tellurium.teconverters package¶
Submodules¶
tellurium.teconverters.antimony_regex module¶
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tellurium.teconverters.antimony_regex.
getFunctionSBORegex
()[source]¶ Return the regex string for a function SBO term. Matches whole line.
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tellurium.teconverters.antimony_regex.
getFunctionStartRegex
()[source]¶ Return the regex string for Antimony model start. Matches whole line.
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tellurium.teconverters.antimony_regex.
getModelEndRegex
()[source]¶ Return the regex string for Antimony model end. Matches whole line.
tellurium.teconverters.antimony_sbo module¶
Helpers to work with SBO terms in antimony.
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class
tellurium.teconverters.antimony_sbo.
antimonySBOConverter
(doc)[source]¶ Bases:
object
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class
tellurium.teconverters.antimony_sbo.
antimonySBOParser
(antimony_str)[source]¶ Bases:
object
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addSBOsToSBML
(sbml_str)[source]¶ Add SBO terms to an SBML string. Must have called elideSBOTerms first to populate self.sbo_map.
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elideSBOTerms
()[source]¶ Remove SBO terms from self.antimony_str. Remove SBO terms for functions. See https://github.com/sys-bio/tellurium/issues/340.
Returns: Antimony string without SBO terms.
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tellurium.teconverters.convert_antimony module¶
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class
tellurium.teconverters.convert_antimony.
antimonyConverter
[source]¶ Bases:
object
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antimonyToSBML
(sb_str, SBO=False)[source]¶ Converts an Antimony string to raw SBML.
Parameters: sb_str – The raw Antimony string Returns: A 2-tuple (module_name, raw_sbml)
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cellmlFileToAntimony
(sbml_path)[source]¶ Converts a CellML file to Antimony source.
Parameters: sbml_path – The path to the CellML file Returns: A 2-tuple (module_name, antimony_source)
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sbmlFileToAntimony
(sbml_path, addSBO=False)[source]¶ Converts a SBML file to Antimony source.
Parameters: sbml_path – The path to the SBML file Returns: A 2-tuple (module_name, antimony_source)
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tellurium.teconverters.convert_omex module¶
Class for working with omex files.
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class
tellurium.teconverters.convert_omex.
Omex
(description='', creator=None)[source]¶ Bases:
object
Wrapper for Combine archives.
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class
tellurium.teconverters.convert_omex.
inlineOmexImporter
(omex)[source]¶ -
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formatPhrasedmlResource
(path)[source]¶ Normalizes path, strips xml extension, and normalizes fs separator.
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classmethod
fromFile
(path)[source]¶ Initialize from a combine archive.
Parameters: path – The path to the omex file
Makes a header for an entry.
Parameters: - entry – Entry in Combine archive (class CaContent)
- type – Can be ‘sbml’ or ‘sedml’
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tellurium.teconverters.convert_phrasedml module¶
tellurium.teconverters.inline_omex module¶
Working with inline omex. This is used in the notebook to provide functionality to the cells.
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class
tellurium.teconverters.inline_omex.
inlineOmex
(sources)[source]¶ Bases:
object
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classmethod
fromString
(omex_str, comp=False)[source]¶ Given mixed Antimony/PhraSEDML, separates out the constituent parts. Assumes that Antimony and PhraSEDML are not mixed on the same line.
Parameters: instr – The input string containing mixed Antimony/PhraSEDML Returns: 2-tuple containing a list of Antimony parts and a list of PhraSEDML parts as strings
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classmethod