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