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docking working version
[django_unres.git] / django_simple / todo / jobfiles.py
diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index 61d2c45..9855b31 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -90,6 +90,12 @@ 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"""
+     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        &
@@ -117,6 +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)\
@@ -146,8 +154,11 @@ CUTOFF=7.00000 WCORR4=0.00000"""
 
           if instance.md_pdbref:
              control_line = control_line+'pdbref '
+             
+          if instance.unres_ff =='NEWCT-9P':
+            control_line = control_line+'tormode=2 cart'
             
-          type_line = 'restart reset_vel=0'\
+          type_line = '        reset_vel=0'\
              +' t_bath='+str(instance.md_temp)\
              +' nstep='+str(instance.md_nstep)\
              +' ntwe='+str(instance.md_ntwe)\
@@ -176,6 +187,9 @@ CUTOFF=7.00000 WCORR4=0.00000"""
            
           if instance.md_pdbref:
              control_line = control_line+'pdbref '
+             
+          if instance.unres_ff =='NEWCT-9P':
+            control_line = control_line+'tormode=2 cart'
           
           cntrl_saxs=''
           if instance.saxs_data != '':
@@ -187,7 +201,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
              cntrl_saxs=' nsaxs='+str(nsaxs)+' scal_rad='+str(instance.scal_rad) 
              control_line += cntrl_saxs             
             
-          type_line = 'restart 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)\
@@ -200,8 +214,8 @@ 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) \
@@ -223,7 +237,7 @@ 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')
@@ -258,13 +272,16 @@ CUTOFF=7.00000 WCORR4=0.00000"""
 
        if instance.type == 'min' or instance.md_start == 'pdbstart':
           if instance.type == 'dock':
-            f.write('model01.pdb\n')
+            f.write('plik1ter.pdb\n')
           else:  
             f.write('plik.pdb\n')
           f.write(write_ssbond(instance.ssbond))
           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':
@@ -286,6 +303,9 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           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)))
 
 
@@ -300,6 +320,9 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           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)))
 
 
@@ -315,6 +338,8 @@ CUTOFF=7.00000 WCORR4=0.00000"""
       os.chdir(instance.jobdirname)
       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)
@@ -323,6 +348,8 @@ CUTOFF=7.00000 WCORR4=0.00000"""
       os.chdir(instance.jobdirname)
       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')
@@ -369,6 +396,8 @@ CUTOFF=7.00000 WCORR4=0.00000"""
       os.chdir(instance.jobdirname)
       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')
@@ -379,7 +408,10 @@ CUTOFF=7.00000 WCORR4=0.00000"""
            f2.write(line.replace('$ssbond',tmp_ss))
           elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock':
             f2.write(line)
-            f2.write('../files/generator_v7 plik.pdb plik2.pdb\n')
+            f2.write('../files/generator_v12a plik.pdb plik2.pdb 0 \n')
+            f2.write("sed '/END/q' plik.pdb |grep ATOM > plik1ter.pdb \n")
+            f2.write("echo TER >>  plik1ter.pdb \n")
+            f2.write("sed '/END/q' plik2.pdb |grep ATOM >> plik1ter.pdb \n")            
           else:
            tmp1=json.loads(instance.remd_multi_t)
            f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
@@ -411,6 +443,8 @@ CUTOFF=7.00000 WCORR4=0.00000"""
                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
           if instance.type == 'dock':
                f.write('{:79}'.format(' n_ene=19 CONSTR_HOMOL=20')+'&\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')
                  
@@ -466,7 +500,10 @@ 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:
@@ -478,6 +515,8 @@ CUTOFF=7.00000 WCORR4=0.00000"""
                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
           if instance.type == 'dock':
                f.write('{:79}'.format(' CONSTR_HOMOL=20')+'&\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')
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