multichain refine ssbond

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

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index be88312..a569298 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -255,15 +255,18 @@ CUTOFF=7.00000 WCORR4=0.00000
         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
         
       tmp_ss=''
-      ix=0
-      if seq[0]=='X':
-       ix=1
       if instance.ssbond!='':
+        ix=[]
+        ii=0
+        for i in range(0,len(seq)):
+           if seq[i]=='X':
+              ii=ii+1
+           ix.append(ii)
         l=[]
         ss=json.loads(instance.ssbond)
         for e in ss:
-           l.append(e[0]-ix)
-           l.append(e[1]-ix)
+           l.append(e[0]-ix[e[0]])
+           l.append(e[1]-ix[e[1]])
         tmp_ss=' '.join(map(str,l))
 
       os.chdir(instance.jobdirname)