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
 129              seq,task.ssbond=from_pdb(task.myfile1)
 130              task.md_seq=""
 131              for i in range(0,len(seq),40):
 132                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 133
 134
 135              task.ready=True
 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              task.save()
 141              return redirect('/')
 142     else:
 143         data= {'name':task.name}
 144         form = TaskForm_min_a(initial=data)
 145     basic_adv=False
 146     p_type='minimization - advanced options'
 147     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 148
 149 @login_required
 150 def add_md(request,task_id):
 151     task = get_object_or_404(Task, id=task_id)
 152     if request.method == 'POST':
 153         form = TaskForm_md(request.POST,request.FILES)
 154         if form.is_valid():
 155              task.name=form.cleaned_data["name"]
 156              task.type="md"
 157              task.md_seed=form.cleaned_data["md_seed"]
 158              task.md_start=form.cleaned_data["md_start"]
 159              task.md_temp=form.cleaned_data["md_temp"]
 160              task.md_nstep=form.cleaned_data["md_nstep"]
 161
 162              task.myfile1=form.cleaned_data["file1"]
 163              task.md_pdbref=form.cleaned_data["md_pdbref"]
 164
 165              task.md_seq=""
 166              if task.md_start == "pdbstart" or task.md_pdbref:
 167                seq,task.ssbond=from_pdb(task.myfile1)
 168              else:
 169                seq=seq_add_x(form.cleaned_data["md_seq"])
 170
 171              for i in range(0,len(seq),40):
 172                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 173
 174              if task.md_start != "pdbstart":
 175                 task.ssbond=''
 176
 177              task.ready=True
 178              basename = str(task.owner)
 179              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 180              task.jobdirname = "_".join([basename, suffix])
 181
 182              task.save()
 183              return redirect('/')
 184     else:
 185         data= {'name':task.name}
 186         form = TaskForm_md(initial=data)
 187     basic_adv=True
 188     p_type='molecular dynamics'
 189     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 190
 191 def add_md_a(request,task_id):
 192     task = get_object_or_404(Task, id=task_id)
 193     if request.method == 'POST':
 194         form = TaskForm_md_a(request.POST,request.FILES)
 195         if form.is_valid():
 196              task.name=form.cleaned_data["name"]
 197              task.type="md"
 198
 199              task.myfile1=form.cleaned_data["file1"]
 200              task.md_start=form.cleaned_data["md_start"]
 201              task.md_pdbref=form.cleaned_data["md_pdbref"]
 202
 203              task.md_seq=""
 204              if task.md_start == "pdbstart" or task.md_pdbref:
 205                seq,task.ssbond=from_pdb(task.myfile1)
 206              else:
 207                seq=seq_add_x(form.cleaned_data["md_seq"])
 208              for i in range(0,len(seq),40):
 209                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 210
 211              if task.md_start != "pdbstart":
 212                 task.ssbond=''
 213
 214              task.md_seed=form.cleaned_data["md_seed"]
 215
 216              task.md_temp=form.cleaned_data["md_temp"]
 217              task.md_nstep=form.cleaned_data["md_nstep"]
 218              task.md_ntwe=form.cleaned_data["md_ntwe"]
 219              task.md_ntwx=form.cleaned_data["md_ntwx"]
 220              task.md_dt=form.cleaned_data["md_dt"]
 221              task.md_lang=form.cleaned_data["md_lang"]
 222              task.md_tau=form.cleaned_data["md_tau"]
 223              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
 224              task.md_mdpdb=form.cleaned_data["md_mdpdb"]
 225
 226
 227              task.ready=True
 228              basename = str(task.owner)
 229              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 230              task.jobdirname = "_".join([basename, suffix])
 231
 232              task.save()
 233              return redirect('/')
 234     else:
 235         data= {'name':task.name}
 236         form = TaskForm_md_a(initial=data)
 237     basic_adv=False
 238     p_type='molecular dynamics - advanced options'
 239     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 240
 241 @login_required
 242 def add_remd(request,task_id):
 243     task = get_object_or_404(Task, id=task_id)
 244     if request.method == 'POST':
 245         form = TaskForm_remd(request.POST,request.FILES)
 246         if form.is_valid():
 247              task.name=form.cleaned_data["name"]
 248              task.type="remd"
 249              task.md_start=form.cleaned_data["md_start"]
 250              task.myfile1=form.cleaned_data["file1"]
 251              task.md_pdbref=form.cleaned_data["md_pdbref"]
 252
 253              task.md_seq=""
 254              if task.md_start == "pdbstart" or task.md_pdbref:
 255                seq,task.ssbond=from_pdb(task.myfile1)
 256              else:
 257                seq=seq_add_x(form.cleaned_data["md_seq"])
 258              for i in range(0,len(seq),40):
 259                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 260
 261              if task.md_start != "pdbstart":
 262                 task.ssbond=''
 263
 264              task.md_seed=form.cleaned_data["md_seed"]
 265
 266              task.md_nstep=form.cleaned_data["md_nstep"]
 267
 268
 269              task.ready=True
 270
 271              basename = str(task.owner)
 272              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 273              task.jobdirname = "_".join([basename, suffix])
 274
 275              task.save()
 276              return redirect('/')
 277     else:
 278         data= {'name':task.name}
 279         form = TaskForm_remd(initial=data)
 280     basic_adv=True
 281     p_type='replica exchange molecular dynamics'
 282     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 283
 284 def add_remd_a(request,task_id):
 285     task = get_object_or_404(Task, id=task_id)
 286     if request.method == 'POST':
 287         form = TaskForm_remd_a(request.POST,request.FILES)
 288         if form.is_valid():
 289              task.name=form.cleaned_data["name"]
 290              task.type="remd"
 291
 292              task.myfile1=form.cleaned_data["file1"]
 293              task.md_start=form.cleaned_data["md_start"]
 294              task.md_pdbref=form.cleaned_data["md_pdbref"]
 295
 296              task.md_seq=""
 297              if task.md_start == "pdbstart" or task.md_pdbref:
 298                seq,task.ssbond=from_pdb(task.myfile1)
 299              else:
 300                seq=seq_add_x(form.cleaned_data["md_seq"])
 301              for i in range(0,len(seq),40):
 302                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 303
 304              if task.md_start != "pdbstart":
 305                 task.ssbond=''
 306
 307              task.md_seed=form.cleaned_data["md_seed"]
 308              task.md_nstep=form.cleaned_data["md_nstep"]
 309              task.md_dt=form.cleaned_data["md_dt"]
 310              task.md_lang=form.cleaned_data["md_lang"]
 311              task.md_tau=form.cleaned_data["md_tau"]
 312              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
 313              task.remd_nrep=form.cleaned_data["remd_nrep"]
 314              task.remd_nstex=form.cleaned_data["remd_nstex"]
 315 #             task.remd_traj1file=form.cleaned_data["remd_traj1file"]
 316 #             task.remd_rest1file=form.cleaned_data["remd_rest1file"]
 317
 318              task.remd_cluter_temp=form.cleaned_data["remd_cluter_temp"]
 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('addmlist',task_id=task.id)
 326     else:
 327         data= {'name':task.name}
 328         form = TaskForm_remd_a(initial=data)
 329     basic_adv=False
 330     p_type='replica exchange molecular dynamics - advanced options'
 331     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 332
 333
 334 def addmlist(request,task_id):
 335     task = get_object_or_404(Task, id=task_id)
 336     if request.method == 'POST':
 337         form = TaskForm_list(task.remd_nrep,request.POST)
 338         if form.is_valid():
 339              task.remd_multi_t=form.cleaned_data["temperatures"]
 340              task.remd_multi_m=form.cleaned_data["multiplexing"]
 341              task.ready=True
 342
 343              task.save()
 344              return redirect('/')
 345     else:
 346         data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
 347         '["1", "1", "1", "1", "1", "1", "1", "1"]',
 348         'temperatures':
 349         '["270", "280", "290", "300", "310", "320", "330", "345"]'
 350         }
 351         form = TaskForm_list(task.remd_nrep,initial=data)
 352     p_type='replica exchange molecular dynamics - advanced options'
 353     return render(request, 'edit_lista.html', {'form': form, 'task':task, 'p_type':p_type})
 354
 355 @login_required
 356 def details(request,task_id):
 357     task = get_object_or_404(Task, id=task_id)
 358     return render(request, "details.html",{'task':task})
 359
 360 @login_required
 361 def delete(request, task_id):
 362     Task.objects.get(id=task_id).delete()
 363     return redirect('/')
 364
 365 @login_required
 366 def refresh_done(request):
 367     user = request.user
 368     tasks = Task.objects.filter(owner=user)
 369     for task in tasks:
 370       if os.path.isfile(task.jobdirname+'/finished') and not task.done:
 371          task.done=True
 372
 373          with open(task.jobdirname+'/file.out_GB000', 'r') as f:
 374
 375            if task.type=='min' or task.type=='md':
 376              text=""
 377              for line in f:
 378                if 'ETOT' in line:
 379                   task.etot=line.split()[1]
 380
 381                if 'RMS deviation' in line:
 382                   text=text+line
 383                   i=1
 384                   for line1 in f:
 385                      text=text+line1
 386                      i+=1
 387                      if i>6:
 388                        break
 389                if 'Total wall' in line:
 390                   text=text+line
 391
 392            elif task.type=='remd':
 393              j=0
 394              text="Acceptance for replica exchanges\n"
 395              for line in f:
 396
 397                if 'ACC' in line:
 398                     j+=1
 399                     text=text+line
 400                     if j==task.remd_nrep:
 401                        j=1
 402                        text="Acceptance for replica exchanges\n"+line
 403
 404                if 'Total wall' in line:
 405                   text=text+line
 406
 407          task.results_text=text
 408
 409
 410          if task.md_pdbref and task.type=='remd':
 411
 412           for i in range(1,6):
 413             with open(task.jobdirname+'/file_wham_T'+str(int(task.remd_cluter_temp))+'K_000'+str(i)+'.pdb', 'r') as f:
 414                  line=f.readline()
 415                  if i==1:
 416                      task.remd_model1=' '.join(line.split()[-6:])
 417                  elif i==2:
 418                      task.remd_model2=' '.join(line.split()[-6:])
 419                  elif i==3:
 420                      task.remd_model3=' '.join(line.split()[-6:])
 421                  elif i==4:
 422                      task.remd_model4=' '.join(line.split()[-6:])
 423                  elif i==5:
 424                      task.remd_model5=' '.join(line.split()[-6:])
 425
 426           for i in range(1,6):
 427             with open(task.jobdirname+'/tmscore'+str(i)+'.out', 'r') as f:
 428                text=''
 429                for line in f:
 430                  if 'RMSD of  the common residues=' in line:
 431                    text=' RMSD='+line.split()[5]
 432                  if 'TM-score    =' in line:
 433                    text=text+' TMscore='+line.split()[2]
 434                  if 'GDT-TS-score=' in line:
 435                    text=text+' GDT_TS='+line.split()[1]
 436
 437                if i==1:
 438                      task.remd_model1=task.remd_model1+text
 439                elif i==2:
 440                      task.remd_model2=task.remd_model2+text
 441                elif i==3:
 442                      task.remd_model3=task.remd_model3+text
 443                elif i==4:
 444                      task.remd_model4=task.remd_model4+text
 445                elif i==5:
 446                      task.remd_model5=task.remd_model5+text
 447
 448
 449
 450          if task.type=='remd':
 451           with open(task.jobdirname+'/file_cluster_clust.out_000', 'r') as f:
 452
 453            for line in f:
 454              if 'sumprob' in line:
 455                 i=0
 456                 for line1 in f:
 457                   i+=1
 458                   if i>6:
 459                        break
 460                   if i==1:
 461                      task.remd_model1=task.remd_model1+' Cluster1 probability= '+line1.split()[2]
 462                   elif i==2:
 463                      task.remd_model2=task.remd_model2+' Cluster2 probability= '+line1.split()[2]
 464                   elif i==3:
 465                      task.remd_model3=task.remd_model3+' Cluster3 probability= '+line1.split()[2]
 466                   elif i==4:
 467                      task.remd_model4=task.remd_model4+' Cluster4 probability= '+line1.split()[2]
 468                   elif i==5:
 469                      task.remd_model5=task.remd_model5+' Cluster5 probability= '+line1.split()[2]
 470
 471
 472
 473          task.save()
 474       elif os.path.isfile(task.jobdirname+'/file_GB000.stat') and not task.done:
 475          if (task.type=='min'):
 476            task.running =1
 477          else:
 478            with open(task.jobdirname+'/file_GB000.stat', 'r') as f:
 479               line=''
 480               for line in f:
 481                 pass
 482               if line != '':
 483                 last = line.split()[0]
 484               else:
 485                 last = 0
 486            task.running=int(1+int(last)*100.0/task.md_nstep)
 487            if task.running>100:
 488              task.running=100
 489          task.save()
 490
 491     proc = subprocess.Popen('/opt/torque/bin/qstat', stdout=subprocess.PIPE)
 492     njob=0
 493     nq=0
 494     for line in proc.stdout:
 495       if 'piasek4' in line:
 496         if line.split()[1]=='test_server':
 497           njob+=1
 498           if line.split()[-2]=='Q':
 499             nq+=1
 500     variable='Idle jobs='+str(nq)+' Total jobs='+str(njob)
 501
 502     return render(request, "index.html", {
 503                 'tasks': tasks ,
 504                 'variable' : variable
 505                         })
 506
 507 #   return redirect('/')