cov-mode parameter to foldseek run

karolamik13 · Nov 11, 2024 · ba342f9 · ba342f9
1 parent f0565f2
commit ba342f9
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/prody/proteins/interactions.py b/prody/proteins/interactions.py
@@ -3430,7 +3430,7 @@ def extract_sequence_from_pdb(pdb_file, chain, output_file):
         'foldseek', 'easy-search', 'inp.pdb', database_folder, 'prot.foldseek',
         'tmp2', '--exhaustive-search', '1', '--format-output',
         "query,target,qstart,qend,tstart,tend,qcov,tcov,qtmscore,ttmscore,rmsd,qaln,taln",
-        '-c', str(cov_threshold)
+        '-c', str(cov_threshold), '--cov-mode', '0'
     ])
 
     # Extract sequence and write to prot.seq