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
  10 res_codes = [
  11                 # 20 canonical amino acids
  12                 ('CYS', 'C'), ('ASP', 'D'), ('SER', 'S'), ('GLN', 'Q'),
  13                 ('LYS', 'K'), ('ILE', 'I'), ('PRO', 'P'), ('THR', 'T'),
  14                 ('PHE', 'F'), ('ASN', 'N'), ('GLY', 'G'), ('HIS', 'H'),
  15                 ('LEU', 'L'), ('ARG', 'R'), ('TRP', 'W'), ('ALA', 'A'),
  16                 ('VAL', 'V'), ('GLU', 'E'), ('TYR', 'Y'), ('MET', 'M'),
  17                 ('HSD', 'H'),('HSE', 'H'),('HSP', 'H'),
  18                 ('HIE', 'H'), ('HID', 'H'),('HIP', 'H'),
  19                 ('CYX', 'C'),
  20                ]
  21
  22 three_to_one = dict(res_codes)
  23
  24 def seq_add_x(sequence):
  25     if sequence[0] != 'G':
  26         sequence='X'+sequence
  27     if sequence[-1] != 'G':
  28         sequence=sequence+'X'
  29     set ='CDSQKIPTFNGHLRWAVEYMX'
  30     sequence = ''.join([c for c in sequence if c in set])
  31
  32     return(sequence)
  33
  34 def from_pdb(file):
  35     sequence = []
  36     ssbond = []
  37     for line in file:
  38             if line[0:6] == 'ATOM  ' and line[13:15] == 'CA':
  39               aa = three_to_one.get(line[17:20])
  40               sequence.append(aa)
  41             if line[0:3] == 'TER':
  42               sequence.append('XX')
  43             if line[0:6] == 'SSBOND':
  44               b=[]
  45               b.append(int(line[17:21]))
  46               b.append(int(line[31:35]))
  47               ssbond.append(b)
  48
  49             if line[0:3] == 'END':
  50               break
  51     while sequence[-1] == 'XX':
  52             del sequence[-1]
  53     if sequence[0] != 'G':
  54             sequence.insert(0,'X')
  55             ssbond=[ [e[0]+1,e[1]+1] for e in ssbond]
  56     if sequence[-1] != 'G':
  57             sequence.append('X')
  58     seq=''.join(sequence)
  59     return seq,ssbond
  60
  61
  62 @login_required
  63 def index(request):
  64     user = request.user
  65     tasks = Task.objects.filter(owner=user)
  66     variable = ''
  67     return render(request, "index.html", {
  68             'tasks': tasks
  69         })
  70
  71 @login_required
  72 def add(request):
  73     if request.method == 'POST':
  74         form = TaskForm(request.POST)
  75         if form.is_valid():
  76             name = form.cleaned_data["name"]
  77             user = request.user
  78             task = Task(name=name,owner=user,ready=False)
  79             task.save()
  80             return redirect('add_min',task_id=task.id)
  81     return redirect('/')
  82
  83
  84 @login_required
  85 def add_min(request,task_id):
  86     task = get_object_or_404(Task, id=task_id)
  87     if request.method == 'POST':
  88         form = TaskForm_min(request.POST,request.FILES)
  89         if form.is_valid():
  90              task.name=form.cleaned_data["name"]
  91              task.type="min"
  92              task.myfile1=form.cleaned_data["file1"]
  93
  94              seq,task.ssbond=from_pdb(task.myfile1)
  95              task.md_seq=""
  96              for i in range(0,len(seq),40):
  97                     task.md_seq=task.md_seq+seq[i:i+40]+" "
  98
  99              task.ready=True
 100              basename = str(task.owner)
 101              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 102              task.jobdirname = "_".join([basename, suffix])
 103
 104              task.save()
 105              return redirect('/')
 106     else:
 107         data= {'name':task.name}
 108         form = TaskForm_min(initial=data)
 109     p_type='minimization'
 110     basic_adv=True
 111     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 112
 113 def add_min_a(request,task_id):
 114     task = get_object_or_404(Task, id=task_id)
 115     if request.method == 'POST':
 116         form = TaskForm_min_a(request.POST,request.FILES)
 117         if form.is_valid():
 118              task.name=form.cleaned_data["name"]
 119              task.type="min"
 120              task.min_choice=form.cleaned_data["min_choice"]
 121              task.min_overlap=form.cleaned_data["min_overlap"]
 122              task.min_searchsc=form.cleaned_data["min_searchsc"]
 123              task.min_maxmin=form.cleaned_data["min_maxmin"]
 124              task.min_maxfun=form.cleaned_data["min_maxfun"]
 125              task.min_pdbout=form.cleaned_data["min_pdbout"]
 126              task.myfile1=form.cleaned_data["file1"]
 127              task.min_unres_pdb=form.cleaned_data["min_unres_pdb"]
 128              task.unres_ff=form.cleaned_data["unres_ff"]
 129
 130              seq,task.ssbond=from_pdb(task.myfile1)
 131              task.md_seq=""
 132              for i in range(0,len(seq),40):
 133                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 134
 135
 136              task.ready=True
 137              basename = str(task.owner)
 138              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 139              task.jobdirname = "_".join([basename, suffix])
 140
 141              task.save()
 142              return redirect('/')
 143     else:
 144         data= {'name':task.name}
 145         form = TaskForm_min_a(initial=data)
 146     basic_adv=False
 147     p_type='minimization - advanced options'
 148     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 149
 150 @login_required
 151 def add_md(request,task_id):
 152     task = get_object_or_404(Task, id=task_id)
 153     if request.method == 'POST':
 154         form = TaskForm_md(request.POST,request.FILES)
 155         if form.is_valid():
 156              task.name=form.cleaned_data["name"]
 157              task.type="md"
 158              task.md_seed=form.cleaned_data["md_seed"]
 159              task.md_start=form.cleaned_data["md_start"]
 160              task.md_temp=form.cleaned_data["md_temp"]
 161              task.md_nstep=form.cleaned_data["md_nstep"]
 162
 163              task.myfile1=form.cleaned_data["file1"]
 164              task.md_pdbref=form.cleaned_data["md_pdbref"]
 165
 166              task.md_seq=""
 167              if task.md_start == "pdbstart" or task.md_pdbref:
 168                seq,task.ssbond=from_pdb(task.myfile1)
 169              else:
 170                seq=seq_add_x(form.cleaned_data["md_seq"])
 171
 172              for i in range(0,len(seq),40):
 173                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 174
 175              if task.md_start != "pdbstart":
 176                 task.ssbond=''
 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_md(initial=data)
 188     basic_adv=True
 189     p_type='molecular dynamics'
 190     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 191
 192 def add_md_a(request,task_id):
 193     task = get_object_or_404(Task, id=task_id)
 194     if request.method == 'POST':
 195         form = TaskForm_md_a(request.POST,request.FILES)
 196         if form.is_valid():
 197              task.name=form.cleaned_data["name"]
 198              task.type="md"
 199
 200              task.myfile1=form.cleaned_data["file1"]
 201              task.md_start=form.cleaned_data["md_start"]
 202              task.md_pdbref=form.cleaned_data["md_pdbref"]
 203
 204              task.md_seq=""
 205              if task.md_start == "pdbstart" or task.md_pdbref:
 206                seq,task.ssbond=from_pdb(task.myfile1)
 207              else:
 208                seq=seq_add_x(form.cleaned_data["md_seq"])
 209              for i in range(0,len(seq),40):
 210                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 211
 212              if task.md_start != "pdbstart":
 213                 task.ssbond=''
 214
 215              task.md_seed=form.cleaned_data["md_seed"]
 216
 217              task.md_temp=form.cleaned_data["md_temp"]
 218              task.md_nstep=form.cleaned_data["md_nstep"]
 219              task.md_ntwe=form.cleaned_data["md_ntwe"]
 220              task.md_ntwx=form.cleaned_data["md_ntwx"]
 221              task.md_dt=form.cleaned_data["md_dt"]
 222              task.md_lang=form.cleaned_data["md_lang"]
 223              task.md_tau=form.cleaned_data["md_tau"]
 224              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
 225              task.md_mdpdb=form.cleaned_data["md_mdpdb"]
 226              task.unres_ff=form.cleaned_data["unres_ff"]
 227
 228              task.ready=True
 229              basename = str(task.owner)
 230              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 231              task.jobdirname = "_".join([basename, suffix])
 232
 233              task.save()
 234              return redirect('/')
 235     else:
 236         data= {'name':task.name}
 237         form = TaskForm_md_a(initial=data)
 238     basic_adv=False
 239     p_type='molecular dynamics - advanced options'
 240     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 241
 242 @login_required
 243 def add_remd(request,task_id):
 244     task = get_object_or_404(Task, id=task_id)
 245     if request.method == 'POST':
 246         form = TaskForm_remd(request.POST,request.FILES)
 247         if form.is_valid():
 248              task.name=form.cleaned_data["name"]
 249              task.type="remd"
 250              task.md_start=form.cleaned_data["md_start"]
 251              task.myfile1=form.cleaned_data["file1"]
 252              task.md_pdbref=form.cleaned_data["md_pdbref"]
 253
 254              task.md_seq=""
 255              if task.md_start == "pdbstart" or task.md_pdbref:
 256                seq,task.ssbond=from_pdb(task.myfile1)
 257              else:
 258                seq=seq_add_x(form.cleaned_data["md_seq"])
 259              for i in range(0,len(seq),40):
 260                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 261
 262              if task.md_start != "pdbstart":
 263                 task.ssbond=''
 264
 265              task.md_seed=form.cleaned_data["md_seed"]
 266
 267              task.md_nstep=form.cleaned_data["md_nstep"]
 268
 269
 270              task.ready=True
 271
 272              basename = str(task.owner)
 273              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 274              task.jobdirname = "_".join([basename, suffix])
 275
 276              task.save()
 277              return redirect('/')
 278     else:
 279         data= {'name':task.name}
 280         form = TaskForm_remd(initial=data)
 281     basic_adv=True
 282     p_type='replica exchange molecular dynamics'
 283     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 284
 285 def add_remd_a(request,task_id):
 286     task = get_object_or_404(Task, id=task_id)
 287     if request.method == 'POST':
 288         form = TaskForm_remd_a(request.POST,request.FILES)
 289         if form.is_valid():
 290              task.name=form.cleaned_data["name"]
 291              task.type="remd"
 292
 293              task.myfile1=form.cleaned_data["file1"]
 294              task.md_start=form.cleaned_data["md_start"]
 295              task.md_pdbref=form.cleaned_data["md_pdbref"]
 296
 297              task.md_seq=""
 298              if task.md_start == "pdbstart" or task.md_pdbref:
 299                seq,task.ssbond=from_pdb(task.myfile1)
 300              else:
 301                seq=seq_add_x(form.cleaned_data["md_seq"])
 302              for i in range(0,len(seq),40):
 303                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 304
 305              if task.md_start != "pdbstart":
 306                 task.ssbond=''
 307
 308              task.md_seed=form.cleaned_data["md_seed"]
 309              task.md_nstep=form.cleaned_data["md_nstep"]
 310              task.md_dt=form.cleaned_data["md_dt"]
 311              task.md_lang=form.cleaned_data["md_lang"]
 312              task.md_tau=form.cleaned_data["md_tau"]
 313              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
 314              task.remd_nrep=form.cleaned_data["remd_nrep"]
 315              task.remd_nstex=form.cleaned_data["remd_nstex"]
 316 #             task.remd_traj1file=form.cleaned_data["remd_traj1file"]
 317 #             task.remd_rest1file=form.cleaned_data["remd_rest1file"]
 318
 319              task.remd_cluter_temp=form.cleaned_data["remd_cluter_temp"]
 320              task.unres_ff=form.cleaned_data["unres_ff"]
 321
 322              basename = str(task.owner)
 323              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 324              task.jobdirname = "_".join([basename, suffix])
 325
 326              task.save()
 327              return redirect('addmlist',task_id=task.id)
 328     else:
 329         data= {'name':task.name}
 330         form = TaskForm_remd_a(initial=data)
 331     basic_adv=False
 332     p_type='replica exchange molecular dynamics - advanced options'
 333     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 334
 335
 336 def addmlist(request,task_id):
 337     task = get_object_or_404(Task, id=task_id)
 338     if request.method == 'POST':
 339         form = TaskForm_list(task.remd_nrep,request.POST)
 340         if form.is_valid():
 341              task.remd_multi_t=form.cleaned_data["temperatures"]
 342              task.remd_multi_m=form.cleaned_data["multiplexing"]
 343              task.ready=True
 344
 345              task.save()
 346              return redirect('/')
 347     else:
 348         data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
 349         '["1", "1", "1", "1", "1", "1", "1", "1"]',
 350         'temperatures':
 351         '["270", "280", "290", "300", "310", "320", "330", "345"]'
 352         }
 353         form = TaskForm_list(task.remd_nrep,initial=data)
 354     p_type='replica exchange molecular dynamics - advanced options'
 355     return render(request, 'edit_lista.html', {'form': form, 'task':task, 'p_type':p_type})
 356
 357 @login_required
 358 def details(request,task_id):
 359     task = get_object_or_404(Task, id=task_id)
 360     return render(request, "details.html",{'task':task})
 361
 362 @login_required
 363 def delete(request, task_id):
 364     Task.objects.get(id=task_id).delete()
 365     return redirect('/')
 366
 367 @login_required
 368 def refresh_done(request):
 369     user = request.user
 370     tasks = Task.objects.filter(owner=user)
 371     for task in tasks:
 372       if os.path.isfile(task.jobdirname+'/finished') and not task.done:
 373          task.done=True
 374
 375          with open(task.jobdirname+'/file.out_GB000', 'r') as f:
 376
 377            if task.type=='min' or task.type=='md':
 378              text=""
 379              for line in f:
 380                if 'ETOT' in line:
 381                   task.etot=line.split()[1]
 382
 383                if 'RMS deviation' in line:
 384                   text=text+line
 385                   i=1
 386                   for line1 in f:
 387                      text=text+line1
 388                      i+=1
 389                      if i>6:
 390                        break
 391                if 'Total wall' in line:
 392                   text=text+line
 393
 394            elif task.type=='remd':
 395              j=0
 396              text="Acceptance for replica exchanges\n"
 397              for line in f:
 398
 399                if 'ACC' in line:
 400                     j+=1
 401                     text=text+line
 402                     if j==task.remd_nrep:
 403                        j=1
 404                        text="Acceptance for replica exchanges\n"+line
 405
 406                if 'Total wall' in line:
 407                   text=text+line
 408
 409          task.results_text=text
 410
 411
 412          if task.md_pdbref and task.type=='remd':
 413
 414           for i in range(1,6):
 415             with open(task.jobdirname+'/file_wham_T'+str(int(task.remd_cluter_temp))+'K_000'+str(i)+'.pdb', 'r') as f:
 416                  line=f.readline()
 417                  if i==1:
 418                      task.remd_model1=' '.join(line.split()[-6:])
 419                  elif i==2:
 420                      task.remd_model2=' '.join(line.split()[-6:])
 421                  elif i==3:
 422                      task.remd_model3=' '.join(line.split()[-6:])
 423                  elif i==4:
 424                      task.remd_model4=' '.join(line.split()[-6:])
 425                  elif i==5:
 426                      task.remd_model5=' '.join(line.split()[-6:])
 427
 428           for i in range(1,6):
 429             with open(task.jobdirname+'/tmscore'+str(i)+'.out', 'r') as f:
 430                text=''
 431                for line in f:
 432                  if 'RMSD of  the common residues=' in line:
 433                    text=' RMSD='+line.split()[5]
 434                  if 'TM-score    =' in line:
 435                    text=text+' TMscore='+line.split()[2]
 436                  if 'GDT-TS-score=' in line:
 437                    text=text+' GDT_TS='+line.split()[1]
 438
 439                if i==1:
 440                      task.remd_model1=task.remd_model1+text
 441                elif i==2:
 442                      task.remd_model2=task.remd_model2+text
 443                elif i==3:
 444                      task.remd_model3=task.remd_model3+text
 445                elif i==4:
 446                      task.remd_model4=task.remd_model4+text
 447                elif i==5:
 448                      task.remd_model5=task.remd_model5+text
 449
 450
 451
 452          if task.type=='remd':
 453           with open(task.jobdirname+'/file_cluster_clust.out_000', 'r') as f:
 454
 455            for line in f:
 456              if 'sumprob' in line:
 457                 i=0
 458                 for line1 in f:
 459                   i+=1
 460                   if i>6:
 461                        break
 462                   if i==1:
 463                      task.remd_model1=task.remd_model1+' Cluster1 probability= '+line1.split()[2]
 464                   elif i==2:
 465                      task.remd_model2=task.remd_model2+' Cluster2 probability= '+line1.split()[2]
 466                   elif i==3:
 467                      task.remd_model3=task.remd_model3+' Cluster3 probability= '+line1.split()[2]
 468                   elif i==4:
 469                      task.remd_model4=task.remd_model4+' Cluster4 probability= '+line1.split()[2]
 470                   elif i==5:
 471                      task.remd_model5=task.remd_model5+' Cluster5 probability= '+line1.split()[2]
 472
 473
 474
 475          task.save()
 476       elif os.path.isfile(task.jobdirname+'/file_GB000.stat') and not task.done:
 477          if (task.type=='min'):
 478            task.running =1
 479          else:
 480            with open(task.jobdirname+'/file_GB000.stat', 'r') as f:
 481               line=''
 482               for line in f:
 483                 pass
 484               if line != '':
 485                 last = line.split()[0]
 486               else:
 487                 last = 0
 488            task.running=int(1+int(last)*100.0/task.md_nstep)
 489            if task.running>100:
 490              task.running=100
 491          task.save()
 492
 493     proc = subprocess.Popen('/opt/torque/bin/qstat', stdout=subprocess.PIPE)
 494     njob=0
 495     nq=0
 496     for line in proc.stdout:
 497       if 'piasek4' in line:
 498         if line.split()[1]=='test_server':
 499           njob+=1
 500           if line.split()[-2]=='Q':
 501             nq+=1
 502     variable='Idle jobs='+str(nq)+' Total jobs='+str(njob)
 503
 504     return render(request, "index.html", {
 505                 'tasks': tasks ,
 506                 'variable' : variable
 507                         })
 508
 509 #   return redirect('/')