problems with json ssbond

[django_unres.git] / django_simple / todo / views.py

diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py
index 90d05e2..4ffb0e7 100644 (file)
--- a/django_simple/todo/views.py
+++ b/django_simple/todo/views.py
@@ -6,6 +6,7 @@ from .models import Task
 import datetime
 import os
 import subprocess
+import json
 
 res_codes = [
                 # 20 canonical amino acids
@@ -34,18 +35,45 @@ def seq_add_x(sequence):
 def from_pdb(file):
     sequence = []
     ssbond = []
+    ssbond_ch = []
+    ires = []
+    chain_start = {}
+    chain_end = {}
+    unres_shift = {}
+    chain=[]
+    ichain=0
+    newchain = True
+    
     for line in file:
+            if line[0:6] == 'COMPND' and line[11:17] == 'CHAIN:':
+              tmp=line[18:]
+              chain_=tmp.split(', ')
+              chain_[-1]=chain_[-1][0]
+              chain.extend(chain_)
+    
             if line[0:6] == 'ATOM  ' and line[13:15] == 'CA':
               aa = three_to_one.get(line[17:20])
-              sequence.append(aa)
+              i = int(line[22:26])
+              if newchain or i!=ires[-1]:
+                sequence.append(aa)
+                ires.append(i)
+                if newchain:
+                 chain_start[chain[ichain]]=i
+                 newchain = False
             if line[0:3] == 'TER':
               sequence.append('XX')
+              chain_end[chain[ichain]]=i
+              ichain=ichain+1
+              newchain = True
             if line[0:6] == 'SSBOND':
               b=[]
               b.append(int(line[17:21]))
               b.append(int(line[31:35]))
               ssbond.append(b)
-                                                                                    
+              c = []
+              c.append((line[15:16]))
+              c.append((line[29:30]))
+              ssbond_ch.append(c)                                                                      
             if line[0:3] == 'END':
               break
     while sequence[-1] == 'XX':
@@ -56,7 +84,15 @@ def from_pdb(file):
     if sequence[-1] != 'G':
             sequence.append('X')
     seq=''.join(sequence)
-    return seq,ssbond
+#    if ires[0] != 1:
+#            ssbond=[ [e[0]-ires[0]+1,e[1]-ires[0]+1] for e in ssbond]
+    i=0
+    for c in chain:
+      unres_shift[c]=i+chain_start[c]
+      i=i-(chain_end[c]-chain_start[c])-3
+    ssbond=[ [e[0]-unres_shift[c[0]]+1,e[1]-unres_shift[c[1]]+1] for e,c in zip(ssbond,ssbond_ch)]     
+
+    return seq,json.dumps(ssbond)
 
 
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