boltz-vsynthes 1.0.1__py3-none-any.whl → 1.0.3__py3-none-any.whl

boltz/main.py

@@ -665,6 +665,14 @@ def process_inputs(
     """
     all_records = []
     
+    # Create processed directory
+    processed_dir = out_dir / "processed"
+    processed_dir.mkdir(parents=True, exist_ok=True)
+    
+    # Create structure directory
+    structure_dir = processed_dir / "structures"
+    structure_dir.mkdir(parents=True, exist_ok=True)
+    
     # Process each input file in its own directory
     for input_file in data:
         # Create a subdirectory for this input file
@@ -687,7 +695,6 @@ def process_inputs(
         # Create output directories for this file
         msa_dir = file_out_dir / "msa"
         records_dir = file_out_dir / "processed" / "records"
-        structure_dir = file_out_dir / "processed" / "structures"
         processed_msa_dir = file_out_dir / "processed" / "msa"
         processed_constraints_dir = file_out_dir / "processed" / "constraints"
         processed_templates_dir = file_out_dir / "processed" / "templates"
@@ -697,7 +704,6 @@ def process_inputs(
         file_out_dir.mkdir(parents=True, exist_ok=True)
         msa_dir.mkdir(parents=True, exist_ok=True)
         records_dir.mkdir(parents=True, exist_ok=True)
-        structure_dir.mkdir(parents=True, exist_ok=True)
         processed_msa_dir.mkdir(parents=True, exist_ok=True)
         processed_constraints_dir.mkdir(parents=True, exist_ok=True)
         processed_templates_dir.mkdir(parents=True, exist_ok=True)
@@ -726,7 +732,7 @@ def process_inputs(
             processed_constraints_dir=processed_constraints_dir,
             processed_templates_dir=processed_templates_dir,
             processed_mols_dir=processed_mols_dir,
-            structure_dir=structure_dir,
+            structure_dir=structure_dir,  # Use the central structure directory
             records_dir=records_dir,
         )
 
@@ -740,7 +746,7 @@ def process_inputs(
 
     # Create combined manifest
     manifest = Manifest(all_records)
-    manifest.dump(out_dir / "processed" / "manifest.json")
+    manifest.dump(processed_dir / "manifest.json")
     return manifest
 
 
@@ -1234,6 +1240,14 @@ def predict(  # noqa: C901, PLR0915, PLR0912
         msg += "s." if len(manifest_filtered.records) > 1 else "."
         click.echo(msg)
 
+        # When skipping structure prediction, we need to ensure structure files exist
+        if skip_structure:
+            for record in manifest_filtered.records:
+                structure_path = out_dir / "predictions" / record.id / f"pre_affinity_{record.id}.npz"
+                if not structure_path.exists():
+                    msg = f"Structure file not found for {record.id}. Cannot run affinity prediction without structure."
+                    raise FileNotFoundError(msg)
+
         pred_writer = BoltzAffinityWriter(
             data_dir=processed.targets_dir,
             output_dir=out_dir / "predictions",

{boltz_vsynthes-1.0.1.dist-info → boltz_vsynthes-1.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.1
+Version: 1.0.3
 Summary: Boltz for V-Synthes
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-1.0.1.dist-info → boltz_vsynthes-1.0.3.dist-info}/RECORD

@@ -1,5 +1,5 @@
 boltz/__init__.py,sha256=F_-so3S40iZrSZ89Ge4TS6aZqwWyZXq_H4AXGDlbA_g,187
-boltz/main.py,sha256=nzakDxdvkrdR3sgvi88wyeRkYHX9Ojhbgt0shGPH23I,40708
+boltz/main.py,sha256=p-iXEzVh_CAkKZs2MJ7EojQQdIZnC9cYXr9Bax_PrU4,41377
 boltz/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 boltz/data/const.py,sha256=1M-88Z6HkfKY6MkNtqcj3b9P-oX9xEXluh3qM_u8dNU,26779
 boltz/data/mol.py,sha256=maOpPHEGX1VVXCIFY6pQNGF7gUBZPAfgSvuPf2QO1yc,34268
@@ -104,9 +104,9 @@ 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-1.0.1.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
-boltz_vsynthes-1.0.1.dist-info/METADATA,sha256=c0VEm3L1a5r4NIo1PIWMre-2AFN4AkqCnTmZxPLCri4,7171
-boltz_vsynthes-1.0.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-boltz_vsynthes-1.0.1.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
-boltz_vsynthes-1.0.1.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
-boltz_vsynthes-1.0.1.dist-info/RECORD,,
+boltz_vsynthes-1.0.3.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
+boltz_vsynthes-1.0.3.dist-info/METADATA,sha256=KQnSi_PP-_Gkz8yG3ED3-a_R4-IUlX92QZxwG8eQe8w,7171
+boltz_vsynthes-1.0.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+boltz_vsynthes-1.0.3.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
+boltz_vsynthes-1.0.3.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
+boltz_vsynthes-1.0.3.dist-info/RECORD,,