User:Remig/plico/tug - Revision history

Remig: Avoid "axis," a newly reserved word

2016-04-12T17:15:22Z

Avoid "axis," a newly reserved word

Remig at 14:35, 11 September 2015

2015-09-11T14:35:30Z

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Remig at 12:27, 27 July 2015

2015-07-27T12:27:16Z

Remig: Remove some debug code

2015-07-25T17:44:23Z

Remove some debug code

Remig: Add menu toggle

2015-07-24T18:36:14Z

Add menu toggle

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Remig at 19:34, 22 July 2014

2014-07-22T19:34:08Z

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Remig: Support multi-frame environment

2014-07-17T16:08:36Z

Support multi-frame environment

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Remig: add plico_prelim param

2014-05-16T16:48:50Z

add plico_prelim param

Remig at 15:08, 16 May 2014

2014-05-16T15:08:49Z

Remig: lc all functions

2014-05-16T15:07:24Z

lc all functions

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@@ Line 8: / Line 8: @@
 Copy and paste the following into a text editor and save in your scripts directory as tug.spt.
 <pre>#   tug - Jmol script by Ron Mignery
-#   v1.19 beta    9/11/2015 -use thisModel
+#   v1.20 beta    4/12/2016 -axis is now a reserved word
+#
 #   Translate or rotate a stretch of a polypeptide against itself
@@ Line 347: / Line 347: @@
              var dt = angle({atomIndex=targetIdx}, {atomIndex=i2}, {atomIndex=i3}, pt)
              var dh = angle({atomIndex=i1}, {atomIndex=i2}, {atomIndex=i3}, {atomIndex=i4})
-             if (dh == "NaN") {
+             if (abs(dh).type == "string") {
                  dh = -50
+             }
@@ Line 868: / Line 868: @@
 # gPlicoRecord is maintained by the macro pilcoRecord
-function rotate_selected_record(pivotIdx, axis, a) {
+function rotate_selected_record(pivotIdx, caxis, a) {
      if (gPlicoRecord != "") {
          plico_record(format("select %s;", {selected}))
          plico_record(format("rotateSelected {atomIndex=%d} @%s @%s;",
-             pivotIdx, axis, a))
+             pivotIdx, caxis, a))
+     }
-     rotateSelected {atomIndex=pivotIdx} @axis @a
+     rotateSelected {atomIndex=pivotIdx} @caxis @a
+}
@@ Line 1,556: / Line 1,556: @@
          var ptd = {@dx @dy 0}
          var pt = (!q)%ptd
-         var axis = {0 0 0}
+         var caxis = {0 0 0}
          if (distance(pt,  {0 0 0}) > 0.004) {
              # If sidechain mode
@@ Line 1,602: / Line 1,602: @@
                      # If two pivots
                      if (g2pivotIdx >= 0) {
-                         axis = {atomIndex=g2pivotIdx}
+                         caxis = {atomIndex=g2pivotIdx}
+                     }
                      # Else
                      else {
-                         axis = cross(pt, {0 0 0}) + {atomIndex=g1pivotIdx}.xyz
+                         caxis = cross(pt, {0 0 0}) + {atomIndex=g1pivotIdx}.xyz
+                     }
@@ Line 1,613: / Line 1,613: @@
                          ? ((dx < 0) ? 2 : -2)
                          : ((dy < 0) ? 2 : -2))
-                     rotate_selected_record(g1pivotIdx, axis, dir)
+                     rotate_selected_record(g1pivotIdx, caxis, dir)
+                 }
@@ Line 1,682: / Line 1,682: @@
                          delay 1
                          if (g1pivotIdx >= 0) {
-                             rotate_selected_record(g1pivotIdx, axis, -a)
+                             rotate_selected_record(g1pivotIdx, caxis, -a)
+                         }
                          else {
@@ Line 2,050: / Line 2,050: @@
      # 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 8: / Line 8: @@
 Copy and paste the following into a text editor and save in your scripts directory as tug.spt.
 <pre>#   tug - Jmol script by Ron Mignery
-#   v1.16 beta    7/24/2015 -add menu toggle
+#   v1.18 beta    7/26/2015 -no adjust with drag2
+#
 #   Translate or rotate a stretch of a polypeptide against itself
@@ Line 1,777: / Line 1,777: @@
      gEcho = "__________TUG__________|ALT-CLICK=mark block|SHIFT-CLICK=anchors" +
          "|ALT-CTRL-CLICK=pivots|ALT-SHIFT-CLICK=dest atom|ALT-DRAG=move" +
-         "|SHIFT-ALT-DRAG=alt move|CLICK bond=freeze|ALT-DOUBLE-CLICK=undo|DOUBLE-CLICK=exit"
+         "|ALT-SHIFT-DRAG=alt move|CLICK bond=freeze|ALT-DOUBLE-CLICK=undo|DOUBLE-CLICK=exit"
      echo @gEcho
@@ Line 1,784: / Line 1,784: @@
      bind "ALT-LEFT-UP" "tug_drag_done_mb";
      bind "ALT-SHIFT-LEFT-DOWN" "tug_mark_mb";
      bind "ALT-LEFT-DRAG" "tug_drag_mb";
      bind "ALT-SHIFT-LEFT-DRAG" "tug_drag_2_mb";

@@ Line 1,270: / Line 1,270: @@
                      gNrotors += aCa.atomIndex
                      gNrotors += aN.atomIndex
+                 }
+             }
@@ Line 1,283: / Line 1,282: @@
                          gNrotors += aN.atomIndex
                          gNrotors += aCp.atomIndex
+                     }
+                 }
@@ Line 1,319: / Line 1,317: @@
                          gCrotors += aCa.atomIndex
                          gCrotors += aC.atomIndex
+                     }
+                 }
@@ Line 1,333: / Line 1,330: @@
                      gCrotors += aC.atomIndex
                      gCrotors += aNn.atomIndex
+                 }
+             }

@@ Line 6: / Line 6: @@
 saved as plicotug.macro in your .jmol/macros directory as described in [[Macro]].
-Copy and paste the following into a text editor and save in your scripts folder as tug.spt.
+Copy and paste the following into a text editor and save in your scripts directory as tug.spt.
 <pre>#   tug - Jmol script by Ron Mignery
-#   v1.11 beta    5/16/2014 -lc all functions
+#   v1.12 beta    5/16/2014 -add plico_prelim param
+#
 #   Translate or rotate a stretch of a polypeptide against itself
@@ Line 332: / Line 332: @@
 # Resolve collisions
-function handle_collisions_2( targetIdx) {
+function handle_collisions( targetIdx) {
      # For all selected atoms
@@ Line 537: / Line 537: @@
                              dt /= 2
+                         }
-                         handle_collisions_2( targetIdx)
+                         handle_collisions( targetIdx)
                          if (not gOk2) {
                              wasCollision = TRUE
@@ Line 954: / Line 954: @@
      }   # endwhile (targetIdx != gNanchorIdx) {
+}
@@ Line 1,476: / Line 1,465: @@
                  var ihc = 0
                  for (ihc = 0; ihc < 10; ihc++) {
-                     handle_collisions_2( idx)
+                     handle_collisions( idx)
                      if (count_collisions(({})).size == 0) {
                          break
@@ Line 1,614: / Line 1,603: @@
                                      var idx = {(atomno=@{{chain=gChain}.atomno.min})
                                          and (chain=gChain)}.atomIndex
-                                     handle_collisions_2( idx)
+                                     handle_collisions( idx)
+                                 }
+                             }
@@ Line 2,008: / Line 1,997: @@
      gPlico = "TUG"
-     plico_prelim()
+     plico_prelim(TRUE)
      gBondPicking = bondPicking
      set bondPicking TRUE

@@ Line 3: / Line 3: @@
 '''Tug''' is a member of the Plico suite of protein folding tools described in [[User:Remig/plico]] . It may be installed and accessed as a macro with the file:
 <pre>Title=PLICO Tug
-Script=script <path to your scripts folder>/tug.spt;plicotug</pre>
+Script=script <path to your scripts folder>/tug.spt;plico_tug</pre>
 saved as plicotug.macro in your .jmol/macros directory as described in [[Macro]].