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 import random
  13
  14 res_codes = [
  15                 # 20 canonical amino acids
  16                 ('CYS', 'C'), ('ASP', 'D'), ('SER', 'S'), ('GLN', 'Q'),
  17                 ('LYS', 'K'), ('ILE', 'I'), ('PRO', 'P'), ('THR', 'T'),
  18                 ('PHE', 'F'), ('ASN', 'N'), ('GLY', 'G'), ('HIS', 'H'),
  19                 ('LEU', 'L'), ('ARG', 'R'), ('TRP', 'W'), ('ALA', 'A'),
  20                 ('VAL', 'V'), ('GLU', 'E'), ('TYR', 'Y'), ('MET', 'M'),
  21                 ('HSD', 'H'),('HSE', 'H'),('HSP', 'H'),
  22                 ('HIE', 'H'), ('HID', 'H'),('HIP', 'H'),
  23                 ('CYX', 'C'),
  24                 ('DCY', 'c'), ('DAS', 'd'), ('DSN', 's'), ('DGN', 'q'),
  25                 ('DLY', 'k'), ('DIL', 'i'), ('DPR', 'p'), ('DTH', 't'),
  26                 ('DPN', 'f'), ('DSG', 'n'), ('DHI', 'h'),
  27                 ('DLE', 'l'), ('DAR', 'r'), ('DTR', 'w'), ('DAL', 'a'),
  28                 ('DVA', 'v'), ('DGL', 'e'), ('DTY', 'y'), ('MED', 'm'),
  29                ]
  30
  31 three_to_one = dict(res_codes)
  32
  33 def dock_box(file):
  34    import math
  35    coord = list()
  36    for line in file:
  37             if line[0:6] == 'ATOM  ' and line[13:15] == 'CA':
  38               x=float(line[30:38])
  39               y=float(line[38:46])
  40               z=float(line[46:54])
  41               coord.append([x, y, z])
  42             if line[0:3] == 'END':
  43               break
  44    maxd=0
  45    l=len(coord)
  46    for i in xrange(l):
  47       for j in xrange(i+1,l):
  48         p1=coord[i]
  49         p2=coord[j]
  50         d=(p1[0]-p2[0])**2 + (p1[1]-p2[1])**2 + (p1[2]-p2[2])**2
  51         if d > maxd:
  52           maxd=d
  53    return math.sqrt(maxd)
  54
  55
  56 def load_pdbid(pdbid,dirname,filename='plik.pdb'):
  57     if (not os.path.isdir(dirname)):
  58        os.mkdir(dirname)
  59     if len(pdbid)==4:
  60        file,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb',
  61                      dirname+'/'+filename)
  62     else:
  63        chain=pdbid[5]
  64        pdbid=pdbid[:4]
  65        pdb_tmp=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
  66        with open(dirname+'/'+filename, 'w') as outfile:
  67         for line in pdb_tmp:
  68           if line[0:6] == 'SSBOND' and line[15] == chain and line[29] == chain:
  69             outfile.write(line)
  70           if line[0:6] == 'ATOM  ' and line[21] == chain:
  71             outfile.write(line)
  72           if line[0:6] == 'ENDMDL':
  73             break
  74        pdb_tmp.close()
  75        file=dirname+'/'+filename
  76
  77     return(file)
  78
  79
  80 def seq_2d_from_pdb(seq_2d,seq):
  81     if seq_2d =='':
  82       return(seq_2d)
  83     seq_2d=seq_2d.replace('C', '-')
  84     seq_2d_tmp=''
  85     ii=0
  86     for i in range(0,len(seq)):
  87       if seq[i]=='X':
  88          seq_2d_tmp=seq_2d_tmp+'-'
  89       else:
  90          if len(seq_2d)>ii:
  91             seq_2d_tmp=seq_2d_tmp+seq_2d[ii]
  92             ii+=1
  93     tmp=''
  94     for i in range(0,len(seq_2d_tmp),40):
  95       tmp=tmp+seq_2d_tmp[i:i+40]+" "
  96     return(tmp)
  97
  98 def seq_2d_add_x(seq_2d,seq,seq_form):
  99     if seq_2d =='':
 100       return(seq_2d)
 101     seq_2d=seq_2d[:len(seq_form)]
 102     seq_2d=seq_2d.replace('C', '-')
 103     if seq_form[0] !='X' and seq[0] == 'X':
 104       seq_2d='-'+seq_2d
 105     if seq_form[-1] !='X' and seq[-1] == 'X':
 106       seq_2d=seq_2d+'-'
 107     seq_2d=seq_2d[:len(seq)]
 108     tmp=''
 109     for i in range(0,len(seq_2d),40):
 110       tmp=tmp+seq_2d[i:i+40]+" "
 111     return(tmp)
 112
 113 def seq_add_x(sequence):
 114     if sequence[0] != 'G' and sequence[0] != 'g' and sequence[0] != 'X':
 115         sequence='X'+sequence
 116     if sequence[-1] != 'G' and sequence[-1] != 'g' and sequence[-1] != 'X':
 117         sequence=sequence+'X'
 118     set ='CDSQKIPTFNGHLRWAVEYMXcdsqkiptfnhlrwaveym'
 119     sequence = ''.join([c for c in sequence if c in set])
 120
 121     return(sequence)
 122
 123 def from_pdb(file):
 124     sequence = []
 125     ssbond = []
 126     ssbond_ch = []
 127     ires = []
 128     chain_start = {}
 129     chain_end = {}
 130     unres_shift = {}
 131     chain_sorted=[]
 132     newchain = True
 133     i=''
 134     for line in file:
 135             if line[0:6] == 'ATOM  ' and line[13:15] == 'CA':
 136               aa = three_to_one.get(line[17:20])
 137               i = int(line[22:26])
 138               ch = line[21:22]
 139               if newchain or i!=ires[-1]:
 140                 sequence.append(aa)
 141                 ires.append(i)
 142                 if newchain:
 143                  chain_start[ch]=i
 144                  chain_sorted.extend(ch)
 145                  newchain = False
 146             if line[0:3] == 'TER' and i != '':
 147               sequence.append('XX')
 148               chain_end[ch]=i
 149               newchain = True
 150             if line[0:6] == 'SSBOND':
 151               b=[]
 152               b.append(int(line[17:21]))
 153               b.append(int(line[31:35]))
 154               ssbond.append(b)
 155               c = []
 156               c.append((line[15:16]))
 157               c.append((line[29:30]))
 158               ssbond_ch.append(c)
 159             if line[0:3] == 'END':
 160               break
 161     if not sequence[-1] == 'XX':
 162             chain_end[ch]=i
 163     while sequence[-1] == 'XX':
 164             del sequence[-1]
 165     if sequence[0] != 'G':
 166             sequence.insert(0,'X')
 167             ssbond=[ [e[0]+1,e[1]+1] for e in ssbond]
 168     if sequence[-1] != 'G':
 169             sequence.append('X')
 170     seq=''.join(sequence)
 171 #    if ires[0] != 1:
 172 #            ssbond=[ [e[0]-ires[0]+1,e[1]-ires[0]+1] for e in ssbond]
 173     i=0
 174     for c in chain_sorted:
 175       unres_shift[c]=i+chain_start[c]
 176       i=i-(chain_end[c]-chain_start[c])-3
 177     ssbond=[ [e[0]-unres_shift[c[0]]+1,e[1]-unres_shift[c[1]]+1] for e,c in zip(ssbond,ssbond_ch)]
 178
 179     return seq,json.dumps(ssbond)
 180
 181
 182 @login_required
 183 def index(request):
 184     user = request.user
 185     tasks = Task.objects.filter(owner=user).order_by('-created_date')
 186     variable = ''
 187     tasks_count = Task.objects.filter(owner=user).count()
 188     return render(request, "index.html", {
 189             'tasks': tasks, 'alldone': 0, 'tasks_count':tasks_count
 190         })
 191
 192 @login_required
 193 def add(request):
 194     if request.method == 'POST':
 195         form = TaskForm(request.POST)
 196         if form.is_valid():
 197             name = form.cleaned_data["name"]
 198             user = request.user
 199             task = Task(name=name,owner=user,ready=False)
 200             task.save()
 201             return redirect('add_min',task_id=task.id)
 202     return redirect('/')
 203
 204 @login_required
 205 def add_min(request,task_id):
 206     task = get_object_or_404(Task, id=task_id)
 207     if request.method == 'POST':
 208      if '_example' in request.POST:
 209         data= {'name':task.name,'pdbid':'1BDD'}
 210         form = TaskForm_min(initial=data)
 211      else:
 212         form = TaskForm_min(request.POST,request.FILES)
 213         if form.is_valid():
 214              task.name=form.cleaned_data["name"]
 215              task.type="min"
 216              pdbid=form.cleaned_data["pdbid"]
 217
 218              basename = str(task.owner)
 219              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 220              task.jobdirname = "_".join([basename, suffix])
 221
 222              if pdbid:
 223               task.myfile1=load_pdbid(pdbid,task.jobdirname)
 224               task.pdbcode=pdbid
 225              else:
 226               task.myfile1=form.cleaned_data["file1"]
 227
 228              seq,task.ssbond=from_pdb(task.myfile1)
 229              task.md_seq=""
 230              for i in range(0,len(seq),40):
 231                     task.md_seq=task.md_seq+seq[i:i+40]+" "
 232
 233              task.ready=True
 234
 235              task.save()
 236              if is_lazy_user(request.user):
 237               return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')
 238              else:
 239               return redirect('/')
 240     else:
 241         data= {'name':task.name}
 242         form = TaskForm_min(initial=data)
 243     p_type='minimization'
 244     basic_adv=True
 245     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 246
 247 @login_required
 248 def add_min_a(request,task_id):
 249     task = get_object_or_404(Task, id=task_id)
 250     if request.method == 'POST':
 251      if '_example' in request.POST:
 252         data= {'name':task.name,'pdbid':'1EI0','unres_ff':'opt-wtfsa-2'}
 253         form = TaskForm_min_a(initial=data)
 254      else:
 255         form = TaskForm_min_a(request.POST,request.FILES)
 256         if form.is_valid():
 257              task.name=form.cleaned_data["name"]
 258              task.type="min"
 259 #             task.min_choice=form.cleaned_data["min_choice"]
 260              task.min_overlap=form.cleaned_data["min_overlap"]
 261              task.min_searchsc=form.cleaned_data["min_searchsc"]
 262              task.min_maxmin=form.cleaned_data["min_maxmin"]
 263              task.min_maxfun=form.cleaned_data["min_maxfun"]
 264              task.min_pdbout=form.cleaned_data["min_pdbout"]
 265
 266              basename = str(task.owner)
 267              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 268              task.jobdirname = "_".join([basename, suffix])
 269
 270              pdbid=form.cleaned_data["pdbid"]
 271              if pdbid:
 272               task.myfile1=load_pdbid(pdbid,task.jobdirname)
 273               task.pdbcode=pdbid
 274              else:
 275               task.myfile1=form.cleaned_data["file1"]
 276
 277              task.min_unres_pdb=form.cleaned_data["min_unres_pdb"]
 278              task.unres_ff=form.cleaned_data["unres_ff"]
 279              task.boxx=form.cleaned_data["boxx"]
 280              task.boxy=form.cleaned_data["boxy"]
 281              task.boxz=form.cleaned_data["boxz"]
 282
 283              seq,task.ssbond=from_pdb(task.myfile1)
 284              task.md_seq=""
 285              for i in range(0,len(seq),40):
 286                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 287
 288              task.ready=True
 289
 290              task.save()
 291              if is_lazy_user(request.user):
 292               return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')
 293              else:
 294               return redirect('/')
 295     else:
 296         data= {'name':task.name}
 297         form = TaskForm_min_a(initial=data)
 298     basic_adv=False
 299     p_type='minimization - advanced options'
 300     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 301
 302 @login_required
 303 def add_md(request,task_id):
 304     task = get_object_or_404(Task, id=task_id)
 305     if request.method == 'POST':
 306      if '_example' in request.POST:
 307         data= {'name':task.name,'pdbid':'1IGD','md_start':'pdbstart',
 308         'md_pdbref':True,'md_temp':200,'md_seed':-39912345}
 309         form = TaskForm_md(initial=data)
 310      else:
 311         form = TaskForm_md(request.POST,request.FILES)
 312         if form.is_valid():
 313              task.name=form.cleaned_data["name"]
 314              task.type="md"
 315              task.md_seed=form.cleaned_data["md_seed"]
 316              task.md_start=form.cleaned_data["md_start"]
 317              task.md_temp=form.cleaned_data["md_temp"]
 318              task.md_nstep=form.cleaned_data["md_nstep"]
 319              task.md_total_steps=task.md_nstep
 320              if task.md_nstep<250000:
 321                  task.md_ntwx=100
 322
 323              basename = str(task.owner)
 324              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 325              task.jobdirname = "_".join([basename, suffix])
 326
 327              pdbid=form.cleaned_data["pdbid"]
 328              if pdbid:
 329               task.myfile1=load_pdbid(pdbid,task.jobdirname)
 330               task.pdbcode=pdbid
 331              else:
 332               task.myfile1=form.cleaned_data["file1"]
 333              task.md_pdbref=form.cleaned_data["md_pdbref"]
 334
 335              task.md_seq=""
 336              if task.md_start == "pdbstart" or task.md_pdbref:
 337                seq,task.ssbond=from_pdb(task.myfile1)
 338              else:
 339                seq=seq_add_x(form.cleaned_data["md_seq"])
 340
 341              for i in range(0,len(seq),40):
 342                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 343
 344              if task.md_start != "pdbstart":
 345                 task.ssbond=''
 346
 347              if any(c.islower() for c in seq):
 348               task.md_respa=False
 349               task.damino=True
 350
 351              task.ready=True
 352
 353              task.save()
 354              if is_lazy_user(request.user):
 355               return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')
 356              else:
 357               return redirect('/')
 358     else:
 359         data= {'name':task.name,'md_seed':-random.randint(10000000,99999999)}
 360         form = TaskForm_md(initial=data)
 361     basic_adv=True
 362     p_type='molecular dynamics'
 363     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 364
 365 @login_required
 366 def add_md_a(request,task_id):
 367     task = get_object_or_404(Task, id=task_id)
 368     if request.method == 'POST':
 369      if '_example' in request.POST:
 370         data= {'name':task.name,'pdbid':'1L2Y','md_start':'extconf',
 371          'md_pdbref':True,'md_mdpdb':True,'md_seed':-39912345}
 372         form = TaskForm_md_a(initial=data)
 373      else:
 374         form = TaskForm_md_a(request.POST,request.FILES)
 375         if form.is_valid():
 376              task.name=form.cleaned_data["name"]
 377              task.type="md"
 378
 379              basename = str(task.owner)
 380              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 381              task.jobdirname = "_".join([basename, suffix])
 382
 383              pdbid=form.cleaned_data["pdbid"]
 384              if pdbid:
 385               task.myfile1=load_pdbid(pdbid,task.jobdirname)
 386               task.pdbcode=pdbid
 387              else:
 388               task.myfile1=form.cleaned_data["file1"]
 389              task.md_start=form.cleaned_data["md_start"]
 390              task.md_pdbref=form.cleaned_data["md_pdbref"]
 391
 392              task.md_seq=""
 393              if task.md_start == "pdbstart" or task.md_pdbref:
 394                seq,task.ssbond=from_pdb(task.myfile1)
 395                task.md_2d=seq_2d_from_pdb(form.cleaned_data["md_2d"],seq)
 396              else:
 397                seq=seq_add_x(form.cleaned_data["md_seq"])
 398                task.md_2d=seq_2d_add_x(form.cleaned_data["md_2d"],seq,form.cleaned_data["md_seq"])
 399
 400              for i in range(0,len(seq),40):
 401                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 402
 403              if task.md_start != "pdbstart":
 404                 task.ssbond=''
 405
 406              task.md_seed=form.cleaned_data["md_seed"]
 407
 408              task.md_temp=form.cleaned_data["md_temp"]
 409              task.md_nstep=form.cleaned_data["md_nstep"]
 410              task.md_total_steps=task.md_nstep
 411              task.md_ntwe=form.cleaned_data["md_ntwe"]
 412              task.md_ntwx=form.cleaned_data["md_ntwx"]
 413              task.md_dt=form.cleaned_data["md_dt"]
 414              task.md_lang=form.cleaned_data["md_lang"]
 415              task.md_tau=form.cleaned_data["md_tau"]
 416              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
 417              task.md_mdpdb=form.cleaned_data["md_mdpdb"]
 418              task.unres_ff=form.cleaned_data["unres_ff"]
 419              task.md_respa=form.cleaned_data["md_respa"]
 420              if any(c.islower() for c in seq):
 421               task.md_respa=False
 422               task.damino=True
 423              task.boxx=form.cleaned_data["boxx"]
 424              task.boxy=form.cleaned_data["boxy"]
 425              task.boxz=form.cleaned_data["boxz"]
 426
 427
 428              task.ready=True
 429
 430              task.save()
 431              if is_lazy_user(request.user):
 432               return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')
 433              else:
 434               return redirect('/')
 435     else:
 436         data= {'name':task.name,'md_seed':-random.randint(10000000,99999999)}
 437         form = TaskForm_md_a(initial=data)
 438     basic_adv=False
 439     p_type='molecular dynamics - advanced options'
 440     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 441
 442 @login_required
 443 def add_remd(request,task_id):
 444     task = get_object_or_404(Task, id=task_id)
 445     if request.method == 'POST':
 446      if '_example' in request.POST:
 447         data= {'name':task.name,'pdbid':'1L2Y','md_pdbref':True,'md_seed':-39912345}
 448         form = TaskForm_remd(initial=data)
 449      else:
 450         form = TaskForm_remd(request.POST,request.FILES)
 451         if form.is_valid():
 452              task.name=form.cleaned_data["name"]
 453              task.type="remd"
 454              task.md_start=form.cleaned_data["md_start"]
 455
 456              basename = str(task.owner)
 457              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 458              task.jobdirname = "_".join([basename, suffix])
 459
 460              pdbid=form.cleaned_data["pdbid"]
 461              if pdbid:
 462               task.myfile1=load_pdbid(pdbid,task.jobdirname)
 463               task.pdbcode=pdbid
 464              else:
 465               task.myfile1=form.cleaned_data["file1"]
 466              task.md_pdbref=form.cleaned_data["md_pdbref"]
 467              task.md_ntwx=task.remd_nstex
 468
 469              task.md_seq=""
 470              if task.md_start == "pdbstart" or task.md_pdbref:
 471                seq,task.ssbond=from_pdb(task.myfile1)
 472              else:
 473                seq=seq_add_x(form.cleaned_data["md_seq"])
 474              for i in range(0,len(seq),40):
 475                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 476
 477              if task.md_start != "pdbstart":
 478                 task.ssbond=''
 479
 480              task.md_seed=form.cleaned_data["md_seed"]
 481
 482              task.md_nstep=form.cleaned_data["md_nstep"]
 483              task.md_total_steps=task.md_nstep
 484
 485              if any(c.islower() for c in seq):
 486               task.md_respa=False
 487               task.damino=True
 488
 489
 490              task.ready=True
 491
 492
 493              task.save()
 494              if is_lazy_user(request.user):
 495               return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')
 496              else:
 497               return redirect('/')
 498     else:
 499         data= {'name':task.name,'md_seed':-random.randint(10000000,99999999)}
 500         form = TaskForm_remd(initial=data)
 501     basic_adv=True
 502     p_type='replica exchange molecular dynamics'
 503     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 504
 505 @login_required
 506 def add_remd_a(request,task_id):
 507     from django.core.files.uploadedfile import UploadedFile
 508     task = get_object_or_404(Task, id=task_id)
 509     if request.method == 'POST':
 510      if '_example' in request.POST:
 511         data= {'name':task.name,'pdbid':'5G3Q:B','md_pdbref':True,
 512          'md_nstep':2000000,'md_lang':'berendsen','unres_ff':'FF2','md_seed':-39912345,
 513          'remd_cluter_temp':290,'md_2d':'--EEEEEEE------EEEEEE------EEEEEE------HHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH---'}
 514         form = TaskForm_remd_a(initial=data)
 515         task.example='casp12'
 516         task.save()
 517      elif '_example_saxs' in request.POST:
 518         data= {'name':task.name,'pdbid':'5UJQ','md_pdbref':True,
 519          'md_nstep':200000,'md_lang':'langevin','unres_ff':'FF2','md_seed':-39912345,
 520          'remd_cluter_temp':270,
 521          'scal_rad':4.0,'wsaxs':100.0,'saxs_data':
 522 """ 0.5     1.33868e-02
 523  1.5     1.95880e-02
 524  2.5     2.68896e-02
 525  3.5     3.43737e-02
 526  4.5     4.07099e-02
 527  5.5     4.47875e-02
 528  6.5     4.63486e-02
 529  7.5     4.60514e-02
 530  8.5     4.49130e-02
 531  9.5     4.36744e-02
 532 10.5     4.26085e-02
 533 11.5     4.17464e-02
 534 12.5     4.11217e-02
 535 13.5     4.07835e-02
 536 14.5     4.06776e-02
 537 15.5     4.06060e-02
 538 16.5     4.03241e-02
 539 17.5     3.96655e-02
 540 18.5     3.85756e-02
 541 19.5     3.70537e-02
 542 20.5     3.50982e-02
 543 21.5     3.27236e-02
 544 22.5     3.00046e-02
 545 23.5     2.70643e-02
 546 24.5     2.40044e-02
 547 25.5     2.08595e-02
 548 26.5     1.76342e-02
 549 27.5     1.43802e-02
 550 28.5     1.12281e-02
 551 29.5     8.34574e-03
 552 30.5     5.87354e-03
 553 31.5     3.88732e-03
 554 32.5     2.39755e-03
 555 33.5     1.36323e-03
 556 34.5     7.06686e-04
 557 35.5     3.30592e-04
 558 36.5     1.38359e-04"""}
 559         form = TaskForm_remd_a(initial=data)
 560      elif '_example_saxs1' in request.POST:
 561         data= {'name':task.name,'pdbid':'2KMS','md_pdbref':True,'md_start':'pdbstart',
 562         'md_2d':'----EEEEEE-EEEEE-------EEEEEEEEE--EEEEEE-EEEE---EEEEEEEEE-----EEEEEEE-EEE-HHHHH-EEEE-EEEEEEEEE----EEEEEE---EEE-----',
 563          'md_nstep':200000,'md_lang':'langevin','unres_ff':'FF2','md_seed':-39912345,
 564          'remd_cluter_temp':280, 'min_maxfun':50,
 565          'scal_rad':5.0,'wsaxs':1000.0,'saxs_data':
 566 """0.7100E-00 0.2036E-03
 567 0.1420E+01 0.4221E-03
 568 0.2130E+01 0.6548E-03
 569 0.2840E+01 0.9001E-03
 570 0.3550E+01 0.1156E-02
 571 0.4260E+01 0.1421E-02
 572 0.4970E+01 0.1692E-02
 573 0.5680E+01 0.1965E-02
 574 0.6390E+01 0.2239E-02
 575 0.7100E+01 0.2509E-02
 576 0.7810E+01 0.2772E-02
 577 0.8520E+01 0.3025E-02
 578 0.9230E+01 0.3265E-02
 579 0.9940E+01 0.3489E-02
 580 0.1065E+02 0.3694E-02
 581 0.1136E+02 0.3878E-02
 582 0.1207E+02 0.4039E-02
 583 0.1278E+02 0.4177E-02
 584 0.1349E+02 0.4289E-02
 585 0.1420E+02 0.4377E-02
 586 0.1491E+02 0.4439E-02
 587 0.1562E+02 0.4478E-02
 588 0.1633E+02 0.4493E-02
 589 0.1704E+02 0.4487E-02
 590 0.1775E+02 0.4461E-02
 591 0.1846E+02 0.4418E-02
 592 0.1917E+02 0.4361E-02
 593 0.1988E+02 0.4291E-02
 594 0.2059E+02 0.4211E-02
 595 0.2130E+02 0.4125E-02
 596 0.2201E+02 0.4034E-02
 597 0.2272E+02 0.3942E-02
 598 0.2343E+02 0.3850E-02
 599 0.2414E+02 0.3761E-02
 600 0.2485E+02 0.3677E-02
 601 0.2556E+02 0.3598E-02
 602 0.2627E+02 0.3526E-02
 603 0.2698E+02 0.3462E-02
 604 0.2769E+02 0.3405E-02
 605 0.2840E+02 0.3356E-02
 606 0.2911E+02 0.3315E-02
 607 0.2982E+02 0.3280E-02
 608 0.3053E+02 0.3251E-02
 609 0.3124E+02 0.3226E-02
 610 0.3195E+02 0.3205E-02
 611 0.3266E+02 0.3186E-02
 612 0.3337E+02 0.3167E-02
 613 0.3408E+02 0.3147E-02
 614 0.3479E+02 0.3125E-02
 615 0.3550E+02 0.3099E-02
 616 0.3621E+02 0.3068E-02
 617 0.3692E+02 0.3031E-02
 618 0.3763E+02 0.2987E-02
 619 0.3834E+02 0.2937E-02
 620 0.3905E+02 0.2878E-02
 621 0.3976E+02 0.2812E-02
 622 0.4047E+02 0.2739E-02
 623 0.4118E+02 0.2658E-02
 624 0.4189E+02 0.2571E-02
 625 0.4260E+02 0.2478E-02
 626 0.4331E+02 0.2381E-02
 627 0.4402E+02 0.2279E-02
 628 0.4473E+02 0.2174E-02
 629 0.4544E+02 0.2068E-02
 630 0.4615E+02 0.1960E-02
 631 0.4686E+02 0.1853E-02
 632 0.4757E+02 0.1748E-02
 633 0.4828E+02 0.1644E-02
 634 0.4899E+02 0.1544E-02
 635 0.4970E+02 0.1447E-02
 636 0.5041E+02 0.1355E-02
 637 0.5112E+02 0.1267E-02
 638 0.5183E+02 0.1184E-02
 639 0.5254E+02 0.1106E-02
 640 0.5325E+02 0.1033E-02
 641 0.5396E+02 0.9646E-03
 642 0.5467E+02 0.9008E-03
 643 0.5538E+02 0.8411E-03
 644 0.5609E+02 0.7852E-03
 645 0.5680E+02 0.7327E-03
 646 0.5751E+02 0.6831E-03
 647 0.5822E+02 0.6360E-03
 648 0.5893E+02 0.5909E-03
 649 0.5964E+02 0.5475E-03
 650 0.6035E+02 0.5055E-03
 651 0.6106E+02 0.4646E-03
 652 0.6177E+02 0.4245E-03
 653 0.6248E+02 0.3853E-03
 654 0.6319E+02 0.3467E-03
 655 0.6390E+02 0.3089E-03
 656 0.6461E+02 0.2719E-03
 657 0.6532E+02 0.2357E-03
 658 0.6603E+02 0.2007E-03
 659 0.6674E+02 0.1669E-03
 660 0.6745E+02 0.1345E-03
 661 0.6816E+02 0.1038E-03
 662 0.6887E+02 0.7482E-04
 663 0.6958E+02 0.4782E-04
 664 0.7029E+02 0.2286E-04"""}
 665         form = TaskForm_remd_a(initial=data)
 666      else:
 667         form = TaskForm_remd_a(request.POST,request.FILES)
 668         if form.is_valid():
 669              task.name=form.cleaned_data["name"]
 670              task.type="remd"
 671
 672              basename = str(task.owner)
 673              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 674              task.jobdirname = "_".join([basename, suffix])
 675
 676              pdbid=form.cleaned_data["pdbid"]
 677              if pdbid:
 678               task.myfile1=load_pdbid(pdbid,task.jobdirname)
 679               task.pdbcode=pdbid
 680              else:
 681               task.myfile1=form.cleaned_data["file1"]
 682              task.md_start=form.cleaned_data["md_start"]
 683              task.md_pdbref=form.cleaned_data["md_pdbref"]
 684
 685              task.md_seq=""
 686              if task.md_start == "pdbstart" or task.md_pdbref:
 687                seq,task.ssbond=from_pdb(task.myfile1)
 688                task.md_2d=seq_2d_from_pdb(form.cleaned_data["md_2d"],seq)
 689              else:
 690                seq=seq_add_x(form.cleaned_data["md_seq"])
 691                task.md_2d=seq_2d_add_x(form.cleaned_data["md_2d"],seq,form.cleaned_data["md_seq"])
 692
 693              for i in range(0,len(seq),40):
 694                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 695
 696              if task.md_start != "pdbstart":
 697                 task.ssbond=''
 698
 699              task.md_seed=form.cleaned_data["md_seed"]
 700              task.md_nstep=form.cleaned_data["md_nstep"]
 701              task.md_total_steps=task.md_nstep
 702              task.md_dt=form.cleaned_data["md_dt"]
 703              task.md_lang=form.cleaned_data["md_lang"]
 704              task.md_tau=form.cleaned_data["md_tau"]
 705              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
 706              task.min_maxfun=form.cleaned_data["min_maxfun"]
 707              task.remd_nrep=form.cleaned_data["remd_nrep"]
 708              task.remd_nstex=form.cleaned_data["remd_nstex"]
 709              task.md_ntwx=form.cleaned_data["md_ntwx"]
 710              task.md_ntwe=form.cleaned_data["md_ntwe"]
 711              task.md_respa=form.cleaned_data["md_respa"]
 712              if any(c.islower() for c in seq):
 713               task.md_respa=False
 714               task.damino=True
 715
 716 #             task.remd_traj1file=form.cleaned_data["remd_traj1file"]
 717 #             task.remd_rest1file=form.cleaned_data["remd_rest1file"]
 718
 719              task.boxx=form.cleaned_data["boxx"]
 720              task.boxy=form.cleaned_data["boxy"]
 721              task.boxz=form.cleaned_data["boxz"]
 722
 723              task.remd_cluter_temp=form.cleaned_data["remd_cluter_temp"]
 724              task.unres_ff=form.cleaned_data["unres_ff"]
 725
 726              task.scal_rad = form.cleaned_data["scal_rad"]
 727              task.saxs_data = form.cleaned_data["saxs_data"]
 728              task.wsaxs = form.cleaned_data["wsaxs"]
 729
 730              task.save()
 731              return redirect('addmlist',task_id=task.id)
 732     else:
 733         data= {'name':task.name,'md_seed':-random.randint(10000000,99999999)}
 734         form = TaskForm_remd_a(initial=data)
 735     basic_adv=False
 736     p_type='replica exchange molecular dynamics - advanced options'
 737     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 738
 739 @login_required
 740 def add_dock(request,task_id):
 741     task = get_object_or_404(Task, id=task_id)
 742     if request.method == 'POST':
 743      if '_example' in request.POST:
 744         data= {'name':task.name,'pdbid':'1BON:A','pdbid2':'1BON:B','md_seed':-12396738,'md_nstep':500000}
 745         form = TaskForm_dock(initial=data)
 746      else:
 747         form = TaskForm_dock(request.POST,request.FILES)
 748         if form.is_valid():
 749              task.name=form.cleaned_data["name"]
 750              task.type="dock"
 751
 752              basename = str(task.owner)
 753              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 754              task.jobdirname = "_".join([basename, suffix])
 755
 756              pdbid=form.cleaned_data["pdbid"]
 757              if pdbid:
 758               task.myfile1=load_pdbid(pdbid,task.jobdirname)
 759               task.pdbcode=pdbid
 760              else:
 761               task.myfile1=form.cleaned_data["file1"]
 762
 763              pdbid2=form.cleaned_data["pdbid2"]
 764              if pdbid2:
 765               task.myfile2=load_pdbid(pdbid2,task.jobdirname,'plik2.pdb')
 766               task.pdbcode2=pdbid2
 767               seq2,ssbond2=from_pdb(task.myfile2)
 768              else:
 769               task.myfile2=form.cleaned_data["file2"]
 770               if not task.myfile2:
 771                 seq2=seq_add_x(form.cleaned_data["md_seq"])
 772                 task.md_seq2=seq2
 773               else:
 774                 seq2,ssbond2=from_pdb(task.myfile2)
 775
 776              task.md_ntwx=task.remd_nstex
 777              task.md_start="pdbstart"
 778              task.remd_multi_m='["3", "3", "3", "3", "3", "3", "3", "3"]'
 779              if task.md_seq2 =='':
 780                task.md_pdbref=True
 781              task.md_respa=False
 782              task.ssbond=""
 783              task.dock_peptide=form.cleaned_data["dock_peptide"]
 784
 785              task.md_seq=""
 786
 787              seq1,ssbond1=from_pdb(task.myfile1)
 788
 789
 790              if seq1[-1]=='X' and seq2[0]=='X':
 791               seq=seq1+seq2
 792              elif seq1[-1]!='X' and seq2[0]!='X':
 793               seq=seq1+'XX'+seq2
 794              else:
 795               seq=seq1+'X'+seq2
 796
 797              for i in range(0,len(seq),40):
 798                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 799
 800              task.md_seed=form.cleaned_data["md_seed"]
 801
 802              task.md_nstep=form.cleaned_data["md_nstep"]
 803              task.md_total_steps=task.md_nstep
 804
 805              if any(c.islower() for c in seq):
 806               task.md_respa=False
 807               task.damino=True
 808
 809              box1=dock_box(task.myfile1)
 810              if task.myfile2:
 811               box2=dock_box(task.myfile2)
 812              else:
 813               box2=len(task.md_seq2)*2.0
 814              task.boxx=(box1+box2)*1.2+20
 815              task.boxy=(box1+box2)*1.2+20
 816              task.boxz=(box1+box2)*1.2+20
 817
 818              task.ready=True
 819
 820
 821
 822              task.save()
 823              if is_lazy_user(request.user):
 824               return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')
 825              else:
 826               return redirect('/')
 827     else:
 828         data= {'name':task.name,'md_seed':-random.randint(10000000,99999999)}
 829         form = TaskForm_dock(initial=data)
 830     basic_adv=True
 831     p_type='docking'
 832     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 833
 834 @login_required
 835 def add_dock_a(request,task_id):
 836     task = get_object_or_404(Task, id=task_id)
 837     if request.method == 'POST':
 838      if '_example' in request.POST:
 839         data= {'name':task.name,'pdbid':'1L2Y','md_pdbref':True,'md_seed':-39912345}
 840         form = TaskForm_dock_a(initial=data)
 841      else:
 842         form = TaskForm_dock_a(request.POST,request.FILES)
 843         if form.is_valid():
 844              task.name=form.cleaned_data["name"]
 845              task.type="dock"
 846
 847              basename = str(task.owner)
 848              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
 849              task.jobdirname = "_".join([basename, suffix])
 850
 851              pdbid=form.cleaned_data["pdbid"]
 852              if pdbid:
 853               task.myfile1=load_pdbid(pdbid,task.jobdirname)
 854               task.pdbcode=pdbid
 855              else:
 856               task.myfile1=form.cleaned_data["file1"]
 857
 858              pdbid2=form.cleaned_data["pdbid2"]
 859              if pdbid2:
 860               task.myfile2=load_pdbid(pdbid2,task.jobdirname,'plik2.pdb')
 861               task.pdbcode2=pdbid2
 862              else:
 863               task.myfile2=form.cleaned_data["file2"]
 864
 865              task.md_ntwx=task.remd_nstex
 866              task.md_start="pdbstart"
 867              task.md_pdbref=True
 868              task.md_respa=False
 869              task.ssbond=""
 870              task.dock_peptide=form.cleaned_data["dock_peptide"]
 871
 872              task.md_seq=""
 873
 874              seq1,ssbond1=from_pdb(task.myfile1)
 875              seq2,ssbond2=from_pdb(task.myfile2)
 876
 877              if seq1[-1]=='X' and seq2[0]=='X':
 878               seq=seq1+seq2
 879              elif seq1[-1]!='X' and seq2[0]!='X':
 880               seq=seq1+'XX'+seq2
 881              else:
 882               seq=seq1+'X'+seq2
 883
 884              for i in range(0,len(seq),40):
 885                 task.md_seq=task.md_seq+seq[i:i+40]+" "
 886
 887              task.md_seed=form.cleaned_data["md_seed"]
 888
 889              task.md_nstep=form.cleaned_data["md_nstep"]
 890              task.md_total_steps=task.md_nstep
 891
 892              task.md_dt=form.cleaned_data["md_dt"]
 893              task.md_lang=form.cleaned_data["md_lang"]
 894              task.md_tau=form.cleaned_data["md_tau"]
 895              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
 896              task.min_maxfun=form.cleaned_data["min_maxfun"]
 897              task.remd_nrep=form.cleaned_data["remd_nrep"]
 898              task.remd_nstex=form.cleaned_data["remd_nstex"]
 899              task.md_ntwx=form.cleaned_data["md_ntwx"]
 900              task.md_ntwe=form.cleaned_data["md_ntwe"]
 901
 902              task.remd_cluter_temp=form.cleaned_data["remd_cluter_temp"]
 903              task.unres_ff=form.cleaned_data["unres_ff"]
 904
 905              if any(c.islower() for c in seq):
 906               task.md_respa=False
 907               task.damino=True
 908
 909              box1=dock_box(task.myfile1)
 910              box2=dock_box(task.myfile2)
 911              task.boxx=(box1+box2)*1.2+20
 912              task.boxy=(box1+box2)*1.2+20
 913              task.boxz=(box1+box2)*1.2+20
 914
 915              task.save()
 916              return redirect('addmlist',task_id=task.id)
 917
 918     else:
 919         data= {'name':task.name,'md_seed':-random.randint(10000000,99999999)}
 920         form = TaskForm_dock_a(initial=data)
 921     basic_adv=False
 922     p_type='docking - advanced options'
 923     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 924
 925
 926
 927 @login_required
 928 def addmlist(request,task_id):
 929     task = get_object_or_404(Task, id=task_id)
 930     if request.method == 'POST':
 931         form = TaskForm_list(task.remd_nrep,request.POST)
 932         if form.is_valid():
 933              task.remd_multi_t=form.cleaned_data["temperatures"]
 934              task.remd_multi_m=form.cleaned_data["multiplexing"]
 935              task.ready=True
 936
 937              task.save()
 938              if is_lazy_user(request.user):
 939               return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')
 940              else:
 941               return redirect('/')
 942     else:
 943       if task.example == 'casp12':
 944         data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
 945         '["2", "2", "2", "2", "2", "2", "2", "2"]',
 946         'temperatures':
 947         '["270", "280", "290", "300", "310", "320", "330", "340"]'
 948         }
 949       elif task.unres_ff == 'FF2':
 950         data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
 951         '["1", "1", "1", "1", "1", "1", "1", "1"]',
 952         'temperatures':
 953         '["270", "280", "290", "300", "310", "320", "330", "345"]'
 954         }
 955       else:
 956         data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
 957         '["1", "1", "1", "1", "1", "1", "1", "1"]',
 958         'temperatures':
 959         '["250", "260", "270", "280", "290", "300", "315", "330"]'
 960         }
 961
 962       form = TaskForm_list(task.remd_nrep,initial=data)
 963     p_type='replica exchange molecular dynamics - advanced options'
 964     return render(request, 'edit_lista.html', {'form': form, 'task':task, 'p_type':p_type})
 965
 966 @login_required
 967 def details(request,task_id):
 968     task = get_object_or_404(Task, id=task_id)
 969     return render(request, "details.html",{'task':task})
 970
 971
 972 def details1(request,user_id,task_id):
 973     task = get_object_or_404(Task, id=task_id)
 974     return render(request, "details1.html",{'task':task})
 975
 976
 977 @login_required
 978 def delete(request, task_id):
 979     Task.objects.get(id=task_id).delete()
 980     return redirect('/')
 981
 982 @login_required
 983 def restart(request, task_id):
 984     task = get_object_or_404(Task, id=task_id)
 985     restart0(task)
 986     return redirect('/')
 987
 988 def add_restart_inp():
 989     with open('file.inp','r') as f1, open ('file.inp.tmp','w') as f2:
 990         for line in f1:
 991           if 'reset_vel=' in line:
 992             f2.write('{:79}'.format('restart'+line[7:]))
 993           else:
 994             f2.write(line)
 995     os.remove('file.inp')
 996     os.rename('file.inp.tmp','file.inp')
 997     return
 998
 999 def restart0(task):
1000     if os.path.isfile(task.jobdirname+'/finished'):
1001       os.remove(task.jobdirname+'/finished')
1002     task.running =1
1003     task.done=False
1004     task.md_total_steps = task.md_total_steps+task.md_nstep
1005     task.save()
1006     if task.type == 'md':
1007       os.chdir(task.jobdirname)
1008       add_restart_inp()
1009       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
1010       os.chdir('..')
1011     elif task.type == 'remd':
1012       os.chdir(task.jobdirname)
1013       add_restart_inp()
1014       tmp1=json.loads(task.remd_multi_m)
1015       nreplicas=sum(map(int, tmp1))
1016       with open('file_wham.inp','r') as f1, open ('file_wham.tmp','w') as f2:
1017         for line in f1:
1018           if 'rec_end=' in line:
1019             rec=task.md_total_steps/task.md_ntwx
1020             f2.write('nfile_cx=1 rec_start='+str(rec/10)
1021                +' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n')
1022           elif 'isampl=' in line:
1023             if task.md_total_steps/task.md_ntwx*nreplicas<=8000:
1024                 isampl=1
1025             else:
1026                 isampl=int(task.md_total_steps/task.md_ntwx*nreplicas/8000)
1027             f2.write('{:79}'.format(' isampl='+str(isampl))+'&\n')
1028           else:
1029             f2.write(line)
1030       os.remove('file_wham.inp')
1031       os.rename('file_wham.tmp','file_wham.inp')
1032       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
1033       os.chdir('..')
1034     return
1035
1036 def restart1(request, user_id, task_id):
1037     task = get_object_or_404(Task, id=task_id)
1038     user = task.owner
1039     restart0(task)
1040     return redirect('/details1/'+str(user)+'/'+str(task.id)+'/')
1041
1042
1043 def refresh_done1(request, task_id):
1044     task = get_object_or_404(Task, id=task_id)
1045     user = task.owner
1046     refresh_done0(task)
1047
1048     proc = subprocess.Popen('/opt/torque/bin/qstat', stdout=subprocess.PIPE)
1049     njob=0
1050     nq=0
1051     for line in proc.stdout:
1052       if 'piasek4' in line:
1053         if line.split()[1]=='test_server':
1054           njob+=1
1055           if line.split()[-2]=='Q':
1056             nq+=1
1057     variable='Idle jobs='+str(nq)+' Total jobs='+str(njob)
1058
1059     return redirect('/details1/'+str(user)+'/'+str(task.id)+'/')
1060
1061
1062 @login_required
1063 def refresh_done(request):
1064     user = request.user
1065     tasks = Task.objects.filter(owner=user).order_by('-created_date')
1066     tasks_count = Task.objects.filter(owner=user).count()
1067     alldone = 1
1068     for task in tasks:
1069       refresh_done0(task)
1070       if not task.done:
1071          alldone=0
1072
1073     proc = subprocess.Popen('/opt/torque/bin/qstat', stdout=subprocess.PIPE)
1074     njob=0
1075     nq=0
1076     for line in proc.stdout:
1077       if 'piasek4' in line:
1078         if line.split()[1]=='test_server':
1079           njob+=1
1080           if line.split()[-2]=='Q':
1081             nq+=1
1082     variable='Idle jobs='+str(nq)+' Total jobs='+str(njob)
1083
1084     if is_lazy_user(request.user):
1085      return redirect('/details1/'+str(user)+'/'+str(task.id)+'/')
1086     else:
1087      return render(request, "index.html", {
1088                 'tasks': tasks ,
1089                 'variable' : variable,
1090                 'alldone': alldone,
1091                 'tasks_count':tasks_count
1092                         })
1093
1094
1095 def refresh_done0(task):
1096       if os.path.isfile(task.jobdirname+'/finished') and not task.done:
1097          task.done=True
1098
1099          with open(task.jobdirname+'/file.out_GB000', 'r') as f:
1100
1101            if task.type=='min' or task.type=='md':
1102              text=""
1103              for line in f:
1104                if 'ETOT' in line:
1105                   task.etot=line.split()[1]
1106
1107                if 'RMS deviation' in line:
1108                   text=text+line
1109                   i=1
1110                   for line1 in f:
1111                      text=text+line1
1112                      i+=1
1113                      if i>6:
1114                        break
1115                if 'Total wall' in line:
1116                   text=text+line
1117
1118            elif task.type=='remd' or task.type=='dock':
1119              j=0
1120              text="Acceptance for replica exchanges and number of exchange attempts\n"
1121              for line in f:
1122
1123                if 'ACC' in line:
1124                     j+=1
1125                     text=text+' '.join(line.split()[2:])+"\n"
1126                     if j==task.remd_nrep:
1127                        j=1
1128                        text="Acceptance for replica exchanges and number of exchange attempts\n"+' '.join(line.split()[2:])+"\n"
1129
1130                if 'Total wall' in line:
1131                   text=text+line
1132
1133          task.results_text=text
1134
1135
1136          if task.md_pdbref and task.type=='remd' or task.type=='dock' and task.md_seq2 == '':
1137
1138           for i in range(1,6):
1139            try:
1140             with open(task.jobdirname+'/file_wham_T'+str(int(task.remd_cluter_temp))+'K_000'+str(i)+'.pdb', 'r') as f:
1141                  line=f.readline()
1142                  if i==1:
1143                      task.remd_model1='Cluster1 '+' '.join(line.split()[-3:])
1144                  elif i==2:
1145                      task.remd_model2='Cluster2 '+' '.join(line.split()[-3:])
1146                  elif i==3:
1147                      task.remd_model3='Cluster3 '+' '.join(line.split()[-3:])
1148                  elif i==4:
1149                      task.remd_model4='Cluster4 '+' '.join(line.split()[-3:])
1150                  elif i==5:
1151                      task.remd_model5='Cluster5 '+' '.join(line.split()[-3:])
1152            except EnvironmentError:
1153             print 'file_wham_T*pdb open error'
1154           for i in range(1,6):
1155             with open(task.jobdirname+'/tmscore'+str(i)+'.out', 'r') as f:
1156                text=''
1157                for line in f:
1158                  if 'RMSD of  the common residues=' in line:
1159                    text=' RMSD='+line.split()[5]
1160                  if 'TM-score    =' in line:
1161                    text=text+' TMscore='+line.split()[2]
1162                  if 'GDT-TS-score=' in line:
1163                    text=text+' GDT_TS='+line.split()[1]
1164
1165                if i==1:
1166                      task.remd_model1=task.remd_model1+text
1167                elif i==2:
1168                      task.remd_model2=task.remd_model2+text
1169                elif i==3:
1170                      task.remd_model3=task.remd_model3+text
1171                elif i==4:
1172                      task.remd_model4=task.remd_model4+text
1173                elif i==5:
1174                      task.remd_model5=task.remd_model5+text
1175
1176           if task.type=='dock':
1177            for i in range(1,6):
1178             with open(task.jobdirname+'/dockq_'+str(i)+'.out', 'r') as f:
1179                text=''
1180                for line in f:
1181                  if 'Fnat' in line:
1182                    text=' Fnat='+line.split()[1]
1183                  if 'iRMS' in line:
1184                    text=text+' iRMS='+line.split()[1]
1185                  if 'LRMS' in line:
1186                    text=text+' LRMS='+line.split()[1]
1187                  if 'CAPRI' in line and not 'DockQ_CAPRI' in line:
1188                    text=text+' CAPRI='+line.split()[1]
1189                  if 'DockQ_CAPRI' in line:
1190                    text=text+' DockQ_CAPRI= '+line.split()[1]
1191                  if 'DockQ ' in line:
1192                    text=text+' DockQ='+line.split()[1]
1193
1194                if i==1:
1195                      task.remd_model1=task.remd_model1+text
1196                elif i==2:
1197                      task.remd_model2=task.remd_model2+text
1198                elif i==3:
1199                      task.remd_model3=task.remd_model3+text
1200                elif i==4:
1201                      task.remd_model4=task.remd_model4+text
1202                elif i==5:
1203                      task.remd_model5=task.remd_model5+text
1204
1205
1206          if task.type=='remd' or task.type=='dock':
1207           with open(task.jobdirname+'/file_cluster_clust.out_000', 'r') as f:
1208
1209            for line in f:
1210              if 'sumprob' in line:
1211                 i=0
1212                 for line1 in f:
1213                   i+=1
1214                   if i>6:
1215                        break
1216                   if i==1:
1217                      task.remd_model1=task.remd_model1+' Cluster1 probability= '+line1.split()[-2]
1218                   elif i==2:
1219                      task.remd_model2=task.remd_model2+' Cluster2 probability= '+line1.split()[-2]
1220                   elif i==3:
1221                      task.remd_model3=task.remd_model3+' Cluster3 probability= '+line1.split()[-2]
1222                   elif i==4:
1223                      task.remd_model4=task.remd_model4+' Cluster4 probability= '+line1.split()[-2]
1224                   elif i==5:
1225                      task.remd_model5=task.remd_model5+' Cluster5 probability= '+line1.split()[-2]
1226
1227
1228
1229          task.save()
1230       elif os.path.isfile(task.jobdirname+'/file_GB000.stat') and not task.done:
1231          if (task.type=='min'):
1232            task.running =1
1233            with open(task.jobdirname+'/file.out_GB000', 'r') as f:
1234               line=''
1235               for line in f:
1236                 pass
1237               if line != '':
1238                 last = line.split()[0]
1239               else:
1240                 last = 0
1241            try:
1242               task.running=int(1+int(last)*100.0/task.min_maxmin)
1243            except:
1244               pass
1245            if task.running>100:
1246               task.running=100
1247          else:
1248            with open(task.jobdirname+'/file_GB000.stat', 'r') as f:
1249               line=''
1250               for line in f:
1251                 pass
1252               if line != '':
1253                 last = line.split()[0]
1254               else:
1255                 last = 0
1256            task.running=int(1+int(last)*100.0/task.md_nstep)
1257            if task.running>100:
1258              task.running=100
1259          task.save()
1260
1261
1262       return
1263
1264 @login_required
1265 def zip_all_files(request, task_id):
1266     import os, zipfile
1267     from django.http import HttpResponse
1268     from wsgiref.util import FileWrapper
1269     from django.core.files.temp import NamedTemporaryFile
1270
1271     task = get_object_or_404(Task, id=task_id)
1272
1273     temp=NamedTemporaryFile()
1274     archive = zipfile.ZipFile(temp, 'w', zipfile.ZIP_DEFLATED)
1275     for (dirpath, dirnames, filenames) in os.walk(task.jobdirname):
1276        for file1 in filenames:
1277          archive.write(dirpath+"/"+file1,file1)
1278     archive.close()
1279     temp.seek(0)
1280     wrapper = FileWrapper(temp)
1281     response = HttpResponse(wrapper, content_type='application/zip')
1282     response['Content-Disposition'] = 'attachment; filename=all.zip'
1283     return response