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:
  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      else:
  94       w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542              &
  95 WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000        &
  96 WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000    &
  97 WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000                      &
  98 CUTOFF=7.00000 WCORR4=0.00000"""
  99
 100
 101      with open(instance.jobdirname+'/file.inp','w') as f:
 102        f.write(instance.name + ' UNRES server job'+ '\n')
 103
 104        if instance.type == 'min' :
 105
 106           control_line = 'SEED='+str(instance.md_seed)+' ' \
 107              + instance.min_choice \
 108              + ' pdbstart pdbref ' \
 109              + ' BOXX='+str(instance.boxx) \
 110              + ' BOXY='+str(instance.boxy) \
 111              + ' BOXZ='+str(instance.boxz) +' '
 112           if not instance.min_overlap:
 113             control_line = control_line+'overlap '
 114           if not instance.min_searchsc:
 115             control_line = control_line+'nosearchsc '
 116           if instance.min_pdbout:
 117             control_line = control_line+'pdbout '
 118           if instance.min_unres_pdb:
 119             control_line = control_line+'unres_pdb '
 120
 121           type_line = 'print_min_ini print_min_res print_min_stat'\
 122             +' MAXMIN='+str(instance.min_maxmin)\
 123             +' MAXFUN='+str(instance.min_maxfun)
 124
 125
 126        seq=instance.md_seq.replace(" ","")
 127        dimen3=len(seq)
 128        if dimen3>1:
 129           if seq[0]=='X':
 130             dimen3-=1
 131           if seq[-1]=='X':
 132             dimen3-=1
 133
 134        nogly ='CDSQKIPTFNHLRWAVEYMcdsqkiptfnhlrwaveym'
 135        seq2 = ''.join([c for c in seq if c in nogly])
 136
 137        dimen3=(dimen3+len(seq2))*3
 138
 139
 140        if instance.type == 'md' :
 141           control_line = 'SEED='+str(instance.md_seed)+' '\
 142            +instance.md_start +' md one_letter'\
 143            + ' BOXX='+str(instance.boxx) \
 144            + ' BOXY='+str(instance.boxy) \
 145            + ' BOXZ='+str(instance.boxz) +' '
 146
 147           if instance.md_pdbref:
 148              control_line = control_line+'pdbref '
 149
 150           type_line = '        reset_vel=0'\
 151              +' t_bath='+str(instance.md_temp)\
 152              +' nstep='+str(instance.md_nstep)\
 153              +' ntwe='+str(instance.md_ntwe)\
 154              +' ntwx='+str(instance.md_ntwx)\
 155              +' dt='+str(instance.md_dt)
 156           if instance.md_lang == 'langevin':
 157             type_line = type_line + ' lang=1 '
 158             type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
 159           if instance.md_lang == 'berendsen':
 160             type_line = type_line + ' lang=0 tbf '
 161             type_line = type_line + 'tau_bath='+str(instance.md_tau)
 162           if instance.md_respa:
 163             type_line = type_line + ' respa '
 164           if instance.md_mdpdb:
 165             type_line = type_line + ' mdpdb '
 166
 167        if instance.type == 'remd' or instance.type == 'dock':
 168           control_line = 'SEED='+str(instance.md_seed)+' '\
 169            +instance.md_start +' re one_letter'\
 170            + ' BOXX='+str(instance.boxx) \
 171            + ' BOXY='+str(instance.boxy) \
 172            + ' BOXZ='+str(instance.boxz) +' '
 173
 174           if instance.type == 'dock':
 175              control_line = control_line+'CONSTR_HOMOL=20 '
 176
 177           if instance.md_pdbref:
 178              control_line = control_line+'pdbref '
 179
 180           cntrl_saxs=''
 181           if instance.saxs_data != '':
 182              lines=instance.saxs_data.split('\n')
 183              nsaxs=0
 184              for line in lines:
 185               if len(line.split())==2:
 186                nsaxs+=1
 187              cntrl_saxs=' nsaxs='+str(nsaxs)+' scal_rad='+str(instance.scal_rad)
 188              control_line += cntrl_saxs
 189
 190           type_line = '        reset_vel='+ str(instance.remd_nstex)\
 191              +' nstep='+str(instance.md_nstep)\
 192              +' ntwe='+str(instance.md_ntwe)\
 193              +' ntwx='+str(instance.md_ntwx)\
 194              +' dt='+str(instance.md_dt)
 195           if instance.md_lang == 'langevin':
 196             type_line = type_line + ' lang=1 '
 197             type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
 198           if instance.md_lang == 'berendsen':
 199             type_line = type_line + ' lang=0 tbf '
 200             type_line = type_line + 'tau_bath='+str(instance.md_tau)
 201           if instance.md_respa:
 202             type_line = type_line + ' respa '
 203 #          if instance.md_mdpdb:
 204 #            type_line = type_line + ' mdpdb '
 205
 206           type_line2 = 'nrep='+str(instance.remd_nrep) \
 207              +' nstex='+str(instance.remd_nstex) \
 208              +' tlist mlist sync nsyn='+str(instance.remd_nstex)\
 209              +' traj1file  rest1file TRAJCACHE=200'
 210
 211        if instance.md_start == 'pdbstart':
 212              type_line = type_line + ' preminim cart'
 213
 214        wrapper = textwrap.TextWrapper(width=70)
 215
 216        word_list = wrapper.wrap(text=control_line)
 217        for element in word_list[:-1]:
 218            f.write('{:79}'.format(element)+'&\n')
 219        f.write(word_list[-1]+'\n')
 220
 221        word_list = wrapper.wrap(text=type_line)
 222        for element in word_list[:-1]:
 223            f.write('{:79}'.format(element)+'&\n')
 224        f.write(word_list[-1]+'\n')
 225
 226        if instance.md_start == 'pdbstart':
 227         if instance.type == 'remd' or instance.type == 'dock':
 228          f.write('print_min_ini print_min_res print_min_stat maxfun='+
 229            str(instance.min_maxfun)+'\n')
 230         else:
 231          f.write('print_min_ini print_min_res print_min_stat\n')
 232
 233
 234        if instance.type == 'remd' or instance.type == 'dock':
 235           word_list = wrapper.wrap(text=type_line2)
 236           for element in word_list[:-1]:
 237               f.write('{:79}'.format(element)+'&\n')
 238           f.write(word_list[-1]+'\n')
 239
 240           tmp1=json.loads(instance.remd_multi_t)
 241           string1=" "
 242           word_list = wrapper.wrap(text=string1.join(tmp1))
 243           for element in word_list[:-1]:
 244               f.write('{:79}'.format(element)+'&\n')
 245           f.write(word_list[-1]+'\n')
 246
 247           tmp1=json.loads(instance.remd_multi_m)
 248           string1=" "
 249           word_list = wrapper.wrap(text=string1.join(tmp1))
 250           for element in word_list[:-1]:
 251               f.write('{:79}'.format(element)+'&\n')
 252           f.write(word_list[-1]+'\n')
 253
 254        if instance.saxs_data != '':
 255          w+=' wsaxs='+str(instance.wsaxs)
 256        f.write(w+'\n')
 257
 258
 259        if instance.type == 'min' or instance.md_start == 'pdbstart':
 260           if instance.type == 'dock':
 261             f.write('model01.pdb\n')
 262           else:
 263             f.write('plik.pdb\n')
 264           f.write(write_ssbond(instance.ssbond))
 265           if instance.md_2d == '':
 266             f.write('0\n')
 267           else:
 268             f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 269
 270        if instance.type == 'dock':
 271           f.write('HOMOL_DIST=0.1    HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0  &\n')
 272           f.write('READ2SIGMA START_FROM_MODELS\n')
 273           for i in range(1,10):
 274            f.write('model0'+str(i)+'.pdb\n')
 275           for i in range(10,21):
 276            f.write('model'+str(i)+'.pdb\n')
 277
 278        if instance.type == 'md' and instance.md_start != 'pdbstart':
 279
 280           if instance.md_pdbref:
 281              f.write('plik.pdb\n')
 282           f.write(str(len(seq))+'\n')
 283           for i in range(0,len(seq),80):
 284              f.write(seq[i:i+80]+'\n')
 285           f.write('0\n')
 286           if instance.md_2d == '':
 287             f.write('0\n')
 288           else:
 289             f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 290
 291
 292        if instance.type == 'remd' and instance.md_start != 'pdbstart':
 293
 294           if instance.md_pdbref:
 295              f.write('plik.pdb\n')
 296           f.write(str(len(seq))+'\n')
 297           for i in range(0,len(seq),80):
 298              f.write(seq[i:i+80]+'\n')
 299           f.write('0\n')
 300           if instance.md_2d == '':
 301             f.write('0\n')
 302           else:
 303             f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 304
 305
 306        if instance.saxs_data != '':
 307              lines=instance.saxs_data.split('\n')
 308              for line in lines:
 309               tmp=line.split()
 310               if len(tmp)==2:
 311                f.write(tmp[0]+' '+tmp[1]+'\n')
 312
 313
 314      if instance.type == 'min':
 315       os.chdir(instance.jobdirname)
 316       if  instance.unres_ff =='FF2':
 317         shutil.copy('../files/pbs.csh','.')
 318       else:
 319         shutil.copy('../files/pbs_new.csh','pbs.csh')
 320       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 321       os.chdir('..')
 322      elif instance.type == 'md':
 323       os.chdir(instance.jobdirname)
 324       if  instance.unres_ff =='FF2':
 325         f1 = open('../files/pbs_md.csh', 'r')
 326       else:
 327         f1 = open('../files/pbs_md_new.csh', 'r')
 328       f2 = open('pbs.csh', 'w')
 329       for line in f1:
 330            f2.write(line.replace('$dimen3',str(dimen3)+' '+str(instance.md_temp) ))
 331       f1.close()
 332       f2.close()
 333
 334       f1 = open('file.seq', 'w')
 335       for i in range(0,len(seq),80):
 336              f1.write(seq[i:i+80]+'\n')
 337       f1.write('\n')
 338       f1.close()
 339
 340       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 341       os.chdir('..')
 342      else:
 343 # instance.type == 'remd'
 344       tmp1=json.loads(instance.remd_multi_m)
 345       nreplicas=sum(map(int, tmp1))
 346 # hardcoded for 4 core nodes with FGPROC=2
 347       nodes=int(nreplicas*2/4)
 348       reszta = nreplicas*2-nodes*4
 349       if reszta == 0 :
 350         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4'
 351       else:
 352         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
 353
 354       tmp_ss=''
 355       if instance.ssbond!='':
 356         ix=[]
 357         ii=0
 358         for i in range(0,len(seq)):
 359            if seq[i]=='X':
 360               ii=ii+1
 361            ix.append(ii)
 362         l=[]
 363         ss=json.loads(instance.ssbond)
 364         for e in ss:
 365            l.append(e[0]-ix[e[0]])
 366            l.append(e[1]-ix[e[1]])
 367         tmp_ss=' '.join(map(str,l))
 368
 369       os.chdir(instance.jobdirname)
 370       if  instance.unres_ff =='FF2':
 371         f1 = open('../files/pbs8.csh', 'r')
 372       else:
 373         f1 = open('../files/pbs8_new.csh', 'r')
 374       f2 = open('pbs8.csh', 'w')
 375       for line in f1:
 376           if '#PBS -l nodes=4:ppn=4' in line:
 377            f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
 378           elif '$ssbond' in line:
 379            f2.write(line.replace('$ssbond',tmp_ss))
 380           elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock':
 381             f2.write(line)
 382             f2.write('../files/generator_v7 plik.pdb plik2.pdb\n')
 383           else:
 384            tmp1=json.loads(instance.remd_multi_t)
 385            f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
 386       f1.close()
 387       f2.close()
 388
 389       f1 = open('file.seq', 'w')
 390       for i in range(0,len(seq),80):
 391              f1.write(seq[i:i+80]+'\n')
 392       f1.write('\n')
 393       f1.close()
 394
 395       os.chdir('..')
 396
 397 # write wham & cluster input
 398       with open(instance.jobdirname+'/file_wham.inp','w') as f:
 399           if instance.md_nstep/instance.md_ntwx*nreplicas<=8000:
 400               isampl=1
 401           else:
 402               isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
 403           f.write('{:79}'.format(' isampl='+str(isampl))+'&\n')
 404           if instance.md_pdbref:
 405             f.write('{:79}'.format('SEED='+str(instance.md_seed)+
 406                ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n')
 407           else:
 408             f.write('{:79}'.format('SEED='+str(instance.md_seed)+
 409               ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n')
 410           if instance.md_2d != '':
 411                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
 412           if instance.type == 'dock':
 413                f.write('{:79}'.format(' n_ene=19 CONSTR_HOMOL=20')+'&\n')
 414           f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
 415                     ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
 416
 417           f.write('nres='+str(len(seq))+' one_letter\n')
 418           for i in range(0,len(seq),80):
 419              f.write(seq[i:i+80]+'\n')
 420
 421           f.write(write_ssbond(instance.ssbond))
 422
 423           if instance.type == 'dock':
 424             f.write('HOMOL_DIST=0.1    HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0  &\n')
 425             f.write('READ2SIGMA \n')
 426             for i in range(1,10):
 427               f.write('model0'+str(i)+'.pdb\n')
 428             for i in range(10,21):
 429               f.write('model'+str(i)+'.pdb\n')
 430
 431           if instance.md_2d != '':
 432              f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 433
 434           if instance.saxs_data != '':
 435              saxs_r=[]
 436              saxs_P=[]
 437              saxs_norm=0
 438              r_last=None
 439              fsaxs = open(instance.jobdirname+'/saxs.data', 'w')
 440              lines=instance.saxs_data.split('\n')
 441              for line in lines:
 442               tmp=line.split()
 443               if len(tmp)==2:
 444                f.write(tmp[0]+' '+tmp[1]+'\n')
 445                saxs_r.append(tmp[0])
 446                saxs_P.append(float(tmp[1]))
 447                if r_last==None:
 448                   r_last=float(tmp[0])
 449                else:
 450                   saxs_norm += float(tmp[1])*(float(tmp[0])-r_last)
 451                   r_last=float(tmp[0])
 452              for r,p in zip(saxs_r,saxs_P):
 453                fsaxs.write('{} {}\n'.format(r,p/saxs_norm))
 454              fsaxs.close()
 455
 456           f.write(w+'\n')
 457           f.write('\n')
 458           f.write('nt='+str(instance.remd_nrep)+' replica read_iset\n')
 459           tmp1=json.loads(instance.remd_multi_t)
 460           for element in tmp1:
 461               f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n')
 462               f.write('kh= 0.0 Q0=0.0\n')
 463           rec=instance.md_nstep/instance.md_ntwx
 464           f.write('nfile_cx=1 rec_start='+str(rec/10)
 465                   +' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n')
 466           f.write('file_MD000\n')
 467           if instance.md_pdbref:
 468              f.write('pdbref\n')
 469              f.write('plik.pdb\n')
 470
 471
 472       with open(instance.jobdirname+'/file_cluster.inp','w') as f:
 473           f.write(instance.name + ' UNRES server job'+ '\n')
 474           f.write('{:79}'.format('nres='+str(len(seq))
 475              +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
 476              +' temper='+str(instance.remd_cluter_temp))+'&\n')
 477           if instance.md_2d != '':
 478                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
 479           if instance.type == 'dock':
 480                f.write('{:79}'.format(' CONSTR_HOMOL=20')+'&\n')
 481           f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
 482                   ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
 483           f.write(w+'\n')
 484           for i in range(0,len(seq),80):
 485              f.write(seq[i:i+80]+'\n')
 486           f.write(write_ssbond(instance.ssbond))
 487           if instance.type == 'dock':
 488             f.write('HOMOL_DIST=0.1    HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0  &\n')
 489             f.write('READ2SIGMA \n')
 490             for i in range(1,10):
 491               f.write('model0'+str(i)+'.pdb\n')
 492             for i in range(10,21):
 493               f.write('model'+str(i)+'.pdb\n')
 494           if instance.md_2d != '':
 495              f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 496           if instance.saxs_data != '':
 497              lines=instance.saxs_data.split('\n')
 498              for line in lines:
 499               tmp=line.split()
 500               if len(tmp)==2:
 501                f.write(tmp[0]+' '+tmp[1]+'\n')
 502
 503       os.chdir(instance.jobdirname)
 504       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 505       os.chdir('..')
 506
 507      print ret_code.stdout.readlines()
 508      logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
 509
 510 @receiver(post_delete, sender=Task)
 511 def delete_on_task_del(sender, instance, **kwargs):
 512    if instance.jobdirname:
 513       if os.path.isdir(instance.jobdirname):
 514          shutil.rmtree(instance.jobdirname)
 515          logger.warning("Dir \"%s\" has been rm." % instance.jobdirname)
 516