django_simple/todo/views.py

   1 from django.contrib.auth.decorators import login_required
   2 from django.shortcuts import redirect, render, get_object_or_404
   3 from django.contrib.auth.models import User
   4 from .forms import *
   5 from .models import Task
   6 import datetime
   7 import os
   8 import subprocess
   9 import json
  10 from lazysignup.decorators import allow_lazy_user
  11 from lazysignup.utils import is_lazy_user
  12
  13 res_codes = [
  14                 # 20 canonical amino acids
  15                 ('CYS', 'C'), ('ASP', 'D'), ('SER', 'S'), ('GLN', 'Q'),
  16                 ('LYS', 'K'), ('ILE', 'I'), ('PRO', 'P'), ('THR', 'T'),
  17                 ('PHE', 'F'), ('ASN', 'N'), ('GLY', 'G'), ('HIS', 'H'),
  18                 ('LEU', 'L'), ('ARG', 'R'), ('TRP', 'W'), ('ALA', 'A'),
  19                 ('VAL', 'V'), ('GLU', 'E'), ('TYR', 'Y'), ('MET', 'M'),
  20                 ('HSD', 'H'),('HSE', 'H'),('HSP', 'H'),
  21                 ('HIE', 'H'), ('HID', 'H'),('HIP', 'H'),
  22                 ('CYX', 'C'),
  23                 ('DCY', 'c'), ('DAS', 'd'), ('DSN', 's'), ('DGN', 'q'),
  24                 ('DLY', 'k'), ('DIL', 'i'), ('DPR', 'p'), ('DTH', 't'),
  25                 ('DPN', 'f'), ('DSG', 'n'), ('DHI', 'h'),
  26                 ('DLE', 'l'), ('DAR', 'r'), ('DTR', 'w'), ('DAL', 'a'),
  27                 ('DVA', 'v'), ('DGL', 'e'), ('DTY', 'y'), ('MED', 'm'),
  28                ]
  29
  30 three_to_one = dict(res_codes)
  31
  32 def seq_add_x(sequence):
  33     if sequence[0] != 'G' and sequence[0] != 'g':
  34         sequence='X'+sequence
  35     if sequence[-1] != 'G' and sequence[-1] != 'g':
  36         sequence=sequence+'X'
  37     set ='CDSQKIPTFNGHLRWAVEYMXcdsqkiptfnghlrwaveym'
  38     sequence = ''.join([c for c in sequence if c in set])
  39
  40     return(sequence)
  41
  42 def from_pdb(file):
  43     sequence = []
  44     ssbond = []
  45     ssbond_ch = []
  46     ires = []
  47     chain_start = {}
  48     chain_end = {}
  49     unres_shift = {}
  50     chain_sorted=[]
  51     newchain = True
  52
  53     for line in file:
  54             if line[0:6] == 'ATOM  ' and line[13:15] == 'CA':
  55               aa = three_to_one.get(line[17:20])
  56               i = int(line[22:26])
  57               ch = line[21:22]
  58               if newchain or i!=ires[-1]:
  59                 sequence.append(aa)
  60                 ires.append(i)
  61                 if newchain:
  62                  chain_start[ch]=i
  63                  chain_sorted.extend(ch)
  64                  newchain = False
  65             if line[0:3] == 'TER':
  66               sequence.append('XX')
  67               chain_end[ch]=i
  68               newchain = True
  69             if line[0:6] == 'SSBOND':
  70               b=[]
  71               b.append(int(line[17:21]))
  72               b.append(int(line[31:35]))
  73               ssbond.append(b)
  74               c = []
  75               c.append((line[15:16]))
  76               c.append((line[29:30]))
  77               ssbond_ch.append(c)
  78             if line[0:3] == 'END':
  79               break
  80     if not sequence[-1] == 'XX':
  81             chain_end[ch]=i
  82     while sequence[-1] == 'XX':
  83             del sequence[-1]
  84     if sequence[0] != 'G':
  85             sequence.insert(0,'X')
  86             ssbond=[ [e[0]+1,e[1]+1] for e in ssbond]
  87     if sequence[-1] != 'G':
  88             sequence.append('X')
  89     seq=''.join(sequence)
  90 #    if ires[0] != 1:
  91 #            ssbond=[ [e[0]-ires[0]+1,e[1]-ires[0]+1] for e in ssbond]
  92     i=0
  93     for c in chain_sorted:
  94       unres_shift[c]=i+chain_start[c]
  95       i=i-(chain_end[c]-chain_start[c])-3
  96     ssbond=[ [e[0]-unres_shift[c[0]]+1,e[1]-unres_shift[c[1]]+1] for e,c in zip(ssbond,ssbond_ch)]
  97
  98     return seq,json.dumps(ssbond)
  99
 100
 101 @login_required
 102 def index(request):
 103     user = request.user
 104     tasks = Task.objects.filter(owner=user).order_by('-created_date')
 105     variable = ''
 106     return render(request, "index.html", {
 107             'tasks': tasks, 'alldone': 0
 108         })
 109
 110 @login_required
 111 def add(request):
 112     if request.method == 'POST':
 113         form = TaskForm(request.POST)
 114         if form.is_valid():
 115             name = form.cleaned_data["name"]
 116             user = request.user
 117             task = Task(name=name,owner=user,ready=False)
 118             task.save()
 119             return redirect('add_min',task_id=task.id)
 120     return redirect('/')
 121
 122 @login_required
 123 def add_min(request,task_id):
 124     task = get_object_or_404(Task, id=task_id)
 125     if request.method == 'POST':
 126      if '_example' in request.POST:
 127         data= {'name':task.name,'pdbid':'1BDD'}
 128         form = TaskForm_min(initial=data)
 129      else:
 130         form = TaskForm_min(request.POST,request.FILES)
 131         if form.is_valid():
 132              task.name=form.cleaned_data["name"]
 133              task.type="min"
 134              pdbid=form.cleaned_data["pdbid"]
 135
 136              basename = str(task.owner)
 137              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 138              task.jobdirname = "_".join([basename, suffix])
 139
 140              if pdbid:
 141               os.mkdir(task.jobdirname)
 142               task.myfile1,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb',
 143                      task.jobdirname+'/plik.pdb')
 144               task.pdbcode=pdbid
 145              else:
 146               task.myfile1=form.cleaned_data["file1"]
 147
 148              seq,task.ssbond=from_pdb(task.myfile1)
 149              task.md_seq=""
 150              for i in range(0,len(seq),40):
 151                     task.md_seq=task.md_seq+seq[i:i+40]+" "
 152
 153              task.ready=True
 154
 155              task.save()
 156              if is_lazy_user(request.user):
 157               return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')
 158              else:
 159               return redirect('/')
 160     else:
 161         data= {'name':task.name}
 162         form = TaskForm_min(initial=data)
 163     p_type='minimization'
 164     basic_adv=True
 165     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 166
 167 @login_required
 168 def add_min_a(request,task_id):
 169     task = get_object_or_404(Task, id=task_id)
 170     if request.method == 'POST':
 171      if '_example' in request.POST:
 172         data= {'name':task.name,'pdbid':'1EI0','unres_ff':'opt-wtfsa-2'}
 173         form = TaskForm_min_a(initial=data)
 174      else:
 175         form = TaskForm_min_a(request.POST,request.FILES)
 176         if form.is_valid():
 177              task.name=form.cleaned_data["name"]
 178              task.type="min"
 179              task.min_choice=form.cleaned_data["min_choice"]
 180              task.min_overlap=form.cleaned_data["min_overlap"]
 181              task.min_searchsc=form.cleaned_data["min_searchsc"]
 182              task.min_maxmin=form.cleaned_data["min_maxmin"]
 183              task.min_maxfun=form.cleaned_data["min_maxfun"]
 184              task.min_pdbout=form.cleaned_data["min_pdbout"]
 185
 186              basename = str(task.owner)
 187              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 188              task.jobdirname = "_".join([basename, suffix])
 189
 190              pdbid=form.cleaned_data["pdbid"]
 191              if pdbid:
 192               os.mkdir(task.jobdirname)
 193               task.myfile1,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb',
 194                      task.jobdirname+'/plik.pdb')
 195               task.pdbcode=pdbid
 196              else:
 197               task.myfile1=form.cleaned_data["file1"]
 198
 199              task.min_unres_pdb=form.cleaned_data["min_unres_pdb"]
 200              task.unres_ff=form.cleaned_data["unres_ff"]
 201              task.boxx=form.cleaned_data["boxx"]
 202              task.boxy=form.cleaned_data["boxy"]
 203              task.boxz=form.cleaned_data["boxz"]
 204
 205              seq,task.ssbond=from_pdb(task.myfile1)
 206              task.md_seq=""
 207              for i in range(0,len(seq),40):
 208                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 209
 210              task.ready=True
 211
 212              task.save()
 213              if is_lazy_user(request.user):
 214               return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')
 215              else:
 216               return redirect('/')
 217     else:
 218         data= {'name':task.name}
 219         form = TaskForm_min_a(initial=data)
 220     basic_adv=False
 221     p_type='minimization - advanced options'
 222     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 223
 224 @login_required
 225 def add_md(request,task_id):
 226     task = get_object_or_404(Task, id=task_id)
 227     if request.method == 'POST':
 228      if '_example' in request.POST:
 229         data= {'name':task.name,'pdbid':'1IGD','md_start':'pdbstart',
 230         'md_pdbref':True,'md_temp':200}
 231         form = TaskForm_md(initial=data)
 232      else:
 233         form = TaskForm_md(request.POST,request.FILES)
 234         if form.is_valid():
 235              task.name=form.cleaned_data["name"]
 236              task.type="md"
 237              task.md_seed=form.cleaned_data["md_seed"]
 238              task.md_start=form.cleaned_data["md_start"]
 239              task.md_temp=form.cleaned_data["md_temp"]
 240              task.md_nstep=form.cleaned_data["md_nstep"]
 241
 242              basename = str(task.owner)
 243              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 244              task.jobdirname = "_".join([basename, suffix])
 245
 246              pdbid=form.cleaned_data["pdbid"]
 247              if pdbid:
 248               os.mkdir(task.jobdirname)
 249               task.myfile1,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb',
 250                      task.jobdirname+'/plik.pdb')
 251               task.pdbcode=pdbid
 252              else:
 253               task.myfile1=form.cleaned_data["file1"]
 254              task.md_pdbref=form.cleaned_data["md_pdbref"]
 255
 256              task.md_seq=""
 257              if task.md_start == "pdbstart" or task.md_pdbref:
 258                seq,task.ssbond=from_pdb(task.myfile1)
 259              else:
 260                seq=seq_add_x(form.cleaned_data["md_seq"])
 261
 262              for i in range(0,len(seq),40):
 263                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 264
 265              if task.md_start != "pdbstart":
 266                 task.ssbond=''
 267
 268              task.ready=True
 269
 270              task.save()
 271              if is_lazy_user(request.user):
 272               return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')
 273              else:
 274               return redirect('/')
 275     else:
 276         data= {'name':task.name}
 277         form = TaskForm_md(initial=data)
 278     basic_adv=True
 279     p_type='molecular dynamics'
 280     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 281
 282 @login_required
 283 def add_md_a(request,task_id):
 284     task = get_object_or_404(Task, id=task_id)
 285     if request.method == 'POST':
 286      if '_example' in request.POST:
 287         data= {'name':task.name,'pdbid':'1L2Y','md_start':'extconf',
 288          'md_pdbref':True,'md_mdpdb':True}
 289         form = TaskForm_md_a(initial=data)
 290      else:
 291         form = TaskForm_md_a(request.POST,request.FILES)
 292         if form.is_valid():
 293              task.name=form.cleaned_data["name"]
 294              task.type="md"
 295
 296              basename = str(task.owner)
 297              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 298              task.jobdirname = "_".join([basename, suffix])
 299
 300              pdbid=form.cleaned_data["pdbid"]
 301              if pdbid:
 302               os.mkdir(task.jobdirname)
 303               task.myfile1,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb',
 304                      task.jobdirname+'/plik.pdb')
 305               task.pdbcode=pdbid
 306              else:
 307               task.myfile1=form.cleaned_data["file1"]
 308              task.md_start=form.cleaned_data["md_start"]
 309              task.md_pdbref=form.cleaned_data["md_pdbref"]
 310
 311              task.md_seq=""
 312              if task.md_start == "pdbstart" or task.md_pdbref:
 313                seq,task.ssbond=from_pdb(task.myfile1)
 314              else:
 315                seq=seq_add_x(form.cleaned_data["md_seq"])
 316              for i in range(0,len(seq),40):
 317                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 318
 319              if task.md_start != "pdbstart":
 320                 task.ssbond=''
 321
 322              task.md_seed=form.cleaned_data["md_seed"]
 323
 324              task.md_temp=form.cleaned_data["md_temp"]
 325              task.md_nstep=form.cleaned_data["md_nstep"]
 326              task.md_ntwe=form.cleaned_data["md_ntwe"]
 327              task.md_ntwx=form.cleaned_data["md_ntwx"]
 328              task.md_dt=form.cleaned_data["md_dt"]
 329              task.md_lang=form.cleaned_data["md_lang"]
 330              task.md_tau=form.cleaned_data["md_tau"]
 331              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
 332              task.md_mdpdb=form.cleaned_data["md_mdpdb"]
 333              task.unres_ff=form.cleaned_data["unres_ff"]
 334              task.md_respa=form.cleaned_data["md_respa"]
 335              task.boxx=form.cleaned_data["boxx"]
 336              task.boxy=form.cleaned_data["boxy"]
 337              task.boxz=form.cleaned_data["boxz"]
 338
 339
 340              task.ready=True
 341
 342              task.save()
 343              if is_lazy_user(request.user):
 344               return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')
 345              else:
 346               return redirect('/')
 347     else:
 348         data= {'name':task.name}
 349         form = TaskForm_md_a(initial=data)
 350     basic_adv=False
 351     p_type='molecular dynamics - advanced options'
 352     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 353
 354 @login_required
 355 def add_remd(request,task_id):
 356     task = get_object_or_404(Task, id=task_id)
 357     if request.method == 'POST':
 358      if '_example' in request.POST:
 359         data= {'name':task.name,'pdbid':'1L2Y','md_pdbref':True}
 360         form = TaskForm_remd(initial=data)
 361      else:
 362         form = TaskForm_remd(request.POST,request.FILES)
 363         if form.is_valid():
 364              task.name=form.cleaned_data["name"]
 365              task.type="remd"
 366              task.md_start=form.cleaned_data["md_start"]
 367
 368              basename = str(task.owner)
 369              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 370              task.jobdirname = "_".join([basename, suffix])
 371
 372              pdbid=form.cleaned_data["pdbid"]
 373              if pdbid:
 374               os.mkdir(task.jobdirname)
 375               task.myfile1,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb',
 376                      task.jobdirname+'/plik.pdb')
 377               task.pdbcode=pdbid
 378              else:
 379               task.myfile1=form.cleaned_data["file1"]
 380              task.md_pdbref=form.cleaned_data["md_pdbref"]
 381              task.md_ntwx=task.remd_nstex
 382
 383              task.md_seq=""
 384              if task.md_start == "pdbstart" or task.md_pdbref:
 385                seq,task.ssbond=from_pdb(task.myfile1)
 386              else:
 387                seq=seq_add_x(form.cleaned_data["md_seq"])
 388              for i in range(0,len(seq),40):
 389                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 390
 391              if task.md_start != "pdbstart":
 392                 task.ssbond=''
 393
 394              task.md_seed=form.cleaned_data["md_seed"]
 395
 396              task.md_nstep=form.cleaned_data["md_nstep"]
 397
 398
 399              task.ready=True
 400
 401
 402              task.save()
 403              if is_lazy_user(request.user):
 404               return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')
 405              else:
 406               return redirect('/')
 407     else:
 408         data= {'name':task.name}
 409         form = TaskForm_remd(initial=data)
 410     basic_adv=True
 411     p_type='replica exchange molecular dynamics'
 412     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 413
 414 @login_required
 415 def add_remd_a(request,task_id):
 416     from django.core.files.uploadedfile import UploadedFile
 417     task = get_object_or_404(Task, id=task_id)
 418     if request.method == 'POST':
 419      if '_example' in request.POST:
 420         data= {'name':task.name,'pdbid':'1E0G','md_pdbref':True,
 421          'md_nstep':500000,'md_lang':'berendsen','unres_ff':'opt-wtfsa-2',
 422          'remd_cluter_temp':280}
 423         form = TaskForm_remd_a(initial=data)
 424      elif '_example_saxs' in request.POST:
 425         data= {'name':task.name,'pdbid':'5UJQ','md_pdbref':True,
 426          'md_nstep':200000,'md_lang':'langevin','unres_ff':'E0LL2Y',
 427          'remd_cluter_temp':270,
 428          'scal_rad':4.0,'wsaxs':100.0,'saxs_data':
 429 """ 0.5     1.33868e-02
 430  1.5     1.95880e-02
 431  2.5     2.68896e-02
 432  3.5     3.43737e-02
 433  4.5     4.07099e-02
 434  5.5     4.47875e-02
 435  6.5     4.63486e-02
 436  7.5     4.60514e-02
 437  8.5     4.49130e-02
 438  9.5     4.36744e-02
 439 10.5     4.26085e-02
 440 11.5     4.17464e-02
 441 12.5     4.11217e-02
 442 13.5     4.07835e-02
 443 14.5     4.06776e-02
 444 15.5     4.06060e-02
 445 16.5     4.03241e-02
 446 17.5     3.96655e-02
 447 18.5     3.85756e-02
 448 19.5     3.70537e-02
 449 20.5     3.50982e-02
 450 21.5     3.27236e-02
 451 22.5     3.00046e-02
 452 23.5     2.70643e-02
 453 24.5     2.40044e-02
 454 25.5     2.08595e-02
 455 26.5     1.76342e-02
 456 27.5     1.43802e-02
 457 28.5     1.12281e-02
 458 29.5     8.34574e-03
 459 30.5     5.87354e-03
 460 31.5     3.88732e-03
 461 32.5     2.39755e-03
 462 33.5     1.36323e-03
 463 34.5     7.06686e-04
 464 35.5     3.30592e-04
 465 36.5     1.38359e-04"""}
 466         form = TaskForm_remd_a(initial=data)
 467      else:
 468         form = TaskForm_remd_a(request.POST,request.FILES)
 469         if form.is_valid():
 470              task.name=form.cleaned_data["name"]
 471              task.type="remd"
 472
 473              basename = str(task.owner)
 474              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 475              task.jobdirname = "_".join([basename, suffix])
 476
 477              pdbid=form.cleaned_data["pdbid"]
 478              if pdbid:
 479               os.mkdir(task.jobdirname)
 480               task.myfile1,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb',
 481                      task.jobdirname+'/plik.pdb')
 482               task.pdbcode=pdbid
 483              else:
 484               task.myfile1=form.cleaned_data["file1"]
 485              task.md_start=form.cleaned_data["md_start"]
 486              task.md_pdbref=form.cleaned_data["md_pdbref"]
 487
 488              task.md_seq=""
 489              if task.md_start == "pdbstart" or task.md_pdbref:
 490                seq,task.ssbond=from_pdb(task.myfile1)
 491              else:
 492                seq=seq_add_x(form.cleaned_data["md_seq"])
 493              for i in range(0,len(seq),40):
 494                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 495
 496              if task.md_start != "pdbstart":
 497                 task.ssbond=''
 498
 499              task.md_seed=form.cleaned_data["md_seed"]
 500              task.md_nstep=form.cleaned_data["md_nstep"]
 501              task.md_dt=form.cleaned_data["md_dt"]
 502              task.md_lang=form.cleaned_data["md_lang"]
 503              task.md_tau=form.cleaned_data["md_tau"]
 504              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
 505              task.remd_nrep=form.cleaned_data["remd_nrep"]
 506              task.remd_nstex=form.cleaned_data["remd_nstex"]
 507              task.md_ntwx=form.cleaned_data["md_ntwx"]
 508              task.md_ntwe=form.cleaned_data["md_ntwe"]
 509              task.md_respa=form.cleaned_data["md_respa"]
 510 #             task.remd_traj1file=form.cleaned_data["remd_traj1file"]
 511 #             task.remd_rest1file=form.cleaned_data["remd_rest1file"]
 512
 513              task.boxx=form.cleaned_data["boxx"]
 514              task.boxy=form.cleaned_data["boxy"]
 515              task.boxz=form.cleaned_data["boxz"]
 516
 517              task.remd_cluter_temp=form.cleaned_data["remd_cluter_temp"]
 518              task.unres_ff=form.cleaned_data["unres_ff"]
 519
 520              task.scal_rad = form.cleaned_data["scal_rad"]
 521              task.saxs_data = form.cleaned_data["saxs_data"]
 522              task.wsaxs = form.cleaned_data["wsaxs"]
 523
 524              task.save()
 525              return redirect('addmlist',task_id=task.id)
 526     else:
 527         data= {'name':task.name}
 528         form = TaskForm_remd_a(initial=data)
 529     basic_adv=False
 530     p_type='replica exchange molecular dynamics - advanced options'
 531     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 532
 533 @login_required
 534 def addmlist(request,task_id):
 535     task = get_object_or_404(Task, id=task_id)
 536     if request.method == 'POST':
 537         form = TaskForm_list(task.remd_nrep,request.POST)
 538         if form.is_valid():
 539              task.remd_multi_t=form.cleaned_data["temperatures"]
 540              task.remd_multi_m=form.cleaned_data["multiplexing"]
 541              task.ready=True
 542
 543              task.save()
 544              if is_lazy_user(request.user):
 545               return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')
 546              else:
 547               return redirect('/')
 548     else:
 549       if task.unres_ff == 'E0LL2Y':
 550         data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
 551         '["1", "1", "1", "1", "1", "1", "1", "1"]',
 552         'temperatures':
 553         '["270", "280", "290", "300", "310", "320", "330", "345"]'
 554         }
 555       else:
 556         data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
 557         '["1", "1", "1", "1", "1", "1", "1", "1"]',
 558         'temperatures':
 559         '["250", "260", "270", "280", "290", "300", "315", "330"]'
 560         }
 561
 562       form = TaskForm_list(task.remd_nrep,initial=data)
 563     p_type='replica exchange molecular dynamics - advanced options'
 564     return render(request, 'edit_lista.html', {'form': form, 'task':task, 'p_type':p_type})
 565
 566 @login_required
 567 def details(request,task_id):
 568     task = get_object_or_404(Task, id=task_id)
 569     return render(request, "details.html",{'task':task})
 570
 571
 572 def details1(request,user_id,task_id):
 573     task = get_object_or_404(Task, id=task_id)
 574     return render(request, "details1.html",{'task':task})
 575
 576
 577 @login_required
 578 def delete(request, task_id):
 579     Task.objects.get(id=task_id).delete()
 580     return redirect('/')
 581
 582 def refresh_done1(request, task_id):
 583     task = get_object_or_404(Task, id=task_id)
 584     user = task.owner
 585     refresh_done0(task)
 586
 587     proc = subprocess.Popen('/opt/torque/bin/qstat', stdout=subprocess.PIPE)
 588     njob=0
 589     nq=0
 590     for line in proc.stdout:
 591       if 'piasek4' in line:
 592         if line.split()[1]=='test_server':
 593           njob+=1
 594           if line.split()[-2]=='Q':
 595             nq+=1
 596     variable='Idle jobs='+str(nq)+' Total jobs='+str(njob)
 597
 598     return redirect('/details1/'+str(user)+'/'+str(task.id)+'/')
 599
 600
 601 @login_required
 602 def refresh_done(request):
 603     user = request.user
 604     tasks = Task.objects.filter(owner=user).order_by('-created_date')
 605     alldone = 1
 606     for task in tasks:
 607       refresh_done0(task)
 608       if not task.done:
 609          alldone=0
 610
 611     proc = subprocess.Popen('/opt/torque/bin/qstat', stdout=subprocess.PIPE)
 612     njob=0
 613     nq=0
 614     for line in proc.stdout:
 615       if 'piasek4' in line:
 616         if line.split()[1]=='test_server':
 617           njob+=1
 618           if line.split()[-2]=='Q':
 619             nq+=1
 620     variable='Idle jobs='+str(nq)+' Total jobs='+str(njob)
 621
 622     if is_lazy_user(request.user):
 623      return redirect('/details1/'+str(user)+'/'+str(task.id)+'/')
 624     else:
 625      return render(request, "index.html", {
 626                 'tasks': tasks ,
 627                 'variable' : variable,
 628                 'alldone': alldone
 629                         })
 630
 631
 632 def refresh_done0(task):
 633       if os.path.isfile(task.jobdirname+'/finished') and not task.done:
 634          task.done=True
 635
 636          with open(task.jobdirname+'/file.out_GB000', 'r') as f:
 637
 638            if task.type=='min' or task.type=='md':
 639              text=""
 640              for line in f:
 641                if 'ETOT' in line:
 642                   task.etot=line.split()[1]
 643
 644                if 'RMS deviation' in line:
 645                   text=text+line
 646                   i=1
 647                   for line1 in f:
 648                      text=text+line1
 649                      i+=1
 650                      if i>6:
 651                        break
 652                if 'Total wall' in line:
 653                   text=text+line
 654
 655            elif task.type=='remd':
 656              j=0
 657              text="Acceptance for replica exchanges and number of exchange attempts\n"
 658              for line in f:
 659
 660                if 'ACC' in line:
 661                     j+=1
 662                     text=text+' '.join(line.split()[2:])+"\n"
 663                     if j==task.remd_nrep:
 664                        j=1
 665                        text="Acceptance for replica exchanges and number of exchange attempts\n"+' '.join(line.split()[2:])+"\n"
 666
 667                if 'Total wall' in line:
 668                   text=text+line
 669
 670          task.results_text=text
 671
 672
 673          if task.md_pdbref and task.type=='remd':
 674
 675           for i in range(1,6):
 676            try:
 677             with open(task.jobdirname+'/file_wham_T'+str(int(task.remd_cluter_temp))+'K_000'+str(i)+'.pdb', 'r') as f:
 678                  line=f.readline()
 679                  if i==1:
 680                      task.remd_model1='Cluster1 '+' '.join(line.split()[-3:])
 681                  elif i==2:
 682                      task.remd_model2='Cluster2 '+' '.join(line.split()[-3:])
 683                  elif i==3:
 684                      task.remd_model3='Cluster3 '+' '.join(line.split()[-3:])
 685                  elif i==4:
 686                      task.remd_model4='Cluster4 '+' '.join(line.split()[-3:])
 687                  elif i==5:
 688                      task.remd_model5='Cluster5 '+' '.join(line.split()[-3:])
 689            except EnvironmentError:
 690             print 'file_wham_T*pdb open error'
 691           for i in range(1,6):
 692             with open(task.jobdirname+'/tmscore'+str(i)+'.out', 'r') as f:
 693                text=''
 694                for line in f:
 695                  if 'RMSD of  the common residues=' in line:
 696                    text=' RMSD='+line.split()[5]
 697                  if 'TM-score    =' in line:
 698                    text=text+' TMscore='+line.split()[2]
 699                  if 'GDT-TS-score=' in line:
 700                    text=text+' GDT_TS='+line.split()[1]
 701
 702                if i==1:
 703                      task.remd_model1=task.remd_model1+text
 704                elif i==2:
 705                      task.remd_model2=task.remd_model2+text
 706                elif i==3:
 707                      task.remd_model3=task.remd_model3+text
 708                elif i==4:
 709                      task.remd_model4=task.remd_model4+text
 710                elif i==5:
 711                      task.remd_model5=task.remd_model5+text
 712
 713
 714
 715          if task.type=='remd':
 716           with open(task.jobdirname+'/file_cluster_clust.out_000', 'r') as f:
 717
 718            for line in f:
 719              if 'sumprob' in line:
 720                 i=0
 721                 for line1 in f:
 722                   i+=1
 723                   if i>6:
 724                        break
 725                   if i==1:
 726                      task.remd_model1=task.remd_model1+' Cluster1 probability= '+line1.split()[2]
 727                   elif i==2:
 728                      task.remd_model2=task.remd_model2+' Cluster2 probability= '+line1.split()[2]
 729                   elif i==3:
 730                      task.remd_model3=task.remd_model3+' Cluster3 probability= '+line1.split()[2]
 731                   elif i==4:
 732                      task.remd_model4=task.remd_model4+' Cluster4 probability= '+line1.split()[2]
 733                   elif i==5:
 734                      task.remd_model5=task.remd_model5+' Cluster5 probability= '+line1.split()[2]
 735
 736
 737
 738          task.save()
 739       elif os.path.isfile(task.jobdirname+'/file_GB000.stat') and not task.done:
 740          if (task.type=='min'):
 741            task.running =1
 742          else:
 743            with open(task.jobdirname+'/file_GB000.stat', 'r') as f:
 744               line=''
 745               for line in f:
 746                 pass
 747               if line != '':
 748                 last = line.split()[0]
 749               else:
 750                 last = 0
 751            task.running=int(1+int(last)*100.0/task.md_nstep)
 752            if task.running>100:
 753              task.running=100
 754          task.save()
 755
 756
 757       return