Skip obsolete PDB templates that don't have a replacement.

Fixes https://github.com/deepmind/alphafold/issues/163.

PiperOrigin-RevId: 395878875
Change-Id: I99a9defa95547582bbfd9fec3ae821386274d77f

alphafold/data/templates.py

@@ -132,19 +132,26 @@ def _is_after_cutoff(
     return False
 
 
-def _parse_obsolete(obsolete_file_path: str) -> Mapping[str, str]:
-  """Parses the data file from PDB that lists which PDB ids are obsolete."""
+def _parse_obsolete(obsolete_file_path: str) -> Mapping[str, Optional[str]]:
+  """Parses the data file from PDB that lists which pdb_ids are obsolete."""
   with open(obsolete_file_path) as f:
     result = {}
     for line in f:
       line = line.strip()
-      # We skip obsolete entries that don't contain a mapping to a new entry.
-      if line.startswith('OBSLTE') and len(line) > 30:
-        # Format:    Date      From     To
-        # 'OBSLTE    31-JUL-94 116L     216L'
-        from_id = line[20:24].lower()
-        to_id = line[29:33].lower()
-        result[from_id] = to_id
+      # Format:    Date      From     To
+      # 'OBSLTE    06-NOV-19 6G9Y'                - Removed, rare
+      # 'OBSLTE    31-JUL-94 116L     216L'       - Replaced, common
+      # 'OBSLTE    26-SEP-06 2H33     2JM5 2OWI'  - Replaced by multiple, rare
+      if line.startswith('OBSLTE'):
+        if len(line) > 30:
+          # Replaced by at least one structure.
+          from_id = line[20:24].lower()
+          to_id = line[29:33].lower()
+          result[from_id] = to_id
+        elif len(line) == 24:
+          # Removed.
+          from_id = line[20:24].lower()
+          result[from_id] = None
     return result
 
 
@@ -673,13 +680,18 @@ def _process_single_hit(
     mmcif_dir: str,
     max_template_date: datetime.datetime,
     release_dates: Mapping[str, datetime.datetime],
-    obsolete_pdbs: Mapping[str, str],
+    obsolete_pdbs: Mapping[str, Optional[str]],
     kalign_binary_path: str,
     strict_error_check: bool = False) -> SingleHitResult:
   """Tries to extract template features from a single HHSearch 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)
 
+  # This hit has been removed (obsoleted) from PDB, skip it.
+  if hit_pdb_code in obsolete_pdbs and obsolete_pdbs[hit_pdb_code] is None:
+    return SingleHitResult(
+        features=None, error=None, warning=f'Hit {hit_pdb_code} is obsolete.')
+
   if hit_pdb_code not in release_dates:
     if hit_pdb_code in obsolete_pdbs:
       hit_pdb_code = obsolete_pdbs[hit_pdb_code]