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 from django.utils.safestring import mark_safe
   8 import json
   9 import urllib
  10
  11 aa_3letter = [
  12      'DPR','DLY','DAR','DHI','DAS','DGL','DSG','DGN','DSN','DTH',
  13      'DAL','DTY','DTR','DVA','DLE','DIL','DPN','MED','DCY',
  14      'CYS','MET','PHE','ILE','LEU','VAL','TRP','TYR','ALA','GLY','THR',
  15      'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO',
  16      'SME','AIB','ABU','DBZ']
  17
  18
  19 def pdb_code_chain(pdbid):
  20
  21     msg=''
  22     chain=''
  23     if len(pdbid)>4:
  24        if pdbid[4]!=':':
  25          return('use : between pdb code and chain id, like 5G3Q:B to select single chain')
  26        chain=pdbid[5]
  27        pdbid=pdbid[:4]
  28
  29     test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
  30     if test.code != 200:
  31           msg = 'wrong pdb code'
  32     else:
  33           msg=pdb_missing_res_chain(test,chain)
  34     test.close()
  35     return(msg)
  36
  37 def pdb_missing_res_chain(file,chain):
  38    msg=''
  39    newchain = True
  40    ires=[]
  41    for line in file:
  42       if line[0:6] == 'ATOM  ' and line[13:15] == 'CA' and (line[21] == chain or chain==''):
  43                i = int(line[22:26])
  44                ch = line[21]
  45                if line[17:20] not in aa_3letter:
  46                  msg='residue '+line[17:20]+' '+str(i)+' not recognized'
  47                  return(msg)
  48                if ires and i==ires[-1]:
  49                  continue
  50                if newchain or i==ires[-1]+1:
  51                  ires.append(i)
  52                  newchain = False
  53                else:
  54                  msg = 'chain breaks between residues '+\
  55                    str(ires[-1])+' and '+str(i)+' of chain '+ch+\
  56                    ', server cannot add missing residues to PDB file - please repair the structure using e.g. Modeller'
  57                  break
  58       if line[0:3] == 'TER':
  59                newchain = True
  60       if line[0:3] == 'END':
  61                break
  62
  63    if len(ires) == 0:
  64         if chain == '':
  65                msg='no CA atoms in this pdb'
  66         else:
  67                msg='wrong chain id'
  68    return(msg)
  69
  70
  71 def code_2d(line):
  72    msg=''
  73    set ='HEC-'
  74    line2 = ''.join([c for c in line if c in set])
  75    if line2 != line:
  76     msg='use only H,E,C or - letters'
  77    return(msg)
  78
  79
  80 class MultiWidgetBasic(forms.MultiWidget):
  81     def __init__(self, count, attrs=None):
  82         self.count=count
  83         widgets = []
  84         for i in range(self.count):
  85            widgets.append(forms.TextInput())
  86         super(MultiWidgetBasic, self).__init__(widgets, attrs)
  87
  88     template_name = 'multi.html'
  89
  90     def decompress(self, value):
  91         if value:
  92             return json.loads(value)
  93         else:
  94             return ['', '']
  95
  96
  97 class MultiExampleField(forms.fields.MultiValueField):
  98     def __init__(self, count, *args, **kwargs):
  99         self.count=count
 100         self.widget = MultiWidgetBasic(self.count)
 101         list_fields = []
 102         for i in range(self.count):
 103            list_fields.append(forms.fields.CharField(max_length=15))
 104         super(MultiExampleField, self).__init__(list_fields, *args, **kwargs)
 105
 106     def compress(self, values):
 107         ## compress list to single object
 108         return json.dumps(values)
 109
 110
 111 class TaskForm(forms.Form):
 112     name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 113
 114
 115 class TaskForm_min(forms.Form):
 116      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 117      file1 = forms.FileField(label='Upload a PDB file',required=False,
 118       help_text='continuous (without breaks) protein chains,use TER to divide chains')
 119      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 120       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 121       label='or PDB code (:chain)')
 122
 123      def clean(self):
 124              cleaned_data = super(TaskForm_min, self).clean()
 125
 126              pdbid = cleaned_data.get("pdbid")
 127              file1 = cleaned_data.get("file1")
 128
 129              if not pdbid and not file1:
 130                 msg = 'provide pdb file or pdb code'
 131                 self.add_error('file1', msg)
 132
 133              if pdbid:
 134                msg=pdb_code_chain(pdbid)
 135                if msg != '':
 136                    self.add_error('pdbid',msg)
 137
 138              if file1:
 139                  msg=pdb_missing_res_chain(file1,'')
 140                  if msg != '':
 141                    self.add_error('file1',msg)
 142
 143
 144 class TaskForm_min_a(forms.Form):
 145      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 146
 147      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 148                            label='Force Field',initial='FF2')
 149 #     min_choice = forms.ChoiceField(choices=MIN_CHOICE,label='minimization algorithm')
 150      min_overlap = forms.BooleanField(required=False,label='remove overlap')
 151      min_searchsc = forms.BooleanField(required=False,label='MC for sidechain overlap')
 152      min_maxmin = forms.IntegerField(label='MAXMIN',initial=10000,
 153                   help_text='maximum number of iterations')
 154      min_maxfun = forms.IntegerField(label='MAXFUN',initial=15000,
 155                   help_text='maximum number of function evaluations')
 156      file1 = forms.FileField(label='Upload a PDB file',required=False,
 157         help_text='continuous (without breaks) protein chains,use TER to divide chains')
 158      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 159       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 160       label='or PDB code (:chain)')
 161
 162      min_unres_pdb = forms.BooleanField(required=False,label='uploaded input unres PDB',
 163                   help_text='(CA and CB atoms only, CB represents SC in UNRES)')
 164      min_pdbout = forms.BooleanField(required=False,label='output PDB',initial='true')
 165      boxx = forms.FloatField(label='Box X',initial=1000.0,
 166                        help_text='box x dimension')
 167      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 168                        help_text='box y dimension')
 169      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 170                        help_text='box z dimension')
 171
 172      def clean(self):
 173              cleaned_data = super(TaskForm_min_a, self).clean()
 174
 175              pdbid = cleaned_data.get("pdbid")
 176              file1 = cleaned_data.get("file1")
 177
 178              if not pdbid and not file1:
 179                 msg = 'provide pdb file or pdb code'
 180                 self.add_error('file1', msg)
 181
 182              if pdbid:
 183                  msg=pdb_code_chain(pdbid)
 184                  if msg != '':
 185                    self.add_error('pdbid',msg)
 186
 187              if file1:
 188                  msg=pdb_missing_res_chain(file1,'')
 189                  if msg != '':
 190                    self.add_error('file1',msg)
 191
 192
 193 class TaskForm_md(forms.Form):
 194      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 195
 196      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 197                       label='starting structure',initial='extconf')
 198      md_seq = forms.CharField(label='Sequence',
 199                      help_text='aminoacid sequence using one letter code<br>'+
 200                      'field is ignored when uploading starting/reference PDB file',
 201                      required=False,
 202                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 203      file1 = forms.FileField(label='Upload a PDB file',required=False,
 204                   help_text='starting structure for pdbstart/reference structure')
 205      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 206       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 207       label='or PDB code (:chain)')
 208      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 209      md_temp = forms.FloatField(label='temperature',initial=300,
 210                   help_text='bath temperature')
 211      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 212                   help_text='total number of steps',max_value=10000000)
 213      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 214                   help_text='seed for random number generator')
 215
 216      def clean(self):
 217              cleaned_data = super(TaskForm_md, self).clean()
 218
 219              md_start = cleaned_data.get("md_start")
 220              file1 = cleaned_data.get("file1")
 221              pdbid = cleaned_data.get("pdbid")
 222              md_seq = cleaned_data.get("md_seq")
 223              md_pdbref = cleaned_data.get("md_pdbref")
 224
 225              if md_start == 'pdbstart' and not (file1 or pdbid):
 226                 msg = 'pdbstart with no PDB file or code'
 227                 self.add_error('file1', msg)
 228
 229              if md_pdbref and not (file1 or pdbid):
 230                 msg = 'pdbref with no PDB file or code'
 231                 self.add_error('file1', msg)
 232
 233
 234              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 235                 msg = 'extended/random chain with no sequence'
 236                 self.add_error('md_seq', msg)
 237
 238              if pdbid:
 239                  msg=pdb_code_chain(pdbid)
 240                  if msg != '':
 241                    self.add_error('pdbid',msg)
 242
 243              if file1:
 244                  msg=pdb_missing_res_chain(file1,'')
 245                  if msg != '':
 246                    self.add_error('file1',msg)
 247
 248
 249 class TaskForm_md_a(forms.Form):
 250      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 251
 252      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 253                            label='Force Field',initial='FF2')
 254      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 255                       label='starting structure',initial='extconf')
 256      md_seq = forms.CharField(label='Sequence',
 257                      help_text='aminoacid sequence using one letter code<br>'+
 258                      'field is ignored when uploading starting/reference PDB file',
 259                      required=False,
 260                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 261      md_2d = forms.CharField(label='Secondary structure restraints',
 262                      help_text='single letter code: H helix, E extended/beta, C or - no restraints',
 263                      required=False,
 264                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 265
 266      file1 = forms.FileField(label='Upload a PDB file',required=False,
 267                   help_text='starting structure for pdbstart/reference structure')
 268      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 269       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 270       label='or PDB code (:chain)')
 271      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 272      md_temp = forms.FloatField(label='temperature',initial=300,
 273                   help_text='bath temperature')
 274      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 275                   help_text='total number of steps',max_value=10000000)
 276      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 277                   help_text='seed for random number generator')
 278
 279      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
 280                help_text='write statfile every ntwe steps')
 281      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,
 282                help_text='write trajectory every ntwe steps',min_value=100)
 283      md_dt = forms.FloatField(label='DT',initial=0.2,
 284                   help_text='time step [mtu=48.9 fs]')
 285      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
 286      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
 287                   help_text='coupling to the thermal bath (Berendsen)')
 288      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
 289                   help_text='scaling of the friction coefficients (Langevin)')
 290      md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
 291      md_mdpdb = forms.BooleanField(required=False,label='trajectory as PDB')
 292
 293      boxx = forms.FloatField(label='Box X',initial=1000.0,
 294                        help_text='box x dimension')
 295      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 296                        help_text='box y dimension')
 297      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 298                        help_text='box z dimension')
 299
 300      def clean(self):
 301              cleaned_data = super(TaskForm_md_a, self).clean()
 302
 303              md_start = cleaned_data.get("md_start")
 304              file1 = cleaned_data.get("file1")
 305              pdbid = cleaned_data.get("pdbid")
 306              md_seq = cleaned_data.get("md_seq")
 307              md_pdbref = cleaned_data.get("md_pdbref")
 308              md_2d = cleaned_data.get("md_2d")
 309
 310              if md_start == 'pdbstart' and not (file1 or pdbid):
 311                 msg = 'pdbstart with no PDB file or code'
 312                 self.add_error('file1', msg)
 313
 314              if md_pdbref and not (file1 or pdbid):
 315                 msg = 'pdbref with no PDB file or code'
 316                 self.add_error('file1', msg)
 317
 318
 319              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 320                 msg = 'extended/random chain with no sequence'
 321                 self.add_error('md_seq', msg)
 322
 323              if pdbid:
 324                  msg=pdb_code_chain(pdbid)
 325                  if msg != '':
 326                    self.add_error('pdbid',msg)
 327
 328              if file1:
 329                  msg=pdb_missing_res_chain(file1,'')
 330                  if msg != '':
 331                    self.add_error('file1',msg)
 332
 333              if md_2d:
 334                  msg=code_2d(md_2d)
 335                  if msg != '':
 336                    self.add_error('md_2d',msg)
 337
 338 class TaskForm_remd(forms.Form):
 339      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 340
 341      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 342                       label='starting structure',initial='extconf')
 343      md_seq = forms.CharField(label='Sequence',
 344                      help_text='aminoacid sequence using one letter code<br>'+
 345                         'field is ignored when uploading starting/reference PDB file',
 346                      required=False,
 347                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 348      file1 = forms.FileField(label='Upload a PDB file',required=False,
 349                   help_text='starting structure for pdbstart/reference structure')
 350      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 351       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 352       label='or PDB code (:chain)')
 353      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 354      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 355                   help_text='total number of steps',max_value=10000000)
 356      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 357                   help_text='seed for random number generator')
 358
 359      def clean(self):
 360              cleaned_data = super(TaskForm_remd, self).clean()
 361
 362              md_start = cleaned_data.get("md_start")
 363              file1 = cleaned_data.get("file1")
 364              pdbid = cleaned_data.get("pdbid")
 365              md_seq = cleaned_data.get("md_seq")
 366              md_pdbref = cleaned_data.get("md_pdbref")
 367
 368              if md_start == 'pdbstart' and not (file1 or pdbid):
 369                 msg = 'pdbstart with no PDB file or code'
 370                 self.add_error('file1', msg)
 371
 372              if md_pdbref and not (file1 or pdbid):
 373                 msg = 'pdbref with no PDB file or code'
 374                 self.add_error('file1', msg)
 375
 376              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 377                 msg = 'extended/random chain with no sequence'
 378                 self.add_error('md_seq', msg)
 379
 380              if pdbid:
 381                  msg=pdb_code_chain(pdbid)
 382                  if msg != '':
 383                    self.add_error('pdbid',msg)
 384
 385              if file1:
 386                  msg=pdb_missing_res_chain(file1,'')
 387                  if msg != '':
 388                    self.add_error('file1',msg)
 389
 390
 391 class TaskForm_remd_a(forms.Form):
 392      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 393
 394      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 395                            label='Force Field',initial='FF2')
 396      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 397                       label='starting structure',initial='extconf')
 398      md_seq = forms.CharField(label='Sequence',
 399                      help_text='aminoacid sequence using one letter code<br>'+
 400                       'field is ignored when uploading starting/reference PDB file',
 401                      required=False,
 402                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 403      md_2d = forms.CharField(label='Secondary structure restraints',
 404                      help_text='single letter code: H helix, E extended/beta, C or - no restraints',
 405                      required=False,
 406                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 407      file1 = forms.FileField(label='Upload a PDB file',required=False,
 408                   help_text='starting structure for pdbstart/reference structure')
 409      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 410       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 411       label='or PDB code (:chain)')
 412      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 413      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 414                   help_text='total number of steps',max_value=10000000)
 415      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 416                   help_text='seed for random number generator')
 417      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
 418                help_text='write statfile every ntwe steps')
 419      md_dt = forms.FloatField(label='DT',initial=0.2,
 420                   help_text='time step [mtu = 48.9 fs]')
 421      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
 422      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
 423                   help_text='coupling to the thermal bath (Berendsen)')
 424      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
 425                   help_text='scaling of the friction coefficients (Langevin)')
 426      min_maxfun = forms.IntegerField(label='MAXFUN',initial=5000,
 427                   help_text='preminim maximum number of function evaluations<br>'+
 428                   'used for start from pdb or random start')
 429      remd_nrep = forms.IntegerField(label='NREP',initial=8,
 430                   help_text='number of replicas')
 431      remd_nstex = forms.IntegerField(label='NSTEX',initial=1000,
 432                   help_text='exchange and write trajectory every nstex steps')
 433      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,min_value=100,
 434                help_text='write trajectory every ntwx steps')
 435      remd_cluter_temp = forms.FloatField(label='TEMPER',
 436                   help_text='temperature for cluster analysis',initial=280)
 437 #     remd_traj1file = forms.BooleanField(required=False,label='single trajectory file',initial='true')
 438 #     remd_rest1file = forms.BooleanField(required=False,label='single restart file',initial='true')
 439
 440      md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
 441
 442      boxx = forms.FloatField(label='Box X',initial=1000.0,
 443                        help_text='box x dimension')
 444      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 445                        help_text='box y dimension')
 446      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 447                        help_text='box z dimension')
 448
 449
 450      wsaxs = forms.FloatField(label='SAXS weight',initial=100.0,
 451                             help_text='weight for SAXS restraint term')
 452      scal_rad = forms.FloatField(label='Scal_rad (SAXS)',initial=1.0,
 453                             help_text='downscaling factor of residue radii used in SAXS restraints')
 454      saxs_data = forms.CharField(label='P(r) SAXS data',
 455                      help_text='distance distribution from SAXS, two columns: r and P(r)',
 456                      required=False,
 457                      widget=forms.Textarea(attrs={'cols': 25, 'rows': 20}))
 458
 459
 460      def clean(self):
 461              cleaned_data = super(TaskForm_remd_a, self).clean()
 462
 463              md_start = cleaned_data.get("md_start")
 464              file1 = cleaned_data.get("file1")
 465              pdbid = cleaned_data.get("pdbid")
 466              md_seq = cleaned_data.get("md_seq")
 467              md_pdbref = cleaned_data.get("md_pdbref")
 468              md_2d = cleaned_data.get("md_2d")
 469
 470              if md_start == 'pdbstart' and not (file1 or pdbid):
 471                 msg = 'pdbstart with no PDB file or code'
 472                 self.add_error('file1', msg)
 473
 474              if md_pdbref and not (file1 or pdbid):
 475                 msg = 'pdbref with no PDB file or code'
 476                 self.add_error('file1', msg)
 477
 478
 479              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 480                 msg = 'extended/random chain with no sequence'
 481                 self.add_error('md_seq', msg)
 482
 483              if pdbid:
 484                  msg=pdb_code_chain(pdbid)
 485                  if msg != '':
 486                    self.add_error('pdbid',msg)
 487
 488              if file1:
 489                  msg=pdb_missing_res_chain(file1,'')
 490                  if msg != '':
 491                    self.add_error('file1',msg)
 492
 493              if md_2d:
 494                  msg=code_2d(md_2d)
 495                  if msg != '':
 496                    self.add_error('md_2d',msg)
 497
 498
 499 class TaskForm_dock(forms.Form):
 500      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 501
 502      file1 = forms.FileField(label='Upload a PDB file1',required=False,
 503                   help_text='starting structure for chain1')
 504      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 505       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 506       label='or PDB code (:chain)')
 507
 508
 509      md_seq = forms.CharField(label=mark_safe('Sequence of chain2 <br /> for dock peptide'),
 510                      help_text='aminoacid sequence using one letter code<br>'+
 511                         'field is ignored when uploading PDB file2',
 512                      required=False,
 513                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 514
 515
 516      file2 = forms.FileField(label='Upload a PDB file2',required=False,
 517                   help_text='starting structure for chain2')
 518      pdbid2 = forms.CharField(min_length=4,max_length=6,required=False,
 519       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 520       label='or PDB code (:chain)')
 521
 522
 523      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 524                   help_text='total number of steps', max_value=10000000)
 525      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 526                   help_text='seed for random number generator')
 527      dock_peptide = forms.BooleanField(required=False,initial=False,
 528             label='dock peptide',help_text='no constraints on chain2')
 529
 530      def clean(self):
 531              cleaned_data = super(TaskForm_dock, self).clean()
 532
 533              file1 = cleaned_data.get("file1")
 534              pdbid = cleaned_data.get("pdbid")
 535              file2 = cleaned_data.get("file2")
 536              pdbid2 = cleaned_data.get("pdbid2")
 537              md_seq = cleaned_data.get("md_seq")
 538
 539
 540              if not (file1 or pdbid):
 541                 msg = 'no PDB file or code for chain1'
 542                 self.add_error('file1', msg)
 543
 544              if not (file2 or pdbid2 or md_seq):
 545                 msg = 'no PDB file or code or sequence for chain2'
 546                 self.add_error('file2', msg)
 547
 548              if pdbid:
 549                  msg=pdb_code_chain(pdbid)
 550                  if msg != '':
 551                    self.add_error('pdbid',msg)
 552
 553              if file1:
 554                  msg=pdb_missing_res_chain(file1,'')
 555                  if msg != '':
 556                    self.add_error('file1',msg)
 557
 558              if pdbid2:
 559                  msg=pdb_code_chain(pdbid2)
 560                  if msg != '':
 561                    self.add_error('pdbid2',msg)
 562
 563              if file2:
 564                  msg=pdb_missing_res_chain(file2,'')
 565                  if msg != '':
 566                    self.add_error('file2',msg)
 567
 568 class TaskForm_dock_a(forms.Form):
 569      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 570
 571      file1 = forms.FileField(label='Upload a PDB file1',required=False,
 572                   help_text='starting structure for chain1')
 573      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 574       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 575       label='or PDB code (:chain)')
 576
 577      md_seq = forms.CharField(label=mark_safe('Sequence of chain2 <br /> for dock peptide'),
 578                      help_text='aminoacid sequence using one letter code<br>'+
 579                         'field is ignored when uploading PDB file2',
 580                      required=False,
 581                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 582
 583
 584      file2 = forms.FileField(label='Upload a PDB file2',required=False,
 585                   help_text='starting structure for chain2')
 586      pdbid2 = forms.CharField(min_length=4,max_length=6,required=False,
 587       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 588       label='or PDB code (:chain)')
 589
 590
 591      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 592                   help_text='total number of steps', max_value=10000000)
 593      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 594                   help_text='seed for random number generator')
 595      dock_peptide = forms.BooleanField(required=False,initial=False,
 596             label='dock peptide',help_text='no constraints on 2nd chain')
 597
 598
 599      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 600                            label='Force Field',initial='FF2')
 601
 602      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
 603                help_text='write statfile every ntwe steps')
 604      md_dt = forms.FloatField(label='DT',initial=0.2,
 605                   help_text='time step [mtu = 48.9 fs]')
 606      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
 607      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
 608                   help_text='coupling to the thermal bath (Berendsen)')
 609      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
 610                   help_text='scaling of the friction coefficients (Langevin)')
 611      min_maxfun = forms.IntegerField(label='MAXFUN',initial=5000,
 612                   help_text='preminim maximum number of function evaluations<br>'+
 613                   'used for start from pdb or random start')
 614      remd_nrep = forms.IntegerField(label='NREP',initial=8,
 615                   help_text='number of replicas')
 616      remd_nstex = forms.IntegerField(label='NSTEX',initial=1000,
 617                   help_text='exchange and write trajectory every nstex steps')
 618      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,min_value=100,
 619                help_text='write trajectory every ntwx steps')
 620      remd_cluter_temp = forms.FloatField(label='TEMPER',
 621                   help_text='temperature for cluster analysis',initial=280)
 622
 623
 624      def clean(self):
 625              cleaned_data = super(TaskForm_dock_a, self).clean()
 626
 627              file1 = cleaned_data.get("file1")
 628              pdbid = cleaned_data.get("pdbid")
 629              file2 = cleaned_data.get("file2")
 630              pdbid2 = cleaned_data.get("pdbid2")
 631              md_seq = cleaned_data.get("md_seq")
 632
 633              if not (file1 or pdbid):
 634                 msg = 'no PDB file or code for chain1'
 635                 self.add_error('file1', msg)
 636
 637              if not (file2 or pdbid2 or md_seq):
 638                 msg = 'no PDB file or code or sequence for chain2'
 639                 self.add_error('file2', msg)
 640
 641              if pdbid:
 642                  msg=pdb_code_chain(pdbid)
 643                  if msg != '':
 644                    self.add_error('pdbid',msg)
 645
 646              if file1:
 647                  msg=pdb_missing_res_chain(file1,'')
 648                  if msg != '':
 649                    self.add_error('file1',msg)
 650
 651              if pdbid2:
 652                  msg=pdb_code_chain(pdbid2)
 653                  if msg != '':
 654                    self.add_error('pdbid2',msg)
 655
 656              if file2:
 657                  msg=pdb_missing_res_chain(file2,'')
 658                  if msg != '':
 659                    self.add_error('file2',msg)
 660
 661
 662 class TaskForm_list(forms.Form):
 663     name = forms.CharField(max_length=40,disabled=True,required=False)
 664     nrep = forms.IntegerField(disabled=True,required=False,label='NREP')
 665
 666     def __init__(self, count, *args, **kwargs):
 667         super(TaskForm_list, self).__init__(*args, **kwargs)
 668         self.count=count
 669         self.fields['temperatures'] = MultiExampleField(self.count)
 670         self.fields['multiplexing'] = MultiExampleField(self.count)
 671
 672
 673