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 c3484fa..a569298 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -14,16 +14,18 @@ logging.basicConfig()
 logger = logging.getLogger(__name__)
 
 def write_ssbond(ssbond):
-     list=[]
+   list=[]
+   if ssbond!='':
+     ssbond=json.loads(ssbond)
      for e in ssbond:
            list.append(e[0])
            list.append(e[1])
      list_sorted=sorted(list)
      
-     if len(list)>0:
+   if len(list)>0:
        return str(len(list))+' '+' '.join(map(str,list_sorted))+'\n'+\
             str(len(ssbond))+' '+' '.join(map(str,list))+'\n'
-     else: 
+   else: 
        return '0\n'
 
 
@@ -251,6 +253,21 @@ CUTOFF=7.00000 WCORR4=0.00000
         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4'
       else:
         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
+        
+      tmp_ss=''
+      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[e[0]])
+           l.append(e[1]-ix[e[1]])
+        tmp_ss=' '.join(map(str,l))
 
       os.chdir(instance.jobdirname)
       if  instance.unres_ff =='E0LL2Y':
@@ -261,6 +278,8 @@ CUTOFF=7.00000 WCORR4=0.00000
       for line in f1:
           if '#PBS -l nodes=4:ppn=4' in line:
            f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
+          elif '$ssbond' in line:
+           f2.write(line.replace('$ssbond',tmp_ss))
           else:
            tmp1=json.loads(instance.remd_multi_t)
            f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))