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 ce0cf44..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'
 
 
@@ -126,7 +128,7 @@ CUTOFF=7.00000 WCORR4=0.00000
           type_line = 'reset_vel='+ str(instance.remd_nstex)\
              +' nstep='+str(instance.md_nstep)\
              +' ntwe='+str(instance.md_ntwe)\
-             +' ntwx='+str(instance.remd_nstex)\
+             +' ntwx='+str(instance.md_ntwx)\
              +' dt='+str(instance.md_dt)
           if instance.md_lang == 'langevin':
             type_line = type_line + ' lang=1 '
@@ -142,7 +144,7 @@ CUTOFF=7.00000 WCORR4=0.00000
           type_line2 = 'nrep='+str(instance.remd_nrep) \
              +' nstex='+str(instance.remd_nstex) \
              +' tlist mlist sync nsyn='+str(instance.remd_nstex)\
-             +' traj1file  rest1file '
+             +' traj1file  rest1file TRAJCACHE=200'
 
        if instance.md_start == 'pdbstart':
              type_line = type_line + ' preminim cart'
@@ -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)))
@@ -270,10 +289,10 @@ CUTOFF=7.00000 WCORR4=0.00000
 
 # write wham & cluster input
       with open(instance.jobdirname+'/file_wham.inp','w') as f:
-          if instance.md_nstep/instance.remd_nstex*nreplicas<=8000:
+          if instance.md_nstep/instance.md_ntwx*nreplicas<=8000:
               isampl=1
           else:
-              isampl=int(instance.md_nstep/instance.remd_nstex*nreplicas/8000)
+              isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
 
           if instance.md_pdbref:
             f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
@@ -295,7 +314,7 @@ CUTOFF=7.00000 WCORR4=0.00000
           for element in tmp1:
               f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n')
               f.write('kh= 0.0 Q0=0.0\n')
-          rec=instance.md_nstep/instance.remd_nstex
+          rec=instance.md_nstep/instance.md_ntwx
           f.write('nfile_cx=1 rec_start='+str(rec/10)
                   +' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n')
           f.write('file_MD000\n')