X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fjobfiles.py;h=44cf4a4edf944fa8247aceabca307d3f3014696b;hb=765fad7872822bd9ddd0b5538694d8eb04a0a116;hp=fd7fd7ce5a6154bac27e00b2b103cdd51c814a07;hpb=18720bfd2db199afb2ebf034b3206fc07f16c1ad;p=django_unres.git

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index fd7fd7c..44cf4a4 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!='':
@@ -43,7 +84,7 @@ 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    &
@@ -90,7 +131,7 @@ 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
@@ -180,6 +221,10 @@ CUTOFF=7.00000 WCORR4=0.00000"""
        f.write(word_list[-1]+'\n')
           
        if instance.md_start == 'pdbstart':
+        if instance.type == 'remd' :
+         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')
 
        
@@ -211,8 +256,10 @@ CUTOFF=7.00000 WCORR4=0.00000"""
        if instance.type == 'min' or instance.md_start == 'pdbstart':
           f.write('plik.pdb\n')
           f.write(write_ssbond(instance.ssbond))
-          f.write('0\n')
-
+          if instance.md_2d == '':
+            f.write('0\n')
+          else:
+            f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 
        if instance.type == 'md' and instance.md_start != 'pdbstart':
 
@@ -221,7 +268,12 @@ 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:
+            f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
+
 
        if instance.type == 'remd' and instance.md_start != 'pdbstart':
 
@@ -230,7 +282,12 @@ 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:
+            f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
+
 
        if instance.saxs_data != '':
              lines=instance.saxs_data.split('\n')
@@ -242,7 +299,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
         
      if instance.type == 'min':
       os.chdir(instance.jobdirname)
-      if  instance.unres_ff =='E0LL2Y':
+      if  instance.unres_ff =='FF2':
         shutil.copy('../files/pbs.csh','.')
       else:
         shutil.copy('../files/pbs_new.csh','pbs.csh')
@@ -250,7 +307,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
       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')
       else:
         f1 = open('../files/pbs_md_new.csh', 'r') 
@@ -263,6 +320,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
       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)      
@@ -295,7 +353,7 @@ 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')
       else:
         f1 = open('../files/pbs8_new.csh', 'r')
@@ -310,6 +368,13 @@ CUTOFF=7.00000 WCORR4=0.00000"""
            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
@@ -322,27 +387,43 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           if instance.md_pdbref:
             f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
                ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n')
-            f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
-                    ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
           else:    
             f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
               ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n')
-            f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
+          if instance.md_2d != '':
+               f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\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))
 
+          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')
-               fsaxs.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')
@@ -366,12 +447,16 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           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')
+          if instance.md_2d != '':
+               f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\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))
+          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: