Support adding R side chains to molecule

rdeditor/molEditWidget.py

@@ -327,6 +327,8 @@ def atom_click(self, atom):
             self.increase_charge(atom)
         elif self.action == "Decrease Charge":
             self.decrease_charge(atom)
+        elif self.action == "Number Atom":
+            self.number_atom(atom)
         elif self.action == "RStoggle":
             self.toogleRS(atom)
         else:
@@ -368,9 +370,15 @@ def add_to_atom(self, atom):
         if self.chemEntityType == "bond":
             self.add_bond_to_atom(atom)
 
+    def getNewAtom(self):
+        newatom = Chem.rdchem.Atom(self.chemEntity)
+        if newatom.GetAtomicNum() == 0:
+            newatom.SetProp("dummyLabel", "R")
+        return newatom
+
     def add_atom_to_atom(self, atom):
         rwmol = Chem.rdchem.RWMol(self.mol)
-        newatom = Chem.rdchem.Atom(self.chemEntity)
+        newatom = self.getNewAtom()
         newidx = rwmol.AddAtom(newatom)
         newbond = rwmol.AddBond(atom.GetIdx(), newidx, Chem.rdchem.BondType.SINGLE)
         self.mol = rwmol
@@ -411,7 +419,7 @@ def add_canvas_atom(self, point):
         if rwmol.GetNumAtoms() == 0:
             point.x = 0.0
             point.y = 0.0
-        newatom = Chem.rdchem.Atom(self.chemEntity)
+        newatom = self.getNewAtom()
         newidx = rwmol.AddAtom(newatom)
         # This should only trigger if we have an empty canvas
         if not rwmol.GetNumConformers():
@@ -469,7 +477,7 @@ def replace_on_atom(self, atom):
 
     def replace_atom(self, atom):
         rwmol = Chem.rdchem.RWMol(self.mol)
-        newatom = Chem.rdchem.Atom(self.chemEntity)
+        newatom = self.getNewAtom()
         rwmol.ReplaceAtom(atom.GetIdx(), newatom)
         self.mol = rwmol
 
@@ -622,6 +630,20 @@ def decrease_charge(self, atom):
         atom.SetFormalCharge(atom.GetFormalCharge() - 1)
         self.molChanged.emit()
 
+    def number_atom(self, atom: Chem.Atom):
+        atomMapNumber = atom.GetIntProp("molAtomMapNumber") if atom.HasProp("molAtomMapNumber") else 0
+        (atomMapNumber, ok) = QtWidgets.QInputDialog.getInt(self, "Number Atom", "Atom number", value=atomMapNumber)
+
+        if not ok:
+            return
+
+        self.backupMol()
+        if atomMapNumber == 0:
+            atom.ClearProp("molAtomMapNumber")
+        else:
+            atom.SetProp("molAtomMapNumber", str(atomMapNumber))
+        self.molChanged.emit()
+
     # self.select_bond(bond)
     def select_bond(self, bond):
         self.logger.debug("Select_bond not implemented")  # TODO

rdeditor/molViewWidget.py

@@ -92,6 +92,15 @@ def mol(self, mol):
             if self._mol is not None:
                 self._prevmol = copy.deepcopy(self._mol)  # Chem.Mol(self._mol.ToBinary())  # Copy
 
+            # Fix pseudo atoms
+            atom: Chem.Atom
+            for atom in mol.GetAtoms():
+                if atom.GetAtomicNum() == 0:
+                    if not atom.HasProp("dummyLabel") or atom.GetProp("dummyLabel") == "*":
+                        atom.SetProp("dummyLabel", "R")
+                    else:
+                        print(atom.GetPropsAsDict())
+
             # # TODO make this failsafe
             # if self._updatepropertycache:
             #     try:

rdeditor/ptable.py

@@ -123,6 +123,7 @@
 }
 
 symboltoint = {
+    "R": 0,
     "Ac": 89,
     "Ag": 47,
     "Al": 13,

rdeditor/ptable_widget.py

@@ -47,6 +47,15 @@ def initUI(self, actionGroup):
                     grid.addWidget(button, 9, key - 54)
                 else:
                     grid.addWidget(button, 10, key - 86)
+        self.atomActions["R"] = QtGui.QAction(
+            "R",
+            self,
+            statusTip="Set atomtype to R",
+            triggered=self.atomtypePush,
+            objectName="R",
+            checkable=True,
+        )
+        actionGroup.addAction(self.atomActions["R"])
         # Ensure spacing between main table and actinides/lathanides
         grid.addWidget(QtWidgets.QLabel(""), 8, 1)
 

rdeditor/rdEditor.py

@@ -174,6 +174,7 @@ def CreateMenus(self):
         self.toolMenu.addAction(self.ezAction)
         self.toolMenu.addAction(self.increaseChargeAction)
         self.toolMenu.addAction(self.decreaseChargeAction)
+        self.toolMenu.addAction(self.numberAtom)
 
         self.toolMenu.addSeparator()
         self.toolMenu.addAction(self.cleanCoordinatesAction)
@@ -262,6 +263,7 @@ def CreateToolBars(self):
         self.mainToolBar.addAction(self.ezAction)
         self.mainToolBar.addAction(self.increaseChargeAction)
         self.mainToolBar.addAction(self.decreaseChargeAction)
+        self.mainToolBar.addAction(self.numberAtom)
         self.mainToolBar.addSeparator()
         self.mainToolBar.addAction(self.cleanCoordinatesAction)
         self.mainToolBar.addAction(self.cleanupMolAction)
@@ -282,6 +284,8 @@ def CreateToolBars(self):
         self.sideToolBar.addAction(self.templateActions["benzene"])
         self.sideToolBar.addAction(self.templateActions["cyclohexane"])
         self.sideToolBar.addSeparator()
+        self.sideToolBar.addAction(self.ptable.atomActions["R"])
+        self.sideToolBar.addSeparator()
         for action in self.atomActions:
             self.sideToolBar.addAction(action)
         self.sideToolBar.addAction(self.openPtableAction)
@@ -706,6 +710,16 @@ def CreateActions(self):
             checkable=True,
         )
         self.actionActionGroup.addAction(self.decreaseChargeAction)
+
+        self.numberAtom = QAction(
+            "A#",
+            self,
+            statusTip="Number Atom",
+            triggered=self.setAction,
+            objectName="Number Atom",
+            checkable=True,
+        )
+        self.actionActionGroup.addAction(self.numberAtom)
         self.addAction.setChecked(True)
 
         # BondTypeActions