From f7d8816f80f57fc6b3c58b0c173fad3f74204d9b Mon Sep 17 00:00:00 2001
From: JamesW <60615431+JWallaceEvotec@users.noreply.github.com>
Date: Tue, 30 Apr 2024 11:54:58 +0100
Subject: [PATCH] Update fragment_types.py to add SanitizeMol calls

This fixes an issue seen where unitialized ring systems confuse the fragmentor
---
 mmpdblib/fragment_types.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/mmpdblib/fragment_types.py b/mmpdblib/fragment_types.py
index c136a11..2232d5c 100644
--- a/mmpdblib/fragment_types.py
+++ b/mmpdblib/fragment_types.py
@@ -258,6 +258,8 @@ def __init__(
         self.max_up_enumerations = max_up_enumerations
 
     def normalize(self, mol):
+        from rdkit import Chem
+        Chem.SanitizeMol(mol)
         # XXX Remove existing isotope labels?
         if self.salt_remover is not None:
             desalted_mol = self.salt_remover.StripMol(mol)
@@ -269,6 +271,8 @@ def normalize(self, mol):
         return None, desalted_mol
 
     def apply_filters(self, mol):
+        from rdkit import Chem
+        Chem.SanitizeMol(mol)
         num_heavies = 0
         for atom in mol.GetAtoms():
             atomic_num = atom.GetAtomicNum()