X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fjobfiles.py;h=c6ab414b64d00a0bc74e367779af00905e3422ae;hb=1b9e4cd5192fafe2213b582fadd19556fb2ecf3a;hp=a569298178995ed94b96e93d0f4127a1f93665a5;hpb=e7ce5a8738d19336986d61d52a8080fe7cb3eefb;p=django_unres.git

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index a569298..c6ab414 100644
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -13,6 +13,47 @@ import textwrap
 logging.basicConfig()
 logger = logging.getLogger(__name__)
 
+def seq_2d_xx(line,seq):
+   line=line.replace(" ","")
+   lista=list(line)
+   for ii in range(0,len(line)):
+    if seq[ii]=='X':
+      if ii>0:
+            lista[ii-1]='-'
+      if ii+1<len(line):
+            lista[ii+1]='-'
+   return("".join(lista)) 
+
+def seq_2d_write(line):
+   line=line.replace(" ", "")
+   out='{:d}\n{:6.1f}\n'.format(len(line),50.0)
+   for i in range(1,4):
+     out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
+   for ii in range(1,len(line)-2):
+     i+=1
+     if line[ii:ii+2]=='HH':
+       out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0)
+     elif line[ii:ii+2]=='EE':
+       out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0)
+     else:
+       out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
+   return(out)
+
+def seq_2d_write_50(line):
+   line=line.replace(" ", "")
+   out='{:d}\n'.format(len(line))
+   for i in range(1,4):
+     out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
+   for ii in range(1,len(line)-2):
+     i+=1
+     if line[ii:ii+2]=='HH':
+       out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0,50.0)
+     elif line[ii:ii+2]=='EE':
+       out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0,50.0)
+     else:
+       out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)     
+   return(out)
+
 def write_ssbond(ssbond):
    list=[]
    if ssbond!='':
@@ -31,7 +72,7 @@ def write_ssbond(ssbond):
 
 @receiver(post_save, sender=Task)
 def write_on_task_save(sender, instance, **kwargs):
-   if instance.ready and not instance.done and instance.running==0:
+   if instance.ready and not instance.done and instance.running==0 and instance.pbsjob=='':
      if (not os.path.isdir(instance.jobdirname)):
         os.mkdir(instance.jobdirname)
 #     os.chdir(instance.jobdirname)
@@ -43,20 +84,24 @@ def write_on_task_save(sender, instance, **kwargs):
 #wrapper = textwrap.TextWrapper(width=70)
 #word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep)))
 
-     if  instance.unres_ff =='E0LL2Y':
+     if  instance.unres_ff =='FF2':
       w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954              &
 WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000        &
 WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000    &
 WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.25                                        &
-CUTOFF=7.00000 WCORR4=0.00000
-"""
+CUTOFF=7.00000 WCORR4=0.00000"""
+     elif  instance.unres_ff =='NEWCT-9P':
+      w="""WSC=0.81230 WSCP=1.20420 WELEC=0.87690 WBOND=1.00000 WANG=1.97730              &
+WSCLOC=0.063657 WTOR=1.41540 WTORD=0.00000 WCORRH=0.00000 WCORR5=0.00000       &
+WCORR6=0.00000 WEL_LOC=0.036638 WTURN3=1.45110 WTURN4=0.00000 WTURN6=0.00000   &
+WSCCOR=0.00000 WVDWPP=0.33393 WHPB=1.00000 WSCP14=0.00000                      &
+CUTOFF=7.00000 WCORR4=0.00000"""
      else:
       w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542              &
 WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000        &
 WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000    &
 WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000                      &
-CUTOFF=7.00000 WCORR4=0.00000
-"""
+CUTOFF=7.00000 WCORR4=0.00000"""
      
 
      with open(instance.jobdirname+'/file.inp','w') as f:
@@ -66,7 +111,10 @@ CUTOFF=7.00000 WCORR4=0.00000
 
           control_line = 'SEED='+str(instance.md_seed)+' ' \
              + instance.min_choice \
-             + ' pdbstart pdbref BOXX=1000. BOXY=1000. BOXZ=1000. '
+             + ' pdbstart pdbref ' \
+             + ' BOXX='+str(instance.boxx) \
+             + ' BOXY='+str(instance.boxy) \
+             + ' BOXZ='+str(instance.boxz) +' '
           if not instance.min_overlap:
             control_line = control_line+'overlap '
           if not instance.min_searchsc:
@@ -75,6 +123,8 @@ CUTOFF=7.00000 WCORR4=0.00000
             control_line = control_line+'pdbout '
           if instance.min_unres_pdb:
             control_line = control_line+'unres_pdb '
+          if instance.unres_ff =='NEWCT-9P':
+            control_line = control_line+'tormode=2 '
             
           type_line = 'print_min_ini print_min_res print_min_stat'\
             +' MAXMIN='+str(instance.min_maxmin)\
@@ -89,7 +139,7 @@ CUTOFF=7.00000 WCORR4=0.00000
           if seq[-1]=='X':
             dimen3-=1
   
-       nogly ='CDSQKIPTFNHLRWAVEYM'
+       nogly ='CDSQKIPTFNHLRWAVEYMcdsqkiptfnhlrwaveym'
        seq2 = ''.join([c for c in seq if c in nogly])
   
        dimen3=(dimen3+len(seq2))*3
@@ -97,11 +147,22 @@ CUTOFF=7.00000 WCORR4=0.00000
             
        if instance.type == 'md' :
           control_line = 'SEED='+str(instance.md_seed)+' '\
-           +instance.md_start +' md one_letter BOXX=1000. BOXY=1000. BOXZ=1000. '
+           +instance.md_start +' md one_letter'\
+           + ' BOXX='+str(instance.boxx) \
+           + ' BOXY='+str(instance.boxy) \
+           + ' BOXZ='+str(instance.boxz) +' '
+
           if instance.md_pdbref:
              control_line = control_line+'pdbref '
+             
+#---v
+          if instance.use_nmr:
+            control_line = control_line+' constr_dist=12 '
+#---^
+          if instance.unres_ff =='NEWCT-9P':
+            control_line = control_line+'tormode=2 cart'
             
-          type_line = 'reset_vel=0'\
+          type_line = '        reset_vel=0'\
              +' t_bath='+str(instance.md_temp)\
              +' nstep='+str(instance.md_nstep)\
              +' ntwe='+str(instance.md_ntwe)\
@@ -118,14 +179,37 @@ CUTOFF=7.00000 WCORR4=0.00000
           if instance.md_mdpdb:
             type_line = type_line + ' mdpdb '
 
-       if instance.type == 'remd' :
+       if instance.type == 'remd' or instance.type == 'dock':
           control_line = 'SEED='+str(instance.md_seed)+' '\
-           +instance.md_start +' re one_letter BOXX=1000. BOXY=1000. BOXZ=1000. '
+           +instance.md_start +' re one_letter'\
+           + ' BOXX='+str(instance.boxx) \
+           + ' BOXY='+str(instance.boxy) \
+           + ' BOXZ='+str(instance.boxz) +' '
+          
+          if instance.type == 'dock':
+             control_line = control_line+'CONSTR_HOMOL=24 '             
+           
           if instance.md_pdbref:
              control_line = control_line+'pdbref '
-           
+             
+          if instance.unres_ff =='NEWCT-9P':
+            control_line = control_line+'tormode=2 cart'
+#---v
+	  if instance.use_nmr:
+	    control_line = control_line+' constr_dist=12 '
+#---^
+          
+          cntrl_saxs=''
+          if instance.saxs_data != '':
+             lines=instance.saxs_data.split('\n')
+             nsaxs=0
+             for line in lines:
+              if len(line.split())==2:
+               nsaxs+=1 
+             cntrl_saxs=' nsaxs='+str(nsaxs)+' scal_rad='+str(instance.scal_rad) 
+             control_line += cntrl_saxs             
             
-          type_line = 'reset_vel='+ str(instance.remd_nstex)\
+          type_line = '        reset_vel='+ str(instance.remd_nstex)\
              +' nstep='+str(instance.md_nstep)\
              +' ntwe='+str(instance.md_ntwe)\
              +' ntwx='+str(instance.md_ntwx)\
@@ -138,8 +222,8 @@ CUTOFF=7.00000 WCORR4=0.00000
             type_line = type_line + 'tau_bath='+str(instance.md_tau)
           if instance.md_respa:
             type_line = type_line + ' respa '
-          if instance.md_mdpdb:
-            type_line = type_line + ' mdpdb '
+#          if instance.md_mdpdb:
+#            type_line = type_line + ' mdpdb '
           
           type_line2 = 'nrep='+str(instance.remd_nrep) \
              +' nstex='+str(instance.remd_nstex) \
@@ -161,11 +245,15 @@ CUTOFF=7.00000 WCORR4=0.00000
            f.write('{:79}'.format(element)+'&\n')
        f.write(word_list[-1]+'\n')
           
-       if instance.md_start == 'pdbstart':
+       if instance.md_start == 'pdbstart' and instance.unres_ff !='NEWCT-9P':
+        if instance.type == 'remd' or instance.type == 'dock':
+         f.write('print_min_ini print_min_res print_min_stat maxfun='+
+           str(instance.min_maxfun)+'\n')
+        else:
          f.write('print_min_ini print_min_res print_min_stat\n')
 
        
-       if instance.type == 'remd' :
+       if instance.type == 'remd' or instance.type == 'dock':
           word_list = wrapper.wrap(text=type_line2)
           for element in word_list[:-1]:
               f.write('{:79}'.format(element)+'&\n')
@@ -184,15 +272,33 @@ CUTOFF=7.00000 WCORR4=0.00000
           for element in word_list[:-1]:
               f.write('{:79}'.format(element)+'&\n')
           f.write(word_list[-1]+'\n')
-
-       f.write(w)
+       
+       if instance.saxs_data != '':
+         w+=' wsaxs='+str(instance.wsaxs)
+       f.write(w+'\n')
 
 
        if instance.type == 'min' or instance.md_start == 'pdbstart':
-          f.write('plik.pdb\n')
+          if instance.type == 'dock':
+            f.write('plik1ter.pdb\n')
+          else:  
+            f.write('plik.pdb\n')
           f.write(write_ssbond(instance.ssbond))
-          f.write('0\n')
-
+          if instance.md_2d == '':
+            f.write('0\n')
+          else:
+           if instance.unres_ff =='NEWCT-9P':
+            f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
+           else:
+            f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
+        
+       if instance.type == 'dock':
+          f.write('HOMOL_DIST=0.1    HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0  &\n')
+          f.write('READ2SIGMA START_FROM_MODELS\n')
+          for i in range(1,10):
+           f.write('model0'+str(i)+'.pdb\n')
+          for i in range(10,25):
+           f.write('model'+str(i)+'.pdb\n')
 
        if instance.type == 'md' and instance.md_start != 'pdbstart':
 
@@ -201,7 +307,31 @@ CUTOFF=7.00000 WCORR4=0.00000
           f.write(str(len(seq))+'\n')
           for i in range(0,len(seq),80):
              f.write(seq[i:i+80]+'\n')
-          f.write('0\n0\n')
+          f.write('0\n')
+          if instance.md_2d == '':
+            f.write('0\n')
+          else:
+           if instance.unres_ff =='NEWCT-9P':
+            f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
+           else:
+            f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
+#---v
+          if instance.use_nmr:
+            f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
+            f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
+            f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
+            if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
+              fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
+              for linmr in fnmr:
+                   f.write(linmr)
+              fnmr.close()
+            else:
+              fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
+              for linmr in fnmr:
+                  f.write(linmr)
+              fnmr.close()
+#---^
+
 
        if instance.type == 'remd' and instance.md_start != 'pdbstart':
 
@@ -210,34 +340,68 @@ CUTOFF=7.00000 WCORR4=0.00000
           f.write(str(len(seq))+'\n')
           for i in range(0,len(seq),80):
              f.write(seq[i:i+80]+'\n')
-          f.write('0\n0\n')
-
-
+          f.write('0\n')
+          if instance.md_2d == '':
+            f.write('0\n')
+          else:
+           if instance.unres_ff =='NEWCT-9P':
+            f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
+           else:
+            f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
+#---v
+          if instance.use_nmr:
+            f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
+            f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
+            f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
+            if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
+              fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
+              for linmr in fnmr:
+                   f.write(linmr)
+              fnmr.close()
+            else:
+              fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
+              for linmr in fnmr:
+                   f.write(linmr)
+              fnmr.close()
+#---^
+
+
+       if instance.saxs_data != '':
+             lines=instance.saxs_data.split('\n')
+             for line in lines:
+              tmp=line.split()
+              if len(tmp)==2:
+               f.write(tmp[0]+' '+tmp[1]+'\n') 
        
         
      if instance.type == 'min':
       os.chdir(instance.jobdirname)
-      if  instance.unres_ff =='E0LL2Y':
+      if  instance.unres_ff =='FF2':
         shutil.copy('../files/pbs.csh','.')
+      elif instance.unres_ff =='NEWCT-9P':
+        shutil.copy('../files/pbs_newct-9p.csh','pbs.csh')
       else:
         shutil.copy('../files/pbs_new.csh','pbs.csh')
       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
       os.chdir('..')
      elif instance.type == 'md':
       os.chdir(instance.jobdirname)
-      if  instance.unres_ff =='E0LL2Y':
+      if  instance.unres_ff =='FF2':
         f1 = open('../files/pbs_md.csh', 'r')
+      elif instance.unres_ff =='NEWCT-9P':
+        f1 = open('../files/pbs_md_newct-9p.csh', 'r')
       else:
         f1 = open('../files/pbs_md_new.csh', 'r') 
       f2 = open('pbs.csh', 'w')
       for line in f1:
-           f2.write(line.replace('$dimen3',str(dimen3) ))
+           f2.write(line.replace('$dimen3',str(dimen3)+' '+str(instance.md_temp) ))
       f1.close()
       f2.close()  
 
       f1 = open('file.seq', 'w')
       for i in range(0,len(seq),80):
              f1.write(seq[i:i+80]+'\n')
+      f1.write('\n')       
       f1.close()
 
       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)      
@@ -270,8 +434,10 @@ CUTOFF=7.00000 WCORR4=0.00000
         tmp_ss=' '.join(map(str,l))
 
       os.chdir(instance.jobdirname)
-      if  instance.unres_ff =='E0LL2Y':
+      if  instance.unres_ff =='FF2':
         f1 = open('../files/pbs8.csh', 'r')
+      elif instance.unres_ff =='NEWCT-9P':
+        f1 = open('../files/pbs8_newct-9p.csh', 'r')
       else:
         f1 = open('../files/pbs8_new.csh', 'r')
       f2 = open('pbs8.csh', 'w')
@@ -280,11 +446,38 @@ CUTOFF=7.00000 WCORR4=0.00000
            f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
           elif '$ssbond' in line:
            f2.write(line.replace('$ssbond',tmp_ss))
+          elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock':
+            f2.write(line)
+            if instance.md_seq2 !='':
+             f2.write("""setenv FGPROCS 2
+setenv POT GB
+setenv PREFIX file2
+setenv OUT1FILE YES
+/users2/local/mpich2-1.4.1p1_intel/bin/mpirun -machinefile $PBS_NODEFILE -np 2 $UNRES_BIN
+/users2/local/pulchra306/pulchra -q -g file2_MD000.pdb
+cat file2_MD000.rebuilt.pdb |grep -v TER |grep -v END > tmp_plik2.pdb
+/users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp_plik2.pdb > act.rebuilt.pdb
+/users2/local/scwrl4/Scwrl4 -h -i act.rebuilt.pdb -o plik2.pdb
+rm tmp_plik2.pdb act.rebuilt.pdb\n""")
+            if instance.dock_peptide:
+             f2.write('../files/generator_v13 plik.pdb plik2.pdb 1 \n')
+            else:
+             f2.write('../files/generator_v13 plik.pdb plik2.pdb 0 \n')
+            f2.write("sed '/END/q' plik.pdb |grep ATOM > plik1ter.pdb \n")
+            f2.write("echo TER >>  plik1ter.pdb \n")
+            f2.write("sed '/END/q' plik2.pdb |grep ATOM >> plik1ter.pdb \n")            
           else:
            tmp1=json.loads(instance.remd_multi_t)
            f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
       f1.close()
       f2.close()
+
+      f1 = open('file.seq', 'w')
+      for i in range(0,len(seq),80):
+             f1.write(seq[i:i+80]+'\n')
+      f1.write('\n')       
+      f1.close()
+      
       os.chdir('..')  
 
 # write wham & cluster input
@@ -293,21 +486,83 @@ CUTOFF=7.00000 WCORR4=0.00000
               isampl=1
           else:
               isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
-
+#---v
+          if instance.use_nmr:
+               f.write('{:79}'.format('with_dist_constr constr_dist=12')+'&\n')
+#---^
+          f.write('{:79}'.format(' isampl='+str(isampl))+'&\n')
           if instance.md_pdbref:
-            f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
-               ' einicheck=1 rescale=2 delta=0.02 cxfile classify\n')
+            f.write('{:79}'.format('SEED='+str(instance.md_seed)+
+               ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n')
           else:    
-            f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
-              ' einicheck=1 rescale=2 delta=0.02 cxfile\n')
+            f.write('{:79}'.format('SEED='+str(instance.md_seed)+
+              ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n')
+          if instance.md_2d != '':
+               f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
+          if instance.type == 'dock':
+               f.write('{:79}'.format(' n_ene=19 CONSTR_HOMOL=24')+'&\n')
+          if instance.unres_ff =='NEWCT-9P':
+               f.write('{:79}'.format('tormode=2 ')+'&\n')
+          f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
+                    ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
+                 
           f.write('nres='+str(len(seq))+' one_letter\n')
           for i in range(0,len(seq),80):
              f.write(seq[i:i+80]+'\n')
 
           f.write(write_ssbond(instance.ssbond))
 
-
-          f.write(w)
+#---v
+          if instance.use_nmr:
+            f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
+            f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
+            f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
+            if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
+              fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
+              for linmr in fnmr:
+                   f.write(linmr)
+              fnmr.close()
+            else:
+              fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
+              for linmr in fnmr:
+                   f.write(linmr)
+              fnmr.close()
+#---^
+
+          if instance.type == 'dock':
+            f.write('HOMOL_DIST=0.1    HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0  &\n')
+            f.write('READ2SIGMA \n')
+            for i in range(1,10):
+              f.write('model0'+str(i)+'.pdb\n')
+            for i in range(10,25):
+              f.write('model'+str(i)+'.pdb\n')
+
+          if instance.md_2d != '':
+             f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
+
+          if instance.saxs_data != '':
+             saxs_r=[]
+             saxs_P=[]
+             saxs_norm=0
+             r_last=None
+             fsaxs = open(instance.jobdirname+'/saxs.data', 'w')
+             lines=instance.saxs_data.split('\n')
+             for line in lines:
+              tmp=line.split()
+              if len(tmp)==2:
+               f.write(tmp[0]+' '+tmp[1]+'\n')
+               saxs_r.append(tmp[0])
+               saxs_P.append(float(tmp[1]))
+               if r_last==None:
+                  r_last=float(tmp[0])
+               else:
+                  saxs_norm += float(tmp[1])*(float(tmp[0])-r_last)
+                  r_last=float(tmp[0])
+             for r,p in zip(saxs_r,saxs_P):
+               fsaxs.write('{} {}\n'.format(r,p/saxs_norm)) 
+             fsaxs.close()
+
+          f.write(w+'\n')
           f.write('\n')
           f.write('nt='+str(instance.remd_nrep)+' replica read_iset\n')
           tmp1=json.loads(instance.remd_multi_t)
@@ -320,30 +575,131 @@ CUTOFF=7.00000 WCORR4=0.00000
           f.write('file_MD000\n')
           if instance.md_pdbref:
              f.write('pdbref\n')
-             f.write('plik.pdb\n')
+             if instance.type == 'dock':
+              f.write('plik1ter.pdb\n')
+             else:
+              f.write('plik.pdb\n')
 
            
       with open(instance.jobdirname+'/file_cluster.inp','w') as f:
           f.write(instance.name + ' UNRES server job'+ '\n')
-          f.write('nres='+str(len(seq))
+          f.write('{:79}'.format('nres='+str(len(seq))
              +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
-             +' temper='+str(instance.remd_cluter_temp)+'\n')
-          f.write(w)
+             +' temper='+str(instance.remd_cluter_temp)
+             +' nclust='+str(instance.remd_cluster_n))+'&\n')
+          if instance.md_2d != '':
+               f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
+#---v
+	  if instance.use_nmr:
+            f.write('{:79}'.format('constr_dist=12 ')+'&\n')
+#---^
+          if instance.type == 'dock':
+               f.write('{:79}'.format(' CONSTR_HOMOL=24')+'&\n')
+          if instance.unres_ff =='NEWCT-9P':
+               f.write('{:79}'.format('tormode=2 ')+'&\n')
+          f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
+                  ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
+          f.write(w+'\n')
           for i in range(0,len(seq),80):
              f.write(seq[i:i+80]+'\n')
           f.write(write_ssbond(instance.ssbond))
+
+#---v
+          if instance.use_nmr:
+            f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
+            f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
+            f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
+            if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
+              fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
+              for linmr in fnmr:
+                   f.write(linmr)
+              fnmr.close()
+            else:
+              fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
+              for linmr in fnmr:
+                   f.write(linmr)
+              fnmr.close()
+#---^
+
+          if instance.type == 'dock':
+            f.write('HOMOL_DIST=0.1    HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0  &\n')
+            f.write('READ2SIGMA \n')
+            for i in range(1,10):
+              f.write('model0'+str(i)+'.pdb\n')
+            for i in range(10,25):
+              f.write('model'+str(i)+'.pdb\n')
+          if instance.md_2d != '':
+             f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
+          if instance.saxs_data != '':
+             lines=instance.saxs_data.split('\n')
+             for line in lines:
+              tmp=line.split()
+              if len(tmp)==2:
+               f.write(tmp[0]+' '+tmp[1]+'\n') 
+      
+      if instance.type == 'dock' and instance.md_seq2 != '':
+         with open(instance.jobdirname+'/file2.inp','w') as f:
+           f.write(instance.name + ' chain2 random start'+ '\n')
+           control_line = 'SEED='+str(instance.md_seed)+' '\
+            +'rand_conf md one_letter'\
+            + ' BOXX=1000 BOXY=1000 BOXZ=1000 '
+           
+           if instance.unres_ff =='NEWCT-9P':
+             control_line = control_line+'tormode=2 cart'
+           
+           type_line = '        reset_vel=0'\
+             +' t_bath=300'\
+             +' nstep=100000'\
+             +' ntwe=10000'\
+             +' ntwx=100000'\
+             +' dt=0.2 lang=1 scal_fric=0.02 respa mdpdb '
+
+           wrapper = textwrap.TextWrapper(width=70)
+           word_list = wrapper.wrap(text=control_line)
+           for element in word_list[:-1]:
+             f.write('{:79}'.format(element)+'&\n')
+           f.write(word_list[-1]+'\n')
+
+           word_list = wrapper.wrap(text=type_line)
+           for element in word_list[:-1]:
+             f.write('{:79}'.format(element)+'&\n')
+           f.write(word_list[-1]+'\n')
+           
+           f.write(w+'\n')
+           
+           seq=instance.md_seq2.replace(" ","")
+           f.write(str(len(seq))+'\n')
+           for i in range(0,len(seq),80):
+             f.write(seq[i:i+80]+'\n')
+           f.write('0\n')
+           f.write('0\n')
+          
       
       os.chdir(instance.jobdirname)  
       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
       os.chdir('..')
+      
+     output = str(ret_code.communicate()[0])
+     output=output.strip()
+     if output=='':
+       output='error'
+     logger.warning("PBS \"%s\" " % output)
+     instance.pbsjob = output
+     instance.save()
      
-     print ret_code.stdout.readlines()
+#     print ret_code.stdout.readlines()
      logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
      
 @receiver(post_delete, sender=Task)
 def delete_on_task_del(sender, instance, **kwargs):     
    if instance.jobdirname:
       if os.path.isdir(instance.jobdirname):
+         if not instance.done:
+           ret_code_qdel = subprocess.Popen(' /opt/torque/bin/qdel '+str(instance.pbsjob), shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+           output = str(ret_code_qdel.communicate()[0])
+           output=output.strip()
+           logger.warning("PBS qdel \"%s\" " % instance.pbsjob)
+           logger.warning("QDEL \"%s\" " % output)
          shutil.rmtree(instance.jobdirname)
          logger.warning("Dir \"%s\" has been rm." % instance.jobdirname)         
-         
\ No newline at end of file
+