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 = 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)
#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:
if 'GENE ASSOCIATION' in note_dict:
del note_dict['GENE ASSOCIATION']
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 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 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 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 = 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)
#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 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 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)
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 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)
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)
