Misc (#485)

* report metabolites without formulas when checking biomass weight

* make MCS dialog persistent

* update tooltip when a reaction is modified

cnapy/core.py

@@ -183,7 +183,7 @@ def make_scenario_feasible(cobra_model: cobra.Model, scen_values: Dict[str, Tupl
                     model.add_cons_vars([gam_slack])
                     for i in range(len(gam_mets)):
                         met = gam_mets[i]
-                        sign = numpy.sign(bm_reaction.metabolites[met])
+                        sign = numpy.sign(bm_reaction.metabolites[met]) # !! FIXME: only correct when gam_base is larger than biomass part !! 
                         met.constraint.set_linear_coefficients({gam_slack: sign*gam_max_change*mue_fixed})
                         gam_mets_sign[i] = sign
                     qp_terms.append(gam_weight * (gam_slack**2))
@@ -322,7 +322,14 @@ def check_biomass_weight(model: cobra.Model, bm_reac_id: str) -> float:
     It only returns a correct value if the molecular weights of all biomass constituents are given.
     """
     bm_coeff = [(m, c) for m,c in model.reactions.get_by_id(bm_reac_id).metabolites.items()]
-    bm_weight = sum(m.formula_weight/1000*-c for m,c in bm_coeff)
+    bm_weight = 0.0
+    for m,c in bm_coeff:
+        w = m.formula_weight
+        if w is None or w == 0:
+            print("Molecular weight of biomass component", m.id, "cannot be calculated from its formula", m.formula)
+        else:
+            bm_weight += w/1000*-c
+#    bm_weight = sum(m.formula_weight/1000*-c for m,c in bm_coeff)
     print("Flux of 1 through the biomass reaction produces", bm_weight, "g biomass.")
     return bm_weight
 
@@ -356,6 +363,7 @@ def replace_ids(dict_list: DictList, annotation_key: str, unambiguous_only: bool
         for new_id in candidates:
             try:
                 entry.id = new_id
+                entry.annotation['original ID'] = old_id
                 break
             except ValueError: # new_id already in use
                 pass

cnapy/gui_elements/main_window.py

@@ -1837,8 +1837,8 @@ def efmtool(self):
         self.efmtool_dialog.exec_()
 
     def mcs(self):
-        self.mcs_dialog = MCSDialog(
-            self.appdata, self.centralWidget())
+        if self.mcs_dialog is None:
+            self.mcs_dialog = MCSDialog(self.appdata, self.centralWidget())
         self.mcs_dialog.show()
 
     def set_onoff(self):

cnapy/gui_elements/reactions_list.py

@@ -88,6 +88,15 @@ def __lt__(self, other):
 #            return super().__lt__(other) # infinite recursion with PySide2, __lt__ is a virtual function of QTreeWidgetItem
             return self.text(column) < other.text(column)
 
+    def update_tooltips(self):
+        text = "Id: " + self.reaction.id + "\nName: " + self.reaction.name \
+            + "\nEquation: " + self.reaction.build_reaction_string()\
+            + "\nLowerbound: " + str(self.reaction.lower_bound) \
+            + "\nUpper bound: " + str(self.reaction.upper_bound) \
+            + "\nObjective coefficient: " + str(self.reaction.objective_coefficient)
+        self.setToolTip(ReactionListColumn.Id, text)
+        self.setToolTip(ReactionListColumn.Name, text)
+
 class ReactionList(QWidget):
     """A list of reaction"""
 
@@ -172,13 +181,7 @@ def add_reaction(self, reaction: cobra.Reaction) -> ReactionListItem:
         item.setFlags(item.flags() | Qt.ItemIsEditable)
         item.setText(ReactionListColumn.Id, reaction.id)
         item.setText(ReactionListColumn.Name, reaction.name)
-        text = "Id: " + reaction.id + "\nName: " + reaction.name \
-            + "\nEquation: " + reaction.build_reaction_string()\
-            + "\nLowerbound: " + str(reaction.lower_bound) \
-            + "\nUpper bound: " + str(reaction.upper_bound) \
-            + "\nObjective coefficient: " + str(reaction.objective_coefficient)
-        item.setToolTip(ReactionListColumn.Id, text)
-        item.setToolTip(ReactionListColumn.Name, text)
+        item.update_tooltips()
         self.update_item(item)
         return item
 
@@ -316,6 +319,7 @@ def handle_changed_reaction(self, reaction: cobra.Reaction):
                 old_id = item.text(ReactionListColumn.Id)
                 item.setText(ReactionListColumn.Id, reaction.id)
                 item.setText(ReactionListColumn.Name, reaction.name)
+                item.update_tooltips()
                 break
 
         self.last_selected = self.reaction_mask.id.text()