libSBML Python API
5.11.0
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▼C_object | |
Clibsbml.ASTNodeList | Class for managing lists of ASTNode objects |
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.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 | This class represents a pair of numerical values where one value represents an absolute value and the other value is a relative value in percent |
▼Clibsbml.SBase | SBML's SBase class, base class of most SBML objects |
Clibsbml.Association | fbc Proposed representation of gene associations |
Clibsbml.BoundingBox | layout A bounding box for an item in a diagram |
Clibsbml.ColorDefinition | LibSBML implementation for the ColorDefinition construct from the SBML render extension |
Clibsbml.Compartment | An SBML compartment, where species are located |
Clibsbml.CompartmentType | A compartment type in SBML Level 2 |
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.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.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 Proposed annotation for gene associations |
Clibsbml.GradientStop | LibSBML implementation of the gradient stop concept from the |
▼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.InitialAssignment | An SBML initial assignment, evaluated once only |
Clibsbml.Input | qual The input to a QualitativeSpecies |
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 | LibSBML implementation for a container which holds zero or more ColorDefinition objects |
Clibsbml.ListOfCompartmentGlyphs | layout A list of CompartmentGlyph objects |
Clibsbml.ListOfCompartments | A list of Compartment objects |
Clibsbml.ListOfCompartmentTypes | A list of CompartmentType objects |
Clibsbml.ListOfConstraints | A list of Constraint objects |
Clibsbml.ListOfCurveElements | A container to store curve elements (RenderPoint and RenderCubicBezier) |
Clibsbml.ListOfDeletions | comp A list of Deletion objects |
Clibsbml.ListOfDrawables | Container class that stores objects derived from Transformation2D |
Clibsbml.ListOfEventAssignments | A list of EventAssignment objects |
Clibsbml.ListOfEvents | A list of Event objects |
Clibsbml.ListOfExternalModelDefinitions | comp A list of ExternalModelDefinition objects |
Clibsbml.ListOfFluxBounds | fbc A list of FluxBound objects |
Clibsbml.ListOfFluxObjectives | fbc A list of FluxObjectives |
Clibsbml.ListOfFunctionDefinitions | A list of FunctionDefinition objects |
Clibsbml.ListOfFunctionTerms | qual A list of FunctionTerm objects |
Clibsbml.ListOfGeneAssociations | fbc A list of GeneAssociation objects |
Clibsbml.ListOfGlobalRenderInformation | Container class that stores GlobalRenderInformation objects |
Clibsbml.ListOfGlobalStyles | ListOfGlobalStyles is the container class that stores GlobalStyles in GlobalRenderInformation objects |
Clibsbml.ListOfGradientDefinitions | Container class that holds a list of gradient definitions |
Clibsbml.ListOfGradientStops | Container that holds zero or more GradientStop objects |
Clibsbml.ListOfGraphicalObjects | layout A list of GraphicalObject objects |
Clibsbml.ListOfInitialAssignments | A list of InitialAssignment objects |
Clibsbml.ListOfInputs | qual A list of Input objects |
Clibsbml.ListOfLayouts | layout A list of Layout objects |
Clibsbml.ListOfLineEndings | Container class to store LineEnding objects |
Clibsbml.ListOfLineSegments | layout A list of LineSegment objects |
Clibsbml.ListOfLocalRenderInformation | Container class that stores LocalRenderInformation objects |
Clibsbml.ListOfLocalStyles | ListOfLocalStyles is the container class that stores LocalStyles in LocalRenderInformation objects |
Clibsbml.ListOfModelDefinitions | comp A list of ModelDefinition objects |
Clibsbml.ListOfObjectives | fbc A list of Objective objects |
Clibsbml.ListOfOutputs | qual A list of Output objects |
▼Clibsbml.ListOfParameters | A list of Parameter objects |
Clibsbml.ListOfLocalParameters | A list of LocalParameter objects |
Clibsbml.ListOfPorts | comp A list of Port 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.ListOfSpeciesGlyphs | layout A list of SpeciesGlyph objects |
Clibsbml.ListOfSpeciesReferenceGlyphs | layout A list of SpeciesReferenceGlyph objects |
Clibsbml.ListOfSpeciesReferences | A list of SpeciesReference 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.Model | An SBML model |
Clibsbml.ModelDefinition | comp A model used in model composition |
Clibsbml.Objective | fbc An objective function |
Clibsbml.Output | qual The output from a QualitativeSpecies |
▼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.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.RenderInformationBase | Abstract base class for local and global render information |
Clibsbml.GlobalRenderInformation | GlobalRenderInformation is the render information stored in the ListOfLayouts |
Clibsbml.LocalRenderInformation | LocalRenderInformation is the render information stored in Layouts |
▼Clibsbml.RenderPoint | Represents a point where the coordinates can be made up of absolute as well as relative values ( |
Clibsbml.RenderCubicBezier | CubicBezier representation for RenderCurve objects and Polygon objects |
▼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.SpeciesType | A species type in SBML Level 2 |
Clibsbml.StoichiometryMath | Stochiometry expressions in SBML Level 2 reactions |
▼Clibsbml.Style | Abstract base class for local and global styles |
Clibsbml.GlobalStyle | Implementation of the GlobalStyle concept of the SBML render extension |
Clibsbml.LocalStyle | Implementation of the LocalStyle concept of the SBML render extension |
▼Clibsbml.Transformation | Implementation of a 3D transformation matrix |
▼Clibsbml.Transformation2D | Implementation of a 2D transformation matrix |
▼Clibsbml.GraphicalPrimitive1D | Base class for all graphical primitives which implements all 1D attributes |
▼Clibsbml.GraphicalPrimitive2D | Constructor which creates a GraphicalPrimitive2D |
Clibsbml.Ellipse | Graphical representation of an ellipse from the SBML render extension |
Clibsbml.LineEnding | LineEnding is a decoration element for the start and/or end of curves in the SBML render extension, e.g |
Clibsbml.Polygon | Class representing a polygon from the SBML render extension |
Clibsbml.Rectangle | Proxy of C++ Rectangle class |
Clibsbml.RenderGroup | The RenderGroup concept from the SBML render extension is used to group graphical primitives together to create composite representations from simple primitives |
Clibsbml.RenderCurve | Implementation of the Curve concept from the SBML render extension |
Clibsbml.Text | Instantiates a new Text object with the given id and position offset |
Clibsbml.Image | Implementation of the Image concept from the SBML render extension |
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.FbcSpeciesPlugin | fbc Extension of Species |
Clibsbml.LayoutModelPlugin | layout Extension of Model |
Clibsbml.LayoutSpeciesReferencePlugin | layout Extension of SpeciesReference |
Clibsbml.QualModelPlugin | qual Extension of Model |
Clibsbml.RenderGraphicalObjectPlugin | Proxy of C++ RenderGraphicalObjectPlugin class |
Clibsbml.RenderLayoutPlugin | Proxy of C++ RenderLayoutPlugin class |
Clibsbml.RenderListOfLayoutsPlugin | Proxy of C++ RenderListOfLayoutsPlugin class |
▼Clibsbml.SBMLDocumentPlugin | Base class for extending SBMLDocument in packages |
Clibsbml.CompSBMLDocumentPlugin | comp Extension of SBMLDocument |
▼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.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.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 | Core 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 package |
Clibsbml.LayoutExtension | layout Base extension class for the package |
Clibsbml.QualExtension | qual Base extension class for the package |
Clibsbml.RenderExtension | Proxy of C++ RenderExtension class |
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.LayoutPkgNamespaces | layout 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 |
▼CASTBase | |
Clibsbml.ASTNode | Abstract Syntax Trees for mathematical expressions |
▼CCompBase | |
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 |
▼CGradientBase | |
Clibsbml.LinearGradient | Representation of a linear gradient object from the SBML render extension |
Clibsbml.RadialGradient | Representation of a radial gradient object from the SBML render extension |
CSBMLReader | File and text-string SBML reader |
CSBMLWriter | File and text-string SBML writer |
▼Ctype | |
Clibsbml.AutoProperty | Auto-detect Python class getX/setX methods |