def info_reactions(self) -> List[Dict[str, Any]]:
"""Information dictionaries for ListOfReactions.
:return: list of info dictionaries for Reactions
"""
data = []
for r in self.model.getListOfReactions(): # type: libsbml.Reaction
info = self.info_sbase(r)
if r.reversible:
reversible = '<td class ="success">⇆</td>'
else:
reversible = '<td class ="danger">➞</td>'
info["reversible"] = reversible
info["equation"] = formating.equationStringFromReaction(r)
modifiers = [mod.getSpecies() for mod in r.getListOfModifiers()]
if modifiers:
modifiers_html = "<br />".join(modifiers)
else:
modifiers_html = empty_html()
info["modifiers"] = modifiers_html
klaw = r.getKineticLaw()
info["formula"] = math(klaw, self.math_render)
info["derived_units"] = derived_units(klaw)
# fbc
info["fbc_bounds"] = formating.boundsStringFromReaction(
r, self.model)
info[
"fbc_gpa"] = formating.geneProductAssociationStringFromReaction(
r)
data.append(info)
return data
def info_parameters(
self, assignment_map: Dict[str, str]) -> List[Dict[str, Any]]:
"""Information dictionaries for Parameters.
:param assignment_map: map of assignments for symbols
:return: list of info dictionaries for Reactions
"""
items = []
for item in self.model.getListOfParameters(
): # type: libsbml.Parameter
info = self.info_sbase(item)
info["units"] = item.units
if item.isSetValue():
value = item.value
else:
value_formula = assignment_map.get(item.id, None)
if value_formula is None:
warnings.warn(
f"No value for parameter via Value, InitialAssignment or "
f"AssignmentRule: {item.id}")
value = math(value_formula, self.math_render)
info["value"] = value
info["derived_units"] = derived_units(item)
info["constant"] = boolean(item.constant)
items.append(info)
return items
def info_compartments(
self, assignment_map: Dict[str, str]) -> List[Dict[str, Any]]:
"""Information dictionaries for Compartments.
:param assignment_map: map of assignments for symbols
:return: list of info dictionaries for Compartments
"""
data = []
for c in self.model.getListOfCompartments(
): # type: libsbml.Compartment
info = self.info_sbase(c)
info["units"] = c.units
if c.isSetSpatialDimensions():
spatial_dimensions = c.spatial_dimensions
else:
spatial_dimensions = empty_html()
info["spatial_dimensions"] = spatial_dimensions
info["constant"] = boolean(c.constant)
info["derived_units"] = derived_units(c)
if c.isSetSize():
size = c.size
else:
size = math(assignment_map.get(c.id, ""), self.math_render)
info["size"] = size
data.append(info)
return data
def info_species(self) -> List[Dict[str, Any]]:
"""Information dictionaries for Species.
:return: list of info dictionaries for Species
"""
data = []
for s in self.model.getListOfSpecies(): # type: libsbml.Species
info = self.info_sbase(s)
info["compartment"] = s.compartment
info["has_only_substance_units"] = boolean(
s.has_only_substance_units)
info["boundary_condition"] = boolean(s.boundary_condition)
info["constant"] = boolean(s.constant)
if s.isSetInitialAmount():
initial_amount = s.initial_amount
else:
initial_amount = empty_html()
info["initial_amount"] = initial_amount
if s.isSetInitialConcentration():
initial_concentration = s.initial_concentration
else:
initial_concentration = empty_html()
info["initial_concentration"] = initial_concentration
info["units"] = s.getUnits()
info["substance_units"] = s.substance_units
info["derived_units"] = derived_units(s)
if s.isSetConversionFactor():
cf_sid = s.getConversionFactor()
cf_p = self.model.getParameter(
cf_sid) # type: libsbml.Parameter
cf_value = cf_p.getValue()
cf_units = cf_p.getUnits()
info["conversion_factor"] = f"{cf_sid}={cf_value} [{cf_units}]"
else:
info["conversion_factor"] = empty_html()
# fbc
sfbc = s.getPlugin("fbc")
if sfbc:
if sfbc.isSetChemicalFormula():
info["fbc_formula"] = sfbc.getChemicalFormula()
if sfbc.isSetCharge():
c = sfbc.getCharge()
if c != 0:
info["fbc_charge"] = f"({sfbc.getCharge()})"
if ("fbc_formula" in info) or ("fbc_charge" in info):
info["fbc"] = f"""
<br />
<code>
{info.get('fbc_formula', '')}{info.get('fbc_charge', '')}
</code>
"""
data.append(info)
return data
def info_rules(self) -> List[Dict[str, Any]]:
"""Information dictionaries for Rules.
:return: list of info dictionaries for Rules
"""
data = []
for rule in self.model.getListOfRules():
info = self.info_sbase(rule)
info["variable"] = formating.ruleVariableToString(rule)
info["assignment"] = math(rule, self.math_render)
info["derived_units"] = derived_units(rule)
data.append(info)
return data
def info_initial_assignments(self) -> List[Dict[str, Any]]:
"""Information dictionaries for InitialAssignments.
:return: list of info dictionaries for InitialAssignments
"""
data = []
for (assignment) in (self.model.getListOfInitialAssignments()
): # type: libsbml.InitialAssignment
info = self.info_sbase(assignment)
info["symbol"] = assignment.symbol
info["assignment"] = math(assignment, self.math_render)
info["derived_units"] = derived_units(assignment)
data.append(info)
return data