new homomer behaviour also in colabfold and higher default settings for sampling and recycling iterations

Author: lhatsk

inference.py

@@ -329,12 +329,12 @@ def to_float(x):
     parser.add_argument(
         "--times",
         type=int,
-        default=10,
+        default=100,
     )
     parser.add_argument(
         "--max_recycling_iters",
         type=int,
-        default=3,
+        default=20,
     )
     parser.add_argument(
         "--num_ensembles",

notebooks/alphalink2.ipynb

@@ -292,14 +292,14 @@
         "  template_results,\n",
         ") = get_msa_and_templates(\n",
         "  target_id,\n",
-        "  unique_sequences,\n",
+        "  sequences,\n",
         "  result_dir=result_dir,\n",
         "  msa_mode=msa_mode,\n",
         "  use_templates=use_templates,\n",
         "  homooligomers_num = homooligomers_num\n",
         ")\n",
         "\n",
-        "for idx, seq in enumerate(unique_sequences):\n",
+        "for idx, seq in enumerate(sequences):\n",
         "    chain_id = PDB_CHAIN_IDS[idx]\n",
         "    sequence_features = pipeline.make_sequence_features(\n",
         "              sequence=seq, description=f'> {jobname} seq {chain_id}', num_res=len(seq)\n",