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 #---v
   9 from django.core.files import File
  10 #---^
  11 import json
  12 import urllib
  13
  14 aa_3letter = [
  15      'DPR','DLY','DAR','DHI','DAS','DGL','DSG','DGN','DSN','DTH',
  16      'DAL','DTY','DTR','DVA','DLE','DIL','DPN','MED','DCY',
  17      'CYS','MET','PHE','ILE','LEU','VAL','TRP','TYR','ALA','GLY','THR',
  18      'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO',
  19      'SME','AIB','ABU','DBZ']
  20
  21
  22 def pdb_code_chain(pdbid):
  23
  24     msg=''
  25     chain=''
  26     if len(pdbid)>4:
  27        if pdbid[4]!=':':
  28          return('use : between pdb code and chain id, like 5G3Q:B to select single chain')
  29        chain=pdbid[5]
  30        pdbid=pdbid[:4]
  31
  32     test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
  33     if test.code != 200:
  34           msg = 'wrong pdb code'
  35     else:
  36           msg=pdb_missing_res_chain(test,chain)
  37     test.close()
  38     return(msg)
  39
  40 def pdb_missing_res_chain(file,chain):
  41    msg=''
  42    newchain = True
  43    ires=[]
  44    for line in file:
  45       if line[0:6] == 'ATOM  ' and line[13:15] == 'CA' and (line[21] == chain or chain==''):
  46                i = int(line[22:26])
  47                ch = line[21]
  48                if line[17:20] not in aa_3letter:
  49                  msg='residue '+line[17:20]+' '+str(i)+' not recognized'
  50                  return(msg)
  51                if ires and i==ires[-1]:
  52                  continue
  53                if newchain or i==ires[-1]+1:
  54                  ires.append(i)
  55                  newchain = False
  56                else:
  57                  msg = 'chain breaks between residues '+\
  58                    str(ires[-1])+' and '+str(i)+' of chain '+ch+\
  59                    ', server cannot add missing residues to PDB file - please repair the structure using e.g. Modeller'
  60                  break
  61       if line[0:3] == 'TER':
  62                newchain = True
  63       if line[0:3] == 'END':
  64                break
  65
  66    if len(ires) == 0:
  67         if chain == '':
  68                msg='no CA atoms in this pdb'
  69         else:
  70                msg='wrong chain id'
  71    return(msg)
  72
  73 #---v
  74 def nmr_bad_cols(file):
  75   msg=''
  76   for line in file:
  77     line=line.rstrip()
  78     if line:
  79       data = line.split()
  80       for x in (0, 1, 2):
  81         lg = data[x].isdigit()
  82         if not lg:
  83           msg = 'NMR shifts data column '+repr(x+1)+' must be integer, not: '+data[x]
  84           return(msg)
  85       dlug = len(data)
  86       if (dlug < 5):
  87         msg = 'There have to be 5 or more columns in NMR shifts data file'
  88         return(msg)
  89       promien = data[3].replace('.', '')
  90       lg2 = promien.isdigit()
  91       if not lg2:
  92           msg ='NMR shifts 4th data column must be decimal or integer radius, not: '+data[3]
  93           return(msg)
  94       lg3 = data[4].startswith('H') or data[4].startswith('Q')
  95       if not lg3:
  96         msg = 'NMR shifts 5th data column must be proton designation, not: '+data[4]
  97         return(msg)
  98     else:
  99       msg = 'NMR shifts data contains blank lines. Remove them.'
 100   return(msg)
 101 #---^
 102
 103
 104 def code_2d(line):
 105    msg=''
 106    set ='HEC-'
 107    line2 = ''.join([c for c in line if c in set])
 108    if line2 != line:
 109     msg='use only H,E,C or - letters'
 110    return(msg)
 111
 112
 113 class MultiWidgetBasic(forms.MultiWidget):
 114     def __init__(self, count, attrs=None):
 115         self.count=count
 116         widgets = []
 117         for i in range(self.count):
 118            widgets.append(forms.TextInput())
 119         super(MultiWidgetBasic, self).__init__(widgets, attrs)
 120
 121     template_name = 'multi.html'
 122
 123     def decompress(self, value):
 124         if value:
 125             return json.loads(value)
 126         else:
 127             return ['', '']
 128
 129
 130 class MultiExampleField(forms.fields.MultiValueField):
 131     def __init__(self, count, *args, **kwargs):
 132         self.count=count
 133         self.widget = MultiWidgetBasic(self.count)
 134         list_fields = []
 135         for i in range(self.count):
 136            list_fields.append(forms.fields.CharField(max_length=15))
 137         super(MultiExampleField, self).__init__(list_fields, *args, **kwargs)
 138
 139     def compress(self, values):
 140         ## compress list to single object
 141         return json.dumps(values)
 142
 143
 144 class TaskForm(forms.Form):
 145     name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 146
 147
 148 class TaskForm_min(forms.Form):
 149      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 150      file1 = forms.FileField(label='Upload a PDB file',required=False,
 151       help_text='continuous (without breaks) protein chains,use TER to divide chains')
 152      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 153       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 154       label='or PDB code (:chain)')
 155
 156      def clean(self):
 157              cleaned_data = super(TaskForm_min, self).clean()
 158
 159              pdbid = cleaned_data.get("pdbid")
 160              file1 = cleaned_data.get("file1")
 161
 162              if not pdbid and not file1:
 163                 msg = 'provide pdb file or pdb code'
 164                 self.add_error('file1', msg)
 165
 166              if pdbid:
 167                msg=pdb_code_chain(pdbid)
 168                if msg != '':
 169                    self.add_error('pdbid',msg)
 170
 171              if file1:
 172                  msg=pdb_missing_res_chain(file1,'')
 173                  if msg != '':
 174                    self.add_error('file1',msg)
 175
 176
 177 class TaskForm_min_a(forms.Form):
 178      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 179
 180      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 181                            label='Force Field',initial='FF2')
 182 #     min_choice = forms.ChoiceField(choices=MIN_CHOICE,label='minimization algorithm')
 183      min_overlap = forms.BooleanField(required=False,label='remove overlap')
 184      min_searchsc = forms.BooleanField(required=False,label='MC for sidechain overlap')
 185      min_maxmin = forms.IntegerField(label='MAXMIN',initial=10000,
 186                   help_text='maximum number of iterations')
 187      min_maxfun = forms.IntegerField(label='MAXFUN',initial=15000,
 188                   help_text='maximum number of function evaluations')
 189      file1 = forms.FileField(label='Upload a PDB file',required=False,
 190         help_text='continuous (without breaks) protein chains,use TER to divide chains')
 191      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 192       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 193       label='or PDB code (:chain)')
 194
 195      min_unres_pdb = forms.BooleanField(required=False,label='uploaded input unres PDB',
 196                   help_text='(CA and CB atoms only, CB represents SC in UNRES)')
 197      min_pdbout = forms.BooleanField(required=False,label='output PDB',initial='true')
 198      boxx = forms.FloatField(label='Box X',initial=1000.0,
 199                        help_text='box x dimension')
 200      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 201                        help_text='box y dimension')
 202      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 203                        help_text='box z dimension')
 204
 205      def clean(self):
 206              cleaned_data = super(TaskForm_min_a, self).clean()
 207
 208              pdbid = cleaned_data.get("pdbid")
 209              file1 = cleaned_data.get("file1")
 210
 211              if not pdbid and not file1:
 212                 msg = 'provide pdb file or pdb code'
 213                 self.add_error('file1', msg)
 214
 215              if pdbid:
 216                  msg=pdb_code_chain(pdbid)
 217                  if msg != '':
 218                    self.add_error('pdbid',msg)
 219
 220              if file1:
 221                  msg=pdb_missing_res_chain(file1,'')
 222                  if msg != '':
 223                    self.add_error('file1',msg)
 224
 225
 226 class TaskForm_md(forms.Form):
 227      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 228
 229      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 230                       label='starting structure',initial='extconf')
 231      md_seq = forms.CharField(label='Sequence',
 232                      help_text='aminoacid sequence using one letter code<br>'+
 233                      'field is ignored when uploading starting/reference PDB file',
 234                      required=False,
 235                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 236      file1 = forms.FileField(label='Upload a PDB file',required=False,
 237                   help_text='starting structure for pdbstart/reference structure')
 238      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 239       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 240       label='or PDB code (:chain)')
 241      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 242      md_temp = forms.FloatField(label='temperature',initial=300,
 243                   help_text='bath temperature')
 244      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 245                   help_text='total number of steps',max_value=10000000)
 246      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 247                   help_text='seed for random number generator')
 248
 249      def clean(self):
 250              cleaned_data = super(TaskForm_md, self).clean()
 251
 252              md_start = cleaned_data.get("md_start")
 253              file1 = cleaned_data.get("file1")
 254              pdbid = cleaned_data.get("pdbid")
 255              md_seq = cleaned_data.get("md_seq")
 256              md_pdbref = cleaned_data.get("md_pdbref")
 257
 258              if md_start == 'pdbstart' and not (file1 or pdbid):
 259                 msg = 'pdbstart with no PDB file or code'
 260                 self.add_error('file1', msg)
 261
 262              if md_pdbref and not (file1 or pdbid):
 263                 msg = 'pdbref with no PDB file or code'
 264                 self.add_error('file1', msg)
 265
 266
 267              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 268                 msg = 'extended/random chain with no sequence'
 269                 self.add_error('md_seq', msg)
 270
 271              if pdbid:
 272                  msg=pdb_code_chain(pdbid)
 273                  if msg != '':
 274                    self.add_error('pdbid',msg)
 275
 276              if file1:
 277                  msg=pdb_missing_res_chain(file1,'')
 278                  if msg != '':
 279                    self.add_error('file1',msg)
 280
 281
 282 class TaskForm_md_a(forms.Form):
 283      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 284
 285      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 286                            label='Force Field',initial='FF2')
 287      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 288                       label='starting structure',initial='extconf')
 289      md_seq = forms.CharField(label='Sequence',
 290                      help_text='aminoacid sequence using one letter code<br>'+
 291                      'field is ignored when uploading starting/reference PDB file',
 292                      required=False,
 293                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 294      md_2d = forms.CharField(label='Secondary structure restraints',
 295                      help_text='single letter code: H helix, E extended/beta, C or - no restraints',
 296                      required=False,
 297                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 298
 299 #---v
 300      use_nmr = forms.BooleanField(required=False,label='use NMR restraints',
 301                   help_text='this option requires the next four fields to be set.')
 302      file3 = forms.FileField(label='Upload a NMR restraints file',required=False,
 303                   help_text='at least 5 columns required:     49      22      1       5.0     HD2     H; <i>Hint: if you are using <u>NMR example data</u> then the field will be filled out automatically</i>')
 304      nmr_scal = forms.IntegerField(label='NMR option: scal_peak',initial=20)
 305      nmr_fordepth = forms.FloatField(label='NMR option: FORDEPTH_PEAK',initial=0.5)
 306      nmr_slope = forms.FloatField(label='NMR option: SLOPE_PEAK',initial=0.05)
 307      file1 = forms.FileField(label='Upload a PDB file',required=False,
 308                   help_text='starting structure for pdbstart/reference structure; <i>Hint: if you are using <u>NMR example data</u> then the field will be filled out automatically</i>')
 309 #---^
 310      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 311       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 312       label='or PDB code (:chain)')
 313      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 314      md_temp = forms.FloatField(label='temperature',initial=300,
 315                   help_text='bath temperature')
 316      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 317                   help_text='total number of steps',max_value=10000000)
 318      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 319                   help_text='seed for random number generator')
 320
 321      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
 322                help_text='write statfile every ntwe steps')
 323      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,
 324                help_text='write trajectory every ntwe steps',min_value=100)
 325      md_dt = forms.FloatField(label='DT',initial=0.2,
 326                   help_text='time step [mtu=48.9 fs]')
 327      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
 328      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
 329                   help_text='coupling to the thermal bath (Berendsen)')
 330      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
 331                   help_text='scaling of the friction coefficients (Langevin)')
 332      md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
 333      md_mdpdb = forms.BooleanField(required=False,label='trajectory as PDB')
 334
 335      boxx = forms.FloatField(label='Box X',initial=1000.0,
 336                        help_text='box x dimension')
 337      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 338                        help_text='box y dimension')
 339      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 340                        help_text='box z dimension')
 341
 342      def clean(self):
 343              cleaned_data = super(TaskForm_md_a, self).clean()
 344
 345 #---v
 346              md_seq = cleaned_data.get("md_seq")
 347              if (md_seq == 'TDELLERLRQLFEELHERGTEIVVEVHINGERDEIRVRNISKEELKKLLERIREKIEREGSSEVEVNVHSGGQTWTFNEK'):
 348                reopn1 = open('files/6msp-from-THR.pdb', 'r')
 349                file1 = File(reopn1)
 350              else:
 351 #---^
 352                file1 = cleaned_data.get("file1")
 353              md_start = cleaned_data.get("md_start")
 354              pdbid = cleaned_data.get("pdbid")
 355              md_seq = cleaned_data.get("md_seq")
 356              md_pdbref = cleaned_data.get("md_pdbref")
 357              md_2d = cleaned_data.get("md_2d")
 358
 359 #---v
 360              if (md_seq == 'TDELLERLRQLFEELHERGTEIVVEVHINGERDEIRVRNISKEELKKLLERIREKIEREGSSEVEVNVHSGGQTWTFNEK'):
 361                reopn = open('files/N1008_AmbiR-trunc.txt', 'r')
 362                file3 = File(reopn)
 363              else:
 364                file3 = cleaned_data.get("file3")
 365              unres_ff = cleaned_data.get("unres_ff")
 366              use_nmr = cleaned_data.get("use_nmr")
 367              nmr_scal = cleaned_data.get("nmr_scal")
 368              nmr_fordepth = cleaned_data.get("nmr_fordepth")
 369              nmr_slope = cleaned_data.get("nmr_slope")
 370              if (use_nmr and file3):
 371                msg=nmr_bad_cols(file3)
 372                if msg != '':
 373                  self.add_error('file3',msg)
 374              else:
 375                if (use_nmr and not file3):
 376                  self.add_error('file3','"Use NMR restarints" and "Upload a NMR restr. file" must be used together')
 377
 378              if (use_nmr and (unres_ff != 'NEWCT-9P')):
 379                self.add_error('unres_ff','"Use NMR restarints" requires NEWCT-9P force field')
 380
 381 #---^
 382              if md_start == 'pdbstart' and not (file1 or pdbid):
 383                 msg = 'pdbstart with no PDB file or code'
 384                 self.add_error('file1', msg)
 385
 386              if md_pdbref and not (file1 or pdbid):
 387                 msg = 'pdbref with no PDB file or code'
 388                 self.add_error('file1', msg)
 389
 390
 391              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 392                 msg = 'extended/random chain with no sequence'
 393                 self.add_error('md_seq', msg)
 394
 395              if pdbid:
 396                  msg=pdb_code_chain(pdbid)
 397                  if msg != '':
 398                    self.add_error('pdbid',msg)
 399
 400              if file1:
 401                  msg=pdb_missing_res_chain(file1,'')
 402                  if msg != '':
 403                    self.add_error('file1',msg)
 404
 405              if md_2d:
 406                  msg=code_2d(md_2d)
 407                  if msg != '':
 408                    self.add_error('md_2d',msg)
 409
 410 class TaskForm_remd(forms.Form):
 411      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 412
 413      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 414                       label='starting structure',initial='extconf')
 415      md_seq = forms.CharField(label='Sequence',
 416                      help_text='aminoacid sequence using one letter code<br>'+
 417                         'field is ignored when uploading starting/reference PDB file',
 418                      required=False,
 419                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 420      file1 = forms.FileField(label='Upload a PDB file',required=False,
 421                   help_text='starting structure for pdbstart/reference structure')
 422      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 423       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 424       label='or PDB code (:chain)')
 425      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 426      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 427                   help_text='total number of steps',max_value=10000000)
 428      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 429                   help_text='seed for random number generator')
 430
 431      def clean(self):
 432              cleaned_data = super(TaskForm_remd, self).clean()
 433
 434              md_start = cleaned_data.get("md_start")
 435              file1 = cleaned_data.get("file1")
 436              pdbid = cleaned_data.get("pdbid")
 437              md_seq = cleaned_data.get("md_seq")
 438              md_pdbref = cleaned_data.get("md_pdbref")
 439
 440              if md_start == 'pdbstart' and not (file1 or pdbid):
 441                 msg = 'pdbstart with no PDB file or code'
 442                 self.add_error('file1', msg)
 443
 444              if md_pdbref and not (file1 or pdbid):
 445                 msg = 'pdbref with no PDB file or code'
 446                 self.add_error('file1', msg)
 447
 448              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 449                 msg = 'extended/random chain with no sequence'
 450                 self.add_error('md_seq', msg)
 451
 452              if pdbid:
 453                  msg=pdb_code_chain(pdbid)
 454                  if msg != '':
 455                    self.add_error('pdbid',msg)
 456
 457              if file1:
 458                  msg=pdb_missing_res_chain(file1,'')
 459                  if msg != '':
 460                    self.add_error('file1',msg)
 461
 462
 463 class TaskForm_remd_a(forms.Form):
 464      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 465
 466      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 467                            label='Force Field',initial='FF2')
 468      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
 469                       label='starting structure',initial='extconf')
 470      md_seq = forms.CharField(label='Sequence',
 471                      help_text='aminoacid sequence using one letter code<br>'+
 472                       'field is ignored when uploading starting/reference PDB file',
 473                      required=False,
 474                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 475      md_2d = forms.CharField(label='Secondary structure restraints',
 476                      help_text='single letter code: H helix, E extended/beta, C or - no restraints',
 477                      required=False,
 478                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 479 #---v
 480      use_nmr = forms.BooleanField(required=False,label='use NMR restraints',
 481                   help_text='this option requires the next four fields to be set.')
 482      file3 = forms.FileField(label='Upload a NMR restraints file',required=False,
 483        help_text='at least 5 columns required:     49      22      1       5.0     HD2     H; <i>Hint: if you are using <u>NMR example data</u> then the field will be filled out automatically</i>')
 484      nmr_scal = forms.IntegerField(label='NMR option: scal_peak',initial=20)
 485      nmr_fordepth = forms.FloatField(label='NMR option: FORDEPTH_PEAK',initial=0.5)
 486      nmr_slope = forms.FloatField(label='NMR option: SLOPE_PEAK',initial=0.05)
 487 #---^
 488      file1 = forms.FileField(label='Upload a PDB file',required=False,
 489                   help_text='starting structure for pdbstart/reference structure; <i>Hint: if you are using <u>NMR example data</u> then the field will be filled out automatically</i>')
 490      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 491       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 492       label='or PDB code (:chain)')
 493      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
 494      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 495                   help_text='total number of steps',max_value=10000000)
 496      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 497                   help_text='seed for random number generator')
 498      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
 499                help_text='write statfile every ntwe steps')
 500      md_dt = forms.FloatField(label='DT',initial=0.2,
 501                   help_text='time step [mtu = 48.9 fs]')
 502      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
 503      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
 504                   help_text='coupling to the thermal bath (Berendsen)')
 505      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
 506                   help_text='scaling of the friction coefficients (Langevin)')
 507      min_maxfun = forms.IntegerField(label='MAXFUN',initial=5000,
 508                   help_text='preminim maximum number of function evaluations<br>'+
 509                   'used for start from pdb or random start')
 510      remd_nrep = forms.IntegerField(label='NREP',initial=8,
 511                   help_text='number of temperatures')
 512      remd_nstex = forms.IntegerField(label='NSTEX',initial=1000,
 513                   help_text='exchange and write trajectory every nstex steps')
 514      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,min_value=100,
 515                help_text='write trajectory every ntwx steps')
 516      remd_cluter_temp = forms.FloatField(label='TEMPER',
 517                   help_text='temperature for cluster analysis',initial=280)
 518 #     remd_traj1file = forms.BooleanField(required=False,label='single trajectory file',initial='true')
 519 #     remd_rest1file = forms.BooleanField(required=False,label='single restart file',initial='true')
 520
 521      md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
 522
 523      boxx = forms.FloatField(label='Box X',initial=1000.0,
 524                        help_text='box x dimension')
 525      boxy = forms.FloatField(label='Box Y',initial=1000.0,
 526                        help_text='box y dimension')
 527      boxz = forms.FloatField(label='Box Z',initial=1000.0,
 528                        help_text='box z dimension')
 529
 530
 531      wsaxs = forms.FloatField(label='SAXS weight',initial=100.0,
 532                             help_text='weight for SAXS restraint term')
 533      scal_rad = forms.FloatField(label='Scal_rad (SAXS)',initial=1.0,
 534                             help_text='downscaling factor of residue radii used in SAXS restraints')
 535      saxs_data = forms.CharField(label='P(r) SAXS data',
 536                      help_text='distance distribution from SAXS, two columns: r and P(r)',
 537                      required=False,
 538                      widget=forms.Textarea(attrs={'cols': 25, 'rows': 20}))
 539
 540
 541      def clean(self):
 542              cleaned_data = super(TaskForm_remd_a, self).clean()
 543
 544              md_start = cleaned_data.get("md_start")
 545 #---v
 546              md_seq = cleaned_data.get("md_seq")
 547              if (md_seq == 'TDELLERLRQLFEELHERGTEIVVEVHINGERDEIRVRNISKEELKKLLERIREKIEREGSSEVEVNVHSGGQTWTFNEK'):
 548                reopn1 = open('files/6msp-from-THR.pdb', 'r')
 549                file1 = File(reopn1)
 550              else:
 551                file1 = cleaned_data.get("file1")
 552 #---^
 553              pdbid = cleaned_data.get("pdbid")
 554              md_pdbref = cleaned_data.get("md_pdbref")
 555              md_2d = cleaned_data.get("md_2d")
 556 #---v
 557              if (md_seq == 'TDELLERLRQLFEELHERGTEIVVEVHINGERDEIRVRNISKEELKKLLERIREKIEREGSSEVEVNVHSGGQTWTFNEK'):
 558                reopn = open('files/N1008_AmbiR-trunc.txt', 'r')
 559                file3 = File(reopn)
 560              else:
 561                file3 = cleaned_data.get("file3")
 562              unres_ff = cleaned_data.get("unres_ff")
 563              use_nmr = cleaned_data.get("use_nmr")
 564              nmr_scal = cleaned_data.get("nmr_scal")
 565              nmr_fordepth = cleaned_data.get("nmr_fordepth")
 566              nmr_slope = cleaned_data.get("nmr_slope")
 567              if (use_nmr and file3):
 568                msg=nmr_bad_cols(file3)
 569                if msg != '':
 570                  self.add_error('file3',msg)
 571              else:
 572                if (use_nmr and not file3):
 573                  self.add_error('file3','"Use NMR restarints" and "Upload a NMR restr. file" must be used together')
 574
 575              if (use_nmr and (unres_ff != 'NEWCT-9P')):
 576                self.add_error('unres_ff','"Use NMR restarints" requires NEWCT-9P force field')
 577
 578 #---^
 579              if md_start == 'pdbstart' and not (file1 or pdbid):
 580                 msg = 'pdbstart with no PDB file or code'
 581                 self.add_error('file1', msg)
 582
 583              if md_pdbref and not (file1 or pdbid):
 584                 msg = 'pdbref with no PDB file or code'
 585                 self.add_error('file1', msg)
 586
 587
 588              if md_start != 'pdbstart' and not md_pdbref and not md_seq:
 589                 msg = 'extended/random chain with no sequence'
 590                 self.add_error('md_seq', msg)
 591
 592              if pdbid:
 593                  msg=pdb_code_chain(pdbid)
 594                  if msg != '':
 595                    self.add_error('pdbid',msg)
 596
 597              if file1:
 598                  msg=pdb_missing_res_chain(file1,'')
 599                  if msg != '':
 600                    self.add_error('file1',msg)
 601
 602              if md_2d:
 603                  msg=code_2d(md_2d)
 604                  if msg != '':
 605                    self.add_error('md_2d',msg)
 606
 607
 608 class TaskForm_dock(forms.Form):
 609      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 610
 611      file1 = forms.FileField(label='Upload a PDB file1',required=False,
 612                   help_text='starting structure for chain1')
 613      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 614       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 615       label='or PDB code (:chain)')
 616
 617
 618      md_seq = forms.CharField(label=mark_safe('Sequence of chain2 <br /> for dock peptide'),
 619                      help_text='aminoacid sequence using one letter code<br>'+
 620                         'field is ignored when uploading PDB file2',
 621                      required=False,
 622                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 623
 624
 625      file2 = forms.FileField(label='Upload a PDB file2',required=False,
 626                   help_text='starting structure for chain2')
 627      pdbid2 = forms.CharField(min_length=4,max_length=6,required=False,
 628       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 629       label='or PDB code (:chain)')
 630
 631
 632      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 633                   help_text='total number of steps', max_value=10000000)
 634      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 635                   help_text='seed for random number generator')
 636      dock_peptide = forms.BooleanField(required=False,initial=False,
 637             label='dock peptide',help_text='no constraints on chain2')
 638
 639      def clean(self):
 640              cleaned_data = super(TaskForm_dock, self).clean()
 641
 642              file1 = cleaned_data.get("file1")
 643              pdbid = cleaned_data.get("pdbid")
 644              file2 = cleaned_data.get("file2")
 645              pdbid2 = cleaned_data.get("pdbid2")
 646              md_seq = cleaned_data.get("md_seq")
 647
 648
 649              if not (file1 or pdbid):
 650                 msg = 'no PDB file or code for chain1'
 651                 self.add_error('file1', msg)
 652
 653              if not (file2 or pdbid2 or md_seq):
 654                 msg = 'no PDB file or code or sequence for chain2'
 655                 self.add_error('file2', msg)
 656
 657              if pdbid:
 658                  msg=pdb_code_chain(pdbid)
 659                  if msg != '':
 660                    self.add_error('pdbid',msg)
 661
 662              if file1:
 663                  msg=pdb_missing_res_chain(file1,'')
 664                  if msg != '':
 665                    self.add_error('file1',msg)
 666
 667              if pdbid2:
 668                  msg=pdb_code_chain(pdbid2)
 669                  if msg != '':
 670                    self.add_error('pdbid2',msg)
 671
 672              if file2:
 673                  msg=pdb_missing_res_chain(file2,'')
 674                  if msg != '':
 675                    self.add_error('file2',msg)
 676
 677 class TaskForm_dock_a(forms.Form):
 678      name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
 679
 680      file1 = forms.FileField(label='Upload a PDB file1',required=False,
 681                   help_text='starting structure for chain1')
 682      pdbid = forms.CharField(min_length=4,max_length=6,required=False,
 683       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 684       label='or PDB code (:chain)')
 685
 686      md_seq = forms.CharField(label=mark_safe('Sequence of chain2 <br /> for dock peptide'),
 687                      help_text='aminoacid sequence using one letter code<br>'+
 688                         'field is ignored when uploading PDB file2',
 689                      required=False,
 690                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
 691
 692
 693      file2 = forms.FileField(label='Upload a PDB file2',required=False,
 694                   help_text='starting structure for chain2')
 695      pdbid2 = forms.CharField(min_length=4,max_length=6,required=False,
 696       widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
 697       label='or PDB code (:chain)')
 698
 699
 700      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
 701                   help_text='total number of steps', max_value=10000000)
 702      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
 703                   help_text='seed for random number generator')
 704      dock_peptide = forms.BooleanField(required=False,initial=False,
 705             label='dock peptide',help_text='no constraints on 2nd chain')
 706
 707
 708      unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
 709                            label='Force Field',initial='FF2')
 710
 711      md_ntwe = forms.IntegerField(label='NTWE',initial=1000,
 712                help_text='write statfile every ntwe steps')
 713      md_dt = forms.FloatField(label='DT',initial=0.2,
 714                   help_text='time step [mtu = 48.9 fs]')
 715      md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
 716      md_tau = forms.FloatField(label='tau_bath',initial=1.0,
 717                   help_text='coupling to the thermal bath (Berendsen)')
 718      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
 719                   help_text='scaling of the friction coefficients (Langevin)')
 720      min_maxfun = forms.IntegerField(label='MAXFUN',initial=5000,
 721                   help_text='preminim maximum number of function evaluations<br>'+
 722                   'used for start from pdb or random start')
 723      remd_nrep = forms.IntegerField(label='NREP',initial=8,
 724                   help_text='number of temperatures')
 725      remd_nstex = forms.IntegerField(label='NSTEX',initial=1000,
 726                   help_text='exchange and write trajectory every nstex steps')
 727      md_ntwx = forms.IntegerField(label='NTWX',initial=1000,min_value=100,
 728                help_text='write trajectory every ntwx steps')
 729      remd_cluter_temp = forms.FloatField(label='TEMPER',
 730                   help_text='temperature for cluster analysis',initial=280)
 731
 732      remd_cluster_n = forms.IntegerField(label='NCLUST',initial=10,min_value=2,
 733                     max_value=50,help_text='number of clusters')
 734
 735      def clean(self):
 736              cleaned_data = super(TaskForm_dock_a, self).clean()
 737
 738              file1 = cleaned_data.get("file1")
 739              pdbid = cleaned_data.get("pdbid")
 740              file2 = cleaned_data.get("file2")
 741              pdbid2 = cleaned_data.get("pdbid2")
 742              md_seq = cleaned_data.get("md_seq")
 743
 744              if not (file1 or pdbid):
 745                 msg = 'no PDB file or code for chain1'
 746                 self.add_error('file1', msg)
 747
 748              if not (file2 or pdbid2 or md_seq):
 749                 msg = 'no PDB file or code or sequence for chain2'
 750                 self.add_error('file2', msg)
 751
 752              if pdbid:
 753                  msg=pdb_code_chain(pdbid)
 754                  if msg != '':
 755                    self.add_error('pdbid',msg)
 756
 757              if file1:
 758                  msg=pdb_missing_res_chain(file1,'')
 759                  if msg != '':
 760                    self.add_error('file1',msg)
 761
 762              if pdbid2:
 763                  msg=pdb_code_chain(pdbid2)
 764                  if msg != '':
 765                    self.add_error('pdbid2',msg)
 766
 767              if file2:
 768                  msg=pdb_missing_res_chain(file2,'')
 769                  if msg != '':
 770                    self.add_error('file2',msg)
 771
 772
 773 class TaskForm_list(forms.Form):
 774     name = forms.CharField(max_length=40,disabled=True,required=False)
 775     nrep = forms.IntegerField(disabled=True,required=False,label='NREP')
 776
 777     def __init__(self, count, *args, **kwargs):
 778         super(TaskForm_list, self).__init__(*args, **kwargs)
 779         self.count=count
 780         self.fields['temperatures'] = MultiExampleField(self.count)
 781         self.fields['multiplexing'] = MultiExampleField(self.count)
 782