def determine_type(obj, parameters, comp_name):
tree = ET.Element("apply")
if isinstance(obj, rxd.rxdmath._Product):
ET.SubElement(tree, "times")
recursive_search(obj._a, tree, parameters, comp_name) # arithmeticed
recursive_search(obj._b, tree, parameters, comp_name) # arithmeticed
elif isinstance(obj, rxd.rxdmath._Quotient):
ET.SubElement(tree, "divide")
recursive_search(obj._a, tree, parameters, comp_name) # arithmeticed
recursive_search(obj._b, tree, parameters, comp_name) # arithmeticed
elif isinstance(obj, rxd.rxdmath._Arithmeticed):
recursive_search(obj, tree, parameters, comp_name)
elif isinstance(obj, rxd.rxdmath._Function):
if function_names[obj._fname] == "exception":
# Do Something bro
if obj._fname == "-":
ET.SubElement(tree, "times")
recursive_search(obj._obj, tree, parameters, comp_name)
ET.SubElement(tree, "cn").text = str(-1)
elif function_names[obj._fname] == "ERROR":
RxDException(obj._fname + " is not supported in this context")
else:
ET.SubElement(tree, function_names[obj._fname])
recursive_search(obj._obj, tree, parameters, comp_name)
elif isinstance(obj, rxd.rxdmath._Function2):
if function_names[obj._fname] == "exception":
if obj._fname == "atan2":
temp = ET.SubElement(tree, function_names["atan"])
applytemp = ET.SubElement(temp, "apply")
temp2 = ET.SubElement(temp, "divide")
recursive_search(obj._obj1, applytemp, parameters, comp_name)
recursive_search(obj._obj2, applytemp, parameters, comp_name)
elif function_names[obj._fname] == "ERROR":
RxDException(obj._fname + " is not supported in this context")
else:
ET.SubElement(tree, function_names[obj._fname])
recursive_search(obj._obj1, tree, parameters, comp_name)
recursive_search(obj._obj2, tree, parameters, comp_name)
return tree
def sbml(segment, filename=None, model_name=None, pretty=True):
rxd.initializer._do_init()
section = segment.sec
if model_name is not None:
output = middle_man(model_name)
else:
output = middle_man(section.name())
regions = section.psection()["regions"]
species = section.psection()["species"]
for i in regions:
node = None
for j in species:
if i in j.regions or j.regions == [None]:
node = j.nodes(segment)[0]
output.add_compartment(i.name, size=node.volume)
for i in species:
if isinstance(i, rxd.Parameter):
node = i.nodes(segment)[0]
tempInitial = i.initial
if i.initial is None:
tempInitial = 0.0
elif not isinstance(tempInitial, float) and not isinstance(
tempInitial, int
):
tempInitial = i.initial(node)
output.add_parameter(i.name, i.initial)
continue
for j in i.regions:
node = i.nodes(segment)[0]
tempInitial = i.initial
if i.initial is None:
tempInitial = 0.0
elif not isinstance(tempInitial, float) and not isinstance(
tempInitial, int
):
tempInitial = i.initial(node)
output.add_species(
name=i.name, compartment=j.name, initial_amount=tempInitial
)
for i in rxd.rxd._all_reactions:
if isinstance(i, rxd.MultiCompartmentReaction):
RxDException("Cannot export MultiCompartmentReactions")
# MIGHT BE A PROBLEM WHEN MULTI COMPARTMENT REACTIONS
reactions = [
r()
for r in rxd.rxd._all_reactions
if (
any(
[
((reg in r()._active_regions) or (reg is None))
for reg in r()._regions
]
)
)
and isinstance(r(), rxd.Reaction)
]
rates = [
r()
for r in rxd.rxd._all_reactions
if (
any(
[
((reg in r()._active_regions) or (reg is None))
for reg in r()._regions
]
)
)
and isinstance(r(), rxd.Rate)
]
num = 0
for react in reactions:
lhs = react._scheme._lhs._items
rhs = react._scheme._rhs._items
reacting_regions = []
if react._regions == [None]:
reacting_regions = regions
else:
reacting_regions = react._regions
for reg in reacting_regions:
reactants = [
[key.name + "_" + reg.name, value]
for key, value in zip(list(lhs.keys()), list(lhs.values()))
]
products = [
[key.name + "_" + reg.name, value]
for key, value in zip(list(rhs.keys()), list(rhs.values()))
]
kineticLaw = ET.Element("kineticLaw")
math = ET.SubElement(
kineticLaw, "math", xmlns="http://www.w3.org/1998/Math/MathML"
)
# adds the region to multiply it by
region_multiple = ET.SubElement(math, "apply")
ET.SubElement(region_multiple, "times")
ET.SubElement(region_multiple, "ci").text = reg.name
parameters_in_react = []
recursive_search(
react._rate_arithmeticed, region_multiple, parameters_in_react, reg.name
)
listOfParameters = ET.Element("listOfParameters")
for i in parameters_in_react:
if i[0] in output.parameters:
continue
ET.SubElement(
listOfParameters, "parameter", id=i[0], name=i[1], value=str(i[2])
)
if list(listOfParameters):
kineticLaw.append(listOfParameters)
output.add_reaction(
"Reaction_" + str(num),
reversible=(react._dir == "<>"),
products=products,
reactants=reactants,
kinetic_law=kineticLaw,
modifiers=[],
)
num += 1
num = 0
for rate in rates:
list_regions = []
if rate._regions == [None]:
list_regions = regions
else:
list_regions = rate._regions
for r in list_regions:
# math = ET.Element("apply")
# ET.SubElement(math,"plus")
# ET.SubElement(math,"cn").text = "0"
# parameters = []
# math_law = ex.recursive_search(rate._original_rate,math,parameters,r.name)
# output.add_rate(rate._species().name + "_" + r.name,math)
products = [[rate._species().name + "_" + r.name, 1]]
reactants = []
modifiers = [
s().name + "_" + r.name
for s in rate._involved_species
if isinstance(s(), rxd.Parameter) == False
and rate._species().name != s().name
]
kineticLaw = ET.Element("kineticLaw")
math = ET.SubElement(
kineticLaw, "math", xmlns="http://www.w3.org/1998/Math/MathML"
)
region_multiple = ET.SubElement(math, "apply")
ET.SubElement(region_multiple, "times")
ET.SubElement(region_multiple, "ci").text = reg.name
parameters = []
recursive_search(rate._original_rate, region_multiple, parameters, r.name)
output.add_reaction(
"Rate_" + str(num),
reversible=True,
products=products,
reactants=reactants,
kinetic_law=kineticLaw,
modifiers=modifiers,
)
num += 1
output.add_unit_def("substance")
output.add_unit("substance", "mole", 1, -3)
output.add_unit_def("time")
output.add_unit("time", "second", 1, -3)
# output.add_unit_def("volume")
# output.add_unit("volume","litre",1,1)
final = output.dump(pretty_print=pretty)
if filename:
with open(filename, "w") as f:
f.write(final)
return final