Model-class: SBML type "Model"
Description
The central SBML element. Contains the Species,
Reactions, Compartments and other
components of the model. See the SBML specification, at the reference, for
further details.Instantiation
Objects can be created by calls of the form new("Model", ...).Slots
id:- Object of class
"character" uniquely identifying this component. name:- Object of class
"character" naming this component. functionDefinitions:- Object of class
"list" containing
FunctionDefinitions. The names of the list
correspond to the IDs of the elements. unitDefinitions:- Object of class
"list" containing
UnitDefinitions. The names of the list
correspond to the IDs of the elements. compartments:- Object of class
"list" containing
Compartments. The names of the list
correspond to the IDs of the elements. species:- Object of class
"list" containing
Speciess. The names of the list
correspond to the IDs of the elements. parameters:- Object of class
"list" containing
Parameters. The names of the list
correspond to the IDs of the elements. rules:- Object of class
"list" containing
Rules. reactions:- Object of class
"list" containing
Reactions. The names of the list
correspond to the IDs of the elements. events:- Object of class
"list" containing
Events. The names of the list
correspond to the IDs of the elements. layouts:- Object of class
"list" containing
Layouts. The names of the list
correspond to the IDs of the elements. speciesTypes:- Object of class
"list" containing
SpeciesTypes. The names of the list
correspond to the IDs of the elements. compartmentTypes:- Object of class
"list" containing
CompartmentTypes. The names of the list
correspond to the IDs of the elements. constraints:- Object of class
"list" containing
Constraints. The names of the list
correspond to the IDs of the elements. initialAssignments:- Object of class
"list" containing
InitialAssignments. modelHistory:- Object of class
ModelHistory recording the history of the
model. metaId:- Object of class
"character" that is an XML ID
"described" by an RDF resource. This links an SBML element to an RDF
resource. RDF may appear anywhere in an SBML element,
but is usually placed inside the annotation element. notes:- Object of class
"character"
containing user-readable XHTML notes about an element. annotation:- Object of class
"character" containing
additional machine-readable information about an element, usually as RDF,
such as BioPAX. This is where application-specific data belongs. cvTerms:- Object of class
"list" containing
instances of CVTerm associated with this
element. sboTerm:- Object of class
"integer" identifying
a term in the Systems Biology Ontology (SBO).
Extends
Class "SBase", directly.Methods
- id
signature(object = "Model"): gets the id slot - id<-
signature(object = "Model"): sets the id slot - name
signature(object = "Model"): gets the name slot - name<-
signature(object = "Model"): sets the name slot - compartments
signature(object = "Model"): gets the compartments slot - compartments<-
signature(object = "Model"): sets the compartments slot - events
signature(object = "Model"): gets the events slot - events<-
signature(object = "Model"): sets the events slot - functionDefinitions
signature(object = "Model"): gets the functionDefinitions slot - functionDefinitions<-
signature(object = "Model"): sets the functionDefinitions slot - layouts
signature(object = "Model"): gets the layouts slot - layouts<-
signature(object = "Model"): sets the layouts slot - parameters
signature(object = "Model"): gets the parameters slot - parameters<-
signature(object = "Model"): sets the parameters slot - species
signature(object = "Model"): gets the species slot - species<-
signature(object = "Model"): sets the species slot - reactions
signature(object = "Model"): gets the reactions slot - reactions<-
signature(object = "Model"): sets the reactions slot - rules
signature(object = "Model"): gets the rules slot - rules<-
signature(object = "Model"): sets the rules slot - unitDefinitions
signature(object = "Model"): gets the unitDefinitions slot - unitDefinitions<-
signature(object = "Model"): sets the unitDefinitions slot - compartmentTypes
signature(object = "Model"): gets the compartmentTypes slot - compartmentTypes<-
signature(object = "Model"): sets the compartmentTypes slot - constraints
signature(object = "Model"): gets the constraints slot - constraints<-
signature(object = "Model"): sets the constraints slot - initialAssignments
signature(object = "Model"): gets the initialAssignments slot - initialAssignments<-
signature(object = "Model"): sets the initialAssignments slot - speciesTypes
signature(object = "Model"): gets the speciesTypes slot - speciesTypes<-
signature(object = "Model"): sets the
speciesTypesslot - modelHistory
signature(object = "Model"): gets the modelHistory slot - modelHistory<-
signature(object = "Model"): sets the modelHistory slot - stoichiometryMatrix
signature(object = "Model"):
calculates the stoichiometry matrix of the model