boltz-vsynthes 1.0.6__tar.gz → 1.0.7__tar.gz

{boltz_vsynthes-1.0.6/src/boltz_vsynthes.egg-info → boltz_vsynthes-1.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.6
+Version: 1.0.7
 Summary: Boltz for V-Synthes
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-1.0.6 → boltz_vsynthes-1.0.7}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "boltz-vsynthes"
-version = "1.0.6"
+version = "1.0.7"
 requires-python = ">=3.10,<3.13"
 description = "Boltz for V-Synthes"
 readme = "README.md"

{boltz_vsynthes-1.0.6 → boltz_vsynthes-1.0.7}/src/boltz/data/parse/schema.py

@@ -1008,7 +1008,7 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
     
     # Keep track of ligand IDs
     ligand_id = 1
-    ligand_id_map = {}  # Maps user-provided IDs to internal LIG1, LIG2, etc.
+    ligand_id_map = {}
 
     # Parse sequences
     for item in schema["sequences"]:
@@ -1067,6 +1067,9 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
                 ligand_id += 1
             else:
                 seq = str(item[entity_type]["ccd"])
+                # For CCD ligands, use the CCD code as the internal ID
+                for id in entity_id:
+                    ligand_id_map[id] = seq
 
         # Group items by entity
         items_to_group.setdefault((entity_type, seq), []).append(item)
@@ -1080,12 +1083,48 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
     # Check if any affinity ligand is present
     affinity_ligands = set()
     properties = schema.get("properties", [])
+    
+    # Get all ligands
+    ligands = []
+    for item in schema["sequences"]:
+        entity_type = list(item.keys())[0]
+        if entity_type == "ligand":
+            entity_id = item[entity_type]["id"]
+            entity_id = [entity_id] if isinstance(entity_id, str) else entity_id
+            ligands.extend(entity_id)
+    
+    # Get user-specified binders
+    specified_binders = set()
     for prop in properties:
         if "affinity" in prop:
             binder = prop["affinity"]["binder"]
-            if binder in ligand_id_map:
-                binder = ligand_id_map[binder]  # Convert to internal LIG1, LIG2, etc.
-            affinity_ligands.add(binder)
+            specified_binders.add(binder)
+    
+    # If no binders specified, use all proteins
+    if not specified_binders:
+        for item in schema["sequences"]:
+            entity_type = list(item.keys())[0]
+            if entity_type == "protein":
+                entity_id = item[entity_type]["id"]
+                entity_id = [entity_id] if isinstance(entity_id, str) else entity_id
+                specified_binders.update(entity_id)
+    
+    # Generate protein-ligand pairs for specified binders
+    new_properties = []
+    for binder in specified_binders:
+        for ligand in ligands:
+            if ligand in ligand_id_map:
+                ligand = ligand_id_map[ligand]  # Convert to internal LIG1, LIG2, etc.
+            affinity_ligands.add(ligand)
+            new_properties.append({
+                "affinity": {
+                    "binder": binder,
+                    "ligand": ligand
+                }
+            })
+    
+    # Update schema with generated properties
+    schema["properties"] = new_properties
 
     # Parse each group
     chains = []

{boltz_vsynthes-1.0.6 → boltz_vsynthes-1.0.7/src/boltz_vsynthes.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.6
+Version: 1.0.7
 Summary: Boltz for V-Synthes
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown