fix wrong chains and error for seq alignment

app.py

@@ -128,7 +128,7 @@ with gr.Blocks() as blocks:
 
     gr.Examples([
             ["TOP7",{"chains": [{"class": "protein","sequence": "MGDIQVQVNIDDNGKNFDYTYTVTTESELQKVLNELMDYIKKQGAKRVRISITARTKKEAEKFAAILIKVFAELGYNDINVTFDGDTVTVEGQLEGGSLEHHHHHH","chain": "A"}], "covMods":[]}], 
-            ["ApixacabanBinder", {"chains": [{"class": "protein","sequence": "SVKSEYAEAAAVGQEAVAVFNTMKAAFQNGDKEAVAQYLARLASLYTRHEELLNRILEKARREGNKEAVTLMNEFTATFQTGKSIFNAMVAAFKNGDDDSFESYLQALEKVTAKGETLADQIAKAL","chain": "A"}, {"class":"ligand", "smiles":"COc1ccc(cc1)n2c3c(c(n2)C(=O)N)CCN(C3=O)c4ccc(cc4)N5CCCCC5=O", "chain": "A"}], "covMods":[]}] 
+            ["ApixacabanBinder", {"chains": [{"class": "protein","sequence": "SVKSEYAEAAAVGQEAVAVFNTMKAAFQNGDKEAVAQYLARLASLYTRHEELLNRILEKARREGNKEAVTLMNEFTATFQTGKSIFNAMVAAFKNGDDDSFESYLQALEKVTAKGETLADQIAKAL","chain": "A"}, {"class":"ligand", "smiles":"COc1ccc(cc1)n2c3c(c(n2)C(=O)N)CCN(C3=O)c4ccc(cc4)N5CCCCC5=O", "sdf":"","name":"","chain": "B"}], "covMods":[]}] 
         ],
     inputs = [jobname, inp]     
     )

msa.py

@@ -148,55 +148,54 @@ def run_mmseqs2(x, prefix, use_env=True, use_filter=True,
   [seqs_unique.append(x) for x in seqs if x not in seqs_unique]
   Ms = [N + seqs_unique.index(seq) for seq in seqs]
   # lets do it!
-  if not os.path.isfile(tar_gz_file):
-    TIME_ESTIMATE = 150 * len(seqs_unique)
-    with tqdm(total=TIME_ESTIMATE, bar_format=TQDM_BAR_FORMAT) as pbar:
-      while REDO:
-        pbar.set_description("SUBMIT")
-
-        # Resubmit job until it goes through
+  TIME_ESTIMATE = 150 * len(seqs_unique)
+  with tqdm(total=TIME_ESTIMATE, bar_format=TQDM_BAR_FORMAT) as pbar:
+    while REDO:
+      pbar.set_description("SUBMIT")
+
+      # Resubmit job until it goes through
+      out = submit(seqs_unique, mode, N)
+      while out["status"] in ["UNKNOWN", "RATELIMIT"]:
+        sleep_time = 5 + random.randint(0, 5)
+        logger.error(f"Sleeping for {sleep_time}s. Reason: {out['status']}")
+        # resubmit
+        time.sleep(sleep_time)
         out = submit(seqs_unique, mode, N)
-        while out["status"] in ["UNKNOWN", "RATELIMIT"]:
-          sleep_time = 5 + random.randint(0, 5)
-          logger.error(f"Sleeping for {sleep_time}s. Reason: {out['status']}")
-          # resubmit
-          time.sleep(sleep_time)
-          out = submit(seqs_unique, mode, N)
 
-        if out["status"] == "ERROR":
-          raise Exception(f'MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.')
+      if out["status"] == "ERROR":
+        raise Exception(f'MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.')
 
-        if out["status"] == "MAINTENANCE":
-          raise Exception(f'MMseqs2 API is undergoing maintenance. Please try again in a few minutes.')
+      if out["status"] == "MAINTENANCE":
+        raise Exception(f'MMseqs2 API is undergoing maintenance. Please try again in a few minutes.')
 
-        # wait for job to finish
-        ID,TIME = out["id"],0
+      # wait for job to finish
+      ID,TIME = out["id"],0
+      pbar.set_description(out["status"])
+      while out["status"] in ["UNKNOWN","RUNNING","PENDING"]:
+        t = 5 + random.randint(0,5)
+        logger.error(f"Sleeping for {t}s. Reason: {out['status']}")
+        time.sleep(t)
+        out = status(ID)
         pbar.set_description(out["status"])
-        while out["status"] in ["UNKNOWN","RUNNING","PENDING"]:
-          t = 5 + random.randint(0,5)
-          logger.error(f"Sleeping for {t}s. Reason: {out['status']}")
-          time.sleep(t)
-          out = status(ID)
-          pbar.set_description(out["status"])
-          if out["status"] == "RUNNING":
-            TIME += t
-            pbar.update(n=t)
-          #if TIME > 900 and out["status"] != "COMPLETE":
-          #  # something failed on the server side, need to resubmit
-          #  N += 1
-          #  break
-
-        if out["status"] == "COMPLETE":
-          if TIME < TIME_ESTIMATE:
-            pbar.update(n=(TIME_ESTIMATE-TIME))
-          REDO = False
-
-        if out["status"] == "ERROR":
-          REDO = False
-          raise Exception(f'MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.')
-
-      # Download results
-      download(ID, tar_gz_file)
+        if out["status"] == "RUNNING":
+          TIME += t
+          pbar.update(n=t)
+        #if TIME > 900 and out["status"] != "COMPLETE":
+        #  # something failed on the server side, need to resubmit
+        #  N += 1
+        #  break
+
+      if out["status"] == "COMPLETE":
+        if TIME < TIME_ESTIMATE:
+          pbar.update(n=(TIME_ESTIMATE-TIME))
+        REDO = False
+
+      if out["status"] == "ERROR":
+        REDO = False
+        raise Exception(f'MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.')
+
+    # Download results
+    download(ID, tar_gz_file)
 
 
     a3m_files = [f"{path}/uniref.a3m"]