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              task.md_ntwx=task.remd_nstex
 254
 255              task.md_seq=""
 256              if task.md_start == "pdbstart" or task.md_pdbref:
 257                seq,task.ssbond=from_pdb(task.myfile1)
 258              else:
 259                seq=seq_add_x(form.cleaned_data["md_seq"])
 260              for i in range(0,len(seq),40):
 261                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 262
 263              if task.md_start != "pdbstart":
 264                 task.ssbond=''
 265
 266              task.md_seed=form.cleaned_data["md_seed"]
 267
 268              task.md_nstep=form.cleaned_data["md_nstep"]
 269
 270
 271              task.ready=True
 272
 273              basename = str(task.owner)
 274              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 275              task.jobdirname = "_".join([basename, suffix])
 276
 277              task.save()
 278              return redirect('/')
 279     else:
 280         data= {'name':task.name}
 281         form = TaskForm_remd(initial=data)
 282     basic_adv=True
 283     p_type='replica exchange molecular dynamics'
 284     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 285
 286 def add_remd_a(request,task_id):
 287     task = get_object_or_404(Task, id=task_id)
 288     if request.method == 'POST':
 289         form = TaskForm_remd_a(request.POST,request.FILES)
 290         if form.is_valid():
 291              task.name=form.cleaned_data["name"]
 292              task.type="remd"
 293
 294              task.myfile1=form.cleaned_data["file1"]
 295              task.md_start=form.cleaned_data["md_start"]
 296              task.md_pdbref=form.cleaned_data["md_pdbref"]
 297
 298              task.md_seq=""
 299              if task.md_start == "pdbstart" or task.md_pdbref:
 300                seq,task.ssbond=from_pdb(task.myfile1)
 301              else:
 302                seq=seq_add_x(form.cleaned_data["md_seq"])
 303              for i in range(0,len(seq),40):
 304                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 305
 306              if task.md_start != "pdbstart":
 307                 task.ssbond=''
 308
 309              task.md_seed=form.cleaned_data["md_seed"]
 310              task.md_nstep=form.cleaned_data["md_nstep"]
 311              task.md_dt=form.cleaned_data["md_dt"]
 312              task.md_lang=form.cleaned_data["md_lang"]
 313              task.md_tau=form.cleaned_data["md_tau"]
 314              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
 315              task.remd_nrep=form.cleaned_data["remd_nrep"]
 316              task.remd_nstex=form.cleaned_data["remd_nstex"]
 317              task.md_ntwx=form.cleaned_data["md_ntwx"]
 318 #             task.remd_traj1file=form.cleaned_data["remd_traj1file"]
 319 #             task.remd_rest1file=form.cleaned_data["remd_rest1file"]
 320
 321              task.remd_cluter_temp=form.cleaned_data["remd_cluter_temp"]
 322              task.unres_ff=form.cleaned_data["unres_ff"]
 323
 324              basename = str(task.owner)
 325              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 326              task.jobdirname = "_".join([basename, suffix])
 327
 328              task.save()
 329              return redirect('addmlist',task_id=task.id)
 330     else:
 331         data= {'name':task.name}
 332         form = TaskForm_remd_a(initial=data)
 333     basic_adv=False
 334     p_type='replica exchange molecular dynamics - advanced options'
 335     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 336
 337
 338 def addmlist(request,task_id):
 339     task = get_object_or_404(Task, id=task_id)
 340     if request.method == 'POST':
 341         form = TaskForm_list(task.remd_nrep,request.POST)
 342         if form.is_valid():
 343              task.remd_multi_t=form.cleaned_data["temperatures"]
 344              task.remd_multi_m=form.cleaned_data["multiplexing"]
 345              task.ready=True
 346
 347              task.save()
 348              return redirect('/')
 349     else:
 350         data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
 351         '["1", "1", "1", "1", "1", "1", "1", "1"]',
 352         'temperatures':
 353         '["270", "280", "290", "300", "310", "320", "330", "345"]'
 354         }
 355         form = TaskForm_list(task.remd_nrep,initial=data)
 356     p_type='replica exchange molecular dynamics - advanced options'
 357     return render(request, 'edit_lista.html', {'form': form, 'task':task, 'p_type':p_type})
 358
 359 @login_required
 360 def details(request,task_id):
 361     task = get_object_or_404(Task, id=task_id)
 362     return render(request, "details.html",{'task':task})
 363
 364 @login_required
 365 def delete(request, task_id):
 366     Task.objects.get(id=task_id).delete()
 367     return redirect('/')
 368
 369 @login_required
 370 def refresh_done(request):
 371     user = request.user
 372     tasks = Task.objects.filter(owner=user)
 373     for task in tasks:
 374       if os.path.isfile(task.jobdirname+'/finished') and not task.done:
 375          task.done=True
 376
 377          with open(task.jobdirname+'/file.out_GB000', 'r') as f:
 378
 379            if task.type=='min' or task.type=='md':
 380              text=""
 381              for line in f:
 382                if 'ETOT' in line:
 383                   task.etot=line.split()[1]
 384
 385                if 'RMS deviation' in line:
 386                   text=text+line
 387                   i=1
 388                   for line1 in f:
 389                      text=text+line1
 390                      i+=1
 391                      if i>6:
 392                        break
 393                if 'Total wall' in line:
 394                   text=text+line
 395
 396            elif task.type=='remd':
 397              j=0
 398              text="Acceptance for replica exchanges\n"
 399              for line in f:
 400
 401                if 'ACC' in line:
 402                     j+=1
 403                     text=text+line
 404                     if j==task.remd_nrep:
 405                        j=1
 406                        text="Acceptance for replica exchanges\n"+line
 407
 408                if 'Total wall' in line:
 409                   text=text+line
 410
 411          task.results_text=text
 412
 413
 414          if task.md_pdbref and task.type=='remd':
 415
 416           for i in range(1,6):
 417             with open(task.jobdirname+'/file_wham_T'+str(int(task.remd_cluter_temp))+'K_000'+str(i)+'.pdb', 'r') as f:
 418                  line=f.readline()
 419                  if i==1:
 420                      task.remd_model1=' '.join(line.split()[-6:])
 421                  elif i==2:
 422                      task.remd_model2=' '.join(line.split()[-6:])
 423                  elif i==3:
 424                      task.remd_model3=' '.join(line.split()[-6:])
 425                  elif i==4:
 426                      task.remd_model4=' '.join(line.split()[-6:])
 427                  elif i==5:
 428                      task.remd_model5=' '.join(line.split()[-6:])
 429
 430           for i in range(1,6):
 431             with open(task.jobdirname+'/tmscore'+str(i)+'.out', 'r') as f:
 432                text=''
 433                for line in f:
 434                  if 'RMSD of  the common residues=' in line:
 435                    text=' RMSD='+line.split()[5]
 436                  if 'TM-score    =' in line:
 437                    text=text+' TMscore='+line.split()[2]
 438                  if 'GDT-TS-score=' in line:
 439                    text=text+' GDT_TS='+line.split()[1]
 440
 441                if i==1:
 442                      task.remd_model1=task.remd_model1+text
 443                elif i==2:
 444                      task.remd_model2=task.remd_model2+text
 445                elif i==3:
 446                      task.remd_model3=task.remd_model3+text
 447                elif i==4:
 448                      task.remd_model4=task.remd_model4+text
 449                elif i==5:
 450                      task.remd_model5=task.remd_model5+text
 451
 452
 453
 454          if task.type=='remd':
 455           with open(task.jobdirname+'/file_cluster_clust.out_000', 'r') as f:
 456
 457            for line in f:
 458              if 'sumprob' in line:
 459                 i=0
 460                 for line1 in f:
 461                   i+=1
 462                   if i>6:
 463                        break
 464                   if i==1:
 465                      task.remd_model1=task.remd_model1+' Cluster1 probability= '+line1.split()[2]
 466                   elif i==2:
 467                      task.remd_model2=task.remd_model2+' Cluster2 probability= '+line1.split()[2]
 468                   elif i==3:
 469                      task.remd_model3=task.remd_model3+' Cluster3 probability= '+line1.split()[2]
 470                   elif i==4:
 471                      task.remd_model4=task.remd_model4+' Cluster4 probability= '+line1.split()[2]
 472                   elif i==5:
 473                      task.remd_model5=task.remd_model5+' Cluster5 probability= '+line1.split()[2]
 474
 475
 476
 477          task.save()
 478       elif os.path.isfile(task.jobdirname+'/file_GB000.stat') and not task.done:
 479          if (task.type=='min'):
 480            task.running =1
 481          else:
 482            with open(task.jobdirname+'/file_GB000.stat', 'r') as f:
 483               line=''
 484               for line in f:
 485                 pass
 486               if line != '':
 487                 last = line.split()[0]
 488               else:
 489                 last = 0
 490            task.running=int(1+int(last)*100.0/task.md_nstep)
 491            if task.running>100:
 492              task.running=100
 493          task.save()
 494
 495     proc = subprocess.Popen('/opt/torque/bin/qstat', stdout=subprocess.PIPE)
 496     njob=0
 497     nq=0
 498     for line in proc.stdout:
 499       if 'piasek4' in line:
 500         if line.split()[1]=='test_server':
 501           njob+=1
 502           if line.split()[-2]=='Q':
 503             nq+=1
 504     variable='Idle jobs='+str(nq)+' Total jobs='+str(njob)
 505
 506     return render(request, "index.html", {
 507                 'tasks': tasks ,
 508                 'variable' : variable
 509                         })
 510
 511 #   return redirect('/')