualified XML name |
| ▼CASTBasePlugin | |
| Clibsbml.MultiASTPlugin | multi Extension of ASTBasePlugin |
| CSBMLReader | File and text-string SBML reader |
| CSBMLWriter | File and text-string SBML writer |
| ▼Ctype | |
| Clibsbml.AutoProperty | Auto-detect Python class getX/setX methods |
| ▼CUserWarning | |
| Clibsbml.PythonAPI2Warning | Custom warning class for warnings generated by libSBML Python API2 |
