boltz-vsynthes 1.0.30__py3-none-any.whl → 1.0.31__py3-none-any.whl

boltz/data/parse/schema.py

@@ -1059,6 +1059,7 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
 
     # Check if any affinity ligand is present
     affinity_ligands = set()
+    affinity_proteins = set()
     properties = schema.get("properties", [])
     if properties and not boltz_2:
         msg = "Affinity prediction is only supported for Boltz2!"
@@ -1069,7 +1070,6 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
         if prop_type == "affinity":
             binder = prop["affinity"]["binder"]
             if not isinstance(binder, str):
-                # TODO: support multi residue ligands and ccd's
                 msg = "Binder must be a single chain."
                 raise ValueError(msg)
 
@@ -1077,18 +1077,21 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
                 msg = f"Could not find binder with name {binder} in the input!"
                 raise ValueError(msg)
 
-            if chain_name_to_entity_type[binder] != "ligand":
+            # Allow both protein and ligand as binders
+            if chain_name_to_entity_type[binder] == "protein":
+                affinity_proteins.add(binder)
+            elif chain_name_to_entity_type[binder] == "ligand":
+                affinity_ligands.add(binder)
+            else:
                 msg = (
-                    f"Chain {binder} is not a ligand! "
-                    "Affinity is currently only supported for ligands."
+                    f"Chain {binder} is not a protein or ligand! "
+                    "Affinity is currently only supported for proteins and ligands."
                 )
                 raise ValueError(msg)
 
-            affinity_ligands.add(binder)
-
-    # Check only one affinity ligand is present
-    if len(affinity_ligands) > 1:
-        msg = "Only one affinity ligand is currently supported!"
+    # Check if any affinity binder is present
+    if len(affinity_proteins) + len(affinity_ligands) > 1:
+        msg = "Only one affinity binder is currently supported!"
         raise ValueError(msg)
 
     # Go through entities and parse them
@@ -1111,12 +1114,15 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
             elif isinstance(item[entity_type]["id"], list):
                 ids.extend(item[entity_type]["id"])
 
-        # Check if any affinity ligand is present
+        # Check if any affinity binder is present
         if len(ids) == 1:
-            affinity = ids[0] in affinity_ligands
+            affinity = ids[0] in affinity_ligands or ids[0] in affinity_proteins
         elif (len(ids) > 1) and any(x in affinity_ligands for x in ids):
             msg = "Cannot compute affinity for a ligand that has multiple copies!"
             raise ValueError(msg)
+        elif (len(ids) > 1) and any(x in affinity_proteins for x in ids):
+            # If binder is a protein, allow multiple ligands
+            affinity = True
         else:
             affinity = False
 
@@ -1215,7 +1221,7 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
             )
 
         # Parse a non-polymer
-        elif (entity_type == "ligand") and ("ccd" in items[0][entity_type]):
+        elif (entity_type == "ligand") and "ccd" in (items[0][entity_type]):
             seq = items[0][entity_type]["ccd"]
 
             if isinstance(seq, str):
@@ -1307,60 +1313,6 @@ 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)

{boltz_vsynthes-1.0.30.dist-info → boltz_vsynthes-1.0.31.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.30
+Version: 1.0.31
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-1.0.30.dist-info → boltz_vsynthes-1.0.31.dist-info}/RECORD

@@ -40,7 +40,7 @@ boltz/data/parse/mmcif.py,sha256=25kEXCkx-OuaawAs7cdz0fxdRu5_CCO0AV00u84PrjQ,368
 boltz/data/parse/mmcif_with_constraints.py,sha256=WHYZckSqUwu-Nb9vmVmxHmC7uxwVrF7AVUeVKsc5wGQ,51473
 boltz/data/parse/pdb.py,sha256=iybk4p2UgUy_ABGprDq_xxyPSdm1HAZsGTM0lhxVEwM,1654
 boltz/data/parse/pdb_download.py,sha256=wge-scX-lOatX0q83W1wOsaql99rYp-6uGWSHEc995M,2718
-boltz/data/parse/schema.py,sha256=kNu28U2_MGiecwWNlcxgaDH3WOcO0P-q2LdoSPSb66w,63826
+boltz/data/parse/schema.py,sha256=9H7ZJpKb22KHXmfJAjG_0jz7VbZ1LAYt5eVp34_nwVw,62176
 boltz/data/parse/sdf.py,sha256=fs3MQVClDcCzxJaeVYiDuoh-fUrYc8Tcd5Bz8ws3FKI,2052
 boltz/data/parse/yaml.py,sha256=GRFRMtDD4PQ4PIpA_S1jj0vRaEu2LlZd_g4rN1zUrNo,1505
 boltz/data/sample/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -107,9 +107,9 @@ boltz/model/optim/scheduler.py,sha256=nB4jz0CZ4pR4n08LQngExL_pNycIdYI8AXVoHPnZWQ
 boltz/model/potentials/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 boltz/model/potentials/potentials.py,sha256=vev8Vjfs-ML1hyrdv_R8DynG4wSFahJ6nzPWp7CYQqw,17507
 boltz/model/potentials/schedules.py,sha256=m7XJjfuF9uTX3bR9VisXv1rvzJjxiD8PobXRpcBBu1c,968
-boltz_vsynthes-1.0.30.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
-boltz_vsynthes-1.0.30.dist-info/METADATA,sha256=LCqHhIkKBAtMf8t6kbT4xoPr54lLZb86Tuy9KOgWYdc,7171
-boltz_vsynthes-1.0.30.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-boltz_vsynthes-1.0.30.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
-boltz_vsynthes-1.0.30.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
-boltz_vsynthes-1.0.30.dist-info/RECORD,,
+boltz_vsynthes-1.0.31.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
+boltz_vsynthes-1.0.31.dist-info/METADATA,sha256=4hMLLLOG2rXQo4bR4F_kU_jxyKnOVVQhrXiwwsHxDtk,7171
+boltz_vsynthes-1.0.31.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+boltz_vsynthes-1.0.31.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
+boltz_vsynthes-1.0.31.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
+boltz_vsynthes-1.0.31.dist-info/RECORD,,