Merge pull request #35 from xchem/ryan_broken_cifs

Ryan broken cifs
xchem · Dec 4, 2024 · b47bb78 · b47bb78
2 parents c263cc7 + 0a979c1
commit b47bb78
Showing 1 changed file with 23 additions and 4 deletions.
diff --git a/src/xchemalign/utils.py b/src/xchemalign/utils.py
@@ -431,10 +431,29 @@ def gen_mols_from_cif(cif_file):
         if not bond_type:
             bond_type = block.find_loop('_chem_comp_bond.value_order')
 
-        for a1, a2, bt in zip(atom1, atom2, bond_type):
-            mol.AddBond(
-                atoms[strip_quotes(a1)].GetIntProp('idx'), atoms[strip_quotes(a2)].GetIntProp('idx'), BOND_TYPES[bt]
-            )
+        try:
+            for a1, a2, bt in zip(atom1, atom2, bond_type):
+                mol.AddBond(
+                    atoms[strip_quotes(a1)].GetIntProp('idx'), atoms[strip_quotes(a2)].GetIntProp('idx'), BOND_TYPES[bt]
+                )
+        except:
+            print('atoms')
+            print(atoms)
+            print('comp ids')
+            print(comp_ids)
+            print('atom symbols')
+            print(atom_symbols)
+            print('atom ids')
+            print(atom_ids)
+            print('x')
+            print(x)
+            print('y')
+            print(y)
+            print('z')
+            print(z)
+            print('charges')
+            print(charges)
+            raise Exception
 
         Chem.SanitizeMol(mol)
         mol.AddConformer(conf)