1 # -*- coding: utf-8 -*-
3 -------------------------------------------------------------------------------
4 UNRESInpGen.py - UNRES graphical input generator v 1.0
5 -------------------------------------------------------------------------------
7 Written by Dawid Jagieła (lightnir@chem.univ.gda.pl) Oct 2012
11 from pymol import cmd,stored
19 UNRESInpGen_version="1.0"
22 self.UNRESInpGenWindow = None
24 self.menuBar.addcascademenu('Plugin', 'UNRESPlugins', 'UNRESPACK Plugins', label='UNRES Plugins')
28 self.menuBar.addmenuitem('UNRESPlugins', 'command','UNRESInpGen',
29 label='UNRES Input Generator',
30 command = lambda s=self: createUNRESInpGen(s) )
32 def createUNRESInpGen(app):
33 if (app.UNRESInpGenWindow == None):
34 app.UNRESInpGenWindow = UNRESInpGenerator(app)
36 app.UNRESInpGenWindow.myToggle()
38 #=================================================================
41 class UNRESInpGenerator(Toplevel):
42 global UNRESInpGen_version
52 writeSSbrige = IntVar()
58 objects_list = ['Select object']
62 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' ]
64 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',
65 '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'},
66 {'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',
67 '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'},
68 {'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',
69 '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'},
70 {'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',
71 'WTURN3':'2.36351', 'WTURN4':'1.34051', 'WTURN6':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
72 {'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',
73 'WTURN3':'2.99827', 'WTURN4':'0.59174', 'WTURN6':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
74 {'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',
75 'WTURN3':'2.00764', 'WTURN4':'0.05345', 'WTURN6':'0.05282', 'WSCCOR':'0.0', 'CUTOFF': '7.00000', 'WCORR4':'0.00000' },
76 {'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',
77 'WTURN4':'0.79171', 'WTURN6':'0.01074', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
78 {'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',
79 'WTURN4':'4.35377', 'WTURN6':'0.10000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
80 {'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',
81 'WTURN4':'0.55588', 'WTURN6':'0.11539', 'CUTOFF':'7.00000', 'WCORR4':'0.0000', 'WTORD':'0.00000', 'WSCCOR':'0.00000'},
82 {'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',
83 'WCORR6':'0.00000', 'SCAL14':'0.40000', 'SCALSCP':'1.00000', 'CUTOFF':'7.00000', 'WSCCOR':'0.00000'}
86 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'}
89 def __init__(self,parent):
90 # Create the GUI window
91 root = Toplevel.__init__(self)
92 self.config(width=400, height=300) # create a root window
93 self.title("UNRES Input Generator v"+UNRESInpGen_version) # Set window title
94 self.resizable(0, 0) # Disable window resize
95 self.geometry('-40+40') # Set window placement
98 self.balloon = Pmw.Balloon(root)
100 #================================
101 # "Main Options" group
103 self.gr1 = Pmw.Group(self,tag_text = 'Main options')
104 self.gr1.grid(row=0, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
106 # - Create title Entryfield & Label
107 #self.l1 = Label(self.gr1.interior(), text="Title:")
108 #self.l1.grid(row=0, column=0,sticky=E)
109 self.e1 = Pmw.EntryField(self.gr1.interior(),
112 validate = {'max': 80 },
113 # value ="(Place input information here)"
115 self.e1.component('entry').config(width=80)
116 self.e1.grid(row=0, column=0,columnspan=4, sticky=E)
118 # - Create "choose method" OptionMenu
119 self.OM1Val.set('MD')
120 self.optmenu1 = Pmw.OptionMenu(self.gr1.interior(),
122 label_text = 'Choose method:',
123 menubutton_textvariable = self.OM1Val,
124 items = ['MD', 'MREMD', 'MINIMIZE' ],
125 command = self.switch_options,
126 menubutton_width = 10
128 self.optmenu1.grid(row=1, column=0,columnspan=2, sticky=E)
132 self.gr1.e1 = Pmw.EntryField(self.gr1.interior(),
135 validate = {'validator' : 'integer', 'min': -2147483648 , 'max' : 0 },
138 self.gr1.e1.component('entry').config(width=8)
139 self.gr1.e1.grid(row=1, column=2, sticky=W)
141 #==================================
144 self.gr1.md = Frame(self.gr1.interior())
145 self.gr1.md.grid(row=2, column=0, columnspan=4,sticky=W+E)
147 # -- nstep entryfield
148 self.gr1.md.e1 = Pmw.EntryField(self.gr1.md,
151 validate = {'validator' : 'integer', 'min': 1 , 'max' : 1000000 },
154 self.balloon.bind(self.gr1.md.e1,'Number of calculation steps')
155 self.gr1.md.e1.component('entry').config(width=8)
156 self.gr1.md.e1.grid(row=0, column=0, sticky=E)
159 self.gr1.md.e2 = Pmw.EntryField(self.gr1.md,
162 validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
165 self.balloon.bind(self.gr1.md.e2,'Frequency of energy output.\nNTWE=0 means no energy dump. ')
166 self.gr1.md.e2.component('entry').config(width=8)
167 self.gr1.md.e2.grid(row=0,column=1, sticky=E)
170 self.gr1.md.e3 = Pmw.EntryField(self.gr1.md,
173 validate = {'validator' : 'integer', 'min': 1 , 'max' : 1000000 },
176 self.balloon.bind(self.gr1.md.e3, "Frequency of coordinate output.")
177 self.gr1.md.e3.component('entry').config(width=8)
178 self.gr1.md.e3.grid(row=0,column=2, sticky=E)
181 self.gr1.md.e4 = Pmw.EntryField(self.gr1.md,
184 validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
186 self.balloon.bind(self.gr1.md.e4, "Time step. \nThe unit is \"molecular time unit\" (mtu)\n 1 mtu = 48.9 fs")
187 self.gr1.md.e4.component('entry').config(width=8)
188 self.gr1.md.e4.grid(row=0,column=3, sticky=E)
190 # -- damax entryfield
191 self.gr1.md.e5 = Pmw.EntryField(self.gr1.md,
194 validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
196 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.")
197 self.gr1.md.e5.component('entry').config(width=8)
198 self.gr1.md.e5.grid(row=1,column=0, sticky=E)
200 # -- dvmax entryfield
201 self.gr1.md.e6 = Pmw.EntryField(self.gr1.md,
204 validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
206 self.balloon.bind(self.gr1.md.e6, "Maximum allowed velocity (in A/mtu).")
207 self.gr1.md.e6.component('entry').config(width=8)
208 self.gr1.md.e6.grid(row=1,column=1, sticky=E)
210 # -- restet_vel entryfield
211 self.gr1.md.e7 = Pmw.EntryField(self.gr1.md,
213 label_text="RESET_VEL",
214 validate = {'validator' : 'integer', 'min': 0 , 'max' : 10000000 },
216 self.balloon.bind(self.gr1.md.e7, "Frequency of resetting velocities to values from Gaussian distribution")
217 self.gr1.md.e7.component('entry').config(width=8)
218 self.gr1.md.e7.grid(row=1,column=2, sticky=E)
221 #=================================
224 self.gr1.th = Frame(self.gr1.interior())
225 self.gr1.th.grid(row=3, column=0, columnspan=5,sticky=W+E)
227 # -- Thermostat optionmenu
228 self.gr1.th.optmenu1 = Pmw.OptionMenu(self.gr1.th,
230 label_text = 'thermostat',
231 items = ['Berendsen', 'Nose-Poincare 1999','Nose-Poincare 2001', 'Nose-Hoover', 'Langevin' ],
232 command=self.set_thermostat,
233 menubutton_width = 15
235 self.gr1.th.optmenu1.pack(side=LEFT)#grid(row=0, column=0, sticky=E)
237 # -- t_bath entryfield
238 self.gr1.th.e1 = Pmw.EntryField(self.gr1.th,
241 validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 10000 },
243 self.balloon.bind(self.gr1.th.e1, "Temperature (in K) of canonical simulation.")
244 self.gr1.th.e1.component('entry').config(width=8)
245 self.gr1.th.e1.pack(side=LEFT)
247 # -- tau_bath entryfield
248 self.gr1.th.e2 = Pmw.EntryField(self.gr1.th,
250 label_text="TAU_BATH",
251 validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 1000000 },
253 self.balloon.bind(self.gr1.th.e2, "(units are mtus; 1mtu=48.9 fs) \nConstant of the coupling to the thermal bath")
254 self.gr1.th.e2.component('entry').config(width=8)
255 self.gr1.th.e2.pack(side=LEFT)
258 self.gr1.th.e3 = Pmw.EntryField(self.gr1.th,
261 validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 1000000 },
263 self.balloon.bind(self.gr1.th.e3, "Mass of the fictitious particle in the calculations with the Nose-Poincare & Nose-Hoover thermostats.")
264 self.gr1.th.e3.component('entry').config(width=8)
265 #self.gr1.th.e2.pack(side=LEFT)
268 #=================================
269 # - Minimization frame
270 self.gr1.mi = Frame(self.gr1.interior())
271 #self.gr1.mi.grid(row=4, column=0, columnspan=5,sticky=W+E)
273 self.gr1.mi.e1 = Pmw.EntryField(self.gr1.mi,
276 validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
278 self.balloon.bind(self.gr1.mi.e1,'Maximum number of iterations of the SUMSL minimizer.')
279 self.gr1.mi.e1.component('entry').config(width=8)
280 self.gr1.mi.e1.pack(side=LEFT)
282 self.gr1.mi.e2 = Pmw.EntryField(self.gr1.mi,
285 validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
287 self.balloon.bind(self.gr1.mi.e2,'Maximum number of function evaluations in a single minimization.')
288 self.gr1.mi.e2.component('entry').config(width=8)
289 self.gr1.mi.e2.pack(side=LEFT)
291 self.gr1.mi.c1 = Checkbutton(self.gr1.mi,
293 variable = self.CART )
294 self.balloon.bind(self.gr1.mi.c1,'Minimize in virtual-bond vectors instead of angles.')
295 self.gr1.mi.c1.pack(side=LEFT)
297 self.gr1.mi.c2 = Checkbutton(self.gr1.mi,
299 variable = self.OVERLAP )
300 self.balloon.bind(self.gr1.mi.c2,'Fix overlaping sidechains.')
301 self.gr1.mi.c2.pack(side=LEFT)
303 self.gr1.mi.c3 = Checkbutton(self.gr1.mi,
305 variable = self.NOSEARCHSC )
306 #self.balloon.bind(self.gr1.mi.c3,'Minimize in virtual-bond vectors instead of angles.')
307 self.gr1.mi.c3.pack(side=LEFT)
311 #=================================
312 # "Force field options" group
314 self.gr2 = Pmw.Group(self,tag_text = 'Force field options')
315 self.gr2.grid(row=2, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
317 # - Create "force field parameters" Option menu
318 self.OM2Val.set('Custom')
319 self.optmenu2 = Pmw.OptionMenu(self.gr2.interior(),
320 label_text = 'Force field parameters:',
322 menubutton_textvariable = self.OM2Val,
323 items = ['Custom','GAB','E0G', '1L2Y_1LE1','4P','3P','CASP5','ALPHABETA','BETA','ALPHA','CASP3' ],
324 initialitem = 'Custom',
325 menubutton_width = 10,
326 command=self.set_force_field
328 self.optmenu2.grid(row=0, column=0,columnspan=4,sticky=E)
330 # Force field parameters Entry Fields
332 for i in range(0,len(self.weights)):
333 self.ef.append(Pmw.EntryField(self.gr2.interior(),
335 label_text=self.weights[i],
336 validate = {'validator' : 'real','min' : 0, 'max' : 10, 'minstrict' : 0},
338 self.ef[i].component('entry').config(width=8)
339 self.ef[i].grid(row=1+(i//9), column=0+(i % 9))
341 self.gr3 = Pmw.Group(self,tag_text = 'Sequence')
342 self.gr3.grid(row=3, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
344 self.gr3.f1 = Frame(self.gr3.interior())
346 self.cb2 = Pmw.ComboBox(self.gr3.f1,
348 #entry_relief = 'raised',
349 label_text = 'Selection/Object',
350 scrolledlist_items = self.objects_list
352 self.cb2.pack(side=LEFT)
354 self.gr3.btn1 = Button(self.gr3.f1, text='Refresh', padx=0, pady=0 , command = self.refresh_list)
355 self.gr3.btn1.pack(side=LEFT)
356 # Get sequence button
357 self.gr3.btn2 = Button(self.gr3.f1, text='Get Sequence', padx=0, pady=0 , command = self.get_seq)
358 self.gr3.btn2.pack(side=LEFT)
360 self.gr3.f1.pack(expand="yes",fill="both")
362 # Disulfide brige checkbox
363 self.gr3.chk = Checkbutton(self.gr3.f1, text="Write disulfide bridges", variable=self.writeSSbrige)
364 self.gr3.chk.pack(side=LEFT)
367 self.gr3.t1 = Pmw.ScrolledText(self.gr3.interior(),
369 columnheader_width = 3,
380 # Sequence text - create the header line
382 for column in range(1,21):
383 headerline = headerline + ('%-4s' % str(column) )
384 self.gr3.t1.component('columnheader').insert('0.0',headerline)
386 self.gr3.t1.pack(expand="yes",fill="both")
389 btn3=Button(self, text='Write Input', padx=0, pady=0, command = self.ok)
390 btn3.grid(row=10, column=0, columnspan=2,sticky=N+W+S+E)
391 btn4=Button(self, text='Close', padx=0, pady=0, command = self.myHide)
392 btn4.grid(row=10, column=2, columnspan=2,sticky=N+W+S+E)
394 # create callback to prevent window kill
395 self.protocol("WM_DELETE_WINDOW", self.myHide)
397 def ToggleColor(self):
398 if self.colorize.get()==1:
399 for i in range(0,len(self.res_states)):
400 UNRESInpGenWindow.ccb[i].config(state=ACTIVE, bg=self.res_states[i][1], activebackground=self.res_states[i][1], relief=RAISED, overrelief=RAISED)
402 for i in range(0,len(self.res_states)):
403 UNRESInpGenWindow.ccb[i].config(state=DISABLED, bg=self.Default_Color , activebackground=self.Default_Color, relief=RAISED, overrelief=RAISED)
412 if self.state() == "normal":
414 elif self.state() == "withdrawn":
417 def get_selections(self):
418 self.objects_list = []
419 for item in cmd.get_names("all"):
420 if cmd.get_type(item)=="object:molecule":
421 self.objects_list.append(item)
422 if cmd.get_type(item)=="selection":
424 self.objects_list.append(item)
426 def get_nonstandard(self):
428 cmd.iterate("(all)","stored.list.append(resn)")
429 stored.list=list(Set(stored.list)) # remove duplicates
430 # Remove standard amino acids and water from list
431 for m in ['HIS','ASP','ARG','PHE','ALA','CYS','GLY','GLN','GLU','LYS','LEU','MET','ASN','SER','TYR','THR','ILE','TRP','PRO','VAL','HOH']:
433 stored.list.remove(m)
436 UNRESInpGenWindow.cbcr1.setlist(stored.list)
438 def refresh_list(self):
440 old = self.objects_list
442 old_cb2=self.cb2.getvalue()[0]
445 self.get_selections()
447 # Update selectionlist if needed
448 if not(old==self.objects_list):
449 self.cb2.setlist(self.objects_list)
450 self.cb2.setlist(self.objects_list)
452 if not(old_cb2 in self.objects_list):
453 # No - clear the combobox entry
454 self.cb2.component('entryfield').clear()
456 # Yes - set the old value
457 self.cb2.selectitem(old_cb2,setentry=1)
461 # Get the number of chains
463 nchains=int(len(cmd.get_chains(self.cb2.getvalue()[0])))
473 for chain in range(0,nchains):
474 # Get only amonoacids, N-terminus acyl and C-terminus amide
475 # example: (1uRC and chain F and (n. ca or (resn ACE and n. C) or (resn NH2 and n. N)))
476 # No chain information or only one chain
478 atomchain=cmd.get_model(str(self.cb2.getvalue()[0])+" & (n. ca|(resn ACE & n. C)|(resn NH2+NHH+NME & n. N))").atom
479 # Chain information is present
481 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
482 # dodaj separator lancuchow
484 self.seq_list.append("D ")
488 # Zamiana chronionych
489 # ACE ALA ALA NH2 D ACE ALA ALA NH2
490 # GLY ALA ALA GLY D GLY ALA ALA GLY
491 # Zamiana niechronionych
493 # D ALA ALA D ALA ALA D
495 # j - licznik pozycji reszty
499 if str(i.resn)=="NH2":
500 self.seq_list.append("GLY")
501 elif str(i.resn)=="NHH":
502 self.seq_list.append("GLY")
503 elif str(i.resn)=="NME":
504 self.seq_list.append("GLY")
505 elif str(i.resn)=="ACE":
506 self.seq_list.append("GLY")
507 elif str(i.resn)=="GLY":
508 self.seq_list.append("GLY")
510 if j==0 and chain==0:
511 self.seq_list.append("D ")
512 self.seq_list.append(str(i.resn))
514 elif j==len(atomchain)-1 and chain==(nchains-1):
515 self.seq_list.append(str(i.resn))
516 self.seq_list.append("D ")
519 self.seq_list.append(str(i.resn))
522 #row_header='0' - old header
525 self.gr3.t1.tag_configure('dummy', background = 'LightBlue1')
527 self.gr3.t1.tag_configure('cysteine', background = 'LightGoldenrod1')
530 for i in range(len(self.seq_list)):
532 if self.seq_list[i]=="D ":
533 tag1 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80))
534 tag2 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80)+3)
538 if self.seq_list[i]=="CYS" or self.seq_list[i]=="CYX":
539 tag1 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80))
540 tag2 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80)+3)
541 CysTagList.append(tag1)
542 CysTagList.append(tag2)
545 seq_data=seq_data+self.seq_list[i]+" "
549 seq_data=seq_data+'\n'
551 #row_header=row_header+'\n'+str(rows*20) - old header
552 row_header=row_header+'\n'+str(rows+1)
555 self.gr3.t1.insert('end',seq_data)
558 apply(self.gr3.t1.tag_add, ('dummy',) + tuple(tagList))
560 apply(self.gr3.t1.tag_add, ('cysteine',) + tuple(CysTagList))
563 self.gr3.t1.component('rowheader').delete(1.0, END)
564 self.gr3.t1.component('rowheader').insert('end',row_header)
567 def switch_options(self,calctype):
569 Displays the options available to set depending on the currently
570 selected calculation type
573 self.gr1.th.grid_remove()
574 self.gr1.md.grid_remove()
575 self.gr1.mi.grid_remove()
577 if self.OM1Val.get()=="MD":
578 self.gr1.md.grid(row=2, column=0, columnspan=5, sticky=W+E)
579 self.gr1.th.grid(row=3, column=0, columnspan=5, sticky=W+E)
580 elif self.OM1Val.get()=="MINIMIZE":
581 self.gr1.mi.grid(row=4,column=0,columnspan=5, sticky=W+E)
584 def set_force_field(self, pole):
586 Enables/disables entryfields for force field perameters depending
587 on the currently selected force field
589 for ff in self.force_fields:
592 for i in range(0,len(self.weights)):
593 if ff.has_key(self.weights[i]):
594 self.ef[i].setvalue(ff.get(self.weights[i]))
595 self.ef[i].component('entry').config(state=NORMAL)
597 self.ef[i].component('entry').config(state=DISABLED)
600 for i in range(0,len(self.weights)):
601 self.ef[i].component('entry').config(state=NORMAL)
603 def set_thermostat(self,thermostat):
605 Display additional widget acording to selected thermostat
608 self.gr1.th.e2.pack_forget()
609 self.gr1.th.e3.pack_forget()
610 if thermostat=='Berendsen':
611 self.gr1.th.e2.pack(side=LEFT)
612 elif thermostat=='Nose-Poincare 1999' or thermostat=='Nose-Poincare 2001' or thermostat=='Nose-Hoover':
613 self.gr1.th.e3.pack(side=LEFT)
615 def fortran_format(self,s):
617 Formats string containing keywords to wrap over 80 columns
622 if column+len(k)+1<80:
626 tmpstr+=" "*(80-column)+"&\n"+k+" "
631 def get_weights(self):
633 Get the force field weights
636 for i in range(0,len(self.weights)):
637 if self.ef[i].component('entry').cget("state")=="normal":
638 s+=self.weights[i]+"="+self.ef[i].getvalue()+" "
641 def get_md_opt(self):
642 s = "NSTEP="+self.gr1.md.e1.getvalue()+" NTWE="+self.gr1.md.e2.getvalue()+" "
643 s+= "NTWX="+self.gr1.md.e3.getvalue()+" DT="+self.gr1.md.e4.getvalue()+" "
644 s+= "DAMAX="+self.gr1.md.e5.getvalue()+" DVMAX="+self.gr1.md.e6.getvalue()+" "
645 s+= "RESET_VEL="+self.gr1.md.e7.getvalue()+" "
648 term=self.gr1.th.optmenu1.getvalue()
650 if term=="Berendsen":
651 s+="TBF TAU_BATH="+self.gr1.th.e2.getvalue()+" "
652 elif term=="Nose-Poincare 1999":
653 s+="NOSEPOINCARE99 Q_NP="+self.gr1.th.e3.getvalue()+" "
654 elif term=="Nose-Poincare 2001":
655 s+="NOSEPOINCARE01 Q_NP="+self.gr1.th.e3.getvalue()+" "
656 elif term=="Nose-Hoover":
657 s+="NOSEHOOVER96 Q_NP="+self.gr1.th.e3.getvalue()+" "
658 elif term=="Langevin":
661 s+="T_BATH="+self.gr1.th.e1.getvalue()+" "
664 def get_minim_opt(self):
665 s = "MAXMIN="+self.gr1.mi.e1.getvalue()+" MAXFUN="+self.gr1.mi.e2.getvalue()
669 def get_seq_data(self):
671 Dumps the sequence and disulfide bridge information
673 # write sequence length
674 s = str(self.seq_length)+"\n"
677 # nchains=int(len(cmd.get_chains(self.cb2.getvalue()[0])))
682 chains=cmd.get_chains(self.cb2.getvalue()[0])
684 #print "chains : ",chains
685 #print "nchains : ",nchains
687 # apply one space before each sequence line
688 seq=self.gr3.t1.get()
689 for line in seq.split('\n'):
691 # remove last newline character
694 # disulfide bridges - get half-cysteines by selection:
695 # sele (bto. ((object) & r. CYS+CYX & n. SG) )& n. SG
696 ncys=cmd.get_model("(bto. (("+str(self.cb2.getvalue()[0])+") & r. CYS+CYX & n. SG)) & n. SG").atom
700 # Is "Write disulfide brige" checked?
702 if self.writeSSbrige.get():
703 # write number of half-cysteines
704 s+=str(len(ncys))+"\n"
706 # No half-cysteines, cys position = 0
709 # Write half-cysteine positions in sequence
712 first=cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+str(chains[0])+" & n. ca")
714 # calculate base offset in first chain (if dummy atom present offset = 1 )
715 if first.atom[0].resn=="GLY":
720 # create dictionary of PDB chain/resi to UNRES_index
723 # calculate residue index offset from first residue in chain containing half-cysteine
724 fresinchain=cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+c.chain+" & n. ca").atom
725 roff=int(c.resi)-int(fresinchain[0].resi)+1
732 resb+=len(cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+r+" & n. ca").atom)
734 # add key/value to dictionary
735 unresidx[c.chain+"/"+str(c.resi)]=boff+resb+coff+roff
736 s+=" "+str(boff+resb+coff+roff)
739 # Write the number of disulfide bridges
740 s+=" "+str(nSSbr)+"\n"
744 # get neibhoring Sulfur atom
745 opis=c.chain+str(c.resi)
746 lista_mostkow.append(opis)
747 nbr=cmd.get_model("(bto. ("+str(self.cb2.getvalue()[0])+" & resi "+str(c.resi)+"& n. SG & chain "+str(c.chain)+")) & n. SG").atom[0]
748 opis2=nbr.chain+str(nbr.resi)
749 if opis2 not in lista_mostkow:
750 # Write witch half-cysteines build the i-th disulfide bridge
751 s+=" "+str(unresidx[c.chain+"/"+str(c.resi)])+" "+str(unresidx[nbr.chain+"/"+str(nbr.resi)])+"\n"
752 #print c.chain, c.resn,c.resi,"-S-S-", nbr.chain, nbr.resn,nbr.resi
761 def write_cshell(self, cshname,prefix):
763 Writes the C-shell script needed to run UNRES calculations
765 s='#!/bin/csh -f\n#\n# C-shell script generated by UNRESInpGen.py\n#\n'
767 # number of processors per energy
768 if self.OM1Val.get()=="MD":
769 s+='setenv FGPROCS 1\n'
772 if self.OM2Val.get()=="CASP3":
778 s+='setenv PREFIX '+prefix+'\n'
781 s+='setenv OUT1FILE YES\n'
783 # force filed parameters
784 s+='#---------------------------------------------------------------------\n'
785 s+='setenv DD $UNRES_ROOT/PARAM\n'
787 if self.OM2Val.get()=="CASP3":
788 s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
789 s+='setenv TORPAR $DD/torsion_cryst.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_LJ.parm\n'
790 s+='setenv ELEPAR $DD/electr.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_GAP.parm\n'
791 s+='setenv SCCORPAR $DD/rotcorr_AM1.parm\n'
792 elif self.OM2Val.get()=="ALPHA" or self.OM2Val.get()=="BETA" or self.OM2Val.get()=="ALPHABETA":
793 s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
794 s+='setenv TORPAR $DD/torsion_ecepp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_GB.parm\n'
795 s+='setenv ELEPAR $DD/electr.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_GAP.parm\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
796 elif self.OM2Val.get()=="CASP5":
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/scinter_GB.parm\n'
799 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'
800 elif self.OM2Val.get()=="3P":
801 s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
802 s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.3P7_iter81_1r\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()=="4P":
805 s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
806 s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.4P5_iter33_3r\n'
807 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'
808 elif self.OM2Val.get()=="GAB":
809 s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
810 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'
811 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'
812 elif self.OM2Val.get()=="E0G":
813 s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
814 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'
815 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'
816 elif self.OM2Val.get()=="1L2Y_1LE1":
817 s+='setenv BONDPAR $DD/bond_AM1.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm\n'
818 s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_$POT.parm\n'
819 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'
820 elif self.OM2Val.get()=="Custom":
821 s+='setenv BONDPAR $DD/.parm\nsetenv THETPAR $DD/.parm\nsetenv ROTPAR $DD/.parm\n'
822 s+='setenv TORPAR $DD/.parm\nsetenv TORDPAR $DD/.parm\nsetenv SIDEPAR $DD/.parm\n'
823 s+='setenv ELEPAR $DD/.parm\nsetenv SCPPAR $DD/.parm\nsetenv FOURIER $DD/.parm\nsetenv SCCORPAR $DD/.parm\n'
827 s+='setenv PATTERN $DD/patterns.cart\n'
828 s+='#---------------------------------------------------------------------\n'
831 f = open(cshname, 'w')
836 def setenv_info(self):
837 print '''IMPORTANT: Remember to set the following envirament variables for your shell before starting calculations:
838 UNRES_ROOT - the root directory where UNRES is installed on your system (should contain PARAM directory)
839 UNRES_BIN - the UNRES binary you want to execute
845 Writes the actual input
848 ('Input files','*.inp'),
851 # Write error handling for empty sequence
853 s=self.gr3.t1.getvalue()
854 if len(s.strip())==0:
855 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\".")
857 # Display dialog window
858 fout = tkFileDialog.asksaveasfile(parent=self,mode='w',filetypes=myFormats,title='Save input')
860 print "Saving input file %s" % fout.name
862 text2save=self.fortran_format(self.e1.get())
864 mainopt="SEED="+self.gr1.e1.get()+" "
865 if self.OM1Val.get()=="MD":
866 mainopt+="MD PDBREF EXTCONF"
867 elif self.OM1Val.get()=="MREMD":
869 elif self.OM1Val.get()=="MINIMIZE":
870 mainopt+="PDBREF MINIMIZE RESCALE_MODE=0"
873 if self.OVERLAP.get():
875 if self.NOSEARCHSC.get():
876 mainopt+=" NOSERARCHSC"
877 text2save+=self.fortran_format(mainopt)
880 if self.OM1Val.get()=="MD":
881 text2save+=self.fortran_format(self.get_md_opt())
882 elif self.OM1Val.get()=="MINIMIZE":
883 text2save+=self.fortran_format(self.get_minim_opt())
885 # Get force fields parameters
886 text2save+=self.fortran_format(self.get_weights())
889 pdbreffn=str(self.cb2.getvalue()[0])+"_pdbref.pdb"
890 text2save+=pdbreffn+"\n"
891 print "Saving PDB reference structure %s" % (os.path.join(os.path.dirname(fout.name),pdbreffn))
892 cmd.save(os.path.join(os.path.dirname(fout.name),pdbreffn), self.cb2.getvalue()[0])
895 cshellfn=os.path.join(os.path.dirname(fout.name),"unres_"+os.path.basename(os.path.splitext(fout.name)[0])+".csh")
896 print "Writing C-shell script %s" % (cshellfn)
897 prefix=os.path.basename(os.path.splitext(fout.name)[0])
898 self.write_cshell(cshellfn,prefix)
901 text2save+=self.get_seq_data()
903 fout.write(text2save)
906 # ENV Varaiables info