boltz-vsynthes 1.0.12__tar.gz → 1.0.14__tar.gz

{boltz_vsynthes-1.0.12/src/boltz_vsynthes.egg-info → boltz_vsynthes-1.0.14}/PKG-INFO

@@ -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 → boltz_vsynthes-1.0.14}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "boltz-vsynthes"
-version = "1.0.12"
+version = "1.0.14"
 requires-python = ">=3.10,<3.13"
 description = "Boltz for VSYNTHES"
 readme = "README.md"

{boltz_vsynthes-1.0.12 → boltz_vsynthes-1.0.14}/src/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 → boltz_vsynthes-1.0.14/src/boltz_vsynthes.egg-info}/PKG-INFO

@@ -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-1.0.14/src/boltz_vsynthes.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

boltz_vsynthes-1.0.12/src/boltz/data/parse/__init__.py

@@ -1,21 +0,0 @@
-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",
-]