django_simple/todo/forms.py

   1 from django import forms
   2 from .models import Task
   3 from .models import MIN_CHOICE
   4 from .models import MD_START
   5 from .models import MD_LANG
   6 from .models import FF_CHOICE
   7 import json
   8 import urllib
   9
  10 def code_2d(line):
  11    msg=''
  12    set ='HEC-'
  13    line2 = ''.join([c for c in line if c in set])
  14    if line2 != line:
  15     msg='use only H,E,C or - letters'
  16    return(msg)
  17
  18 def pdb_missing_res(file):
  19    msg=''
  20    newchain = True
  21    ires=[]
  22    for line in file:
  23       if line[0:6] == 'ATOM  ' and line[13:15] == 'CA':
  24                i = int(line[22:26])
  25                if ires and i==ires[-1]:
  26                  continue
  27                if newchain or i==ires[-1]+1:
  28                  ires.append(i)
  29                  newchain = False
  30                else:
  31                  msg = 'chain breaks between residues '+\
  32                    str(ires[-1])+' and '+str(i)+\
  33                    ', server cannot add missing residues to PDB file - please repair the structure using e.g. Modeller'
  34                  break
  35       if line[0:3] == 'TER':
  36                newchain = True
  37       if line[0:3] == 'END':
  38                break
  39
  40    return(msg)
  41
  42 class MultiWidgetBasic(forms.MultiWidget):
  43     def __init__(self, count, attrs=None):
  44         self.count=count
  45         widgets = []
  46         for i in range(self.count):
  47            widgets.append(forms.TextInput())
  48         super(MultiWidgetBasic, self).__init__(widgets, attrs)
  49
  50     template_name = 'multi.html'
  51
  52     def decompress(self, value):
  53         if value:
  54             return json.loads(value)
  55         else:
  56             return ['', '']
  57
  58
  59 class MultiExampleField(forms.fields.MultiValueField):
  60     def __init__(self, count, *args, **kwargs):
  61         self.count=count
  62         self.widget = MultiWidgetBasic(self.count)
  63         list_fields = []
  64         for i in range(self.count):
  65            list_fields.append(forms.fields.CharField(max_length=15))
  66         super(MultiExampleField, self).__init__(list_fields, *args, **kwargs)
  67
  68     def compress(self, values):
  69         ## compress list to single object
  70         return json.dumps(values)
  71
  72
  73 class TaskForm(forms.Form):
  74     name = forms.CharField(max_length=20)
  75
  76
  77 class TaskForm_min(forms.Form):
  78      name = forms.CharField(max_length=20)
  79      file1 = forms.FileField(label='Upload a PDB file',required=False,
  80       help_text='continuous (without breaks) protein chains,use TER to divide chains')
  81      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
  82       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
  83       label='or PDB code')
  84
  85      def clean(self):
  86              cleaned_data = super(TaskForm_min, self).clean()
  87
  88              pdbid = cleaned_data.get("pdbid")
  89              file1 = cleaned_data.get("file1")
  90
  91              if not pdbid and not file1:
  92                 msg = 'provide pdb file or pdb code'
  93                 self.add_error('file1', msg)
  94
  95              if pdbid:
  96                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
  97                if test.code != 200:
  98                  msg = 'wrong pdb code'
  99                  self.add_error('pdbid', msg)
 100                else:
 101                  msg=pdb_missing_res(test)
 102                  if msg != '':
 103                    self.add_error('pdbid',msg)
 104                test.close()
 105
 106              if file1:
 107                  msg=pdb_missing_res(file1)
 108                  if msg != '':
 109                    self.add_error('file1',msg)
 110
 111
 112 class TaskForm_min_a(forms.Form):
 113      name = forms.CharField(max_length=20)
 114
 115      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 116                            label='Force Field',initial='FF2')
 117 #     min_choice = forms.ChoiceField(choices=MIN_CHOICE,label='minimization algorithm')
 118      min_overlap = forms.BooleanField(required=False,label='remove overlap')
 119      min_searchsc = forms.BooleanField(required=False,label='MC for sidechain overlap')
 120      min_maxmin = forms.IntegerField(label='MAXMIN',initial=10000,
 121                   help_text='maximum number of iterations')
 122      min_maxfun = forms.IntegerField(label='MAXFUN',initial=15000,
 123                   help_text='maximum number of function evaluations')
 124      file1 = forms.FileField(label='Upload a PDB file',required=False,
 125         help_text='continuous (without breaks) protein chains,use TER to divide chains')
 126      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
 127       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
 128       label='or PDB code')
 129
 130      min_unres_pdb = forms.BooleanField(required=False,label='uploaded input unres PDB',
 131                   help_text='(CA and CB atoms only, CB represents SC in UNRES)')
 132      min_pdbout = forms.BooleanField(required=False,label='output PDB',initial='true')
 133      boxx = forms.FloatField(label='Box X',initial=1000.0,
 134                        help_text='box x dimension')
 135      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 136                        help_text='box y dimension')
 137      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 138                        help_text='box z dimension')
 139
 140      def clean(self):
 141              cleaned_data = super(TaskForm_min_a, self).clean()
 142
 143              pdbid = cleaned_data.get("pdbid")
 144              file1 = cleaned_data.get("file1")
 145
 146              if not pdbid and not file1:
 147                 msg = 'provide pdb file or pdb code'
 148                 self.add_error('file1', msg)
 149
 150              if pdbid:
 151                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 152                if test.code != 200:
 153                  msg = 'wrong pdb code'
 154                  self.add_error('pdbid', msg)
 155                else:
 156                  msg=pdb_missing_res(test)
 157                  if msg != '':
 158                    self.add_error('pdbid',msg)
 159                test.close()
 160
 161              if file1:
 162                  msg=pdb_missing_res(file1)
 163                  if msg != '':
 164                    self.add_error('file1',msg)
 165
 166
 167 class TaskForm_md(forms.Form):
 168      name = forms.CharField(max_length=20)
 169
 170      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 171                       label='starting structure',initial='extconf')
 172      md_seq = forms.CharField(label='Sequence',
 173                      help_text='aminoacid sequence using one letter code<br>'+
 174                      'field is ignored when uploading starting/reference PDB file',
 175                      required=False,
 176                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 177      file1 = forms.FileField(label='Upload a PDB file',required=False,
 178                   help_text='starting structure for pdbstart/reference structure')
 179      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
 180       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
 181       label='or PDB code')
 182      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 183      md_temp = forms.FloatField(label='temperature',initial=300,
 184                   help_text='bath temperature')
 185      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 186                   help_text='total number of steps')
 187      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 188                   help_text='seed for random number generator')
 189
 190      def clean(self):
 191              cleaned_data = super(TaskForm_md, self).clean()
 192
 193              md_start = cleaned_data.get("md_start")
 194              file1 = cleaned_data.get("file1")
 195              pdbid = cleaned_data.get("pdbid")
 196              md_seq = cleaned_data.get("md_seq")
 197              md_pdbref = cleaned_data.get("md_pdbref")
 198
 199              if md_start == 'pdbstart' and not (file1 or pdbid):
 200                 msg = 'pdbstart with no PDB file or code'
 201                 self.add_error('file1', msg)
 202
 203              if md_pdbref and not (file1 or pdbid):
 204                 msg = 'pdbref with no PDB file or code'
 205                 self.add_error('file1', msg)
 206
 207
 208              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 209                 msg = 'extended/random chain with no sequence'
 210                 self.add_error('md_seq', msg)
 211
 212              if pdbid:
 213                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 214                if test.code != 200:
 215                  msg = 'wrong pdb code'
 216                  self.add_error('pdbid', msg)
 217                else:
 218                  msg=pdb_missing_res(test)
 219                  if msg != '':
 220                    self.add_error('pdbid',msg)
 221                test.close()
 222
 223              if file1:
 224                  msg=pdb_missing_res(file1)
 225                  if msg != '':
 226                    self.add_error('file1',msg)
 227
 228
 229 class TaskForm_md_a(forms.Form):
 230      name = forms.CharField(max_length=20)
 231
 232      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 233                            label='Force Field',initial='FF2')
 234      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 235                       label='starting structure',initial='extconf')
 236      md_seq = forms.CharField(label='Sequence',
 237                      help_text='aminoacid sequence using one letter code<br>'+
 238                      'field is ignored when uploading starting/reference PDB file',
 239                      required=False,
 240                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 241      md_2d = forms.CharField(label='Secondary structure restraints',
 242                      help_text='single letter code: H - helix, E - extended/beta, C or - no restraints',
 243                      required=False,
 244                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 245
 246      file1 = forms.FileField(label='Upload a PDB file',required=False,
 247                   help_text='starting structure for pdbstart/reference structure')
 248      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
 249       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
 250       label='or PDB code')
 251      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 252      md_temp = forms.FloatField(label='temperature',initial=300,
 253                   help_text='bath temperature')
 254      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 255                   help_text='total number of steps')
 256      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 257                   help_text='seed for random number generator')
 258
 259      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
 260                help_text='write statfile every ntwe steps')
 261      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,
 262                help_text='write trajectory every ntwe steps')
 263      md_dt = forms.FloatField(label='DT',initial=0.2,
 264                   help_text='time step [mtu=48.9 fs]')
 265      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
 266      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
 267                   help_text='coupling to the thermal bath (Berendsen)')
 268      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
 269                   help_text='scaling of the friction coefficients (Langevin)')
 270      md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
 271      md_mdpdb = forms.BooleanField(required=False,label='trajectory as PDB')
 272
 273      boxx = forms.FloatField(label='Box X',initial=1000.0,
 274                        help_text='box x dimension')
 275      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 276                        help_text='box y dimension')
 277      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 278                        help_text='box z dimension')
 279
 280      def clean(self):
 281              cleaned_data = super(TaskForm_md_a, self).clean()
 282
 283              md_start = cleaned_data.get("md_start")
 284              file1 = cleaned_data.get("file1")
 285              pdbid = cleaned_data.get("pdbid")
 286              md_seq = cleaned_data.get("md_seq")
 287              md_pdbref = cleaned_data.get("md_pdbref")
 288              md_2d = cleaned_data.get("md_2d")
 289
 290              if md_start == 'pdbstart' and not (file1 or pdbid):
 291                 msg = 'pdbstart with no PDB file or code'
 292                 self.add_error('file1', msg)
 293
 294              if md_pdbref and not (file1 or pdbid):
 295                 msg = 'pdbref with no PDB file or code'
 296                 self.add_error('file1', msg)
 297
 298
 299              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 300                 msg = 'extended/random chain with no sequence'
 301                 self.add_error('md_seq', msg)
 302
 303              if pdbid:
 304                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 305                if test.code != 200:
 306                  msg = 'wrong pdb code'
 307                  self.add_error('pdbid', msg)
 308                else:
 309                  msg=pdb_missing_res(test)
 310                  if msg != '':
 311                    self.add_error('pdbid',msg)
 312                test.close()
 313
 314              if file1:
 315                  msg=pdb_missing_res(file1)
 316                  if msg != '':
 317                    self.add_error('file1',msg)
 318
 319              if md_2d:
 320                  msg=code_2d(md_2d)
 321                  if msg != '':
 322                    self.add_error('md_2d',msg)
 323
 324 class TaskForm_remd(forms.Form):
 325      name = forms.CharField(max_length=20)
 326
 327      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 328                       label='starting structure',initial='extconf')
 329      md_seq = forms.CharField(label='Sequence',
 330                      help_text='aminoacid sequence using one letter code<br>'+
 331                         'field is ignored when uploading starting/reference PDB file',
 332                      required=False,
 333                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 334      file1 = forms.FileField(label='Upload a PDB file',required=False,
 335                   help_text='starting structure for pdbstart/reference structure')
 336      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
 337       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
 338       label='or PDB code')
 339      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 340      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 341                   help_text='total number of steps')
 342      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 343                   help_text='seed for random number generator')
 344
 345      def clean(self):
 346              cleaned_data = super(TaskForm_remd, self).clean()
 347
 348              md_start = cleaned_data.get("md_start")
 349              file1 = cleaned_data.get("file1")
 350              pdbid = cleaned_data.get("pdbid")
 351              md_seq = cleaned_data.get("md_seq")
 352              md_pdbref = cleaned_data.get("md_pdbref")
 353
 354              if md_start == 'pdbstart' and not (file1 or pdbid):
 355                 msg = 'pdbstart with no PDB file or code'
 356                 self.add_error('file1', msg)
 357
 358              if md_pdbref and not (file1 or pdbid):
 359                 msg = 'pdbref with no PDB file or code'
 360                 self.add_error('file1', msg)
 361
 362              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 363                 msg = 'extended/random chain with no sequence'
 364                 self.add_error('md_seq', msg)
 365
 366              if pdbid:
 367                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 368                if test.code != 200:
 369                  msg = 'wrong pdb code'
 370                  self.add_error('pdbid', msg)
 371                else:
 372                  msg=pdb_missing_res(test)
 373                  if msg != '':
 374                    self.add_error('pdbid',msg)
 375                test.close()
 376
 377              if file1:
 378                  msg=pdb_missing_res(file1)
 379                  if msg != '':
 380                    self.add_error('file1',msg)
 381
 382
 383 class TaskForm_remd_a(forms.Form):
 384      name = forms.CharField(max_length=20)
 385
 386      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 387                            label='Force Field',initial='FF2')
 388      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 389                       label='starting structure',initial='extconf')
 390      md_seq = forms.CharField(label='Sequence',
 391                      help_text='aminoacid sequence using one letter code<br>'+
 392                       'field is ignored when uploading starting/reference PDB file',
 393                      required=False,
 394                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 395      md_2d = forms.CharField(label='Secondary structure restraints',
 396                      help_text='single letter code: H - helix, E - extended/beta, C or - no restraints',
 397                      required=False,
 398                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 399      file1 = forms.FileField(label='Upload a PDB file',required=False,
 400                   help_text='starting structure for pdbstart/reference structure')
 401      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
 402       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
 403       label='or PDB code')
 404      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 405      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 406                   help_text='total number of steps')
 407      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 408                   help_text='seed for random number generator')
 409      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
 410                help_text='write statfile every ntwe steps')
 411      md_dt = forms.FloatField(label='DT',initial=0.2,
 412                   help_text='time step [mtu = 48.9 fs]')
 413      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
 414      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
 415                   help_text='coupling to the thermal bath (Berendsen)')
 416      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
 417                   help_text='scaling of the friction coefficients (Langevin)')
 418      remd_nrep = forms.IntegerField(label='NREP',initial=8,
 419                   help_text='number of replicas')
 420      remd_nstex = forms.IntegerField(label='NSTEX',initial=1000,
 421                   help_text='exchange and write trajectory every nstex steps')
 422      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,
 423                help_text='write trajectory every ntwx steps')
 424      remd_cluter_temp = forms.FloatField(label='TEMPER',
 425                   help_text='temperature for cluster analysis',initial=280)
 426 #     remd_traj1file = forms.BooleanField(required=False,label='single trajectory file',initial='true')
 427 #     remd_rest1file = forms.BooleanField(required=False,label='single restart file',initial='true')
 428
 429      md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
 430
 431      boxx = forms.FloatField(label='Box X',initial=1000.0,
 432                        help_text='box x dimension')
 433      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 434                        help_text='box y dimension')
 435      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 436                        help_text='box z dimension')
 437
 438
 439      wsaxs = forms.FloatField(label='SAXS weight',initial=100.0,
 440                             help_text='weight for SAXS restraint term')
 441      scal_rad = forms.FloatField(label='Scal_rad (SAXS)',initial=1.0,
 442                             help_text='downscaling factor of residue radii used in SAXS restraints')
 443      saxs_data = forms.CharField(label='P(r) SAXS data',
 444                      help_text='distance distribution from SAXS, two columns: r and P(r)',
 445                      required=False,
 446                      widget=forms.Textarea(attrs={'cols': 25, 'rows': 20}))
 447
 448
 449      def clean(self):
 450              cleaned_data = super(TaskForm_remd_a, self).clean()
 451
 452              md_start = cleaned_data.get("md_start")
 453              file1 = cleaned_data.get("file1")
 454              pdbid = cleaned_data.get("pdbid")
 455              md_seq = cleaned_data.get("md_seq")
 456              md_pdbref = cleaned_data.get("md_pdbref")
 457              md_2d = cleaned_data.get("md_2d")
 458
 459              if md_start == 'pdbstart' and not (file1 or pdbid):
 460                 msg = 'pdbstart with no PDB file or code'
 461                 self.add_error('file1', msg)
 462
 463              if md_pdbref and not (file1 or pdbid):
 464                 msg = 'pdbref with no PDB file or code'
 465                 self.add_error('file1', msg)
 466
 467
 468              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 469                 msg = 'extended/random chain with no sequence'
 470                 self.add_error('md_seq', msg)
 471
 472              if pdbid:
 473                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 474                if test.code != 200:
 475                  msg = 'wrong pdb code'
 476                  self.add_error('pdbid', msg)
 477                else:
 478                  msg=pdb_missing_res(test)
 479                  if msg != '':
 480                    self.add_error('pdbid',msg)
 481                test.close()
 482
 483              if file1:
 484                  msg=pdb_missing_res(file1)
 485                  if msg != '':
 486                    self.add_error('file1',msg)
 487
 488              if md_2d:
 489                  msg=code_2d(md_2d)
 490                  if msg != '':
 491                    self.add_error('md_2d',msg)
 492
 493
 494
 495 class TaskForm_list(forms.Form):
 496     name = forms.CharField(max_length=20,disabled=True,required=False)
 497     nrep = forms.IntegerField(disabled=True,required=False,label='NREP')
 498
 499     def __init__(self, count, *args, **kwargs):
 500         super(TaskForm_list, self).__init__(*args, **kwargs)
 501         self.count=count
 502         self.fields['temperatures'] = MultiExampleField(self.count)
 503         self.fields['multiplexing'] = MultiExampleField(self.count)
 504
 505
 506