boltz-vsynthes 1.0.32__py3-none-any.whl → 1.0.34__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
@@ -1221,7 +1222,7 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
             )
 
         # Parse a non-polymer
-        elif (entity_type == "ligand") and "ccd" in (items[0][entity_type]):
+        elif (entity_type == "ligand") and ("ccd" in items[0][entity_type]):
             seq = items[0][entity_type]["ccd"]
 
             if isinstance(seq, str):
@@ -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/main.py

@@ -27,9 +27,6 @@ from boltz.data.msa.mmseqs2 import run_mmseqs2
 from boltz.data.parse.a3m import parse_a3m
 from boltz.data.parse.csv import parse_csv
 from boltz.data.parse.fasta import parse_fasta
-from boltz.data.parse.pdb import parse_pdb
-from boltz.data.parse.pdb_download import parse_pdb_id
-from boltz.data.parse.sdf import parse_sdf
 from boltz.data.parse.yaml import parse_yaml
 from boltz.data.types import MSA, Manifest, Record
 from boltz.data.write.writer import BoltzAffinityWriter, BoltzWriter
@@ -294,28 +291,20 @@ def check_inputs(data: Path) -> list[Path]:
     if data.is_dir():
         data: list[Path] = list(data.glob("*"))
 
-        # Filter out non .fasta, .yaml, .pdb, or .sdf files, raise
+        # Filter out non .fasta or .yaml files, raise
         # an error on directory and other file types
         for d in data:
             if d.is_dir():
-                msg = f"Found directory {d} instead of .fasta, .yaml, .pdb, or .sdf."
+                msg = f"Found directory {d} instead of .fasta or .yaml."
                 raise RuntimeError(msg)
-            if d.suffix not in (".fa", ".fas", ".fasta", ".yml", ".yaml", ".pdb", ".sdf"):
+            if d.suffix not in (".fa", ".fas", ".fasta", ".yml", ".yaml"):
                 msg = (
                     f"Unable to parse filetype {d.suffix}, "
-                    "please provide a .fasta, .yaml, .pdb, or .sdf file."
+                    "please provide a .fasta or .yaml file."
                 )
                 raise RuntimeError(msg)
     else:
-        # Check if input is a PDB ID (4 characters)
-        if len(data.stem) == 4 and data.stem.isalnum():
-            # Create a temporary file to store the PDB ID
-            temp_file = data.parent / f"{data.stem}.pdb"
-            with temp_file.open("w") as f:
-                f.write(data.stem)
-            data = [temp_file]
-        else:
-            data = [data]
+        data = [data]
 
     return data
 
@@ -508,23 +497,13 @@ def process_input(  # noqa: C901, PLR0912, PLR0915, D103
             target = parse_fasta(path, ccd, mol_dir, boltz2)
         elif path.suffix in (".yml", ".yaml"):
             target = parse_yaml(path, ccd, mol_dir, boltz2)
-        elif path.suffix == ".pdb":
-            # Check if this is a PDB ID file
-            if path.stat().st_size <= 4:  # File only contains PDB ID
-                with path.open("r") as f:
-                    pdb_id = f.read().strip()
-                target = parse_pdb_id(pdb_id, ccd, mol_dir, path.parent, boltz2)
-            else:
-                target = parse_pdb(path, ccd, mol_dir, boltz2)
-        elif path.suffix == ".sdf":
-            target = parse_sdf(path, ccd, mol_dir, boltz2)
         elif path.is_dir():
-            msg = f"Found directory {path} instead of .fasta, .yaml, .pdb, or .sdf, skipping."
+            msg = f"Found directory {path} instead of .fasta or .yaml, skipping."
             raise RuntimeError(msg)  # noqa: TRY301
         else:
             msg = (
                 f"Unable to parse filetype {path.suffix}, "
-                "please provide a .fasta, .yaml, .pdb, or .sdf file."
+                "please provide a .fasta or .yaml file."
             )
             raise RuntimeError(msg)  # noqa: TRY301
 

{boltz_vsynthes-1.0.32.dist-info → boltz_vsynthes-1.0.34.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.32
+Version: 1.0.34
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-1.0.32.dist-info → boltz_vsynthes-1.0.34.dist-info}/RECORD

@@ -1,5 +1,5 @@
 boltz/__init__.py,sha256=F_-so3S40iZrSZ89Ge4TS6aZqwWyZXq_H4AXGDlbA_g,187
-boltz/main.py,sha256=fFXeW6PmVsbZtx0EVGBiczf3ulncuheeai1wpRVEhOI,40803
+boltz/main.py,sha256=AMYdcqTLOL5Mbo8P2ix1KeNwTijH5fWNzKUnLHBNtn0,39735
 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
@@ -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=1saQOFI15H6TqoEupjsjnbX77UQfuST174kIErThdwY,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-1.0.34.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
+boltz_vsynthes-1.0.34.dist-info/METADATA,sha256=h-T8W9FPQG5hynUMxYWhnJN4Ztt1XWoX4LgorJCEEYY,7171
+boltz_vsynthes-1.0.34.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+boltz_vsynthes-1.0.34.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
+boltz_vsynthes-1.0.34.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
+boltz_vsynthes-1.0.34.dist-info/RECORD,,