fake Se as S for RDKit Gasteiger charges

forlilab · Jul 24, 2023 · 88d640f · 88d640f
1 parent b8b4e05
commit 88d640f
Showing 1 changed file with 6 additions and 2 deletions.
diff --git a/meeko/molsetup.py b/meeko/molsetup.py
@@ -648,8 +648,12 @@ def init_atom(self, assign_charges, coords):
         """ initialize the atom table information """
         # extract/generate charges
         if assign_charges:
-            rdPartialCharges.ComputeGasteigerCharges(self.mol)
-            charges = [a.GetDoubleProp('_GasteigerCharge') for a in self.mol.GetAtoms()]
+            copy_mol = Chem.Mol(self.mol)
+            for atom in copy_mol.GetAtoms():
+                if atom.GetAtomicNum() == 34:
+                    atom.SetAtomicNum(16)
+            rdPartialCharges.ComputeGasteigerCharges(copy_mol)
+            charges = [a.GetDoubleProp('_GasteigerCharge') for a in copy_mol.GetAtoms()]
         else:
             charges = [0.0] * self.mol.GetNumAtoms()
         # perceive chirality