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' :
 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.md_pdbref:
 175              control_line = control_line+'pdbref '
 176
 177           cntrl_saxs=''
 178           if instance.saxs_data != '':
 179              lines=instance.saxs_data.split('\n')
 180              nsaxs=0
 181              for line in lines:
 182               if len(line.split())==2:
 183                nsaxs+=1
 184              cntrl_saxs=' nsaxs='+str(nsaxs)+' scal_rad='+str(instance.scal_rad)
 185              control_line += cntrl_saxs
 186
 187           type_line = 'reset_vel='+ str(instance.remd_nstex)\
 188              +' nstep='+str(instance.md_nstep)\
 189              +' ntwe='+str(instance.md_ntwe)\
 190              +' ntwx='+str(instance.md_ntwx)\
 191              +' dt='+str(instance.md_dt)
 192           if instance.md_lang == 'langevin':
 193             type_line = type_line + ' lang=1 '
 194             type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
 195           if instance.md_lang == 'berendsen':
 196             type_line = type_line + ' lang=0 tbf '
 197             type_line = type_line + 'tau_bath='+str(instance.md_tau)
 198           if instance.md_respa:
 199             type_line = type_line + ' respa '
 200           if instance.md_mdpdb:
 201             type_line = type_line + ' mdpdb '
 202
 203           type_line2 = 'nrep='+str(instance.remd_nrep) \
 204              +' nstex='+str(instance.remd_nstex) \
 205              +' tlist mlist sync nsyn='+str(instance.remd_nstex)\
 206              +' traj1file  rest1file TRAJCACHE=200'
 207
 208        if instance.md_start == 'pdbstart':
 209              type_line = type_line + ' preminim cart'
 210
 211        wrapper = textwrap.TextWrapper(width=70)
 212
 213        word_list = wrapper.wrap(text=control_line)
 214        for element in word_list[:-1]:
 215            f.write('{:79}'.format(element)+'&\n')
 216        f.write(word_list[-1]+'\n')
 217
 218        word_list = wrapper.wrap(text=type_line)
 219        for element in word_list[:-1]:
 220            f.write('{:79}'.format(element)+'&\n')
 221        f.write(word_list[-1]+'\n')
 222
 223        if instance.md_start == 'pdbstart':
 224          f.write('print_min_ini print_min_res print_min_stat\n')
 225
 226
 227        if instance.type == 'remd' :
 228           word_list = wrapper.wrap(text=type_line2)
 229           for element in word_list[:-1]:
 230               f.write('{:79}'.format(element)+'&\n')
 231           f.write(word_list[-1]+'\n')
 232
 233           tmp1=json.loads(instance.remd_multi_t)
 234           string1=" "
 235           word_list = wrapper.wrap(text=string1.join(tmp1))
 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_m)
 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        if instance.saxs_data != '':
 248          w+=' wsaxs='+str(instance.wsaxs)
 249        f.write(w+'\n')
 250
 251
 252        if instance.type == 'min' or instance.md_start == 'pdbstart':
 253           f.write('plik.pdb\n')
 254           f.write(write_ssbond(instance.ssbond))
 255           if instance.md_2d == '':
 256             f.write('0\n')
 257           else:
 258             f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 259
 260        if instance.type == 'md' and instance.md_start != 'pdbstart':
 261
 262           if instance.md_pdbref:
 263              f.write('plik.pdb\n')
 264           f.write(str(len(seq))+'\n')
 265           for i in range(0,len(seq),80):
 266              f.write(seq[i:i+80]+'\n')
 267           f.write('0\n')
 268           if instance.md_2d == '':
 269             f.write('0\n')
 270           else:
 271             f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 272
 273
 274        if instance.type == 'remd' and instance.md_start != 'pdbstart':
 275
 276           if instance.md_pdbref:
 277              f.write('plik.pdb\n')
 278           f.write(str(len(seq))+'\n')
 279           for i in range(0,len(seq),80):
 280              f.write(seq[i:i+80]+'\n')
 281           f.write('0\n')
 282           if instance.md_2d == '':
 283             f.write('0\n')
 284           else:
 285             f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 286
 287
 288        if instance.saxs_data != '':
 289              lines=instance.saxs_data.split('\n')
 290              for line in lines:
 291               tmp=line.split()
 292               if len(tmp)==2:
 293                f.write(tmp[0]+' '+tmp[1]+'\n')
 294
 295
 296      if instance.type == 'min':
 297       os.chdir(instance.jobdirname)
 298       if  instance.unres_ff =='FF2':
 299         shutil.copy('../files/pbs.csh','.')
 300       else:
 301         shutil.copy('../files/pbs_new.csh','pbs.csh')
 302       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 303       os.chdir('..')
 304      elif instance.type == 'md':
 305       os.chdir(instance.jobdirname)
 306       if  instance.unres_ff =='FF2':
 307         f1 = open('../files/pbs_md.csh', 'r')
 308       else:
 309         f1 = open('../files/pbs_md_new.csh', 'r')
 310       f2 = open('pbs.csh', 'w')
 311       for line in f1:
 312            f2.write(line.replace('$dimen3',str(dimen3)+' '+str(instance.md_temp) ))
 313       f1.close()
 314       f2.close()
 315
 316       f1 = open('file.seq', 'w')
 317       for i in range(0,len(seq),80):
 318              f1.write(seq[i:i+80]+'\n')
 319       f1.close()
 320
 321       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 322       os.chdir('..')
 323      else:
 324 # instance.type == 'remd'
 325       tmp1=json.loads(instance.remd_multi_m)
 326       nreplicas=sum(map(int, tmp1))
 327 # hardcoded for 4 core nodes with FGPROC=2
 328       nodes=int(nreplicas*2/4)
 329       reszta = nreplicas*2-nodes*4
 330       if reszta == 0 :
 331         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4'
 332       else:
 333         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
 334
 335       tmp_ss=''
 336       if instance.ssbond!='':
 337         ix=[]
 338         ii=0
 339         for i in range(0,len(seq)):
 340            if seq[i]=='X':
 341               ii=ii+1
 342            ix.append(ii)
 343         l=[]
 344         ss=json.loads(instance.ssbond)
 345         for e in ss:
 346            l.append(e[0]-ix[e[0]])
 347            l.append(e[1]-ix[e[1]])
 348         tmp_ss=' '.join(map(str,l))
 349
 350       os.chdir(instance.jobdirname)
 351       if  instance.unres_ff =='FF2':
 352         f1 = open('../files/pbs8.csh', 'r')
 353       else:
 354         f1 = open('../files/pbs8_new.csh', 'r')
 355       f2 = open('pbs8.csh', 'w')
 356       for line in f1:
 357           if '#PBS -l nodes=4:ppn=4' in line:
 358            f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
 359           elif '$ssbond' in line:
 360            f2.write(line.replace('$ssbond',tmp_ss))
 361           else:
 362            tmp1=json.loads(instance.remd_multi_t)
 363            f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
 364       f1.close()
 365       f2.close()
 366       os.chdir('..')
 367
 368 # write wham & cluster input
 369       with open(instance.jobdirname+'/file_wham.inp','w') as f:
 370           if instance.md_nstep/instance.md_ntwx*nreplicas<=8000:
 371               isampl=1
 372           else:
 373               isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
 374
 375           if instance.md_pdbref:
 376             f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
 377                ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n')
 378           else:
 379             f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
 380               ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n')
 381           if instance.md_2d != '':
 382                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
 383           f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
 384                     ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
 385
 386           f.write('nres='+str(len(seq))+' one_letter\n')
 387           for i in range(0,len(seq),80):
 388              f.write(seq[i:i+80]+'\n')
 389
 390           f.write(write_ssbond(instance.ssbond))
 391
 392           if instance.md_2d != '':
 393              f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 394
 395           if instance.saxs_data != '':
 396              fsaxs = open(instance.jobdirname+'/saxs.data', 'w')
 397              lines=instance.saxs_data.split('\n')
 398              for line in lines:
 399               tmp=line.split()
 400               if len(tmp)==2:
 401                f.write(tmp[0]+' '+tmp[1]+'\n')
 402                fsaxs.write(tmp[0]+' '+tmp[1]+'\n')
 403              fsaxs.close()
 404
 405           f.write(w+'\n')
 406           f.write('\n')
 407           f.write('nt='+str(instance.remd_nrep)+' replica read_iset\n')
 408           tmp1=json.loads(instance.remd_multi_t)
 409           for element in tmp1:
 410               f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n')
 411               f.write('kh= 0.0 Q0=0.0\n')
 412           rec=instance.md_nstep/instance.md_ntwx
 413           f.write('nfile_cx=1 rec_start='+str(rec/10)
 414                   +' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n')
 415           f.write('file_MD000\n')
 416           if instance.md_pdbref:
 417              f.write('pdbref\n')
 418              f.write('plik.pdb\n')
 419
 420
 421       with open(instance.jobdirname+'/file_cluster.inp','w') as f:
 422           f.write(instance.name + ' UNRES server job'+ '\n')
 423           f.write('{:79}'.format('nres='+str(len(seq))
 424              +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
 425              +' temper='+str(instance.remd_cluter_temp))+'&\n')
 426           if instance.md_2d != '':
 427                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
 428           f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
 429                   ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
 430           f.write(w+'\n')
 431           for i in range(0,len(seq),80):
 432              f.write(seq[i:i+80]+'\n')
 433           f.write(write_ssbond(instance.ssbond))
 434           if instance.md_2d != '':
 435              f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 436           if instance.saxs_data != '':
 437              lines=instance.saxs_data.split('\n')
 438              for line in lines:
 439               tmp=line.split()
 440               if len(tmp)==2:
 441                f.write(tmp[0]+' '+tmp[1]+'\n')
 442
 443       os.chdir(instance.jobdirname)
 444       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 445       os.chdir('..')
 446
 447      print ret_code.stdout.readlines()
 448      logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
 449
 450 @receiver(post_delete, sender=Task)
 451 def delete_on_task_del(sender, instance, **kwargs):
 452    if instance.jobdirname:
 453       if os.path.isdir(instance.jobdirname):
 454          shutil.rmtree(instance.jobdirname)
 455          logger.warning("Dir \"%s\" has been rm." % instance.jobdirname)
 456