X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fjobfiles.py;h=61d2c45b4347c8bbb984e4ac87fa5c532eb60c24;hb=5a52e318fbba09f787c91fadc8d364d16c2d452d;hp=be88312d735de04d824c0d22338c920fb6d22c38;hpb=ae2ca9f762ec4db6c91066465f347fc3678cddae;p=django_unres.git

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index be88312..61d2c45 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!='':
@@ -43,20 +84,18 @@ 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"""
      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 +105,10 @@ 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:
@@ -89,7 +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
@@ -97,11 +139,15 @@ 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 '
             
-          type_line = 'reset_vel=0'\
+          type_line = 'restart reset_vel=0'\
              +' t_bath='+str(instance.md_temp)\
              +' nstep='+str(instance.md_nstep)\
              +' ntwe='+str(instance.md_ntwe)\
@@ -118,14 +164,30 @@ 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=20 '             
+           
           if instance.md_pdbref:
              control_line = control_line+'pdbref '
-           
+          
+          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 = 'restart reset_vel='+ str(instance.remd_nstex)\
              +' nstep='+str(instance.md_nstep)\
              +' ntwe='+str(instance.md_ntwe)\
              +' ntwx='+str(instance.md_ntwx)\
@@ -162,10 +224,14 @@ CUTOFF=7.00000 WCORR4=0.00000
        f.write(word_list[-1]+'\n')
           
        if instance.md_start == 'pdbstart':
+        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 +250,30 @@ 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('model01.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:
+            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(10,21):
+           f.write('model'+str(i)+'.pdb\n')
 
        if instance.type == 'md' and instance.md_start != 'pdbstart':
 
@@ -201,7 +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.type == 'remd' and instance.md_start != 'pdbstart':
 
@@ -210,14 +296,24 @@ 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')
+             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','.')
       else:
         shutil.copy('../files/pbs_new.csh','pbs.csh')
@@ -225,19 +321,20 @@ 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') 
       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)      
@@ -255,19 +352,22 @@ CUTOFF=7.00000 WCORR4=0.00000
         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
         
       tmp_ss=''
-      ix=0
-      if seq[0]=='X':
-       ix=1
       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)
-           l.append(e[1]-ix)
+           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':
+      if  instance.unres_ff =='FF2':
         f1 = open('../files/pbs8.csh', 'r')
       else:
         f1 = open('../files/pbs8_new.csh', 'r')
@@ -277,11 +377,21 @@ 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 $PBS_O_WORKDIR' in line and instance.type == 'dock':
+            f2.write(line)
+            f2.write('../files/generator_v7 plik.pdb plik2.pdb\n')
           else:
            tmp1=json.loads(instance.remd_multi_t)
            f2.write(line.replace('$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
@@ -290,21 +400,60 @@ CUTOFF=7.00000 WCORR4=0.00000
               isampl=1
           else:
               isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
-
+          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=20')+'&\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)
+          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(10,21):
+              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)
@@ -322,13 +471,34 @@ CUTOFF=7.00000 WCORR4=0.00000
            
       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))+'&\n')
+          if instance.md_2d != '':
+               f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
+          if instance.type == 'dock':
+               f.write('{:79}'.format(' CONSTR_HOMOL=20')+'&\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.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(10,21):
+              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') 
       
       os.chdir(instance.jobdirname)  
       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)