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_code_chain(pdbid):
  11
  12     msg=''
  13     chain=''
  14     if len(pdbid)>4:
  15        if pdbid[4]!=':':
  16          return('use : between pdb code and chain id, like 5G3Q:B to select single chain')
  17        chain=pdbid[5]
  18        pdbid=pdbid[:4]
  19
  20     test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
  21     if test.code != 200:
  22           msg = 'wrong pdb code'
  23     else:
  24           msg=pdb_missing_res_chain(test,chain)
  25     test.close()
  26     return(msg)
  27
  28 def pdb_missing_res_chain(file,chain):
  29    msg=''
  30    newchain = True
  31    ires=[]
  32    for line in file:
  33       if line[0:6] == 'ATOM  ' and line[13:15] == 'CA' and (line[21] == chain or chain==''):
  34                i = int(line[22:26])
  35                ch = line[21]
  36                if ires and i==ires[-1]:
  37                  continue
  38                if newchain or i==ires[-1]+1:
  39                  ires.append(i)
  40                  newchain = False
  41                else:
  42                  msg = 'chain breaks between residues '+\
  43                    str(ires[-1])+' and '+str(i)+' of chain '+ch+\
  44                    ', server cannot add missing residues to PDB file - please repair the structure using e.g. Modeller'
  45                  break
  46       if line[0:3] == 'TER':
  47                newchain = True
  48       if line[0:3] == 'END':
  49                break
  50
  51    if len(ires) == 0:
  52                msg='wrong chain id'
  53    return(msg)
  54
  55
  56 def code_2d(line):
  57    msg=''
  58    set ='HEC-'
  59    line2 = ''.join([c for c in line if c in set])
  60    if line2 != line:
  61     msg='use only H,E,C or - letters'
  62    return(msg)
  63
  64 def pdb_missing_res(file):
  65    msg=''
  66    newchain = True
  67    ires=[]
  68    for line in file:
  69       if line[0:6] == 'ATOM  ' and line[13:15] == 'CA':
  70                i = int(line[22:26])
  71                if ires and i==ires[-1]:
  72                  continue
  73                if newchain or i==ires[-1]+1:
  74                  ires.append(i)
  75                  newchain = False
  76                else:
  77                  msg = 'chain breaks between residues '+\
  78                    str(ires[-1])+' and '+str(i)+\
  79                    ', server cannot add missing residues to PDB file - please repair the structure using e.g. Modeller'
  80                  break
  81       if line[0:3] == 'TER':
  82                newchain = True
  83       if line[0:3] == 'END':
  84                break
  85
  86    return(msg)
  87
  88 class MultiWidgetBasic(forms.MultiWidget):
  89     def __init__(self, count, attrs=None):
  90         self.count=count
  91         widgets = []
  92         for i in range(self.count):
  93            widgets.append(forms.TextInput())
  94         super(MultiWidgetBasic, self).__init__(widgets, attrs)
  95
  96     template_name = 'multi.html'
  97
  98     def decompress(self, value):
  99         if value:
 100             return json.loads(value)
 101         else:
 102             return ['', '']
 103
 104
 105 class MultiExampleField(forms.fields.MultiValueField):
 106     def __init__(self, count, *args, **kwargs):
 107         self.count=count
 108         self.widget = MultiWidgetBasic(self.count)
 109         list_fields = []
 110         for i in range(self.count):
 111            list_fields.append(forms.fields.CharField(max_length=15))
 112         super(MultiExampleField, self).__init__(list_fields, *args, **kwargs)
 113
 114     def compress(self, values):
 115         ## compress list to single object
 116         return json.dumps(values)
 117
 118
 119 class TaskForm(forms.Form):
 120     name = forms.CharField(max_length=20)
 121
 122
 123 class TaskForm_min(forms.Form):
 124      name = forms.CharField(max_length=20)
 125      file1 = forms.FileField(label='Upload a PDB file',required=False,
 126       help_text='continuous (without breaks) protein chains,use TER to divide chains')
 127      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 128       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 129       label='or PDB code (:chain)')
 130
 131      def clean(self):
 132              cleaned_data = super(TaskForm_min, self).clean()
 133
 134              pdbid = cleaned_data.get("pdbid")
 135              file1 = cleaned_data.get("file1")
 136
 137              if not pdbid and not file1:
 138                 msg = 'provide pdb file or pdb code'
 139                 self.add_error('file1', msg)
 140
 141              if pdbid:
 142                msg=pdb_code_chain(pdbid)
 143                if msg != '':
 144                    self.add_error('pdbid',msg)
 145
 146              if file1:
 147                  msg=pdb_missing_res(file1)
 148                  if msg != '':
 149                    self.add_error('file1',msg)
 150
 151
 152 class TaskForm_min_a(forms.Form):
 153      name = forms.CharField(max_length=20)
 154
 155      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 156                            label='Force Field',initial='FF2')
 157 #     min_choice = forms.ChoiceField(choices=MIN_CHOICE,label='minimization algorithm')
 158      min_overlap = forms.BooleanField(required=False,label='remove overlap')
 159      min_searchsc = forms.BooleanField(required=False,label='MC for sidechain overlap')
 160      min_maxmin = forms.IntegerField(label='MAXMIN',initial=10000,
 161                   help_text='maximum number of iterations')
 162      min_maxfun = forms.IntegerField(label='MAXFUN',initial=15000,
 163                   help_text='maximum number of function evaluations')
 164      file1 = forms.FileField(label='Upload a PDB file',required=False,
 165         help_text='continuous (without breaks) protein chains,use TER to divide chains')
 166      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 167       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 168       label='or PDB code (:chain)')
 169
 170      min_unres_pdb = forms.BooleanField(required=False,label='uploaded input unres PDB',
 171                   help_text='(CA and CB atoms only, CB represents SC in UNRES)')
 172      min_pdbout = forms.BooleanField(required=False,label='output PDB',initial='true')
 173      boxx = forms.FloatField(label='Box X',initial=1000.0,
 174                        help_text='box x dimension')
 175      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 176                        help_text='box y dimension')
 177      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 178                        help_text='box z dimension')
 179
 180      def clean(self):
 181              cleaned_data = super(TaskForm_min_a, self).clean()
 182
 183              pdbid = cleaned_data.get("pdbid")
 184              file1 = cleaned_data.get("file1")
 185
 186              if not pdbid and not file1:
 187                 msg = 'provide pdb file or pdb code'
 188                 self.add_error('file1', msg)
 189
 190              if pdbid:
 191                  msg=pdb_code_chain(pdbid)
 192                  if msg != '':
 193                    self.add_error('pdbid',msg)
 194
 195              if file1:
 196                  msg=pdb_missing_res(file1)
 197                  if msg != '':
 198                    self.add_error('file1',msg)
 199
 200
 201 class TaskForm_md(forms.Form):
 202      name = forms.CharField(max_length=20)
 203
 204      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 205                       label='starting structure',initial='extconf')
 206      md_seq = forms.CharField(label='Sequence',
 207                      help_text='aminoacid sequence using one letter code<br>'+
 208                      'field is ignored when uploading starting/reference PDB file',
 209                      required=False,
 210                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 211      file1 = forms.FileField(label='Upload a PDB file',required=False,
 212                   help_text='starting structure for pdbstart/reference structure')
 213      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 214       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 215       label='or PDB code (:chain)')
 216      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 217      md_temp = forms.FloatField(label='temperature',initial=300,
 218                   help_text='bath temperature')
 219      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 220                   help_text='total number of steps')
 221      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 222                   help_text='seed for random number generator')
 223
 224      def clean(self):
 225              cleaned_data = super(TaskForm_md, self).clean()
 226
 227              md_start = cleaned_data.get("md_start")
 228              file1 = cleaned_data.get("file1")
 229              pdbid = cleaned_data.get("pdbid")
 230              md_seq = cleaned_data.get("md_seq")
 231              md_pdbref = cleaned_data.get("md_pdbref")
 232
 233              if md_start == 'pdbstart' and not (file1 or pdbid):
 234                 msg = 'pdbstart with no PDB file or code'
 235                 self.add_error('file1', msg)
 236
 237              if md_pdbref and not (file1 or pdbid):
 238                 msg = 'pdbref with no PDB file or code'
 239                 self.add_error('file1', msg)
 240
 241
 242              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 243                 msg = 'extended/random chain with no sequence'
 244                 self.add_error('md_seq', msg)
 245
 246              if pdbid:
 247                  msg=pdb_code_chain(pdbid)
 248                  if msg != '':
 249                    self.add_error('pdbid',msg)
 250
 251              if file1:
 252                  msg=pdb_missing_res(file1)
 253                  if msg != '':
 254                    self.add_error('file1',msg)
 255
 256
 257 class TaskForm_md_a(forms.Form):
 258      name = forms.CharField(max_length=20)
 259
 260      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 261                            label='Force Field',initial='FF2')
 262      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 263                       label='starting structure',initial='extconf')
 264      md_seq = forms.CharField(label='Sequence',
 265                      help_text='aminoacid sequence using one letter code<br>'+
 266                      'field is ignored when uploading starting/reference PDB file',
 267                      required=False,
 268                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 269      md_2d = forms.CharField(label='Secondary structure restraints',
 270                      help_text='single letter code: H - helix, E - extended/beta, C or - no restraints',
 271                      required=False,
 272                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 273
 274      file1 = forms.FileField(label='Upload a PDB file',required=False,
 275                   help_text='starting structure for pdbstart/reference structure')
 276      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 277       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 278       label='or PDB code (:chain)')
 279      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 280      md_temp = forms.FloatField(label='temperature',initial=300,
 281                   help_text='bath temperature')
 282      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 283                   help_text='total number of steps')
 284      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 285                   help_text='seed for random number generator')
 286
 287      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
 288                help_text='write statfile every ntwe steps')
 289      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,
 290                help_text='write trajectory every ntwe steps')
 291      md_dt = forms.FloatField(label='DT',initial=0.2,
 292                   help_text='time step [mtu=48.9 fs]')
 293      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
 294      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
 295                   help_text='coupling to the thermal bath (Berendsen)')
 296      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
 297                   help_text='scaling of the friction coefficients (Langevin)')
 298      md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
 299      md_mdpdb = forms.BooleanField(required=False,label='trajectory as PDB')
 300
 301      boxx = forms.FloatField(label='Box X',initial=1000.0,
 302                        help_text='box x dimension')
 303      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 304                        help_text='box y dimension')
 305      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 306                        help_text='box z dimension')
 307
 308      def clean(self):
 309              cleaned_data = super(TaskForm_md_a, self).clean()
 310
 311              md_start = cleaned_data.get("md_start")
 312              file1 = cleaned_data.get("file1")
 313              pdbid = cleaned_data.get("pdbid")
 314              md_seq = cleaned_data.get("md_seq")
 315              md_pdbref = cleaned_data.get("md_pdbref")
 316              md_2d = cleaned_data.get("md_2d")
 317
 318              if md_start == 'pdbstart' and not (file1 or pdbid):
 319                 msg = 'pdbstart with no PDB file or code'
 320                 self.add_error('file1', msg)
 321
 322              if md_pdbref and not (file1 or pdbid):
 323                 msg = 'pdbref with no PDB file or code'
 324                 self.add_error('file1', msg)
 325
 326
 327              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 328                 msg = 'extended/random chain with no sequence'
 329                 self.add_error('md_seq', msg)
 330
 331              if pdbid:
 332                  msg=pdb_code_chain(pdbid)
 333                  if msg != '':
 334                    self.add_error('pdbid',msg)
 335
 336              if file1:
 337                  msg=pdb_missing_res(file1)
 338                  if msg != '':
 339                    self.add_error('file1',msg)
 340
 341              if md_2d:
 342                  msg=code_2d(md_2d)
 343                  if msg != '':
 344                    self.add_error('md_2d',msg)
 345
 346 class TaskForm_remd(forms.Form):
 347      name = forms.CharField(max_length=20)
 348
 349      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 350                       label='starting structure',initial='extconf')
 351      md_seq = forms.CharField(label='Sequence',
 352                      help_text='aminoacid sequence using one letter code<br>'+
 353                         'field is ignored when uploading starting/reference PDB file',
 354                      required=False,
 355                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 356      file1 = forms.FileField(label='Upload a PDB file',required=False,
 357                   help_text='starting structure for pdbstart/reference structure')
 358      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 359       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 360       label='or PDB code (:chain)')
 361      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 362      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 363                   help_text='total number of steps')
 364      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 365                   help_text='seed for random number generator')
 366
 367      def clean(self):
 368              cleaned_data = super(TaskForm_remd, self).clean()
 369
 370              md_start = cleaned_data.get("md_start")
 371              file1 = cleaned_data.get("file1")
 372              pdbid = cleaned_data.get("pdbid")
 373              md_seq = cleaned_data.get("md_seq")
 374              md_pdbref = cleaned_data.get("md_pdbref")
 375
 376              if md_start == 'pdbstart' and not (file1 or pdbid):
 377                 msg = 'pdbstart with no PDB file or code'
 378                 self.add_error('file1', msg)
 379
 380              if md_pdbref and not (file1 or pdbid):
 381                 msg = 'pdbref with no PDB file or code'
 382                 self.add_error('file1', msg)
 383
 384              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 385                 msg = 'extended/random chain with no sequence'
 386                 self.add_error('md_seq', msg)
 387
 388              if pdbid:
 389                  msg=pdb_code_chain(pdbid)
 390                  if msg != '':
 391                    self.add_error('pdbid',msg)
 392
 393              if file1:
 394                  msg=pdb_missing_res(file1)
 395                  if msg != '':
 396                    self.add_error('file1',msg)
 397
 398
 399 class TaskForm_remd_a(forms.Form):
 400      name = forms.CharField(max_length=20)
 401
 402      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 403                            label='Force Field',initial='FF2')
 404      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 405                       label='starting structure',initial='extconf')
 406      md_seq = forms.CharField(label='Sequence',
 407                      help_text='aminoacid sequence using one letter code<br>'+
 408                       'field is ignored when uploading starting/reference PDB file',
 409                      required=False,
 410                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 411      md_2d = forms.CharField(label='Secondary structure restraints',
 412                      help_text='single letter code: H - helix, E - extended/beta, C or - no restraints',
 413                      required=False,
 414                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 415      file1 = forms.FileField(label='Upload a PDB file',required=False,
 416                   help_text='starting structure for pdbstart/reference structure')
 417      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 418       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 419       label='or PDB code (:chain)')
 420      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 421      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 422                   help_text='total number of steps')
 423      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 424                   help_text='seed for random number generator')
 425      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
 426                help_text='write statfile every ntwe steps')
 427      md_dt = forms.FloatField(label='DT',initial=0.2,
 428                   help_text='time step [mtu = 48.9 fs]')
 429      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
 430      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
 431                   help_text='coupling to the thermal bath (Berendsen)')
 432      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
 433                   help_text='scaling of the friction coefficients (Langevin)')
 434      remd_nrep = forms.IntegerField(label='NREP',initial=8,
 435                   help_text='number of replicas')
 436      remd_nstex = forms.IntegerField(label='NSTEX',initial=1000,
 437                   help_text='exchange and write trajectory every nstex steps')
 438      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,
 439                help_text='write trajectory every ntwx steps')
 440      remd_cluter_temp = forms.FloatField(label='TEMPER',
 441                   help_text='temperature for cluster analysis',initial=280)
 442 #     remd_traj1file = forms.BooleanField(required=False,label='single trajectory file',initial='true')
 443 #     remd_rest1file = forms.BooleanField(required=False,label='single restart file',initial='true')
 444
 445      md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
 446
 447      boxx = forms.FloatField(label='Box X',initial=1000.0,
 448                        help_text='box x dimension')
 449      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 450                        help_text='box y dimension')
 451      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 452                        help_text='box z dimension')
 453
 454
 455      wsaxs = forms.FloatField(label='SAXS weight',initial=100.0,
 456                             help_text='weight for SAXS restraint term')
 457      scal_rad = forms.FloatField(label='Scal_rad (SAXS)',initial=1.0,
 458                             help_text='downscaling factor of residue radii used in SAXS restraints')
 459      saxs_data = forms.CharField(label='P(r) SAXS data',
 460                      help_text='distance distribution from SAXS, two columns: r and P(r)',
 461                      required=False,
 462                      widget=forms.Textarea(attrs={'cols': 25, 'rows': 20}))
 463
 464
 465      def clean(self):
 466              cleaned_data = super(TaskForm_remd_a, self).clean()
 467
 468              md_start = cleaned_data.get("md_start")
 469              file1 = cleaned_data.get("file1")
 470              pdbid = cleaned_data.get("pdbid")
 471              md_seq = cleaned_data.get("md_seq")
 472              md_pdbref = cleaned_data.get("md_pdbref")
 473              md_2d = cleaned_data.get("md_2d")
 474
 475              if md_start == 'pdbstart' and not (file1 or pdbid):
 476                 msg = 'pdbstart with no PDB file or code'
 477                 self.add_error('file1', msg)
 478
 479              if md_pdbref and not (file1 or pdbid):
 480                 msg = 'pdbref with no PDB file or code'
 481                 self.add_error('file1', msg)
 482
 483
 484              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 485                 msg = 'extended/random chain with no sequence'
 486                 self.add_error('md_seq', msg)
 487
 488              if pdbid:
 489                  msg=pdb_code_chain(pdbid)
 490                  if msg != '':
 491                    self.add_error('pdbid',msg)
 492
 493              if file1:
 494                  msg=pdb_missing_res(file1)
 495                  if msg != '':
 496                    self.add_error('file1',msg)
 497
 498              if md_2d:
 499                  msg=code_2d(md_2d)
 500                  if msg != '':
 501                    self.add_error('md_2d',msg)
 502
 503
 504
 505 class TaskForm_list(forms.Form):
 506     name = forms.CharField(max_length=20,disabled=True,required=False)
 507     nrep = forms.IntegerField(disabled=True,required=False,label='NREP')
 508
 509     def __init__(self, count, *args, **kwargs):
 510         super(TaskForm_list, self).__init__(*args, **kwargs)
 511         self.count=count
 512         self.fields['temperatures'] = MultiExampleField(self.count)
 513         self.fields['multiplexing'] = MultiExampleField(self.count)
 514
 515
 516