From b1c5b379267f2d9313ddccd8b035406c83056773 Mon Sep 17 00:00:00 2001
From: Esben Jannik Bjerrum <esbenjannik@rocketmai.com>
Date: Mon, 29 Jul 2024 20:42:15 +0200
Subject: [PATCH] Fixed a bug where molstereo was shown as active, even if
 molecule editied to be nonisomeric. Updating of Stereo now runs everytime mol
 event is triggered.

---
 rdeditor/molEditWidget.py | 14 +-------------
 rdeditor/molViewWidget.py | 13 +++++++++++++
 rdeditor/rdEditor.py      |  2 --
 3 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/rdeditor/molEditWidget.py b/rdeditor/molEditWidget.py
index 2618896..67b1bdf 100644
--- a/rdeditor/molEditWidget.py
+++ b/rdeditor/molEditWidget.py
@@ -504,11 +504,8 @@ def toogleRS(self, atom):
         self.logger.debug("New stereotype set to %s" % atom.GetChiralTag())
         # rdDepictor.Compute2DCoords(self._mol)
         # self._mol.ClearComputedProps()
-        self._mol.UpdatePropertyCache()
+        self._mol.UpdatePropertyCache(strict=False)
         rdDepictor.Compute2DCoords(self._mol)
-        if atom.HasProp("_CIPCode"):
-            atom.ClearProp("_CIPCode")
-        Chem.rdCIPLabeler.AssignCIPLabels(self._mol)
         self.molChanged.emit()
 
     def assert_stereo_atoms(self, bond):
@@ -546,12 +543,6 @@ def assign_stereo_atoms(self, mol: Chem.Mol):
                         stereoatoms[1], stereoatoms[0]
                     )  # Not sure why this can get the wrong way. Seem to now work correctly for Absisic Acid
 
-    def updateMolStereo(self, mol):
-        self.logger.debug("Updating stereo info")
-        Chem.rdmolops.SetDoubleBondNeighborDirections(mol)
-        mol.UpdatePropertyCache()
-        Chem.rdCIPLabeler.AssignCIPLabels(mol)
-
     def toogleEZ(self, bond: Chem.Bond):
         self.backupMol()
 
@@ -579,9 +570,6 @@ def toogleEZ(self, bond: Chem.Bond):
         self.logger.debug(f"StereoAtoms are {list(bond.GetStereoAtoms())}")
         self.logger.debug(f"Bond properties are {bond.GetPropsAsDict(includePrivate=True, includeComputed=True)}")
 
-        bond.ClearProp("_CIPCode")
-        self.updateMolStereo(self._mol)
-
         self.logger.debug(f"StereoAtoms are {list(bond.GetStereoAtoms())}")
         self.logger.debug(f"Bond properties are {bond.GetPropsAsDict(includePrivate=True, includeComputed=True)}")
 
diff --git a/rdeditor/molViewWidget.py b/rdeditor/molViewWidget.py
index 74fe058..63be035 100644
--- a/rdeditor/molViewWidget.py
+++ b/rdeditor/molViewWidget.py
@@ -235,10 +235,23 @@ def canon_coords_and_draw(self):
         self._drawmol = copy.deepcopy(self._mol)  # Chem.Mol(self._mol.ToBinary())
         self.draw()
 
+    def updateStereo(self):
+        self.logger.debug("Updating stereo info")
+        for atom in self.mol.GetAtoms():
+            if atom.HasProp("_CIPCode"):
+                atom.ClearProp("_CIPCode")
+        for bond in self.mol.GetBonds():
+            if bond.HasProp("_CIPCode"):
+                bond.ClearProp("_CIPCode")
+        Chem.rdmolops.SetDoubleBondNeighborDirections(self.mol)
+        self.mol.UpdatePropertyCache(strict=False)
+        Chem.rdCIPLabeler.AssignCIPLabels(self.mol)
+
     sanitizeSignal = QtCore.Signal(str, name="sanitizeSignal")
 
     @QtCore.Slot()
     def sanitizeDrawMol(self, kekulize=False, drawkekulize=False):
+        self.updateStereo()
         self.computeNewCoords()
         # self._drawmol_test = Chem.Mol(self._mol.ToBinary())  # Is this necessary?
         # self._drawmol = Chem.Mol(self._mol.ToBinary())  # Is this necessary?
diff --git a/rdeditor/rdEditor.py b/rdeditor/rdEditor.py
index 5d1b7c0..088d328 100644
--- a/rdeditor/rdEditor.py
+++ b/rdeditor/rdEditor.py
@@ -366,8 +366,6 @@ def paste(self):
             self.editor.assign_stereo_atoms(mol)
             Chem.rdmolops.SetBondStereoFromDirections(mol)
 
-            self.editor.updateMolStereo(mol)
-
             self.editor.mol = mol
         else:
             self.editor.logger.warning(f"Failed to parse the content of the clipboard as a SMILES: {repr(text)}")