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