Read Partial Charges from mol2 and SDF

meeko/cli/mk_prepare_ligand.py

@@ -78,6 +78,11 @@ def cmd_lineparser():
         "--name_from_prop",
         help="set molecule name from RDKit/SDF property",
     )
+    io_group.add_argument(
+        "--charge_from_prop",
+        nargs="*",
+        help="set atom partial charges from the input file. The default is PartialCharge for SDF and _TriposPartialCharge for MOL2 unless overriden by a user defined property name. ",
+    )
     io_group.add_argument(
         "-o",
         "--out",
@@ -214,7 +219,7 @@ def cmd_lineparser():
     )
     config_group.add_argument(
         "--charge_model",
-        choices=("gasteiger", "espaloma", "zero"),
+        choices=("gasteiger", "espaloma", "zero", "read"),
         help="default is 'gasteiger', 'zero' sets all zeros",
         default="gasteiger",
     )
@@ -551,6 +556,19 @@ def main():
     nr_failures = 0
     is_after_first = False
     preparator = MoleculePreparation.from_config(config)
+
+    if args.charge_from_prop is not None: 
+        if args.charge_model != "read": 
+            print('--charge_from_prop must be used with --charge_model "read"')
+            sys.exit(1)
+
+        preparator.charge_model = "read"
+        if args.charge_from_prop: 
+            preparator.charge_atom_prop = args.charge_from_prop[0]
+        else:
+            if ext=="mol2": 
+                preparator.charge_atom_prop = "_TriposPartialCharge"
+
     for mol in mol_supplier:
         if is_after_first and output.is_multimol == False:
             print("Processed only the first molecule of multiple molecule input.")

meeko/molsetup.py

@@ -1724,17 +1724,22 @@ def init_atom(self, compute_gasteiger_charges: bool, read_charges_from_prop: str
                         ok_charges[i] += chrg_by_heavy_atom[newidx]
                 charges = ok_charges
         elif read_charges_from_prop is not None: 
-            if not isinstance(read_charges_from_prop, str): 
+            if not isinstance(read_charges_from_prop, str) or not read_charges_from_prop: 
                 raise ValueError(
-                    f"Invalid value for read_charges_from_prop: expected a string (str), but got {type(read_charges_from_prop).__name__} instead. "
+                    f"Invalid atom property name for read_charges_from_prop: expected a nonempty string (str), but got {type(read_charges_from_prop).__name__} instead. "
                 )
-            if not read_charges_from_prop: 
-                read_charges_from_prop = "_TriposPartialCharge"
-                raise Warning(
-                    "The charge_model of MoleculePreparation is set to be 'read', but a valid charge_propname is not given. " + eol + 
-                    "The default property name ('_TriposPartialCharge') will be used. " 
-                )
-            charges = [float(atom.GetProp(read_charges_from_prop)) for atom in self.mol.GetAtoms()]
+            charges = [
+                        float(atom.GetProp(read_charges_from_prop)) 
+                        if atom.HasProp(read_charges_from_prop) else None
+                        for atom in self.mol.GetAtoms()
+                    ]
+            if None in charges: 
+                for idx, charge in enumerate(charges):
+                    if charge is None:
+                        print(f"Charge at index {idx} is None.")
+                raise ValueError(
+                    f"The list of charges based on atom property name {read_charges_from_prop} contains None. "
+                )  
         else:
             charges = [0.0] * self.mol.GetNumAtoms()
         # register atom

meeko/preparation.py

@@ -86,7 +86,7 @@ def __init__(
         input_offatom_params=None,
         load_offatom_params=None,
         charge_model="gasteiger",
-        charge_propname=None,
+        charge_atom_prop=None,
         dihedral_model=None,
         reactive_smarts=None,
         reactive_smarts_idx=None,
@@ -156,24 +156,24 @@ def __init__(
             )
 
         self.charge_model = charge_model
-        self.charge_propname = charge_propname
+        self.charge_atom_prop = charge_atom_prop
 
-        if self.charge_model!="read" and self.charge_propname: 
+        if self.charge_model!="read" and self.charge_atom_prop: 
             raise ValueError(
-                "A charge_propname (%s) is given to MoleculePreparation but its current charge_model is %s. " + eol + 
-                "To read charges from atom properties in the input mol, set charge_model to 'read' and name the property in 'charge_propname'. " 
-                % (charge_propname, charge_model)
+                "A charge_atom_prop (%s) is given to MoleculePreparation but its current charge_model is %s. " + eol + 
+                "To read charges from atom properties in the input mol, set charge_model to 'read' and name the property as 'charge_atom_prop'. " 
+                % (charge_atom_prop, charge_model)
             )
         if self.charge_model=="read":
-            if not self.charge_propname: 
-                self.charge_propname = "_TriposPartialCharge"
-                raise Warning(
-                    "The charge_model of MoleculePreparation is set to be 'read', but a valid charge_propname is not given. " + eol + 
-                    "The default property name ('_TriposPartialCharge') will be used. " 
+            if not self.charge_atom_prop: 
+                self.charge_atom_prop = "PartialCharge"
+                warnings.warn(
+                    "The charge_model of MoleculePreparation is set to be 'read', but a valid charge_atom_prop is not given. " + eol + 
+                    "The default atom property ('PartialCharge') will be used. "
                 )
-            elif not isinstance(self.charge_propname, str): 
+            elif not isinstance(self.charge_atom_prop, str): 
                 raise ValueError(
-                    f"Invalid value for charge_propname: expected a string (str), but got {type(self.charge_propname).__name__} instead. "
+                    f"Invalid value for charge_atom_prop: expected a string (str), but got {type(self.charge_atom_prop).__name__} instead. "
                 )
 
         allowed_dihedral_models = [None, "openff", "espaloma"]
@@ -511,7 +511,7 @@ def prepare(
             keep_chorded_rings=self.keep_chorded_rings,
             keep_equivalent_rings=self.keep_equivalent_rings,
             compute_gasteiger_charges=self.charge_model == "gasteiger",
-            read_charges_from_prop=self.charge_propname,
+            read_charges_from_prop=self.charge_atom_prop,
             conformer_id=conformer_id,
         )