Set coordination bond order to single

oddt/toolkits/extras/rdkit.py

@@ -1,6 +1,7 @@
 from __future__ import absolute_import, print_function
 from math import isnan, isinf
 
+import rdkit
 from rdkit import Chem
 from rdkit.Chem import AllChem
 
@@ -55,6 +56,17 @@ def MolFromPDBBlock(molBlock,
                             bond.SetBondType(Chem.BondType.DOUBLE)
                             break
 
+    # Set metal coordination (zero order) bond orders to single
+    if rdkit.__version__ >= '2018.03':
+        for bond in mol.GetBonds():
+            if bond.GetBondType() == Chem.BondType.ZERO:
+                a1 = bond.GetBeginAtom()
+                a2 = bond.GetEndAtom()
+                if a1.GetAtomicNum() in _metals:
+                    bond.SetBondType(Chem.BondType.SINGLE)
+                elif a2.GetAtomicNum() in _metals:
+                    bond.SetBondType(Chem.BondType.SINGLE)
+
     if sanitize:
         result = Chem.SanitizeMol(mol)
         if result != 0: