From bca9c761500850b3d413fe5b78cea2a7dc4eb90b Mon Sep 17 00:00:00 2001
From: Joana Pereira <joanapereira@4414.bioz.unibas.ch>
Date: Wed, 10 May 2023 14:10:42 +0200
Subject: [PATCH] implemented the detection of OMBBs that form complexes with
OMBBs. it also works with input pdbs now.
---
barrOs_library.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/barrOs_library.py b/barrOs_library.py
index 9841695..f1d8fb7 100644
--- a/barrOs_library.py
+++ b/barrOs_library.py
@@ -2271,11 +2271,13 @@ def run_barros(arguments, offset = 1, step = 2, local_angle_threshold = 25, dist
for i, pdbID in enumerate(in_queue):
deleted_it = False
+ isfile = False
print(" ... Taking care of '{}' (job {}) ({}/{})".format(pdbID, job_number+1, i+1, len(in_queue)))
if '.pdb' in pdbID or '.ent' in pdbID:
+ isfile = True
pdb_file = pdbID
chains_inpdb = get_chains_in_pdb(pdb_file, source_pdb=False)[0]
try:
@@ -2302,7 +2304,7 @@ def run_barros(arguments, offset = 1, step = 2, local_angle_threshold = 25, dist
target_chains = []
if len(chains_inpdb) > 1:
for chainID in chains_inpdb:
- if '.pdb' in pdbID or '.ent' in pdbID:
+ if isfile:
chain_pdb, _ = extract_chain(pdb_file, chain, outpdb = 'downloaded_pdbs/{}_{}.pdb'.format(pdbID, chainID))
target_chains.append([pdbID.split('.')[0], chainID, chain_pdb, protein_type, membrane_thickness])
else:
--
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