django_simple/todo/jobfiles.py

   1 import logging
   2
   3 from django.db.models.signals import post_save, post_delete
   4 from django.dispatch import receiver
   5 from .models import Task
   6 import os
   7 import shutil
   8 import subprocess
   9 import json
  10 from string import Template
  11 import textwrap
  12
  13 logging.basicConfig()
  14 logger = logging.getLogger(__name__)
  15
  16 def seq_2d_xx(line,seq):
  17    line=line.replace(" ","")
  18    lista=list(line)
  19    for ii in range(0,len(line)):
  20     if seq[ii]=='X':
  21       if ii>0:
  22             lista[ii-1]='-'
  23       if ii+1<len(line):
  24             lista[ii+1]='-'
  25    return("".join(lista))
  26
  27 def seq_2d_write(line):
  28    line=line.replace(" ", "")
  29    out='{:d}\n{:6.1f}\n'.format(len(line),50.0)
  30    for i in range(1,4):
  31      out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
  32    for ii in range(1,len(line)-2):
  33      i+=1
  34      if line[ii:ii+2]=='HH':
  35        out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0)
  36      elif line[ii:ii+2]=='EE':
  37        out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0)
  38      else:
  39        out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
  40    return(out)
  41
  42 def seq_2d_write_50(line):
  43    line=line.replace(" ", "")
  44    out='{:d}\n'.format(len(line))
  45    for i in range(1,4):
  46      out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
  47    for ii in range(1,len(line)-2):
  48      i+=1
  49      if line[ii:ii+2]=='HH':
  50        out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0,50.0)
  51      elif line[ii:ii+2]=='EE':
  52        out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0,50.0)
  53      else:
  54        out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
  55    return(out)
  56
  57 def write_ssbond(ssbond):
  58    list=[]
  59    if ssbond!='':
  60      ssbond=json.loads(ssbond)
  61      for e in ssbond:
  62            list.append(e[0])
  63            list.append(e[1])
  64      list_sorted=sorted(list)
  65
  66    if len(list)>0:
  67        return str(len(list))+' '+' '.join(map(str,list_sorted))+'\n'+\
  68             str(len(ssbond))+' '+' '.join(map(str,list))+'\n'
  69    else:
  70        return '0\n'
  71
  72
  73 @receiver(post_save, sender=Task)
  74 def write_on_task_save(sender, instance, **kwargs):
  75    if instance.ready and not instance.done and instance.running==0 and instance.pbsjob=='':
  76      if (not os.path.isdir(instance.jobdirname)):
  77         os.mkdir(instance.jobdirname)
  78 #     os.chdir(instance.jobdirname)
  79
  80
  81
  82 #md=Template('nstep=$nstep ntwe=100  ntwx=100   dt=0.20 damax=10.0 lang=1'+
  83 #   't_bath=300 reset_vel=0 respa ntime_split=1 maxtime_split=512 mdpdb')
  84 #wrapper = textwrap.TextWrapper(width=70)
  85 #word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep)))
  86
  87      if  instance.unres_ff =='FF2':
  88       w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954              &
  89 WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000        &
  90 WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000    &
  91 WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.25                                        &
  92 CUTOFF=7.00000 WCORR4=0.00000"""
  93      elif  instance.unres_ff =='NEWCT-9P':
  94       w="""WSC=0.81230 WSCP=1.20420 WELEC=0.87690 WBOND=1.00000 WANG=1.97730              &
  95 WSCLOC=0.063657 WTOR=1.41540 WTORD=0.00000 WCORRH=0.00000 WCORR5=0.00000       &
  96 WCORR6=0.00000 WEL_LOC=0.036638 WTURN3=1.45110 WTURN4=0.00000 WTURN6=0.00000   &
  97 WSCCOR=0.00000 WVDWPP=0.33393 WHPB=1.00000 WSCP14=0.00000                      &
  98 CUTOFF=7.00000 WCORR4=0.00000"""
  99      else:
 100       w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542              &
 101 WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000        &
 102 WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000    &
 103 WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000                      &
 104 CUTOFF=7.00000 WCORR4=0.00000"""
 105
 106
 107      with open(instance.jobdirname+'/file.inp','w') as f:
 108        f.write(instance.name + ' UNRES server job'+ '\n')
 109
 110        if instance.type == 'min' :
 111
 112           control_line = 'SEED='+str(instance.md_seed)+' ' \
 113              + instance.min_choice \
 114              + ' pdbstart pdbref ' \
 115              + ' BOXX='+str(instance.boxx) \
 116              + ' BOXY='+str(instance.boxy) \
 117              + ' BOXZ='+str(instance.boxz) +' '
 118           if not instance.min_overlap:
 119             control_line = control_line+'overlap '
 120           if not instance.min_searchsc:
 121             control_line = control_line+'nosearchsc '
 122           if instance.min_pdbout:
 123             control_line = control_line+'pdbout '
 124           if instance.min_unres_pdb:
 125             control_line = control_line+'unres_pdb '
 126           if instance.unres_ff =='NEWCT-9P':
 127             control_line = control_line+'tormode=2 '
 128
 129           type_line = 'print_min_ini print_min_res print_min_stat'\
 130             +' MAXMIN='+str(instance.min_maxmin)\
 131             +' MAXFUN='+str(instance.min_maxfun)
 132
 133
 134        seq=instance.md_seq.replace(" ","")
 135        dimen3=len(seq)
 136        if dimen3>1:
 137           if seq[0]=='X':
 138             dimen3-=1
 139           if seq[-1]=='X':
 140             dimen3-=1
 141
 142        nogly ='CDSQKIPTFNHLRWAVEYMcdsqkiptfnhlrwaveym'
 143        seq2 = ''.join([c for c in seq if c in nogly])
 144
 145        dimen3=(dimen3+len(seq2))*3
 146
 147
 148        if instance.type == 'md' :
 149           control_line = 'SEED='+str(instance.md_seed)+' '\
 150            +instance.md_start +' md one_letter'\
 151            + ' BOXX='+str(instance.boxx) \
 152            + ' BOXY='+str(instance.boxy) \
 153            + ' BOXZ='+str(instance.boxz) +' '
 154
 155           if instance.md_pdbref:
 156              control_line = control_line+'pdbref '
 157
 158           if instance.unres_ff =='NEWCT-9P':
 159             control_line = control_line+'tormode=2 cart'
 160
 161           type_line = '        reset_vel=0'\
 162              +' t_bath='+str(instance.md_temp)\
 163              +' nstep='+str(instance.md_nstep)\
 164              +' ntwe='+str(instance.md_ntwe)\
 165              +' ntwx='+str(instance.md_ntwx)\
 166              +' dt='+str(instance.md_dt)
 167           if instance.md_lang == 'langevin':
 168             type_line = type_line + ' lang=1 '
 169             type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
 170           if instance.md_lang == 'berendsen':
 171             type_line = type_line + ' lang=0 tbf '
 172             type_line = type_line + 'tau_bath='+str(instance.md_tau)
 173           if instance.md_respa:
 174             type_line = type_line + ' respa '
 175           if instance.md_mdpdb:
 176             type_line = type_line + ' mdpdb '
 177
 178        if instance.type == 'remd' or instance.type == 'dock':
 179           control_line = 'SEED='+str(instance.md_seed)+' '\
 180            +instance.md_start +' re one_letter'\
 181            + ' BOXX='+str(instance.boxx) \
 182            + ' BOXY='+str(instance.boxy) \
 183            + ' BOXZ='+str(instance.boxz) +' '
 184
 185           if instance.type == 'dock':
 186              control_line = control_line+'CONSTR_HOMOL=24 '
 187
 188           if instance.md_pdbref:
 189              control_line = control_line+'pdbref '
 190
 191           if instance.unres_ff =='NEWCT-9P':
 192             control_line = control_line+'tormode=2 cart'
 193
 194           cntrl_saxs=''
 195           if instance.saxs_data != '':
 196              lines=instance.saxs_data.split('\n')
 197              nsaxs=0
 198              for line in lines:
 199               if len(line.split())==2:
 200                nsaxs+=1
 201              cntrl_saxs=' nsaxs='+str(nsaxs)+' scal_rad='+str(instance.scal_rad)
 202              control_line += cntrl_saxs
 203
 204           type_line = '        reset_vel='+ str(instance.remd_nstex)\
 205              +' nstep='+str(instance.md_nstep)\
 206              +' ntwe='+str(instance.md_ntwe)\
 207              +' ntwx='+str(instance.md_ntwx)\
 208              +' dt='+str(instance.md_dt)
 209           if instance.md_lang == 'langevin':
 210             type_line = type_line + ' lang=1 '
 211             type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
 212           if instance.md_lang == 'berendsen':
 213             type_line = type_line + ' lang=0 tbf '
 214             type_line = type_line + 'tau_bath='+str(instance.md_tau)
 215           if instance.md_respa:
 216             type_line = type_line + ' respa '
 217 #          if instance.md_mdpdb:
 218 #            type_line = type_line + ' mdpdb '
 219
 220           type_line2 = 'nrep='+str(instance.remd_nrep) \
 221              +' nstex='+str(instance.remd_nstex) \
 222              +' tlist mlist sync nsyn='+str(instance.remd_nstex)\
 223              +' traj1file  rest1file TRAJCACHE=200'
 224
 225        if instance.md_start == 'pdbstart':
 226              type_line = type_line + ' preminim cart'
 227
 228        wrapper = textwrap.TextWrapper(width=70)
 229
 230        word_list = wrapper.wrap(text=control_line)
 231        for element in word_list[:-1]:
 232            f.write('{:79}'.format(element)+'&\n')
 233        f.write(word_list[-1]+'\n')
 234
 235        word_list = wrapper.wrap(text=type_line)
 236        for element in word_list[:-1]:
 237            f.write('{:79}'.format(element)+'&\n')
 238        f.write(word_list[-1]+'\n')
 239
 240        if instance.md_start == 'pdbstart' and instance.unres_ff !='NEWCT-9P':
 241         if instance.type == 'remd' or instance.type == 'dock':
 242          f.write('print_min_ini print_min_res print_min_stat maxfun='+
 243            str(instance.min_maxfun)+'\n')
 244         else:
 245          f.write('print_min_ini print_min_res print_min_stat\n')
 246
 247
 248        if instance.type == 'remd' or instance.type == 'dock':
 249           word_list = wrapper.wrap(text=type_line2)
 250           for element in word_list[:-1]:
 251               f.write('{:79}'.format(element)+'&\n')
 252           f.write(word_list[-1]+'\n')
 253
 254           tmp1=json.loads(instance.remd_multi_t)
 255           string1=" "
 256           word_list = wrapper.wrap(text=string1.join(tmp1))
 257           for element in word_list[:-1]:
 258               f.write('{:79}'.format(element)+'&\n')
 259           f.write(word_list[-1]+'\n')
 260
 261           tmp1=json.loads(instance.remd_multi_m)
 262           string1=" "
 263           word_list = wrapper.wrap(text=string1.join(tmp1))
 264           for element in word_list[:-1]:
 265               f.write('{:79}'.format(element)+'&\n')
 266           f.write(word_list[-1]+'\n')
 267
 268        if instance.saxs_data != '':
 269          w+=' wsaxs='+str(instance.wsaxs)
 270        f.write(w+'\n')
 271
 272
 273        if instance.type == 'min' or instance.md_start == 'pdbstart':
 274           if instance.type == 'dock':
 275             f.write('plik1ter.pdb\n')
 276           else:
 277             f.write('plik.pdb\n')
 278           f.write(write_ssbond(instance.ssbond))
 279           if instance.md_2d == '':
 280             f.write('0\n')
 281           else:
 282            if instance.unres_ff =='NEWCT-9P':
 283             f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 284            else:
 285             f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 286
 287        if instance.type == 'dock':
 288           f.write('HOMOL_DIST=0.1    HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0  &\n')
 289           f.write('READ2SIGMA START_FROM_MODELS\n')
 290           for i in range(1,10):
 291            f.write('model0'+str(i)+'.pdb\n')
 292           for i in range(10,25):
 293            f.write('model'+str(i)+'.pdb\n')
 294
 295        if instance.type == 'md' and instance.md_start != 'pdbstart':
 296
 297           if instance.md_pdbref:
 298              f.write('plik.pdb\n')
 299           f.write(str(len(seq))+'\n')
 300           for i in range(0,len(seq),80):
 301              f.write(seq[i:i+80]+'\n')
 302           f.write('0\n')
 303           if instance.md_2d == '':
 304             f.write('0\n')
 305           else:
 306            if instance.unres_ff =='NEWCT-9P':
 307             f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 308            else:
 309             f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 310
 311
 312        if instance.type == 'remd' and instance.md_start != 'pdbstart':
 313
 314           if instance.md_pdbref:
 315              f.write('plik.pdb\n')
 316           f.write(str(len(seq))+'\n')
 317           for i in range(0,len(seq),80):
 318              f.write(seq[i:i+80]+'\n')
 319           f.write('0\n')
 320           if instance.md_2d == '':
 321             f.write('0\n')
 322           else:
 323            if instance.unres_ff =='NEWCT-9P':
 324             f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 325            else:
 326             f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 327
 328
 329        if instance.saxs_data != '':
 330              lines=instance.saxs_data.split('\n')
 331              for line in lines:
 332               tmp=line.split()
 333               if len(tmp)==2:
 334                f.write(tmp[0]+' '+tmp[1]+'\n')
 335
 336
 337      if instance.type == 'min':
 338       os.chdir(instance.jobdirname)
 339       if  instance.unres_ff =='FF2':
 340         shutil.copy('../files/pbs.csh','.')
 341       elif instance.unres_ff =='NEWCT-9P':
 342         shutil.copy('../files/pbs_newct-9p.csh','pbs.csh')
 343       else:
 344         shutil.copy('../files/pbs_new.csh','pbs.csh')
 345       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 346       os.chdir('..')
 347      elif instance.type == 'md':
 348       os.chdir(instance.jobdirname)
 349       if  instance.unres_ff =='FF2':
 350         f1 = open('../files/pbs_md.csh', 'r')
 351       elif instance.unres_ff =='NEWCT-9P':
 352         f1 = open('../files/pbs_md_newct-9p.csh', 'r')
 353       else:
 354         f1 = open('../files/pbs_md_new.csh', 'r')
 355       f2 = open('pbs.csh', 'w')
 356       for line in f1:
 357            f2.write(line.replace('$dimen3',str(dimen3)+' '+str(instance.md_temp) ))
 358       f1.close()
 359       f2.close()
 360
 361       f1 = open('file.seq', 'w')
 362       for i in range(0,len(seq),80):
 363              f1.write(seq[i:i+80]+'\n')
 364       f1.write('\n')
 365       f1.close()
 366
 367       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 368       os.chdir('..')
 369      else:
 370 # instance.type == 'remd'
 371       tmp1=json.loads(instance.remd_multi_m)
 372       nreplicas=sum(map(int, tmp1))
 373 # hardcoded for 4 core nodes with FGPROC=2
 374       nodes=int(nreplicas*2/4)
 375       reszta = nreplicas*2-nodes*4
 376       if reszta == 0 :
 377         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4'
 378       else:
 379         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
 380
 381       tmp_ss=''
 382       if instance.ssbond!='':
 383         ix=[]
 384         ii=0
 385         for i in range(0,len(seq)):
 386            if seq[i]=='X':
 387               ii=ii+1
 388            ix.append(ii)
 389         l=[]
 390         ss=json.loads(instance.ssbond)
 391         for e in ss:
 392            l.append(e[0]-ix[e[0]])
 393            l.append(e[1]-ix[e[1]])
 394         tmp_ss=' '.join(map(str,l))
 395
 396       os.chdir(instance.jobdirname)
 397       if  instance.unres_ff =='FF2':
 398         f1 = open('../files/pbs8.csh', 'r')
 399       elif instance.unres_ff =='NEWCT-9P':
 400         f1 = open('../files/pbs8_newct-9p.csh', 'r')
 401       else:
 402         f1 = open('../files/pbs8_new.csh', 'r')
 403       f2 = open('pbs8.csh', 'w')
 404       for line in f1:
 405           if '#PBS -l nodes=4:ppn=4' in line:
 406            f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
 407           elif '$ssbond' in line:
 408            f2.write(line.replace('$ssbond',tmp_ss))
 409           elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock':
 410             f2.write(line)
 411             if instance.md_seq2 !='':
 412              f2.write("""setenv FGPROCS 2
 413 setenv POT GB
 414 setenv PREFIX file2
 415 setenv OUT1FILE YES
 416 /users2/local/mpich2-1.4.1p1_intel/bin/mpirun -machinefile $PBS_NODEFILE -np 2 $UNRES_BIN
 417 /users2/local/pulchra306/pulchra -q -g file2_MD000.pdb
 418 cat file2_MD000.rebuilt.pdb |grep -v TER |grep -v END > tmp_plik2.pdb
 419 /users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp_plik2.pdb > act.rebuilt.pdb
 420 /users2/local/scwrl4/Scwrl4 -h -i act.rebuilt.pdb -o plik2.pdb
 421 rm tmp_plik2.pdb act.rebuilt.pdb\n""")
 422             if instance.dock_peptide:
 423              f2.write('../files/generator_v13 plik.pdb plik2.pdb 1 \n')
 424             else:
 425              f2.write('../files/generator_v13 plik.pdb plik2.pdb 0 \n')
 426             f2.write("sed '/END/q' plik.pdb |grep ATOM > plik1ter.pdb \n")
 427             f2.write("echo TER >>  plik1ter.pdb \n")
 428             f2.write("sed '/END/q' plik2.pdb |grep ATOM >> plik1ter.pdb \n")
 429           else:
 430            tmp1=json.loads(instance.remd_multi_t)
 431            f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
 432       f1.close()
 433       f2.close()
 434
 435       f1 = open('file.seq', 'w')
 436       for i in range(0,len(seq),80):
 437              f1.write(seq[i:i+80]+'\n')
 438       f1.write('\n')
 439       f1.close()
 440
 441       os.chdir('..')
 442
 443 # write wham & cluster input
 444       with open(instance.jobdirname+'/file_wham.inp','w') as f:
 445           if instance.md_nstep/instance.md_ntwx*nreplicas<=8000:
 446               isampl=1
 447           else:
 448               isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
 449           f.write('{:79}'.format(' isampl='+str(isampl))+'&\n')
 450           if instance.md_pdbref:
 451             f.write('{:79}'.format('SEED='+str(instance.md_seed)+
 452                ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n')
 453           else:
 454             f.write('{:79}'.format('SEED='+str(instance.md_seed)+
 455               ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n')
 456           if instance.md_2d != '':
 457                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
 458           if instance.type == 'dock':
 459                f.write('{:79}'.format(' n_ene=19 CONSTR_HOMOL=24')+'&\n')
 460           if instance.unres_ff =='NEWCT-9P':
 461                f.write('{:79}'.format('tormode=2 ')+'&\n')
 462           f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
 463                     ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
 464
 465           f.write('nres='+str(len(seq))+' one_letter\n')
 466           for i in range(0,len(seq),80):
 467              f.write(seq[i:i+80]+'\n')
 468
 469           f.write(write_ssbond(instance.ssbond))
 470
 471           if instance.type == 'dock':
 472             f.write('HOMOL_DIST=0.1    HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0  &\n')
 473             f.write('READ2SIGMA \n')
 474             for i in range(1,10):
 475               f.write('model0'+str(i)+'.pdb\n')
 476             for i in range(10,25):
 477               f.write('model'+str(i)+'.pdb\n')
 478
 479           if instance.md_2d != '':
 480              f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 481
 482           if instance.saxs_data != '':
 483              saxs_r=[]
 484              saxs_P=[]
 485              saxs_norm=0
 486              r_last=None
 487              fsaxs = open(instance.jobdirname+'/saxs.data', 'w')
 488              lines=instance.saxs_data.split('\n')
 489              for line in lines:
 490               tmp=line.split()
 491               if len(tmp)==2:
 492                f.write(tmp[0]+' '+tmp[1]+'\n')
 493                saxs_r.append(tmp[0])
 494                saxs_P.append(float(tmp[1]))
 495                if r_last==None:
 496                   r_last=float(tmp[0])
 497                else:
 498                   saxs_norm += float(tmp[1])*(float(tmp[0])-r_last)
 499                   r_last=float(tmp[0])
 500              for r,p in zip(saxs_r,saxs_P):
 501                fsaxs.write('{} {}\n'.format(r,p/saxs_norm))
 502              fsaxs.close()
 503
 504           f.write(w+'\n')
 505           f.write('\n')
 506           f.write('nt='+str(instance.remd_nrep)+' replica read_iset\n')
 507           tmp1=json.loads(instance.remd_multi_t)
 508           for element in tmp1:
 509               f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n')
 510               f.write('kh= 0.0 Q0=0.0\n')
 511           rec=instance.md_nstep/instance.md_ntwx
 512           f.write('nfile_cx=1 rec_start='+str(rec/10)
 513                   +' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n')
 514           f.write('file_MD000\n')
 515           if instance.md_pdbref:
 516              f.write('pdbref\n')
 517              if instance.type == 'dock':
 518               f.write('plik1ter.pdb\n')
 519              else:
 520               f.write('plik.pdb\n')
 521
 522
 523       with open(instance.jobdirname+'/file_cluster.inp','w') as f:
 524           f.write(instance.name + ' UNRES server job'+ '\n')
 525           f.write('{:79}'.format('nres='+str(len(seq))
 526              +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
 527              +' temper='+str(instance.remd_cluter_temp))+'&\n')
 528           if instance.md_2d != '':
 529                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
 530           if instance.type == 'dock':
 531                f.write('{:79}'.format(' CONSTR_HOMOL=24')+'&\n')
 532           if instance.unres_ff =='NEWCT-9P':
 533                f.write('{:79}'.format('tormode=2 ')+'&\n')
 534           f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
 535                   ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
 536           f.write(w+'\n')
 537           for i in range(0,len(seq),80):
 538              f.write(seq[i:i+80]+'\n')
 539           f.write(write_ssbond(instance.ssbond))
 540           if instance.type == 'dock':
 541             f.write('HOMOL_DIST=0.1    HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0  &\n')
 542             f.write('READ2SIGMA \n')
 543             for i in range(1,10):
 544               f.write('model0'+str(i)+'.pdb\n')
 545             for i in range(10,25):
 546               f.write('model'+str(i)+'.pdb\n')
 547           if instance.md_2d != '':
 548              f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 549           if instance.saxs_data != '':
 550              lines=instance.saxs_data.split('\n')
 551              for line in lines:
 552               tmp=line.split()
 553               if len(tmp)==2:
 554                f.write(tmp[0]+' '+tmp[1]+'\n')
 555
 556       if instance.type == 'dock' and instance.md_seq2 != '':
 557          with open(instance.jobdirname+'/file2.inp','w') as f:
 558            f.write(instance.name + ' chain2 random start'+ '\n')
 559            control_line = 'SEED='+str(instance.md_seed)+' '\
 560             +'rand_conf md one_letter'\
 561             + ' BOXX=1000 BOXY=1000 BOXZ=1000 '
 562
 563            if instance.unres_ff =='NEWCT-9P':
 564              control_line = control_line+'tormode=2 cart'
 565
 566            type_line = '        reset_vel=0'\
 567              +' t_bath=300'\
 568              +' nstep=100000'\
 569              +' ntwe=10000'\
 570              +' ntwx=100000'\
 571              +' dt=0.2 lang=1 scal_fric=0.02 respa mdpdb '
 572
 573            wrapper = textwrap.TextWrapper(width=70)
 574            word_list = wrapper.wrap(text=control_line)
 575            for element in word_list[:-1]:
 576              f.write('{:79}'.format(element)+'&\n')
 577            f.write(word_list[-1]+'\n')
 578
 579            word_list = wrapper.wrap(text=type_line)
 580            for element in word_list[:-1]:
 581              f.write('{:79}'.format(element)+'&\n')
 582            f.write(word_list[-1]+'\n')
 583
 584            f.write(w+'\n')
 585
 586            seq=instance.md_seq2.replace(" ","")
 587            f.write(str(len(seq))+'\n')
 588            for i in range(0,len(seq),80):
 589              f.write(seq[i:i+80]+'\n')
 590            f.write('0\n')
 591            f.write('0\n')
 592
 593
 594       os.chdir(instance.jobdirname)
 595       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 596       os.chdir('..')
 597
 598      output = str(ret_code.communicate()[0])
 599      output=output.strip()
 600      if output=='':
 601        output='error'
 602      logger.warning("PBS \"%s\" " % output)
 603      instance.pbsjob = output
 604      instance.save()
 605
 606 #     print ret_code.stdout.readlines()
 607      logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
 608
 609 @receiver(post_delete, sender=Task)
 610 def delete_on_task_del(sender, instance, **kwargs):
 611    if instance.jobdirname:
 612       if os.path.isdir(instance.jobdirname):
 613          if not instance.done:
 614            ret_code_qdel = subprocess.Popen(' /opt/torque/bin/qdel '+str(instance.pbsjob), shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 615            output = str(ret_code_qdel.communicate()[0])
 616            output=output.strip()
 617            logger.warning("PBS qdel \"%s\" " % instance.pbsjob)
 618            logger.warning("QDEL \"%s\" " % output)
 619          shutil.rmtree(instance.jobdirname)
 620          logger.warning("Dir \"%s\" has been rm." % instance.jobdirname)
 621