boltz-vsynthes 1.0.27__py3-none-any.whl → 1.0.29__py3-none-any.whl

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/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/data/parse/schema.py

@@ -1024,12 +1024,12 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
                     # 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)
-                    seq = target.sequences[0]  # Access sequence directly from the dictionary
+                    seq = target["sequences"][0]["protein"]["sequence"]  # Access sequence from dict
                 else:
                     # This is a PDB file
                     from boltz.data.parse.pdb import parse_pdb
                     target = parse_pdb(pdb_path, ccd, mol_dir)
-                    seq = target.sequences[0]  # Access sequence directly from the dictionary
+                    seq = target["sequences"][0]["protein"]["sequence"]  # Access sequence from dict
             else:
                 msg = f"Protein must have either 'sequence' or 'pdb' field: {item}"
                 raise ValueError(msg)
@@ -1041,9 +1041,7 @@ 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)
+                seq = target["sequences"][0]["ligand"]["smiles"]  # Access sequence from dict
             elif "ccd" in item[entity_type]:
                 seq = str(item[entity_type]["ccd"])
             else:

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-1.0.27.dist-info → boltz_vsynthes-1.0.29.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.27
+Version: 1.0.29
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-1.0.27.dist-info → boltz_vsynthes-1.0.29.dist-info}/RECORD

@@ -38,10 +38,10 @@ boltz/data/parse/csv.py,sha256=Hcq8rJW2njczahEr8jfd_o-zxLaNSgJ3YIoC9srIqpw,2518
 boltz/data/parse/fasta.py,sha256=taI4s_CqPtyF0XaLJAsVAJHCL0GXm2g1g8Qeccdxikk,3906
 boltz/data/parse/mmcif.py,sha256=25kEXCkx-OuaawAs7cdz0fxdRu5_CCO0AV00u84PrjQ,36822
 boltz/data/parse/mmcif_with_constraints.py,sha256=WHYZckSqUwu-Nb9vmVmxHmC7uxwVrF7AVUeVKsc5wGQ,51473
-boltz/data/parse/pdb.py,sha256=X4u1ZzSFk0Xy8LRbCCMVlbAzWeGddo2O4SQuk_WyS-k,1656
-boltz/data/parse/pdb_download.py,sha256=YLxCidVkRLlvZ0uCCSnRTP7Yz1-AYv9hz_SO3_xecWk,2769
-boltz/data/parse/schema.py,sha256=578YHuUxV-L9LooF-ONet1zuX2HjRp8crMbIJBYw-cM,60899
-boltz/data/parse/sdf.py,sha256=9hi4mfc4oCbNtXsKhU3HmI3hclwsxu7YaT8tSyi7IlY,2107
+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=CcK-9F7h3fG7VI5zMNzhi2Yjqfq30z-ndBstO_2mx8o,60908
+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
 boltz/data/sample/cluster.py,sha256=9Sx8qP7zGZOAyEspwYFtCTbGTBZnuN-zfCKFbbA_6oI,8175
@@ -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-1.0.27.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
-boltz_vsynthes-1.0.27.dist-info/METADATA,sha256=64rc6owSGyTbtm6xvq_aRDGSkp3LRrz8_CbL_TUv3ws,7171
-boltz_vsynthes-1.0.27.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-boltz_vsynthes-1.0.27.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
-boltz_vsynthes-1.0.27.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
-boltz_vsynthes-1.0.27.dist-info/RECORD,,
+boltz_vsynthes-1.0.29.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
+boltz_vsynthes-1.0.29.dist-info/METADATA,sha256=2NGfvz95nz21zJeUKD-q9ymclZarT3dPCq4dxFXQztw,7171
+boltz_vsynthes-1.0.29.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+boltz_vsynthes-1.0.29.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
+boltz_vsynthes-1.0.29.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
+boltz_vsynthes-1.0.29.dist-info/RECORD,,