sbmlsim.simulation.base
¶
BaseObjects for SED-ML and simulation.
Module Contents¶
Classes¶
Base class for SED-ML bases. |
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Base class for SED-ML bases with required sid. |
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Target class. |
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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) –