def obtainSCT(
self,
fileName,
reactionDefinitions,
useID,
namingConventions,
speciesEquivalences=None,
):
"""
one of the library's main entry methods. Process data from a file
to obtain the species composition table, a dictionary describing
the chemical history of different elements in the system
"""
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(fileName)
parser = SBML2BNGL(document.getModel(), useID)
database = structures.Databases()
database.forceModificationFlag = True
database = mc.createSpeciesCompositionGraph(
parser,
database,
reactionDefinitions,
namingConventions,
speciesEquivalences=speciesEquivalences,
bioGridFlag=False,
)
return database.prunnedDependencyGraph, database, document
def obtainSCT(self, fileName, reactionDefinitions, useID, namingConventions,speciesEquivalences=None):
'''
one of the library's main entry methods. Process data from a file
to obtain the species composition table, a dictionary describing
the chemical history of different elements in the system
'''
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(fileName)
parser = SBML2BNGL(document.getModel(),useID)
database = structures.Databases()
database.forceModificationFlag = True
database = mc.createSpeciesCompositionGraph(parser, database, reactionDefinitions,namingConventions,
speciesEquivalences=speciesEquivalences,bioGridFlag=False)
return database.prunnedDependencyGraph, database,document
def obtainSCT(fileName,reactionDefinitions,useID,namingConventions):
'''
one of the library's main entry methods. Process data from a file
'''
logMess.log = []
logMess.counter = -1
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(fileName)
parser =SBML2BNGL(document.getModel(),useID)
database = structures.Databases()
database.forceModificationFlag = True
sct,database = mc.createSpeciesCompositionGraph(parser, database, reactionDefinitions,namingConventions,
speciesEquivalences=None,bioGridFlag=False)
return sct,database,document
def obtainSCT(fileName, reactionDefinitions, useID, namingConventions):
'''
one of the library's main entry methods. Process data from a file
'''
logMess.log = []
logMess.counter = -1
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(fileName)
parser = SBML2BNGL(document.getModel(), useID)
database = structures.Databases()
database.forceModificationFlag = True
sct, database = mc.createSpeciesCompositionGraph(parser,
database,
reactionDefinitions,
namingConventions,
speciesEquivalences=None,
bioGridFlag=False)
return sct, database, document