Bug fix #4: Obsolete PDBs were not getting replaced by newer ones.

openfold/data/templates.py

@@ -798,6 +798,8 @@ def _process_single_hit(
     hit: parsers.TemplateHit,
     mmcif_dir: str,
     max_template_date: datetime.datetime,
+    release_dates: Mapping[str, datetime.datetime],
+    obsolete_pdbs: Mapping[str, str],
     kalign_binary_path: str,
     strict_error_check: bool = False,
 ) -> SingleHitResult:
@@ -805,6 +807,10 @@ def _process_single_hit(
     # Fail hard if we can't get the PDB ID and chain name from the hit.
     hit_pdb_code, hit_chain_id = _get_pdb_id_and_chain(hit)
 
+    if hit_pdb_code not in release_dates:
+        if hit_pdb_code in obsolete_pdbs:
+            hit_pdb_code = obsolete_pdbs[hit_pdb_code]
+
     mapping = _build_query_to_hit_index_mapping(
         hit.query,
         hit.hit_sequence,
@@ -1054,6 +1060,8 @@ class TemplateHitFeaturizer:
                 hit=hit,
                 mmcif_dir=self._mmcif_dir,
                 max_template_date=template_cutoff_date,
+                release_dates=self._release_dates,
+                obsolete_pdbs=self._obsolete_pdbs,
                 strict_error_check=self._strict_error_check,
                 kalign_binary_path=self._kalign_binary_path,
             )