sbmlsh package

Submodules

sbmlsh.mod2sbml module

mod2sbml version 3.1.1.1

Copyright (C) 2005-2024, Darren J Wilkinson

Includes modifications by:

Jeremy Purvis (jep@thefoldingproblem.com) Carole Proctor (c.j.proctor@ncl.ac.uk) Mark Muldoon (m.muldoon@man.ac.uk) Lukas Endler (lukas@ebi.ac.uk)

Module for parsing SBML-shorthand model files, version 3.1.1, and all previous versions

Typical usage: >>> import sbmlsh >>> p=mod2sbml.Parser() >>> p.parseStream(sys.stdin)

Raises error “ParseError” on a fatal parsing error.

class sbmlsh.mod2sbml.Parser

Bases: object

Parser class Has constructor: Parser() and the following public methods: parseStream(inStream) parse(inString)

COMPARTMENTS = 4

EVENTS = 12

MODEL = 2

PARAMETERS = 6

REAC1 = 8

REAC2 = 9

REAC3 = 10

REAC4 = 11

RULES = 7

SBML = 1

SPECIES = 5

UNITS = 3

binaryOp(op, bits)

handleCompartments(line, name)

handleEvents(line, name)

handleModel(line, name)

handleNewContext(line, name)

handleParameters(line, name)

handleReac1(line, name)

handleReac2(line, name)

handleReac3(line, name)

handleRules(line, name)

handleSbml(line, name)

handleSpecies(line, name)

handleTerms(side, left)

handleUnits(line, name)

parse(inString)

Parse a string containing SBML-shorthand

Create an SBML model from a string containing a model in SBML-shorthand.

Parameters

inStringstring

String containing a SBML-shorthand model

Returns

A libSBML SBMLDocument object.

Examples

>>> from sbmlsh import mod2sbml
>>> p = mod2sbml.Parser()
>>> sbml = p.parse(inString)

parseStream(inS)

Parse a stream containing SBML-shorthand

Create an SBML model from a stream containing a model in SBML-shorthand.

Parameters

inSstream

Input stream containing a SBML-shorthand model

Returns

A libSBML SBMLDocument object.

Examples

>>> from sbmlsh import mod2sbml
>>> p = mod2sbml.Parser()
>>> inS = open("myModel.mod", 'r')
>>> sbml = p.parseStream(inS)

replaceTime(ast)

trigMangle(trig)

sbmlsh.mod2sbml.main()

sbmlsh.roundtrip module

sbmlsh.roundtrip.roundtrip(filename)

sbmlsh.sbml-latex-extract module

sbmlsh.sbml2latex module

sbml2latex version 1.0

Copyright (C) 2008, Darren J Wilkinson

d.j.wilkinson@ncl.ac.uk http://www.staff.ncl.ac.uk/d.j.wilkinson/

This is GNU Free Software (General Public License)

Module for converting SBML to LaTeX, version 1.0 Typical usage: >>> from sbml2latex import Parser >>> p=Parser(sbmldoc) >>> p.parseStream(sys.stdout)

Raises error “ParseError” on a fatal parsing error.

class sbmlsh.sbml2latex.Parser(d)

Bases: object

Parser class Has constructor: Parser(sbmldoc) where sbmldoc is a libsbml sbmldocument object, and the following public methods: parseStream(outStream) parse()

parse()

Parses the SBML (L2) model and returns a string containing the corresponding LaTeX

parseStream(outStream)

parses SBML model and writes LaTeX to outStream

sbmlsh.sbml2mod module

sbml2mod version 3.1.1.1

Copyright (C) 2005-2024, Darren J Wilkinson

Includes modifications by:

Jeremy Purvis (jep@thefoldingproblem.com) Carole Proctor (c.j.proctor@ncl.ac.uk) Mark Muldoon (m.muldoon@man.ac.uk) Lukas Endler (lukas@ebi.ac.uk)

Module for converting SBML to SBML-shorthand model files, version 3.1.1 Typical usage: >>> import sbmlsh >>> p=sbml2mod.Parser(sbmldoc) >>> p.parseStream(sys.stdout)

Raises error “ParseError” on a fatal parsing error.

class sbmlsh.sbml2mod.Parser(d)

Bases: object

Parser class Has constructor: Parser(sbmldoc) where sbmldoc is a libsbml sbmldocument object, and the following public methods: parseStream(outStream) parse()

parse()

Convert SBML to SBML-shorthand

Convert the SBML model to a string containing a model in SBML-shorthand.

Parameters

None.

Returns

A string containing SBML-shorthand

Examples

>>> from sbmlsh import sbml2mod
>>> p = sbml2mod.Parser(sbmlDoc)
>>> sbmlSH = p.parse()

parseStream(outS)

Convert an SBML document to an SBML-shorthand output stream

Create and return an SBML-shorthand model as an output stream based on an SBML document.

Parameters

outSstream

Output stream containing a SBML-shorthand model

Returns

Nothing.

Examples

>>> from sbmlsh import sbml2mod
>>> p = sbml2mod.Parser(sbmlDoc)
>>> outS = open("myModel.mod", 'w')
>>> p.parseStream(outS)

sbmlsh.sbml2mod.main()

Module contents