boltz-vsynthes 1.0.6__py3-none-any.whl → 1.0.7__py3-none-any.whl

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.dist-info → boltz_vsynthes-1.0.7.dist-info}/METADATA

@@ -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.dist-info → boltz_vsynthes-1.0.7.dist-info}/RECORD

@@ -38,7 +38,7 @@ 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/schema.py,sha256=dE4Cew9JrU4rifyZmFHQM2jglwJq7xHcxtA_-wSxj3w,41995
+boltz/data/parse/schema.py,sha256=DvMwh1Brn4ELzBuLEk89fdYv4XBx5bX3Fq2_TMeZ-08,43352
 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
@@ -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-1.0.6.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
-boltz_vsynthes-1.0.6.dist-info/METADATA,sha256=wfKFFAABcO0tFOYgorKiqdUMwzUnFFUYcDy12CwxF1g,7171
-boltz_vsynthes-1.0.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-boltz_vsynthes-1.0.6.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
-boltz_vsynthes-1.0.6.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
-boltz_vsynthes-1.0.6.dist-info/RECORD,,
+boltz_vsynthes-1.0.7.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
+boltz_vsynthes-1.0.7.dist-info/METADATA,sha256=AQB7KiKkpIvaBZ2aMiTw1wfHE8_Vm_4D7cbJMN80J2U,7171
+boltz_vsynthes-1.0.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+boltz_vsynthes-1.0.7.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
+boltz_vsynthes-1.0.7.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
+boltz_vsynthes-1.0.7.dist-info/RECORD,,