def addAntimony(self, antimonyStr, filename=None):
""" Adds SBML file as Antimony into COMBINE archive.
:param antimonyStr: antimony string
"""
warnings.warn('Use inline_omex instead.', DeprecationWarning)
sbmlStr = te.antimonyToSBML(antimonyStr)
self.addSBML(sbmlStr, filename)
def get_sbml(self):
return te.antimonyToSBML(f"""
model {self.model_name()}
r1: S1 -> S2 ; k1*S1*Stim;
r2: S2 -> S1 ; k2*S2;
Stim = 0;
S1 = 10;
S2 = 0;
k1 = 0.1
k2 = 0.1
end
""")
def _setReferencedSBML(self, phrasedmlStr):
""" Set phrasedml referenced SBML for given phrasedml String. """
modelNames = []
for aStr in self.antimonyList:
r = te.loada(aStr)
name = r.getModel().getModelName()
modelNames.append(name)
sources = self._modelsFromPhrasedml(phrasedmlStr)
for source, name in sources.iteritems():
# not a antimony model
if name not in modelNames:
continue
# set as referenced model
aStr = self.antimonyList[modelNames.index(name)]
phrasedml.setReferencedSBML(source, te.antimonyToSBML(aStr))
def _setReferencedSBML(self, phrasedmlStr):
""" Set phrasedml referenced SBML for given phrasedml String. """
modelNames = []
for aStr in self.antimonyList:
r = te.loada(aStr)
name = r.getModel().getModelName()
modelNames.append(name)
sources = self._modelsFromPhrasedml(phrasedmlStr)
for source, name in sources.iteritems():
# not a antimony model
if name not in modelNames:
continue
# set as referenced model
aStr = self.antimonyList[modelNames.index(name)]
phrasedml.setReferencedSBML(source, te.antimonyToSBML(aStr))
def addPhrasedml(self, phrasedmlStr, antimonyStr, arcname=None):
""" Adds phrasedml via conversion to SEDML. """
# FIXME: This does not work for multiple referenced models !.
reModel = r"""(\w*) = model ('|")(.*)('|")"""
phrasedmllines = phrasedmlStr.splitlines()
for k, line in enumerate(phrasedmllines):
reSearchModel = re.split(reModel, line)
if len(reSearchModel) > 1:
modelsource = str(reSearchModel[3])
modelname = os.path.basename(modelsource)
modelname = str(modelname).replace(".xml", '')
phrasedml.setReferencedSBML(modelsource, te.antimonyToSBML(antimonyStr))
sedmlstr = phrasedml.convertString(phrasedmlStr)
if sedmlstr is None:
raise Exception(phrasedml.getLastError())
phrasedml.clearReferencedSBML()
self.addSEDML(sedmlstr, arcname)
def addPhrasedml(self, phrasedmlStr, antimonyStr, arcname=None):
""" Adds SEDML file as phraSEDML string into COMBINE archive.
:param phrasedmlStr: phraSEDML string
:param antimonyStr: antimony string to be referenced
:param arcname: (optional) desired name of SEDML file
"""
warnings.warn('Use inline_omex instead.', DeprecationWarning)
# FIXME: This does not work for multiple referenced models !.
reModel = r"""(\w*) = model ('|")(.*)('|")"""
phrasedmllines = phrasedmlStr.splitlines()
for k, line in enumerate(phrasedmllines):
reSearchModel = re.split(reModel, line)
if len(reSearchModel) > 1:
modelsource = str(reSearchModel[3])
modelname = os.path.basename(modelsource)
modelname = str(modelname).replace(".xml", '')
phrasedml.setReferencedSBML(modelsource, te.antimonyToSBML(antimonyStr))
sedmlstr = phrasedml.convertString(phrasedmlStr)
if sedmlstr is None:
raise Exception(phrasedml.getLastError())
phrasedml.clearReferencedSBML()
self.addSEDML(sedmlstr, arcname)
def addPhrasedml(self, phrasedmlStr, antimonyStr, arcname=None):
""" Adds SEDML file as phraSEDML string into COMBINE archive.
:param phrasedmlStr: phraSEDML string
:param antimonyStr: antimony string to be referenced
:param arcname: (optional) desired name of SEDML file
"""
# FIXME: This does not work for multiple referenced models !.
reModel = r"""(\w*) = model ('|")(.*)('|")"""
phrasedmllines = phrasedmlStr.splitlines()
for k, line in enumerate(phrasedmllines):
reSearchModel = re.split(reModel, line)
if len(reSearchModel) > 1:
modelsource = str(reSearchModel[3])
modelname = os.path.basename(modelsource)
modelname = str(modelname).replace(".xml", '')
phrasedml.setReferencedSBML(modelsource,
te.antimonyToSBML(antimonyStr))
sedmlstr = phrasedml.convertString(phrasedmlStr)
if sedmlstr is None:
raise Exception(phrasedml.getLastError())
phrasedml.clearReferencedSBML()
self.addSEDML(sedmlstr, arcname)
# In[1]:
#!!! DO NOT CHANGE !!! THIS FILE WAS CREATED AUTOMATICALLY FROM NOTEBOOKS !!! CHANGES WILL BE OVERWRITTEN !!! CHANGE CORRESPONDING NOTEBOOK FILE !!!
from __future__ import print_function
import tellurium as te
# antimony model
ant_model = """
S1 -> S2; k1*S1;
S2 -> S3; k2*S2;
k1= 0.1; k2 = 0.2;
S1 = 10; S2 = 0; S3 = 0;
"""
# convert to SBML
sbml_model = te.antimonyToSBML(ant_model)
# convert to CellML
cellml_model = te.antimonyToCellML(ant_model)
# or from the sbml
cellml_model = te.sbmlToCellML(sbml_model)
# In[2]:
def addAntimony(self, antimonyStr):
""" Add antimony to archive. """
sbmlStr = te.antimonyToSBML(antimonyStr)
self.addSBML(sbmlStr)
def test_antimonyToSBML_str(self):
sbml = te.antimonyToSBML(self.ant_str)
self.assertIsNotNone(sbml)
def test_antimonyToSBML_file(self):
sbml = te.antimonyToSBML(self.ant_file)
self.assertIsNotNone(sbml)
def setUp(self) -> None:
self.sbml = te.antimonyToSBML(TEST_MODEL1)
self.yaml_file = os.path.join(os.path.dirname(__file__), 'config.yaml')
# sbml = te.antimonyToSBML(antimony_string())
# print(sbml)
if __name__ == '__main__':
working_directory = os.path.dirname(__file__)
model_combinations = create_combinations(new_reaction1(), new_reaction2())
reactions_map = {0: new_reaction1(), 1: new_reaction2()}
fnames = []
for model_id, topology in model_combinations:
reactions_string = ''
for reaction in topology:
reactions_string += reactions_map[reaction] + '\n'
model_string = antimony_string(reactions_string)
sbml = te.antimonyToSBML(model_string)
fname = os.path.join(working_directory,
'topology{}.sbml'.format(model_id))
with open(fname, 'w') as f:
f.write(sbml)
print('file written to "{}"'.format(fname))
fnames.append(fname)
for f in fnames:
assert os.path.isfile(f)
# Here's a simple example with a fake model I use for testing'
# Back to the main [Index](../index.ipynb)
# #### Antimony, SBML, CellML
# In[1]:
#!!! DO NOT CHANGE !!! THIS FILE WAS CREATED AUTOMATICALLY FROM NOTEBOOKS !!! CHANGES WILL BE OVERWRITTEN !!! CHANGE CORRESPONDING NOTEBOOK FILE !!!
from __future__ import print_function
import tellurium as te
# antimony model
ant_model = """
S1 -> S2; k1*S1;
S2 -> S3; k2*S2;
k1= 0.1; k2 = 0.2;
S1 = 10; S2 = 0; S3 = 0;
"""
# convert to SBML
sbml_model = te.antimonyToSBML(ant_model)
# convert to CellML
cellml_model = te.antimonyToCellML(ant_model)
# or from the sbml
cellml_model = te.sbmlToCellML(sbml_model)
# In[2]:
def test_antimonyToSBML_file(self):
sbml = te.antimonyToSBML(self.ant_file)
self.assertIsNotNone(sbml)
model myModel
S1 -> S2; k1*S1
S1 = 10; S2 = 0
k1 = 1
end
'''
phrasedml_str = '''
model1 = model "myModel"
sim1 = simulate uniform(0, 5, 100)
task1 = run sim1 on model1
plot "Figure 1" time vs S1, S2
'''
# create the sedml xml string from the phrasedml
sbml_str = te.antimonyToSBML(antimony_str)
phrasedml.setReferencedSBML("myModel", sbml_str)
sedml_str = phrasedml.convertString(phrasedml_str)
if sedml_str == None:
print(phrasedml.getLastPhrasedError())
print(sedml_str)
# In[2]:
# Create the temporary files and execute the code
import tempfile
f_sbml = tempfile.NamedTemporaryFile(prefix="myModel", suffix=".xml")
f_sbml.write(sbml_str)
f_sbml.flush()
def test_antimonyToSBML_str(self):
sbml = te.antimonyToSBML(self.ant_str)
self.assertIsNotNone(sbml)
"""
Create SBML bipartite graph with tellurium/antimony.
Read the antimony tutorial for details.
reversibility:
reversible reaction: '->'
irreversible reaction: '=>'
One class is R (reaction) the other class S (species).
"""
import tellurium as te
ant = """
model graph()
// bipartite reaction-species graph (R-S graph)
// all ingoing edges on the left, outgoing on the right
R1: A + B => C;
R2: C => D;
R3: D => E;
end
"""
sbml = te.antimonyToSBML(ant)
with open("bipartite-graph.xml", "w") as f:
f.write(sbml)
def addAntimony(self, antimonyStr, filename=None):
""" Adds SBML file as Antimony into COMBINE archive.
:param antimonyStr: antimony string
"""
sbmlStr = te.antimonyToSBML(antimonyStr)
self.addSBML(sbmlStr, filename)
model1 = model "test1"
model2 = model "test2"
model3 = model model1 with S1=S2+20
sim1 = simulate uniform(0, 6, 100)
task1 = run sim1 on model1
task2 = run sim1 on model2
plot "Timecourse test1" task1.time vs task1.S1, task1.S2
plot "Timecourse test2" task2.time vs task2.X1, task2.X2
"""
# phrasedml.setReferencedSBML("test1")
exp = te.experiment(phrasedmlList=[phrasedmlStr], antimonyList=[antTest1Str])
print(exp)
# set first model
phrasedml.setReferencedSBML("test1", te.antimonyToSBML(antTest1Str))
phrasedml.setReferencedSBML("test2", te.antimonyToSBML(antTest2Str))
sedmlstr = phrasedml.convertString(phrasedmlStr)
if sedmlstr is None:
raise Exception(phrasedml.getLastError())
print(sedmlstr)
# In[3]:
# In[3]:
model myModel
S1 -> S2; k1*S1
S1 = 10; S2 = 0
k1 = 1
end
'''
phrasedml_str = '''
model1 = model "myModel"
sim1 = simulate uniform(0, 5, 100)
task1 = run sim1 on model1
plot "Figure 1" time vs S1, S2
'''
# create the sedml xml string from the phrasedml
sbml_str = te.antimonyToSBML(antimony_str)
phrasedml.setReferencedSBML("myModel", sbml_str)
sedml_str = phrasedml.convertString(phrasedml_str)
if sedml_str == None:
print(phrasedml.getLastPhrasedError())
print(sedml_str)
# In[2]:
# Create the temporary files and execute the code
import tempfile
f_sbml = tempfile.NamedTemporaryFile(prefix="myModel", suffix=".xml")
f_sbml.write(sbml_str)
f_sbml.flush()
print(f_sbml.name)
def setUp(self) -> None:
self.sbml = te.antimonyToSBML(TEST_MODEL2)
self.config = Config(self.sbml)
