From bd3e83049021ad4594aa630e349668ca7ab9f6b0 Mon Sep 17 00:00:00 2001
From: Joana Pereira <joanapereira@4414.bioz.unibas.ch>
Date: Sat, 6 May 2023 13:44:04 +0200
Subject: [PATCH] implemented the detection of OMBBs that form complexes with
OMBBs
---
barrOs_library.py | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/barrOs_library.py b/barrOs_library.py
index b47c212..4b04741 100644
--- a/barrOs_library.py
+++ b/barrOs_library.py
@@ -719,7 +719,6 @@ def get_secondary_structure(pdb_file):
run_dssp = sp.Popen(['mkdssp', '-i', pdb_file, '-o', out_file], stdout=sp.PIPE, stderr=sp.PIPE, stdin=sp.PIPE)
stdout, stderr = run_dssp.communicate()
- print(stderr)
if len(stderr) > 0:
run_dssp = sp.Popen(['dssp', '-i', pdb_file, '-o', out_file], stdout=sp.PIPE, stderr=sp.PIPE, stdin=sp.PIPE)
stdout, stderr = run_dssp.communicate()
@@ -2322,10 +2321,10 @@ def run_barros(arguments, offset = 1, step = 2, local_angle_threshold = 25, dist
for pdbID, chainID, pdb_file, protein_type, membrane_thickness in target_chains:
- try:
- pdb_sequence, barrel_topology, chains, num_bb_regions, pdb_file = process_barrel(pdb_file, ID = pdbID, chainID = chainID, offset = offset, step = step, local_angle_threshold = local_angle_threshold, distance_threshold = distance_threshold, multimer_only=multimer_only)
- except:
- num_bb_regions = 0
+ # try:
+ pdb_sequence, barrel_topology, chains, num_bb_regions, pdb_file = process_barrel(pdb_file, ID = pdbID, chainID = chainID, offset = offset, step = step, local_angle_threshold = local_angle_threshold, distance_threshold = distance_threshold, multimer_only=multimer_only)
+ # except:
+ num_bb_regions = 0
# check if it has a barrel. If so, continue
if num_bb_regions > 0 and len(pdb_sequence) < 10000:
--
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