minor tweaks to allow PDBQT writing for receptor with Co2+

meeko/chemtempgen.py

@@ -395,28 +395,29 @@ def from_cif(cls, source_cif: str, resname: str):
                            'value_order', # bond order
                            ]
         bond_table = block.find(bond_category, bond_attributes)
-        bond_cols = {attr: bond_table.find_column(f"{bond_category}{attr}") for attr in bond_attributes}
-
-        # Connect atoms by bonds
-        bond_type_mapping = {
-            'SING': Chem.BondType.SINGLE,
-            'DOUB': Chem.BondType.DOUBLE,
-            'TRIP': Chem.BondType.TRIPLE,
-            'AROM': Chem.BondType.AROMATIC
-        }
-        bond_types = bond_cols['value_order']
-
-        for bond_i, bond_type in enumerate(bond_types):
-            rwmol.AddBond(name_to_idx_mapping[bond_cols['atom_id_1'][bond_i].strip('"')], 
-                          name_to_idx_mapping[bond_cols['atom_id_2'][bond_i].strip('"')], 
-                          bond_type_mapping.get(bond_type, Chem.BondType.UNSPECIFIED))
-
-        # Try recharging mol (for metals)
-        try:
-            rwmol = recharge(rwmol)
-        except Exception as e:
-            logger.error(f"Failed to recharge rdkitmol. Error: {e} -> template for {resname} will be None. ")
-            return None
+        if bond_table: 
+            bond_cols = {attr: bond_table.find_column(f"{bond_category}{attr}") for attr in bond_attributes}
+
+            # Connect atoms by bonds
+            bond_type_mapping = {
+                'SING': Chem.BondType.SINGLE,
+                'DOUB': Chem.BondType.DOUBLE,
+                'TRIP': Chem.BondType.TRIPLE,
+                'AROM': Chem.BondType.AROMATIC
+            }
+            bond_types = bond_cols['value_order']
+
+            for bond_i, bond_type in enumerate(bond_types):
+                rwmol.AddBond(name_to_idx_mapping[bond_cols['atom_id_1'][bond_i].strip('"')], 
+                            name_to_idx_mapping[bond_cols['atom_id_2'][bond_i].strip('"')], 
+                            bond_type_mapping.get(bond_type, Chem.BondType.UNSPECIFIED))
+
+            # Try recharging mol (for metals)
+            try:
+                rwmol = recharge(rwmol)
+            except Exception as e:
+                logger.error(f"Failed to recharge rdkitmol. Error: {e} -> template for {resname} will be None. ")
+                return None
 
         # Finish eidting mol 
         try:    

meeko/data/params/ad4_types.json

@@ -18,6 +18,7 @@
     {"smarts": "[#30]",             "atype": "Zn"},
     {"smarts": "[#35]",             "atype": "Br"},
     {"smarts": "[#53]",             "atype": "I"},
+    {"smarts": "[#27]",             "atype": "Co"},
     {"smarts": "[#7X3v3][a]",       "atype": "N",  "comment": "pyrrole, aniline"},
     {"smarts": "[#7X3v3][#6X3v4]",  "atype": "N",  "comment": "amide"},
     {"smarts": "[#7X3v3][NX2]=[*]", "atype": "N",  "comment": "triazene"},

meeko/utils/rdkitutils.py

@@ -272,4 +272,5 @@ def react_and_map(reactants: tuple[Chem.Mol], rxn: rdChemReactions.ChemicalReact
     # 34: 1.20,
     35: 1.20,
     53: 1.39,
+    27: 0.00,
 }