Merge branch 'JSON_parsable_base' into scratch_bond

forlilab · Jan 12, 2025 · d166afc · d166afc
2 parents 0a81777 + 761e829
commit d166afc
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Showing 2 changed files with 11 additions and 11 deletions.
diff --git a/meeko/molsetup.py b/meeko/molsetup.py
@@ -533,21 +533,21 @@ def _decode_object(cls, obj: dict[str, Any]):
         molsetup = cls(name, is_sidechain)
 
         molsetup.pseudoatom_count = obj["pseudoatom_count"]
-        molsetup.atoms = [Atom.json_decoder(x) for x in obj["atoms"]]
+        molsetup.atoms = [Atom.from_dict(x) for x in obj["atoms"]]
         molsetup.bond_info = {
-            string_to_tuple(k, int): Bond.json_decoder(v)
+            string_to_tuple(k, int): Bond.from_dict(v)
             for k, v in obj["bond_info"].items()
         }
         molsetup.rings = {
-            string_to_tuple(k, int): Ring.json_decoder(v) for k, v in obj["rings"].items()
+            string_to_tuple(k, int): Ring.from_dict(v) for k, v in obj["rings"].items()
         }
         molsetup.ring_closure_info = RingClosureInfo(
             obj["ring_closure_info"]["bonds_removed"],
             obj["ring_closure_info"]["pseudos_by_atom"],
         )
         molsetup.rotamers = [convert_to_tuple_keyed_dict(rotamer, int) for rotamer in obj["rotamers"]]
         molsetup.atom_params = obj["atom_params"]
-        molsetup.restraints = [Restraint.json_decoder(x) for x in obj["restraints"]]
+        molsetup.restraints = [Restraint.from_dict(x) for x in obj["restraints"]]
         molsetup.flexibility_model = obj["flexibility_model"]
         if "rigid_body_connectivity" in molsetup.flexibility_model:
             tuples_rigid_body_connectivity = {
@@ -1554,7 +1554,7 @@ def json_encoder(cls, obj: "RDKitMoleculeSetup") -> Optional[dict[str, Any]]:
     @classmethod
     def _decode_object(cls, obj: dict[str, Any]): 
 
-        base_molsetup = MoleculeSetup.json_decoder(obj)
+        base_molsetup = MoleculeSetup.from_dict(obj)
         rdkit_molsetup = cls(source = base_molsetup)
 
         # Restores RDKitMoleculeSetup-specific attributes from the json dict

diff --git a/meeko/polymer.py b/meeko/polymer.py
@@ -617,9 +617,9 @@ def _decode_object(cls, obj: dict[str, Any]):
 
         # Extracting the constructor args from the json representation and creating a ResidueChemTemplates instance
         templates = {
-            k: ResidueTemplate.json_decoder(v, check_keys=False) for k, v in obj["residue_templates"].items()
+            k: ResidueTemplate.from_dict(v) for k, v in obj["residue_templates"].items()
         }
-        padders = {k: ResiduePadder.json_decoder(v, check_keys=False) for k, v in obj["padders"].items()}
+        padders = {k: ResiduePadder.from_dict(v) for k, v in obj["padders"].items()}
 
         residue_chem_templates = cls(templates, padders, obj["ambiguous"])
 
@@ -963,14 +963,14 @@ def _decode_object(cls, obj: dict[str, Any]):
 
         # Deserializes ResidueChemTemplates from the dict to use as an input, then constructs a Polymer object
         # and sets its values using deserialized JSON values.
-        residue_chem_templates = ResidueChemTemplates.json_decoder(
+        residue_chem_templates = ResidueChemTemplates.from_dict(
             obj["residue_chem_templates"]
         )
 
         polymer = cls({}, {}, residue_chem_templates)
 
         polymer.monomers = {
-            k: Monomer.json_decoder(v, check_keys=False) for k, v in obj["monomers"].items()
+            k: Monomer.from_dict(v) for k, v in obj["monomers"].items()
         }
         polymer.log = obj["log"]
 
@@ -2130,9 +2130,9 @@ def _decode_object(cls, obj: dict[str, Any]):
         rdkit_mol = rdkit_mol_from_json(obj["rdkit_mol"])
         padded_mol = rdkit_mol_from_json(obj["padded_mol"])
 
-        molsetup = RDKitMoleculeSetup.json_decoder(obj["molsetup"])
+        molsetup = RDKitMoleculeSetup.from_dict(obj["molsetup"])
         if not isinstance(molsetup, RDKitMoleculeSetup):
-            molsetup = MoleculeSetup.json_decoder(obj["molsetup"])
+            molsetup = MoleculeSetup.from_dict(obj["molsetup"])
 
         mapidx_to_raw = convert_to_int_keyed_dict(obj["mapidx_to_raw"])
         molsetup_mapidx = convert_to_int_keyed_dict(obj["molsetup_mapidx"])