def test_KineticLaw_copyConstructor(self):
o1 = libsbml.KineticLaw(2,4)
p = libsbml.Parameter(2,4)
p.setId("jake")
o1.addParameter(p)
p = None
self.assert_( o1.getNumParameters() == 1 )
self.assert_( o1.getParameter(0).getId() == "jake" )
o2 = libsbml.KineticLaw(o1)
self.assert_( o2.getNumParameters() == 1 )
self.assert_( o2.getParameter(0).getId() == "jake" )
self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() )
o2 = None
o1 = None
pass
def test_L3_KineticLaw_addParameter1(self):
kl = libsbml.KineticLaw(3, 1)
p = libsbml.Parameter(3, 1)
i = self.KL.addParameter(p)
self.assert_(i == libsbml.LIBSBML_INVALID_OBJECT)
p.setId("p")
i = self.KL.addParameter(p)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(self.KL.getNumParameters() == 1)
self.assert_(self.KL.getNumLocalParameters() == 1)
self.assert_(kl.getNumParameters() == 0)
self.assert_(kl.getNumLocalParameters() == 0)
i = kl.addParameter(p)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(self.KL.getNumParameters() == 1)
self.assert_(self.KL.getNumLocalParameters() == 1)
self.assert_(kl.getNumParameters() == 1)
self.assert_(kl.getNumLocalParameters() == 1)
_dummyList = [p]
_dummyList[:] = []
del _dummyList
_dummyList = [kl]
_dummyList[:] = []
del _dummyList
pass
def test_KineticLaw_getParameterById(self):
k1 = libsbml.Parameter(2, 4)
k2 = libsbml.Parameter(2, 4)
k1.setId("k1")
k2.setId("k2")
k1.setValue(3.14)
k2.setValue(2.72)
self.M.addParameter(k1)
self.M.addParameter(k2)
r1 = libsbml.Reaction(2, 4)
r1.setId("reaction_1")
kl = libsbml.KineticLaw(2, 4)
kl.setFormula("k1 * X0")
k3 = libsbml.Parameter(2, 4)
k4 = libsbml.Parameter(2, 4)
k3.setId("k1")
k4.setId("k2")
k3.setValue(2.72)
k4.setValue(3.14)
kl.addParameter(k3)
kl.addParameter(k4)
r1.setKineticLaw(kl)
self.M.addReaction(r1)
kl1 = self.M.getReaction(0).getKineticLaw()
self.assert_(kl1.getParameter("k1") != k3)
self.assert_(kl1.getParameter("k1") != k1)
self.assert_(kl1.getParameter("k2") != k4)
self.assert_(kl1.getParameter("k3") == None)
pass
def test_KineticLaw_setTimeUnits4(self):
kl1 = libsbml.KineticLaw(1,2)
i = kl1.setTimeUnits("")
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
self.assertEqual( False, kl1.isSetTimeUnits() )
_dummyList = [ kl1 ]; _dummyList[:] = []; del _dummyList
pass
def test_KineticLaw(self):
kl = libsbml.KineticLaw(2,4)
self.assertEqual( False, (kl.hasRequiredElements()) )
kl.setMath(libsbml.parseFormula("kl"))
self.assertEqual( True, kl.hasRequiredElements() )
kl = None
pass
def test_KineticLaw_L1(self):
kl = libsbml.KineticLaw(1, 2)
self.assertEqual(False, (kl.hasRequiredAttributes()))
kl.setFormula("kl")
self.assertEqual(True, kl.hasRequiredAttributes())
kl = None
pass
def test_KineticLaw_createParameter(self): self.kl = libsbml.KineticLaw(2,2) p = self.kl.createParameter() self.assert_( self.kl.getNumParameters() == 1 ) self.assert_( (p).getLevel() == 2 ) self.assert_( (p).getVersion() == 2 ) _dummyList = [ self.kl ]; _dummyList[:] = []; del _dummyList pass
def test_KineticLaw_addParameter4(self): self.kl = libsbml.KineticLaw(2,2) p = None i = self.kl.addParameter(p) self.assert_( i == libsbml.LIBSBML_OPERATION_FAILED ) self.assert_( self.kl.getNumParameters() == 0 ) _dummyList = [ self.kl ]; _dummyList[:] = []; del _dummyList pass
def test_KineticLaw_parent_add(self):
kl = libsbml.KineticLaw(2, 4)
kl.setMath(libsbml.parseFormula("1"))
r = libsbml.Reaction(2, 4)
r.setKineticLaw(kl)
self.assert_(r == r.getKineticLaw().getParentSBMLObject())
r = None
pass
def test_KineticLaw_addParameter3(self): self.kl = libsbml.KineticLaw(2,2) p = libsbml.Parameter(1,2) p.setId( "p") i = self.kl.addParameter(p) self.assert_( i == libsbml.LIBSBML_LEVEL_MISMATCH ) self.assert_( self.kl.getNumParameters() == 0 ) _dummyList = [ p ]; _dummyList[:] = []; del _dummyList _dummyList = [ self.kl ]; _dummyList[:] = []; del _dummyList pass
def test_KineticLaw_setSubstanceUnits2(self): kl1 = libsbml.KineticLaw(1,2) i = kl1.setSubstanceUnits( "mole") self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( True, kl1.isSetSubstanceUnits() ) i = kl1.unsetSubstanceUnits() self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( False, kl1.isSetSubstanceUnits() ) _dummyList = [ kl1 ]; _dummyList[:] = []; del _dummyList pass
def test_Reaction_setKineticLaw2(self):
kl = libsbml.KineticLaw(1, 1)
kl.setMath(libsbml.parseFormula("1"))
i = self.R.setKineticLaw(kl)
self.assert_(i == libsbml.LIBSBML_VERSION_MISMATCH)
self.assertEqual(False, self.R.isSetKineticLaw())
_dummyList = [kl]
_dummyList[:] = []
del _dummyList
pass
def test_KineticLaw_setTimeUnits3(self): kl1 = libsbml.KineticLaw(1,2) i = kl1.setTimeUnits( "1second") self.assert_( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE ) self.assertEqual( False, kl1.isSetTimeUnits() ) i = kl1.unsetTimeUnits() self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( False, kl1.isSetTimeUnits() ) _dummyList = [ kl1 ]; _dummyList[:] = []; del _dummyList pass
def test_Reaction_setKineticLaw3(self):
kl = libsbml.KineticLaw(1, 2)
kl.setMath(libsbml.parseFormula("1"))
i = self.R.setKineticLaw(kl)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assertEqual(True, self.R.isSetKineticLaw())
_dummyList = [kl]
_dummyList[:] = []
del _dummyList
pass
def test_KineticLaw_Parameter_parent_create(self):
kl = libsbml.KineticLaw(2, 4)
p = kl.createParameter()
self.assert_(kl.getNumParameters() == 1)
lop = kl.getListOfParameters()
self.assert_(kl == lop.getParentSBMLObject())
self.assert_(lop == p.getParentSBMLObject())
self.assert_(lop == kl.getParameter(0).getParentSBMLObject())
kl = None
pass
def test_KineticLaw_ancestor_add(self):
kl = libsbml.KineticLaw(2,4)
kl.setMath(libsbml.parseFormula("1"))
r = libsbml.Reaction(2,4)
r.setKineticLaw(kl)
obj = r.getKineticLaw()
self.assert_( obj.getAncestorOfType(libsbml.SBML_REACTION) == r )
self.assert_( obj.getAncestorOfType(libsbml.SBML_MODEL) == None )
self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None )
r = None
pass
def test_KineticLaw_addParameter1(self): self.kl = libsbml.KineticLaw(2,2) p = libsbml.Parameter(2,2) i = self.kl.addParameter(p) self.assert_( i == libsbml.LIBSBML_INVALID_OBJECT ) p.setId( "p") i = self.kl.addParameter(p) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( self.kl.getNumParameters() == 1 ) _dummyList = [ p ]; _dummyList[:] = []; del _dummyList _dummyList = [ self.kl ]; _dummyList[:] = []; del _dummyList pass
def test_KineticLaw_Parameter_parent_add(self):
kl = libsbml.KineticLaw(2, 4)
p = libsbml.Parameter(2, 4)
p.setId("jake")
kl.addParameter(p)
p = None
self.assert_(kl.getNumParameters() == 1)
self.assert_(kl.getParameter(0).getId() == "jake")
lop = kl.getListOfParameters()
self.assert_(kl == lop.getParentSBMLObject())
self.assert_(lop == kl.getParameter(0).getParentSBMLObject())
kl = None
pass
def test_KineticLaw_Parameter_ancestor_add(self):
kl = libsbml.KineticLaw(2,4)
p = libsbml.Parameter(2,4)
p.setId("jake")
kl.addParameter(p)
p = None
lop = kl.getListOfParameters()
obj = kl.getParameter(0)
self.assert_( obj.getAncestorOfType(libsbml.SBML_KINETIC_LAW) == kl )
self.assert_( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lop )
self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None )
self.assert_( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == None )
kl = None
pass
def test_KineticLaw_addParameter2(self):
self.kl = libsbml.KineticLaw(2, 2)
p = libsbml.Parameter(2, 1)
p.setId("p")
i = self.kl.addParameter(p)
self.assert_(i == libsbml.LIBSBML_VERSION_MISMATCH)
self.assert_(self.kl.getNumParameters() == 0)
_dummyList = [p]
_dummyList[:] = []
del _dummyList
_dummyList = [self.kl]
_dummyList[:] = []
del _dummyList
pass
def test_KineticLaw_Parameter_ancestor_create(self): kl = libsbml.KineticLaw(2,4) p = kl.createParameter() self.assert_( kl.getNumParameters() == 1 ) lop = kl.getListOfParameters() self.assert_( p.getAncestorOfType(libsbml.SBML_KINETIC_LAW) == kl ) self.assert_( p.getAncestorOfType(libsbml.SBML_LIST_OF) == lop ) self.assert_( p.getAncestorOfType(libsbml.SBML_DOCUMENT) == None ) self.assert_( p.getAncestorOfType(libsbml.SBML_COMPARTMENT) == None ) obj = kl.getParameter(0) self.assert_( obj.getAncestorOfType(libsbml.SBML_KINETIC_LAW) == kl ) self.assert_( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lop ) self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None ) self.assert_( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == None ) kl = None pass
def test_internal_consistency_check_99911_kl(self):
d = libsbml.SBMLDocument(2,4)
d.setLevelAndVersion(2,1,False)
m = d.createModel()
r = m.createReaction()
r.setId("r")
sr = r.createReactant()
sr.setSpecies("s")
kl = libsbml.KineticLaw(2,4)
kl.setSBOTerm(2)
p = kl.createParameter()
p.setId("p")
r.setKineticLaw(kl)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_internal_consistency_check_99904_kl(self):
d = libsbml.SBMLDocument(2,4)
kl = libsbml.KineticLaw(2,4)
m = d.createModel()
d.setLevelAndVersion(1,2,False)
c = m.createCompartment()
c.setId("cc")
r = m.createReaction()
r.setId("r")
sr = r.createReactant()
sr.setSpecies("s")
kl.setFormula("2")
kl.setMetaId("mmm")
r.setKineticLaw(kl)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_KineticLaw_createWithNS(self):
xmlns = libsbml.XMLNamespaces()
xmlns.add("http://www.sbml.org", "testsbml")
sbmlns = libsbml.SBMLNamespaces(2, 1)
sbmlns.addNamespaces(xmlns)
object = libsbml.KineticLaw(sbmlns)
self.assert_(object.getTypeCode() == libsbml.SBML_KINETIC_LAW)
self.assert_(object.getMetaId() == "")
self.assert_(object.getNotes() == None)
self.assert_(object.getAnnotation() == None)
self.assert_(object.getLevel() == 2)
self.assert_(object.getVersion() == 1)
self.assert_(object.getNamespaces() != None)
self.assert_(object.getNamespaces().getLength() == 2)
_dummyList = [object]
_dummyList[:] = []
del _dummyList
pass
def test_Reaction_copyConstructor(self):
o1 = libsbml.Reaction(2,4)
o1.setId("c")
self.assert_( o1.getId() == "c" )
kl = libsbml.KineticLaw(2,4)
kl.setMath(libsbml.parseFormula("1"))
o1.setKineticLaw(kl)
kl = None
self.assert_( o1.isSetKineticLaw() == True )
self.assert_( o1.getKineticLaw() != None )
o2 = libsbml.Reaction(o1)
self.assert_( o2.getId() == "c" )
self.assert_( o2.isSetKineticLaw() == True )
self.assert_( o2.getKineticLaw() != None )
self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() )
o2 = None
o1 = None
pass
def get_and_set(self, reaction_name, lista, category):
# Prendo tutti i reagenti con i loro valori stechiometrici
elements = []
for element in lista:
# Ottengo un oggetto SpeciesReference
# Devo ottenere il valore stechiometrico
stoichiometry_value = element.getStoichiometry()
if stoichiometry_value == 1.0 and element.isSetStoichiometryMath():
tmp_kinetic = libsbml.KineticLaw(2, 4)
tmp_kinetic.setMath(element.getStoichiometryMath().getMath())
stoichiometry_value = tmp_kinetic.getFormula()
if category == "r":
self.species_dict[element.getSpecies()].add_reaction_as_reactant(
reaction_name, stoichiometry_value
)
elif category == "p":
self.species_dict[element.getSpecies()].add_reaction_as_product(
reaction_name, stoichiometry_value
)
elements.append(element.getSpecies())
return elements
def test_L3_KineticLaw_addParameter2(self):
kl = libsbml.KineticLaw(3, 1)
lp = libsbml.LocalParameter(3, 1)
lp1 = libsbml.LocalParameter(3, 1)
i = kl.addLocalParameter(lp)
self.assert_(i == libsbml.LIBSBML_INVALID_OBJECT)
lp.setId("p")
lp1.setId("p1")
i = kl.addLocalParameter(lp)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(kl.getNumParameters() == 1)
self.assert_(kl.getNumLocalParameters() == 1)
i = kl.addParameter(lp1)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(kl.getNumParameters() == 2)
self.assert_(kl.getNumLocalParameters() == 2)
_dummyList = [lp]
_dummyList[:] = []
del _dummyList
_dummyList = [kl]
_dummyList[:] = []
del _dummyList
pass
def test_KineticLaw(self):
kl = libsbml.KineticLaw(2, 4)
self.assertEqual(True, kl.hasRequiredAttributes())
kl = None
pass
def get_libsbml_document(cobra_model,
sbml_level=2, sbml_version=1,
print_time=False,
use_fbc_package=True):
""" Return a libsbml document object for writing to a file. This function
is used by write_cobra_model_to_sbml_file(). """
note_start_tag, note_end_tag = '<p>', '</p>'
if sbml_level > 2 or (sbml_level == 2 and sbml_version == 4):
note_start_tag, note_end_tag = '<html:p>', '</html:p>'
sbml_doc = libsbml.SBMLDocument(sbml_level, sbml_version)
sbml_model = sbml_doc.createModel(cobra_model.id.split('.')[0])
# Note need to set units
reaction_units = 'mmol_per_gDW_per_hr'
model_units = sbml_model.createUnitDefinition()
model_units.setId(reaction_units)
sbml_unit = model_units.createUnit()
sbml_unit.setKind(libsbml.UNIT_KIND_MOLE)
sbml_unit.setScale(-3)
sbml_unit = model_units.createUnit()
sbml_unit.setKind(libsbml.UNIT_KIND_GRAM)
sbml_unit.setExponent(-1)
sbml_unit = model_units.createUnit()
sbml_unit.setKind(libsbml.UNIT_KIND_SECOND)
sbml_unit.setMultiplier(1.0 / 60 / 60)
sbml_unit.setExponent(-1)
# Add in the common compartment abbreviations. If there are additional
# compartments they also need to be added.
if not cobra_model.compartments:
cobra_model.compartments = {'c': 'cytosol',
'p': 'periplasm',
'e': 'extracellular'}
for the_key in cobra_model.compartments.keys():
sbml_comp = sbml_model.createCompartment()
sbml_comp.setId(the_key)
sbml_comp.setName(cobra_model.compartments[the_key])
sbml_comp.setSize(1) # Just to get rid of warnings
if print_time:
warn("print_time is deprecated", DeprecationWarning)
# Use this dict to allow for fast look up of species id
# for references created in the reaction section.
metabolite_dict = {}
for cobra_metabolite in cobra_model.metabolites:
metabolite_dict[cobra_metabolite.id] = add_sbml_species(
sbml_model, cobra_metabolite, note_start_tag=note_start_tag,
note_end_tag=note_end_tag)
for the_reaction in cobra_model.reactions:
# This is probably the culprit. Including cobra.Reaction
# objects explicitly in cobra.Model will speed this up.
sbml_reaction = sbml_model.createReaction()
# Need to remove - for proper SBML. Replace with __
the_reaction_id = 'R_' + the_reaction.id.replace('-', '__')
sbml_reaction.setId(the_reaction_id)
# The reason we are not using the Reaction.reversibility property
# is because the SBML definition of reversibility does not quite
# match with the cobra definition. In cobra, reversibility implies
# that both positive and negative flux values are feasible. However,
# SBML requires negative-flux-only reactions to still be classified
# as reversible. To quote from the SBML Level 3 Version 1 Spec:
# > However, labeling a reaction as irreversible is interpreted as
# > an assertion that the rate expression will not have negative
# > values during a simulation.
# (Page 60 lines 44-45)
sbml_reaction.setReversible(the_reaction.lower_bound < 0)
if the_reaction.name:
sbml_reaction.setName(the_reaction.name)
else:
sbml_reaction.setName(the_reaction.id)
# Add in the reactant/product references
for the_metabolite, the_coefficient in \
iteritems(the_reaction._metabolites):
sbml_stoichiometry = the_coefficient
metabolite_id = str(metabolite_dict[the_metabolite.id])
# Each SpeciesReference must have a unique id
if sbml_stoichiometry < 0:
species_reference = sbml_reaction.createReactant()
else:
species_reference = sbml_reaction.createProduct()
species_reference.setId(metabolite_id + '_' + the_reaction_id)
species_reference.setSpecies(metabolite_id)
species_reference.setStoichiometry(abs(sbml_stoichiometry))
# Deal with the case where the reaction is a boundary reaction
if len(the_reaction._metabolites) == 1:
the_metabolite, the_coefficient = list(
the_reaction._metabolites.items())[0]
metabolite_id = add_sbml_species(sbml_model, the_metabolite,
note_start_tag=note_start_tag,
note_end_tag=note_end_tag,
boundary_metabolite=True)
sbml_stoichiometry = -the_coefficient
# Each SpeciesReference must have a unique id
if sbml_stoichiometry < 0:
species_reference = sbml_reaction.createReactant()
else:
species_reference = sbml_reaction.createProduct()
species_reference.setId(metabolite_id + '_' + the_reaction_id)
species_reference.setSpecies(metabolite_id)
species_reference.setStoichiometry(abs(sbml_stoichiometry))
# Add in the kineticLaw
sbml_law = libsbml.KineticLaw(sbml_level, sbml_version)
if hasattr(sbml_law, 'setId'):
sbml_law.setId('FLUX_VALUE')
sbml_law.setFormula('FLUX_VALUE')
reaction_parameter_dict = {
'LOWER_BOUND': [the_reaction.lower_bound, reaction_units],
'UPPER_BOUND': [the_reaction.upper_bound, reaction_units],
'FLUX_VALUE': [0, reaction_units],
'OBJECTIVE_COEFFICIENT': [the_reaction.objective_coefficient,
'dimensionless']}
for k, v in reaction_parameter_dict.items():
sbml_parameter = libsbml.Parameter(sbml_level, sbml_version)
sbml_parameter.setId(k)
if hasattr(v, '__iter__'):
sbml_parameter.setValue(v[0])
sbml_parameter.setUnits(v[1])
else:
sbml_parameter.setValue(v)
sbml_law.addParameter(sbml_parameter)
sbml_reaction.setKineticLaw(sbml_law)
# Checks if GPR and Subsystem annotations are present in the notes
# section and if they are the same as those in the reaction's
# gene_reaction_rule/ subsystem attribute. If they are not identical,
# they are set to be identical
note_dict = the_reaction.notes.copy()
if the_reaction.gene_reaction_rule:
note_dict['GENE_ASSOCIATION'] = [
str(the_reaction.gene_reaction_rule)]
if the_reaction.subsystem:
note_dict['SUBSYSTEM'] = [str(the_reaction.subsystem)]
# In a cobrapy model the notes section is stored as a dictionary. The
# following section turns the key-value-pairs of the dictionary into a
# string and replaces recurring symbols so that the string has the i
# required syntax for an SBML doc.
note_str = str(list(iteritems(note_dict)))
note_start_tag, note_end_tag, note_delimiter = '<p>', '</p>', ':'
note_str = note_str.replace('(\'', note_start_tag)
note_str = note_str.replace('\']),', note_end_tag)
note_str = note_str.replace('\',', note_delimiter)
note_str = note_str.replace('\']', '')
note_str = note_str.replace('[\'', '')
note_str = note_str.replace(
'[', '<html xmlns="http://www.w3.org/1999/xhtml">')
note_str = note_str.replace(')]', note_end_tag + '</html>')
sbml_reaction.setNotes(note_str)
if use_fbc_package:
try:
from libsbml import ConversionProperties, LIBSBML_OPERATION_SUCCESS
conversion_properties = ConversionProperties()
conversion_properties.addOption(
"convert cobra", True, "Convert Cobra model")
result = sbml_doc.convert(conversion_properties)
if result != LIBSBML_OPERATION_SUCCESS:
raise Exception("Conversion of COBRA to SBML+fbc failed")
except Exception as e:
error_string = 'Error saving as SBML+fbc. %s'
try:
# Check whether the FbcExtension is there
from libsbml import FbcExtension
error_string = error_string % e
except ImportError:
error_string = error_string % "FbcExtension not available in "
"libsbml. If use_fbc_package == True then libsbml must be "
"compiled with the fbc extension."
from libsbml import getLibSBMLDottedVersion
_sbml_version = getLibSBMLDottedVersion()
_major, _minor, _patch = map(int, _sbml_version.split('.'))
if _major < 5 or (_major == 5 and _minor < 8):
error_string += "You've got libsbml %s installed. "
"You need 5.8.0 or later with the fbc package"
raise Exception(error_string)
return sbml_doc
def toSBMLString(net):
metaId = 0
try:
m = libsbml.Model(net.id)
except NotImplementedError:
m = libsbml.Model(sbml_level, sbml_version)
m.setId(net.id)
m.setName(net.name)
m.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
for id, fd in list(net.functionDefinitions.items()):
try:
sfd = libsbml.FunctionDefinition(id)
except:
sfd = libsbml.FunctionDefinition(sbml_level, sbml_version)
sfd.setId(id)
sfd.setName(fd.name)
formula = fd.math
formula = formula.replace('**', '^')
formula = 'lambda(%s, %s)' % (','.join(fd.variables), formula)
sfd.setMath(libsbml.parseFormula(formula))
sfd.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addFunctionDefinition(sfd)
for id, c in list(net.compartments.items()):
try:
sc = libsbml.Compartment(id)
except NotImplementedError:
sc = libsbml.Compartment(sbml_level, sbml_version)
sc.setId(id)
sc.setName(c.name)
sc.setConstant(c.is_constant)
sc.setSize(c.initialValue)
sc.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addCompartment(sc)
for id, s in list(net.species.items()):
try:
ss = libsbml.Species(id)
except NotImplementedError:
ss = libsbml.Species(sbml_level, sbml_version)
ss.setId(id)
ss.setName(s.name)
ss.setCompartment(s.compartment)
if s.initialValue is not None and not isinstance(s.initialValue, str):
ss.setInitialConcentration(s.initialValue)
ss.setBoundaryCondition(s.is_boundary_condition)
ss.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addSpecies(ss)
for id, p in list(net.parameters.items()):
try:
sp = libsbml.Parameter(id)
except NotImplementedError:
sp = libsbml.Parameter(sbml_level, sbml_version)
sp.setId(id)
sp.setName(p.name)
if p.initialValue is not None:
sp.setValue(p.initialValue)
sp.setConstant(p.is_constant)
sp.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addParameter(sp)
for id, r in list(net.rateRules.items()):
try:
sr = libsbml.RateRule()
except NotImplementedError:
sr = libsbml.RateRule(sbml_level, sbml_version)
sr.setVariable(id)
formula = r.replace('**', '^')
sr.setMath(libsbml.parseFormula(formula))
sr.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addRule(sr)
for id, r in list(net.assignmentRules.items()):
try:
sr = libsbml.AssignmentRule()
except NotImplementedError:
sr = libsbml.AssignmentRule(sbml_level, sbml_version)
sr.setVariable(id)
formula = r.replace('**', '^')
sr.setMath(libsbml.parseFormula(formula))
sr.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addRule(sr)
for r, r in list(net.algebraicRules.items()):
try:
sr = libsbml.AlgebraicRule()
except NotImplementedError:
sr = libsbml.AlgebraicRule(sbml_level, sbml_version)
formula = r.replace('**', '^')
sr.setMath(libsbml.parseFormula(formula))
sr.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addRule(sr)
for id, rxn in list(net.reactions.items()):
# Need to identify modifiers in kinetic law and add them to
# stoichiometry
kl_vars = ExprManip.extract_vars(rxn.kineticLaw)
species_in_kl = kl_vars.intersection(list(net.species.keys()))
for s in species_in_kl:
if s not in rxn.stoichiometry:
rxn.stoichiometry[s] = 0
try:
srxn = libsbml.Reaction(id)
except NotImplementedError:
srxn = libsbml.Reaction(sbml_level, sbml_version)
srxn.setId(id)
srxn.setName(rxn.name)
# Handle the case where the model was originally read in from an
# SBML file, so that the reactants and products of the Reaction
# object are explicitly set.
if rxn.reactant_stoichiometry != None and \
rxn.product_stoichiometry != None:
for rid, stoich_list in list(rxn.reactant_stoichiometry.items()):
for stoich in stoich_list:
rxn_add_stoich(srxn, rid, -float(stoich), is_product=False)
for rid, stoich_list in list(rxn.product_stoichiometry.items()):
for stoich in stoich_list:
rxn_add_stoich(srxn, rid, stoich, is_product=True)
# Handle the case where the model was created using the SloppyCell
# API, in which case reactants and products are inferred from their
# stoichiometries
else:
for rid, stoich in list(rxn.stoichiometry.items()):
rxn_add_stoich(srxn, rid, stoich)
formula = rxn.kineticLaw.replace('**', '^')
try:
kl = libsbml.KineticLaw(formula)
except NotImplementedError:
kl = libsbml.KineticLaw(sbml_level, sbml_version)
kl.setFormula(formula)
srxn.setKineticLaw(kl)
srxn.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addReaction(srxn)
for id, e in list(net.events.items()):
try:
se = libsbml.Event(id)
except NotImplementedError:
se = libsbml.Event(sbml_level, sbml_version)
se.setId(id)
se.setName(e.name)
formula = e.trigger.replace('**', '^')
formula = formula.replace('and_func(', 'and(')
formula = formula.replace('or_func(', 'or(')
ast = libsbml.parseFormula(formula)
if ast is None:
raise ValueError('Problem parsing event trigger: %s. Problem may '
'be use of relational operators (< and >) rather '
'than libsbml-friendly functions lt and gt.' %
formula)
try:
se.setTrigger(ast)
except TypeError:
try:
trigger = libsbml.Trigger(ast)
except NotImplementedError:
trigger = libsbml.Trigger(sbml_level, sbml_version)
trigger.setMath(ast)
se.setTrigger(trigger)
formula = str(e.delay).replace('**', '^')
try:
se.setDelay(libsbml.parseFormula(formula))
except TypeError:
try:
se.setDelay(libsbml.Delay(libsbml.parseFormula(formula)))
except NotImplementedError:
delay = libsbml.Delay(sbml_level, sbml_version)
delay.setMath(libsbml.parseFormula(formula))
se.setDelay(delay)
for varId, formula in list(e.event_assignments.items()):
try:
sea = libsbml.EventAssignment()
except NotImplementedError:
sea = libsbml.EventAssignment(sbml_level, sbml_version)
sea.setVariable(varId)
formula = str(formula).replace('**', '^')
formula = formula.replace('and_func(', 'and(')
formula = formula.replace('or_func(', 'or(')
ast = libsbml.parseFormula(formula)
replaceTime(ast)
sea.setMath(ast)
se.addEventAssignment(sea)
se.setMetaId('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addEvent(se)
for id, con in list(net.constraints.items()):
try:
scon = libsbml.Constraint()
except NotImplementedError:
scon = libsbml.Constraint(sbml_level, sbml_version)
scon.setId(con.id)
scon.setName(con.name)
formula = con.trigger.replace('**', '^')
ast = libsbml.parseFormula(formula)
if ast is None:
raise ValueError(
'Problem parsing constraint math: %s. Problem may '
'be use of relational operators (< and >) rather '
'than libsbml-friendly functions lt and gt.' % formula)
scon.setMath(ast)
se.setcon('SloppyCell_{0:05d}'.format(metaId))
metaId += 1
m.addConstraint(scon)
d = libsbml.SBMLDocument(sbml_level, sbml_version)
d.setModel(m)
sbmlStr = libsbml.writeSBMLToString(d)
return sbmlStr