fix several isses

example/nanobody_scaffolds/7eow.yaml

@@ -17,37 +17,26 @@ structure_groups:
       visibility: 0
       res_index: 26..34,52..59,98..118
 
-# Flexible lengths for CDR 1
 exclude: 
   - chain:
       id: B
       res_index: 26..28 # take out 3
+  - chain:
+      id: B
+      res_index: 52..54 # take out 3
+  - chain:
+      id: B
+      res_index: 98..104 # take out seven
 
 design_insertions:
   - insertion:
       id: B
       res_index: 26 # The res_index'th residue will be a designed one (starting to count from 1)
       num_residues: 1..5
-
-# Flexible lengths for CDR 2
-exclude: 
-  - chain:
-      id: B
-      res_index: 52..54 # take out 3
-
-design_insertions:
   - insertion:
       id: B
       res_index: 52 # The res_index'th residue will be a designed one (starting to count from 1)
       num_residues: 1..5
-
-# Flexible lengths for CDR 3
-exclude: 
-  - chain:
-      id: B
-      res_index: 98..104 # take out seven
-
-design_insertions:
   - insertion:
       id: B
       res_index: 98 # The res_index'th residue will be a designed one (starting to count from 1)

example/nanobody_scaffolds/7xl0.yaml

@@ -17,41 +17,31 @@ structure_groups:
       res_index: 26..33,51..57,97..110
 
 
-# Flexible lengths for CDR 1
 exclude: 
   - chain:
       id: A
       res_index: 26..28 # take out 3
-
-design_insertions:
-  - insertion:
-      id: A
-      res_index: 26 # The res_index'th residue will be a designed one (starting to count from 1)
-      num_residues: 1..5
-
-# Flexible lengths for CDR 2
-exclude: 
   - chain:
       id: A
       res_index: 51..53 # take out 3
-
-design_insertions:
-  - insertion:
-      id: A
-      res_index: 51 # The res_index'th residue will be a designed one (starting to count from 1)
-      num_residues: 1..5
-
-# Flexible lengths for CDR 3
-exclude: 
   - chain:
       id: A
       res_index: 97..102 # take out 6
 
 design_insertions:
+  - insertion:
+      id: A
+      res_index: 26 # The res_index'th residue will be a designed one (starting to count from 1)
+      num_residues: 1..5
+  - insertion:
+      id: A
+      res_index: 51 # The res_index'th residue will be a designed one (starting to count from 1)
+      num_residues: 1..5
   - insertion:
       id: A
       res_index: 97 # The res_index'th residue will be a designed one (starting to count from 1)
       num_residues: 1..12
+  
 
 # reindex the residue index which is used in the positional encoding
 reset_res_index:

example/nanobody_scaffolds/8coh.yaml

@@ -18,37 +18,26 @@ structure_groups:
       res_index: 26..33,51..58,97..115
 
 
-# Flexible lengths for CDR 1
 exclude: 
   - chain:
       id: A
       res_index: 26..28 # take out 3
+  - chain:
+      id: A
+      res_index: 51..53 # take out 3
+  - chain:
+      id: A
+      res_index: 97..103 # take out seven
 
 design_insertions:
   - insertion:
       id: A
       res_index: 26 # The res_index'th residue will be a designed one (starting to count from 1)
       num_residues: 1..5
-
-# Flexible lengths for CDR 2
-exclude: 
-  - chain:
-      id: A
-      res_index: 51..53 # take out 3
-
-design_insertions:
   - insertion:
       id: A
       res_index: 51 # The res_index'th residue will be a designed one (starting to count from 1)
       num_residues: 1..5
-
-# Flexible lengths for CDR 3
-exclude: 
-  - chain:
-      id: A
-      res_index: 97..103 # take out seven
-
-design_insertions:
   - insertion:
       id: A
       res_index: 98 # The res_index'th residue will be a designed one (starting to count from 1)

example/nanobody_scaffolds/8z8v.yaml

@@ -16,39 +16,26 @@ structure_groups:
       visibility: 0
       res_index: 26..33,51..58,98..108
 
-
-
-# Flexible lengths for CDR 1
 exclude: 
   - chain:
       id: B
       res_index: 26..28 # take out 3
+  - chain:
+      id: B
+      res_index: 51..53 # take out 3
+  - chain:
+      id: B
+      res_index: 98..100 # take out 3
 
 design_insertions:
   - insertion:
       id: B
       res_index: 26 # The res_index'th residue will be a designed one (starting to count from 1)
       num_residues: 1..5
-
-# Flexible lengths for CDR 2
-exclude: 
-  - chain:
-      id: B
-      res_index: 51..53 # take out 3
-
-design_insertions:
   - insertion:
       id: B
       res_index: 51 # The res_index'th residue will be a designed one (starting to count from 1)
       num_residues: 1..5
-
-# Flexible lengths for CDR 3
-exclude: 
-  - chain:
-      id: B
-      res_index: 98..100 # take out 3
-
-design_insertions:
   - insertion:
       id: B
       res_index: 98 # The res_index'th residue will be a designed one (starting to count from 1)

pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "boltzgen"
-requires-python = ">=3.10"
+requires-python = ">=3.9"
 #dynamic = ["version"]
 version = "0.1.2"
 dependencies = [
@@ -37,7 +37,7 @@ dependencies = [
     "cuequivariance_ops_torch_cu12>=0.5.0",
     "cuequivariance_torch>=0.5.0",
     "huggingface_hub",
-    "biopython",
+    "biopython", 
 ]
 
 # Enables the usage of setuptools_scm

src/boltzgen/cli/boltzgen.py

@@ -322,12 +322,6 @@ def add_configure_arguments(
         help="Threshold used for RMSD-based filters (lower is better).",
         default=None,
     )
-    p.add_argument(
-        "--local_files_only",
-        action="store_true",
-        help="Run in offline mode, use model weights and data from the local cache.",
-        default=False,
-    )
 
 
 def add_models_download_options(p: argparse.ArgumentParser) -> None:
@@ -1297,7 +1291,6 @@ def get_artifact_path(
             library_name="boltzgen",
             force_download=args.force_download,
             token=args.models_token,
-            local_files_only=args.local_files_only,
             cache_dir=args.cache,
         )
         result = Path(result)

src/boltzgen/data/parse/schema.py

@@ -1394,15 +1394,6 @@ class YamlDesignParser:
                             )
                         new_chain_to_msa[renamed_id] = msa
                     chain_to_msa.update(new_chain_to_msa)
-                    # Update chain_to_msa dictionary. Set defaults given by file_msa_flag for proteins. Insert -1 (no msa) for {dna, rna, ligand}.
-                    for chain in data.chains:
-                        chain_id = chain["name"].item()
-                        if chain_id not in chain_to_msa:
-                            if chain["mol_type"] == const.chain_type_ids["PROTEIN"]:
-                                chain_to_msa[chain_id] = file_msa_flag
-                            else:
-                                chain_to_msa[chain_id] = -1
-                    chain_to_msa.update(new_chain_to_msa)
                 else:
                     path = item["file"]["path"]
                     (

src/boltzgen/task/predict/data_protein_binder.py

@@ -1,4 +1,5 @@
 from dataclasses import dataclass
+from boltzgen.data.data import StructureInfo
 from pathlib import Path
 import re
 from typing import Dict, List, Optional
@@ -286,7 +287,7 @@ class PredictionDataset(torch.utils.data.Dataset):
 
         # Load record
         record = load_record(pdb_id, self.dataset.record_dir)
-
+        
         # Get the structure
         try:
             if self.inverse_fold: