boltz-vsynthes 1.0.12__py3-none-any.whl → 1.0.14__py3-none-any.whl

boltz/data/parse/__init__.py

@@ -1,21 +1 @@
-from boltz.data.parse.pdb import parse_pdb
-from boltz.data.parse.sdf import parse_sdf
-from boltz.data.parse.pdb_download import parse_pdb_id
-from boltz.data.parse.yaml import parse_yaml
-from boltz.data.parse.fasta import parse_fasta
-from boltz.data.parse.a3m import parse_a3m
-from boltz.data.parse.csv import parse_csv
-from boltz.data.parse.mmcif import parse_mmcif
-from boltz.data.parse.mmcif_with_constraints import parse_mmcif_with_constraints
 
-__all__ = [
-    "parse_pdb",
-    "parse_sdf",
-    "parse_pdb_id",
-    "parse_yaml",
-    "parse_fasta",
-    "parse_a3m",
-    "parse_csv",
-    "parse_mmcif",
-    "parse_mmcif_with_constraints",
-]

boltz/data/parse/schema.py

@@ -1015,14 +1015,39 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
 
         # Get sequence
         if entity_type in {"protein", "dna", "rna"}:
-            seq = str(item[entity_type]["sequence"])
+            if "sequence" in item[entity_type]:
+                seq = str(item[entity_type]["sequence"])
+            elif "pdb" in item[entity_type]:
+                # Handle PDB file
+                pdb_path = Path(item[entity_type]["pdb"])
+                if len(pdb_path.stem) == 4 and pdb_path.stem.isalnum():
+                    # This is a PDB ID
+                    from boltz.data.parse.pdb_download import parse_pdb_id
+                    target = parse_pdb_id(pdb_path.stem, ccd, mol_dir, pdb_path.parent, boltz2)
+                else:
+                    # This is a PDB file
+                    from boltz.data.parse.pdb import parse_pdb
+                    target = parse_pdb(pdb_path, ccd, mol_dir, boltz2)
+                # Get sequence from the first chain
+                seq = target.sequences[0]
+            else:
+                msg = f"Protein must have either 'sequence' or 'pdb' field: {item}"
+                raise ValueError(msg)
         elif entity_type == "ligand":
-            assert "smiles" in item[entity_type] or "ccd" in item[entity_type]
-            assert "smiles" not in item[entity_type] or "ccd" not in item[entity_type]
             if "smiles" in item[entity_type]:
                 seq = str(item[entity_type]["smiles"])
-            else:
+            elif "sdf" in item[entity_type]:
+                # Handle SDF file
+                sdf_path = Path(item[entity_type]["sdf"])
+                from boltz.data.parse.sdf import parse_sdf
+                target = parse_sdf(sdf_path, ccd, mol_dir, boltz2)
+                # Get sequence from the first ligand
+                seq = target.sequences[0]
+            elif "ccd" in item[entity_type]:
                 seq = str(item[entity_type]["ccd"])
+            else:
+                msg = f"Ligand must have 'smiles', 'sdf', or 'ccd' field: {item}"
+                raise ValueError(msg)
 
         # Group items by entity
         items_to_group.setdefault((entity_type, seq), []).append(item)

{boltz_vsynthes-1.0.12.dist-info → boltz_vsynthes-1.0.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.12
+Version: 1.0.14
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-1.0.12.dist-info → boltz_vsynthes-1.0.14.dist-info}/RECORD

@@ -32,7 +32,7 @@ boltz/data/module/training.py,sha256=iNzmq9ufs20S4M947CCzdYzGTFjmCTf2tFExJ2PtXnA
 boltz/data/module/trainingv2.py,sha256=ZsYUHYXxfuPgIpbTwCj5QLO0XK__xjsqIw6GARSNGW0,21276
 boltz/data/msa/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 boltz/data/msa/mmseqs2.py,sha256=Im3s0h9lQVl-bXDfn4T6X6bxhLyF3XEyUXDjWFCjsvs,8202
-boltz/data/parse/__init__.py,sha256=28ltwqi_0kqIjgnjUr7b730rqcEykh73rTYph7Mt3n8,642
+boltz/data/parse/__init__.py,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
 boltz/data/parse/a3m.py,sha256=I5nD16kYVW1NPKeLEMm7I4GnEQrtZk9bFtxw89wmKi0,3318
 boltz/data/parse/csv.py,sha256=Hcq8rJW2njczahEr8jfd_o-zxLaNSgJ3YIoC9srIqpw,2518
 boltz/data/parse/fasta.py,sha256=taI4s_CqPtyF0XaLJAsVAJHCL0GXm2g1g8Qeccdxikk,3906
@@ -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=o2gGGVDxLaKhqPaZjuwfY6gdIyu4iUxczmkvDnEnNls,1808
 boltz/data/parse/pdb_download.py,sha256=FJTX7qHKJ_sBRcHg1PLKlqy6gVuluPDAWOAuYKI4-gM,2931
-boltz/data/parse/schema.py,sha256=gnHZBy0Io2Ecrw3KAD1lE1-cKnWL4ypKUI3EmeV5FDQ,59566
+boltz/data/parse/schema.py,sha256=yvUG5rrYzK5FJGwKBY5N1lihCpuUzh6-fZenjcrtMoc,60825
 boltz/data/parse/sdf.py,sha256=myFA3bL6MkdPdMFfZHotxJ8yNMGpsc_u6w06YFadeiw,1364
 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-1.0.12.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
-boltz_vsynthes-1.0.12.dist-info/METADATA,sha256=cjkpORB6zM1s9yoflOv7VCepyxy5UKby5vA2S13a4K0,7171
-boltz_vsynthes-1.0.12.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-boltz_vsynthes-1.0.12.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
-boltz_vsynthes-1.0.12.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
-boltz_vsynthes-1.0.12.dist-info/RECORD,,
+boltz_vsynthes-1.0.14.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
+boltz_vsynthes-1.0.14.dist-info/METADATA,sha256=SOWlJpcwXqF4NaRyohkVa7egBqD1kF3UobSkWeHRFdc,7171
+boltz_vsynthes-1.0.14.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+boltz_vsynthes-1.0.14.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
+boltz_vsynthes-1.0.14.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
+boltz_vsynthes-1.0.14.dist-info/RECORD,,