Fix _fetch_upkb_cached in translate2modelcif.py

projects/PP2A-B55-design/translate2modelcif.py

@@ -363,19 +363,24 @@ def _check_sequence(up_ac, sequence):
 # for cache below
 upkb_entry_cache = {} # key = (up_ac, up_version, mdl_sequence)
 def _fetch_upkb_cached(sqe, up_ac, up_version=None):
-    """Get versioned UniProtKB entry (version=None means latest).
+    """Get best matching UniProtKB entry for sequence sqe.
     Get it from cache if already fetched.
-    Return None if failed to parse entry.
+    up_version defines starting version in UP to check.
+    Note that the returned UP entry may be a different version than the one in up_version.
+    Returned UP data includes result of _align_sequences.
+    If no perfect match found, it prints a warning.
     """
     # check if in cache already
     cache_key = (up_ac, up_version, sqe)
     if cache_key in upkb_entry_cache:
         return upkb_entry_cache[cache_key]
-    # fetch and parse
+    # fetch and parse first guess
     if up_version is None:
         up_data = _fetch_upkb_entry(up_ac)
+    else:
+        up_data = _fetch_unisave_entry(up_ac, up_version)
+    # find best match starting from first guess
     min_up_data = None
-
     while True:
         mismatches, up_range, mdl_range, covered_aln,  mdl_seqres = _align_sequences(
             sqe, up_data["up_sequence"], atomseq_aln=False)
@@ -415,14 +420,6 @@ def _fetch_upkb_cached(sqe, up_ac, up_version=None):
             _warn_msg(msg)
             # raise RuntimeError(msg)
             break
-    '''else:
-        try:
-            # note: can fail to parse very old UP versions...
-            up_data = _fetch_unisave_entry(up_ac, up_version)
-        except RuntimeError as ex:
-            #_warn_msg(f"Error in parsing v{next_v} of {up_ac}:\n{ex}")
-            up_data = None
-    '''
 
     # keep in cache
     upkb_entry_cache[cache_key] = up_data