pdb without CHAIN working again and plot fluct+bfactor

diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py
index 4ffb0e7..4f3b4e5 100644 (file)
--- a/django_simple/todo/views.py
+++ b/django_simple/todo/views.py
@@ -58,11 +58,13 @@ def from_pdb(file):
                 sequence.append(aa)
                 ires.append(i)
                 if newchain:
-                 chain_start[chain[ichain]]=i
+                 if len(chain)>0:
+                  chain_start[chain[ichain]]=i
                  newchain = False
             if line[0:3] == 'TER':
               sequence.append('XX')
-              chain_end[chain[ichain]]=i
+              if len(chain)>0:
+               chain_end[chain[ichain]]=i
               ichain=ichain+1
               newchain = True
             if line[0:6] == 'SSBOND':

diff --git a/files/fluct_plot.py b/files/fluct_plot.py
index b05ede1..8d6e214 100755 (executable)
--- a/files/fluct_plot.py
+++ b/files/fluct_plot.py
@@ -6,7 +6,7 @@ import matplotlib
 #matplotlib.use('GTK')
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
-
+import os.path
 
 iatom=0
 nmol=0
@@ -48,9 +48,22 @@ for i in range(1,natom+1):
    x.append(i)
    y.append(fluct)
 
+b=[]
+if os.path.exists('plik.pdb'):
+ with open('plik.pdb') as f:
+   for line in f:
+      if line[0:4]=='ATOM' and line[13:15]=='CA':
+#         print line
+         b.append(math.sqrt(float(line[60:66])*3/8/math.pi/math.pi))
+                  
+
+
 plt.xlabel('residue')
 plt.ylabel('fluctuations')
 plt.xlim(0,natom+1)
 plt.plot(x,y,'-')
+if len(b)!=0:
+ plt.plot(x,b,'-',c='red')
+ plt.legend(['fluctuations','sqrt(3*bfactor/8*pi^2)'])
 plt.savefig('fluct_plot.png')
                                
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