source/pymol/UNRESInpGen.py

   1 # -*- coding: utf-8 -*-
   2 '''
   3 -------------------------------------------------------------------------------
   4  UNRESInpGen.py - UNRES graphical input generator v 1.0
   5 -------------------------------------------------------------------------------
   6
   7  Written by Dawid Jagieła (lightnir@chem.univ.gda.pl)  Oct 2012
   8
   9 '''
  10
  11 from pymol import cmd,stored
  12 from Tkinter import *
  13 import tkFileDialog
  14 import tkMessageBox
  15 import Pmw
  16 import string
  17 import os
  18
  19 UNRESInpGen_version="1.0"
  20
  21 def __init__(self):
  22         self.UNRESInpGenWindow = None
  23         try:
  24                 self.menuBar.addcascademenu('Plugin', 'UNRESPlugins', 'UNRESPACK Plugins', label='UNRES Plugins')
  25         except:
  26                 pass
  27
  28         self.menuBar.addmenuitem('UNRESPlugins', 'command','UNRESInpGen',
  29                 label='UNRES Input Generator',
  30                 command = lambda s=self: createUNRESInpGen(s) )
  31
  32 def createUNRESInpGen(app):
  33         if (app.UNRESInpGenWindow == None):
  34                 app.UNRESInpGenWindow = UNRESInpGenerator(app)
  35         else:
  36                 app.UNRESInpGenWindow.myToggle()
  37
  38 #=================================================================
  39
  40
  41 class UNRESInpGenerator(Toplevel):
  42         global UNRESInpGen_version
  43         # Class variables
  44         """
  45         cv = IntVar()
  46         pp = IntVar()
  47         cp = IntVar()
  48         rv = IntVar()
  49         colorize = IntVar()
  50         """
  51         seq_letter = IntVar()
  52         writeSSbrige = IntVar()
  53         OM1Val = StringVar()
  54         OM2Val = StringVar()
  55         objects_list = ['Select object']
  56         seq_list=[]
  57         seq_length=0
  58
  59         weights = ['WLONG','WSCC','WSCP','WELEC','WVDWPP','WEL_LOC','WCORR4','WCORR5','WCORR6','WTURN3','WTURN4','WTURN6','WSCCOR','WSTRAIN','WBOND','WTOR','WTORD','WANG','WSCLOC','SCAL14','SCALSCP','WCORRH','CUTOFF' ]
  60
  61         force_fields = [ {'FF':'GAB', 'WLONG' :'1.35279', 'WSCP'   :'1.59304', 'WELEC' :'0.71534', 'WBOND' :'1.00000', 'WANG'  :'1.13873', 'WSCLOC':'0.16258', 'WTOR':'1.98599', 'WTORD':'1.57069', 'WCORRH':'0.42887', 'WCORR5':'0.00000',
  62                                         'WCORR6':'0.00000', 'WEL_LOC':'0.16036', 'WTURN3':'1.68722', 'WTURN4':'0.66230', 'WTURN6':'0.00000', 'WVDWPP':'0.11371', 'WHPB':'1.00000', 'WCORR4':'0.00000', 'CUTOFF':'7.00000'},
  63                     {'FF':'E0G', 'WLONG':'1.70905', 'WSCP':'2.18310', 'WELEC':'1.06684', 'WBOND':'1.00000', 'WANG':'1.17536', 'WSCLOC':'0.22070', 'WTOR':'2.65798', 'WTORD':'2.00646', 'WCORRH':'0.23541', 'WCORR5':'0.00000',
  64                                         'WCORR6':'0.00000', 'WEL_LOC':'0.42789', 'WTURN3':'1.68126', 'WTURN4':'0.75080', 'WTURN6':'0.00000', 'WVDWPP':'0.27044', 'WHPB':'1.00000', 'WSCP14':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000'},
  65                     {'FF':'1L2Y_1LE1', 'WLONG' :'1.00000', 'WSCP'    :'1.23315', 'WELEC' : '0.84476', 'WBOND' :'1.00000', 'WANG'  :'0.62954', 'WSCLOC': '0.10554', 'WTOR': '1.84316', 'WTORD' : '1.26571', 'WCORRH': '0.19212', 'WCORR5': '0.00000',
  66                                         'WCORR6':'0.00000', 'WEL_LOC':'0.37357', 'WTURN3':'1.40323', 'WTURN4':'0.64673', 'WTURN6':'0.00000', 'WVDWPP': '0.23173', 'WHPB': '1.00000', 'WSCCOR': '0.00000', 'CUTOFF': '7.00000', 'WCORR4': '0.00000'},
  67                     {'FF':'4P',  'WSC':'1.00000', 'WSCP':'2.73684', 'WELEC':'0.06833', 'WANG':'4.15526', 'WSCLOC':'0.16761', 'WTOR':'2.99546', 'WTORD':'2.89720', 'WCORRH':'1.98989', 'WCORR5':'0.00000', 'WCORR6':'0.00000', 'WEL_LOC':'1.60072',
  68                                         'WTURN3':'2.36351', 'WTURN4':'1.34051', 'WTURN6':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  69                     {'FF':'3P',  'WSC':'1.00000', 'WSCP':'2.85111', 'WELEC':'0.36281', 'WANG':'3.95152', 'WSCLOC':'0.15244', 'WTOR':'3.00008', 'WTORD':'2.89863', 'WCORRH':'1.91423', 'WCORR5':'0.00000', 'WCORR6':'0.00000', 'WEL_LOC':'1.72128',
  70                                         'WTURN3':'2.99827', 'WTURN4':'0.59174', 'WTURN6':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  71                         {'FF':'CASP5',          'WSC':'1.00000',        'WSCP':'1.54864', 'WELEC':'0.20016', 'WANG': '1.00572', 'WSCLOC': '0.06764', 'WTOR':'1.70537', 'WTORD':'1.24442', 'WCORRH':'0.91583', 'WCORR5':'0.00607', 'WCORR6':'0.02316', 'WEL_LOC':'1.51083',
  72                                         'WTURN3':'2.00764', 'WTURN4':'0.05345', 'WTURN6':'0.05282', 'WSCCOR':'0.0', 'CUTOFF': '7.00000', 'WCORR4':'0.00000' },
  73                         {'FF':'ALPHABETA',      'WSC':'1.00000', 'WSCP':'1.43178', 'WELEC':'0.41501', 'WANG':'0.37790', 'WSCLOC':'0.12880', 'WTOR':'1.98784', 'WCORRH':'2.50526', 'WCORR5':'0.23873', 'WCORR6':'0.76327', 'WEL_LOC':'2.97687', 'WTURN3':'0.09261',
  74                                         'WTURN4':'0.79171', 'WTURN6':'0.01074', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  75                         {'FF':'BETA', 'WSC':'1.00000', 'WSCP':'1.10684', 'WELEC':'0.70000', 'WANG':'0.80775', 'WSCLOC':'1.91939', 'WTOR':'3.36070', 'WCORRH':'2.50000', 'WCORR5':'0.99949', 'WCORR6':'0.46247', 'WEL_LOC':'2.50000', 'WTURN3':'1.80121',
  76                                         'WTURN4':'4.35377', 'WTURN6':'0.10000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  77                         {'FF':'ALPHA', 'WSC':'1.00000', 'WSCP':'0.72364', 'WELEC':'1.10890', 'WANG':'0.68702', 'WSCLOC':'1.79888', 'WTOR':'0.30562', 'WCORRH':'1.09616', 'WCORR5':'0.17452', 'WCORR6':'0.36878', 'WEL_LOC':'0.19508', 'WTURN3':'0.00000',
  78                                         'WTURN4':'0.55588', 'WTURN6':'0.11539', 'CUTOFF':'7.00000', 'WCORR4':'0.0000', 'WTORD':'0.00000', 'WSCCOR':'0.00000'},
  79                         {'FF':'CASP3', 'WELEC':'1.50000', 'WSTRAIN':'1.00000', 'WTOR':'0.08617', 'WANG':'0.10384', 'WSCLOC':'0.10384', 'WCORR':'1.50000', 'WTURN3':'0.00000', 'WTURN4':'0.00000', 'WTURN6':'0.00000', 'WEL_LOC':'0.00000', 'WCORR5':'0.00000',
  80                                         'WCORR6':'0.00000', 'SCAL14':'0.40000', 'SCALSCP':'1.00000', 'CUTOFF':'7.00000', 'WSCCOR':'0.00000'}
  81         ]
  82
  83         one_letter ={'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', 'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y', 'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A', 'GLY':'G', 'PRO':'P', 'CYS':'C'}
  84
  85
  86         def __init__(self,parent):
  87                 # Create the GUI window
  88                 root = Toplevel.__init__(self)
  89                 self.config(width=400, height=300)              # create a root window
  90                 self.title("UNRES Input Generator v"+UNRESInpGen_version)                 # Set window title
  91                 self.resizable(0, 0)                                # Disable window resize
  92                 self.geometry('-40+40')                             # Set window placement
  93
  94                 # Create the Balloon.
  95                 self.balloon = Pmw.Balloon(root)
  96
  97                 #================================
  98                 # "Main Options" group
  99                 #
 100                 self.gr1 = Pmw.Group(self,tag_text = 'Main options')
 101                 self.gr1.grid(row=0, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
 102
 103                 # - Create title Entryfield & Label
 104                 #self.l1 = Label(self.gr1.interior(), text="Title:")
 105                 #self.l1.grid(row=0, column=0,sticky=E)
 106                 self.e1 = Pmw.EntryField(self.gr1.interior(),
 107                         labelpos='w',
 108                         label_text="Title:",
 109                         validate = {'max': 80 },
 110                 #       value ="(Place input information here)"
 111                 )
 112                 self.e1.component('entry').config(width=80)
 113                 self.e1.grid(row=0, column=0,columnspan=4, sticky=E)
 114
 115                 # - Create "choose method" OptionMenu
 116                 self.OM1Val.set('MD')
 117                 self.optmenu1 =  Pmw.OptionMenu(self.gr1.interior(),
 118                         labelpos = 'w',
 119                         label_text = 'Choose method:',
 120                         menubutton_textvariable = self.OM1Val,
 121                         items = ['MD', 'MREMD' ],
 122                         command = self.switch_options,
 123                         menubutton_width = 10
 124                 )
 125                 self.optmenu1.grid(row=1, column=0,columnspan=2, sticky=E)
 126
 127
 128                 # - Seed entryfield
 129                 self.gr1.e1 = Pmw.EntryField(self.gr1.interior(),
 130                         labelpos='w',
 131                         label_text="Seed",
 132                         validate = {'validator' : 'integer', 'min': -2147483648 , 'max' : 0 },
 133                         value = "-1111333"
 134                 )
 135                 self.gr1.e1.component('entry').config(width=8)
 136                 self.gr1.e1.grid(row=1, column=2, sticky=W)
 137
 138                 #==================================
 139                 # - MD options frame
 140                 #
 141                 self.gr1.md = Frame(self.gr1.interior())
 142                 self.gr1.md.grid(row=2, column=0, columnspan=4,sticky=W+E)
 143
 144                 # -- nstep entryfield
 145                 self.gr1.md.e1 = Pmw.EntryField(self.gr1.md,
 146                         labelpos='w',
 147                         label_text="NSTEP",
 148                         validate = {'validator' : 'integer', 'min': 1 , 'max' : 1000000 },
 149                         value = "500000"
 150                 )
 151                 self.balloon.bind(self.gr1.md.e1,'Number of calculation steps')
 152                 self.gr1.md.e1.component('entry').config(width=8)
 153                 self.gr1.md.e1.grid(row=0, column=0, sticky=E)
 154
 155                 # -- ntwe entryfield
 156                 self.gr1.md.e2 = Pmw.EntryField(self.gr1.md,
 157                         labelpos='w',
 158                         label_text="NTWE",
 159                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
 160                         value = "100"
 161                 )
 162                 self.balloon.bind(self.gr1.md.e2,'Frequency of energy output.\nNTWE=0 means no energy dump. ')
 163                 self.gr1.md.e2.component('entry').config(width=8)
 164                 self.gr1.md.e2.grid(row=0,column=1, sticky=E)
 165
 166                 # -- ntwx entryfield
 167                 self.gr1.md.e3 = Pmw.EntryField(self.gr1.md,
 168                         labelpos='w',
 169                         label_text="NTWX",
 170                         validate = {'validator' : 'integer', 'min': 1 , 'max' : 1000000 },
 171                         value = "1000"
 172                 )
 173                 self.balloon.bind(self.gr1.md.e3, "Frequency of coordinate output.")
 174                 self.gr1.md.e3.component('entry').config(width=8)
 175                 self.gr1.md.e3.grid(row=0,column=2, sticky=E)
 176
 177                 # -- dt entryfield
 178                 self.gr1.md.e4 = Pmw.EntryField(self.gr1.md,
 179                         labelpos='w',
 180                         label_text="DT",
 181                         validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
 182                         value = "0.1")
 183                 self.balloon.bind(self.gr1.md.e4, "Time step. \nThe unit is \"molecular time unit\" (mtu)\n 1 mtu = 48.9 fs")
 184                 self.gr1.md.e4.component('entry').config(width=8)
 185                 self.gr1.md.e4.grid(row=0,column=3, sticky=E)
 186
 187                 # -- damax entryfield
 188                 self.gr1.md.e5 = Pmw.EntryField(self.gr1.md,
 189                         labelpos='w',
 190                         label_text="DAMAX",
 191                         validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
 192                         value = "1.0")
 193                 self.balloon.bind(self.gr1.md.e5, "Maximum allowed change of acceleration during a single time step.\nThe time step gets scaled down, if this is exceeded.")
 194                 self.gr1.md.e5.component('entry').config(width=8)
 195                 self.gr1.md.e5.grid(row=1,column=0, sticky=E)
 196
 197                 # -- dvmax entryfield
 198                 self.gr1.md.e6 = Pmw.EntryField(self.gr1.md,
 199                         labelpos='w',
 200                         label_text="DVMAX",
 201                         validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
 202                         value = "20.0")
 203                 self.balloon.bind(self.gr1.md.e6, "Maximum allowed velocity (in A/mtu).")
 204                 self.gr1.md.e6.component('entry').config(width=8)
 205                 self.gr1.md.e6.grid(row=1,column=1, sticky=E)
 206
 207                 # -- restet_vel entryfield
 208                 self.gr1.md.e7 = Pmw.EntryField(self.gr1.md,
 209                         labelpos='w',
 210                         label_text="RESET_VEL",
 211                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 10000000 },
 212                         value = "1000")
 213                 self.balloon.bind(self.gr1.md.e7, "Frequency of resetting velocities to values from Gaussian distribution")
 214                 self.gr1.md.e7.component('entry').config(width=8)
 215                 self.gr1.md.e7.grid(row=1,column=2, sticky=E)
 216
 217
 218                 #=================================
 219                 #  - thermostat frame
 220                 #
 221                 self.gr1.th = Frame(self.gr1.interior())
 222                 self.gr1.th.grid(row=3, column=0, columnspan=5,sticky=W+E)
 223
 224                 # -- Thermostat optionmenu
 225                 self.gr1.th.optmenu1 =  Pmw.OptionMenu(self.gr1.th,
 226                         labelpos = 'w',
 227                         label_text = 'thermostat',
 228                         items = ['Berendsen', 'Nose-Poincare 1999','Nose-Poincare 2001', 'Nose-Hoover', 'Langevin' ],
 229                         command=self.set_thermostat,
 230                         menubutton_width = 15
 231                 )
 232                 self.gr1.th.optmenu1.pack(side=LEFT)#grid(row=0, column=0, sticky=E)
 233
 234                 # -- t_bath entryfield
 235                 self.gr1.th.e1 = Pmw.EntryField(self.gr1.th,
 236                         labelpos='w',
 237                         label_text="T_BATH",
 238                         validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 10000 },
 239                         value = "300.0")
 240                 self.balloon.bind(self.gr1.th.e1, "Temperature (in K) of canonical simulation.")
 241                 self.gr1.th.e1.component('entry').config(width=8)
 242                 self.gr1.th.e1.pack(side=LEFT)
 243
 244                 # -- tau_bath entryfield
 245                 self.gr1.th.e2 = Pmw.EntryField(self.gr1.th,
 246                         labelpos='w',
 247                         label_text="TAU_BATH",
 248                         validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 1000000 },
 249                         value = "1.0")
 250                 self.balloon.bind(self.gr1.th.e2, "(units are mtus; 1mtu=48.9 fs) \nConstant of the coupling to the thermal bath")
 251                 self.gr1.th.e2.component('entry').config(width=8)
 252                 self.gr1.th.e2.pack(side=LEFT)
 253
 254                 # -- q_np entryfield
 255                 self.gr1.th.e3 = Pmw.EntryField(self.gr1.th,
 256                         labelpos='w',
 257                         label_text="Q_NP",
 258                         validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 1000000 },
 259                         value = "0.1")
 260                 self.balloon.bind(self.gr1.th.e3, "Mass of the fictitious particle in the calculations with the Nose-Poincare & Nose-Hoover thermostats.")
 261                 self.gr1.th.e3.component('entry').config(width=8)
 262                 #self.gr1.th.e2.pack(side=LEFT)
 263
 264
 265                 #=================================
 266                 # "Force field options" group
 267                 #
 268                 self.gr2 = Pmw.Group(self,tag_text = 'Force field options')
 269                 self.gr2.grid(row=2, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
 270
 271                 # - Create "force field parameters" Option menu
 272                 self.OM2Val.set('Custom')
 273                 self.optmenu2 = Pmw.OptionMenu(self.gr2.interior(),
 274                 label_text = 'Force field parameters:',
 275                         labelpos = 'w',
 276                         menubutton_textvariable = self.OM2Val,
 277                         items = ['Custom','GAB','E0G', '1L2Y_1LE1','4P','3P','CASP5','ALPHABETA','BETA','ALPHA','CASP3' ],
 278                         initialitem = 'Custom',
 279                         menubutton_width = 10,
 280                         command=self.set_force_field
 281                 )
 282                 self.optmenu2.grid(row=0, column=0,columnspan=4,sticky=E)
 283
 284                 # Force field parameters Entry Fields
 285                 self.ef = []
 286                 for i in range(0,len(self.weights)):
 287                         self.ef.append(Pmw.EntryField(self.gr2.interior(),
 288                         labelpos='n',
 289                         label_text=self.weights[i],
 290                         validate = {'validator' : 'real','min' : 0, 'max' : 10, 'minstrict' : 0},
 291                         value = '1.00000'))
 292                         self.ef[i].component('entry').config(width=8)
 293                         self.ef[i].grid(row=1+(i//9), column=0+(i % 9))
 294                 # "Sequence" group
 295                 self.gr3 = Pmw.Group(self,tag_text = 'Sequence')
 296                 self.gr3.grid(row=3, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
 297
 298                 self.gr3.f1 = Frame(self.gr3.interior())
 299                 # Object List
 300                 self.cb2 = Pmw.ComboBox(self.gr3.f1,
 301                         labelpos = 'w',
 302                         #entry_relief = 'raised',
 303                         label_text = 'Selection/Object',
 304                         scrolledlist_items = self.objects_list
 305                 )
 306                 self.cb2.pack(side=LEFT)
 307                 # refresh button
 308                 self.gr3.btn1 = Button(self.gr3.f1, text='Refresh', padx=0, pady=0 , command = self.refresh_list)
 309                 self.gr3.btn1.pack(side=LEFT)
 310                 # Get sequence button
 311                 self.gr3.btn2 = Button(self.gr3.f1, text='Get Sequence', padx=0, pady=0 , command = self.get_seq)
 312                 self.gr3.btn2.pack(side=LEFT)
 313
 314                 self.gr3.f1.pack(expand="yes",fill="both")
 315
 316                 # Disulfide brige checkbox
 317                 self.gr3.chk = Checkbutton(self.gr3.f1, text="Write disulfide bridges", variable=self.writeSSbrige)
 318                 self.gr3.chk.pack(side=LEFT)
 319
 320                 # Sequence text
 321                 self.gr3.t1 = Pmw.ScrolledText(self.gr3.interior(),
 322                         columnheader = 1,
 323                         columnheader_width = 3,
 324                         rowheader = 1,
 325                         rowheader_width = 4,
 326                         usehullsize=1,
 327                         hull_width=30,
 328                         hull_height=180,
 329                         text_padx = 4,
 330                         text_pady = 4,
 331                         Header_padx = 4,
 332                         rowheader_pady = 4,
 333                 )
 334                 # Sequence text - create the header line
 335                 headerline = ''
 336                 for column in range(1,21):
 337                         headerline = headerline + ('%-4s' % str(column) )
 338                 self.gr3.t1.component('columnheader').insert('0.0',headerline)
 339
 340                 self.gr3.t1.pack(expand="yes",fill="both")
 341
 342                 # Add some buttons
 343                 btn3=Button(self, text='Write Input', padx=0, pady=0, command = self.ok)
 344                 btn3.grid(row=10, column=0, columnspan=2,sticky=N+W+S+E)
 345                 btn4=Button(self, text='Close', padx=0, pady=0, command = self.myHide)
 346                 btn4.grid(row=10, column=2, columnspan=2,sticky=N+W+S+E)
 347
 348                 # create callback to prevent window kill
 349                 self.protocol("WM_DELETE_WINDOW", self.myHide)
 350
 351         def ToggleColor(self):
 352                 if self.colorize.get()==1:
 353                         for i in range(0,len(self.res_states)):
 354                                 UNRESInpGenWindow.ccb[i].config(state=ACTIVE, bg=self.res_states[i][1], activebackground=self.res_states[i][1], relief=RAISED, overrelief=RAISED)
 355                 else:
 356                         for i in range(0,len(self.res_states)):
 357                                 UNRESInpGenWindow.ccb[i].config(state=DISABLED, bg=self.Default_Color , activebackground=self.Default_Color, relief=RAISED, overrelief=RAISED)
 358
 359         def myShow(self):
 360                 self.deiconify()
 361
 362         def myHide(self):
 363                 self.withdraw()
 364
 365         def myToggle(self):
 366                 if self.state() == "normal":
 367                         self.myHide()
 368                 elif self.state() == "withdrawn":
 369                         self.myShow()
 370
 371         def get_selections(self):
 372                 self.objects_list = []
 373                 for item in cmd.get_names("all"):
 374                         if cmd.get_type(item)=="object:molecule":
 375                                 self.objects_list.append(item)
 376                         if cmd.get_type(item)=="selection":
 377                                 if item[0]<>"_":
 378                                         self.objects_list.append(item)
 379
 380         def get_nonstandard(self):
 381                 stored.list=[]
 382                 cmd.iterate("(all)","stored.list.append(resn)")
 383                 stored.list=list(Set(stored.list))  # remove duplicates
 384                 # Remove standard amino acids and water from list
 385                 for m in ['HIS','ASP','ARG','PHE','ALA','CYS','GLY','GLN','GLU','LYS','LEU','MET','ASN','SER','TYR','THR','ILE','TRP','PRO','VAL','HOH']:
 386                         try:
 387                                 stored.list.remove(m)
 388                         except ValueError:
 389                                 pass
 390                 UNRESInpGenWindow.cbcr1.setlist(stored.list)
 391
 392         def refresh_list(self):
 393                 # Save old values
 394                 old = self.objects_list
 395                 try:
 396                         old_cb2=self.cb2.getvalue()[0]
 397                 except:
 398                         old_cb2=''
 399                 self.get_selections()
 400
 401                 # Update selectionlist if needed
 402                 if not(old==self.objects_list):
 403                         self.cb2.setlist(self.objects_list)
 404                         self.cb2.setlist(self.objects_list)
 405
 406                 if not(old_cb2 in self.objects_list):
 407                         # No - clear the combobox entry
 408                         self.cb2.component('entryfield').clear()
 409                 else:
 410                         # Yes - set the old value
 411                         self.cb2.selectitem(old_cb2,setentry=1)
 412
 413
 414         def get_seq(self):
 415                 # Get the number of chains
 416                 try:
 417                         nchains=int(len(cmd.get_chains(self.cb2.getvalue()[0])))
 418                 except:
 419                         nchains=0
 420                 pass
 421
 422                 if (nchains>0):
 423                         self.seq_list=[]
 424                 offset=0
 425                 seq_data=''
 426                 self.seq_length=0
 427                 for chain in range(0,nchains):
 428                         # Get only amonoacids, N-terminus acyl and C-terminus amide
 429                         # example:      (1uRC and chain F and (n. ca or (resn ACE and n. C) or (resn NH2 and n. N)))
 430                         # No chain information or only one chain
 431                         if nchains==1:
 432                                 atomchain=cmd.get_model(str(self.cb2.getvalue()[0])+" & (n. ca|(resn ACE & n. C)|(resn NH2+NHH+NME & n. N))").atom
 433                         # Chain information is present
 434                         else:
 435                                 atomchain=cmd.get_model(str(self.cb2.getvalue()[0])+" & chain "+cmd.get_chains(self.cb2.getvalue()[0])[chain]+" & (n. ca|(resn ACE & n. C)|(resn NH2+NHH+NME & n. N))").atom
 436                         # dodaj separator lancuchow
 437                         if chain>0:
 438                                 self.seq_list.append("D  ")
 439                                 self.seq_length+=1
 440
 441
 442                         # Zamiana chronionych
 443                         # ACE ALA ALA NH2 D   ACE ALA ALA NH2
 444                         # GLY ALA ALA GLY D   GLY ALA ALA GLY
 445                         # Zamiana niechronionych
 446                         #     ALA ALA     D       ALA ALA
 447                         # D   ALA ALA     D       ALA ALA D
 448                         #
 449                         # j - licznik pozycji reszty
 450                         j=0
 451                         for i in atomchain:
 452                                 self.seq_length+=1
 453                                 if str(i.resn)=="NH2":
 454                                         self.seq_list.append("GLY")
 455                                 elif str(i.resn)=="NHH":
 456                                         self.seq_list.append("GLY")
 457                                 elif str(i.resn)=="NME":
 458                                         self.seq_list.append("GLY")
 459                                 elif str(i.resn)=="ACE":
 460                                         self.seq_list.append("GLY")
 461                                 elif str(i.resn)=="GLY":
 462                                         self.seq_list.append("GLY")
 463                                 else:
 464                                         if j==0 and chain==0:
 465                                                 self.seq_list.append("D  ")
 466                                                 self.seq_list.append(str(i.resn))
 467                                                 self.seq_length+=1
 468                                         elif j==len(atomchain)-1 and chain==(nchains-1):
 469                                                 self.seq_list.append(str(i.resn))
 470                                                 self.seq_list.append("D  ")
 471                                                 self.seq_length+=1
 472                                         else:
 473                                                 self.seq_list.append(str(i.resn))
 474                                 j+=1
 475                 rows=0
 476                 #row_header='0'  - old header
 477                 row_header='1'
 478                 # tag setup
 479                 self.gr3.t1.tag_configure('dummy', background = 'LightBlue1')
 480                 tagList=[]
 481                 self.gr3.t1.tag_configure('cysteine', background = 'LightGoldenrod1')
 482                 CysTagList=[]
 483
 484                 for i in range(len(self.seq_list)):
 485                         # Dummy tag
 486                         if self.seq_list[i]=="D  ":
 487                                 tag1 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80))
 488                                 tag2 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80)+3)
 489                                 tagList.append(tag1)
 490                                 tagList.append(tag2)
 491                         # Cysteine tag
 492                         if self.seq_list[i]=="CYS" or self.seq_list[i]=="CYX":
 493                                 tag1 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80))
 494                                 tag2 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80)+3)
 495                                 CysTagList.append(tag1)
 496                                 CysTagList.append(tag2)
 497                         #
 498                         offset+=1
 499                         seq_data=seq_data+self.seq_list[i]+" "
 500                         # Line Wrap
 501                         if offset>19:
 502                                 offset=0
 503                                 seq_data=seq_data+'\n'
 504                                 rows+=1
 505                                 #row_header=row_header+'\n'+str(rows*20)    - old header
 506                                 row_header=row_header+'\n'+str(rows+1)
 507
 508                 self.gr3.t1.clear()
 509                 self.gr3.t1.insert('end',seq_data)
 510                 # Apply tags
 511                 if len(tagList):
 512                         apply(self.gr3.t1.tag_add, ('dummy',) + tuple(tagList))
 513                 if len(CysTagList):
 514                         apply(self.gr3.t1.tag_add, ('cysteine',) + tuple(CysTagList))
 515
 516                 # Show row header
 517                 self.gr3.t1.component('rowheader').delete(1.0, END)
 518                 self.gr3.t1.component('rowheader').insert('end',row_header)
 519
 520
 521         def switch_options(self,calctype):
 522                 '''
 523                         Displays the options available to set depending on the currently
 524                         selected calculation type
 525                 '''
 526                 # Hide all
 527                 self.gr1.th.grid_remove()
 528                 self.gr1.md.grid_remove()
 529                 if  self.OM1Val.get()=="MD":
 530                         self.gr1.md.grid(row=2, column=0, columnspan=5, sticky=W+E)
 531                         self.gr1.th.grid(row=3, column=0, columnspan=5, sticky=W+E)
 532
 533
 534         def set_force_field(self, pole):
 535                 '''
 536                         Enables/disables entryfields for force field perameters depending
 537                         on the currently selected force field
 538                 '''
 539                 for ff in self.force_fields:
 540                         if ff['FF']==pole:
 541                                 #print ff
 542                                 for i in range(0,len(self.weights)):
 543                                         if ff.has_key(self.weights[i]):
 544                                                 self.ef[i].setvalue(ff.get(self.weights[i]))
 545                                                 self.ef[i].component('entry').config(state=NORMAL)
 546                                         else:
 547                                                 self.ef[i].component('entry').config(state=DISABLED)
 548                         # Custom force field
 549                         elif pole=='Custom':
 550                                 for i in range(0,len(self.weights)):
 551                                         self.ef[i].component('entry').config(state=NORMAL)
 552
 553         def set_thermostat(self,thermostat):
 554                 '''
 555                         Display additional widget acording to selected thermostat
 556                 '''
 557                 #print thermostat
 558                 self.gr1.th.e2.pack_forget()
 559                 self.gr1.th.e3.pack_forget()
 560                 if thermostat=='Berendsen':
 561                         self.gr1.th.e2.pack(side=LEFT)
 562                 elif thermostat=='Nose-Poincare 1999' or thermostat=='Nose-Poincare 2001' or thermostat=='Nose-Hoover':
 563                         self.gr1.th.e3.pack(side=LEFT)
 564
 565         def fortran_format(self,s):
 566                 '''
 567                     Formats string containing keywords to wrap over 80 columns
 568                 '''
 569                 tmpstr=''
 570                 column=1
 571                 for k in s.split():
 572                         if column+len(k)+1<80:
 573                                 tmpstr+=k+' '
 574                                 column+=len(k)+1
 575                         else:
 576                                 tmpstr+=" "*(80-column)+"&\n"+k+" "
 577                                 column=len(k)+2
 578                 tmpstr+='\n'
 579                 return tmpstr
 580
 581         def get_weights(self):
 582                 '''
 583                         Get the force field weights
 584                 '''
 585                 s = ''
 586                 for i in range(0,len(self.weights)):
 587                         if self.ef[i].component('entry').cget("state")=="normal":
 588                                 s+=self.weights[i]+"="+self.ef[i].getvalue()+" "
 589                 return s
 590
 591         def get_md_opt(self):
 592                 s = "NSTEP="+self.gr1.md.e1.getvalue()+" NTWE="+self.gr1.md.e2.getvalue()+" "
 593                 s+= "NTWX="+self.gr1.md.e3.getvalue()+" DT="+self.gr1.md.e4.getvalue()+" "
 594                 s+= "DAMAX="+self.gr1.md.e5.getvalue()+" DVMAX="+self.gr1.md.e6.getvalue()+" "
 595                 s+= "RESET_VEL="+self.gr1.md.e7.getvalue()+" "
 596
 597                 # Thermostat options
 598                 term=self.gr1.th.optmenu1.getvalue()
 599                 #print term
 600                 if term=="Berendsen":
 601                         s+="TBF TAU_BATH="+self.gr1.th.e2.getvalue()+" "
 602                 elif term=="Nose-Poincare 1999":
 603                         s+="NOSEPOINCARE99 Q_NP="+self.gr1.th.e3.getvalue()+" "
 604                 elif term=="Nose-Poincare 2001":
 605                         s+="NOSEPOINCARE01 Q_NP="+self.gr1.th.e3.getvalue()+" "
 606                 elif term=="Nose-Hoover":
 607                         s+="NOSEHOOVER96 Q_NP="+self.gr1.th.e3.getvalue()+" "
 608                 elif term=="Langevin":
 609                         s+="LANG=1 "
 610
 611                 s+="T_BATH="+self.gr1.th.e1.getvalue()+" "
 612                 return s
 613
 614
 615         def get_seq_data(self):
 616                 '''
 617                         Dumps the sequence and disulfide bridge information
 618                 '''
 619                 # write sequence length
 620                 s = str(self.seq_length)+"\n"
 621                 #
 622                 #try:
 623                 #       nchains=int(len(cmd.get_chains(self.cb2.getvalue()[0])))
 624                 #except:
 625                 #       nchains=0
 626                 #pass
 627
 628                 chains=cmd.get_chains(self.cb2.getvalue()[0])
 629                 nchains=len(chains)
 630                 #print "chains  : ",chains
 631                 #print "nchains : ",nchains
 632
 633                 # apply one space before each sequence line
 634                 seq=self.gr3.t1.get()
 635                 for line in seq.split('\n'):
 636                         s+=" "+line+"\n"
 637                 # remove last newline character
 638                 s = s[:-1]
 639
 640                 # disulfide bridges - get half-cysteines by selection:
 641         # sele (bto. ((object) & r. CYS+CYX & n. SG) )& n. SG
 642                 ncys=cmd.get_model("(bto. (("+str(self.cb2.getvalue()[0])+") & r. CYS+CYX & n. SG)) & n. SG").atom
 643                 nSSbr=len(ncys)/2
 644
 645
 646                 # Is "Write disulfide brige" checked?
 647                 # yes
 648                 if self.writeSSbrige.get():
 649                         # write number of half-cysteines
 650                         s+=str(len(ncys))+"\n"
 651                         if len(ncys)==0:
 652                                 # No half-cysteines, cys position = 0
 653                                 s+=" 0\n"
 654                         else:
 655                                 # Write half-cysteine positions in sequence
 656                                 #
 657                                 # get first chain
 658                                 first=cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+str(chains[0])+" & n. ca")
 659
 660                                 # calculate base offset in first chain (if dummy atom present offset = 1 )
 661                                 if first.atom[0].resn=="GLY":
 662                                         boff=0
 663                                 else:
 664                                         boff=1
 665
 666                                 # create dictionary of PDB chain/resi to UNRES_index
 667                                 unresidx={}
 668                                 for c in ncys:
 669                                         # calculate residue index offset from first residue in chain containing half-cysteine
 670                                         fresinchain=cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+c.chain+" & n. ca").atom
 671                                         roff=int(c.resi)-int(fresinchain[0].resi)+1
 672
 673                                         resb=0
 674                                         coff=0
 675                                         for r in chains:
 676                                                 if c.chain==r:
 677                                                         break
 678                                                 resb+=len(cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+r+" & n. ca").atom)
 679                                                 coff+=1
 680                                         # add key/value to dictionary
 681                                         unresidx[c.chain+"/"+str(c.resi)]=boff+resb+coff+roff
 682                                         s+=" "+str(boff+resb+coff+roff)
 683                                 s+="\n"
 684
 685                                 # Write the number of disulfide bridges
 686                                 s+=" "+str(nSSbr)+"\n"
 687
 688                                 lista_mostkow=[]
 689                                 for c in ncys:
 690                                         # get neibhoring Sulfur atom
 691                                         opis=c.chain+str(c.resi)
 692                                         lista_mostkow.append(opis)
 693                                         nbr=cmd.get_model("(bto. ("+str(self.cb2.getvalue()[0])+" & resi "+str(c.resi)+"& n. SG & chain "+str(c.chain)+")) & n. SG").atom[0]
 694                                         opis2=nbr.chain+str(nbr.resi)
 695                                         if opis2 not in lista_mostkow:
 696                                                 # Write witch half-cysteines build the i-th disulfide bridge
 697                                                 s+=" "+str(unresidx[c.chain+"/"+str(c.resi)])+" "+str(unresidx[nbr.chain+"/"+str(nbr.resi)])+"\n"
 698                                                 #print c.chain, c.resn,c.resi,"-S-S-", nbr.chain, nbr.resn,nbr.resi
 699                 # Don't writeSSbrige
 700                 else:
 701                         s+="0\n 0\n"
 702
 703
 704                 return s
 705
 706
 707         def write_cshell(self, cshname,prefix):
 708                 '''
 709                         Writes the C-shell script needed to run UNRES calculations
 710                 '''
 711                 s='#!/bin/csh -f\n#\n# C-shell script generated by UNRESInpGen.py\n#\n'
 712
 713                 # number of processors per energy
 714                 if self.OM1Val.get()=="MD":
 715                         s+='setenv FGPROCS 1\n'
 716
 717                 # Potential
 718                 if self.OM2Val.get()=="CASP3":
 719                         s+='setenv POT LJ\n'
 720                 else:
 721                         s+='setenv POT GB\n'
 722
 723                 # input file
 724                 s+='setenv PREFIX '+prefix+'\n'
 725
 726                 # Parallel stuff
 727                 s+='setenv OUT1FILE YES\n'
 728
 729                 # force filed parameters
 730                 s+='#---------------------------------------------------------------------\n'
 731                 s+='setenv DD $UNRES_ROOT/PARAM\n'
 732
 733                 if self.OM2Val.get()=="CASP3":
 734                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 735                         s+='setenv TORPAR $DD/torsion_cryst.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_LJ.parm\n'
 736                         s+='setenv ELEPAR $DD/electr.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_GAP.parm\n'
 737                         s+='setenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 738                 elif self.OM2Val.get()=="ALPHA" or self.OM2Val.get()=="BETA" or self.OM2Val.get()=="ALPHABETA":
 739                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 740                         s+='setenv TORPAR $DD/torsion_ecepp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_GB.parm\n'
 741                         s+='setenv ELEPAR $DD/electr.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_GAP.parm\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 742                 elif self.OM2Val.get()=="CASP5":
 743                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 744                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_GB.parm\n'
 745                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_iter7n_c\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 746                 elif self.OM2Val.get()=="3P":
 747                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 748                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.3P7_iter81_1r\n'
 749                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 750                 elif self.OM2Val.get()=="4P":
 751                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 752                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.4P5_iter33_3r\n'
 753                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 754                 elif self.OM2Val.get()=="GAB":
 755                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 756                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k\n'
 757                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 758                 elif self.OM2Val.get()=="E0G":
 759                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 760                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.1e0g-52-17k-2k-newclass-shan1e9_gap8g-sc\n'
 761                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 762                 elif self.OM2Val.get()=="1L2Y_1LE1":
 763                         s+='setenv BONDPAR $DD/bond_AM1.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm\n'
 764                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_$POT.parm\n'
 765                         s+='setenv ELEPAR $DD/electr_631Gdp.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_opt.parm.1igd_hc_iter3_3\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 766                 elif self.OM2Val.get()=="Custom":
 767                         s+='setenv BONDPAR $DD/.parm\nsetenv THETPAR $DD/.parm\nsetenv ROTPAR $DD/.parm\n'
 768                         s+='setenv TORPAR $DD/.parm\nsetenv TORDPAR $DD/.parm\nsetenv SIDEPAR $DD/.parm\n'
 769                         s+='setenv ELEPAR $DD/.parm\nsetenv SCPPAR $DD/.parm\nsetenv FOURIER $DD/.parm\nsetenv SCCORPAR $DD/.parm\n'
 770
 771
 772
 773                 s+='setenv PATTERN $DD/patterns.cart\n'
 774                 s+='#---------------------------------------------------------------------\n'
 775                 s+='$UNRES_BIN $*\n'
 776
 777                 f = open(cshname, 'w')
 778                 f.write(s)
 779                 f.close()
 780
 781
 782         def setenv_info(self):
 783                 print '''IMPORTANT: Remember to set the following envirament variables for your shell before starting calculations:
 784                   UNRES_ROOT - the root directory where UNRES is installed on your system (should contain PARAM directory)
 785                   UNRES_BIN  - the UNRES binary you want to execute
 786                 '''
 787
 788
 789         def ok(self):
 790                 '''
 791                     Writes the actual input
 792                 '''
 793                 myFormats = [
 794                     ('Input files','*.inp'),
 795                         ('All files','*.*')
 796                 ]
 797                 # Write error handling for empty sequence
 798                 #
 799                 s=self.gr3.t1.getvalue()
 800                 if len(s.strip())==0:
 801                         tkMessageBox.showerror("NEED SEQUENCE DATA!", "NEED SEQUENCE DATA!\n\nYou have not loaded the sequence information. Please click \"Refresh\", choose an object from the list and click \"Get sequence\".")
 802                 else:
 803                         # Display dialog window
 804                         fout = tkFileDialog.asksaveasfile(parent=self,mode='w',filetypes=myFormats,title='Save input')
 805                         if fout:
 806                                 print "Saving input file %s" % fout.name
 807                                 # Get input header
 808                                 text2save=self.fortran_format(self.e1.get())
 809                                 # Get main options
 810                                 mainopt="SEED="+self.gr1.e1.get()+" "
 811                                 if self.OM1Val.get()=="MD":
 812                                         mainopt+="MD PDBREF EXTCONF"
 813                                 elif self.OM1Val.get()=="MREMD":
 814                                         mainopt+="RE "
 815                                 text2save+=self.fortran_format(mainopt)
 816                                 # Get aux options
 817
 818                                 if self.OM1Val.get()=="MD":
 819                                         text2save+=self.fortran_format(self.get_md_opt())
 820
 821                                 # Get force fields parameters
 822                                 text2save+=self.fortran_format(self.get_weights())
 823
 824                                 # PDB reference
 825                                 pdbreffn=str(self.cb2.getvalue()[0])+"_pdbref.pdb"
 826                                 text2save+=pdbreffn+"\n"
 827                                 print "Saving PDB reference structure %s" % (os.path.join(os.path.dirname(fout.name),pdbreffn))
 828                                 cmd.save(os.path.join(os.path.dirname(fout.name),pdbreffn), self.cb2.getvalue()[0])
 829
 830                                 # C-shell script
 831                                 cshellfn=os.path.join(os.path.dirname(fout.name),"unres_"+os.path.basename(os.path.splitext(fout.name)[0])+".csh")
 832                                 print "Writing C-shell script %s" % (cshellfn)
 833                                 prefix=os.path.basename(os.path.splitext(fout.name)[0])
 834                                 self.write_cshell(cshellfn,prefix)
 835
 836                                 # Get sequence data
 837                                 text2save+=self.get_seq_data()
 838
 839                                 fout.write(text2save)
 840                                 fout.close()
 841
 842                                 # ENV Varaiables info
 843                                 self.setenv_info()