def flattenMotif(combined):
#flatten the combined model by converting it to sbml and then converting back to Antimony
antimony.clearPreviousLoads()
code = antimony.loadAntimonyString(combined)
if code <= 0:
textfile = open('combined.txt', 'w')
textfile.write(combined)
textfile.close()
raise AssertionError(
'combined model is not flattenable. Are you using the right species names? '
+ 'Combined model saved as: ' + str(os.getcwd()) +
'\\combined.txt')
sbmlStr = antimony.getSBMLString('combined')
antimony.loadSBMLString(sbmlStr)
flatComb = antimony.getAntimonyString('combined')
####TODO
#Delete extraneous mRNA -> Protein reactions at P_c connections
#look for p_c#, regex
#delete second equation with occurance of p_c#curr, regex
#todo: remove extraneous species + parameters in the removed equation
####TODO
return (flatComb)
def cellmlStrToAntimony(CellMLStr):
"""Convert a cellml string into the
equivalent antimony string:
ant = cellMLStrToAntimony('mymodel.cellml')
"""
if antimony.loadCellMLFile(CellMLStr) < 0:
raise Exception("Error calling cellMLStrToAntimony" + antimony.getLastError())
return antimony.getAntimonyString(None)
def cellmlFileToAntimony(CellMLFileName):
"""Load a cellml file and return the
equivalent antimony string:
ant = cellMLToAntimony('mymodel.cellml')
"""
if antimony.loadCellMLFile(CellMLFileName) == -1:
raise Exception("Error calling loadCellMLFile")
antimony.loadCellMLFile(CellMLFileName)
return antimony.getAntimonyString(None)
def sbmlToAntimony(str):
"""Convert a SBML string into Antimony:
sbmlStr = sbmlToAntimony (antimonyStr)
"""
err = antimony.loadSBMLString(str)
if err < 0:
raise Exception("Antimony: " + antimony.getLastError())
return antimony.getAntimonyString(None)
def translate_sbml(cls, sbml_file: str):
"""
Translate SBML file to Antimony model specification.
cayenne's model specification is loosely based on Antimony's model
specification.
"""
er_code = sb.loadSBMLFile(sbml_file)
if er_code == -1:
raise ModelError("Error while parsing model")
sb_module = sb.getMainModuleName()
sb_string = sb.getAntimonyString(sb_module)
return sb_string
def cellmlToAntimony(cellml):
""" Convert CellML to antimony string.
:param cellml: CellML string or file
:type cellml: str | file
:return: antimony
:rtype: str
"""
if os.path.isfile(cellml):
code = antimony.loadCellMLFile(cellml)
else:
code = antimony.loadCellMLString(cellml)
_checkAntimonyReturnCode(code)
return antimony.getAntimonyString(None)
def sbmlToAntimony(sbml):
""" Convert SBML to antimony string.
:param sbml: SBML string or file
:type sbml: str | file
:return: Antimony
:rtype: str
"""
if os.path.isfile(sbml):
code = antimony.loadSBMLFile(sbml)
else:
code = antimony.loadSBMLString(sbml)
_checkAntimonyReturnCode(code)
return antimony.getAntimonyString(None)
def cellmlToAntimony(cellml):
""" Convert CellML to antimony string.
:param cellml: CellML string or file
:type cellml: str | file
:return: antimony
:rtype: str
"""
if os.path.isfile(cellml):
code = antimony.loadCellMLFile(cellml)
else:
code = antimony.loadCellMLString(cellml)
_checkAntimonyReturnCode(code)
return antimony.getAntimonyString(None)
def sbmlToAntimony(sbml):
""" Convert SBML to antimony string.
:param sbml: SBML string or file
:type sbml: str | file
:return: Antimony
:rtype: str
"""
if os.path.isfile(sbml):
code = antimony.loadSBMLFile(sbml)
else:
code = antimony.loadSBMLString(sbml)
_checkAntimonyReturnCode(code)
return antimony.getAntimonyString(None)
def cellmlFileToAntimony(self, sbml_path):
""" Converts a CellML file to Antimony source.
:param sbml_path: The path to the CellML file
:returns: A 2-tuple (module_name, antimony_source)
"""
import antimony as sb
# try to load the Antimony code`
code = sb.loadCellMLFile(sbml_path)
# if errors, bail
if self.checkAntimonyReturnCode(code):
errors = sb.getLastError()
raise RuntimeError('Errors encountered when trying to load model:\n{}'.format(errors))
module = sb.getMainModuleName()
sb_source = sb.getAntimonyString(module)
return (module, sb_source)
def cellmlFileToAntimony(self, sbml_path):
""" Converts a CellML file to Antimony source.
:param sbml_path: The path to the CellML file
:returns: A 2-tuple (module_name, antimony_source)
"""
import antimony as sb
# try to load the Antimony code`
code = sb.loadCellMLFile(sbml_path)
# if errors, bail
if self.checkAntimonyReturnCode(code):
errors = sb.getLastError()
raise RuntimeError('Errors encountered when trying to load model:\n{}'.format(errors))
module = sb.getMainModuleName()
sb_source = sb.getAntimonyString(module)
return (module, sb_source)
def sbmlToAntimony(self, sbml, addSBO=False):
""" Converts a raw SBML string to Antimony source.
:param sbml: The raw SBML string
:returns: A 2-tuple (module_name, antimony_source)
"""
import antimony as sb
# try to load the Antimony code`
code = sb.loadSBMLString(sbml)
# if errors, bail
if self.checkAntimonyReturnCode(code):
errors = sb.getLastError()
raise RuntimeError('Errors encountered when trying to load model:\n{}'.format(errors))
module = sb.getMainModuleName()
sb_source = sb.getAntimonyString(module)
if addSBO:
sb_source = self.tryAddSBOTerms(sb_source, sbml_str=sbml)
return (module, sb_source)
def sbmlToAntimony(self, sbml, addSBO=False):
""" Converts a raw SBML string to Antimony source.
:param sbml: The raw SBML string
:returns: A 2-tuple (module_name, antimony_source)
"""
import antimony as sb
# try to load the Antimony code`
code = sb.loadSBMLString(sbml)
# if errors, bail
if self.checkAntimonyReturnCode(code):
errors = sb.getLastError()
raise RuntimeError('Errors encountered when trying to load model:\n{}'.format(errors))
module = sb.getMainModuleName()
sb_source = sb.getAntimonyString(module)
if addSBO:
sb_source = self.tryAddSBOTerms(sb_source, sbml_str=sbml)
return (module, sb_source)
# A : model1();
# B : model2();
# #repeat for all models I have
# #specify a global input node
# var species p_c;
# A.p_input is p_c;
# B.p_output is p_c;
# #repeat for n-1 modules
# end
# '''
#properly flatten the combined model
antimony.loadAntimonyString(combined)
sbmlstr = antimony.getSBMLString('combined')
antimony.loadSBMLString(sbmlstr)
flatcomb = antimony.getAntimonyString('combined')
r = te.loada(flatcomb)
r.exportToAntimony('combined.txt')
r.draw(layout='dot')
#combined = reads + '''
#model combined
# var species p_c;
# #!!module names have to be identical to model names from imported models!!
# A : ffl1();
# B : ffl1();
# A.p_input is p_c;
# B.p_output is p_c;
#end
#'''
