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 #---v
 159           if instance.use_nmr:
 160             control_line = control_line+' constr_dist=12 '
 161 #---^
 162           if instance.unres_ff =='NEWCT-9P':
 163             control_line = control_line+'tormode=2 cart'
 164
 165           type_line = '        reset_vel=0'\
 166              +' t_bath='+str(instance.md_temp)\
 167              +' nstep='+str(instance.md_nstep)\
 168              +' ntwe='+str(instance.md_ntwe)\
 169              +' ntwx='+str(instance.md_ntwx)\
 170              +' dt='+str(instance.md_dt)
 171           if instance.md_lang == 'langevin':
 172             type_line = type_line + ' lang=1 '
 173             type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
 174           if instance.md_lang == 'berendsen':
 175             type_line = type_line + ' lang=0 tbf '
 176             type_line = type_line + 'tau_bath='+str(instance.md_tau)
 177           if instance.md_respa:
 178             type_line = type_line + ' respa '
 179           if instance.md_mdpdb:
 180             type_line = type_line + ' mdpdb '
 181
 182        if instance.type == 'remd' or instance.type == 'dock':
 183           control_line = 'SEED='+str(instance.md_seed)+' '\
 184            +instance.md_start +' re one_letter'\
 185            + ' BOXX='+str(instance.boxx) \
 186            + ' BOXY='+str(instance.boxy) \
 187            + ' BOXZ='+str(instance.boxz) +' '
 188
 189           if instance.type == 'dock':
 190              control_line = control_line+'CONSTR_HOMOL=24 '
 191
 192           if instance.md_pdbref:
 193              control_line = control_line+'pdbref '
 194
 195           if instance.unres_ff =='NEWCT-9P':
 196             control_line = control_line+'tormode=2 cart'
 197 #---v
 198           if instance.use_nmr:
 199             control_line = control_line+' constr_dist=12 '
 200 #---^
 201
 202           cntrl_saxs=''
 203           if instance.saxs_data != '':
 204              lines=instance.saxs_data.split('\n')
 205              nsaxs=0
 206              for line in lines:
 207               if len(line.split())==2:
 208                nsaxs+=1
 209              cntrl_saxs=' nsaxs='+str(nsaxs)+' scal_rad='+str(instance.scal_rad)
 210              control_line += cntrl_saxs
 211
 212           type_line = '        reset_vel='+ str(instance.remd_nstex)\
 213              +' nstep='+str(instance.md_nstep)\
 214              +' ntwe='+str(instance.md_ntwe)\
 215              +' ntwx='+str(instance.md_ntwx)\
 216              +' dt='+str(instance.md_dt)
 217           if instance.md_lang == 'langevin':
 218             type_line = type_line + ' lang=1 '
 219             type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
 220           if instance.md_lang == 'berendsen':
 221             type_line = type_line + ' lang=0 tbf '
 222             type_line = type_line + 'tau_bath='+str(instance.md_tau)
 223           if instance.md_respa:
 224             type_line = type_line + ' respa '
 225 #          if instance.md_mdpdb:
 226 #            type_line = type_line + ' mdpdb '
 227
 228           type_line2 = 'nrep='+str(instance.remd_nrep) \
 229              +' nstex='+str(instance.remd_nstex) \
 230              +' tlist mlist sync nsyn='+str(instance.remd_nstex)\
 231              +' traj1file  rest1file TRAJCACHE=200'
 232
 233        if instance.md_start == 'pdbstart':
 234              type_line = type_line + ' preminim cart'
 235
 236        wrapper = textwrap.TextWrapper(width=70)
 237
 238        word_list = wrapper.wrap(text=control_line)
 239        for element in word_list[:-1]:
 240            f.write('{:79}'.format(element)+'&\n')
 241        f.write(word_list[-1]+'\n')
 242
 243        word_list = wrapper.wrap(text=type_line)
 244        for element in word_list[:-1]:
 245            f.write('{:79}'.format(element)+'&\n')
 246        f.write(word_list[-1]+'\n')
 247
 248        if instance.md_start == 'pdbstart' and instance.unres_ff !='NEWCT-9P':
 249         if instance.type == 'remd' or instance.type == 'dock':
 250          f.write('print_min_ini print_min_res print_min_stat maxfun='+
 251            str(instance.min_maxfun)+'\n')
 252         else:
 253          f.write('print_min_ini print_min_res print_min_stat\n')
 254
 255
 256        if instance.type == 'remd' or instance.type == 'dock':
 257           word_list = wrapper.wrap(text=type_line2)
 258           for element in word_list[:-1]:
 259               f.write('{:79}'.format(element)+'&\n')
 260           f.write(word_list[-1]+'\n')
 261
 262           tmp1=json.loads(instance.remd_multi_t)
 263           string1=" "
 264           word_list = wrapper.wrap(text=string1.join(tmp1))
 265           for element in word_list[:-1]:
 266               f.write('{:79}'.format(element)+'&\n')
 267           f.write(word_list[-1]+'\n')
 268
 269           tmp1=json.loads(instance.remd_multi_m)
 270           string1=" "
 271           word_list = wrapper.wrap(text=string1.join(tmp1))
 272           for element in word_list[:-1]:
 273               f.write('{:79}'.format(element)+'&\n')
 274           f.write(word_list[-1]+'\n')
 275
 276        if instance.saxs_data != '':
 277          w+=' wsaxs='+str(instance.wsaxs)
 278        f.write(w+'\n')
 279
 280
 281        if instance.type == 'min' or instance.md_start == 'pdbstart':
 282           if instance.type == 'dock':
 283             f.write('plik1ter.pdb\n')
 284           else:
 285             f.write('plik.pdb\n')
 286           f.write(write_ssbond(instance.ssbond))
 287           if instance.md_2d == '':
 288             f.write('0\n')
 289           else:
 290            if instance.unres_ff =='NEWCT-9P':
 291             f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 292            else:
 293             f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 294
 295        if instance.type == 'dock':
 296           f.write('HOMOL_DIST=0.1    HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0  &\n')
 297           f.write('READ2SIGMA START_FROM_MODELS\n')
 298           for i in range(1,10):
 299            f.write('model0'+str(i)+'.pdb\n')
 300           for i in range(10,25):
 301            f.write('model'+str(i)+'.pdb\n')
 302
 303        if instance.type == 'md' and instance.md_start != 'pdbstart':
 304
 305           if instance.md_pdbref:
 306              f.write('plik.pdb\n')
 307           f.write(str(len(seq))+'\n')
 308           for i in range(0,len(seq),80):
 309              f.write(seq[i:i+80]+'\n')
 310           f.write('0\n')
 311           if instance.md_2d == '':
 312             f.write('0\n')
 313           else:
 314            if instance.unres_ff =='NEWCT-9P':
 315             f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 316            else:
 317             f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 318 #---v
 319           if instance.use_nmr:
 320             f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
 321             f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
 322             f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
 323             if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
 324               fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
 325               for linmr in fnmr:
 326                    f.write(linmr)
 327               fnmr.close()
 328             else:
 329               fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
 330               for linmr in fnmr:
 331                   f.write(linmr)
 332               fnmr.close()
 333 #---^
 334
 335
 336        if instance.type == 'remd' and instance.md_start != 'pdbstart':
 337
 338           if instance.md_pdbref:
 339              f.write('plik.pdb\n')
 340           f.write(str(len(seq))+'\n')
 341           for i in range(0,len(seq),80):
 342              f.write(seq[i:i+80]+'\n')
 343           f.write('0\n')
 344           if instance.md_2d == '':
 345             f.write('0\n')
 346           else:
 347            if instance.unres_ff =='NEWCT-9P':
 348             f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 349            else:
 350             f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 351 #---v
 352           if instance.use_nmr:
 353             f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
 354             f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
 355             f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
 356             if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
 357               fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
 358               for linmr in fnmr:
 359                    f.write(linmr)
 360               fnmr.close()
 361             else:
 362               fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
 363               for linmr in fnmr:
 364                    f.write(linmr)
 365               fnmr.close()
 366 #---^
 367
 368
 369        if instance.saxs_data != '':
 370              lines=instance.saxs_data.split('\n')
 371              for line in lines:
 372               tmp=line.split()
 373               if len(tmp)==2:
 374                f.write(tmp[0]+' '+tmp[1]+'\n')
 375
 376
 377      if instance.type == 'min':
 378       os.chdir(instance.jobdirname)
 379       if  instance.unres_ff =='FF2':
 380         shutil.copy('../files/pbs.csh','.')
 381       elif instance.unres_ff =='NEWCT-9P':
 382         shutil.copy('../files/pbs_newct-9p.csh','pbs.csh')
 383       else:
 384         shutil.copy('../files/pbs_new.csh','pbs.csh')
 385       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 386       os.chdir('..')
 387      elif instance.type == 'md':
 388       os.chdir(instance.jobdirname)
 389       if  instance.unres_ff =='FF2':
 390         f1 = open('../files/pbs_md.csh', 'r')
 391       elif instance.unres_ff =='NEWCT-9P':
 392         f1 = open('../files/pbs_md_newct-9p.csh', 'r')
 393       else:
 394         f1 = open('../files/pbs_md_new.csh', 'r')
 395       f2 = open('pbs.csh', 'w')
 396       for line in f1:
 397            f2.write(line.replace('$dimen3',str(dimen3)+' '+str(instance.md_temp) ))
 398       f1.close()
 399       f2.close()
 400
 401       f1 = open('file.seq', 'w')
 402       for i in range(0,len(seq),80):
 403              f1.write(seq[i:i+80]+'\n')
 404       f1.write('\n')
 405       f1.close()
 406
 407       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 408       os.chdir('..')
 409      else:
 410 # instance.type == 'remd'
 411       tmp1=json.loads(instance.remd_multi_m)
 412       nreplicas=sum(map(int, tmp1))
 413 # hardcoded for 4 core nodes with FGPROC=2
 414       nodes=int(nreplicas*2/4)
 415       reszta = nreplicas*2-nodes*4
 416       if reszta == 0 :
 417         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4'
 418       else:
 419         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
 420
 421       tmp_ss=''
 422       if instance.ssbond!='':
 423         ix=[]
 424         ii=0
 425         for i in range(0,len(seq)):
 426            if seq[i]=='X':
 427               ii=ii+1
 428            ix.append(ii)
 429         l=[]
 430         ss=json.loads(instance.ssbond)
 431         for e in ss:
 432            l.append(e[0]-ix[e[0]])
 433            l.append(e[1]-ix[e[1]])
 434         tmp_ss=' '.join(map(str,l))
 435
 436       os.chdir(instance.jobdirname)
 437       if  instance.unres_ff =='FF2':
 438         f1 = open('../files/pbs8.csh', 'r')
 439       elif instance.unres_ff =='NEWCT-9P':
 440         f1 = open('../files/pbs8_newct-9p.csh', 'r')
 441       else:
 442         f1 = open('../files/pbs8_new.csh', 'r')
 443       f2 = open('pbs8.csh', 'w')
 444       for line in f1:
 445           if '#PBS -l nodes=4:ppn=4' in line:
 446            f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
 447           elif '$ssbond' in line:
 448            f2.write(line.replace('$ssbond',tmp_ss))
 449           elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock':
 450             f2.write(line)
 451             if instance.md_seq2 !='':
 452              f2.write("""setenv FGPROCS 2
 453 setenv POT GB
 454 setenv PREFIX file2
 455 setenv OUT1FILE YES
 456 /users2/local/mpich2-1.4.1p1_intel/bin/mpirun -machinefile $PBS_NODEFILE -np 2 $UNRES_BIN
 457 /users2/local/pulchra306/pulchra -q -g file2_MD000.pdb
 458 cat file2_MD000.rebuilt.pdb |grep -v TER |grep -v END > tmp_plik2.pdb
 459 /users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp_plik2.pdb > act.rebuilt.pdb
 460 /users2/local/scwrl4/Scwrl4 -h -i act.rebuilt.pdb -o plik2.pdb
 461 rm tmp_plik2.pdb act.rebuilt.pdb\n""")
 462             if instance.dock_peptide:
 463              f2.write('../files/generator_v13 plik.pdb plik2.pdb 1 \n')
 464             else:
 465              f2.write('../files/generator_v13 plik.pdb plik2.pdb 0 \n')
 466             f2.write("sed '/END/q' plik.pdb |grep ATOM > plik1ter.pdb \n")
 467             f2.write("echo TER >>  plik1ter.pdb \n")
 468             f2.write("sed '/END/q' plik2.pdb |grep ATOM >> plik1ter.pdb \n")
 469           else:
 470            tmp1=json.loads(instance.remd_multi_t)
 471            f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
 472       f1.close()
 473       f2.close()
 474
 475       f1 = open('file.seq', 'w')
 476       for i in range(0,len(seq),80):
 477              f1.write(seq[i:i+80]+'\n')
 478       f1.write('\n')
 479       f1.close()
 480
 481       os.chdir('..')
 482
 483 # write wham & cluster input
 484       with open(instance.jobdirname+'/file_wham.inp','w') as f:
 485           if instance.md_nstep/instance.md_ntwx*nreplicas<=8000:
 486               isampl=1
 487           else:
 488               isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
 489 #---v
 490           if instance.use_nmr:
 491                f.write('{:79}'.format('with_dist_constr constr_dist=12')+'&\n')
 492 #---^
 493           f.write('{:79}'.format(' isampl='+str(isampl))+'&\n')
 494           if instance.md_pdbref:
 495             f.write('{:79}'.format('SEED='+str(instance.md_seed)+
 496                ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n')
 497           else:
 498             f.write('{:79}'.format('SEED='+str(instance.md_seed)+
 499               ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n')
 500           if instance.md_2d != '':
 501                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
 502           if instance.type == 'dock':
 503                f.write('{:79}'.format(' n_ene=19 CONSTR_HOMOL=24')+'&\n')
 504           if instance.unres_ff =='NEWCT-9P':
 505                f.write('{:79}'.format('tormode=2 ')+'&\n')
 506           f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
 507                     ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
 508
 509           f.write('nres='+str(len(seq))+' one_letter\n')
 510           for i in range(0,len(seq),80):
 511              f.write(seq[i:i+80]+'\n')
 512
 513           f.write(write_ssbond(instance.ssbond))
 514
 515 #---v
 516           if instance.use_nmr:
 517             f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
 518             f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
 519             f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
 520             if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
 521               fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
 522               for linmr in fnmr:
 523                    f.write(linmr)
 524               fnmr.close()
 525             else:
 526               fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
 527               for linmr in fnmr:
 528                    f.write(linmr)
 529               fnmr.close()
 530 #---^
 531
 532           if instance.type == 'dock':
 533             f.write('HOMOL_DIST=0.1    HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0  &\n')
 534             f.write('READ2SIGMA \n')
 535             for i in range(1,10):
 536               f.write('model0'+str(i)+'.pdb\n')
 537             for i in range(10,25):
 538               f.write('model'+str(i)+'.pdb\n')
 539
 540           if instance.md_2d != '':
 541              f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 542
 543           if instance.saxs_data != '':
 544              saxs_r=[]
 545              saxs_P=[]
 546              saxs_norm=0
 547              r_last=None
 548              fsaxs = open(instance.jobdirname+'/saxs.data', 'w')
 549              lines=instance.saxs_data.split('\n')
 550              for line in lines:
 551               tmp=line.split()
 552               if len(tmp)==2:
 553                f.write(tmp[0]+' '+tmp[1]+'\n')
 554                saxs_r.append(tmp[0])
 555                saxs_P.append(float(tmp[1]))
 556                if r_last==None:
 557                   r_last=float(tmp[0])
 558                else:
 559                   saxs_norm += float(tmp[1])*(float(tmp[0])-r_last)
 560                   r_last=float(tmp[0])
 561              for r,p in zip(saxs_r,saxs_P):
 562                fsaxs.write('{} {}\n'.format(r,p/saxs_norm))
 563              fsaxs.close()
 564
 565           f.write(w+'\n')
 566           f.write('\n')
 567           f.write('nt='+str(instance.remd_nrep)+' replica read_iset\n')
 568           tmp1=json.loads(instance.remd_multi_t)
 569           for element in tmp1:
 570               f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n')
 571               f.write('kh= 0.0 Q0=0.0\n')
 572           rec=instance.md_nstep/instance.md_ntwx
 573           f.write('nfile_cx=1 rec_start='+str(rec/10)
 574                   +' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n')
 575           f.write('file_MD000\n')
 576           if instance.md_pdbref:
 577              f.write('pdbref\n')
 578              if instance.type == 'dock':
 579               f.write('plik1ter.pdb\n')
 580              else:
 581               f.write('plik.pdb\n')
 582
 583
 584       with open(instance.jobdirname+'/file_cluster.inp','w') as f:
 585           f.write(instance.name + ' UNRES server job'+ '\n')
 586           f.write('{:79}'.format('nres='+str(len(seq))
 587              +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
 588              +' temper='+str(instance.remd_cluter_temp)
 589              +' nclust='+str(instance.remd_cluster_n))+'&\n')
 590           if instance.md_2d != '':
 591                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
 592 #---v
 593           if instance.use_nmr:
 594             f.write('{:79}'.format('constr_dist=12 ')+'&\n')
 595 #---^
 596           if instance.type == 'dock':
 597                f.write('{:79}'.format(' CONSTR_HOMOL=24')+'&\n')
 598           if instance.unres_ff =='NEWCT-9P':
 599                f.write('{:79}'.format('tormode=2 ')+'&\n')
 600           f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
 601                   ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
 602           f.write(w+'\n')
 603           for i in range(0,len(seq),80):
 604              f.write(seq[i:i+80]+'\n')
 605           f.write(write_ssbond(instance.ssbond))
 606
 607 #---v
 608           if instance.use_nmr:
 609             f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
 610             f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
 611             f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
 612             if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
 613               fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
 614               for linmr in fnmr:
 615                    f.write(linmr)
 616               fnmr.close()
 617             else:
 618               fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
 619               for linmr in fnmr:
 620                    f.write(linmr)
 621               fnmr.close()
 622 #---^
 623
 624           if instance.type == 'dock':
 625             f.write('HOMOL_DIST=0.1    HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0  &\n')
 626             f.write('READ2SIGMA \n')
 627             for i in range(1,10):
 628               f.write('model0'+str(i)+'.pdb\n')
 629             for i in range(10,25):
 630               f.write('model'+str(i)+'.pdb\n')
 631           if instance.md_2d != '':
 632              f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 633           if instance.saxs_data != '':
 634              lines=instance.saxs_data.split('\n')
 635              for line in lines:
 636               tmp=line.split()
 637               if len(tmp)==2:
 638                f.write(tmp[0]+' '+tmp[1]+'\n')
 639
 640       if instance.type == 'dock' and instance.md_seq2 != '':
 641          with open(instance.jobdirname+'/file2.inp','w') as f:
 642            f.write(instance.name + ' chain2 random start'+ '\n')
 643            control_line = 'SEED='+str(instance.md_seed)+' '\
 644             +'rand_conf md one_letter'\
 645             + ' BOXX=1000 BOXY=1000 BOXZ=1000 '
 646
 647            if instance.unres_ff =='NEWCT-9P':
 648              control_line = control_line+'tormode=2 cart'
 649
 650            type_line = '        reset_vel=0'\
 651              +' t_bath=300'\
 652              +' nstep=100000'\
 653              +' ntwe=10000'\
 654              +' ntwx=100000'\
 655              +' dt=0.2 lang=1 scal_fric=0.02 respa mdpdb '
 656
 657            wrapper = textwrap.TextWrapper(width=70)
 658            word_list = wrapper.wrap(text=control_line)
 659            for element in word_list[:-1]:
 660              f.write('{:79}'.format(element)+'&\n')
 661            f.write(word_list[-1]+'\n')
 662
 663            word_list = wrapper.wrap(text=type_line)
 664            for element in word_list[:-1]:
 665              f.write('{:79}'.format(element)+'&\n')
 666            f.write(word_list[-1]+'\n')
 667
 668            f.write(w+'\n')
 669
 670            seq=instance.md_seq2.replace(" ","")
 671            f.write(str(len(seq))+'\n')
 672            for i in range(0,len(seq),80):
 673              f.write(seq[i:i+80]+'\n')
 674            f.write('0\n')
 675            f.write('0\n')
 676
 677
 678       os.chdir(instance.jobdirname)
 679       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 680       os.chdir('..')
 681
 682      output = str(ret_code.communicate()[0])
 683      output=output.strip()
 684      if output=='':
 685        output='error'
 686      logger.warning("PBS \"%s\" " % output)
 687      instance.pbsjob = output
 688      instance.save()
 689
 690 #     print ret_code.stdout.readlines()
 691      logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
 692
 693 @receiver(post_delete, sender=Task)
 694 def delete_on_task_del(sender, instance, **kwargs):
 695    if instance.jobdirname:
 696       if os.path.isdir(instance.jobdirname):
 697          if not instance.done:
 698            ret_code_qdel = subprocess.Popen(' /opt/torque/bin/qdel '+str(instance.pbsjob), shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 699            output = str(ret_code_qdel.communicate()[0])
 700            output=output.strip()
 701            logger.warning("PBS qdel \"%s\" " % instance.pbsjob)
 702            logger.warning("QDEL \"%s\" " % output)
 703          shutil.rmtree(instance.jobdirname)
 704          logger.warning("Dir \"%s\" has been rm." % instance.jobdirname)
 705