--- /dev/null
+# -*- coding: utf-8 -*-
+'''
+-------------------------------------------------------------------------------
+ UNRESInpGen.py - UNRES graphical input generator v 1.0
+-------------------------------------------------------------------------------
+
+ Written by Dawid Jagieła (lightnir@chem.univ.gda.pl) Oct 2012
+
+'''
+
+from pymol import cmd,stored
+from Tkinter import *
+import tkFileDialog
+import tkMessageBox
+import Pmw
+import string
+import os
+
+UNRESInpGen_version="1.0"
+
+def __init__(self):
+ self.UNRESInpGenWindow = None
+ try:
+ self.menuBar.addcascademenu('Plugin', 'UNRESPlugins', 'UNRESPACK Plugins', label='UNRES Plugins')
+ except:
+ pass
+
+ self.menuBar.addmenuitem('UNRESPlugins', 'command','UNRESInpGen',
+ label='UNRES Input Generator',
+ command = lambda s=self: createUNRESInpGen(s) )
+
+def createUNRESInpGen(app):
+ if (app.UNRESInpGenWindow == None):
+ app.UNRESInpGenWindow = UNRESInpGenerator(app)
+ else:
+ app.UNRESInpGenWindow.myToggle()
+
+#=================================================================
+
+
+class UNRESInpGenerator(Toplevel):
+ global UNRESInpGen_version
+ # Class variables
+ """
+ cv = IntVar()
+ pp = IntVar()
+ cp = IntVar()
+ rv = IntVar()
+ colorize = IntVar()
+ """
+ seq_letter = IntVar()
+ writeSSbrige = IntVar()
+ OM1Val = StringVar()
+ OM2Val = StringVar()
+ objects_list = ['Select object']
+ seq_list=[]
+ seq_length=0
+
+ 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' ]
+
+ 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',
+ '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'},
+ {'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',
+ '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'},
+ {'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',
+ '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'},
+ {'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',
+ 'WTURN3':'2.36351', 'WTURN4':'1.34051', 'WTURN6':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
+ {'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',
+ 'WTURN3':'2.99827', 'WTURN4':'0.59174', 'WTURN6':'0.00000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
+ {'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',
+ 'WTURN3':'2.00764', 'WTURN4':'0.05345', 'WTURN6':'0.05282', 'WSCCOR':'0.0', 'CUTOFF': '7.00000', 'WCORR4':'0.00000' },
+ {'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',
+ 'WTURN4':'0.79171', 'WTURN6':'0.01074', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
+ {'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',
+ 'WTURN4':'4.35377', 'WTURN6':'0.10000', 'CUTOFF':'7.00000', 'WCORR4':'0.00000', 'WSCCOR':'0.00000'},
+ {'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',
+ 'WTURN4':'0.55588', 'WTURN6':'0.11539', 'CUTOFF':'7.00000', 'WCORR4':'0.0000', 'WTORD':'0.00000', 'WSCCOR':'0.00000'},
+ {'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',
+ 'WCORR6':'0.00000', 'SCAL14':'0.40000', 'SCALSCP':'1.00000', 'CUTOFF':'7.00000', 'WSCCOR':'0.00000'}
+ ]
+
+ 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'}
+
+
+ def __init__(self,parent):
+ # Create the GUI window
+ root = Toplevel.__init__(self)
+ self.config(width=400, height=300) # create a root window
+ self.title("UNRES Input Generator v"+UNRESInpGen_version) # Set window title
+ self.resizable(0, 0) # Disable window resize
+ self.geometry('-40+40') # Set window placement
+
+ # Create the Balloon.
+ self.balloon = Pmw.Balloon(root)
+
+ #================================
+ # "Main Options" group
+ #
+ self.gr1 = Pmw.Group(self,tag_text = 'Main options')
+ self.gr1.grid(row=0, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
+
+ # - Create title Entryfield & Label
+ #self.l1 = Label(self.gr1.interior(), text="Title:")
+ #self.l1.grid(row=0, column=0,sticky=E)
+ self.e1 = Pmw.EntryField(self.gr1.interior(),
+ labelpos='w',
+ label_text="Title:",
+ validate = {'max': 80 },
+ # value ="(Place input information here)"
+ )
+ self.e1.component('entry').config(width=80)
+ self.e1.grid(row=0, column=0,columnspan=4, sticky=E)
+
+ # - Create "choose method" OptionMenu
+ self.OM1Val.set('MD')
+ self.optmenu1 = Pmw.OptionMenu(self.gr1.interior(),
+ labelpos = 'w',
+ label_text = 'Choose method:',
+ menubutton_textvariable = self.OM1Val,
+ items = ['MD', 'MREMD' ],
+ command = self.switch_options,
+ menubutton_width = 10
+ )
+ self.optmenu1.grid(row=1, column=0,columnspan=2, sticky=E)
+
+
+ # - Seed entryfield
+ self.gr1.e1 = Pmw.EntryField(self.gr1.interior(),
+ labelpos='w',
+ label_text="Seed",
+ validate = {'validator' : 'integer', 'min': -2147483648 , 'max' : 0 },
+ value = "-1111333"
+ )
+ self.gr1.e1.component('entry').config(width=8)
+ self.gr1.e1.grid(row=1, column=2, sticky=W)
+
+ #==================================
+ # - MD options frame
+ #
+ self.gr1.md = Frame(self.gr1.interior())
+ self.gr1.md.grid(row=2, column=0, columnspan=4,sticky=W+E)
+
+ # -- nstep entryfield
+ self.gr1.md.e1 = Pmw.EntryField(self.gr1.md,
+ labelpos='w',
+ label_text="NSTEP",
+ validate = {'validator' : 'integer', 'min': 1 , 'max' : 1000000 },
+ value = "500000"
+ )
+ self.balloon.bind(self.gr1.md.e1,'Number of calculation steps')
+ self.gr1.md.e1.component('entry').config(width=8)
+ self.gr1.md.e1.grid(row=0, column=0, sticky=E)
+
+ # -- ntwe entryfield
+ self.gr1.md.e2 = Pmw.EntryField(self.gr1.md,
+ labelpos='w',
+ label_text="NTWE",
+ validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
+ value = "100"
+ )
+ self.balloon.bind(self.gr1.md.e2,'Frequency of energy output.\nNTWE=0 means no energy dump. ')
+ self.gr1.md.e2.component('entry').config(width=8)
+ self.gr1.md.e2.grid(row=0,column=1, sticky=E)
+
+ # -- ntwx entryfield
+ self.gr1.md.e3 = Pmw.EntryField(self.gr1.md,
+ labelpos='w',
+ label_text="NTWX",
+ validate = {'validator' : 'integer', 'min': 1 , 'max' : 1000000 },
+ value = "1000"
+ )
+ self.balloon.bind(self.gr1.md.e3, "Frequency of coordinate output.")
+ self.gr1.md.e3.component('entry').config(width=8)
+ self.gr1.md.e3.grid(row=0,column=2, sticky=E)
+
+ # -- dt entryfield
+ self.gr1.md.e4 = Pmw.EntryField(self.gr1.md,
+ labelpos='w',
+ label_text="DT",
+ validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
+ value = "0.1")
+ self.balloon.bind(self.gr1.md.e4, "Time step. \nThe unit is \"molecular time unit\" (mtu)\n 1 mtu = 48.9 fs")
+ self.gr1.md.e4.component('entry').config(width=8)
+ self.gr1.md.e4.grid(row=0,column=3, sticky=E)
+
+ # -- damax entryfield
+ self.gr1.md.e5 = Pmw.EntryField(self.gr1.md,
+ labelpos='w',
+ label_text="DAMAX",
+ validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
+ value = "1.0")
+ 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.")
+ self.gr1.md.e5.component('entry').config(width=8)
+ self.gr1.md.e5.grid(row=1,column=0, sticky=E)
+
+ # -- dvmax entryfield
+ self.gr1.md.e6 = Pmw.EntryField(self.gr1.md,
+ labelpos='w',
+ label_text="DVMAX",
+ validate = {'validator' : 'real', 'min': 0.001 , 'max' : 1000 },
+ value = "20.0")
+ self.balloon.bind(self.gr1.md.e6, "Maximum allowed velocity (in A/mtu).")
+ self.gr1.md.e6.component('entry').config(width=8)
+ self.gr1.md.e6.grid(row=1,column=1, sticky=E)
+
+ # -- restet_vel entryfield
+ self.gr1.md.e7 = Pmw.EntryField(self.gr1.md,
+ labelpos='w',
+ label_text="RESET_VEL",
+ validate = {'validator' : 'integer', 'min': 0 , 'max' : 10000000 },
+ value = "1000")
+ self.balloon.bind(self.gr1.md.e7, "Frequency of resetting velocities to values from Gaussian distribution")
+ self.gr1.md.e7.component('entry').config(width=8)
+ self.gr1.md.e7.grid(row=1,column=2, sticky=E)
+
+
+ #=================================
+ # - thermostat frame
+ #
+ self.gr1.th = Frame(self.gr1.interior())
+ self.gr1.th.grid(row=3, column=0, columnspan=5,sticky=W+E)
+
+ # -- Thermostat optionmenu
+ self.gr1.th.optmenu1 = Pmw.OptionMenu(self.gr1.th,
+ labelpos = 'w',
+ label_text = 'thermostat',
+ items = ['Berendsen', 'Nose-Poincare 1999','Nose-Poincare 2001', 'Nose-Hoover', 'Langevin' ],
+ command=self.set_thermostat,
+ menubutton_width = 15
+ )
+ self.gr1.th.optmenu1.pack(side=LEFT)#grid(row=0, column=0, sticky=E)
+
+ # -- t_bath entryfield
+ self.gr1.th.e1 = Pmw.EntryField(self.gr1.th,
+ labelpos='w',
+ label_text="T_BATH",
+ validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 10000 },
+ value = "300.0")
+ self.balloon.bind(self.gr1.th.e1, "Temperature (in K) of canonical simulation.")
+ self.gr1.th.e1.component('entry').config(width=8)
+ self.gr1.th.e1.pack(side=LEFT)
+
+ # -- tau_bath entryfield
+ self.gr1.th.e2 = Pmw.EntryField(self.gr1.th,
+ labelpos='w',
+ label_text="TAU_BATH",
+ validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 1000000 },
+ value = "1.0")
+ self.balloon.bind(self.gr1.th.e2, "(units are mtus; 1mtu=48.9 fs) \nConstant of the coupling to the thermal bath")
+ self.gr1.th.e2.component('entry').config(width=8)
+ self.gr1.th.e2.pack(side=LEFT)
+
+ # -- q_np entryfield
+ self.gr1.th.e3 = Pmw.EntryField(self.gr1.th,
+ labelpos='w',
+ label_text="Q_NP",
+ validate = {'validator' : 'real', 'min': 0.000001 , 'max' : 1000000 },
+ value = "0.1")
+ self.balloon.bind(self.gr1.th.e3, "Mass of the fictitious particle in the calculations with the Nose-Poincare & Nose-Hoover thermostats.")
+ self.gr1.th.e3.component('entry').config(width=8)
+ #self.gr1.th.e2.pack(side=LEFT)
+
+
+ #=================================
+ # "Force field options" group
+ #
+ self.gr2 = Pmw.Group(self,tag_text = 'Force field options')
+ self.gr2.grid(row=2, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
+
+ # - Create "force field parameters" Option menu
+ self.OM2Val.set('Custom')
+ self.optmenu2 = Pmw.OptionMenu(self.gr2.interior(),
+ label_text = 'Force field parameters:',
+ labelpos = 'w',
+ menubutton_textvariable = self.OM2Val,
+ items = ['Custom','GAB','E0G', '1L2Y_1LE1','4P','3P','CASP5','ALPHABETA','BETA','ALPHA','CASP3' ],
+ initialitem = 'Custom',
+ menubutton_width = 10,
+ command=self.set_force_field
+ )
+ self.optmenu2.grid(row=0, column=0,columnspan=4,sticky=E)
+
+ # Force field parameters Entry Fields
+ self.ef = []
+ for i in range(0,len(self.weights)):
+ self.ef.append(Pmw.EntryField(self.gr2.interior(),
+ labelpos='n',
+ label_text=self.weights[i],
+ validate = {'validator' : 'real','min' : 0, 'max' : 10, 'minstrict' : 0},
+ value = '1.00000'))
+ self.ef[i].component('entry').config(width=8)
+ self.ef[i].grid(row=1+(i//9), column=0+(i % 9))
+ # "Sequence" group
+ self.gr3 = Pmw.Group(self,tag_text = 'Sequence')
+ self.gr3.grid(row=3, column=0,columnspan=4,sticky=W+E,padx=10, pady=5)
+
+ self.gr3.f1 = Frame(self.gr3.interior())
+ # Object List
+ self.cb2 = Pmw.ComboBox(self.gr3.f1,
+ labelpos = 'w',
+ #entry_relief = 'raised',
+ label_text = 'Selection/Object',
+ scrolledlist_items = self.objects_list
+ )
+ self.cb2.pack(side=LEFT)
+ # refresh button
+ self.gr3.btn1 = Button(self.gr3.f1, text='Refresh', padx=0, pady=0 , command = self.refresh_list)
+ self.gr3.btn1.pack(side=LEFT)
+ # Get sequence button
+ self.gr3.btn2 = Button(self.gr3.f1, text='Get Sequence', padx=0, pady=0 , command = self.get_seq)
+ self.gr3.btn2.pack(side=LEFT)
+
+ self.gr3.f1.pack(expand="yes",fill="both")
+
+ # Disulfide brige checkbox
+ self.gr3.chk = Checkbutton(self.gr3.f1, text="Write disulfide bridges", variable=self.writeSSbrige)
+ self.gr3.chk.pack(side=LEFT)
+
+ # Sequence text
+ self.gr3.t1 = Pmw.ScrolledText(self.gr3.interior(),
+ columnheader = 1,
+ columnheader_width = 3,
+ rowheader = 1,
+ rowheader_width = 4,
+ usehullsize=1,
+ hull_width=30,
+ hull_height=180,
+ text_padx = 4,
+ text_pady = 4,
+ Header_padx = 4,
+ rowheader_pady = 4,
+ )
+ # Sequence text - create the header line
+ headerline = ''
+ for column in range(1,21):
+ headerline = headerline + ('%-4s' % str(column) )
+ self.gr3.t1.component('columnheader').insert('0.0',headerline)
+
+ self.gr3.t1.pack(expand="yes",fill="both")
+
+ # Add some buttons
+ btn3=Button(self, text='Write Input', padx=0, pady=0, command = self.ok)
+ btn3.grid(row=10, column=0, columnspan=2,sticky=N+W+S+E)
+ btn4=Button(self, text='Close', padx=0, pady=0, command = self.myHide)
+ btn4.grid(row=10, column=2, columnspan=2,sticky=N+W+S+E)
+
+ # create callback to prevent window kill
+ self.protocol("WM_DELETE_WINDOW", self.myHide)
+
+ def ToggleColor(self):
+ if self.colorize.get()==1:
+ for i in range(0,len(self.res_states)):
+ UNRESInpGenWindow.ccb[i].config(state=ACTIVE, bg=self.res_states[i][1], activebackground=self.res_states[i][1], relief=RAISED, overrelief=RAISED)
+ else:
+ for i in range(0,len(self.res_states)):
+ UNRESInpGenWindow.ccb[i].config(state=DISABLED, bg=self.Default_Color , activebackground=self.Default_Color, relief=RAISED, overrelief=RAISED)
+
+ def myShow(self):
+ self.deiconify()
+
+ def myHide(self):
+ self.withdraw()
+
+ def myToggle(self):
+ if self.state() == "normal":
+ self.myHide()
+ elif self.state() == "withdrawn":
+ self.myShow()
+
+ def get_selections(self):
+ self.objects_list = []
+ for item in cmd.get_names("all"):
+ if cmd.get_type(item)=="object:molecule":
+ self.objects_list.append(item)
+ if cmd.get_type(item)=="selection":
+ if item[0]<>"_":
+ self.objects_list.append(item)
+
+ def get_nonstandard(self):
+ stored.list=[]
+ cmd.iterate("(all)","stored.list.append(resn)")
+ stored.list=list(Set(stored.list)) # remove duplicates
+ # Remove standard amino acids and water from list
+ for m in ['HIS','ASP','ARG','PHE','ALA','CYS','GLY','GLN','GLU','LYS','LEU','MET','ASN','SER','TYR','THR','ILE','TRP','PRO','VAL','HOH']:
+ try:
+ stored.list.remove(m)
+ except ValueError:
+ pass
+ UNRESInpGenWindow.cbcr1.setlist(stored.list)
+
+ def refresh_list(self):
+ # Save old values
+ old = self.objects_list
+ try:
+ old_cb2=self.cb2.getvalue()[0]
+ except:
+ old_cb2=''
+ self.get_selections()
+
+ # Update selectionlist if needed
+ if not(old==self.objects_list):
+ self.cb2.setlist(self.objects_list)
+ self.cb2.setlist(self.objects_list)
+
+ if not(old_cb2 in self.objects_list):
+ # No - clear the combobox entry
+ self.cb2.component('entryfield').clear()
+ else:
+ # Yes - set the old value
+ self.cb2.selectitem(old_cb2,setentry=1)
+
+
+ def get_seq(self):
+ # Get the number of chains
+ try:
+ nchains=int(len(cmd.get_chains(self.cb2.getvalue()[0])))
+ except:
+ nchains=0
+ pass
+
+ if (nchains>0):
+ self.seq_list=[]
+ offset=0
+ seq_data=''
+ self.seq_length=0
+ for chain in range(0,nchains):
+ # Get only amonoacids, N-terminus acyl and C-terminus amide
+ # example: (1uRC and chain F and (n. ca or (resn ACE and n. C) or (resn NH2 and n. N)))
+ # No chain information or only one chain
+ if nchains==1:
+ atomchain=cmd.get_model(str(self.cb2.getvalue()[0])+" & (n. ca|(resn ACE & n. C)|(resn NH2+NHH+NME & n. N))").atom
+ # Chain information is present
+ else:
+ 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
+ # dodaj separator lancuchow
+ if chain>0:
+ self.seq_list.append("D ")
+ self.seq_length+=1
+
+
+ # Zamiana chronionych
+ # ACE ALA ALA NH2 D ACE ALA ALA NH2
+ # GLY ALA ALA GLY D GLY ALA ALA GLY
+ # Zamiana niechronionych
+ # ALA ALA D ALA ALA
+ # D ALA ALA D ALA ALA D
+ #
+ # j - licznik pozycji reszty
+ j=0
+ for i in atomchain:
+ self.seq_length+=1
+ if str(i.resn)=="NH2":
+ self.seq_list.append("GLY")
+ elif str(i.resn)=="NHH":
+ self.seq_list.append("GLY")
+ elif str(i.resn)=="NME":
+ self.seq_list.append("GLY")
+ elif str(i.resn)=="ACE":
+ self.seq_list.append("GLY")
+ elif str(i.resn)=="GLY":
+ self.seq_list.append("GLY")
+ else:
+ if j==0 and chain==0:
+ self.seq_list.append("D ")
+ self.seq_list.append(str(i.resn))
+ self.seq_length+=1
+ elif j==len(atomchain)-1 and chain==(nchains-1):
+ self.seq_list.append(str(i.resn))
+ self.seq_list.append("D ")
+ self.seq_length+=1
+ else:
+ self.seq_list.append(str(i.resn))
+ j+=1
+ rows=0
+ #row_header='0' - old header
+ row_header='1'
+ # tag setup
+ self.gr3.t1.tag_configure('dummy', background = 'LightBlue1')
+ tagList=[]
+ self.gr3.t1.tag_configure('cysteine', background = 'LightGoldenrod1')
+ CysTagList=[]
+
+ for i in range(len(self.seq_list)):
+ # Dummy tag
+ if self.seq_list[i]=="D ":
+ tag1 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80))
+ tag2 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80)+3)
+ tagList.append(tag1)
+ tagList.append(tag2)
+ # Cysteine tag
+ if self.seq_list[i]=="CYS" or self.seq_list[i]=="CYX":
+ tag1 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80))
+ tag2 = '%d.%d' % (rows+1, ((len(seq_data)-rows)%80)+3)
+ CysTagList.append(tag1)
+ CysTagList.append(tag2)
+ #
+ offset+=1
+ seq_data=seq_data+self.seq_list[i]+" "
+ # Line Wrap
+ if offset>19:
+ offset=0
+ seq_data=seq_data+'\n'
+ rows+=1
+ #row_header=row_header+'\n'+str(rows*20) - old header
+ row_header=row_header+'\n'+str(rows+1)
+
+ self.gr3.t1.clear()
+ self.gr3.t1.insert('end',seq_data)
+ # Apply tags
+ if len(tagList):
+ apply(self.gr3.t1.tag_add, ('dummy',) + tuple(tagList))
+ if len(CysTagList):
+ apply(self.gr3.t1.tag_add, ('cysteine',) + tuple(CysTagList))
+
+ # Show row header
+ self.gr3.t1.component('rowheader').delete(1.0, END)
+ self.gr3.t1.component('rowheader').insert('end',row_header)
+
+
+ def switch_options(self,calctype):
+ '''
+ Displays the options available to set depending on the currently
+ selected calculation type
+ '''
+ # Hide all
+ self.gr1.th.grid_remove()
+ self.gr1.md.grid_remove()
+ if self.OM1Val.get()=="MD":
+ self.gr1.md.grid(row=2, column=0, columnspan=5, sticky=W+E)
+ self.gr1.th.grid(row=3, column=0, columnspan=5, sticky=W+E)
+
+
+ def set_force_field(self, pole):
+ '''
+ Enables/disables entryfields for force field perameters depending
+ on the currently selected force field
+ '''
+ for ff in self.force_fields:
+ if ff['FF']==pole:
+ #print ff
+ for i in range(0,len(self.weights)):
+ if ff.has_key(self.weights[i]):
+ self.ef[i].setvalue(ff.get(self.weights[i]))
+ self.ef[i].component('entry').config(state=NORMAL)
+ else:
+ self.ef[i].component('entry').config(state=DISABLED)
+ # Custom force field
+ elif pole=='Custom':
+ for i in range(0,len(self.weights)):
+ self.ef[i].component('entry').config(state=NORMAL)
+
+ def set_thermostat(self,thermostat):
+ '''
+ Display additional widget acording to selected thermostat
+ '''
+ #print thermostat
+ self.gr1.th.e2.pack_forget()
+ self.gr1.th.e3.pack_forget()
+ if thermostat=='Berendsen':
+ self.gr1.th.e2.pack(side=LEFT)
+ elif thermostat=='Nose-Poincare 1999' or thermostat=='Nose-Poincare 2001' or thermostat=='Nose-Hoover':
+ self.gr1.th.e3.pack(side=LEFT)
+
+ def fortran_format(self,s):
+ '''
+ Formats string containing keywords to wrap over 80 columns
+ '''
+ tmpstr=''
+ column=1
+ for k in s.split():
+ if column+len(k)+1<80:
+ tmpstr+=k+' '
+ column+=len(k)+1
+ else:
+ tmpstr+=" "*(80-column)+"&\n"+k+" "
+ column=len(k)+2
+ tmpstr+='\n'
+ return tmpstr
+
+ def get_weights(self):
+ '''
+ Get the force field weights
+ '''
+ s = ''
+ for i in range(0,len(self.weights)):
+ if self.ef[i].component('entry').cget("state")=="normal":
+ s+=self.weights[i]+"="+self.ef[i].getvalue()+" "
+ return s
+
+ def get_md_opt(self):
+ s = "NSTEP="+self.gr1.md.e1.getvalue()+" NTWE="+self.gr1.md.e2.getvalue()+" "
+ s+= "NTWX="+self.gr1.md.e3.getvalue()+" DT="+self.gr1.md.e4.getvalue()+" "
+ s+= "DAMAX="+self.gr1.md.e5.getvalue()+" DVMAX="+self.gr1.md.e6.getvalue()+" "
+ s+= "RESET_VEL="+self.gr1.md.e7.getvalue()+" "
+
+ # Thermostat options
+ term=self.gr1.th.optmenu1.getvalue()
+ #print term
+ if term=="Berendsen":
+ s+="TBF TAU_BATH="+self.gr1.th.e2.getvalue()+" "
+ elif term=="Nose-Poincare 1999":
+ s+="NOSEPOINCARE99 Q_NP="+self.gr1.th.e3.getvalue()+" "
+ elif term=="Nose-Poincare 2001":
+ s+="NOSEPOINCARE01 Q_NP="+self.gr1.th.e3.getvalue()+" "
+ elif term=="Nose-Hoover":
+ s+="NOSEHOOVER96 Q_NP="+self.gr1.th.e3.getvalue()+" "
+ elif term=="Langevin":
+ s+="LANG=1 "
+
+ s+="T_BATH="+self.gr1.th.e1.getvalue()+" "
+ return s
+
+
+ def get_seq_data(self):
+ '''
+ Dumps the sequence and disulfide bridge information
+ '''
+ # write sequence length
+ s = str(self.seq_length)+"\n"
+ #
+ #try:
+ # nchains=int(len(cmd.get_chains(self.cb2.getvalue()[0])))
+ #except:
+ # nchains=0
+ #pass
+
+ chains=cmd.get_chains(self.cb2.getvalue()[0])
+ nchains=len(chains)
+ #print "chains : ",chains
+ #print "nchains : ",nchains
+
+ # apply one space before each sequence line
+ seq=self.gr3.t1.get()
+ for line in seq.split('\n'):
+ s+=" "+line+"\n"
+ # remove last newline character
+ s = s[:-1]
+
+ # disulfide bridges - get half-cysteines by selection:
+ # sele (bto. ((object) & r. CYS+CYX & n. SG) )& n. SG
+ ncys=cmd.get_model("(bto. (("+str(self.cb2.getvalue()[0])+") & r. CYS+CYX & n. SG)) & n. SG").atom
+ nSSbr=len(ncys)/2
+
+
+ # Is "Write disulfide brige" checked?
+ # yes
+ if self.writeSSbrige.get():
+ # write number of half-cysteines
+ s+=str(len(ncys))+"\n"
+ if len(ncys)==0:
+ # No half-cysteines, cys position = 0
+ s+=" 0\n"
+ else:
+ # Write half-cysteine positions in sequence
+ #
+ # get first chain
+ first=cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+str(chains[0])+" & n. ca")
+
+ # calculate base offset in first chain (if dummy atom present offset = 1 )
+ if first.atom[0].resn=="GLY":
+ boff=0
+ else:
+ boff=1
+
+ # create dictionary of PDB chain/resi to UNRES_index
+ unresidx={}
+ for c in ncys:
+ # calculate residue index offset from first residue in chain containing half-cysteine
+ fresinchain=cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+c.chain+" & n. ca").atom
+ roff=int(c.resi)-int(fresinchain[0].resi)+1
+
+ resb=0
+ coff=0
+ for r in chains:
+ if c.chain==r:
+ break
+ resb+=len(cmd.get_model(str(self.cb2.getvalue()[0])+"& chain "+r+" & n. ca").atom)
+ coff+=1
+ # add key/value to dictionary
+ unresidx[c.chain+"/"+str(c.resi)]=boff+resb+coff+roff
+ s+=" "+str(boff+resb+coff+roff)
+ s+="\n"
+
+ # Write the number of disulfide bridges
+ s+=" "+str(nSSbr)+"\n"
+
+ lista_mostkow=[]
+ for c in ncys:
+ # get neibhoring Sulfur atom
+ opis=c.chain+str(c.resi)
+ lista_mostkow.append(opis)
+ nbr=cmd.get_model("(bto. ("+str(self.cb2.getvalue()[0])+" & resi "+str(c.resi)+"& n. SG & chain "+str(c.chain)+")) & n. SG").atom[0]
+ opis2=nbr.chain+str(nbr.resi)
+ if opis2 not in lista_mostkow:
+ # Write witch half-cysteines build the i-th disulfide bridge
+ s+=" "+str(unresidx[c.chain+"/"+str(c.resi)])+" "+str(unresidx[nbr.chain+"/"+str(nbr.resi)])+"\n"
+ #print c.chain, c.resn,c.resi,"-S-S-", nbr.chain, nbr.resn,nbr.resi
+ # Don't writeSSbrige
+ else:
+ s+="0\n 0\n"
+
+
+ return s
+
+
+ def write_cshell(self, cshname,prefix):
+ '''
+ Writes the C-shell script needed to run UNRES calculations
+ '''
+ s='#!/bin/csh -f\n#\n# C-shell script generated by UNRESInpGen.py\n#\n'
+
+ # number of processors per energy
+ if self.OM1Val.get()=="MD":
+ s+='setenv FGPROCS 1\n'
+
+ # Potential
+ if self.OM2Val.get()=="CASP3":
+ s+='setenv POT LJ\n'
+ else:
+ s+='setenv POT GB\n'
+
+ # input file
+ s+='setenv PREFIX '+prefix+'\n'
+
+ # Parallel stuff
+ s+='setenv OUT1FILE YES\n'
+
+ # force filed parameters
+ s+='#---------------------------------------------------------------------\n'
+ s+='setenv DD $UNRES_ROOT/PARAM\n'
+
+ if self.OM2Val.get()=="CASP3":
+ s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
+ s+='setenv TORPAR $DD/torsion_cryst.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_LJ.parm\n'
+ s+='setenv ELEPAR $DD/electr.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_GAP.parm\n'
+ s+='setenv SCCORPAR $DD/rotcorr_AM1.parm\n'
+ elif self.OM2Val.get()=="ALPHA" or self.OM2Val.get()=="BETA" or self.OM2Val.get()=="ALPHABETA":
+ s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
+ s+='setenv TORPAR $DD/torsion_ecepp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_GB.parm\n'
+ s+='setenv ELEPAR $DD/electr.parm\nsetenv SCPPAR $DD/scp.parm\nsetenv FOURIER $DD/fourier_GAP.parm\nsetenv SCCORPAR $DD/rotcorr_AM1.parm\n'
+ elif self.OM2Val.get()=="CASP5":
+ s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
+ s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_GB.parm\n'
+ 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'
+ elif self.OM2Val.get()=="3P":
+ s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
+ s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.3P7_iter81_1r\n'
+ 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'
+ elif self.OM2Val.get()=="4P":
+ s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
+ s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/sc_GB_opt.4P5_iter33_3r\n'
+ 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'
+ elif self.OM2Val.get()=="GAB":
+ s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
+ 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'
+ 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'
+ elif self.OM2Val.get()=="E0G":
+ s+='setenv BONDPAR $DD/bond.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/scgauss.parm\n'
+ 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'
+ 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'
+ elif self.OM2Val.get()=="1L2Y_1LE1":
+ s+='setenv BONDPAR $DD/bond_AM1.parm\nsetenv THETPAR $DD/thetaml.5parm\nsetenv ROTPAR $DD/rotamers_AM1_aura.10022007.parm\n'
+ s+='setenv TORPAR $DD/torsion_631Gdp.parm\nsetenv TORDPAR $DD/torsion_double_631Gdp.parm\nsetenv SIDEPAR $DD/scinter_$POT.parm\n'
+ 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'
+ elif self.OM2Val.get()=="Custom":
+ s+='setenv BONDPAR $DD/.parm\nsetenv THETPAR $DD/.parm\nsetenv ROTPAR $DD/.parm\n'
+ s+='setenv TORPAR $DD/.parm\nsetenv TORDPAR $DD/.parm\nsetenv SIDEPAR $DD/.parm\n'
+ s+='setenv ELEPAR $DD/.parm\nsetenv SCPPAR $DD/.parm\nsetenv FOURIER $DD/.parm\nsetenv SCCORPAR $DD/.parm\n'
+
+
+
+ s+='setenv PATTERN $DD/patterns.cart\n'
+ s+='#---------------------------------------------------------------------\n'
+ s+='$UNRES_BIN $*\n'
+
+ f = open(cshname, 'w')
+ f.write(s)
+ f.close()
+
+
+ def setenv_info(self):
+ print '''IMPORTANT: Remember to set the following envirament variables for your shell before starting calculations:
+ UNRES_ROOT - the root directory where UNRES is installed on your system (should contain PARAM directory)
+ UNRES_BIN - the UNRES binary you want to execute
+ '''
+
+
+ def ok(self):
+ '''
+ Writes the actual input
+ '''
+ myFormats = [
+ ('Input files','*.inp'),
+ ('All files','*.*')
+ ]
+ # Write error handling for empty sequence
+ #
+ s=self.gr3.t1.getvalue()
+ if len(s.strip())==0:
+ 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\".")
+ else:
+ # Display dialog window
+ fout = tkFileDialog.asksaveasfile(parent=self,mode='w',filetypes=myFormats,title='Save input')
+ if fout:
+ print "Saving input file %s" % fout.name
+ # Get input header
+ text2save=self.fortran_format(self.e1.get())
+ # Get main options
+ mainopt="SEED="+self.gr1.e1.get()+" "
+ if self.OM1Val.get()=="MD":
+ mainopt+="MD PDBREF EXTCONF"
+ elif self.OM1Val.get()=="MREMD":
+ mainopt+="RE "
+ text2save+=self.fortran_format(mainopt)
+ # Get aux options
+
+ if self.OM1Val.get()=="MD":
+ text2save+=self.fortran_format(self.get_md_opt())
+
+ # Get force fields parameters
+ text2save+=self.fortran_format(self.get_weights())
+
+ # PDB reference
+ pdbreffn=str(self.cb2.getvalue()[0])+"_pdbref.pdb"
+ text2save+=pdbreffn+"\n"
+ print "Saving PDB reference structure %s" % (os.path.join(os.path.dirname(fout.name),pdbreffn))
+ cmd.save(os.path.join(os.path.dirname(fout.name),pdbreffn), self.cb2.getvalue()[0])
+
+ # C-shell script
+ cshellfn=os.path.join(os.path.dirname(fout.name),"unres_"+os.path.basename(os.path.splitext(fout.name)[0])+".csh")
+ print "Writing C-shell script %s" % (cshellfn)
+ prefix=os.path.basename(os.path.splitext(fout.name)[0])
+ self.write_cshell(cshellfn,prefix)
+
+ # Get sequence data
+ text2save+=self.get_seq_data()
+
+ fout.write(text2save)
+ fout.close()
+
+ # ENV Varaiables info
+ self.setenv_info()
projects / unres.git / commitdiff