def translate_to_sbml_string(self, model_file: str = '', model_string: str = ''):
"""
Returns string of SBML model specification translated from Antimony or CellML model specification file or string
:param model_file: relative path to model specification file
:param model_string: model specification string
:return {str,str}: string of SBML model specification, string of main module name
"""
# Just to be sure, call clear previous loads
antimony.clearPreviousLoads()
# Loading from model string or file?
if model_file == '':
res_load = antimony.loadString(model_string)
else:
model_path_normalized = self.normalize_path(model_file)
res_load = antimony.loadFile(model_path_normalized)
if res_load == -1:
AntimonyTranslatorError(self, getAntimonyMessage=True)
# Get main loaded module
main_module_name = antimony.getMainModuleName()
if not main_module_name:
AntimonyTranslatorError(self, getAntimonyMessage=True)
# Return string of SBML model specification
translated_model_string = antimony.getSBMLString(main_module_name)
if not translated_model_string:
AntimonyTranslatorError(self, getAntimonyMessage=True)
else:
return translated_model_string, main_module_name
import antimony
with open('transcription.sb') as f:
sb = f.read()
#print(sb)
res = antimony.loadString(sb)
if res < 0:
print(antimony.getLastError())
#print(res)
#print(antimony.getModuleNames())
#print(antimony.getModuleNames()[-1])
sbml = antimony.getSBMLString(antimony.getModuleNames()[-1])
with open('transcription_sbml.xml', 'w') as f:
f.write(sbml)
import antimony
with open('../model/rnadecay.sb') as f:
sb = f.read()
print(sb)
res = antimony.loadString(sb)
if res < 0:
print(antimony.getLastError())
print(res)
print(antimony.getModuleNames())
print(antimony.getModuleNames()[-1])
sbml = antimony.getSBMLString(antimony.getModuleNames()[-1])
with open('../model/rnadecay_sbml.xml', 'w') as f:
f.write(sbml)
def getSBMLStr(self):
antimony.clearPreviousLoads()
antimony.loadString(self.getRawStr())
return antimony.getSBMLString(antimony.getModuleNames()[-1])
// Species initializations:
var species S3;
var species S4;
S3 = 0.5;
PP_S = 0.0;
S4 := 2*S3;
// Rule for S1
K1 = 0.5;
// Additional events for triggering re-integration
E1: at(time>=2): S3=5;
end
"""
model = antimony.loadString(model_txt)
sbml_file = "event_time.xml"
antimony.writeSBMLFile("event_time.xml", "event_time")
# load model in roadrunner and define the selection
r = roadrunner.RoadRunner(sbml_file)
r.selections = list(
itertools.chain(
["time"], r.model.getBoundarySpeciesIds(), r.model.getFloatingSpeciesIds(), r.model.getReactionIds()
)
)
print(r.selections)
absTol = 1e-6 * min(r.model.getCompartmentVolumes())
relTol = 1e-6
r.reset()