def save_sbml(filename, model, y0=None, volume=1.0, is_valid=True):
"""
Save a model in the SBML format.
Parameters
----------
model : NetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume.
is_valid : bool, optional
Check if the generated model is valid. True as a default.
"""
y0 = y0 or {}
import libsbml
document = export_sbml(model, y0, volume, is_valid)
# with open(filename, 'w') as fout:
# fout.write(libsbml.writeSBMLToString(document))
# writer = libsbml.SBMLWriter()
# writer.writeSBML(document, filename)
libsbml.writeSBML(document, filename)
def createFluxObj(self):
rpsbml = rpSBML.rpSBML('test', None, '../cache')
rpsbml.genericModel('RetroPath_heterologous_pathway', 'rp_model',
self.compXref)
for meta in set([
i for step in steps for lr in ['left', 'right']
for i in step[lr]
]):
try:
inchi = rp_inchi[meta]
except KeyError:
inchi = None
try:
smiles = rp_smiles[meta]
except KeyError:
smiles = None
rpsbml.createSpecies(meta, self.chemXref, None, inchi, smiles,
'MNXC3', 0, '')
rpsbml.createPathway(path_id)
step_id = 0
for stepNum in range(len(steps)):
rpsbml.createReaction('RP_' + str(stepNum), 'B_999999',
'B__999999', steps[stepNum],
reaction_smiles[stepNum], self.reacXref,
'testRid', 0.0, None, rpsbml.hetero_group,
None)
step_id += 1
rpsbml.createFluxObj('flux1', 'RP_1', 2.0, True)
libsbml.writeSBML(rpsbml.document,
self.outputPath + 'test_createFluxObj.sbml')
def save_sbml(filename, model, y0=None, volume=1.0, is_valid=True):
"""
Save a model in the SBML format.
Parameters
----------
model : NetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume.
is_valid : bool, optional
Check if the generated model is valid. True as a default.
"""
y0 = y0 or {}
import libsbml
document = export_sbml(model, y0, volume, is_valid)
# with open(filename, 'w') as fout:
# fout.write(libsbml.writeSBMLToString(document))
# writer = libsbml.SBMLWriter()
# writer.writeSBML(document, filename)
libsbml.writeSBML(document, filename)
def test_WriteL3SBML_zip(self):
file = []
file.append("../../../examples/sample-models/from-spec/level-3/algebraicrules.xml")
file.append("../../../examples/sample-models/from-spec/level-3/assignmentrules.xml")
file.append("../../../examples/sample-models/from-spec/level-3/boundarycondition.xml")
file.append("../../../examples/sample-models/from-spec/level-3/delay.xml")
file.append("../../../examples/sample-models/from-spec/level-3/dimerization.xml")
file.append("../../../examples/sample-models/from-spec/level-3/enzymekinetics.xml")
file.append("../../../examples/sample-models/from-spec/level-3/events.xml")
file.append("../../../examples/sample-models/from-spec/level-3/functiondef.xml")
file.append("../../../examples/sample-models/from-spec/level-3/multicomp.xml")
file.append("../../../examples/sample-models/from-spec/level-3/overdetermined.xml")
file.append("../../../examples/sample-models/from-spec/level-3/twodimensional.xml")
file.append("../../../examples/sample-models/from-spec/level-3/units.xml")
zipfile = "test.xml.zip"
for f in file:
d = libsbml.readSBML(f)
self.assert_( d != None )
if not libsbml.SBMLWriter.hasZlib():
self.assert_( libsbml.writeSBML(d,zipfile) == 0 )
d = None
continue
result = libsbml.writeSBML(d,zipfile)
self.assertEqual( 1, result )
dg = libsbml.readSBML(zipfile)
self.assert_( dg != None )
self.assert_( ( dg.toSBML() != d.toSBML() ) == False )
d = None
dg = None
pass
def write_cobra_model_to_sbml_file(cobra_model, sbml_filename,
sbml_level=2, sbml_version=1,
print_time=False,
use_fbc_package=True):
"""Write a cobra.Model object to an SBML XML file.
cobra_model: :class:`~cobra.core.Model.Model` object
sbml_filename: The file to write the SBML XML to.
sbml_level: 2 is the only level supported at the moment.
sbml_version: 1 is the only version supported at the moment.
use_fbc_package: Boolean.
Convert the model to the FBC package format to improve portability.
http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_(flux)
TODO: Update the NOTES to match the SBML standard and provide support for
Level 2 Version 4
"""
sbml_doc = get_libsbml_document(cobra_model,
sbml_level=sbml_level, sbml_version=sbml_version,
print_time=print_time,
use_fbc_package=use_fbc_package)
writeSBML(sbml_doc, sbml_filename)
def createMergeModels(self):
rpsbml = rpSBML.rpSBML('test', None, '../cache')
rpsbml.genericModel('RetroPath_heterologous_pathway', 'rp_model',
self.compXref)
for meta in set([
i for step in steps for lr in ['left', 'right']
for i in step[lr]
]):
try:
inchi = rp_inchi[meta]
except KeyError:
inchi = None
try:
smiles = rp_smiles[meta]
except KeyError:
smiles = None
rpsbml.createSpecies(meta, self.chemXref, None, inchi, smiles,
'MNXC3', 0, '')
rp_pathway = rpsbml.createPathway(path_id)
#reactions
step_id = 0
for stepNum in range(len(steps)):
rpsbml.createReaction('RP_' + str(stepNum), 'B_999999',
'B__999999', steps[stepNum],
reaction_smiles[stepNum], self.reacXref,
'testRid', 0.0, None, rpsbml.hetero_group,
None)
step_id += 1
#other model
document = libsbml.readSBML(self.outputPath +
'bigg_iMM904.COBRA-sbml3.xml')
model = document.getModel()
rpsbml.mergeModels(model)
libsbml.writeSBML(document, self.outputPath + 'test_mergeModels.sbml')
def write_cobra_model_to_sbml_file(cobra_model,
sbml_filename,
sbml_level=2,
sbml_version=1,
print_time=False,
use_fbc_package=True):
"""Write a cobra.Model object to an SBML XML file.
cobra_model: :class:`~cobra.core.Model.Model` object
sbml_filename: The file to write the SBML XML to.
sbml_level: 2 is the only level supported at the moment.
sbml_version: 1 is the only version supported at the moment.
use_fbc_package: Boolean.
Convert the model to the FBC package format to improve portability.
http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_(flux)
TODO: Update the NOTES to match the SBML standard and provide support for
Level 2 Version 4
"""
sbml_doc = get_libsbml_document(cobra_model,
sbml_level=sbml_level,
sbml_version=sbml_version,
print_time=print_time,
use_fbc_package=use_fbc_package)
writeSBML(sbml_doc, sbml_filename)
def createUnit(self):
rpsbml = rpSBML.rpSBML('test', None, '../cache')
rpsbml.createModel('RetroPath_heterologous_pathway', 'rp_model')
unitDef = rpsbml.createUnitDefinition('mmol_per_gDW_per_hr')
rpsbml.createUnit(unitDef, libsbml.UNIT_KIND_MOLE, 1, -3, 1)
rpsbml.createUnit(unitDef, libsbml.UNIT_KIND_GRAM, 1, 0, 1)
rpsbml.createUnit(unitDef, libsbml.UNIT_KIND_SECOND, 1, 0, 3600)
libsbml.writeSBML(rpsbml.document,
self.outputPath + 'test_createUnit.sbml')
def main(args):
"""Usage: replaceOneFD filename functionDefinitionId reactionId outfile
"""
if (len(args) != 5):
print(
"Usage: replaceOneFD filename functionDefinitionId reactionId outfile"
)
return 1
filename = args[1]
outFile = args[4]
functionDefinitionId = args[2]
reactionId = args[3]
document = libsbml.readSBML(filename)
if (document.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0):
print(
"The models contains errors, please correct them before continuing."
)
document.printErrors()
return 1
model = document.getModel()
functionDefinition = model.getFunctionDefinition(functionDefinitionId)
if (functionDefinition == None):
print()
print("No functiondefinition with the given id can be found.")
return 1
reaction = model.getReaction(reactionId)
if (reaction == None):
print()
print("No reaction with the given id can be found.")
return 1
if (reaction.isSetKineticLaw() == False
or reaction.getKineticLaw().isSetMath() == False):
print()
print("The reaction has no math set. ")
return 1
# Until here it was all setup, all we needed was an ASTNode, in which we wanted to
# replace calls to a function definition, with the function definitions content.
#
libsbml.SBMLTransforms.replaceFD(reaction.getKineticLaw().getMath(),
functionDefinition)
# finally write to file
libsbml.writeSBML(document, outFile)
def write_sbml(self, outfile = ''):
if not outfile:
outfile = self.filename + '.xml'
docu = libsbml.SBMLDocument()
model = docu.createModel()
model.setId(self.id)
model.setName(self.pathway)
model.setAnnotation(
"a pathway from MetaFishNet project")
"""
ectype = libsbml.SpeciesType("enzyme")
cpdtype = libsbml.SpeciesType("compound")
model.addSpeciesType(ectype)
model.addSpeciesType(cpdtype)
"""
ectype = model.createSpeciesType()
ectype.setId("enzyme")
cpdtype = model.createSpeciesType()
cpdtype.setId("compound")
for ec in self.eclist:
sp = model.createSpecies()
sp.setId(sidify(ec))
sp.setName(ec)
sp.setSpeciesType("enzyme")
for cpd in self.cmpds:
ss = model.createSpecies()
ss.setId(sidify(cpd))
ss.setName(cpd)
ss.setSpeciesType("compound")
for rxn in self.rxns:
sbmrxn = model.createReaction()
sbmrxn.setId(rxn.ID)
m = sbmrxn.createModifier()
if rxn.ecstr:
m.setId(sidify(rxn.ecstr))
#m.setName(rxn.ecstr)
for sub in rxn.reactants:
r = sbmrxn.createReactant()
r.setId(sidify(sub))
for prd in rxn.products:
p = sbmrxn.createProduct()
p.setId(sidify(prd))
#docu.setModel(model)
libsbml.writeSBML(docu, outfile)
def writeExampleSBML(sbmlDoc, filename):
result = libsbml.writeSBML(sbmlDoc, filename)
if result == 1:
print ("Wrote file '" + filename + "'")
return True
else:
print ("Failed to write '" + filename + "'")
return False
def main (args):
"""Usage: replaceOneFD filename functionDefinitionId reactionId outfile
"""
if (len(args) != 5):
print("Usage: replaceOneFD filename functionDefinitionId reactionId outfile");
return 1;
filename = args[1];
outFile = args[4];
functionDefinitionId = args[2];
reactionId = args[3];
document = libsbml.readSBML(filename);
if (document.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0):
print("The models contains errors, please correct them before continuing.");
document.printErrors();
return 1;
model = document.getModel();
functionDefinition = model.getFunctionDefinition(functionDefinitionId);
if (functionDefinition == None):
print();
print("No functiondefinition with the given id can be found.");
return 1;
reaction = model.getReaction(reactionId);
if (reaction == None):
print();
print("No reaction with the given id can be found.");
return 1;
if (reaction.isSetKineticLaw() == False or reaction.getKineticLaw().isSetMath()== False):
print();
print("The reaction has no math set. ");
return 1;
# Until here it was all setup, all we needed was an ASTNode, in which we wanted to
# replace calls to a function definition, with the function definitions content.
#
libsbml.SBMLTransforms.replaceFD(reaction.getKineticLaw().getMath(), functionDefinition);
# finally write to file
libsbml.writeSBML(document, outFile);
def convert(self, kgml, sbml):
"""input kgml file, output sbml file"""
w = open(kgml)
tree = ElementTree.parse(w)
note_dict = dict(tree.getroot().items())
model = self.docu.createModel()
model.setName(note_dict['name'])
model.setAnnotation(self.d2note(note_dict))
rxns = tree.findall('reaction')
rlist = [self.parseRxn(x) for x in rxns]
all_enzymes, all_cpds = [], []
for r in rlist:
all_enzymes += r.enzymes
all_cpds += r.cpds
all_enzymes, all_cpds = set(all_enzymes), set(all_cpds)
for ec in all_enzymes:
sp = model.createSpecies()
sp.setId(sidify(ec))
sp.setName(ec)
sp.setSpeciesType("enzyme")
for cpd in all_cpds:
ss = model.createSpecies()
ss.setId(sidify(cpd))
ss.setName(cpd)
ss.setSpeciesType("compound")
for rxn in rlist:
sbmrxn = model.createReaction()
sbmrxn.setName(rxn.ID)
for enz in rxn.enzymes:
m = sbmrxn.createModifier()
m.setId(sidify(enz))
for sub in rxn.reactants:
r = sbmrxn.createReactant()
r.setId(sidify(sub))
for prd in rxn.products:
p = sbmrxn.createProduct()
p.setId(sidify(prd))
libsbml.writeSBML(self.docu, sbml)
def createSpecies(self):
rpsbml = rpSBML.rpSBML('test', None, '../cache')
rpsbml.genericModel('RetroPath_heterologous_pathway', 'rp_model',
self.compXref)
for meta in set([
i for step in steps for lr in ['left', 'right']
for i in step[lr]
]):
try:
inchi = rp_inchi[meta]
except KeyError:
inchi = None
try:
smiles = rp_smiles[meta]
except KeyError:
smiles = None
rpsbml.createSpecies(meta, self.chemXref, None, inchi, smiles,
'MNXC3', 0, '')
libsbml.writeSBML(rpsbml.document,
self.outputPath + 'test_createSpecies.sbml')
def write_sbml_file(self, filename, **kwargs):
self.set_volumes()
if self.volume:
kwargs['volume'] = self.volume
document, _ = self.crn.generate_sbml_model(**kwargs)
else:
document, _ = self.crn.generate_sbml_model(**kwargs)
if document.getNumErrors() and self.warning_print:
warnings.warn('SBML document has errors. It is recommended that you fix them before generating this model.')
status = libsbml.writeSBML(document, filename)
if status == libsbml.LIBSBML_OPERATION_SUCCESS:
print('SBML file written successfully to {0}'.format(filename))
return document
def write_cobra_model_to_sbml_file(cobra_model,
sbml_filename,
sbml_level=2,
sbml_version=1,
print_time=False,
use_fbc_package=True):
"""Write a cobra.Model object to an SBML XML file.
Parameters
----------
cobra_model : cobra.core.Model.Model
The model object to write
sbml_filename : string
The file to write the SBML XML to.
sbml_level : int
2 is the only supported level.
sbml_version : int
1 is the only supported version.
print_time : bool
deprecated
use_fbc_package : bool
Convert the model to the FBC package format to improve portability.
http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_(flux)
Notes
-----
TODO: Update the NOTES to match the SBML standard and provide support for
Level 2 Version 4
"""
if not libsbml:
raise ImportError('write_cobra_model_to_sbml_file '
'requires python-libsbml')
sbml_doc = get_libsbml_document(cobra_model,
sbml_level=sbml_level,
sbml_version=sbml_version,
print_time=print_time,
use_fbc_package=use_fbc_package)
libsbml.writeSBML(sbml_doc, sbml_filename)
def save_sbml(filename, model, y0={}, volume=1.0):
"""
Save a model in the SBML format.
Parameters
----------
model : NetworkModel or ODENetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume.
"""
import libsbml
document = export_sbml(model, y0, volume)
# with open(filename, 'w') as fout:
# fout.write(libsbml.writeSBMLToString(document))
# writer = libsbml.SBMLWriter()
# writer.writeSBML(document, filename)
libsbml.writeSBML(document, filename)
def main (args):
"""Usage: printNotes filename
"""
if (len(args) != 3):
print("Usage: inlineInitialAssignments filename outFile");
return 1;
filename = args[1];
outFile = args[2];
document = libsbml.readSBML(filename);
if (document.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0):
print("The models contains errors, please correct them before continuing.");
document.printErrors();
return 1;
model = document.getModel();
libsbml.SBMLTransforms.expandInitialAssignments(model);
libsbml.writeSBML(document, outFile);
def write_cobra_model_to_sbml_file(cobra_model, sbml_filename,
sbml_level=2, sbml_version=1,
print_time=False,
use_fbc_package=True):
"""Write a cobra.Model object to an SBML XML file.
Parameters
----------
cobra_model : cobra.core.Model.Model
The model object to write
sbml_filename : string
The file to write the SBML XML to.
sbml_level : int
2 is the only supported level.
sbml_version : int
1 is the only supported version.
print_time : bool
deprecated
use_fbc_package : bool
Convert the model to the FBC package format to improve portability.
http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_(flux)
Notes
-----
TODO: Update the NOTES to match the SBML standard and provide support for
Level 2 Version 4
"""
if not libsbml:
raise ImportError('write_cobra_model_to_sbml_file '
'requires python-libsbml')
sbml_doc = get_libsbml_document(cobra_model,
sbml_level=sbml_level,
sbml_version=sbml_version,
print_time=print_time,
use_fbc_package=use_fbc_package)
libsbml.writeSBML(sbml_doc, sbml_filename)
def main(args):
"""Usage: printNotes filename
"""
if (len(args) != 3):
print("Usage: inlineInitialAssignments filename outFile")
return 1
filename = args[1]
outFile = args[2]
document = libsbml.readSBML(filename)
if (document.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0):
print(
"The models contains errors, please correct them before continuing."
)
document.printErrors()
return 1
model = document.getModel()
libsbml.SBMLTransforms.expandInitialAssignments(model)
libsbml.writeSBML(document, outFile)
def save_sbml(filename, model, y0=None, volume=1.0):
"""
Save a model in the SBML format.
Parameters
----------
model : NetworkModel or ODENetworkModel
y0 : dict
Initial condition.
volume : Real or Real3, optional
A size of the simulation volume.
"""
y0 = y0 or {}
import libsbml
document = export_sbml(model, y0, volume)
# with open(filename, 'w') as fout:
# fout.write(libsbml.writeSBMLToString(document))
# writer = libsbml.SBMLWriter()
# writer.writeSBML(document, filename)
libsbml.writeSBML(document, filename)
def write_sbml_file(self, filename, **kwargs):
warnings.warn(
"CRNLab is deprecated and will cease to function with future releases: to save a CRN to SBML, please use ChemicalReactionNetwork.write_sbml_file()",
DeprecationWarning)
self.set_volumes()
if self.volume:
kwargs['volume'] = self.volume
document, _ = self.crn.generate_sbml_model(**kwargs)
else:
document, _ = self.crn.generate_sbml_model(**kwargs)
if document.getNumErrors() and self.warning_print:
warnings.warn(
'SBML document has errors. It is recommended that you fix them before generating this model.'
)
status = libsbml.writeSBML(document, filename)
if status == libsbml.LIBSBML_OPERATION_SUCCESS:
print('SBML file written successfully to {0}'.format(filename))
return document
def to_SBML_l2v1(from_name, to_name):
"""
Convert an SBML file to level 2, version 1 using lisbml.
from_name Name of file to read SBML from.
to_name File to output SBML to.
"""
doc = libsbml.readSBML(os.path.abspath(from_name))
if isinstance(doc, int):
logger.critical('Fatal Errors reading SBML from file %s!' % from_name)
_print_sbml_fatals(doc)
errors = doc.setLevel(2)
if errors:
logger.critical('Fatal Errors converting %f to level 2!' % from_name)
_print_sbml_fatals(doc)
errors = doc.setVersion(1)
if errors:
logger.critical('Fatal Errors converting %f to level 2, version 1!' %
from_name)
_print_sbml_fatals(doc)
success = libsbml.writeSBML(doc, to_name)
if not success:
logger.critical('Error writing to %s' % to_name)
def to_SBML_l2v1(from_name, to_name):
"""
Convert an SBML file to level 2, version 1 using lisbml.
from_name Name of file to read SBML from.
to_name File to output SBML to.
"""
doc = libsbml.readSBML(os.path.abspath(from_name))
if isinstance(doc, int):
logger.critical('Fatal Errors reading SBML from file %s!' % from_name)
_print_sbml_fatals(doc)
errors = doc.setLevel(2)
if errors:
logger.critical('Fatal Errors converting %f to level 2!' % from_name)
_print_sbml_fatals(doc)
errors = doc.setVersion(1)
if errors:
logger.critical('Fatal Errors converting %f to level 2, version 1!'
% from_name)
_print_sbml_fatals(doc)
success = libsbml.writeSBML(doc, to_name)
if not success:
logger.critical('Error writing to %s' % to_name)
sbml_model = sbml_doc.getModel()
for par in sbml_model.getListOfParameters():
if par.getName() == 'pPROT':
phosphoId = par.getId()
phosphoRule = \
sbml_model.getAssignmentRuleByVariable(
phosphoId
).getFormula()
totalId = [
par.getId() for par in sbml_model.getListOfParameters()
if par.getName() == 'tPROT'
][0]
totalRule = \
sbml_model.getAssignmentRuleByVariable(
totalId
).getFormula()
new_phosphoRule = '(' + phosphoRule + ')/(' + totalRule + ')'
sbml_model.getAssignmentRuleByVariable(phosphoId).setFormula(
new_phosphoRule)
sbml_model.getAssignmentRuleByVariable(totalId).removeFromParentAndDelete()
sbml_model.getParameter(totalId).removeFromParentAndDelete()
libsbml.writeSBML(sbml_doc, outfile)
def createModel(self):
rpsbml = rpSBML.rpSBML('test', None, '../cache')
rpsbml.createModel('RetroPath_heterologous_pathway', 'rp_model')
libsbml.writeSBML(rpsbml.document,
self.outputPath + 'test_createModel.sbml')
def printSBML(self, ofile, ver=['2', '3']):
'''
Output the model to SBML.
LibSBML must be installed.
Arguments
--
ofile: if specifed, output to this file
ver: version of SBML
'''
if sbml:
p, r, s, v = self.parameters, self.reactions, self.species, self.variables
# preliminaries: including SBML version, such as 2.3
document = libsbml.SBMLDocument(eval(ver[0]), eval(ver[1]))
model = document.createModel()
c = model.createCompartment()
c.setId('cell')
c.setVolume(1.0)
# create species
for spec in self.alphspecies:
ss = model.createSpecies()
ss.setId(spec)
ss.setCompartment('cell')
ss.setInitialAmount(eval(s[spec]['initial amount']))
# create parameters
for par in p.keys():
pp = model.createParameter()
pp.setId(par)
pp.setConstant(True)
pp.setValue(eval(p[par]['value']))
# variables must first be defined as parameters
for var in v.keys():
pp = model.createParameter()
pp.setId(var)
pp.setConstant(False)
# define all rate constants as parameters
for reac in r.keys():
rvalue = r[reac]['rate value']
if rvalue:
# a new rate constant is defined
newrate = r[reac]['rate constant']
pp = model.createParameter()
pp.setId(newrate)
if self.isfloat(rvalue):
# defined numerically
pp.setConstant(True)
pp.setValue(eval(rvalue))
else:
# defined algebraically
pp.setConstant(False)
vv = model.createAssignmentRule()
value = libsbml.parseFormula(rvalue)
vv.setVariable(newrate)
vv.setMath(value)
# create variables
for var in v.keys():
vv = model.createAssignmentRule()
value = libsbml.parseFormula(v[var]['value'])
vv.setVariable(var)
vv.setMath(value)
# create reactions
for reac in r.keys():
rr = model.createReaction()
rr.setId('r_' + reac)
rr.setCompartment('cell')
rr.setReversible(False)
for i in range(len(r[reac]['reactants'])):
rrr = rr.createReactant()
rrr.setSpecies(r[reac]['reactants'][i])
for i in range(len(r[reac]['products'])):
rrp = rr.createProduct()
rrp.setSpecies(r[reac]['products'][i])
if r[reac]['mass action']:
# find rate by mass action
rrate = r[reac]['rate constant']
for reactant in r[reac]['reactants']:
rrate += '*' + reactant
mods = self.findmodifiers(rrate,
exclude=list(
set(r[reac]['reactants'])))
else:
# rate already specified
rrate = r[reac]['rate constant']
mods = self.findmodifiers(rrate)
# add modifiers
for mod in mods:
mdf = rr.createModifier()
mdf.setSpecies(mod)
rrk = rr.createKineticLaw()
rrk.setFormula(rrate)
# write file
document.setModel(model)
if ofile:
libsbml.writeSBMLToFile(document, ofile + '.xml')
else:
libsbml.writeSBML(document, sys.stdout)
else:
print(
'sencillo: libSBML cannot be imported. SBML cannot be created.'
)
#
olevel = document.getLevel();
oversion = document.getVersion();
success = False;
outputFile = os.path.join(d, modelfile.replace('l3v1', 'l2v4'))
print ("Attempting to convert Level " + str(olevel) + " Version " + str(oversion)
+ " model to Level 2 Version 4." + "\n", file=sys.stderr);
success = document.setLevelAndVersion(2, 4);
errors = document.getNumErrors();
if (not success):
print("Unable to perform conversion due to the following:" + "\n", file=sys.stderr);
document.printErrors();
print("\n", file=sys.stderr);
print("Conversion skipped. Either libSBML does not (yet)" + "\n"
+ "have the ability to convert this model or (automatic)" + "\n"
+ "conversion is not possible in this case." + "\n", file=sys.stderr);
break
elif (errors > 0):
print("Information may have been lost in conversion; but a valid model ", file=sys.stderr);
print("was produced by the conversion.\nThe following information ", file=sys.stderr);
print("was provided:\n", file=sys.stderr);
document.printErrors();
writeSBML(document, outputFile);
else:
print("Conversion completed." + "\n", file=sys.stderr);
writeSBML(document, outputFile);
def createCompartent(self):
rpsbml = rpSBML.rpSBML('test', None, '../cache')
rpsbml.createModel('RetroPath_heterologous_pathway', 'rp_model')
rpsbml.createCompartment(1, 'MNXC3', 'cytoplasm', self.compXref)
libsbml.writeSBML(rpsbml.document,
self.outputPath + 'test_createCompartent.sbml')
def genericModel(self):
rpsbml = rpSBML.rpSBML('test', None, '../cache')
rpsbml.genericModel('RetroPath_heterologous_pathway', 'rp_model',
self.compXref)
libsbml.writeSBML(rpsbml.document,
self.outputPath + 'test_genericModel.sbml')
print("Attempting to convert Level " + str(olevel) + " Version " +
str(oversion) + " model to Level 2 Version 4." + "\n",
file=sys.stderr)
success = document.setLevelAndVersion(2, 4)
errors = document.getNumErrors()
if (not success):
print("Unable to perform conversion due to the following:" + "\n",
file=sys.stderr)
document.printErrors()
print("\n", file=sys.stderr)
print("Conversion skipped. Either libSBML does not (yet)" + "\n" +
"have the ability to convert this model or (automatic)" + "\n" +
"conversion is not possible in this case." + "\n",
file=sys.stderr)
break
elif (errors > 0):
print(
"Information may have been lost in conversion; but a valid model ",
file=sys.stderr)
print("was produced by the conversion.\nThe following information ",
file=sys.stderr)
print("was provided:\n", file=sys.stderr)
document.printErrors()
writeSBML(document, outputFile)
else:
print("Conversion completed." + "\n", file=sys.stderr)
writeSBML(document, outputFile)
def saveAsSBML( self, filename ):
aSBMLDocument = self.convertEMLToSBML()
libsbml.writeSBML( aSBMLDocument, filename )
def write_cobra_model_to_sbml_file(cobra_model,
sbml_filename,
sbml_level=2,
sbml_version=1,
print_time=False,
use_fbc_package=True):
"""Write a cobra.Model object to an SBML XML file.
cobra_model: :class:`~cobra.core.Model.Model` object
sbml_filename: The file to write the SBML XML to.
sbml_level: 2 is the only level supported at the moment.
sbml_version: 1 is the only version supported at the moment.
use_fbc_package: Boolean.
Convert the model to the FBC package format to improve portability.
http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_(flux)
TODO: Update the NOTES to match the SBML standard and provide support for
Level 2 Version 4
"""
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 = 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(UNIT_KIND_MOLE)
sbml_unit.setScale(-3)
sbml_unit = model_units.createUnit()
sbml_unit.setKind(UNIT_KIND_GRAM)
sbml_unit.setExponent(-1)
sbml_unit = model_units.createUnit()
sbml_unit.setKind(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")
#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 the_reaction._metabolites.items(
):
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 = 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 = 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)
sbml_reaction.setNotes(
'<html xmlns="http://www.w3.org/1999/xhtml">%sGENE_ASSOCIATION: %s%s%sSUBSYSTEM: %s%s</html>'
% (note_start_tag, the_reaction.gene_reaction_rule, note_end_tag,
note_start_tag, the_reaction.subsystem, note_end_tag))
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))
writeSBML(sbml_doc, sbml_filename)
def createUnitDefinition(self):
rpsbml = rpSBML.rpSBML('test', None, '../cache')
rpsbml.createModel('RetroPath_heterologous_pathway', 'rp_model')
unitDef = rpsbml.createUnitDefinition('mmol_per_gDW_per_hr')
libsbml.writeSBML(rpsbml.document,
self.outputPath + 'test_createUnitDefinition.sbml')
def enzyme_note(enzyme_list):
result = '<body xmlns="http://www.w3.org/1999/xhtml"><p>GENE_ASSOCIATION: ('
result += ' and '.join(enzyme_list)
return result + ')</p></body>\n'
if __name__ == "__main__":
# read sbml
sbml = libsbml.readSBML('metabolism.xml')
# update metabolite names
for s in sbml.model.species:
s.setId(metabolite_name(s.id))
for r in sbml.model.reactions:
for sr in itertools.chain(r.reactants, r.products):
sr.setSpecies(metabolite_name(sr.species))
# add notes with enzyme compositions
enzymes = etree.parse('enzymes.xml')
enzyme_list = {}
for e in enzymes.iterfind('listOfEnzymes/enzyme'):
id_ = e.attrib['id']
enzyme_list[id_] = [
sr.attrib['species']
for sr in e.find('machineryComposition/listOfReactants')
if not sr.attrib['species'].startswith('m_')
]
for r in sbml.model.reactions:
r.setNotes(enzyme_note(enzyme_list[r.id]))
# write sbml
libsbml.writeSBML(sbml, 'sbml.xml')
def write_cobra_model_to_sbml_file(cobra_model,
sbml_filename,
sbml_level=2,
sbml_version=1,
print_time=False):
"""Write a cobra.Model object to an SBML XML file.
cobra_model: A cobra.Model object
sbml_filename: The file to write the SBML XML to.
sbml_level: 2 is the only level supported at the moment.
sbml_version: 1 is the only version supported at the moment.
print_time: Boolean. Print the time requirements for different sections
TODO: Update the NOTES to match the SBML standard and provide support for
Level 2 Version 4
"""
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 = SBMLDocument(sbml_level, sbml_version)
sbml_model = sbml_doc.createModel(cobra_model.description.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(UNIT_KIND_MOLE)
sbml_unit.setScale(-3)
sbml_unit = model_units.createUnit()
sbml_unit.setKind(UNIT_KIND_GRAM)
sbml_unit.setExponent(-1)
sbml_unit = model_units.createUnit()
sbml_unit.setKind(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:
start_time = time()
#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)
if print_time:
print 'Adding %s took %1.2f seconds' % ('metabolites',
time() - start_time)
if print_time:
start_time = time()
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)
sbml_reaction.setReversible(the_reaction.reversibility)
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 the_reaction._metabolites.items(
):
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 = the_reaction._metabolites.items(
)[0]
the_metabolite = the_metabolite.copy()
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 = 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 = 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)
sbml_reaction.setNotes(
'<html xmlns="http://www.w3.org/1999/xhtml">%sGENE_ASSOCIATION: %s%s%sSUBSYSTEM: %s%s</html>'
% (note_start_tag, the_reaction.gene_reaction_rule, note_end_tag,
note_start_tag, the_reaction.subsystem, note_end_tag))
if print_time:
print 'Adding %s took %1.2f seconds' % ('reactions',
time() - start_time)
writeSBML(sbml_doc, sbml_filename)
def _writeDBModelToSBML(conn, database_path, sbml_output_path, modelRow):
c = conn.cursor()
# check table existence
c.execute('SELECT name FROM sqlite_master WHERE type="table"')
db_tables = [row[0] for row in c.fetchall()]
expected_tables = ['Components', 'Regulations', 'Parametrizations']
if len(set(expected_tables).difference(set(db_tables))) != 0:
raise Exception("[Error] writeDBModelToSBML, {0} : Cannot find table(s) {1} in database.".
format(database_path, set(expected_tables).difference(set(db_tables))))
# check model row existence
rowcount = c.execute("SELECT COUNT (*) FROM Parametrizations").fetchone()[0]
if modelRow > rowcount:
raise Exception(
"[Error] writeDBModelToSBML, {0} : Cannot select row {1} from table Parametrizations with {2} rows. Aborting model export.\n".format(
database_path, modelRow, rowcount))
# Create an SBMLNamespaces object with the given SBML level, version,
# package name, package version.
sbmlns = libsbml.SBMLNamespaces(3, 1, "qual", 1)
# Creates an SBMLDocument object
document = libsbml.SBMLDocument(sbmlns)
# mark qual as required
document.setPackageRequired("qual", True)
# create the Model
model = document.createModel()
# get a QualModelPlugin object plugged into the model object (enables qualSBML interface).
mplugin = model.getPlugin("qual")
# extract regulatory context descriptions from table Parametrizations
# get the column names from table Parametrizations
column_name_list = [tuple[0] for tuple in c.execute(
"SELECT * FROM Parametrizations").description] # TO DO: exception for invalid/missing model
# create a list of all column names which represent regulatory contexts
context_name_list = [column_name for column_name in column_name_list if
column_name[0:2] == 'K_'] # TO DO: index dependent = bad
# create a list of "targets" (components with incoming regulations)
target_list = [target for target, in
c.execute('SELECT DISTINCT Target FROM Regulations ORDER BY Target').fetchall()]
# create an internal list of regulatory context descriptions
context_list = []
for context_name in context_name_list:
# find the target component matching the context name
target_match_list = [target for target in target_list if context_name[2:].find(
target) != -1] # can find multiple targets: e.g. context_name="K_RafB_012" will match species Raf and RafB
target = [match for match in target_match_list if len(match) == max(map(len, target_match_list))][
0] # take the longest match, now "K_RafB_012" will only match RafB and not Raf
# extract the threshold states of the regulatory context from the context name
# regular expression pattern: find all digits following "K_RafB_" where RafB is the current context target
pattern = r'(?<=K_{0}_)\d+'.format(target)
# thresholds_name: string of threshold state digits (e.g. "012" for context_name K_RafB_012)
thresholds_name = re.search(pattern, context_name).group(0) # WILL NOT WORK for components with MaxActivity > 9
threshold_list = [int(d) for d in thresholds_name]
context = [context_name, target]
context.extend(threshold_list) # each context = list of format ['K_Raf_031', 'Raf', 0, 3, 1]
context_list.append(context)
# write to qualSBML model
# set a default compartment (required for all models)
compartment = model.createCompartment()
compartment.setId("default")
compartment.setConstant(True)
# set QualitativeSpecies from Components table
for name, maxActivity in c.execute('SELECT Name, MaxActivity FROM Components ORDER BY Name').fetchall():
# create a qualSBML QualitativeSpecies
qs = mplugin.createQualitativeSpecies()
qs.setId(name) # Id is required to be unique
qs.setCompartment("default")
qs.setConstant(False) # components without inputs are usually set constant, however this is not required
qs.setMaxLevel(maxActivity)
qs.setName(name) # name is not required to be set or to be unique
# set Transitions from Regulations and Parametrizations tables
# qualSBML Transitions have a list for input and an output QualitativeSpecies. Usually each transition only has one output (target).
# Components with identical regulation may be described using only one Transition with multiple outputs
# but this is not required and this function creates a transition for each target component.
for target, in c.execute('SELECT DISTINCT Target FROM Regulations ORDER BY Target').fetchall():
# create a Transition: one qualSBML Transition per TREMPPI component with >= 1 regulators
t = mplugin.createTransition()
# create qualSBML transition output for transition t
o = t.createOutput()
o.setQualitativeSpecies(target)
o.setTransitionEffect(
1) # transitionEffect=1 means 'assignmentLevel'. Required for logical/multi valued models.
# save a list of all regulator/input-species-names (string) for this target component
source_list = []
for source, in c.execute('SELECT DISTINCT Source FROM Regulations WHERE Target=? ORDER BY Source',
(target,)).fetchall():
# create qualSBML transition input for transition t
i = t.createInput()
i.setQualitativeSpecies(source)
i.setTransitionEffect(0) # transitionEffect=0 means 'none'. Required for logical/multi valued models.
# also append this input to our regulator/input-name list
source_list.append(source)
# setup a ASTNode representation for the qualSBML Transition.FunctionTerm.Math element from TREMPPI regulatory context information
# get all regulatory contexts for this target component
target_context_list = [context for context in context_list if context[1] == target]
# Each regulatory context is represented in qualSBML by one Transition.FunctionTerm or by the Transition.DefaultTerm.
# FunctionTerm definitions hold the (in-)equalities to define source/input states leading to a target/output value.
# This function creates a FunctionTerm even for unobservable contexts as long as they are defined in table Parametrizations.
# This leads to more FunctionTerm definitions than necessary but allows to recreate the whole network from the qualSBML file.
for context in target_context_list:
# list of regulator threshold states for this context
source_tstate_list = context[2:]
# parameter target value of this context
param = \
c.execute('SELECT {0} FROM Parametrizations WHERE rowid={1}'.format(context[0], modelRow)).fetchall()[0][0]
# If this context is the context with threshold level = 0 for all regulators, use it as Transition.DefaultTerm in qualSBML
# Transitions default to this target value if none of the FunctionTerm definitions apply to a system state
if sum(source_tstate_list) == 0:
# create qualSBML transition DefaultTerm for transition t
d = t.createDefaultTerm()
d.setResultLevel(param) # ResultLevel is the qualSBML equivalent of a target value
# else create a Transition.FunctionTerm term with math element
else:
# create qualSBML transition FunctionTerm for transition t
f = t.createFunctionTerm()
f.setResultLevel(param)
# list of the ASTNode-tree inequality representations of each regulatory context
f_ASTNode_list = []
# find lower and upper thresholds (activity interval) of each source/regulator in this context and build an ASTNode tree of the resulting inequalities
# for each source index
for source_index in range(0, len(source_list)):
source = source_list[source_index]
source_tstate = source_tstate_list[
source_index] # threshold state for this source (e.g. 0 for the first regulator of RafB in K_RafB_012)
# list of thresholds for this source -> target regulation
threshold_list = c.execute(
'SELECT Threshold FROM Regulations WHERE Target=? AND Source=? ORDER BY Threshold',
(target, source)).fetchall()
lower_t = 0 # Initialize the lower bound of the interval with 0.
# If the activity interval includes 0 as lower bound, it is the leftmost (lowest) activity interval.
# If it includes the highest threshold of the regulator as its lower bound, it is the rightmost (largest) activity interval.
leftmost = True # initialize as leftmost
rightmost = False
threshold_index = 0 # index of the current regulator threshold
# Traverse regulator thresholds and reset lower_t until lower_t matches the threshold state in this context
# and set threshold_index to the index of the next higher threshold.
while source_tstate > lower_t:
lower_t = threshold_list[threshold_index][0]
threshold_index += 1
leftmost = False # If lower_t is not 0, this is not the lowest activity interval.
# If this is not the rightmost (highest) interval, set upper_t to the next higher threshold of this regulator.
if len(threshold_list) > threshold_index:
upper_t = threshold_list[threshold_index][0]
# Otherwise, set upper_t to the maximum activity of the regulator.
else:
upper_t = c.execute('SELECT MaxActivity FROM Components WHERE Name=?', (source,)).fetchall()[0]
rightmost = True
# build ASTNode tree
# if this is the leftmost activity interval create inequality: source < upper bound
if leftmost:
ast = buildASTInequality(source, 'lt', upper_t)
# else if this is the rightmost activity interval create inequality: source >= lower bound
elif rightmost:
ast = buildASTInequality(source, 'geq', lower_t)
# otherwise create inequalities: (source >= lower bound) AND (source < upper bound)
else:
# create AND ASTNode
ast = libsbml.ASTNode(libsbml.AST_LOGICAL_AND)
# create (source >= lower bound) AST subtree
lower_t_ASTNode = buildASTInequality(source, 'geq', lower_t)
# create (source < upper bound) AST subtree
upper_t_ASTNode = buildASTInequality(source, 'lt', upper_t)
# add subtries to AND node
ast.addChild(lower_t_ASTNode)
ast.addChild(upper_t_ASTNode)
# Add the complete AST tree of this source/regulator to the list of inequality definitions for this context/FunctionTerm
f_ASTNode_list.append(ast)
# If this context depends on more than one source/regulator, add an additional AND node as root of the context/FunctionTerm AST tree
# and add all regulator subtrees as children (MathML's AND allows more than 2 children)
if (len(f_ASTNode_list) > 1):
topASTNode = libsbml.ASTNode(libsbml.AST_LOGICAL_AND)
for ast in f_ASTNode_list:
topASTNode.addChild(ast)
# otherwise make the first (and only) ASTNode in the list the root
else:
topASTNode = f_ASTNode_list[0]
# set the complete AST tree as the Math-element of this FunctionTerm
f.setMath(topASTNode)
# Check document consistency
document.checkInternalConsistency()
if document.getNumErrors() > 0:
raise Exception(
"[Error] writeDBModelToSBML: Exported SBML model invalid or inconsistant, aborting model export.\n Error Log from libSBML:\n{0}".format(
document.getErrorLog().toString()))
# Write the document to the specified output file path
libsbml.writeSBML(document, sbml_output_path)
def write_cobra_model_to_sbml_file(cobra_model, sbml_filename,
sbml_level=2, sbml_version=1,
print_time=False):
"""Write a cobra.Model object to an SBML XML file.
cobra_model: A cobra.Model object
sbml_filename: The file to write the SBML XML to.
sbml_level: 2 is the only level supported at the moment.
sbml_version: 1 is the only version supported at the moment.
print_time: Boolean. Print the time requirements for different sections
TODO: Update the NOTES to match the SBML standard and provide support for
Level 2 Version 4
"""
#Add in the common compartment abbreviations. If there are additional compartments
#they also need to be added.
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>'
if not hasattr(cobra_model, 'compartments'):
cobra_model.compartments = {'c': 'cytosol',
'p': 'periplasm',
'e': 'extracellular'}
sbml_doc = SBMLDocument(sbml_level, sbml_version)
sbml_model = sbml_doc.createModel(cobra_model.description.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(UNIT_KIND_MOLE)
sbml_unit.setScale(-3)
sbml_unit = model_units.createUnit()
sbml_unit.setKind(UNIT_KIND_GRAM)
sbml_unit.setExponent(-1)
sbml_unit = model_units.createUnit()
sbml_unit.setKind(UNIT_KIND_SECOND)
sbml_unit.setMultiplier(1.0/60/60)
sbml_unit.setExponent(-1)
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:
start_time = time()
#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)
if print_time:
print 'Adding %s took %1.2f seconds'%('metabolites',
time()-start_time)
if print_time:
start_time = time()
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)
if the_reaction.reversibility == 1:
sbml_reaction.setReversible(True)
else:
sbml_reaction.setReversible(False)
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 the_reaction._metabolites.items():
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 = the_reaction._metabolites.items()[0]
the_metabolite = the_metabolite.copy()
metabolite_id = add_sbml_species(sbml_model, the_metabolite,
note_start_tag=note_start_tag,
note_end_tag=note_end_tag,
boundary_metabolite=True)
the_coefficient *= -1
#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 = KineticLaw(sbml_level, sbml_version)
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 = 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)
sbml_reaction.setNotes('<html xmlns="http://www.w3.org/1999/xhtml">%sGENE_ASSOCIATION: %s%s%sSUBSYSTEM: %s%s</html>'%(note_start_tag,
the_reaction.gene_reaction_rule,
note_end_tag,
note_start_tag,
the_reaction.subsystem,
note_end_tag))
if print_time:
print 'Adding %s took %1.2f seconds'%('reactions',
time()-start_time)
writeSBML(sbml_doc, sbml_filename)
def createParameter(self):
rpsbml = rpSBML.rpSBML('test', None, '../cache')
rpsbml.createModel('RetroPath_heterologous_pathway', 'rp_model')
upInfParam = rpsbml.createParameter('B_999999', 999999.0, 'kj_per_mol')
libsbml.writeSBML(rpsbml.document,
self.outputPath + 'test_createParameter.sbml')
def add_metainfo(original_file, output_file, name_of_model, is_kegg, objective_fn, gap_filling_rxns, rxn_to_ec, rxn_to_gene, rxns_of_interest, \
seq_similarity_reactions, spontaneous_reactions, user_defined_reactions, all_reaction_to_attribute, all_metabolite_to_attribute):
"""This function reads the information in original_file, and modifies it and outputs it to output_file.
The following additional parameters need to be specified:
name_of_model: the name of the model.
is_kegg: True (uses KEGG reaction database) or False (uses BiGG database)
objective_fn: the name of the objective function for this model.
gap_filling_rxns: the list of gap-filling reactions.
rxn_to_ec: mapping of reaction to EC.
rxn_to_gene: mapping of reaction to gene.
rxns_of_interest: high-confidence reactions + gap-filling reactions.
seq_similarity_reactions: reactions that are being added based on sequence similarity (this is for models reconstructed using the BiGG database).
spontaneous_reactions: reactions that are always added as they are non-enzymatic.
"""
# Add compartments if this is a BiGG model.
compart_info = ["<listOfCompartments>"]
if not is_kegg:
ids = ["c", "p", "e"]
names = ["cytosol", "periplasm", "extracellular space"]
else:
# Have only one compartment if KEGG.
ids = ["c"]
names = ["cytosol"]
for curr_id, curr_name in zip(ids, names):
#<compartment id="c" name="cytosol" size="1" constant="true"/>
curr_string = '<compartment metaid="'+ curr_id + '" id="' + curr_id + '" name="' + curr_name + '" size="1" constant="true"/>'
compart_info.append(curr_string)
compart_info.append("</listOfCompartments>")
add_information_after("<model id=", compart_info, output_file, original_file)
# Set flux objective
flux_obj_str_lst = ['<fbc:listOfObjectives fbc:activeObjective="obj">']
flux_obj_str_lst.append('<fbc:objective fbc:id="obj" fbc:type="maximize">')
flux_obj_str_lst.append('<fbc:listOfFluxObjectives>')
flux_obj_str_lst.append('<fbc:fluxObjective fbc:reaction="' + objective_fn + '" fbc:coefficient="1"/>')
flux_obj_str_lst.append('</fbc:listOfFluxObjectives>')
flux_obj_str_lst.append('</fbc:objective>')
flux_obj_str_lst.append('</fbc:listOfObjectives>')
add_information_after("</listOfReactions>", flux_obj_str_lst, output_file)
# Set the FBC information on the second line.
# and change the name of the model.
line_num_to_new_info = {}
new_name_of_model = name_of_model
line_num_to_new_info[2] = '<model metaid="' + new_name_of_model + '" id="' + new_name_of_model + '" fbc:strict="true">'
new_info = '<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" ' +\
'xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" ' + \
'level="3" version="1" fbc:required="false" groups:required="false">'
line_num_to_new_info[1] = new_info
replace_information(line_num_to_new_info, output_file)
# Add the compartment for the metabolites if model is made using KEGG.
if is_kegg:
change_metabolite_attribute(output_file)
# Get the lower and upper bounds possible at all.
bound_to_id, rxn_to_lb, rxn_to_ub = read_bounds(original_file)
# Then, re-write the file while dispensing of "kineticLaw" parameters
# and add the upper and lower bounds to the individual reactions.
# Also add attributes for each reaction (description/name).
fix_bounds(output_file, bound_to_id, rxn_to_lb, rxn_to_ub, all_reaction_to_attribute, is_kegg)
# Add metaId and attributes for each compound (description/name).
fix_cpd(output_file, all_metabolite_to_attribute, is_kegg)
# Now, add the reaction to gene association information.
add_genes_to_file(rxn_to_gene, rxns_of_interest, output_file)
# Add any pathway information. Leave out global pathways, as these are generic pathways.
generic_pathways = ["rn01100", "rn01110", "rn01120", "rn01200", "rn01210", "rn01212", "rn01230", "rn01240", "rn01220"]
pathwayID_to_name, pathwayID_to_reaction_of_int = get_pathway_to_reaction(all_reaction_to_attribute, rxns_of_interest, is_kegg)
add_pathway_information(pathwayID_to_name, pathwayID_to_reaction_of_int, generic_pathways, output_file)
document = libsbml.readSBML(output_file)
# Add reaction to EC information plus other dblinks
i = 0
while i < len(document.model.reactions):
rxn = document.model.getReaction(i)
if rxn.id in rxn_to_ec:
ecs = rxn_to_ec[rxn.id]
add_annotation_for_rxn(rxn, ecs)
if rxn.id in gap_filling_rxns:
add_confidence_for_rxn(rxn, "Gap-filling")
elif rxn.id in user_defined_reactions:
add_confidence_for_rxn(rxn, "User-defined reaction")
elif rxn.id in seq_similarity_reactions:
add_confidence_for_rxn(rxn, "Non-EC associated reaction added based on sequence similarity")
elif rxn.id in spontaneous_reactions:
add_confidence_for_rxn(rxn, "Spontaneous reaction")
else:
if rxn.id in rxn_to_ec:
add_confidence_for_rxn(rxn, "Added due to associated high-confidence EC prediction")
# Add attributes.
if is_kegg:
temp_identifier = rxn.id.split("_")[0]
else:
temp_identifier = rxn.id
if (temp_identifier[-2] == "_") and (temp_identifier[-1].isalpha()):
temp_identifier = temp_identifier[:-2]
if temp_identifier.startswith("R_"):
temp_identifier = temp_identifier[2:]
# print (temp_identifier)
# input()
if temp_identifier in all_reaction_to_attribute:
# print (all_reaction_to_attribute[temp_identifier])
curr_dblinks = all_reaction_to_attribute[temp_identifier]["DB_LINKS"]
add_elem_dblinks(rxn, curr_dblinks)
i += 1
# Add metabolite attributes
i = 0
while i < len(document.model.species):
met = document.model.getSpecies(i)
if is_kegg:
temp_identifier = met.id.split("[")[0]
else:
temp_identifier = met.id
if (temp_identifier[-2] == "_") and (temp_identifier[-1].isalpha()):
temp_identifier = temp_identifier[:-2]
if temp_identifier.startswith("M_"):
temp_identifier = temp_identifier[2:]
if temp_identifier in all_metabolite_to_attribute:
curr_dblinks = all_metabolite_to_attribute[temp_identifier]["DB_LINKS"]
add_elem_dblinks(met, curr_dblinks)
i += 1
libsbml.writeSBML(document, output_file)
def write_cobra_model_to_sbml_file(cobra_model, sbml_filename,
sbml_level=2, sbml_version=1,
print_time=False,
use_fbc_package=True):
"""Write a cobra.Model object to an SBML XML file.
cobra_model: :class:`~cobra.core.Model.Model` object
sbml_filename: The file to write the SBML XML to.
sbml_level: 2 is the only level supported at the moment.
sbml_version: 1 is the only version supported at the moment.
use_fbc_package: Boolean.
Convert the model to the FBC package format to improve portability.
http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_(flux)
TODO: Update the NOTES to match the SBML standard and provide support for
Level 2 Version 4
"""
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 = SBMLDocument(sbml_level, sbml_version)
sbml_model = sbml_doc.createModel(cobra_model.description.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(UNIT_KIND_MOLE)
sbml_unit.setScale(-3)
sbml_unit = model_units.createUnit()
sbml_unit.setKind(UNIT_KIND_GRAM)
sbml_unit.setExponent(-1)
sbml_unit = model_units.createUnit()
sbml_unit.setKind(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")
#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)
sbml_reaction.setReversible(the_reaction.reversibility)
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 the_reaction._metabolites.items():
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]
the_metabolite = the_metabolite.copy()
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 = 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 = 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)
sbml_reaction.setNotes('<html xmlns="http://www.w3.org/1999/xhtml">%sGENE_ASSOCIATION: %s%s%sSUBSYSTEM: %s%s</html>'%(note_start_tag,
the_reaction.gene_reaction_rule,
note_end_tag,
note_start_tag,
the_reaction.subsystem,
note_end_tag))
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))
writeSBML(sbml_doc, sbml_filename)