Added release info for UniRef90

projects/novelfams/translate2modelcif.py

@@ -342,20 +342,20 @@ def _get_entities(pdb_file, fam_name, trg_seq):
 
     # NOTE: can have gaps to accommodate "X" in ref_seq
     exp_seq = sqe_gaps.replace("-", "X")
-    len_diff = len(trg_seq.string) - len(exp_seq)
+    trg_seq = trg_seq.string
+    len_diff = len(trg_seq) - len(exp_seq)
     if len_diff > 0:
         exp_seq += "X" * len_diff
-    if exp_seq != trg_seq.string:
-        print(
+    if exp_seq != trg_seq:
+        # ToDo: turn into an exception once we got the correct sequence list.
+        _warn_msg(
             f"Sequence in {os.path.splitext(os.path.basename(pdb_file))[0]} "
-            + "does not match target.",
-            exp_seq,
+            + "does not match target. Falling back to residue-based sequence."
         )
-        # ToDo: re-enable check
-        # raise RuntimeError(f"Sequence in {pdb_file} does not match target.")
+        trg_seq = exp_seq
 
     cif_ent = {
-        "seqres": trg_seq.string,
+        "seqres": trg_seq,
         "pdb_sequence": sqe_gaps,
         "pdb_chain_id": [_get_ch_name(chn, False)],
         "fam_name": fam_name,
@@ -509,8 +509,8 @@ def _get_sequence_dbs_alphafold(seq_dbs):
             "UniRef90",
             "ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/"
             + "uniref90.fasta.gz",
-            version=None,
-            release_date=None,
+            version="2021_4",
+            release_date=datetime.datetime(2021, 11, 17),
         ),
         "BFD": modelcif.ReferenceDatabase(
             "BFD",
@@ -970,6 +970,10 @@ def _read_sequences(path):
                 continue
             sqnz += line
 
+    if len(sqnz) > 0:
+        sqnz = sqnz.rstrip("*")
+        sqnz_lst.AddSequence(seq.CreateSequence(name, sqnz))
+
     return sqnz_lst
 
 
@@ -1008,11 +1012,6 @@ def _main():
             )
         except (_InvalidCoordinateError, _NoEntitiesError):
             continue
-        except Exception as exc:
-            # ToDo: remove catching ALL exceptions
-            _warn_msg(f"Uncaught exception for '{f_name}':")
-            print(str(exc))
-            continue
 
         # report progress after a bit of time
         if timer() - tmstmp > 60: