From 728b3bec41c583fcc1c046b5d98d03736c67ddd1 Mon Sep 17 00:00:00 2001
From: Joana Pereira <joanapereira@4414.bioz.unibas.ch>
Date: Tue, 4 Apr 2023 16:12:42 +0200
Subject: [PATCH] minor bug fix
---
barrOs_library.py | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/barrOs_library.py b/barrOs_library.py
index 9c66f95..7f41808 100644
--- a/barrOs_library.py
+++ b/barrOs_library.py
@@ -1534,14 +1534,13 @@ def draw_graph(graph, labels, fig_label):
## 9. TO CALCULATE THE SHEAR NUMBER (Project by Roger Bamert)
-def shear_number(inpdb_file, show_path = False):
+def shear_number(pdb_file, show_path = False):
- chains_in_barrel = get_chains_in_pdb(inpdb_file, source_pdb=False)[0]
- pdb_file, _ = extract_chain(inpdb_file, chains_in_barrel[0], outpdb='/tmp/{}_{}'.format(inpdb_file.split('/')[-1], chains_in_barrel[0]))
+ # chains_in_barrel = get_chains_in_pdb(inpdb_file, source_pdb=False)[0]
+ # pdb_file, _ = extract_chain(inpdb_file, chains_in_barrel[0], outpdb='/tmp/{}_{}'.format(inpdb_file.split('/')[-1], chains_in_barrel[0]))
CA_coordinates, res_nums = get_CA_coordinates(pdb_file)
regions = find_regions(res_nums)
- print(regions)
angles_matrix, alpha_angles = calculateAnglesMatrix(CA_coordinates, regions)
adj_matrix = create_adjacency_matrix(CA_coordinates, angles_matrix, regions)
@@ -1575,7 +1574,7 @@ def shear_number(inpdb_file, show_path = False):
print('........Error: Was not able to find or build any path')
return None
- os.system('rm {}'.format(pdb_file))
+ # os.system('rm {}'.format(pdb_file))
return shear
--
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