restart for md and remd

[django_unres.git] / django_simple / todo / jobfiles.py

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index 9284dd3..61d2c45 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -147,7 +147,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           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)\
@@ -164,12 +164,15 @@ 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='+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 '
@@ -184,7 +187,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
              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)\
@@ -221,14 +224,14 @@ CUTOFF=7.00000 WCORR4=0.00000"""
        f.write(word_list[-1]+'\n')
           
        if instance.md_start == 'pdbstart':
-        if instance.type == 'remd' :
+        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')
@@ -254,12 +257,23 @@ CUTOFF=7.00000 WCORR4=0.00000"""
 
 
        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))
           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':
 
@@ -363,11 +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
@@ -376,15 +400,17 @@ 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('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
+            f.write('{:79}'.format('SEED='+str(instance.md_seed)+
                ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n')
           else:    
-            f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
+            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')
                  
@@ -394,6 +420,14 @@ CUTOFF=7.00000 WCORR4=0.00000"""
 
           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)))
 
@@ -442,12 +476,21 @@ CUTOFF=7.00000 WCORR4=0.00000"""
              +' 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 != '':