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
  11 class MultiWidgetBasic(forms.MultiWidget):
  12     def __init__(self, count, attrs=None):
  13         self.count=count
  14         widgets = []
  15         for i in range(self.count):
  16            widgets.append(forms.TextInput())
  17         super(MultiWidgetBasic, self).__init__(widgets, attrs)
  18
  19     template_name = 'multi.html'
  20
  21     def decompress(self, value):
  22         if value:
  23             return json.loads(value)
  24         else:
  25             return ['', '']
  26
  27
  28 class MultiExampleField(forms.fields.MultiValueField):
  29     def __init__(self, count, *args, **kwargs):
  30         self.count=count
  31         self.widget = MultiWidgetBasic(self.count)
  32         list_fields = []
  33         for i in range(self.count):
  34            list_fields.append(forms.fields.CharField(max_length=15))
  35         super(MultiExampleField, self).__init__(list_fields, *args, **kwargs)
  36
  37     def compress(self, values):
  38         ## compress list to single object
  39         return json.dumps(values)
  40
  41
  42 class TaskForm(forms.Form):
  43     name = forms.CharField(max_length=20)
  44
  45
  46 class TaskForm_min(forms.Form):
  47      name = forms.CharField(max_length=20)
  48      file1 = forms.FileField(label='Upload a PDB file',required=False,
  49       help_text='continuous (without breaks) protein chains,use TER to divide chains')
  50      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
  51       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
  52       label='or PDB code')
  53
  54      def clean(self):
  55              cleaned_data = super(TaskForm_min, self).clean()
  56
  57              pdbid = cleaned_data.get("pdbid")
  58              file1 = cleaned_data.get("file1")
  59
  60              if not pdbid and not file1:
  61                 msg = 'provide pdb file or pdb code'
  62                 self.add_error('file1', msg)
  63
  64              if pdbid:
  65                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
  66                if test.code != 200:
  67                  msg = 'wrong pdb code'
  68                  self.add_error('pdbid', msg)
  69                test.close()
  70
  71 class TaskForm_min_a(forms.Form):
  72      name = forms.CharField(max_length=20)
  73
  74      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
  75                            label='Force Field',initial='E0LL2Y')
  76      min_choice = forms.ChoiceField(choices=MIN_CHOICE,label='minimization algorithm')
  77      min_overlap = forms.BooleanField(required=False,label='remove overlap')
  78      min_searchsc = forms.BooleanField(required=False,label='MC for sidechain overlap')
  79      min_maxmin = forms.IntegerField(label='MAXMIN',initial=10000,
  80                   help_text='maximum number of iterations')
  81      min_maxfun = forms.IntegerField(label='MAXFUN',initial=15000,
  82                   help_text='maximum number of function evaluations')
  83      file1 = forms.FileField(label='Upload a PDB file',required=False,
  84         help_text='continuous (without breaks) protein chains,use TER to divide chains')
  85      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
  86       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
  87       label='or PDB code')
  88
  89      min_unres_pdb = forms.BooleanField(required=False,label='uploaded input unres PDB',
  90                   help_text='(CA and CB atoms only, CB represents SC in UNRES)')
  91      min_pdbout = forms.BooleanField(required=False,label='output PDB',initial='true')
  92      boxx = forms.FloatField(label='Box X',initial=1000.0,
  93                        help_text='box x dimension')
  94      boxy = forms.FloatField(label='Box Y',initial=1000.0,
  95                        help_text='box y dimension')
  96      boxz = forms.FloatField(label='Box Z',initial=1000.0,
  97                        help_text='box z dimension')
  98
  99      def clean(self):
 100              cleaned_data = super(TaskForm_min_a, self).clean()
 101
 102              pdbid = cleaned_data.get("pdbid")
 103              file1 = cleaned_data.get("file1")
 104
 105              if not pdbid and not file1:
 106                 msg = 'provide pdb file or pdb code'
 107                 self.add_error('file1', msg)
 108
 109              if pdbid:
 110                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 111                if test.code != 200:
 112                  msg = 'wrong pdb code'
 113                  self.add_error('pdbid', msg)
 114                test.close()
 115
 116
 117 class TaskForm_md(forms.Form):
 118      name = forms.CharField(max_length=20)
 119
 120      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 121                       label='starting structure',initial='extconf')
 122      md_seq = forms.CharField(label='Sequence',
 123                      help_text='aminoacid sequence using one letter code<br>'+
 124                      'field is ignored when uploading starting/reference PDB file',
 125                      required=False,
 126                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 127      file1 = forms.FileField(label='Upload a PDB file',required=False,
 128                   help_text='starting structure for pdbstart/reference structure')
 129      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
 130       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
 131       label='or PDB code')
 132      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 133      md_temp = forms.FloatField(label='temperature',initial=300,
 134                   help_text='bath temperature')
 135      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 136                   help_text='total number of steps')
 137      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 138                   help_text='seed for random number generator')
 139
 140      def clean(self):
 141              cleaned_data = super(TaskForm_md, self).clean()
 142
 143              md_start = cleaned_data.get("md_start")
 144              file1 = cleaned_data.get("file1")
 145              pdbid = cleaned_data.get("pdbid")
 146              md_seq = cleaned_data.get("md_seq")
 147              md_pdbref = cleaned_data.get("md_pdbref")
 148
 149              if md_start == 'pdbstart' and not (file1 or pdbid):
 150                 msg = 'pdbstart with no PDB file or code'
 151                 self.add_error('file1', msg)
 152
 153              if md_pdbref and not (file1 or pdbid):
 154                 msg = 'pdbref with no PDB file or code'
 155                 self.add_error('file1', msg)
 156
 157
 158              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 159                 msg = 'extended/random chain with no sequence'
 160                 self.add_error('md_seq', msg)
 161
 162              if pdbid:
 163                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 164                if test.code != 200:
 165                  msg = 'wrong pdb code'
 166                  self.add_error('pdbid', msg)
 167                test.close()
 168
 169
 170 class TaskForm_md_a(forms.Form):
 171      name = forms.CharField(max_length=20)
 172
 173      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 174                            label='Force Field',initial='E0LL2Y')
 175      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 176                       label='starting structure',initial='extconf')
 177      md_seq = forms.CharField(label='Sequence',
 178                      help_text='aminoacid sequence using one letter code<br>'+
 179                      'field is ignored when uploading starting/reference PDB file',
 180                      required=False,
 181                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 182      file1 = forms.FileField(label='Upload a PDB file',required=False,
 183                   help_text='starting structure for pdbstart/reference structure')
 184      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
 185       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
 186       label='or PDB code')
 187      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 188      md_temp = forms.FloatField(label='temperature',initial=300,
 189                   help_text='bath temperature')
 190      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 191                   help_text='total number of steps')
 192      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 193                   help_text='seed for random number generator')
 194
 195      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
 196                help_text='write statfile every ntwe steps')
 197      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,
 198                help_text='write trajectory every ntwe steps')
 199      md_dt = forms.FloatField(label='DT',initial=0.2,
 200                   help_text='time step [mtu]')
 201      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
 202      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
 203                   help_text='coupling to the thermal bath (Berendsen)')
 204      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
 205                   help_text='scaling of the friction coefficients (Langevin)')
 206      md_mdpdb = forms.BooleanField(required=False,label='trajectory as PDB')
 207
 208      boxx = forms.FloatField(label='Box X',initial=1000.0,
 209                        help_text='box x dimension')
 210      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 211                        help_text='box y dimension')
 212      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 213                        help_text='box z dimension')
 214
 215      def clean(self):
 216              cleaned_data = super(TaskForm_md_a, 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                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 239                if test.code != 200:
 240                  msg = 'wrong pdb code'
 241                  self.add_error('pdbid', msg)
 242                test.close()
 243
 244
 245 class TaskForm_remd(forms.Form):
 246      name = forms.CharField(max_length=20)
 247
 248      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 249                       label='starting structure',initial='extconf')
 250      md_seq = forms.CharField(label='Sequence',
 251                      help_text='aminoacid sequence using one letter code<br>'+
 252                         'field is ignored when uploading starting/reference PDB file',
 253                      required=False,
 254                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 255      file1 = forms.FileField(label='Upload a PDB file',required=False,
 256                   help_text='starting structure for pdbstart/reference structure')
 257      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
 258       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
 259       label='or PDB code')
 260      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 261      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 262                   help_text='total number of steps')
 263      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 264                   help_text='seed for random number generator')
 265
 266      def clean(self):
 267              cleaned_data = super(TaskForm_remd, self).clean()
 268
 269              md_start = cleaned_data.get("md_start")
 270              file1 = cleaned_data.get("file1")
 271              pdbid = cleaned_data.get("pdbid")
 272              md_seq = cleaned_data.get("md_seq")
 273              md_pdbref = cleaned_data.get("md_pdbref")
 274
 275              if md_start == 'pdbstart' and not (file1 or pdbid):
 276                 msg = 'pdbstart with no PDB file or code'
 277                 self.add_error('file1', msg)
 278
 279              if md_pdbref and not (file1 or pdbid):
 280                 msg = 'pdbref with no PDB file or code'
 281                 self.add_error('file1', msg)
 282
 283              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 284                 msg = 'extended/random chain with no sequence'
 285                 self.add_error('md_seq', msg)
 286
 287              if pdbid:
 288                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 289                if test.code != 200:
 290                  msg = 'wrong pdb code'
 291                  self.add_error('pdbid', msg)
 292                test.close()
 293
 294
 295 class TaskForm_remd_a(forms.Form):
 296      name = forms.CharField(max_length=20)
 297
 298      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 299                            label='Force Field',initial='E0LL2Y')
 300      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 301                       label='starting structure',initial='extconf')
 302      md_seq = forms.CharField(label='Sequence',
 303                      help_text='aminoacid sequence using one letter code<br>'+
 304                       'field is ignored when uploading starting/reference PDB file',
 305                      required=False,
 306                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 307      file1 = forms.FileField(label='Upload a PDB file',required=False,
 308                   help_text='starting structure for pdbstart/reference structure')
 309      pdbid = forms.CharField(min_length=4,max_length=4,required=False,
 310       widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
 311       label='or PDB code')
 312      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 313      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 314                   help_text='total number of steps')
 315      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 316                   help_text='seed for random number generator')
 317      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
 318                help_text='write statfile every ntwe steps')
 319      md_dt = forms.FloatField(label='DT',initial=0.2,
 320                   help_text='time step [mtu]')
 321      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
 322      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
 323                   help_text='coupling to the thermal bath (Berendsen)')
 324      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
 325                   help_text='scaling of the friction coefficients (Langevin)')
 326      remd_nrep = forms.IntegerField(label='NREP',initial=8,
 327                   help_text='number of replicas')
 328      remd_nstex = forms.IntegerField(label='NSTEX',initial=1000,
 329                   help_text='exchange and write trajectory every nstex steps')
 330      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,
 331                help_text='write trajectory every ntwx steps')
 332      remd_cluter_temp = forms.FloatField(label='TEMPER',
 333                   help_text='temperature for cluster analysis',initial=280)
 334 #     remd_traj1file = forms.BooleanField(required=False,label='single trajectory file',initial='true')
 335 #     remd_rest1file = forms.BooleanField(required=False,label='single restart file',initial='true')
 336
 337      boxx = forms.FloatField(label='Box X',initial=1000.0,
 338                        help_text='box x dimension')
 339      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 340                        help_text='box y dimension')
 341      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 342                        help_text='box z dimension')
 343
 344
 345      def clean(self):
 346              cleaned_data = super(TaskForm_remd_a, self).clean()
 347
 348              md_start = cleaned_data.get("md_start")
 349              file1 = cleaned_data.get("file1")
 350              pdbid = cleaned_data.get("pdbid")
 351              md_seq = cleaned_data.get("md_seq")
 352              md_pdbref = cleaned_data.get("md_pdbref")
 353
 354              if md_start == 'pdbstart' and not (file1 or pdbid):
 355                 msg = 'pdbstart with no PDB file or code'
 356                 self.add_error('file1', msg)
 357
 358              if md_pdbref and not (file1 or pdbid):
 359                 msg = 'pdbref with no PDB file or code'
 360                 self.add_error('file1', msg)
 361
 362
 363              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 364                 msg = 'extended/random chain with no sequence'
 365                 self.add_error('md_seq', msg)
 366
 367              if pdbid:
 368                test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
 369                if test.code != 200:
 370                  msg = 'wrong pdb code'
 371                  self.add_error('pdbid', msg)
 372                test.close()
 373
 374
 375
 376 class TaskForm_list(forms.Form):
 377     name = forms.CharField(max_length=20,disabled=True,required=False)
 378     nrep = forms.IntegerField(disabled=True,required=False,label='NREP')
 379
 380     def __init__(self, count, *args, **kwargs):
 381         super(TaskForm_list, self).__init__(*args, **kwargs)
 382         self.count=count
 383         self.fields['temperatures'] = MultiExampleField(self.count)
 384         self.fields['multiplexing'] = MultiExampleField(self.count)
 385
 386
 387