modelmage.model.Model

Class Model

Instance Methods

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__init__(self, document=None, filename=None, history=None)

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getSbmlDocument(self)

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setSbmlDocument(self, document)

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getIdNameMap(self)

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getNameIdMap(self)

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getStoich(self)

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setStoich(self, pair, stoich)

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getGraph(self)

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none

__buildGraph(self)
Reads a model and returns a directed bipartite graph containing the reactions and species in the file.

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({str}{str})

__buildMaps(self, model)
Creates the dicts for the mapping of species to names and the other way round.

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[str]

getModelElement(self, element='Species', attr='id')
Returns the given attributes of the given type of elements. source code

([string],[string])

inspectKineticLaw(self, reaction, species, globalParameters)
Examines the formula of a kinetic law and returns lists of the substrates and parameters.

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writeSBML(self, filename)
Writes SBML document to a file and automatically determines the filename if wanted.

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getNewFilename(self, base=None)

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sbml.SBMLDocuments

readSBML(self, filename, verbose=False)
Reads SBML document from a file or a string and checks if the document is consistent.

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Class Variables

[hide private]

__sbmlDocument = None

__graph = None

history = None

filename = None

__idNameMap = {}

__nameIdMap = {}

__stoich = {}

reactionId = {}

speciesId = {}

functions = []

reactionFunctions = {}

reactionSubPar = {}

__buildMaps(self, model)

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Creates the dicts for the mapping of species to names and the other way round.

Returns: ({str}{str}): Dicts that map ids to names and the other way round. The maps include species, reactions and parameters.

getModelElement(self, element=`'Species'`, attr=`'id'`)

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Returns the given attributes of the given type of elements.

Returns: [str]: list of attributes

inspectKineticLaw(self, reaction, species, globalParameters)

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Examines the formula of a kinetic law and returns lists of the substrates and parameters.

Returns: ([string],[string]): Tupel of lists of substrates/modifiers and parameters

writeSBML(self, filename)

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Writes SBML document to a file and automatically determines the filename if wanted.

Parameters:

filename (str) - the base of the filename, removed will be added to this

readSBML(self, filename, verbose=False)

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Reads SBML document from a file or a string and checks if the document is consistent.

Parameters:

filename (str) - the path to the file which should be read

Returns: sbml.SBMLDocuments

the SBML document which was contained in the file

Class Model

__buildMaps(self, model)

getModelElement(self, element='Species', attr='id')

inspectKineticLaw(self, reaction, species, globalParameters)

writeSBML(self, filename)

readSBML(self, filename, verbose=False)

getModelElement(self, element=`'Species'`, attr=`'id'`)