Merge pull request #351 from DiODeProject/missing-rate

Fixes #321 and fixes #322

Author: jarmarshall

mumot/models.py

@@ -1706,11 +1706,20 @@ def _get_solutions(self):
             self._solutions = solve(iter(self._equations.values()), self._reactants, force=False, positive=False, set=False)
         return self._solutions
 
+    def _get_rates_from_stoichiometry(self):
+        rates = set()
+        for reaction in self._stoichiometry.values():
+            if reaction['rate']: 
+                for symb in reaction['rate'].atoms():
+                    if isinstance(symb, Symbol):
+                        rates.add( symb )
+        return rates
+
     def _create_free_param_dictionary_for_controller(self, inputParams, initWidgets=None, showSystemSize=False, showPlotLimits=False):
         initWidgetsSympy = {parse_latex(paramName): paramValue for paramName, paramValue in initWidgets.items()} if initWidgets is not None else {}
 
         paramValuesDict = {}
-        for freeParam in self._rates.union(self._constantReactants):
+        for freeParam in self._get_rates_from_stoichiometry().union(self._constantReactants):
             paramValuesDict[str(freeParam)] = utils._parse_input_keyword_for_numeric_widgets(
                 inputValue=utils._get_item_from_params_list(inputParams, str(freeParam)),
                 defaultValueRangeStep=[defaults.MuMoTdefault._initialRateValue, defaults.MuMoTdefault._rateLimits[0], defaults.MuMoTdefault._rateLimits[1], defaults.MuMoTdefault._rateStep],
@@ -1837,7 +1846,7 @@ def _getFuncs(self):
                 argList.append(reactant)
             for reactant in self._constantReactants:
                 argList.append(reactant)
-            for rate in self._rates:
+            for rate in self._get_rates_from_stoichiometry():
                 argList.append(rate)
             if self._systemSize is not None:
                 argList.append(self._systemSize)

mumot/views.py

@@ -188,7 +188,7 @@ def _get_params(self, refModel=None):
         for name, value in self._fixedParams.items():
             # if name == 'systemSize' or name == 'plotLimits':
             #     continue
-            if name not in self._mumotModel._rates and name not in self._mumotModel._constantReactants:
+            if name not in self._mumotModel._get_rates_from_stoichiometry() and name not in self._mumotModel._constantReactants:
                 continue
             name = repr(name)
             if name in model._ratesLaTeX: