From 08dac33deffc6008b1616ef41a0fc5ab15bac961 Mon Sep 17 00:00:00 2001
From: Dawid Jagiela <lightnir@chem.univ.gda.pl>
Date: Thu, 7 Mar 2013 13:10:51 +0100
Subject: [PATCH] added OVERLAP and NOSEARCHSC options in UNRESInpGen.py

---
 source/pymol/UNRESInpGen.py |   22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/source/pymol/UNRESInpGen.py b/source/pymol/UNRESInpGen.py
index da99f5a..5e355a7 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
@@ -292,6 +294,20 @@ 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)
+
+
+
 		#================================= 
 		# "Force field options" group
 		#     
@@ -851,9 +867,13 @@ class UNRESInpGenerator(Toplevel):
 				elif self.OM1Val.get()=="MREMD":
 					mainopt+="RE "
 				elif self.OM1Val.get()=="MINIMIZE":
-					mainopt+="PDBREF MINIMIZE "
+					mainopt+="PDBREF 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
 
-- 
1.7.9.5