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 pdb_missing_res(file):
  11    msg=''
  12    newchain = True
  13    ires=[]
  14    for line in file:
  15       if line[0:6] == 'ATOM  ' and line[13:15] == 'CA':
  16                i = int(line[22:26])
  17                if ires and i==ires[-1]:
  18                  continue
  19                if newchain or i==ires[-1]+1:
  20                  ires.append(i)
  21                  newchain = False
  22                else:
  23                  msg = 'chain breaks between residues '+\
  24                    str(ires[-1])+' and '+str(i)+\
  25                    ', server cannot add missing residues to PDB file - please repair the structure using e.g. Modeller'
  26                  break
  27       if line[0:3] == 'TER':
  28                newchain = True
  29       if line[0:3] == 'END':
  30                break
  31
  32    return(msg)
  33
  34 class MultiWidgetBasic(forms.MultiWidget):
  35     def __init__(self, count, attrs=None):
  36         self.count=count
  37         widgets = []
  38         for i in range(self.count):
  39            widgets.append(forms.TextInput())
  40         super(MultiWidgetBasic, self).__init__(widgets, attrs)
  41
  42     template_name = 'multi.html'
  43
  44     def decompress(self, value):
  45         if value:
  46             return json.loads(value)
  47         else:
  48             return ['', '']
  49
  50
  51 class MultiExampleField(forms.fields.MultiValueField):
  52     def __init__(self, count, *args, **kwargs):
  53         self.count=count
  54         self.widget = MultiWidgetBasic(self.count)
  55         list_fields = []
  56         for i in range(self.count):
  57            list_fields.append(forms.fields.CharField(max_length=15))
  58         super(MultiExampleField, self).__init__(list_fields, *args, **kwargs)
  59
  60     def compress(self, values):
  61         ## compress list to single object
  62         return json.dumps(values)
  63
  64
  65 class TaskForm(forms.Form):
  66     name = forms.CharField(max_length=20)
  67
  68
  69 class TaskForm_min(forms.Form):
  70      name = forms.CharField(max_length=20)
  71      file1 = forms.FileField(label='Upload a PDB file',required=False,
  72       help_text='continuous (without breaks) protein chains,use TER to divide chains')
  73      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
  74       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
  75       label='or PDB code')
  76
  77      def clean(self):
  78              cleaned_data = super(TaskForm_min, self).clean()
  79
  80              pdbid = cleaned_data.get("pdbid")
  81              file1 = cleaned_data.get("file1")
  82
  83              if not pdbid and not file1:
  84                 msg = 'provide pdb file or pdb code'
  85                 self.add_error('file1', msg)
  86
  87              if pdbid:
  88                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
  89                if test.code != 200:
  90                  msg = 'wrong pdb code'
  91                  self.add_error('pdbid', msg)
  92                else:
  93                  msg=pdb_missing_res(test)
  94                  if msg != '':
  95                    self.add_error('pdbid',msg)
  96                test.close()
  97
  98              if file1:
  99                  msg=pdb_missing_res(file1)
 100                  if msg != '':
 101                    self.add_error('file1',msg)
 102
 103
 104 class TaskForm_min_a(forms.Form):
 105      name = forms.CharField(max_length=20)
 106
 107      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 108                            label='Force Field',initial='E0LL2Y')
 109      min_choice = forms.ChoiceField(choices=MIN_CHOICE,label='minimization algorithm')
 110      min_overlap = forms.BooleanField(required=False,label='remove overlap')
 111      min_searchsc = forms.BooleanField(required=False,label='MC for sidechain overlap')
 112      min_maxmin = forms.IntegerField(label='MAXMIN',initial=10000,
 113                   help_text='maximum number of iterations')
 114      min_maxfun = forms.IntegerField(label='MAXFUN',initial=15000,
 115                   help_text='maximum number of function evaluations')
 116      file1 = forms.FileField(label='Upload a PDB file',required=False,
 117         help_text='continuous (without breaks) protein chains,use TER to divide chains')
 118      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
 119       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
 120       label='or PDB code')
 121
 122      min_unres_pdb = forms.BooleanField(required=False,label='uploaded input unres PDB',
 123                   help_text='(CA and CB atoms only, CB represents SC in UNRES)')
 124      min_pdbout = forms.BooleanField(required=False,label='output PDB',initial='true')
 125      boxx = forms.FloatField(label='Box X',initial=1000.0,
 126                        help_text='box x dimension')
 127      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 128                        help_text='box y dimension')
 129      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 130                        help_text='box z dimension')
 131
 132      def clean(self):
 133              cleaned_data = super(TaskForm_min_a, self).clean()
 134
 135              pdbid = cleaned_data.get("pdbid")
 136              file1 = cleaned_data.get("file1")
 137
 138              if not pdbid and not file1:
 139                 msg = 'provide pdb file or pdb code'
 140                 self.add_error('file1', msg)
 141
 142              if pdbid:
 143                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 144                if test.code != 200:
 145                  msg = 'wrong pdb code'
 146                  self.add_error('pdbid', msg)
 147                else:
 148                  msg=pdb_missing_res(test)
 149                  if msg != '':
 150                    self.add_error('pdbid',msg)
 151                test.close()
 152
 153              if file1:
 154                  msg=pdb_missing_res(file1)
 155                  if msg != '':
 156                    self.add_error('file1',msg)
 157
 158
 159 class TaskForm_md(forms.Form):
 160      name = forms.CharField(max_length=20)
 161
 162      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 163                       label='starting structure',initial='extconf')
 164      md_seq = forms.CharField(label='Sequence',
 165                      help_text='aminoacid sequence using one letter code<br>'+
 166                      'field is ignored when uploading starting/reference PDB file',
 167                      required=False,
 168                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 169      file1 = forms.FileField(label='Upload a PDB file',required=False,
 170                   help_text='starting structure for pdbstart/reference structure')
 171      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
 172       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
 173       label='or PDB code')
 174      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 175      md_temp = forms.FloatField(label='temperature',initial=300,
 176                   help_text='bath temperature')
 177      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 178                   help_text='total number of steps')
 179      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 180                   help_text='seed for random number generator')
 181
 182      def clean(self):
 183              cleaned_data = super(TaskForm_md, self).clean()
 184
 185              md_start = cleaned_data.get("md_start")
 186              file1 = cleaned_data.get("file1")
 187              pdbid = cleaned_data.get("pdbid")
 188              md_seq = cleaned_data.get("md_seq")
 189              md_pdbref = cleaned_data.get("md_pdbref")
 190
 191              if md_start == 'pdbstart' and not (file1 or pdbid):
 192                 msg = 'pdbstart with no PDB file or code'
 193                 self.add_error('file1', msg)
 194
 195              if md_pdbref and not (file1 or pdbid):
 196                 msg = 'pdbref with no PDB file or code'
 197                 self.add_error('file1', msg)
 198
 199
 200              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 201                 msg = 'extended/random chain with no sequence'
 202                 self.add_error('md_seq', msg)
 203
 204              if pdbid:
 205                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 206                if test.code != 200:
 207                  msg = 'wrong pdb code'
 208                  self.add_error('pdbid', msg)
 209                else:
 210                  msg=pdb_missing_res(test)
 211                  if msg != '':
 212                    self.add_error('pdbid',msg)
 213                test.close()
 214
 215              if file1:
 216                  msg=pdb_missing_res(file1)
 217                  if msg != '':
 218                    self.add_error('file1',msg)
 219
 220
 221 class TaskForm_md_a(forms.Form):
 222      name = forms.CharField(max_length=20)
 223
 224      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 225                            label='Force Field',initial='E0LL2Y')
 226      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 227                       label='starting structure',initial='extconf')
 228      md_seq = forms.CharField(label='Sequence',
 229                      help_text='aminoacid sequence using one letter code<br>'+
 230                      'field is ignored when uploading starting/reference PDB file',
 231                      required=False,
 232                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 233      file1 = forms.FileField(label='Upload a PDB file',required=False,
 234                   help_text='starting structure for pdbstart/reference structure')
 235      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
 236       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
 237       label='or PDB code')
 238      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 239      md_temp = forms.FloatField(label='temperature',initial=300,
 240                   help_text='bath temperature')
 241      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 242                   help_text='total number of steps')
 243      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 244                   help_text='seed for random number generator')
 245
 246      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
 247                help_text='write statfile every ntwe steps')
 248      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,
 249                help_text='write trajectory every ntwe steps')
 250      md_dt = forms.FloatField(label='DT',initial=0.2,
 251                   help_text='time step [mtu]')
 252      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
 253      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
 254                   help_text='coupling to the thermal bath (Berendsen)')
 255      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
 256                   help_text='scaling of the friction coefficients (Langevin)')
 257      md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
 258      md_mdpdb = forms.BooleanField(required=False,label='trajectory as PDB')
 259
 260      boxx = forms.FloatField(label='Box X',initial=1000.0,
 261                        help_text='box x dimension')
 262      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 263                        help_text='box y dimension')
 264      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 265                        help_text='box z dimension')
 266
 267      def clean(self):
 268              cleaned_data = super(TaskForm_md_a, self).clean()
 269
 270              md_start = cleaned_data.get("md_start")
 271              file1 = cleaned_data.get("file1")
 272              pdbid = cleaned_data.get("pdbid")
 273              md_seq = cleaned_data.get("md_seq")
 274              md_pdbref = cleaned_data.get("md_pdbref")
 275
 276              if md_start == 'pdbstart' and not (file1 or pdbid):
 277                 msg = 'pdbstart with no PDB file or code'
 278                 self.add_error('file1', msg)
 279
 280              if md_pdbref and not (file1 or pdbid):
 281                 msg = 'pdbref with no PDB file or code'
 282                 self.add_error('file1', msg)
 283
 284
 285              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 286                 msg = 'extended/random chain with no sequence'
 287                 self.add_error('md_seq', msg)
 288
 289              if pdbid:
 290                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 291                if test.code != 200:
 292                  msg = 'wrong pdb code'
 293                  self.add_error('pdbid', msg)
 294                else:
 295                  msg=pdb_missing_res(test)
 296                  if msg != '':
 297                    self.add_error('pdbid',msg)
 298                test.close()
 299
 300              if file1:
 301                  msg=pdb_missing_res(file1)
 302                  if msg != '':
 303                    self.add_error('file1',msg)
 304
 305
 306 class TaskForm_remd(forms.Form):
 307      name = forms.CharField(max_length=20)
 308
 309      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 310                       label='starting structure',initial='extconf')
 311      md_seq = forms.CharField(label='Sequence',
 312                      help_text='aminoacid sequence using one letter code<br>'+
 313                         'field is ignored when uploading starting/reference PDB file',
 314                      required=False,
 315                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 316      file1 = forms.FileField(label='Upload a PDB file',required=False,
 317                   help_text='starting structure for pdbstart/reference structure')
 318      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
 319       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
 320       label='or PDB code')
 321      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 322      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 323                   help_text='total number of steps')
 324      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 325                   help_text='seed for random number generator')
 326
 327      def clean(self):
 328              cleaned_data = super(TaskForm_remd, self).clean()
 329
 330              md_start = cleaned_data.get("md_start")
 331              file1 = cleaned_data.get("file1")
 332              pdbid = cleaned_data.get("pdbid")
 333              md_seq = cleaned_data.get("md_seq")
 334              md_pdbref = cleaned_data.get("md_pdbref")
 335
 336              if md_start == 'pdbstart' and not (file1 or pdbid):
 337                 msg = 'pdbstart with no PDB file or code'
 338                 self.add_error('file1', msg)
 339
 340              if md_pdbref and not (file1 or pdbid):
 341                 msg = 'pdbref with no PDB file or code'
 342                 self.add_error('file1', msg)
 343
 344              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 345                 msg = 'extended/random chain with no sequence'
 346                 self.add_error('md_seq', msg)
 347
 348              if pdbid:
 349                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 350                if test.code != 200:
 351                  msg = 'wrong pdb code'
 352                  self.add_error('pdbid', msg)
 353                else:
 354                  msg=pdb_missing_res(test)
 355                  if msg != '':
 356                    self.add_error('pdbid',msg)
 357                test.close()
 358
 359              if file1:
 360                  msg=pdb_missing_res(file1)
 361                  if msg != '':
 362                    self.add_error('file1',msg)
 363
 364
 365 class TaskForm_remd_a(forms.Form):
 366      name = forms.CharField(max_length=20)
 367
 368      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 369                            label='Force Field',initial='E0LL2Y')
 370      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 371                       label='starting structure',initial='extconf')
 372      md_seq = forms.CharField(label='Sequence',
 373                      help_text='aminoacid sequence using one letter code<br>'+
 374                       'field is ignored when uploading starting/reference PDB file',
 375                      required=False,
 376                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 377      file1 = forms.FileField(label='Upload a PDB file',required=False,
 378                   help_text='starting structure for pdbstart/reference structure')
 379      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
 380       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
 381       label='or PDB code')
 382      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 383      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 384                   help_text='total number of steps')
 385      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 386                   help_text='seed for random number generator')
 387      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
 388                help_text='write statfile every ntwe steps')
 389      md_dt = forms.FloatField(label='DT',initial=0.2,
 390                   help_text='time step [mtu]')
 391      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
 392      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
 393                   help_text='coupling to the thermal bath (Berendsen)')
 394      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
 395                   help_text='scaling of the friction coefficients (Langevin)')
 396      remd_nrep = forms.IntegerField(label='NREP',initial=8,
 397                   help_text='number of replicas')
 398      remd_nstex = forms.IntegerField(label='NSTEX',initial=1000,
 399                   help_text='exchange and write trajectory every nstex steps')
 400      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,
 401                help_text='write trajectory every ntwx steps')
 402      remd_cluter_temp = forms.FloatField(label='TEMPER',
 403                   help_text='temperature for cluster analysis',initial=280)
 404 #     remd_traj1file = forms.BooleanField(required=False,label='single trajectory file',initial='true')
 405 #     remd_rest1file = forms.BooleanField(required=False,label='single restart file',initial='true')
 406
 407      md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
 408
 409      boxx = forms.FloatField(label='Box X',initial=1000.0,
 410                        help_text='box x dimension')
 411      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 412                        help_text='box y dimension')
 413      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 414                        help_text='box z dimension')
 415
 416
 417      wsaxs = forms.FloatField(label='SAXS weight',initial=100.0,
 418                             help_text='weight for SAXS restraint term')
 419      scal_rad = forms.FloatField(label='Scal_rad (SAXS)',initial=1.0,
 420                             help_text='downscaling factor of residue radii used in SAXS restraints')
 421      saxs_data = forms.CharField(label='P(r) SAXS data',
 422                      help_text='distance distribution from SAXS, two columns: r and P(r)',
 423                      required=False,
 424                      widget=forms.Textarea(attrs={'cols': 25, 'rows': 20}))
 425
 426
 427      def clean(self):
 428              cleaned_data = super(TaskForm_remd_a, self).clean()
 429
 430              md_start = cleaned_data.get("md_start")
 431              file1 = cleaned_data.get("file1")
 432              pdbid = cleaned_data.get("pdbid")
 433              md_seq = cleaned_data.get("md_seq")
 434              md_pdbref = cleaned_data.get("md_pdbref")
 435
 436              if md_start == 'pdbstart' and not (file1 or pdbid):
 437                 msg = 'pdbstart with no PDB file or code'
 438                 self.add_error('file1', msg)
 439
 440              if md_pdbref and not (file1 or pdbid):
 441                 msg = 'pdbref with no PDB file or code'
 442                 self.add_error('file1', msg)
 443
 444
 445              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 446                 msg = 'extended/random chain with no sequence'
 447                 self.add_error('md_seq', msg)
 448
 449              if pdbid:
 450                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 451                if test.code != 200:
 452                  msg = 'wrong pdb code'
 453                  self.add_error('pdbid', msg)
 454                else:
 455                  msg=pdb_missing_res(test)
 456                  if msg != '':
 457                    self.add_error('pdbid',msg)
 458                test.close()
 459
 460              if file1:
 461                  msg=pdb_missing_res(file1)
 462                  if msg != '':
 463                    self.add_error('file1',msg)
 464
 465
 466
 467 class TaskForm_list(forms.Form):
 468     name = forms.CharField(max_length=20,disabled=True,required=False)
 469     nrep = forms.IntegerField(disabled=True,required=False,label='NREP')
 470
 471     def __init__(self, count, *args, **kwargs):
 472         super(TaskForm_list, self).__init__(*args, **kwargs)
 473         self.count=count
 474         self.fields['temperatures'] = MultiExampleField(self.count)
 475         self.fields['multiplexing'] = MultiExampleField(self.count)
 476
 477
 478