From fdf491c6c5e2f140c111542135de7bbdd210a2e6 Mon Sep 17 00:00:00 2001
From: KAPAKAYALA ANJI BABU <anjibabu480@gmail.com>
Date: Mon, 11 Mar 2019 17:36:08 +0800
Subject: [PATCH 1/6] Update README.md

---
 README.md | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index 3cb49d2..aabb5e7 100644
--- a/README.md
+++ b/README.md
@@ -1,17 +1,12 @@
 
-**Enhaced_Sampling_Methods_Tutorials**
+#         Enhaced Sampling Methods Tutorials
 
 
-
-
-
-
-* Molecular Dynamics(**MD**):     Will be updated soon
+* Molecular Dynamics(**MD**)     :     Will be updated soon
 * Umbrella Sampling([**US**](https://github.com/NNairIITK/Enhanced_Sampling_Methods_Tutorials/tree/master/Umbrella_Sampling))                         :     will be updated soon 
 * Metadynamics([**METAD**](https://github.com/NNairIITK/Enhanced_Sampling_Methods_Tutorials/tree/master/Metadynamics))                           :     Will be updated soon
 * Replica Exchange MD([**REMD**](https://github.com/NNairIITK/Enhanced_Sampling_Methods_Tutorials/tree/master/Replica_Exchange_MD))                                                         
                                                     :     Updated
-* Well Sliced Metadynamics(**WS-METAD**)            :     Will be updated soon
 * Replica Exchange Solute Scaling([**REST2**](https://github.com/NNairIITK/Enhanced_Sampling_Methods_Tutorials/tree/master/REST2))           
                                                     :     Updated
 * Temperature Accelerated Sliced Sampling([**TASS**](https://github.com/NNairIITK/Enhanced_Sampling_Methods_Tutorials/tree/master/TASS)) :     Updated
@@ -20,10 +15,8 @@
     
     
     
-    
-  
-    
-** Keep looking at this page for more updates** 
+       
+**Keep looking at this page for more updates** 
         
         Cheers !!!
         Anji Babu

From 4e32033c55058f86588742bf650c2a7546aadfb2 Mon Sep 17 00:00:00 2001
From: KAPAKAYALA ANJI BABU <anjibabu480@gmail.com>
Date: Fri, 5 Feb 2021 23:57:33 +0530
Subject: [PATCH 2/6] script to choose hot atoms

---
 REST2/Process_topology_REST2.sh | 71 +++++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 REST2/Process_topology_REST2.sh

diff --git a/REST2/Process_topology_REST2.sh b/REST2/Process_topology_REST2.sh
new file mode 100644
index 0000000..76c1410
--- /dev/null
+++ b/REST2/Process_topology_REST2.sh
@@ -0,0 +1,71 @@
+#-------------------------------------------------------------------------------#
+#    Bash script to Process the topology for REST2 setup
+#    Selects the hot atoms for RESt2
+#
+#    Author: Anji Babu Kapakayala
+#             IIT Kanpur, India.
+#-------------------------------------------------------------------------------#
+#!/bin/bash
+#file="unfolded.top"
+file="$1"
+resid=0
+while read line;do
+
+#---->
+res=`echo $line|awk '{print $2}'`
+if [ "$res" == 'residue' ] 
+then
+resid=`echo $line|awk '{print $3}'`
+resid_ref=$resid
+fi
+#<---
+resid_new=`echo $line|awk '{print $3}'`
+
+if [ "$line" != "" ];then
+   if [ "$resid_new" != "" ];then
+      if [ "$resid_new" == "$resid_ref" ];then
+         C1=`echo $line|awk '{print $1}'`
+	 C2=`echo $line|awk '{print $2}'`
+	 C4=`echo $line|awk '{print $4}'`
+	 C5=`echo $line|awk '{print $5}'`
+	 C6=`echo $line|awk '{print $6}'`
+	 C7=`echo $line|awk '{print $7}'`
+	 C8=`echo $line|awk '{print $8}'`
+	 C9=`echo $line|awk '{print $9}'`
+	 C10=`echo $line|awk '{print $10}'`
+	 C11=`echo $line|awk '{print $11}'`
+
+            if [ "$res" != 'residue' ] ;then
+#               echo "  $C1  ${C2}_ $resid_new $C4 $C5 $C6 $C7 $C8 $C9 $C10 $C11 " >> unfolded_scaled.top
+               echo $C1$'\t'${C2}_$'\t'$resid_new$'\t'$C4$'\t'$C5$'\t'$C6$'\t'$C7$'\t'$C8$'\t'$C9$'\t'$C10$'\t' $C11  >> unfolded_scaled.top
+            else
+               echo $line >> unfolded_scaled.top
+            fi
+      else
+	 echo $line >> unfolded_scaled.top
+      fi
+   else
+      echo $line >> unfolded_scaled.top
+   fi
+else
+echo $line >> unfolded_scaled.top
+fi
+
+first=`echo $line|awk '{print $1}'`
+if [ "$first" == "[" ];then
+#resid_new="X"
+resid_ref="Y"
+fi
+done<$file
+
+
+#awk '{for(i=1; i<=NR; i++) 
+#{if($i=="; residue") print $0
+
+
+
+
+#}#if
+
+#}' $file
+

From afff4f42e811d9b31355b7457370d4959f347427 Mon Sep 17 00:00:00 2001
From: KAPAKAYALA ANJI BABU <anjibabu480@gmail.com>
Date: Sat, 6 Feb 2021 12:08:17 +0530
Subject: [PATCH 3/6] Selects HOT atoms

---
 REST2/Process_topology_REST2.sh | 48 +++++++++++++++++----------------
 1 file changed, 25 insertions(+), 23 deletions(-)

diff --git a/REST2/Process_topology_REST2.sh b/REST2/Process_topology_REST2.sh
index 76c1410..666118d 100644
--- a/REST2/Process_topology_REST2.sh
+++ b/REST2/Process_topology_REST2.sh
@@ -1,16 +1,25 @@
 #-------------------------------------------------------------------------------#
 #    Bash script to Process the topology for REST2 setup
-#    Selects the hot atoms for RESt2
+#    Selects the HOT atoms for REST2
 #
 #    Author: Anji Babu Kapakayala
 #             IIT Kanpur, India.
+#
+#    USAGE : bash Process_topology_REST2.sh topol.top
 #-------------------------------------------------------------------------------#
 #!/bin/bash
-#file="unfolded.top"
-file="$1"
+infile="$1"
+#infile="trp_processed.top"
 resid=0
-while read line;do
 
+#---> Setting output filename
+fname=`echo "$infile"|cut -d "." -f1`
+outfile="${fname}_processed.top"
+
+#---> Make lines starts with * to ;*
+sed -i "s/\*/;\*/g" $infile
+
+while read line;do
 #---->
 res=`echo $line|awk '{print $2}'`
 if [ "$res" == 'residue' ] 
@@ -20,7 +29,6 @@ resid_ref=$resid
 fi
 #<---
 resid_new=`echo $line|awk '{print $3}'`
-
 if [ "$line" != "" ];then
    if [ "$resid_new" != "" ];then
       if [ "$resid_new" == "$resid_ref" ];then
@@ -36,19 +44,18 @@ if [ "$line" != "" ];then
 	 C11=`echo $line|awk '{print $11}'`
 
             if [ "$res" != 'residue' ] ;then
-#               echo "  $C1  ${C2}_ $resid_new $C4 $C5 $C6 $C7 $C8 $C9 $C10 $C11 " >> unfolded_scaled.top
-               echo $C1$'\t'${C2}_$'\t'$resid_new$'\t'$C4$'\t'$C5$'\t'$C6$'\t'$C7$'\t'$C8$'\t'$C9$'\t'$C10$'\t' $C11  >> unfolded_scaled.top
+               echo $C1$'\t'${C2}_$'\t'$resid_new$'\t'$C4$'\t'$C5$'\t'$C6$'\t'$C7$'\t'$C8$'\t'$C9$'\t'$C10$'\t' $C11  >> $outfile
             else
-               echo $line >> unfolded_scaled.top
+               echo $line >> $outfile
             fi
       else
-	 echo $line >> unfolded_scaled.top
+	 echo $line >> $outfile
       fi
    else
-      echo $line >> unfolded_scaled.top
+      echo $line >> $outfile
    fi
 else
-echo $line >> unfolded_scaled.top
+echo $line >> $outfile
 fi
 
 first=`echo $line|awk '{print $1}'`
@@ -56,16 +63,11 @@ if [ "$first" == "[" ];then
 #resid_new="X"
 resid_ref="Y"
 fi
-done<$file
-
-
-#awk '{for(i=1; i<=NR; i++) 
-#{if($i=="; residue") print $0
-
-
-
-
-#}#if
-
-#}' $file
+done<$infile
 
+#---> Make lines starts with ;* to *
+sed -i "s/;\*/\*/g" $infile
+sed -i "s/;\*/\*/g" $outfile
+#---------------------------------------------------------#
+#      <========== ANJI BABU KAPAKAYALA ==========>
+#---------------------------------------------------------#

From a2802fd3798b9d3372bad5164e467efcc5e897d7 Mon Sep 17 00:00:00 2001
From: KAPAKAYALA ANJI BABU <anjibabu480@gmail.com>
Date: Sat, 6 Feb 2021 16:20:15 +0530
Subject: [PATCH 4/6] Update Process_topology_REST2.sh

---
 REST2/Process_topology_REST2.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/REST2/Process_topology_REST2.sh b/REST2/Process_topology_REST2.sh
index 666118d..6f2fdde 100644
--- a/REST2/Process_topology_REST2.sh
+++ b/REST2/Process_topology_REST2.sh
@@ -6,6 +6,7 @@
 #             IIT Kanpur, India.
 #
 #    USAGE : bash Process_topology_REST2.sh topol.top
+#    Equilant Command using vim   :%s/\%V /_/g
 #-------------------------------------------------------------------------------#
 #!/bin/bash
 infile="$1"

From a98f558f440e1c3cf30233e38fcf5845c677e332 Mon Sep 17 00:00:00 2001
From: KAPAKAYALA ANJI BABU <anjibabu480@gmail.com>
Date: Wed, 10 Feb 2021 15:27:15 +0530
Subject: [PATCH 5/6] fixed format issue

---
 REST2/Process_topology_REST2.sh | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/REST2/Process_topology_REST2.sh b/REST2/Process_topology_REST2.sh
index 6f2fdde..9f2717a 100644
--- a/REST2/Process_topology_REST2.sh
+++ b/REST2/Process_topology_REST2.sh
@@ -6,7 +6,9 @@
 #             IIT Kanpur, India.
 #
 #    USAGE : bash Process_topology_REST2.sh topol.top
-#    Equilant Command using vim   :%s/\%V /_/g
+#
+#    Equilant command in vim: :%s/\%V /_/g
+#
 #-------------------------------------------------------------------------------#
 #!/bin/bash
 infile="$1"
@@ -15,7 +17,7 @@ resid=0
 
 #---> Setting output filename
 fname=`echo "$infile"|cut -d "." -f1`
-outfile="${fname}_processed.top"
+outfile="${fname}_hot.top"
 
 #---> Make lines starts with * to ;*
 sed -i "s/\*/;\*/g" $infile
@@ -47,16 +49,16 @@ if [ "$line" != "" ];then
             if [ "$res" != 'residue' ] ;then
                echo $C1$'\t'${C2}_$'\t'$resid_new$'\t'$C4$'\t'$C5$'\t'$C6$'\t'$C7$'\t'$C8$'\t'$C9$'\t'$C10$'\t' $C11  >> $outfile
             else
-               echo $line >> $outfile
+               echo "$line" >> $outfile
             fi
       else
-	 echo $line >> $outfile
+	 echo "$line" >> $outfile
       fi
    else
-      echo $line >> $outfile
+      echo "$line" >> $outfile
    fi
 else
-echo $line >> $outfile
+echo "$line" >> $outfile
 fi
 
 first=`echo $line|awk '{print $1}'`

From 57dbc48c215a7bc276f6643d7ce5885005ad5a6f Mon Sep 17 00:00:00 2001
From: KAPAKAYALA ANJI BABU <anjibabu480@gmail.com>
Date: Thu, 11 Feb 2021 22:08:16 +0530
Subject: [PATCH 6/6] selection of range of residues are implemented

---
 REST2/process_for_resid.sh | 119 +++++++++++++++++++++++++++++++++++++
 1 file changed, 119 insertions(+)
 create mode 100644 REST2/process_for_resid.sh

diff --git a/REST2/process_for_resid.sh b/REST2/process_for_resid.sh
new file mode 100644
index 0000000..c601cf7
--- /dev/null
+++ b/REST2/process_for_resid.sh
@@ -0,0 +1,119 @@
+#-------------------------------------------------------------------------------#
+#    Bash script to Process the topology for REST2 setup
+#    Selects the HOT atoms for REST2
+#
+#    Author: Anji Babu Kapakayala
+#             IIT Kanpur, India.
+#
+#    USAGE : bash Process_topology_REST2.sh topol.top 
+#            bash process_topology_REST2.sh toptl.top --resid 1-5
+#
+#    Equilant command in vim: :%s/\%V /_/g
+#
+#-------------------------------------------------------------------------------#
+#!/bin/bash
+infile="$1"
+#infile="trp_processed.top"
+resid=$3
+
+#---> Setting output filename
+fname=`echo "$infile"|cut -d "." -f1`
+outfile="${fname}_hot.top"
+touch $outfile
+
+#---> Make lines starts with * to ;*
+sed -i "s/\*/;\*/g" $infile
+
+#-------------------------------------------------------------------------------#
+function select_hot_atoms() {
+
+while read line;do
+     echo "Processing for Resid: $resid"
+#---->
+res=`echo $line|awk '{print $2}'`
+if [ "$res" == 'residue' ] 
+then
+#--->
+  if [ "$1" == "all" ];then
+     resid=`echo $line|awk '{print $3}'`
+     resid_ref=$resid
+  else
+     resid_ref=$1
+     echo "Processing for Resid: $1"
+  fi
+#<---  
+fi
+#<---
+resid_new=`echo $line|awk '{print $3}'`
+if [ "$line" != "" ];then
+   if [ "$resid_new" != "" ];then
+      if [ "$resid_new" == "$resid_ref" ];then
+         C1=`echo $line|awk '{print $1}'`
+	 C2=`echo $line|awk '{print $2}'`
+	 C4=`echo $line|awk '{print $4}'`
+	 C5=`echo $line|awk '{print $5}'`
+	 C6=`echo $line|awk '{print $6}'`
+	 C7=`echo $line|awk '{print $7}'`
+	 C8=`echo $line|awk '{print $8}'`
+	 C9=`echo $line|awk '{print $9}'`
+	 C10=`echo $line|awk '{print $10}'`
+	 C11=`echo $line|awk '{print $11}'`
+
+            if [ "$res" != 'residue' ] ;then
+               echo $C1$'\t'${C2}_$'\t'$resid_new$'\t'$C4$'\t'$C5$'\t'$C6$'\t'$C7$'\t'$C8$'\t'$C9$'\t'$C10$'\t' $C11  >> $outfile
+            else
+               echo "$line" >> $outfile
+            fi
+      else
+	 echo "$line" >> $outfile
+      fi
+   else
+      echo "$line" >> $outfile
+   fi
+else
+echo "$line" >> $outfile
+fi
+
+first=`echo $line|awk '{print $1}'`
+if [ "$first" == "[" ];then
+#resid_new="X"
+resid_ref="Y"
+fi
+done<$infile
+}
+#-------------------------------------------------------------------------------#
+# <========================== MAIN CODE ====================================>
+#-------------------------------------------------------------------------------#
+if [ "$2" == "" ];then
+     echo "Processing All Residues"
+   select_hot_atoms all
+else
+   case "$2" in 
+        --resid|-r) echo "Resid : $resid"
+	      if [ "$3" != "" ];then
+		 r1=`echo $3|cut -d "-" -f1`
+		 r2=`echo $3|cut -d "-" -f2`
+                 echo "Initial Resid: $r1"
+                 echo "Final   Resid: $r2"
+	  		for i in `seq $r1 1 $r2`;do
+		           select_hot_atoms $i
+			   mv $outfile tmp
+ 			   infile="tmp"
+			       done
+	         
+	      else			  
+		 echo "Invalid resid.";exit
+	      fi
+   ;;
+     *) echo " Invalid Argument.";;   
+   esac
+fi
+
+#-------------------------------------------------------------------------------#
+#---> Make lines starts with ;* to *
+sed -i "s/;\*/\*/g" $infile
+sed -i "s/;\*/\*/g" $outfile
+mv tmp $outfile
+#-------------------------------------------------------------------------------#
+#      <========== ANJI BABU KAPAKAYALA ==========>
+#-------------------------------------------------------------------------------#