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
  12 res_codes = [
  13                 # 20 canonical amino acids
  14                 ('CYS', 'C'), ('ASP', 'D'), ('SER', 'S'), ('GLN', 'Q'),
  15                 ('LYS', 'K'), ('ILE', 'I'), ('PRO', 'P'), ('THR', 'T'),
  16                 ('PHE', 'F'), ('ASN', 'N'), ('GLY', 'G'), ('HIS', 'H'),
  17                 ('LEU', 'L'), ('ARG', 'R'), ('TRP', 'W'), ('ALA', 'A'),
  18                 ('VAL', 'V'), ('GLU', 'E'), ('TYR', 'Y'), ('MET', 'M'),
  19                 ('HSD', 'H'),('HSE', 'H'),('HSP', 'H'),
  20                 ('HIE', 'H'), ('HID', 'H'),('HIP', 'H'),
  21                 ('CYX', 'C'),
  22                ]
  23
  24 three_to_one = dict(res_codes)
  25
  26 def seq_add_x(sequence):
  27     if sequence[0] != 'G':
  28         sequence='X'+sequence
  29     if sequence[-1] != 'G':
  30         sequence=sequence+'X'
  31     set ='CDSQKIPTFNGHLRWAVEYMX'
  32     sequence = ''.join([c for c in sequence if c in set])
  33
  34     return(sequence)
  35
  36 def from_pdb(file):
  37     sequence = []
  38     ssbond = []
  39     ssbond_ch = []
  40     ires = []
  41     chain_start = {}
  42     chain_end = {}
  43     unres_shift = {}
  44     chain=[]
  45     ichain=0
  46     newchain = True
  47
  48     for line in file:
  49             if line[0:6] == 'COMPND' and line[11:17] == 'CHAIN:':
  50               tmp=line[18:]
  51               chain_=tmp.split(', ')
  52               chain_[-1]=chain_[-1][0]
  53               chain.extend(chain_)
  54
  55             if line[0:6] == 'ATOM  ' and line[13:15] == 'CA':
  56               aa = three_to_one.get(line[17:20])
  57               i = int(line[22:26])
  58               if newchain or i!=ires[-1]:
  59                 sequence.append(aa)
  60                 ires.append(i)
  61                 if newchain:
  62                  if len(chain)>0:
  63                   chain_start[chain[ichain]]=i
  64                  newchain = False
  65             if line[0:3] == 'TER':
  66               sequence.append('XX')
  67               if len(chain)>0:
  68                chain_end[chain[ichain]]=i
  69               ichain=ichain+1
  70               newchain = True
  71             if line[0:6] == 'SSBOND':
  72               b=[]
  73               b.append(int(line[17:21]))
  74               b.append(int(line[31:35]))
  75               ssbond.append(b)
  76               c = []
  77               c.append((line[15:16]))
  78               c.append((line[29:30]))
  79               ssbond_ch.append(c)
  80             if line[0:3] == 'END':
  81               break
  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:
  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
 108         })
 109
 110 @allow_lazy_user
 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         form = TaskForm_min(request.POST,request.FILES)
 127         if form.is_valid():
 128              task.name=form.cleaned_data["name"]
 129              task.type="min"
 130              task.myfile1=form.cleaned_data["file1"]
 131
 132              seq,task.ssbond=from_pdb(task.myfile1)
 133              task.md_seq=""
 134              for i in range(0,len(seq),40):
 135                     task.md_seq=task.md_seq+seq[i:i+40]+" "
 136
 137              task.ready=True
 138              basename = str(task.owner)
 139              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 140              task.jobdirname = "_".join([basename, suffix])
 141
 142              task.save()
 143              return redirect('/')
 144     else:
 145         data= {'name':task.name}
 146         form = TaskForm_min(initial=data)
 147     p_type='minimization'
 148     basic_adv=True
 149     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 150
 151 @login_required
 152 def add_min_a(request,task_id):
 153     task = get_object_or_404(Task, id=task_id)
 154     if request.method == 'POST':
 155         form = TaskForm_min_a(request.POST,request.FILES)
 156         if form.is_valid():
 157              task.name=form.cleaned_data["name"]
 158              task.type="min"
 159              task.min_choice=form.cleaned_data["min_choice"]
 160              task.min_overlap=form.cleaned_data["min_overlap"]
 161              task.min_searchsc=form.cleaned_data["min_searchsc"]
 162              task.min_maxmin=form.cleaned_data["min_maxmin"]
 163              task.min_maxfun=form.cleaned_data["min_maxfun"]
 164              task.min_pdbout=form.cleaned_data["min_pdbout"]
 165              task.myfile1=form.cleaned_data["file1"]
 166              task.min_unres_pdb=form.cleaned_data["min_unres_pdb"]
 167              task.unres_ff=form.cleaned_data["unres_ff"]
 168              task.boxx=form.cleaned_data["boxx"]
 169              task.boxy=form.cleaned_data["boxy"]
 170              task.boxz=form.cleaned_data["boxz"]
 171
 172              seq,task.ssbond=from_pdb(task.myfile1)
 173              task.md_seq=""
 174              for i in range(0,len(seq),40):
 175                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 176
 177
 178              task.ready=True
 179              basename = str(task.owner)
 180              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 181              task.jobdirname = "_".join([basename, suffix])
 182
 183              task.save()
 184              return redirect('/')
 185     else:
 186         data= {'name':task.name}
 187         form = TaskForm_min_a(initial=data)
 188     basic_adv=False
 189     p_type='minimization - advanced options'
 190     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 191
 192 @login_required
 193 def add_md(request,task_id):
 194     task = get_object_or_404(Task, id=task_id)
 195     if request.method == 'POST':
 196         form = TaskForm_md(request.POST,request.FILES)
 197         if form.is_valid():
 198              task.name=form.cleaned_data["name"]
 199              task.type="md"
 200              task.md_seed=form.cleaned_data["md_seed"]
 201              task.md_start=form.cleaned_data["md_start"]
 202              task.md_temp=form.cleaned_data["md_temp"]
 203              task.md_nstep=form.cleaned_data["md_nstep"]
 204
 205              task.myfile1=form.cleaned_data["file1"]
 206              task.md_pdbref=form.cleaned_data["md_pdbref"]
 207
 208              task.md_seq=""
 209              if task.md_start == "pdbstart" or task.md_pdbref:
 210                seq,task.ssbond=from_pdb(task.myfile1)
 211              else:
 212                seq=seq_add_x(form.cleaned_data["md_seq"])
 213
 214              for i in range(0,len(seq),40):
 215                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 216
 217              if task.md_start != "pdbstart":
 218                 task.ssbond=''
 219
 220              task.ready=True
 221              basename = str(task.owner)
 222              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 223              task.jobdirname = "_".join([basename, suffix])
 224
 225              task.save()
 226              return redirect('/')
 227     else:
 228         data= {'name':task.name}
 229         form = TaskForm_md(initial=data)
 230     basic_adv=True
 231     p_type='molecular dynamics'
 232     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 233
 234 @login_required
 235 def add_md_a(request,task_id):
 236     task = get_object_or_404(Task, id=task_id)
 237     if request.method == 'POST':
 238         form = TaskForm_md_a(request.POST,request.FILES)
 239         if form.is_valid():
 240              task.name=form.cleaned_data["name"]
 241              task.type="md"
 242
 243              task.myfile1=form.cleaned_data["file1"]
 244              task.md_start=form.cleaned_data["md_start"]
 245              task.md_pdbref=form.cleaned_data["md_pdbref"]
 246
 247              task.md_seq=""
 248              if task.md_start == "pdbstart" or task.md_pdbref:
 249                seq,task.ssbond=from_pdb(task.myfile1)
 250              else:
 251                seq=seq_add_x(form.cleaned_data["md_seq"])
 252              for i in range(0,len(seq),40):
 253                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 254
 255              if task.md_start != "pdbstart":
 256                 task.ssbond=''
 257
 258              task.md_seed=form.cleaned_data["md_seed"]
 259
 260              task.md_temp=form.cleaned_data["md_temp"]
 261              task.md_nstep=form.cleaned_data["md_nstep"]
 262              task.md_ntwe=form.cleaned_data["md_ntwe"]
 263              task.md_ntwx=form.cleaned_data["md_ntwx"]
 264              task.md_dt=form.cleaned_data["md_dt"]
 265              task.md_lang=form.cleaned_data["md_lang"]
 266              task.md_tau=form.cleaned_data["md_tau"]
 267              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
 268              task.md_mdpdb=form.cleaned_data["md_mdpdb"]
 269              task.unres_ff=form.cleaned_data["unres_ff"]
 270              task.boxx=form.cleaned_data["boxx"]
 271              task.boxy=form.cleaned_data["boxy"]
 272              task.boxz=form.cleaned_data["boxz"]
 273
 274
 275              task.ready=True
 276              basename = str(task.owner)
 277              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 278              task.jobdirname = "_".join([basename, suffix])
 279
 280              task.save()
 281              return redirect('/')
 282     else:
 283         data= {'name':task.name}
 284         form = TaskForm_md_a(initial=data)
 285     basic_adv=False
 286     p_type='molecular dynamics - advanced options'
 287     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 288
 289 @login_required
 290 def add_remd(request,task_id):
 291     task = get_object_or_404(Task, id=task_id)
 292     if request.method == 'POST':
 293         form = TaskForm_remd(request.POST,request.FILES)
 294         if form.is_valid():
 295              task.name=form.cleaned_data["name"]
 296              task.type="remd"
 297              task.md_start=form.cleaned_data["md_start"]
 298              task.myfile1=form.cleaned_data["file1"]
 299              task.md_pdbref=form.cleaned_data["md_pdbref"]
 300              task.md_ntwx=task.remd_nstex
 301
 302              task.md_seq=""
 303              if task.md_start == "pdbstart" or task.md_pdbref:
 304                seq,task.ssbond=from_pdb(task.myfile1)
 305              else:
 306                seq=seq_add_x(form.cleaned_data["md_seq"])
 307              for i in range(0,len(seq),40):
 308                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 309
 310              if task.md_start != "pdbstart":
 311                 task.ssbond=''
 312
 313              task.md_seed=form.cleaned_data["md_seed"]
 314
 315              task.md_nstep=form.cleaned_data["md_nstep"]
 316
 317
 318              task.ready=True
 319
 320              basename = str(task.owner)
 321              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 322              task.jobdirname = "_".join([basename, suffix])
 323
 324              task.save()
 325              return redirect('/')
 326     else:
 327         data= {'name':task.name}
 328         form = TaskForm_remd(initial=data)
 329     basic_adv=True
 330     p_type='replica exchange molecular dynamics'
 331     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 332
 333 @login_required
 334 def add_remd_a(request,task_id):
 335     task = get_object_or_404(Task, id=task_id)
 336     if request.method == 'POST':
 337         form = TaskForm_remd_a(request.POST,request.FILES)
 338         if form.is_valid():
 339              task.name=form.cleaned_data["name"]
 340              task.type="remd"
 341
 342              task.myfile1=form.cleaned_data["file1"]
 343              task.md_start=form.cleaned_data["md_start"]
 344              task.md_pdbref=form.cleaned_data["md_pdbref"]
 345
 346              task.md_seq=""
 347              if task.md_start == "pdbstart" or task.md_pdbref:
 348                seq,task.ssbond=from_pdb(task.myfile1)
 349              else:
 350                seq=seq_add_x(form.cleaned_data["md_seq"])
 351              for i in range(0,len(seq),40):
 352                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 353
 354              if task.md_start != "pdbstart":
 355                 task.ssbond=''
 356
 357              task.md_seed=form.cleaned_data["md_seed"]
 358              task.md_nstep=form.cleaned_data["md_nstep"]
 359              task.md_dt=form.cleaned_data["md_dt"]
 360              task.md_lang=form.cleaned_data["md_lang"]
 361              task.md_tau=form.cleaned_data["md_tau"]
 362              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
 363              task.remd_nrep=form.cleaned_data["remd_nrep"]
 364              task.remd_nstex=form.cleaned_data["remd_nstex"]
 365              task.md_ntwx=form.cleaned_data["md_ntwx"]
 366              task.md_ntwe=form.cleaned_data["md_ntwe"]
 367 #             task.remd_traj1file=form.cleaned_data["remd_traj1file"]
 368 #             task.remd_rest1file=form.cleaned_data["remd_rest1file"]
 369
 370              task.boxx=form.cleaned_data["boxx"]
 371              task.boxy=form.cleaned_data["boxy"]
 372              task.boxz=form.cleaned_data["boxz"]
 373
 374
 375              task.remd_cluter_temp=form.cleaned_data["remd_cluter_temp"]
 376              task.unres_ff=form.cleaned_data["unres_ff"]
 377
 378              basename = str(task.owner)
 379              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 380              task.jobdirname = "_".join([basename, suffix])
 381
 382              task.save()
 383              return redirect('addmlist',task_id=task.id)
 384     else:
 385         data= {'name':task.name}
 386         form = TaskForm_remd_a(initial=data)
 387     basic_adv=False
 388     p_type='replica exchange molecular dynamics - advanced options'
 389     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 390
 391 @login_required
 392 def addmlist(request,task_id):
 393     task = get_object_or_404(Task, id=task_id)
 394     if request.method == 'POST':
 395         form = TaskForm_list(task.remd_nrep,request.POST)
 396         if form.is_valid():
 397              task.remd_multi_t=form.cleaned_data["temperatures"]
 398              task.remd_multi_m=form.cleaned_data["multiplexing"]
 399              task.ready=True
 400
 401              task.save()
 402              return redirect('/')
 403     else:
 404       if task.unres_ff == 'E0LL2Y':
 405         data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
 406         '["1", "1", "1", "1", "1", "1", "1", "1"]',
 407         'temperatures':
 408         '["270", "280", "290", "300", "310", "320", "330", "345"]'
 409         }
 410       else:
 411         data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
 412         '["1", "1", "1", "1", "1", "1", "1", "1"]',
 413         'temperatures':
 414         '["250", "260", "270", "280", "290", "300", "315", "330"]'
 415         }
 416
 417       form = TaskForm_list(task.remd_nrep,initial=data)
 418     p_type='replica exchange molecular dynamics - advanced options'
 419     return render(request, 'edit_lista.html', {'form': form, 'task':task, 'p_type':p_type})
 420
 421 def details(request,task_id):
 422     task = get_object_or_404(Task, id=task_id)
 423     return render(request, "details.html",{'task':task})
 424
 425 @login_required
 426 def delete(request, task_id):
 427     Task.objects.get(id=task_id).delete()
 428     return redirect('/')
 429
 430 @login_required
 431 def refresh_done(request):
 432     user = request.user
 433     tasks = Task.objects.filter(owner=user).order_by('-created_date')
 434     for task in tasks:
 435       if os.path.isfile(task.jobdirname+'/finished') and not task.done:
 436          task.done=True
 437
 438          with open(task.jobdirname+'/file.out_GB000', 'r') as f:
 439
 440            if task.type=='min' or task.type=='md':
 441              text=""
 442              for line in f:
 443                if 'ETOT' in line:
 444                   task.etot=line.split()[1]
 445
 446                if 'RMS deviation' in line:
 447                   text=text+line
 448                   i=1
 449                   for line1 in f:
 450                      text=text+line1
 451                      i+=1
 452                      if i>6:
 453                        break
 454                if 'Total wall' in line:
 455                   text=text+line
 456
 457            elif task.type=='remd':
 458              j=0
 459              text="Acceptance for replica exchanges\n"
 460              for line in f:
 461
 462                if 'ACC' in line:
 463                     j+=1
 464                     text=text+line
 465                     if j==task.remd_nrep:
 466                        j=1
 467                        text="Acceptance for replica exchanges\n"+line
 468
 469                if 'Total wall' in line:
 470                   text=text+line
 471
 472          task.results_text=text
 473
 474
 475          if task.md_pdbref and task.type=='remd':
 476
 477           for i in range(1,6):
 478            try:
 479             with open(task.jobdirname+'/file_wham_T'+str(int(task.remd_cluter_temp))+'K_000'+str(i)+'.pdb', 'r') as f:
 480                  line=f.readline()
 481                  if i==1:
 482                      task.remd_model1=' '.join(line.split()[-6:])
 483                  elif i==2:
 484                      task.remd_model2=' '.join(line.split()[-6:])
 485                  elif i==3:
 486                      task.remd_model3=' '.join(line.split()[-6:])
 487                  elif i==4:
 488                      task.remd_model4=' '.join(line.split()[-6:])
 489                  elif i==5:
 490                      task.remd_model5=' '.join(line.split()[-6:])
 491            except EnvironmentError:
 492             print 'file_wham_T*pdb open error'
 493           for i in range(1,6):
 494             with open(task.jobdirname+'/tmscore'+str(i)+'.out', 'r') as f:
 495                text=''
 496                for line in f:
 497                  if 'RMSD of  the common residues=' in line:
 498                    text=' RMSD='+line.split()[5]
 499                  if 'TM-score    =' in line:
 500                    text=text+' TMscore='+line.split()[2]
 501                  if 'GDT-TS-score=' in line:
 502                    text=text+' GDT_TS='+line.split()[1]
 503
 504                if i==1:
 505                      task.remd_model1=task.remd_model1+text
 506                elif i==2:
 507                      task.remd_model2=task.remd_model2+text
 508                elif i==3:
 509                      task.remd_model3=task.remd_model3+text
 510                elif i==4:
 511                      task.remd_model4=task.remd_model4+text
 512                elif i==5:
 513                      task.remd_model5=task.remd_model5+text
 514
 515
 516
 517          if task.type=='remd':
 518           with open(task.jobdirname+'/file_cluster_clust.out_000', 'r') as f:
 519
 520            for line in f:
 521              if 'sumprob' in line:
 522                 i=0
 523                 for line1 in f:
 524                   i+=1
 525                   if i>6:
 526                        break
 527                   if i==1:
 528                      task.remd_model1=task.remd_model1+' Cluster1 probability= '+line1.split()[2]
 529                   elif i==2:
 530                      task.remd_model2=task.remd_model2+' Cluster2 probability= '+line1.split()[2]
 531                   elif i==3:
 532                      task.remd_model3=task.remd_model3+' Cluster3 probability= '+line1.split()[2]
 533                   elif i==4:
 534                      task.remd_model4=task.remd_model4+' Cluster4 probability= '+line1.split()[2]
 535                   elif i==5:
 536                      task.remd_model5=task.remd_model5+' Cluster5 probability= '+line1.split()[2]
 537
 538
 539
 540          task.save()
 541       elif os.path.isfile(task.jobdirname+'/file_GB000.stat') and not task.done:
 542          if (task.type=='min'):
 543            task.running =1
 544          else:
 545            with open(task.jobdirname+'/file_GB000.stat', 'r') as f:
 546               line=''
 547               for line in f:
 548                 pass
 549               if line != '':
 550                 last = line.split()[0]
 551               else:
 552                 last = 0
 553            task.running=int(1+int(last)*100.0/task.md_nstep)
 554            if task.running>100:
 555              task.running=100
 556          task.save()
 557
 558     proc = subprocess.Popen('/opt/torque/bin/qstat', stdout=subprocess.PIPE)
 559     njob=0
 560     nq=0
 561     for line in proc.stdout:
 562       if 'piasek4' in line:
 563         if line.split()[1]=='test_server':
 564           njob+=1
 565           if line.split()[-2]=='Q':
 566             nq+=1
 567     variable='Idle jobs='+str(nq)+' Total jobs='+str(njob)
 568
 569     return render(request, "index.html", {
 570                 'tasks': tasks ,
 571                 'variable' : variable
 572                         })
 573
 574 #   return redirect('/')