boltz-vsynthes 1.0.26__tar.gz → 1.0.28__tar.gz

{boltz_vsynthes-1.0.26/src/boltz_vsynthes.egg-info → boltz_vsynthes-1.0.28}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.26
+Version: 1.0.28
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-1.0.26 → boltz_vsynthes-1.0.28}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "boltz-vsynthes"
-version = "1.0.26"
+version = "1.0.28"
 requires-python = ">=3.10,<3.13"
 description = "Boltz for VSYNTHES"
 readme = "README.md"

{boltz_vsynthes-1.0.26 → boltz_vsynthes-1.0.28}/src/boltz/data/parse/pdb.py

@@ -5,6 +5,7 @@ from typing import Optional
 from Bio import PDB
 from Bio.PDB.PDBParser import PDBParser
 from Bio.PDB.Polypeptide import PPBuilder
+from Bio.Data.IUPACData import protein_letters_3to1
 from rdkit import Chem
 from rdkit.Chem.rdchem import Mol
 
@@ -17,7 +18,7 @@ def parse_pdb(
     ccd: dict[str, Mol],
     mol_dir: Path,
     boltz2: bool = False,
-) -> Target:
+) -> dict:
     """Parse a PDB file.
 
     Parameters
@@ -33,8 +34,8 @@ def parse_pdb(
 
     Returns
     -------
-    Target
-        The parsed target.
+    dict
+        Dictionary containing sequences and bonds.
     """
     # Read PDB file
     parser = PDBParser(QUIET=True)
@@ -56,10 +57,8 @@ def parse_pdb(
                         }
                     })
 
-    data = {
+    return {
         "sequences": sequences,
         "bonds": [],
         "version": 1,
-    }
-
-    return parse_boltz_schema(pdb_path.stem, data, ccd, mol_dir, boltz2) 
+    } 

{boltz_vsynthes-1.0.26 → boltz_vsynthes-1.0.28}/src/boltz/data/parse/pdb_download.py

@@ -55,7 +55,7 @@ def parse_pdb_id(
     mol_dir: Path,
     cache_dir: Path,
     boltz2: bool = False,
-) -> Target:
+) -> dict:
     """Parse a PDB file by ID.
 
     Parameters
@@ -73,12 +73,12 @@ def parse_pdb_id(
 
     Returns
     -------
-    Target
-        The parsed target.
+    dict
+        Dictionary containing sequences and bonds.
     """
     # Download PDB file
     pdb_path = download_pdb(pdb_id, cache_dir)
-    
+
     # Read PDB file
     parser = PDBParser(QUIET=True)
     structure = parser.get_structure("protein", str(pdb_path))
@@ -99,10 +99,8 @@ def parse_pdb_id(
                         }
                     })
 
-    data = {
+    return {
         "sequences": sequences,
         "bonds": [],
         "version": 1,
-    }
-
-    return parse_boltz_schema(pdb_id, data, ccd, mol_dir, boltz2) 
+    } 

{boltz_vsynthes-1.0.26 → boltz_vsynthes-1.0.28}/src/boltz/data/parse/schema.py

@@ -1041,7 +1041,9 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
                 sdf_path = Path(item[entity_type]["sdf"])
                 from boltz.data.parse.sdf import parse_sdf
                 target = parse_sdf(sdf_path, ccd, mol_dir)
+                print(target)
                 seq = target.sequences[0]
+                print(seq)
             elif "ccd" in item[entity_type]:
                 seq = str(item[entity_type]["ccd"])
             else:

{boltz_vsynthes-1.0.26 → boltz_vsynthes-1.0.28}/src/boltz/data/parse/sdf.py

@@ -48,7 +48,7 @@ def parse_sdf(
     ccd: dict[str, Mol],
     mol_dir: Path,
     boltz2: bool = False,
-) -> Target:
+) -> dict:
     """Parse an SDF file.
 
     Parameters
@@ -64,8 +64,8 @@ def parse_sdf(
 
     Returns
     -------
-    Target
-        The parsed target.
+    dict
+        Dictionary containing sequences and bonds.
     """
     # Process SDF file
     mol_dict = _process_sdf(str(sdf_path))
@@ -81,10 +81,8 @@ def parse_sdf(
             }
         })
 
-    data = {
+    return {
         "sequences": sequences,
         "bonds": [],
         "version": 1,
-    }
-
-    return parse_boltz_schema(sdf_path.stem, data, ccd, mol_dir, boltz2) 
+    } 

{boltz_vsynthes-1.0.26 → boltz_vsynthes-1.0.28/src/boltz_vsynthes.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.26
+Version: 1.0.28
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown