boltz-vsynthes 1.0.39__tar.gz → 1.0.40__tar.gz

{boltz_vsynthes-1.0.39/src/boltz_vsynthes.egg-info → boltz_vsynthes-1.0.40}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.39
+Version: 1.0.40
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-1.0.39 → boltz_vsynthes-1.0.40}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "boltz-vsynthes"
-version = "1.0.39"
+version = "1.0.40"
 requires-python = ">=3.10,<3.13"
 description = "Boltz for VSYNTHES"
 readme = "README.md"

{boltz_vsynthes-1.0.39 → boltz_vsynthes-1.0.40}/src/boltz/data/parse/schema.py

@@ -1326,6 +1326,60 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
                 "cyclic", False
             ), "Cyclic flag is not supported for ligands"
 
+        elif (entity_type == "ligand") and ("sdf" in items[0][entity_type]):
+            # Handle SDF file
+            sdf_path = Path(items[0][entity_type]["sdf"])
+            from boltz.data.parse.sdf import parse_sdf
+            target = parse_sdf(sdf_path, ccd, mol_dir)
+            mol = target["sequences"][0]["ligand"]["smiles"]
+
+            if affinity:
+                mol = standardize(mol)
+
+            mol = AllChem.MolFromSmiles(mol)
+            mol = AllChem.AddHs(mol)
+
+            # Set atom names
+            canonical_order = AllChem.CanonicalRankAtoms(mol)
+            for atom, can_idx in zip(mol.GetAtoms(), canonical_order):
+                atom_name = atom.GetSymbol().upper() + str(can_idx + 1)
+                if len(atom_name) > 4:
+                    msg = (
+                        f"{mol} has an atom with a name longer than "
+                        f"4 characters: {atom_name}."
+                    )
+                    raise ValueError(msg)
+                atom.SetProp("name", atom_name)
+
+            success = compute_3d_conformer(mol)
+            if not success:
+                msg = f"Failed to compute 3D conformer for {mol}"
+                raise ValueError(msg)
+
+            mol_no_h = AllChem.RemoveHs(mol, sanitize=False)
+            affinity_mw = AllChem.Descriptors.MolWt(mol_no_h) if affinity else None
+            extra_mols[f"LIG{ligand_id}"] = mol_no_h
+            residue = parse_ccd_residue(
+                name=f"LIG{ligand_id}",
+                ref_mol=mol,
+                res_idx=0,
+            )
+
+            ligand_id += 1
+            parsed_chain = ParsedChain(
+                entity=entity_id,
+                residues=[residue],
+                type=const.chain_type_ids["NONPOLYMER"],
+                cyclic_period=0,
+                sequence=None,
+                affinity=affinity,
+                affinity_mw=affinity_mw,
+            )
+
+            assert not items[0][entity_type].get(
+                "cyclic", False
+            ), "Cyclic flag is not supported for ligands"
+
         else:
             msg = f"Invalid entity type: {entity_type}"
             raise ValueError(msg)
@@ -1393,15 +1447,6 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
                 chain_id=asym_id,
                 mw=chain.affinity_mw,
             )
-            # Save affinity info if output directory is specified
-            if output_dir is not None:
-                affinity_path = subfolder / "affinity_info.json"
-                with open(affinity_path, "w") as f:
-                    json.dump({
-                        "chain_id": asym_id,
-                        "mw": chain.affinity_mw,
-                        "chain_name": chain_name
-                    }, f)
 
         # Find all copies of this chain in the assembly
         entity_id = int(chain.entity)

{boltz_vsynthes-1.0.39 → boltz_vsynthes-1.0.40/src/boltz_vsynthes.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.39
+Version: 1.0.40
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown