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