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()
55 objects_list = ['Select object']
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' ]
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'}
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'}
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
95 self.balloon = Pmw.Balloon(root)
97 #================================
98 # "Main Options" group
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)
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(),
109 validate = {'max': 80 },
110 # value ="(Place input information here)"
112 self.e1.component('entry').config(width=80)
113 self.e1.grid(row=0, column=0,columnspan=4, sticky=E)
115 # - Create "choose method" OptionMenu
116 self.OM1Val.set('MD')
117 self.optmenu1 = Pmw.OptionMenu(self.gr1.interior(),
119 label_text = 'Choose method:',
120 menubutton_textvariable = self.OM1Val,
121 items = ['MD', 'MREMD' ],
122 command = self.switch_options,
123 menubutton_width = 10
125 self.optmenu1.grid(row=1, column=0,columnspan=2, sticky=E)
129 self.gr1.e1 = Pmw.EntryField(self.gr1.interior(),
132 validate = {'validator' : 'integer', 'min': -2147483648 , 'max' : 0 },
135 self.gr1.e1.component('entry').config(width=8)
136 self.gr1.e1.grid(row=1, column=2, sticky=W)
138 #==================================
141 self.gr1.md = Frame(self.gr1.interior())
142 self.gr1.md.grid(row=2, column=0, columnspan=4,sticky=W+E)
144 # -- nstep entryfield
145 self.gr1.md.e1 = Pmw.EntryField(self.gr1.md,
148 validate = {'validator' : 'integer', 'min': 1 , 'max' : 1000000 },
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)
156 self.gr1.md.e2 = Pmw.EntryField(self.gr1.md,
159 validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
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)
167 self.gr1.md.e3 = Pmw.EntryField(self.gr1.md,
170 validate = {'validator' : 'integer', 'min': 1 , 'max' : 1000000 },
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)
178 self.gr1.md.e4 = Pmw.EntryField(self.gr1.md,
181 validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
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)
187 # -- damax entryfield
188 self.gr1.md.e5 = Pmw.EntryField(self.gr1.md,
191 validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
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)
197 # -- dvmax entryfield
198 self.gr1.md.e6 = Pmw.EntryField(self.gr1.md,
201 validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
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)
207 # -- restet_vel entryfield
208 self.gr1.md.e7 = Pmw.EntryField(self.gr1.md,
210 label_text="RESET_VEL",
211 validate = {'validator' : 'integer', 'min': 0 , 'max' : 10000000 },
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)
218 #=================================
221 self.gr1.th = Frame(self.gr1.interior())
222 self.gr1.th.grid(row=3, column=0, columnspan=5,sticky=W+E)
224 # -- Thermostat optionmenu
225 self.gr1.th.optmenu1 = Pmw.OptionMenu(self.gr1.th,
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
232 self.gr1.th.optmenu1.pack(side=LEFT)#grid(row=0, column=0, sticky=E)
234 # -- t_bath entryfield
235 self.gr1.th.e1 = Pmw.EntryField(self.gr1.th,
238 validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 10000 },
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)
244 # -- tau_bath entryfield
245 self.gr1.th.e2 = Pmw.EntryField(self.gr1.th,
247 label_text="TAU_BATH",
248 validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 1000000 },
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)
255 self.gr1.th.e3 = Pmw.EntryField(self.gr1.th,
258 validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 1000000 },
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)
265 #=================================
266 # "Force field options" group
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)
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:',
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
282 self.optmenu2.grid(row=0, column=0,columnspan=4,sticky=E)
284 # Force field parameters Entry Fields
286 for i in range(0,len(self.weights)):
287 self.ef.append(Pmw.EntryField(self.gr2.interior(),
289 label_text=self.weights[i],
290 validate = {'validator' : 'real','min' : 0, 'max' : 10, 'minstrict' : 0},
292 self.ef[i].component('entry').config(width=8)
293 self.ef[i].grid(row=1+(i//9), column=0+(i % 9))
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)
298 self.gr3.f1 = Frame(self.gr3.interior())
300 self.cb2 = Pmw.ComboBox(self.gr3.f1,
302 #entry_relief = 'raised',
303 label_text = 'Selection/Object',
304 scrolledlist_items = self.objects_list
306 self.cb2.pack(side=LEFT)
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)
314 self.gr3.f1.pack(expand="yes",fill="both")
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)
321 self.gr3.t1 = Pmw.ScrolledText(self.gr3.interior(),
323 columnheader_width = 3,
334 # Sequence text - create the header line
336 for column in range(1,21):
337 headerline = headerline + ('%-4s' % str(column) )
338 self.gr3.t1.component('columnheader').insert('0.0',headerline)
340 self.gr3.t1.pack(expand="yes",fill="both")
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)
348 # create callback to prevent window kill
349 self.protocol("WM_DELETE_WINDOW", self.myHide)
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)
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)
366 if self.state() == "normal":
368 elif self.state() == "withdrawn":
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":
378 self.objects_list.append(item)
380 def get_nonstandard(self):
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']:
387 stored.list.remove(m)
390 UNRESInpGenWindow.cbcr1.setlist(stored.list)
392 def refresh_list(self):
394 old = self.objects_list
396 old_cb2=self.cb2.getvalue()[0]
399 self.get_selections()
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)
406 if not(old_cb2 in self.objects_list):
407 # No - clear the combobox entry
408 self.cb2.component('entryfield').clear()
410 # Yes - set the old value
411 self.cb2.selectitem(old_cb2,setentry=1)
415 # Get the number of chains
417 nchains=int(len(cmd.get_chains(self.cb2.getvalue()[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
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
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
438 self.seq_list.append("D ")
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
447 # D ALA ALA D ALA ALA D
449 # j - licznik pozycji reszty
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")
464 if j==0 and chain==0:
465 self.seq_list.append("D ")
466 self.seq_list.append(str(i.resn))
468 elif j==len(atomchain)-1 and chain==(nchains-1):
469 self.seq_list.append(str(i.resn))
470 self.seq_list.append("D ")
473 self.seq_list.append(str(i.resn))
476 #row_header='0' - old header
479 self.gr3.t1.tag_configure('dummy', background = 'LightBlue1')
481 self.gr3.t1.tag_configure('cysteine', background = 'LightGoldenrod1')
484 for i in range(len(self.seq_list)):
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)
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)
499 seq_data=seq_data+self.seq_list[i]+" "
503 seq_data=seq_data+'\n'
505 #row_header=row_header+'\n'+str(rows*20) - old header
506 row_header=row_header+'\n'+str(rows+1)
509 self.gr3.t1.insert('end',seq_data)
512 apply(self.gr3.t1.tag_add, ('dummy',) + tuple(tagList))
514 apply(self.gr3.t1.tag_add, ('cysteine',) + tuple(CysTagList))
517 self.gr3.t1.component('rowheader').delete(1.0, END)
518 self.gr3.t1.component('rowheader').insert('end',row_header)
521 def switch_options(self,calctype):
523 Displays the options available to set depending on the currently
524 selected calculation type
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)
534 def set_force_field(self, pole):
536 Enables/disables entryfields for force field perameters depending
537 on the currently selected force field
539 for ff in self.force_fields:
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)
547 self.ef[i].component('entry').config(state=DISABLED)
550 for i in range(0,len(self.weights)):
551 self.ef[i].component('entry').config(state=NORMAL)
553 def set_thermostat(self,thermostat):
555 Display additional widget acording to selected 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)
565 def fortran_format(self,s):
567 Formats string containing keywords to wrap over 80 columns
572 if column+len(k)+1<80:
576 tmpstr+=" "*(80-column)+"&\n"+k+" "
581 def get_weights(self):
583 Get the force field weights
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()+" "
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()+" "
598 term=self.gr1.th.optmenu1.getvalue()
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":
611 s+="T_BATH="+self.gr1.th.e1.getvalue()+" "
615 def get_seq_data(self):
617 Dumps the sequence and disulfide bridge information
619 # write sequence length
620 s = str(self.seq_length)+"\n"
623 # nchains=int(len(cmd.get_chains(self.cb2.getvalue()[0])))
628 chains=cmd.get_chains(self.cb2.getvalue()[0])
630 #print "chains : ",chains
631 #print "nchains : ",nchains
633 # apply one space before each sequence line
634 seq=self.gr3.t1.get()
635 for line in seq.split('\n'):
637 # remove last newline character
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
646 # Is "Write disulfide brige" checked?
648 if self.writeSSbrige.get():
649 # write number of half-cysteines
650 s+=str(len(ncys))+"\n"
652 # No half-cysteines, cys position = 0
655 # Write half-cysteine positions in sequence
658 first=cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+str(chains[0])+" & n. ca")
660 # calculate base offset in first chain (if dummy atom present offset = 1 )
661 if first.atom[0].resn=="GLY":
666 # create dictionary of PDB chain/resi to UNRES_index
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
678 resb+=len(cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+r+" & n. ca").atom)
680 # add key/value to dictionary
681 unresidx[c.chain+"/"+str(c.resi)]=boff+resb+coff+roff
682 s+=" "+str(boff+resb+coff+roff)
685 # Write the number of disulfide bridges
686 s+=" "+str(nSSbr)+"\n"
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
707 def write_cshell(self, cshname,prefix):
709 Writes the C-shell script needed to run UNRES calculations
711 s='#!/bin/csh -f\n#\n# C-shell script generated by UNRESInpGen.py\n#\n'
713 # number of processors per energy
714 if self.OM1Val.get()=="MD":
715 s+='setenv FGPROCS 1\n'
718 if self.OM2Val.get()=="CASP3":
724 s+='setenv PREFIX '+prefix+'\n'
727 s+='setenv OUT1FILE YES\n'
729 # force filed parameters
730 s+='#---------------------------------------------------------------------\n'
731 s+='setenv DD $UNRES_ROOT/PARAM\n'
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'
773 s+='setenv PATTERN $DD/patterns.cart\n'
774 s+='#---------------------------------------------------------------------\n'
777 f = open(cshname, 'w')
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
791 Writes the actual input
794 ('Input files','*.inp'),
797 # Write error handling for empty sequence
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\".")
803 # Display dialog window
804 fout = tkFileDialog.asksaveasfile(parent=self,mode='w',filetypes=myFormats,title='Save input')
806 print "Saving input file %s" % fout.name
808 text2save=self.fortran_format(self.e1.get())
810 mainopt="SEED="+self.gr1.e1.get()+" "
811 if self.OM1Val.get()=="MD":
812 mainopt+="MD PDBREF EXTCONF"
813 elif self.OM1Val.get()=="MREMD":
815 text2save+=self.fortran_format(mainopt)
818 if self.OM1Val.get()=="MD":
819 text2save+=self.fortran_format(self.get_md_opt())
821 # Get force fields parameters
822 text2save+=self.fortran_format(self.get_weights())
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])
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)
837 text2save+=self.get_seq_data()
839 fout.write(text2save)
842 # ENV Varaiables info