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         CART = IntVar()
  56         objects_list = ['Select object']
  57         seq_list=[]
  58         seq_length=0
  59
  60         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' ]
  61
  62         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',
  63                                         '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'},
  64                     {'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',
  65                                         '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'},
  66                     {'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',
  67                                         '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'},
  68                     {'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',
  69                                         'WTURN3':'2.36351', 'WTURN4':'1.34051', 'WTURN6':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  70                     {'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',
  71                                         'WTURN3':'2.99827', 'WTURN4':'0.59174', 'WTURN6':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  72                         {'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',
  73                                         'WTURN3':'2.00764', 'WTURN4':'0.05345', 'WTURN6':'0.05282', 'WSCCOR':'0.0', 'CUTOFF': '7.00000', 'WCORR4':'0.00000' },
  74                         {'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',
  75                                         'WTURN4':'0.79171', 'WTURN6':'0.01074', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  76                         {'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',
  77                                         'WTURN4':'4.35377', 'WTURN6':'0.10000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
  78                         {'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',
  79                                         'WTURN4':'0.55588', 'WTURN6':'0.11539', 'CUTOFF':'7.00000', 'WCORR4':'0.0000', 'WTORD':'0.00000', 'WSCCOR':'0.00000'},
  80                         {'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',
  81                                         'WCORR6':'0.00000', 'SCAL14':'0.40000', 'SCALSCP':'1.00000', 'CUTOFF':'7.00000', 'WSCCOR':'0.00000'}
  82         ]
  83
  84         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'}
  85
  86
  87         def __init__(self,parent):
  88                 # Create the GUI window
  89                 root = Toplevel.__init__(self)
  90                 self.config(width=400, height=300)              # create a root window
  91                 self.title("UNRES Input Generator v"+UNRESInpGen_version)                 # Set window title
  92                 self.resizable(0, 0)                                # Disable window resize
  93                 self.geometry('-40+40')                             # Set window placement
  94
  95                 # Create the Balloon.
  96                 self.balloon = Pmw.Balloon(root)
  97
  98                 #================================
  99                 # "Main Options" group
 100                 #
 101                 self.gr1 = Pmw.Group(self,tag_text = 'Main options')
 102                 self.gr1.grid(row=0, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
 103
 104                 # - Create title Entryfield & Label
 105                 #self.l1 = Label(self.gr1.interior(), text="Title:")
 106                 #self.l1.grid(row=0, column=0,sticky=E)
 107                 self.e1 = Pmw.EntryField(self.gr1.interior(),
 108                         labelpos='w',
 109                         label_text="Title:",
 110                         validate = {'max': 80 },
 111                 #       value ="(Place input information here)"
 112                 )
 113                 self.e1.component('entry').config(width=80)
 114                 self.e1.grid(row=0, column=0,columnspan=4, sticky=E)
 115
 116                 # - Create "choose method" OptionMenu
 117                 self.OM1Val.set('MD')
 118                 self.optmenu1 =  Pmw.OptionMenu(self.gr1.interior(),
 119                         labelpos = 'w',
 120                         label_text = 'Choose method:',
 121                         menubutton_textvariable = self.OM1Val,
 122                         items = ['MD', 'MREMD', 'MINIMIZE' ],
 123                         command = self.switch_options,
 124                         menubutton_width = 10
 125                 )
 126                 self.optmenu1.grid(row=1, column=0,columnspan=2, sticky=E)
 127
 128
 129                 # - Seed entryfield
 130                 self.gr1.e1 = Pmw.EntryField(self.gr1.interior(),
 131                         labelpos='w',
 132                         label_text="Seed",
 133                         validate = {'validator' : 'integer', 'min': -2147483648 , 'max' : 0 },
 134                         value = "-1111333"
 135                 )
 136                 self.gr1.e1.component('entry').config(width=8)
 137                 self.gr1.e1.grid(row=1, column=2, sticky=W)
 138
 139                 #==================================
 140                 # - MD options frame
 141                 #
 142                 self.gr1.md = Frame(self.gr1.interior())
 143                 self.gr1.md.grid(row=2, column=0, columnspan=4,sticky=W+E)
 144
 145                 # -- nstep entryfield
 146                 self.gr1.md.e1 = Pmw.EntryField(self.gr1.md,
 147                         labelpos='w',
 148                         label_text="NSTEP",
 149                         validate = {'validator' : 'integer', 'min': 1 , 'max' : 1000000 },
 150                         value = "500000"
 151                 )
 152                 self.balloon.bind(self.gr1.md.e1,'Number of calculation steps')
 153                 self.gr1.md.e1.component('entry').config(width=8)
 154                 self.gr1.md.e1.grid(row=0, column=0, sticky=E)
 155
 156                 # -- ntwe entryfield
 157                 self.gr1.md.e2 = Pmw.EntryField(self.gr1.md,
 158                         labelpos='w',
 159                         label_text="NTWE",
 160                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
 161                         value = "100"
 162                 )
 163                 self.balloon.bind(self.gr1.md.e2,'Frequency of energy output.\nNTWE=0 means no energy dump. ')
 164                 self.gr1.md.e2.component('entry').config(width=8)
 165                 self.gr1.md.e2.grid(row=0,column=1, sticky=E)
 166
 167                 # -- ntwx entryfield
 168                 self.gr1.md.e3 = Pmw.EntryField(self.gr1.md,
 169                         labelpos='w',
 170                         label_text="NTWX",
 171                         validate = {'validator' : 'integer', 'min': 1 , 'max' : 1000000 },
 172                         value = "1000"
 173                 )
 174                 self.balloon.bind(self.gr1.md.e3, "Frequency of coordinate output.")
 175                 self.gr1.md.e3.component('entry').config(width=8)
 176                 self.gr1.md.e3.grid(row=0,column=2, sticky=E)
 177
 178                 # -- dt entryfield
 179                 self.gr1.md.e4 = Pmw.EntryField(self.gr1.md,
 180                         labelpos='w',
 181                         label_text="DT",
 182                         validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
 183                         value = "0.1")
 184                 self.balloon.bind(self.gr1.md.e4, "Time step. \nThe unit is \"molecular time unit\" (mtu)\n 1 mtu = 48.9 fs")
 185                 self.gr1.md.e4.component('entry').config(width=8)
 186                 self.gr1.md.e4.grid(row=0,column=3, sticky=E)
 187
 188                 # -- damax entryfield
 189                 self.gr1.md.e5 = Pmw.EntryField(self.gr1.md,
 190                         labelpos='w',
 191                         label_text="DAMAX",
 192                         validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
 193                         value = "1.0")
 194                 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.")
 195                 self.gr1.md.e5.component('entry').config(width=8)
 196                 self.gr1.md.e5.grid(row=1,column=0, sticky=E)
 197
 198                 # -- dvmax entryfield
 199                 self.gr1.md.e6 = Pmw.EntryField(self.gr1.md,
 200                         labelpos='w',
 201                         label_text="DVMAX",
 202                         validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
 203                         value = "20.0")
 204                 self.balloon.bind(self.gr1.md.e6, "Maximum allowed velocity (in A/mtu).")
 205                 self.gr1.md.e6.component('entry').config(width=8)
 206                 self.gr1.md.e6.grid(row=1,column=1, sticky=E)
 207
 208                 # -- restet_vel entryfield
 209                 self.gr1.md.e7 = Pmw.EntryField(self.gr1.md,
 210                         labelpos='w',
 211                         label_text="RESET_VEL",
 212                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 10000000 },
 213                         value = "1000")
 214                 self.balloon.bind(self.gr1.md.e7, "Frequency of resetting velocities to values from Gaussian distribution")
 215                 self.gr1.md.e7.component('entry').config(width=8)
 216                 self.gr1.md.e7.grid(row=1,column=2, sticky=E)
 217
 218
 219                 #=================================
 220                 #  - thermostat frame
 221                 #
 222                 self.gr1.th = Frame(self.gr1.interior())
 223                 self.gr1.th.grid(row=3, column=0, columnspan=5,sticky=W+E)
 224
 225                 # -- Thermostat optionmenu
 226                 self.gr1.th.optmenu1 =  Pmw.OptionMenu(self.gr1.th,
 227                         labelpos = 'w',
 228                         label_text = 'thermostat',
 229                         items = ['Berendsen', 'Nose-Poincare 1999','Nose-Poincare 2001', 'Nose-Hoover', 'Langevin' ],
 230                         command=self.set_thermostat,
 231                         menubutton_width = 15
 232                 )
 233                 self.gr1.th.optmenu1.pack(side=LEFT)#grid(row=0, column=0, sticky=E)
 234
 235                 # -- t_bath entryfield
 236                 self.gr1.th.e1 = Pmw.EntryField(self.gr1.th,
 237                         labelpos='w',
 238                         label_text="T_BATH",
 239                         validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 10000 },
 240                         value = "300.0")
 241                 self.balloon.bind(self.gr1.th.e1, "Temperature (in K) of canonical simulation.")
 242                 self.gr1.th.e1.component('entry').config(width=8)
 243                 self.gr1.th.e1.pack(side=LEFT)
 244
 245                 # -- tau_bath entryfield
 246                 self.gr1.th.e2 = Pmw.EntryField(self.gr1.th,
 247                         labelpos='w',
 248                         label_text="TAU_BATH",
 249                         validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 1000000 },
 250                         value = "1.0")
 251                 self.balloon.bind(self.gr1.th.e2, "(units are mtus; 1mtu=48.9 fs) \nConstant of the coupling to the thermal bath")
 252                 self.gr1.th.e2.component('entry').config(width=8)
 253                 self.gr1.th.e2.pack(side=LEFT)
 254
 255                 # -- q_np entryfield
 256                 self.gr1.th.e3 = Pmw.EntryField(self.gr1.th,
 257                         labelpos='w',
 258                         label_text="Q_NP",
 259                         validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 1000000 },
 260                         value = "0.1")
 261                 self.balloon.bind(self.gr1.th.e3, "Mass of the fictitious particle in the calculations with the Nose-Poincare & Nose-Hoover thermostats.")
 262                 self.gr1.th.e3.component('entry').config(width=8)
 263                 #self.gr1.th.e2.pack(side=LEFT)
 264
 265
 266                 #=================================
 267                 # - Minimization frame
 268                 self.gr1.mi = Frame(self.gr1.interior())
 269                 #self.gr1.mi.grid(row=4, column=0, columnspan=5,sticky=W+E)
 270
 271                 self.gr1.mi.e1 = Pmw.EntryField(self.gr1.mi,
 272                         labelpos='w',
 273                         label_text="MAXMIN",
 274                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
 275                         value = "2000" )
 276                 self.balloon.bind(self.gr1.mi.e1,'Maximum number of iterations of the SUMSL minimizer.')
 277                 self.gr1.mi.e1.component('entry').config(width=8)
 278                 self.gr1.mi.e1.pack(side=LEFT)
 279
 280                 self.gr1.mi.e2 = Pmw.EntryField(self.gr1.mi,
 281                         labelpos='w',
 282                         label_text="MAXFUN",
 283                         validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
 284                         value = "5000" )
 285                 self.balloon.bind(self.gr1.mi.e2,'Maximum number of function evaluations in a single minimization.')
 286                 self.gr1.mi.e2.component('entry').config(width=8)
 287                 self.gr1.mi.e2.pack(side=LEFT)
 288
 289                 self.gr1.mi.c1 = Checkbutton(self.gr1.mi,
 290                         text = "CART",
 291                         variable = self.CART )
 292                 self.balloon.bind(self.gr1.mi.c1,'Minimize in virtual-bond vectors instead of angles.')
 293                 self.gr1.mi.c1.pack(side=LEFT)
 294
 295                 #=================================
 296                 # "Force field options" group
 297                 #
 298                 self.gr2 = Pmw.Group(self,tag_text = 'Force field options')
 299                 self.gr2.grid(row=2, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
 300
 301                 # - Create "force field parameters" Option menu
 302                 self.OM2Val.set('Custom')
 303                 self.optmenu2 = Pmw.OptionMenu(self.gr2.interior(),
 304                 label_text = 'Force field parameters:',
 305                         labelpos = 'w',
 306                         menubutton_textvariable = self.OM2Val,
 307                         items = ['Custom','GAB','E0G', '1L2Y_1LE1','4P','3P','CASP5','ALPHABETA','BETA','ALPHA','CASP3' ],
 308                         initialitem = 'Custom',
 309                         menubutton_width = 10,
 310                         command=self.set_force_field
 311                 )
 312                 self.optmenu2.grid(row=0, column=0,columnspan=4,sticky=E)
 313
 314                 # Force field parameters Entry Fields
 315                 self.ef = []
 316                 for i in range(0,len(self.weights)):
 317                         self.ef.append(Pmw.EntryField(self.gr2.interior(),
 318                         labelpos='n',
 319                         label_text=self.weights[i],
 320                         validate = {'validator' : 'real','min' : 0, 'max' : 10, 'minstrict' : 0},
 321                         value = '1.00000'))
 322                         self.ef[i].component('entry').config(width=8)
 323                         self.ef[i].grid(row=1+(i//9), column=0+(i % 9))
 324                 # "Sequence" group
 325                 self.gr3 = Pmw.Group(self,tag_text = 'Sequence')
 326                 self.gr3.grid(row=3, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
 327
 328                 self.gr3.f1 = Frame(self.gr3.interior())
 329                 # Object List
 330                 self.cb2 = Pmw.ComboBox(self.gr3.f1,
 331                         labelpos = 'w',
 332                         #entry_relief = 'raised',
 333                         label_text = 'Selection/Object',
 334                         scrolledlist_items = self.objects_list
 335                 )
 336                 self.cb2.pack(side=LEFT)
 337                 # refresh button
 338                 self.gr3.btn1 = Button(self.gr3.f1, text='Refresh', padx=0, pady=0 , command = self.refresh_list)
 339                 self.gr3.btn1.pack(side=LEFT)
 340                 # Get sequence button
 341                 self.gr3.btn2 = Button(self.gr3.f1, text='Get Sequence', padx=0, pady=0 , command = self.get_seq)
 342                 self.gr3.btn2.pack(side=LEFT)
 343
 344                 self.gr3.f1.pack(expand="yes",fill="both")
 345
 346                 # Disulfide brige checkbox
 347                 self.gr3.chk = Checkbutton(self.gr3.f1, text="Write disulfide bridges", variable=self.writeSSbrige)
 348                 self.gr3.chk.pack(side=LEFT)
 349
 350                 # Sequence text
 351                 self.gr3.t1 = Pmw.ScrolledText(self.gr3.interior(),
 352                         columnheader = 1,
 353                         columnheader_width = 3,
 354                         rowheader = 1,
 355                         rowheader_width = 4,
 356                         usehullsize=1,
 357                         hull_width=30,
 358                         hull_height=180,
 359                         text_padx = 4,
 360                         text_pady = 4,
 361                         Header_padx = 4,
 362                         rowheader_pady = 4,
 363                 )
 364                 # Sequence text - create the header line
 365                 headerline = ''
 366                 for column in range(1,21):
 367                         headerline = headerline + ('%-4s' % str(column) )
 368                 self.gr3.t1.component('columnheader').insert('0.0',headerline)
 369
 370                 self.gr3.t1.pack(expand="yes",fill="both")
 371
 372                 # Add some buttons
 373                 btn3=Button(self, text='Write Input', padx=0, pady=0, command = self.ok)
 374                 btn3.grid(row=10, column=0, columnspan=2,sticky=N+W+S+E)
 375                 btn4=Button(self, text='Close', padx=0, pady=0, command = self.myHide)
 376                 btn4.grid(row=10, column=2, columnspan=2,sticky=N+W+S+E)
 377
 378                 # create callback to prevent window kill
 379                 self.protocol("WM_DELETE_WINDOW", self.myHide)
 380
 381         def ToggleColor(self):
 382                 if self.colorize.get()==1:
 383                         for i in range(0,len(self.res_states)):
 384                                 UNRESInpGenWindow.ccb[i].config(state=ACTIVE, bg=self.res_states[i][1], activebackground=self.res_states[i][1], relief=RAISED, overrelief=RAISED)
 385                 else:
 386                         for i in range(0,len(self.res_states)):
 387                                 UNRESInpGenWindow.ccb[i].config(state=DISABLED, bg=self.Default_Color , activebackground=self.Default_Color, relief=RAISED, overrelief=RAISED)
 388
 389         def myShow(self):
 390                 self.deiconify()
 391
 392         def myHide(self):
 393                 self.withdraw()
 394
 395         def myToggle(self):
 396                 if self.state() == "normal":
 397                         self.myHide()
 398                 elif self.state() == "withdrawn":
 399                         self.myShow()
 400
 401         def get_selections(self):
 402                 self.objects_list = []
 403                 for item in cmd.get_names("all"):
 404                         if cmd.get_type(item)=="object:molecule":
 405                                 self.objects_list.append(item)
 406                         if cmd.get_type(item)=="selection":
 407                                 if item[0]<>"_":
 408                                         self.objects_list.append(item)
 409
 410         def get_nonstandard(self):
 411                 stored.list=[]
 412                 cmd.iterate("(all)","stored.list.append(resn)")
 413                 stored.list=list(Set(stored.list))  # remove duplicates
 414                 # Remove standard amino acids and water from list
 415                 for m in ['HIS','ASP','ARG','PHE','ALA','CYS','GLY','GLN','GLU','LYS','LEU','MET','ASN','SER','TYR','THR','ILE','TRP','PRO','VAL','HOH']:
 416                         try:
 417                                 stored.list.remove(m)
 418                         except ValueError:
 419                                 pass
 420                 UNRESInpGenWindow.cbcr1.setlist(stored.list)
 421
 422         def refresh_list(self):
 423                 # Save old values
 424                 old = self.objects_list
 425                 try:
 426                         old_cb2=self.cb2.getvalue()[0]
 427                 except:
 428                         old_cb2=''
 429                 self.get_selections()
 430
 431                 # Update selectionlist if needed
 432                 if not(old==self.objects_list):
 433                         self.cb2.setlist(self.objects_list)
 434                         self.cb2.setlist(self.objects_list)
 435
 436                 if not(old_cb2 in self.objects_list):
 437                         # No - clear the combobox entry
 438                         self.cb2.component('entryfield').clear()
 439                 else:
 440                         # Yes - set the old value
 441                         self.cb2.selectitem(old_cb2,setentry=1)
 442
 443
 444         def get_seq(self):
 445                 # Get the number of chains
 446                 try:
 447                         nchains=int(len(cmd.get_chains(self.cb2.getvalue()[0])))
 448                 except:
 449                         nchains=0
 450                 pass
 451
 452                 if (nchains>0):
 453                         self.seq_list=[]
 454                 offset=0
 455                 seq_data=''
 456                 self.seq_length=0
 457                 for chain in range(0,nchains):
 458                         # Get only amonoacids, N-terminus acyl and C-terminus amide
 459                         # example:      (1uRC and chain F and (n. ca or (resn ACE and n. C) or (resn NH2 and n. N)))
 460                         # No chain information or only one chain
 461                         if nchains==1:
 462                                 atomchain=cmd.get_model(str(self.cb2.getvalue()[0])+" & (n. ca|(resn ACE & n. C)|(resn NH2+NHH+NME & n. N))").atom
 463                         # Chain information is present
 464                         else:
 465                                 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
 466                         # dodaj separator lancuchow
 467                         if chain>0:
 468                                 self.seq_list.append("D  ")
 469                                 self.seq_length+=1
 470
 471
 472                         # Zamiana chronionych
 473                         # ACE ALA ALA NH2 D   ACE ALA ALA NH2
 474                         # GLY ALA ALA GLY D   GLY ALA ALA GLY
 475                         # Zamiana niechronionych
 476                         #     ALA ALA     D       ALA ALA
 477                         # D   ALA ALA     D       ALA ALA D
 478                         #
 479                         # j - licznik pozycji reszty
 480                         j=0
 481                         for i in atomchain:
 482                                 self.seq_length+=1
 483                                 if str(i.resn)=="NH2":
 484                                         self.seq_list.append("GLY")
 485                                 elif str(i.resn)=="NHH":
 486                                         self.seq_list.append("GLY")
 487                                 elif str(i.resn)=="NME":
 488                                         self.seq_list.append("GLY")
 489                                 elif str(i.resn)=="ACE":
 490                                         self.seq_list.append("GLY")
 491                                 elif str(i.resn)=="GLY":
 492                                         self.seq_list.append("GLY")
 493                                 else:
 494                                         if j==0 and chain==0:
 495                                                 self.seq_list.append("D  ")
 496                                                 self.seq_list.append(str(i.resn))
 497                                                 self.seq_length+=1
 498                                         elif j==len(atomchain)-1 and chain==(nchains-1):
 499                                                 self.seq_list.append(str(i.resn))
 500                                                 self.seq_list.append("D  ")
 501                                                 self.seq_length+=1
 502                                         else:
 503                                                 self.seq_list.append(str(i.resn))
 504                                 j+=1
 505                 rows=0
 506                 #row_header='0'  - old header
 507                 row_header='1'
 508                 # tag setup
 509                 self.gr3.t1.tag_configure('dummy', background = 'LightBlue1')
 510                 tagList=[]
 511                 self.gr3.t1.tag_configure('cysteine', background = 'LightGoldenrod1')
 512                 CysTagList=[]
 513
 514                 for i in range(len(self.seq_list)):
 515                         # Dummy tag
 516                         if self.seq_list[i]=="D  ":
 517                                 tag1 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80))
 518                                 tag2 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80)+3)
 519                                 tagList.append(tag1)
 520                                 tagList.append(tag2)
 521                         # Cysteine tag
 522                         if self.seq_list[i]=="CYS" or self.seq_list[i]=="CYX":
 523                                 tag1 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80))
 524                                 tag2 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80)+3)
 525                                 CysTagList.append(tag1)
 526                                 CysTagList.append(tag2)
 527                         #
 528                         offset+=1
 529                         seq_data=seq_data+self.seq_list[i]+" "
 530                         # Line Wrap
 531                         if offset>19:
 532                                 offset=0
 533                                 seq_data=seq_data+'\n'
 534                                 rows+=1
 535                                 #row_header=row_header+'\n'+str(rows*20)    - old header
 536                                 row_header=row_header+'\n'+str(rows+1)
 537
 538                 self.gr3.t1.clear()
 539                 self.gr3.t1.insert('end',seq_data)
 540                 # Apply tags
 541                 if len(tagList):
 542                         apply(self.gr3.t1.tag_add, ('dummy',) + tuple(tagList))
 543                 if len(CysTagList):
 544                         apply(self.gr3.t1.tag_add, ('cysteine',) + tuple(CysTagList))
 545
 546                 # Show row header
 547                 self.gr3.t1.component('rowheader').delete(1.0, END)
 548                 self.gr3.t1.component('rowheader').insert('end',row_header)
 549
 550
 551         def switch_options(self,calctype):
 552                 '''
 553                         Displays the options available to set depending on the currently
 554                         selected calculation type
 555                 '''
 556                 # Hide all
 557                 self.gr1.th.grid_remove()
 558                 self.gr1.md.grid_remove()
 559                 self.gr1.mi.grid_remove()
 560                 # Show MD stuff
 561                 if  self.OM1Val.get()=="MD":
 562                         self.gr1.md.grid(row=2, column=0, columnspan=5, sticky=W+E)
 563                         self.gr1.th.grid(row=3, column=0, columnspan=5, sticky=W+E)
 564                 elif self.OM1Val.get()=="MINIMIZE":
 565                         self.gr1.mi.grid(row=4,column=0,columnspan=5, sticky=W+E)
 566
 567
 568         def set_force_field(self, pole):
 569                 '''
 570                         Enables/disables entryfields for force field perameters depending
 571                         on the currently selected force field
 572                 '''
 573                 for ff in self.force_fields:
 574                         if ff['FF']==pole:
 575                                 #print ff
 576                                 for i in range(0,len(self.weights)):
 577                                         if ff.has_key(self.weights[i]):
 578                                                 self.ef[i].setvalue(ff.get(self.weights[i]))
 579                                                 self.ef[i].component('entry').config(state=NORMAL)
 580                                         else:
 581                                                 self.ef[i].component('entry').config(state=DISABLED)
 582                         # Custom force field
 583                         elif pole=='Custom':
 584                                 for i in range(0,len(self.weights)):
 585                                         self.ef[i].component('entry').config(state=NORMAL)
 586
 587         def set_thermostat(self,thermostat):
 588                 '''
 589                         Display additional widget acording to selected thermostat
 590                 '''
 591                 #print thermostat
 592                 self.gr1.th.e2.pack_forget()
 593                 self.gr1.th.e3.pack_forget()
 594                 if thermostat=='Berendsen':
 595                         self.gr1.th.e2.pack(side=LEFT)
 596                 elif thermostat=='Nose-Poincare 1999' or thermostat=='Nose-Poincare 2001' or thermostat=='Nose-Hoover':
 597                         self.gr1.th.e3.pack(side=LEFT)
 598
 599         def fortran_format(self,s):
 600                 '''
 601                     Formats string containing keywords to wrap over 80 columns
 602                 '''
 603                 tmpstr=''
 604                 column=1
 605                 for k in s.split():
 606                         if column+len(k)+1<80:
 607                                 tmpstr+=k+' '
 608                                 column+=len(k)+1
 609                         else:
 610                                 tmpstr+=" "*(80-column)+"&\n"+k+" "
 611                                 column=len(k)+2
 612                 tmpstr+='\n'
 613                 return tmpstr
 614
 615         def get_weights(self):
 616                 '''
 617                         Get the force field weights
 618                 '''
 619                 s = ''
 620                 for i in range(0,len(self.weights)):
 621                         if self.ef[i].component('entry').cget("state")=="normal":
 622                                 s+=self.weights[i]+"="+self.ef[i].getvalue()+" "
 623                 return s
 624
 625         def get_md_opt(self):
 626                 s = "NSTEP="+self.gr1.md.e1.getvalue()+" NTWE="+self.gr1.md.e2.getvalue()+" "
 627                 s+= "NTWX="+self.gr1.md.e3.getvalue()+" DT="+self.gr1.md.e4.getvalue()+" "
 628                 s+= "DAMAX="+self.gr1.md.e5.getvalue()+" DVMAX="+self.gr1.md.e6.getvalue()+" "
 629                 s+= "RESET_VEL="+self.gr1.md.e7.getvalue()+" "
 630
 631                 # Thermostat options
 632                 term=self.gr1.th.optmenu1.getvalue()
 633                 #print term
 634                 if term=="Berendsen":
 635                         s+="TBF TAU_BATH="+self.gr1.th.e2.getvalue()+" "
 636                 elif term=="Nose-Poincare 1999":
 637                         s+="NOSEPOINCARE99 Q_NP="+self.gr1.th.e3.getvalue()+" "
 638                 elif term=="Nose-Poincare 2001":
 639                         s+="NOSEPOINCARE01 Q_NP="+self.gr1.th.e3.getvalue()+" "
 640                 elif term=="Nose-Hoover":
 641                         s+="NOSEHOOVER96 Q_NP="+self.gr1.th.e3.getvalue()+" "
 642                 elif term=="Langevin":
 643                         s+="LANG=1 "
 644
 645                 s+="T_BATH="+self.gr1.th.e1.getvalue()+" "
 646                 return s
 647
 648         def get_minim_opt(self):
 649                 s = "MAXMIN="+self.gr1.mi.e1.getvalue()+" MAXFUN="+self.gr1.mi.e2.getvalue()
 650                 return s
 651
 652
 653         def get_seq_data(self):
 654                 '''
 655                         Dumps the sequence and disulfide bridge information
 656                 '''
 657                 # write sequence length
 658                 s = str(self.seq_length)+"\n"
 659                 #
 660                 #try:
 661                 #       nchains=int(len(cmd.get_chains(self.cb2.getvalue()[0])))
 662                 #except:
 663                 #       nchains=0
 664                 #pass
 665
 666                 chains=cmd.get_chains(self.cb2.getvalue()[0])
 667                 nchains=len(chains)
 668                 #print "chains  : ",chains
 669                 #print "nchains : ",nchains
 670
 671                 # apply one space before each sequence line
 672                 seq=self.gr3.t1.get()
 673                 for line in seq.split('\n'):
 674                         s+=" "+line+"\n"
 675                 # remove last newline character
 676                 s = s[:-1]
 677
 678                 # disulfide bridges - get half-cysteines by selection:
 679         # sele (bto. ((object) & r. CYS+CYX & n. SG) )& n. SG
 680                 ncys=cmd.get_model("(bto. (("+str(self.cb2.getvalue()[0])+") & r. CYS+CYX & n. SG)) & n. SG").atom
 681                 nSSbr=len(ncys)/2
 682
 683
 684                 # Is "Write disulfide brige" checked?
 685                 # yes
 686                 if self.writeSSbrige.get():
 687                         # write number of half-cysteines
 688                         s+=str(len(ncys))+"\n"
 689                         if len(ncys)==0:
 690                                 # No half-cysteines, cys position = 0
 691                                 s+=" 0\n"
 692                         else:
 693                                 # Write half-cysteine positions in sequence
 694                                 #
 695                                 # get first chain
 696                                 first=cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+str(chains[0])+" & n. ca")
 697
 698                                 # calculate base offset in first chain (if dummy atom present offset = 1 )
 699                                 if first.atom[0].resn=="GLY":
 700                                         boff=0
 701                                 else:
 702                                         boff=1
 703
 704                                 # create dictionary of PDB chain/resi to UNRES_index
 705                                 unresidx={}
 706                                 for c in ncys:
 707                                         # calculate residue index offset from first residue in chain containing half-cysteine
 708                                         fresinchain=cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+c.chain+" & n. ca").atom
 709                                         roff=int(c.resi)-int(fresinchain[0].resi)+1
 710
 711                                         resb=0
 712                                         coff=0
 713                                         for r in chains:
 714                                                 if c.chain==r:
 715                                                         break
 716                                                 resb+=len(cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+r+" & n. ca").atom)
 717                                                 coff+=1
 718                                         # add key/value to dictionary
 719                                         unresidx[c.chain+"/"+str(c.resi)]=boff+resb+coff+roff
 720                                         s+=" "+str(boff+resb+coff+roff)
 721                                 s+="\n"
 722
 723                                 # Write the number of disulfide bridges
 724                                 s+=" "+str(nSSbr)+"\n"
 725
 726                                 lista_mostkow=[]
 727                                 for c in ncys:
 728                                         # get neibhoring Sulfur atom
 729                                         opis=c.chain+str(c.resi)
 730                                         lista_mostkow.append(opis)
 731                                         nbr=cmd.get_model("(bto. ("+str(self.cb2.getvalue()[0])+" & resi "+str(c.resi)+"& n. SG & chain "+str(c.chain)+")) & n. SG").atom[0]
 732                                         opis2=nbr.chain+str(nbr.resi)
 733                                         if opis2 not in lista_mostkow:
 734                                                 # Write witch half-cysteines build the i-th disulfide bridge
 735                                                 s+=" "+str(unresidx[c.chain+"/"+str(c.resi)])+" "+str(unresidx[nbr.chain+"/"+str(nbr.resi)])+"\n"
 736                                                 #print c.chain, c.resn,c.resi,"-S-S-", nbr.chain, nbr.resn,nbr.resi
 737                 # Don't writeSSbrige
 738                 else:
 739                         s+="0\n 0\n"
 740
 741
 742                 return s
 743
 744
 745         def write_cshell(self, cshname,prefix):
 746                 '''
 747                         Writes the C-shell script needed to run UNRES calculations
 748                 '''
 749                 s='#!/bin/csh -f\n#\n# C-shell script generated by UNRESInpGen.py\n#\n'
 750
 751                 # number of processors per energy
 752                 if self.OM1Val.get()=="MD":
 753                         s+='setenv FGPROCS 1\n'
 754
 755                 # Potential
 756                 if self.OM2Val.get()=="CASP3":
 757                         s+='setenv POT LJ\n'
 758                 else:
 759                         s+='setenv POT GB\n'
 760
 761                 # input file
 762                 s+='setenv PREFIX '+prefix+'\n'
 763
 764                 # Parallel stuff
 765                 s+='setenv OUT1FILE YES\n'
 766
 767                 # force filed parameters
 768                 s+='#---------------------------------------------------------------------\n'
 769                 s+='setenv DD $UNRES_ROOT/PARAM\n'
 770
 771                 if self.OM2Val.get()=="CASP3":
 772                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 773                         s+='setenv TORPAR $DD/torsion_cryst.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_LJ.parm\n'
 774                         s+='setenv ELEPAR $DD/electr.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_GAP.parm\n'
 775                         s+='setenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 776                 elif self.OM2Val.get()=="ALPHA" or self.OM2Val.get()=="BETA" or self.OM2Val.get()=="ALPHABETA":
 777                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 778                         s+='setenv TORPAR $DD/torsion_ecepp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_GB.parm\n'
 779                         s+='setenv ELEPAR $DD/electr.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_GAP.parm\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
 780                 elif self.OM2Val.get()=="CASP5":
 781                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 782                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_GB.parm\n'
 783                         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'
 784                 elif self.OM2Val.get()=="3P":
 785                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 786                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.3P7_iter81_1r\n'
 787                         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'
 788                 elif self.OM2Val.get()=="4P":
 789                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 790                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.4P5_iter33_3r\n'
 791                         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'
 792                 elif self.OM2Val.get()=="GAB":
 793                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 794                         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'
 795                         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'
 796                 elif self.OM2Val.get()=="E0G":
 797                         s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
 798                         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'
 799                         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'
 800                 elif self.OM2Val.get()=="1L2Y_1LE1":
 801                         s+='setenv BONDPAR $DD/bond_AM1.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm\n'
 802                         s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_$POT.parm\n'
 803                         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'
 804                 elif self.OM2Val.get()=="Custom":
 805                         s+='setenv BONDPAR $DD/.parm\nsetenv THETPAR $DD/.parm\nsetenv ROTPAR $DD/.parm\n'
 806                         s+='setenv TORPAR $DD/.parm\nsetenv TORDPAR $DD/.parm\nsetenv SIDEPAR $DD/.parm\n'
 807                         s+='setenv ELEPAR $DD/.parm\nsetenv SCPPAR $DD/.parm\nsetenv FOURIER $DD/.parm\nsetenv SCCORPAR $DD/.parm\n'
 808
 809
 810
 811                 s+='setenv PATTERN $DD/patterns.cart\n'
 812                 s+='#---------------------------------------------------------------------\n'
 813                 s+='$UNRES_BIN $*\n'
 814
 815                 f = open(cshname, 'w')
 816                 f.write(s)
 817                 f.close()
 818
 819
 820         def setenv_info(self):
 821                 print '''IMPORTANT: Remember to set the following envirament variables for your shell before starting calculations:
 822                   UNRES_ROOT - the root directory where UNRES is installed on your system (should contain PARAM directory)
 823                   UNRES_BIN  - the UNRES binary you want to execute
 824                 '''
 825
 826
 827         def ok(self):
 828                 '''
 829                     Writes the actual input
 830                 '''
 831                 myFormats = [
 832                     ('Input files','*.inp'),
 833                         ('All files','*.*')
 834                 ]
 835                 # Write error handling for empty sequence
 836                 #
 837                 s=self.gr3.t1.getvalue()
 838                 if len(s.strip())==0:
 839                         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\".")
 840                 else:
 841                         # Display dialog window
 842                         fout = tkFileDialog.asksaveasfile(parent=self,mode='w',filetypes=myFormats,title='Save input')
 843                         if fout:
 844                                 print "Saving input file %s" % fout.name
 845                                 # Get input header
 846                                 text2save=self.fortran_format(self.e1.get())
 847                                 # Get main options
 848                                 mainopt="SEED="+self.gr1.e1.get()+" "
 849                                 if self.OM1Val.get()=="MD":
 850                                         mainopt+="MD PDBREF EXTCONF"
 851                                 elif self.OM1Val.get()=="MREMD":
 852                                         mainopt+="RE "
 853                                 elif self.OM1Val.get()=="MINIMIZE":
 854                                         mainopt+="PDBREF MINIMIZE "
 855                                         if self.CART.get():
 856                                                 mainopt+=" CART"
 857                                 text2save+=self.fortran_format(mainopt)
 858                                 # Get aux options
 859
 860                                 if self.OM1Val.get()=="MD":
 861                                         text2save+=self.fortran_format(self.get_md_opt())
 862                                 elif self.OM1Val.get()=="MINIMIZE":
 863                                         text2save+=self.fortran_format(self.get_minim_opt())
 864
 865                                 # Get force fields parameters
 866                                 text2save+=self.fortran_format(self.get_weights())
 867
 868                                 # PDB reference
 869                                 pdbreffn=str(self.cb2.getvalue()[0])+"_pdbref.pdb"
 870                                 text2save+=pdbreffn+"\n"
 871                                 print "Saving PDB reference structure %s" % (os.path.join(os.path.dirname(fout.name),pdbreffn))
 872                                 cmd.save(os.path.join(os.path.dirname(fout.name),pdbreffn), self.cb2.getvalue()[0])
 873
 874                                 # C-shell script
 875                                 cshellfn=os.path.join(os.path.dirname(fout.name),"unres_"+os.path.basename(os.path.splitext(fout.name)[0])+".csh")
 876                                 print "Writing C-shell script %s" % (cshellfn)
 877                                 prefix=os.path.basename(os.path.splitext(fout.name)[0])
 878                                 self.write_cshell(cshellfn,prefix)
 879
 880                                 # Get sequence data
 881                                 text2save+=self.get_seq_data()
 882
 883                                 fout.write(text2save)
 884                                 fout.close()
 885
 886                                 # ENV Varaiables info
 887                                 self.setenv_info()