fix reactive typing for ligands

meeko/preparation.py

@@ -418,7 +418,12 @@ def setup(self):
             " MoleculePreparation.prepare() returns a list of MoleculeSetup instances."
         )
         warnings.warn(msg, DeprecationWarning)
-        return self.deprecated_setup_access
+        if len(self.deprecated_setup_access) > 1:
+            raise RuntimeError(
+                "got multiple setups, use new api: molsetup_list = mk_prep(mol)"
+            )
+
+        return self.deprecated_setup_access[0]
 
     @classmethod
     def get_defaults_dict(cls):
@@ -551,20 +556,22 @@ def prepare(
                 self.reactive_smarts,
                 self.reactive_smarts_idx,
             )
+
+            if len(reactive_types_dicts) == 0:
+                raise RuntimeError("reactive SMARTS didn't match")
+
             setups = []
             for r in reactive_types_dicts:
                 new_setup = setup.copy()
                 # There is no guarantee that the addition order in the dictionary will be the correct order to
                 # create the list in, so first sorts the keys from the dictionary then extracts the values in order
                 # to construct the new atom type list.
-                sorted_keys = list(r.keys())
-                sorted_keys.sort()
-                new_setup_atom_type = [r[idx] for idx in sorted_keys]
-                new_setup.atom_type = new_setup_atom_type
+                for idx, atom_type in r.items():
+                    new_setup.atoms[idx].atom_type = atom_type
                 setups.append(new_setup)
 
         # for a gentle introduction of the new API
-        self.deprecated_setup_access = setups[0]
+        self.deprecated_setup_access = setups
 
         return setups
 

meeko/reactive.py

@@ -131,7 +131,7 @@ def atom_name_to_molsetup_index(chorizo_residue, atom_name):
     return index
 
 
-def assign_x(molsetup, reactive_atom_index, get_reactive_atype=get_reactive_atype):
+def assign_reactive_types_by_index(molsetup, reactive_atom_index, get_reactive_atype=get_reactive_atype):
 
     atypes = {atom.index: atom.atom_type for atom in molsetup.atoms}
 
@@ -166,7 +166,7 @@ def assign_reactive_types(
     for atom_indices in molsetup.find_pattern(smarts):
 
         reactive_atom_index = atom_indices[smarts_idx]
-        atypes = assign_x(
+        atypes = assign_reactive_types_by_index(
             molsetup,
             reactive_atom_index,
             get_reactive_atype

scripts/mk_prepare_receptor.py

@@ -10,7 +10,8 @@
 
 import numpy as np
 
-from meeko.reactive import atom_name_to_molsetup_index, assign_x
+from meeko.reactive import atom_name_to_molsetup_index
+from meeko.reactive import assign_reactive_types_by_index
 from meeko import PDBQTMolecule
 from meeko import RDKitMolCreate
 from meeko import MoleculePreparation
@@ -441,7 +442,7 @@ def get_args():
     # get reactive atom types
     reactive_aname = reactive_flexres_name[res_id]
     reactive_atomi = atom_name_to_molsetup_index(chorizo.residues[res_id], reactive_aname)
-    reactive_atypes = assign_x(chorizo.residues[res_id].molsetup, reactive_atomi)
+    reactive_atypes = assign_reactive_types_by_index(chorizo.residues[res_id].molsetup, reactive_atomi)
     # set reactive atom types
     nr_atom = len(chorizo.residues[res_id].molsetup.atoms)
     for atom_index in range(nr_atom):