boltz-vsynthes 1.0.32__py3-none-any.whl → 1.0.33__py3-none-any.whl

boltz/data/parse/schema.py

@@ -2,6 +2,7 @@ from collections.abc import Mapping
 from dataclasses import dataclass
 from pathlib import Path
 from typing import Optional
+import json
 
 import click
 import numpy as np
@@ -1425,15 +1426,43 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
             protein_chains.add(chain_name)
 
         # Add affinity info
-        if chain.affinity and affinity_info is not None:
-            msg = "Cannot compute affinity for multiple ligands!"
-            raise ValueError(msg)
-
         if chain.affinity:
-            affinity_info = AffinityInfo(
-                chain_id=asym_id,
-                mw=chain.affinity_mw,
-            )
+            # If this is a protein binder, we need to create affinity info for each ligand
+            if chain_name in affinity_proteins:
+                # Find all ligand chains
+                ligand_chains = [
+                    (name, c) for name, c in chains.items() 
+                    if c.type == const.chain_type_ids["NONPOLYMER"]
+                ]
+                if not ligand_chains:
+                    msg = "No ligand chains found for protein binder!"
+                    raise ValueError(msg)
+                
+                # Create affinity info for each ligand
+                for ligand_name, ligand_chain in ligand_chains:
+                    affinity_info = AffinityInfo(
+                        chain_id=asym_id,
+                        mw=chain.affinity_mw,
+                    )
+                    # Save the affinity info in a subfolder named after the ligand
+                    output_dir = Path(f"output/{ligand_name}")
+                    output_dir.mkdir(parents=True, exist_ok=True)
+                    # Save the affinity info
+                    with open(output_dir / "affinity_info.json", "w") as f:
+                        json.dump({
+                            "chain_id": asym_id,
+                            "mw": chain.affinity_mw,
+                            "ligand_name": ligand_name
+                        }, f)
+            else:
+                # This is a ligand binder
+                if affinity_info is not None:
+                    msg = "Cannot compute affinity for multiple ligands!"
+                    raise ValueError(msg)
+                affinity_info = AffinityInfo(
+                    chain_id=asym_id,
+                    mw=chain.affinity_mw,
+                )
 
         # Find all copies of this chain in the assembly
         entity_id = int(chain.entity)

{boltz_vsynthes-1.0.32.dist-info → boltz_vsynthes-1.0.33.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.32
+Version: 1.0.33
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-1.0.32.dist-info → boltz_vsynthes-1.0.33.dist-info}/RECORD

@@ -40,7 +40,7 @@ boltz/data/parse/mmcif.py,sha256=25kEXCkx-OuaawAs7cdz0fxdRu5_CCO0AV00u84PrjQ,368
 boltz/data/parse/mmcif_with_constraints.py,sha256=WHYZckSqUwu-Nb9vmVmxHmC7uxwVrF7AVUeVKsc5wGQ,51473
 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=liL6Dl4P1bEq-nYwm8DOAXPfl32yYi84MgrcFXpR-0M,64220
+boltz/data/parse/schema.py,sha256=5eU-_NR-g2XTtDpYXoREAy84DWTyHN8yRiXngd4BShs,65676
 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
@@ -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-1.0.32.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
-boltz_vsynthes-1.0.32.dist-info/METADATA,sha256=mGtHYvFndm8HdHsMfvXFMu5x4CwNVAAgdP5o_CVGBgU,7171
-boltz_vsynthes-1.0.32.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-boltz_vsynthes-1.0.32.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
-boltz_vsynthes-1.0.32.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
-boltz_vsynthes-1.0.32.dist-info/RECORD,,
+boltz_vsynthes-1.0.33.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
+boltz_vsynthes-1.0.33.dist-info/METADATA,sha256=XadtfwQoBLRNyaCe61wdMoCixayUE05BNfA7Y7hblgI,7171
+boltz_vsynthes-1.0.33.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+boltz_vsynthes-1.0.33.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
+boltz_vsynthes-1.0.33.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
+boltz_vsynthes-1.0.33.dist-info/RECORD,,