Gets the value assigned to the input string. The input string can be a species name/Id, parameter name/Id, compartment name/Id.
The returns 1 if the input string appears in the sbml document otherwise 0. The input string can be a species name/Id, parameter name/Id, compartment name/Id.
Loads the sbml document. The input string must be a valid sbml document. An exception will be thrown if there are fatal errors in the input string.
Validates the input sbml document. The input string must be a valid sbml document. An exception will be thrown if there are fatal errors in the input string.
Returns the currently loaded sbml document
Modifies the names of local parameters by adding reaction name at the beginning and promotes them to global.
Returns the modelName/Id given in sbml document
Returns the modelId/Name given in sbml document
Returns the number offunction Definitions listed in the sbml document
Returns the number of compartments listed in the sbml document
Returns the number of reactions listed in the sbml document
Returns the number of floating species in the sbml document
Returns the number of boundary species in the sbml document
Returns the number of global parameters in the sbml document
The return type is a list containing {functionId, list of arguments, function body}. The index can vary from 0 to (numOfFunctionDefinitions-1). If the index exceeds the total number of function Definitions then the method throws an exception
The return type is a list containing {species id's} where the species modify the reaction. The index can vary from 0 to (numReactions-1). If the index exceeds the total number of reactions then the method throws an exception
The return type is a list containing lists of {species id's and stoichiometry} that are reactants of the reaction. The index can vary from 0 to (numReactions-1). If the index exceeds the total number of reactions then the method throws an exception
The return type is a list containing lists of {species id's and stoichiometry} that are products of the reaction. The index can vary from 0 to (numReactions-1). If the index exceeds the total number of reactions then the method throws an exception
Returns the name of compartment for the input index. The index can vary from 0 to (numOfCompartments-1). If the index exceeds the total number of compartments then the method throws an exception
Returns the Id of compartment for the input index. The index can vary from 0 to (numOfCompartments-1). If the index exceeds the total number of compartments then the method throws an exception
Returns the outside compartment for the input. The input should be a compartment name for level 1 and compartment id for level 2. Throws an exception if the id or name is not found.
Returns a list of all the floating speciesIds.
Returns a list of all the floating species and their values together with and indicator whether this value is a concentration (true) or an amount (false). The return type will be a list of lists ex:- {{“S1”,1.0,True},{“S2”,2.0,False}}
Returns the name of the floatingSpecies for the input index. The index can vary from 0 to (numOfFloatingSpecies-1). If the index exceeds the total number of floatingSpecies then the method throws an exception
Returns the id of the floatingSpecies for the input index. The index can vary from 0 to (numOfFloatingSpecies-1). If the index exceeds the total number of floatingSpecies then the method throws an exception
Returns a list of all the Boundary speciesIds.
Returns a list of all the boundary species and their values together with and indicator whether this value is a concentration (true) or an amount (false). The return type will be a list of lists ex:- {{“S1”,1.0,True},{“S2”,2.0,False}}
Returns the name of the boundarySpecies for the input index. The index can vary from 0 to (numOfBoundarySpecies-1). If the index exceeds the total number of boundarySpecies then the method throws an exception
Returns the id of the boundarySpecies for the input index. The index can vary from 0 to (numOfBoundarySpecies-1). If the index exceeds the total number of boundarySpecies then the method throws an exception
Returns the name/Id of the compartment where the Species with the given speciesId is located
Returns the name of the compartment where the floatingSpecies with the given index is located
Returns the name of the compartment where the floatingSpecies with the given index is located
Returns 1 if the reaction for the input index value is reversible and 0 otherwise. The index can vary from 0 to (numOfReactions-1). If the index exceeds the total number of Reactions then the method throws an exception
Returns the name of the reaction for the input index value. The index can vary from 0 to (numOfReactions-1). If the index exceeds the total number of Reactions then the method throws an exception
Returns the id of the reaction for the input index value. The index can vary from 0 to (numOfReactions-1). If the index exceeds the total number of Reactions then the method throws an exception
Returns the number of reactants for tbe reaction index. The index can vary from 0 to (numOfReactions-1). If the index exceeds the total number of Reactions then the method throws an exception
Returns the number of products for tbe reaction index. The index can vary from 0 to (numOfReactions-1). If the index exceeds the total number of Reactions then the method throws an exception
Returns the name of reactant for the indicies values provided. The first input is the reaction index and it can vary from 0 to (numOfReactions-1). The second index varies from 0 to (numberOfReactants-1) of the input reaction index. If the first index exceeds the total number of Reactions or the second index exceeds the total number of reactants of the reaction then the method throws an exception
Returns the name of product for the indicies values provided. The first input is the reaction index and it can vary from 0 to (numOfReactions-1). The second index varies from 0 to (numberOfProducts-1) of the input reaction index. If the first index exceeds the total number of Reactions or the second index exceeds the total number of products of the reaction then the method throws an exception
Returns the Kineticlaw of reaction at the index value provided. The index can vary from 0 to (numOfReactions-1). If the index exceeds the total number of Reactions then the method throws an exception
Returns the name of stoichiometry value for the indicies values provided. The first input is the reaction index and it can vary from 0 to (numOfReactions-1). The second index varies from 0 to (numberOfReactants-1) of the input reaction index. If the first index exceeds the total number of Reactions or the second index exceeds the total number of products of the reaction then the method throws an exception
Returns the name of stoichiometry value for the indicies values provided. The first input is the reaction index and it can vary from 0 to (numOfReactions-1). The second index varies from 0 to (numberOfProducts-1) of the input reaction index. If the first index exceeds the total number of Reactions or the second index exceeds the total number of products of the reaction then the method throws an exception
Returns the name of stoichiometry value for the indicies values provided. The first input is the reaction index and it can vary from 0 to (numOfReactions-1). The second index varies from 0 to (numberOfReactants-1) of the input reaction index. If the first index exceeds the total number of Reactions or the second index exceeds the total number of products of the reaction then the method throws an exception
Returns the name of stoichiometry value for the indicies values provided. The first input is the reaction index and it can vary from 0 to (numOfReactions-1). The second index varies from 0 to (numberOfProducts-1) of the input reaction index. If the first index exceeds the total number of Reactions or the second index exceeds the total number of products of the reaction then the method throws an exception
Returns a list of both the global & local parameters and their values. The return type will be a list of lists ex:- {{“K1”,1.0},{“K2”,2.0}}
Returns the total number of local parameters for the input reaction index.
Returns the name of the parameter for the indicies values provided. The first input is the reaction index and it can vary from 0 to (numOfReactions-1). The second index varies from 0 to (localParameters-1) of the input reaction index. If the first index exceeds the total number of Reactions or the second index exceeds the total number of Parameters of the reaction then the method throws an exception
Returns the id of the parameter for the indicies values provided. The first input is the reaction index and it can vary from 0 to (numOfReactions-1). The second index varies from 0 to (localParameters-1) of the input reaction index. If the first index exceeds the total number of Reactions or the second index exceeds the total number of Parameters of the reaction then the method throws an exception
Returns the value of parameter for the indicies values provided. The first input is the reaction index and it can vary from 0 to (numOfReactions-1). The second index varies from 0 to (numberOfParameters-1) of the input reaction index. If the first index exceeds the total number of Reactions or the second index exceeds the total number of Parameters of the reaction then the method throws an exception
Returns 1 if a value is assigned to the parameter for the indicies values provided and 0 otherwise. The first input is the reaction index and it can vary from 0 to (numOfReactions-1). The second index varies from 0 to (numberOfParameters-1) of the input reaction index. If the first index exceeds the total number of Reactions or the second index exceeds the total number of Parameters of the reaction then the method throws an exception
Returns the name of the global parameter at index values provided. The index can vary from 0 to (numOfGlobalParameters-1). If the index exceeds the total number of Global Parameters then the method throws an exception
Returns the id of the global parameter at index values provided. The index can vary from 0 to (numOfGlobalParameters-1). If the index exceeds the total number of Global Parameters then the method throws an exception
Returns the total number of Rules in the sbml.
Returns the rule at the index value provided. The index can vary from 0 to (numOfRules-1). If the index exceeds the total number of rules then the method throws an exception.
The return string indicates the type of rule at the index provided. Eg., 'Assignment_Rule', 'Algebraic_Rule', 'Rate_Rule', 'Parameter_Rule'; 'Species_Concentration_Rule'; 'Compartment_Volume_Rule'. The index can vary from 0 to (numOfRules-1). If the index exceeds the total number of rules then the method throws an exception.
Returns the total number of Event in the sbml.
Returns the event at the index value provided. The return type is a list containing {trigger, delay, {lValue_eventAssignment1, rValue_eventAssignment1}, {lValue_eventAssignment2, rValue_eventAssignment2}, …} The index can vary from 0 to (numOfEvents-1). If the index exceeds the total number of events then the method throws an exception.
Returns the 1 if the input string has a value and 0 otherwise. The input string can be a species name/Id, parameter name/Id, compartment name/Id.
Returns the description of the builtin funtion for the input string provided.
Returns a list of strings of all the builtin functions.
Converts a MathML string to mathematical infix expression.
Converts a mathematical infix expression to a MathML string.
Converts a SBML level 1 document to level2 document.
Converts a SBML level 2 document to level1 document.
Converts a power tag to \^. The input is a valid sbml string. The output is also an sbml string with power expressions converted.
Sets the value of the species name/Id, parameter name/Id, compartment name/Id to the given value.
Returns True if the given species name/Id has an initial amount set, False otherwise.
Returns True if the given species name/Id has an initial concentration set, False otherwise.
