Added a separate AlignmentRunner for handling seq_emb mode.

- In `seq_emb` mode, the AlignmentRunner works only on generating templates.

run_pretrained_openfold.py

@@ -73,6 +73,15 @@ def precompute_alignments(tags, seqs, alignment_dir, args):
 
             os.makedirs(local_alignment_dir)
 
+            if args.use_single_seq_mode:
+                alignment_runner = data_pipeline.AlignmentRunner(
+                    jackhmmer_binary_path=args.jackhmmer_binary_path,
+                    hhsearch_binary_path=args.hhsearch_binary_path,
+                    uniref90_database_path=args.uniref90_database_path,
+                    pdb70_database_path=args.pdb70_database_path,
+                    no_cpus=args.cpus,
+                )
+            else:
                 alignment_runner = data_pipeline.AlignmentRunner(
                     jackhmmer_binary_path=args.jackhmmer_binary_path,
                     hhblits_binary_path=args.hhblits_binary_path,