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ssbond with 1st res <> 1
author
Cezary Czaplewski
<czarek@chem.univ.gda.pl>
Thu, 7 Sep 2017 15:35:43 +0000
(17:35 +0200)
committer
Cezary Czaplewski
<czarek@chem.univ.gda.pl>
Thu, 7 Sep 2017 15:35:43 +0000
(17:35 +0200)
django_simple/todo/views.py
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diff --git
a/django_simple/todo/views.py
b/django_simple/todo/views.py
index
90d05e2
..
37f4dd1
100644
(file)
--- a/
django_simple/todo/views.py
+++ b/
django_simple/todo/views.py
@@
-34,10
+34,13
@@
def seq_add_x(sequence):
def from_pdb(file):
sequence = []
ssbond = []
+ ires = []
for line in file:
if line[0:6] == 'ATOM ' and line[13:15] == 'CA':
aa = three_to_one.get(line[17:20])
sequence.append(aa)
+ i = int(line[24:26])
+ ires.append(i)
if line[0:3] == 'TER':
sequence.append('XX')
if line[0:6] == 'SSBOND':
@@
-56,6
+59,9
@@
def from_pdb(file):
if sequence[-1] != 'G':
sequence.append('X')
seq=''.join(sequence)
+ if ires[0] != 1:
+ ssbond=[ [e[0]-ires[0]+1,e[1]-ires[0]+1] for e in ssbond]
+
return seq,ssbond