User:Remig/plico/toab - Revision history

Remig at 17:07, 12 April 2016

2016-04-12T17:07:20Z

Remig at 15:07, 11 September 2015

2015-09-11T15:07:37Z

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Remig: Add single AA mode

2015-07-27T21:15:01Z

Add single AA mode

Remig: Add toggle menu

2015-07-24T18:48:37Z

Add toggle menu

Remig: Handle multi-frame environment

2014-07-22T19:32:04Z

Handle multi-frame environment

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Remig at 16:32, 16 May 2014

2014-05-16T16:32:35Z

Remig: lc all functions

2014-05-16T16:28:55Z

lc all functions

Remig: Do not var globals

2014-04-03T16:00:47Z

Do not var globals

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Remig: Undo revision 8464 by Remig (talk)

2014-04-03T15:53:08Z

Undo revision 8464 by Remig (talk)

Remig: Undo revision 8463 by Remig (talk)

2014-04-03T15:51:04Z

Undo revision 8463 by Remig (talk)

@@ Line 10: / Line 10: @@
 Copy and paste the following into a text editor and save in your scripts directory as toab.spt.
 <pre>#   toAlphaBeta - Jmol script by Ron Mignery
-#   v1.6 beta    9/11/2015 -use thisModel
+#   v1.7 beta    4/12/2016 -require latest common includes
+#
 #   Move a stretch of polypeptide from alpha to beta or vice versa
@@ Line 268: / Line 268: @@
      # Load common functions if not already
-     if (kCommon < 6) {
+     if (kCommon < 7) {
          script $SCRIPT_PATH$plicoCommon.spt
-         if (kCommon < 6) {
+         if (kCommon < 7) {
              prompt ("A newer version of plicoCommon.SPT is required")
              quit
+         }

@@ Line 9: / Line 9: @@
 Copy and paste the following into a text editor and save in your scripts directory as toab.spt.
-<pre>#   toAB - Jmol script by Ron Mignery
+<pre>#   toAlphaBeta - Jmol script by Ron Mignery
-#   v1.4 beta    7/24/2015 -add menu toggle
+#   v1.5 beta    7/27/2015 -add single aa mode
+#
 #   Move a stretch of polypeptide from alpha to beta or vice versa
+#
 gToab = false
@@ Line 108: / Line 109: @@
                      var caIdx = get_cward_bb_idx(nIdx, gChain)
                      var cIdx = get_cward_bb_idx(caIdx, gChain)
-                     var dh= angle({atomIndex=ncIdx}, {atomIndex=nIdx},
+                     if (ncIdx >= 0) {
-                        {atomIndex=caIdx}, {atomIndex=cIdx})
+                        var dh= angle({atomIndex=ncIdx}, {atomIndex=nIdx},
-                    var dir = ((phi > dh) ? abs(8*dx) : -(abs(8*dx)))
+                            {atomIndex=caIdx}, {atomIndex=cIdx})
-                    if (not gToabAlt) {
+                        var dir = ((phi > dh) ? abs(8*dx) : -(abs(8*dx)))
-                        select_nward_idx(nIdx, ((gNanchorIdx >= 0) ? gNcargoIdx : minIdx))
+                        if (not gToabAlt) {
+                            select_nward_idx(nIdx, ((gNanchorIdx >= 0) ? gNcargoIdx : minIdx))
-                    else {
-                        select_cward_idx(caIdx, ((gCanchorIdx >= 0) ? gCcargoIdx : maxIdx))
+                        else {
+                            select_cward_idx(caIdx, ((gCanchorIdx >= 0) ? gCcargoIdx : maxIdx))
-                    if (abs(phi-dh) > 0.5) {
-                        rotate_selected_record(caIdx, {atomIndex=nIdx}, dir)
+                        if (abs(phi-dh) > 0.5) {
+                     }
@@ Line 187: / Line 190: @@
 function to_ab_cargo_mb() {
      gToab = true
-     tug_cargo_mb
+     tug_cargo_mb()
+}
@@ Line 212: / Line 261: @@
      plico_prelim(true)
-     gEcho = ("____Alpha <==> Beta____|ALT-CLICK=mark block|DOUBLE-CLICK=exit")
+     gEcho = ("______Alpha <==> Beta______|ALT-CLICK=mark block" +
      echo @gEcho
      gChain = ""
@@ Line 220: / Line 271: @@
      bind "ALT-LEFT-CLICK" "_pickAtom";
      bind "ALT-LEFT-CLICK" "+:to_ab_cargo_mb";
      bind "DOUBLE" "plico_exit";
      bind "LEFT-CLICK" "+:plico_menu_toggle";

@@ Line 9: / Line 9: @@
 Copy and paste the following into a text editor and save in your scripts directory as toab.spt.
-<pre>#   toAlphBeta - Jmol script by Ron Mignery
+<pre>#   toAB - Jmol script by Ron Mignery
-#   v1.3 beta    7/22/2014 -handle multi-frame environment
+#   v1.4 beta    7/24/2015 -add menu toggle
+#
 #   Move a stretch of polypeptide from alpha to beta or vice versa
@@ Line 66: / Line 66: @@
              if (gSCidx >= 0) {
                  if ({atomIndex=gSCidx}.atomName == "O") {
-                     dir = ((abs(dx) > abs(dy))
+                     var dir = ((abs(dx) > abs(dy))
                          ? ((dx < 0) ? 2 : -2)
                          : ((dy < 0) ? 2 : -2))
@@ Line 154: / Line 154: @@
          if (lcset.size > 0) {
              for (var i = 1; i <= lcset.size; i++) {
-                 handleCollisions2(lcset[i].atomIndex)
+                 handle_collisions(lcset[i].atomIndex)
+             }
+         }
@@ Line 186: / Line 186: @@
 # Bound to ALT-LEFT-CLICK by plico_to_ab
 function to_ab_cargo_mb() {
      gToab = true
      tug_cargo_mb
@@ Line 195: / Line 194: @@
      # Load common functions if not already
-     if (kCommon < 3) {
+     if (kCommon < 6) {
          script $SCRIPT_PATH$plicoCommon.spt
-         if (kCommon < 3) {
+         if (kCommon < 6) {
              prompt ("A newer version of plicoCommon.SPT is required")
              quit
@@ Line 216: / Line 215: @@
      echo @gEcho
      gChain = ""
      unbind
@@ Line 221: / Line 221: @@
      bind "ALT-LEFT-CLICK" "+:to_ab_cargo_mb";
      bind "DOUBLE" "plico_exit";
+}
 # End of TOAB.SPT</pre>

@@ Line 3: / Line 3: @@
 '''ToAlphaBeta''' is a member of the Plico suite of protein folding tools described [[User:Remig/plico|here]]. It may be installed and accessed as a macro with the file:
 <pre>Title=PLICO To Alpha/Beta
-Script=script <path to your scripts directory>/toab.spt;plicoToab
+Script=script <path to your scripts directory>/toab.spt;plico_to_ab
 </pre>saved as plicotoab.macro in your .jmol/macros directory as described in [[Macro]].
 Copy and paste the following into a text editor and save in your scripts directory as toab.spt.

@@ Line 5: / Line 5: @@
 Script=script <path to your scripts directory>/toab.spt;plicoToab
 </pre>saved as plicotoab.macro in your .jmol/macros directory as described in [[Macro]].
 Copy and paste the following into a text editor and save in your scripts directory as toab.spt.
 <pre>#   toAlphBeta - Jmol script by Ron Mignery
-#   v1.1 beta    3/4/2014 for Jmol 14 -do not var globals for Jmol 14.0.13+
+#   v1.2 beta    5/16/2014 -lc all functions
+#
 #   Move a stretch of polypeptide from alpha to beta or vice versa
@@ Line 14: / Line 15: @@
 gToabAlt = FALSE
-# Bound to LEFT-UP by toabEnableDrag
+# Bound to LEFT-UP by to_ab_enable_drag
-function toabDragDoneMB() {
+function to_ab_drag_done_mb() {
      if (not gToabAlt) {
          if (gNanchorIdx >= 0) {
@@ Line 28: / Line 29: @@
+}
-# Bound to ALT-SHIFT-LEFT-DRAG by toabEnableDrag
+# Bound to ALT-SHIFT-LEFT-DRAG by to_ab_enable_drag
-function toabDrag2MB() {
+function to_ab_drag_2_mb() {
      gToabAlt = TRUE
-     toabDrag()
+     to_ab_drag()
+}
-# Bound to ALT-LEFT-DRAG by toabEnableDrag
+# Bound to ALT-LEFT-DRAG by to_ab_enable_drag
 function toabDragMB() {
      gToabAlt = FALSE
-     toabDrag()
+     to_ab_drag()
+}
-function toabDrag() {
+function to_ab_drag() {
      if (not gBusy) {
          gBusy = TRUE
@@ Line 151: / Line 152: @@
 # Called by tugCargoMB when gToab is true
-function toabEnableDrag() {
+function to_ab_enable_drag() {
      gEcho = "____Alpha <==> Beta____|ALT-CLICK=mark block|SHIFT-CLICK=anchors" +
          "|ALT-DRAG=move|SHIFT-ALT-DRAG=alt move|DOUBLE-CLICK=exit"
@@ Line 160: / Line 161: @@
      bind "ALT-LEFT-UP" "tugDragDoneMB";
      bind "ALT-LEFT-DRAG" "toabDragMB";
-     bind "ALT-SHIFT-LEFT-UP" "toabDragDoneMB";
+     bind "ALT-SHIFT-LEFT-UP" "to_ab_drag_done_mb";
-     bind "ALT-SHIFT-LEFT-DRAG" "toabDrag2MB";
+     bind "ALT-SHIFT-LEFT-DRAG" "to_ab_drag_2_mb";
      unbind "SHIFT-LEFT-CLICK"
@@ Line 169: / Line 170: @@
+}
-# Bound to ALT-LEFT-CLICK by plicoToab
+# Bound to ALT-LEFT-CLICK by plico_to_ab
-function toabCargoMB() {
+function to_ab_cargo_mb() {
-print "toabCargoMB()"#TBD
+print "to_ab_cargo_mb()"#TBD
      gToab = TRUE
      tugCargoMB
@@ Line 177: / Line 178: @@
 # Top level of ToAlphaBeta
-function plicoToab() {
+function plico_to_ab() {
      # Load tug functions if not already
@@ Line 189: / Line 190: @@
      gPlico = "TO ALPHA/BETA"
-     plicoPrelim()
+     plico_prelim(TRUE)
      gEcho = ("____Alpha <==> Beta____|ALT-CLICK=mark block|DOUBLE-CLICK=exit")
@@ Line 197: / Line 198: @@
      bind "ALT-LEFT-CLICK" "_pickAtom";
-     bind "ALT-LEFT-CLICK" "+:toabCargoMB";
+     bind "ALT-LEFT-CLICK" "+:to_ab_cargo_mb";
-     bind "DOUBLE" "plicoExit";
+     bind "DOUBLE" "plico_exit";
+}
-# End of TOAB.SPT
+# End of TOAB.SPT</pre>