From 3db37e7d130a2197a9dd843a0023c641c74618f3 Mon Sep 17 00:00:00 2001
From: uzman2406 <anushauzma@gmail.com>
Date: Tue, 3 Feb 2026 12:26:31 +0000
Subject: [PATCH] Backbone standardization using RDKit could modify the nature
 of the functional groups #70

---
 prolif/molecule.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/prolif/molecule.py b/prolif/molecule.py
index 258248b7..3138bffb 100644
--- a/prolif/molecule.py
+++ b/prolif/molecule.py
@@ -369,7 +369,12 @@ def _adjust_hydrogens(template: Chem.Mol, pdbqt_mol: Chem.Mol) -> Chem.Mol:
         mol = rwmol.GetMol()
         # sanitize
         mol.UpdatePropertyCache()
-        Chem.SanitizeMol(mol)
+        Chem.SanitizeMol(
+            mol,
+            sanitizeOps=Chem.SanitizeFlags.SANITIZE_ALL
+            ^ Chem.SanitizeFlags.SANITIZE_KEKULIZE
+        )
+
         return mol
 
     def __len__(self) -> int: