sbmlsim.simulation.base

BaseObjects for SED-ML and simulation.

Module Contents

Classes

BaseObject

Base class for SED-ML bases.

BaseObjectSIdRequired

Base class for SED-ML bases with required sid.

Target

Target class.

Symbol

Symbol class.

class sbmlsim.simulation.base.BaseObject(sid, name)[source]

Bases: abc.ABC

Base class for SED-ML bases.

FIXME: support annotations and notes

Parameters
  • sid (Optional[str]) –

  • name (Optional[str]) –

class sbmlsim.simulation.base.BaseObjectSIdRequired(sid, name)[source]

Bases: BaseObject

Base class for SED-ML bases with required sid.

Parameters
  • sid (str) –

  • name (Optional[str]) –

class sbmlsim.simulation.base.Target(target)[source]

Target class.

An instance of Variable can refer to a model constituent inside a particular model through the address stored in the target attribute, such as an XPath expression. Note that while it is possible to write XPath expressions that select multiple nodes within a referenced model, when used within a target attribute, a single element or attribute must be selected by the expression. The target attribute may also be used in three situations to reference another SED-ML element with mathematical meaning, by containing a fragment identifier consisting of a hash character (#) followed by the SId of the element (i.e. “#id001”).

Parameters

target (str) –

class sbmlsim.simulation.base.Symbol(symbol)[source]

Symbol class.

The symbol attribute of type string is used to refer either to a predefined, implicit variable or to a predefined implicit function to be performed on the target. In both cases, the symbol should be a kisaoID (and follow the format of that attribute) that represents that variable’s concept. The notion of implicit variables is explained in Section 3.2.5. For backwards compatibility, the old string “urn:sedml:symbol:time” is also allowed, though interpreters should interpret “KISAO:0000832” as meaning the same thing.

Parameters

symbol (str) –

values = ['KISAO:0000832', 'KISAO:0000836', 'KISAO:0000837', 'KISAO:0000838', 'KISAO:0000654',...[source]