X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Fpymol%2FUNRESInpGen.py;h=ca8c51664b9fabe03c37866812b5f142aab0cf36;hb=dd88fb4db4946bb579a66ab65dc1213cb33ec12a;hp=da99f5afce7d0bf50144fa0ec6cd356728d0a835;hpb=2237ba279d1c0254140eefb1683d7a63c53478e9;p=unres.git

diff --git a/source/pymol/UNRESInpGen.py b/source/pymol/UNRESInpGen.py
index da99f5a..ca8c516 100755
--- a/source/pymol/UNRESInpGen.py
+++ b/source/pymol/UNRESInpGen.py
@@ -53,6 +53,8 @@ class UNRESInpGenerator(Toplevel):
 	OM1Val = StringVar()
 	OM2Val = StringVar()
 	CART = IntVar()
+	OVERLAP = IntVar()
+	NOSEARCHSC = IntVar()
 	objects_list = ['Select object']    
 	seq_list=[]
 	seq_length=0
@@ -119,7 +121,7 @@ class UNRESInpGenerator(Toplevel):
 			labelpos = 'w',
 			label_text = 'Choose method:',
 			menubutton_textvariable = self.OM1Val,
-			items = ['MD', 'MREMD', 'MINIMIZE' ],
+			items = ['MD', 'REMD/MREMD', 'MINIMIZE' ],
 			command = self.switch_options,
 			menubutton_width = 10
 		)
@@ -214,7 +216,15 @@ class UNRESInpGenerator(Toplevel):
 		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)
-
+		
+		# -- initial structure
+		self.gr1.md.om1 = Pmw.OptionMenu(self.gr1.md,
+			labelpos = 'w',
+			label_text = 'Start from',
+			items = ['PDB', 'extended', 'random' ],
+			menubutton_width = 8,
+		)
+		self.gr1.md.om1.grid(row=1,column=3, sticky=E)
 
 		#=================================
 		#  - thermostat frame
@@ -292,6 +302,105 @@ class UNRESInpGenerator(Toplevel):
 		self.balloon.bind(self.gr1.mi.c1,'Minimize in virtual-bond vectors instead of angles.')
 		self.gr1.mi.c1.pack(side=LEFT)
 
+		self.gr1.mi.c2 = Checkbutton(self.gr1.mi,
+			text = "OVERLAP",
+			variable = self.OVERLAP )
+		self.balloon.bind(self.gr1.mi.c2,'Fix overlaping sidechains.')
+		self.gr1.mi.c2.pack(side=LEFT)
+
+		self.gr1.mi.c3 = Checkbutton(self.gr1.mi,
+			text = "NOSEARCHSC",
+			variable = self.NOSEARCHSC )
+		#self.balloon.bind(self.gr1.mi.c3,'Minimize in virtual-bond vectors instead of angles.')
+		self.gr1.mi.c3.pack(side=LEFT)
+
+
+		#=================================
+		# - REMD frame
+		self.gr1.re = Frame(self.gr1.interior())
+		#self.gr1.re.grid(row=5, column=0, columnspan=5,sticky=W+E)
+
+		self.gr1.re.e1 = Pmw.EntryField(self.gr1.re,
+			labelpos = 'w',
+			label_text = "NREP",
+			validate = {'validator' : 'integer', 'min': 1 , 'max' : 32 },
+			command = self.set_replica_widgets,
+			value = "16" )
+		self.balloon.bind(self.gr1.re.e1,'Number of replicas in a REMD/MREMD run.')
+		self.gr1.re.e1.component('entry').config(width=8)
+		self.gr1.re.e1.grid(row=0, column=0, sticky=W)
+		
+		self.gr1.re.e2 = Pmw.EntryField(self.gr1.re,
+			labelpos = 'w',
+			label_text = "NSTEX",
+			validate = {'validator' : 'integer', 'min': 0 , 'max' : 1000000 },
+			value = "1000" )
+		self.balloon.bind(self.gr1.re.e2,'Number of steps after which exchange is performed in REMD/MREMD runs.')
+		self.gr1.re.e2.component('entry').config(width=8)
+		self.gr1.re.e2.grid(row=0, column=1, sticky=W)
+
+		# -- radio select
+		self.gr1.re.rs = Pmw.RadioSelect(self.gr1.re,
+			labelpos = 'w',
+			label_text = 'Replica temperatures',
+			command = self.sel_replica_mode,
+			buttontype = 'radiobutton'
+			#frame_borderwidth = 2,
+			#frame_relief = 'ridge' 
+			)
+		self.gr1.re.rs.grid(row=1, column=0, columnspan=4,sticky=W)
+
+		for text in ('Manual', 'Range'):
+			self.gr1.re.rs.add(text)
+		
+		# --- range
+		self.gr1.re.tf1 = Frame(self.gr1.re, bg="blue")
+		self.gr1.re.tf1.grid(row=2,column=0, columnspan=4, sticky=W)
+
+		self.gr1.re.tf1.e1 = Pmw.EntryField(self.gr1.re.tf1,
+			labelpos = 'w',
+			label_text = "RETMIN",
+			validate = {'validator' : 'real', 'min': 0 , 'max' : 1000000 },
+			value = "10" )
+		self.balloon.bind(self.gr1.re.tf1.e1,'Minimum temperature in a REMD/MREMD run.')
+		self.gr1.re.tf1.e1.component('entry').config(width=8)
+		self.gr1.re.tf1.e1.grid(row=0, column=0, sticky=W)
+
+		self.gr1.re.tf1.e2 = Pmw.EntryField(self.gr1.re.tf1,
+			labelpos = 'w',
+			label_text = "RETMAX",
+			validate = {'validator' : 'real', 'min': 0 , 'max' : 1000000 },
+			value = "1000" )
+		self.balloon.bind(self.gr1.re.tf1.e2,'Maxmum temperature in a REMD/MREMD run.')
+		self.gr1.re.tf1.e2.component('entry').config(width=8)
+		self.gr1.re.tf1.e2.grid(row=0, column=1, sticky=W)
+		
+		# --- manual
+		self.gr1.re.tf2 = Frame(self.gr1.re) 
+		self.gr1.re.tf2.grid(row=3,column=0, columnspan=4, sticky=W)
+
+		self.gr1.re.tf2.te = []
+		for i in range(0,32): #int(self.gr1.re.e1.get())):
+			self.gr1.re.tf2.te.append(Pmw.EntryField(self.gr1.re.tf2,
+				labelpos='n',
+				label_text='T%02d' % (i+1),
+				validate = {'validator' : 'real','min' : 0, 'max' : 1000, 'minstrict' : 0},
+				value = '%d' % (200+i*10)))
+			self.gr1.re.tf2.te[i].component('entry').config(width=3)
+			self.gr1.re.tf2.te[i].grid(row=1+(i//16), column=0+(i % 16))
+
+		self.gr1.re.tf2.nre = Pmw.EntryField(self.gr1.re.tf2, 
+			labelpos ='n',
+			label_text='Rep. in Temp.',
+			validate = {'validator' : 'integer','min' : 1, 'max' : 100 },
+			value = '2')
+		self.gr1.re.tf2.nre.component('entry').config(width=3)
+		self.gr1.re.tf2.nre.grid(row=1, column=17)
+
+		# display manual replica options 
+		self.gr1.re.e1.invoke()
+		self.gr1.re.rs.invoke('Manual')
+
 		#================================= 
 		# "Force field options" group
 		#     
@@ -321,7 +430,10 @@ class UNRESInpGenerator(Toplevel):
 			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)
 				
@@ -557,13 +669,47 @@ class UNRESInpGenerator(Toplevel):
 		self.gr1.th.grid_remove()
 		self.gr1.md.grid_remove()
 		self.gr1.mi.grid_remove()
+		self.gr1.re.grid_remove()
 		# Show MD stuff
 		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)
+		elif self.OM1Val.get()=="REMD/MREMD":
+			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)
+			self.gr1.re.grid(row=5, column=0, columnspan=5, sticky=W+E)
 		elif self.OM1Val.get()=="MINIMIZE":
 			self.gr1.mi.grid(row=4,column=0,columnspan=5, sticky=W+E)
 
+	def sel_replica_mode(self,mode):
+		'''
+			Display replica temperatures settings
+		'''
+		try:
+			self.gr1.re.tf1.grid_remove()
+			self.gr1.re.tf2.grid_remove()
+			if mode=="Range":
+				self.gr1.re.tf1.grid(row=2,column=0, columnspan=4, sticky=W)	
+			elif mode=="Manual":
+				self.gr1.re.tf2.grid(row=3,column=0, columnspan=4, sticky=W)
+		except:
+			pass
+
+	def set_replica_widgets(self):
+		'''
+			Refresh list of available temperature widgets in manual mode
+		'''
+		#print self.gr1.re.e1.get()
+		for i in range(0,32): #int(self.gr1.re.e1.get())):
+			try:
+				if i<int(self.gr1.re.e1.get()):
+					self.gr1.re.tf2.te[i].component('entry').config(state=NORMAL)
+				else:
+					self.gr1.re.tf2.te[i].component('entry').config(state=DISABLED)
+			except:
+				pass
+
+
 
 	def set_force_field(self, pole):
 		'''
@@ -598,7 +744,8 @@ class UNRESInpGenerator(Toplevel):
 
 	def fortran_format(self,s):
 		'''
-		    Formats string containing keywords to wrap over 80 columns 
+		    Formats string containing keywords to wrap over 80 columns.
+			Input string should be one line.
 		'''
 		tmpstr=''
 		column=1
@@ -623,6 +770,9 @@ class UNRESInpGenerator(Toplevel):
 		return s
 
 	def get_md_opt(self):
+		'''
+			Get MD options for main input
+		'''
 		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()+" " 
@@ -646,27 +796,56 @@ class UNRESInpGenerator(Toplevel):
 		return s
 
 	def get_minim_opt(self):
+		'''
+			Get minimization options
+		'''
 		s = "MAXMIN="+self.gr1.mi.e1.getvalue()+" MAXFUN="+self.gr1.mi.e2.getvalue()
 		return s
 
 
+	def get_mremd_opt(self):
+		'''
+			Generates a sting containing REMD?MREMD main options for input
+		'''
+		s = "NREP="+self.gr1.re.e1.get()+" NSTEX="+self.gr1.re.e2.get()+" "
+		if self.gr1.re.rs.getvalue()=="Range":
+			s+="RETMIN="+self.gr1.re.tf1.e1.get()+"RETMAX="+self.gr1.re.tf1.e2.get()
+		else:
+			s+="TLIST MLIST" 
+		s+=" TRAJ1FILE REST1FILE SYNC"
+
+		return s
+
+	def get_mremd_temp_opt(self):
+		'''
+			Generate a strong containing temperatures for REMD/MREMD "manual mode"
+		'''
+		s=""
+		for i in range(0,int(self.gr1.re.e1.get())):
+			s+=self.gr1.re.tf2.te[i].get()+" "	
+
+		return s
+
+	def get_mremd_replicas(self):
+		'''
+			Generates a string containing number of replicas in every temperature for REMD/MREMD calculations.
+			For REMD calculations contains only sequence of ones.
+		'''
+		s=""
+		for i in range(0,int(self.gr1.re.e1.get())):
+			s+=self.gr1.re.tf2.nre.get()+" "
+		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()
@@ -737,7 +916,6 @@ class UNRESInpGenerator(Toplevel):
 		# Don't writeSSbrige 	
 		else:
 			s+="0\n 0\n"
-				
 
 		return s
 
@@ -746,7 +924,13 @@ class UNRESInpGenerator(Toplevel):
 		'''
 			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'
+		s='#!/bin/csh -f\n#\n# C-shell script generated by UNRESInpGen.py v'+UNRESInpGen_version+' \n#\n'
+	
+		s+='#--------------------------------------------------------------------\n'
+		s+='# Uncomment and set these variables to run MPI versions of UNRES\n'
+		s+='#setenv UNRES_ROOT /path/to/root/directory/of/unrespack\n'
+		s+='#setenv UNRES_BIN /path/to/unres_binary.exe\n'
+		s+='#--------------------------------------------------------------------\n'
 		
 		# number of processors per energy
 		if self.OM1Val.get()=="MD":
@@ -792,7 +976,7 @@ class UNRESInpGenerator(Toplevel):
 		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'
+			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/sccor_pdb_shelly.dat\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'
@@ -800,7 +984,7 @@ class UNRESInpGenerator(Toplevel):
 		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'
+			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/sccor_pdb_shelly.dat\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'
@@ -847,18 +1031,40 @@ class UNRESInpGenerator(Toplevel):
 				# 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 "
+					mainopt+="MD PDBREF"
+					if self.gr1.md.om1.getvalue()=="PDB":
+						mainopt+=" PDBSTART"
+					elif self.gr1.md.om1.getvalue()=="extended":
+						mainopt+=" EXTCONF"
+					else:
+						mainopt+=" RAND_CONF"
+				elif self.OM1Val.get()=="REMD/MREMD":
+					mainopt+="RE PDBREF"
+					if self.gr1.md.om1.getvalue()=="PDB":
+						mainopt+=" PDBSTART"
+					elif self.gr1.md.om1.getvalue()=="extended":
+						mainopt+=" EXTCONF"
+					else:
+						mainopt+=" RAND_CONF"
+				
 				elif self.OM1Val.get()=="MINIMIZE":
-					mainopt+="PDBREF MINIMIZE "
+					mainopt+="PDBREF PDBSTART MINIMIZE RESCALE_MODE=0"
 					if self.CART.get():
 						mainopt+=" CART"
+					if self.OVERLAP.get():
+						mainopt+=" OVERLAP"
+					if self.NOSEARCHSC.get():
+						mainopt+=" NOSERARCHSC"
 				text2save+=self.fortran_format(mainopt)
 				# Get aux options
 
 				if self.OM1Val.get()=="MD":
 					text2save+=self.fortran_format(self.get_md_opt())
+				elif self.OM1Val.get()=="REMD/MREMD":
+					text2save+=self.fortran_format(self.get_md_opt())
+					text2save+=self.fortran_format(self.get_mremd_opt())
+					text2save+=self.fortran_format(self.get_mremd_temp_opt())
+					text2save+=self.fortran_format(self.get_mremd_replicas())
 				elif self.OM1Val.get()=="MINIMIZE":
 					text2save+=self.fortran_format(self.get_minim_opt())