User:Remig/plico/plicoCommon - Revision history

Remig: Avoid "axis," a newly reserved word

2016-04-12T17:08:47Z

Avoid "axis," a newly reserved word

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Remig at 14:27, 11 September 2015

2015-09-11T14:27:36Z

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Remig at 12:00, 27 July 2015

2015-07-27T12:00:24Z

Remig: Add menu toggle

2015-07-24T18:25:05Z

Add menu toggle

Remig: Add double-bonding support

2015-07-13T18:32:20Z

Add double-bonding support

Remig: atom_rcn() => get_atom_rcn()

2014-11-18T21:29:45Z

atom_rcn() => get_atom_rcn()

Remig at 17:44, 18 August 2014

2014-08-18T17:44:26Z

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Remig at 16:04, 17 July 2014

2014-07-17T16:04:43Z

Remig: Add stuff

2014-07-16T14:45:04Z

Add stuff

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Remig: add plico-prelim param

2014-05-16T16:43:42Z

add plico-prelim param

@@ Line 3: / Line 3: @@
 Copy and paste the following into a text editor and save in your scripts folder as plicoCommon.spt.
 <pre>#   plicoCommon - Jmol script by Ron Mignery
-#   v1.9 beta    7/24/2015 -add menu toggle
+#   v1.9 beta    7/26/2015 -add menu toggle
+#
 #   Routines and values common to all Plico suite scripts
@@ Line 352: / Line 352: @@
      if (gPlico.size > 0) {
          p = prompt(format("Exit %s?", gPlico), "Yes|No|Undo all", true)
-         if (p == "Undo") {
+         if (p == "Undo all") {
              load plico_save.pdb
              script inline gZoom

@@ Line 1: / Line 1: @@
 This script contains routines used by other scripts of the Plico suite.  It must be located in the same directory as any script that uses these routines.
 Copy and paste the following into a text editor and save in your scripts folder as plicoCommon.spt.
 <pre>#   plicoCommon - Jmol script by Ron Mignery
-#   v1.8 beta    7/13/2015 -add double-bond routine
+#   v1.9 beta    7/24/2015 -add menu toggle
+#
 #   Routines and values common to all Plico suite scripts
 #   Must be present in the same directory as other Plico scripts that use it
-kCommon = 5
+kCommon = 6
 kDtolerance = 0.1
 kAtolerance = 5.0
@@ Line 21: / Line 21: @@
 gAltScheme = "Rasmol"
 gBusy = false
 # Return L tetrahedron point if i1<i2<i3, else R point
@@ Line 132: / Line 134: @@
          and (file=f) and (model=m)}.atomName == "C") { # if psi
          add_sc_to_select(lastno-1, false, false, iChain)
+     }
+}
@@ Line 189: / Line 208: @@
              var lcAtoms = (within(kCtolerance, false, {atomIndex=idx})
                  and {atomIndex > idx}
                  and not connected({atomIndex=idx}))
              if (lcAtoms.size > 0) {
@@ Line 245: / Line 263: @@
 function hi {
      hover "%D %U"
+}
@@ Line 288: / Line 325: @@
      gZoom = script("show zoom")
      gRotate = script("show rotation")
-     write tugsave.pdb
+     write plico_save.pdb
      select none
@@ Line 314: / Line 351: @@
      var done = false
      if (gPlico.size > 0) {
-         p = prompt(format("Exit %s?", gPlico), "Yes|No|Undo", true)
+         p = prompt(format("Exit %s?", gPlico), "Yes|No|Undo all", true)
          if (p == "Undo") {
-             load tugsave.pdb
+             load plico_save.pdb
              script inline gZoom
              rotate @gRotate
              echo Tug session undone
              if (gPlicoRecord != "") {
-                 plico_record("load tugsave.pdb;")
+                 plico_record("load plico_save.pdb;")
+             }
+         }
@@ Line 338: / Line 375: @@
          gBusy = false
          background ECHO yellow
          done = true
@@ Line 437: / Line 475: @@
+     }
+}
-# end of plicocommon.spt
 # end of plicocommon.spt</pre>

@@ Line 3: / Line 3: @@
 Copy and paste the following into a text editor and save in your scripts folder as plicoCommon.spt.
 <pre>#   plicoCommon - Jmol script by Ron Mignery
-#   v1.7 beta    11/18/2014 -atom_rcn() => get_atom_rcn()
+#   v1.8 beta    7/13/2015 -add double-bond routine
+#
 #   Routines and values common to all Plico suite scripts
 #   Must be present in the same directory as other Plico scripts that use it
-kCommon = 4
+kCommon = 5
 kDtolerance = 0.1
 kAtolerance = 5.0
@@ Line 54: / Line 54: @@
 function abs( x) {
-     if (x < 0) {
+     return ((x < 0) ? -x : x)
+}
 # Selected must include second parameter but not the first
 function set_distance_atoms( static, mobile, desired) {
@@ Line 197: / Line 195: @@
                  if (rc == true) {
                      print format("Collision of idx=%d with %s", idx, lcAtoms)
+                 }
+             }
@@ Line 243: / Line 244: @@
 # A handy debug routine
 function hi {
-     print "hoverLabel=%D %U (atomIndex...)"
+     hover "%D %U"
+}
@@ Line 379: / Line 376: @@
      echo "vx = phi        vy = previous psi"
+}
 # end of plicocommon.spt</pre>

@@ Line 3: / Line 3: @@
 Copy and paste the following into a text editor and save in your scripts folder as plicoCommon.spt.
 <pre>#   plicoCommon - Jmol script by Ron Mignery
-#   v1.6 beta    7/16/2014 -handle multiple frames+
+#   v1.7 beta    11/18/2014 -atom_rcn() => get_atom_rcn()
+#
 #   Routines and values common to all Plico suite scripts
 #   Must be present in the same directory as other Plico scripts that use it
-kCommon = 3
+kCommon = 4
 kDtolerance = 0.1
 kAtolerance = 5.0
@@ Line 226: / Line 226: @@
 # Utility
-function atom_rcn( iResno, iChain, iName) {
+function get_atom_rcn( iResno, iChain, iName) {
      var f = (_frameID/1000000)
      var m = (_frameID%1000000)
@@ Line 347: / Line 347: @@
+     }
      return done
+}
 # end of plicocommon.spt</pre>

@@ Line 3: / Line 3: @@
 Copy and paste the following into a text editor and save in your scripts folder as plicoCommon.spt.
 <pre>#   plicoCommon - Jmol script by Ron Mignery
-#   v1.5 beta    7/16/2014 -handle multiple frames
+#   v1.5 beta    7/16/2014 -handle multiple frames+
+#
 #   Routines and values common to all Plico suite scripts
@@ Line 316: / Line 316: @@
 function plico_exit() {
      var p = ""
      if (gPlico.size > 0) {
          p = prompt(format("Exit %s?", gPlico), "Yes|No|Undo", TRUE)
@@ Line 341: / Line 342: @@
          gBusy = FALSE
          background ECHO yellow
          # Pop selected
          select gSelSaves
+     }
+}
 # end of plicocommon.spt</pre>

@@ Line 3: / Line 3: @@
 Copy and paste the following into a text editor and save in your scripts folder as plicoCommon.spt.
 <pre>#   plicoCommon - Jmol script by Ron Mignery
-#   v1.3 beta    5/16/2014 -lc all functions
+#   v1.4 beta    5/16/2014 - add plico-prelim param
+#
 #   Routines and values common to all Plico suite scripts
@@ Line 180: / Line 180: @@
+}
-function plico_prelim() {
+function plico_prelim(repair) {
      # Push selected
@@ Line 187: / Line 187: @@
      # Bad idea to proceed when collisions present
-     while (TRUE) {
+     while (repair) {
          var cc = count_collisions(({})).size
          if (cc > 0) {
@@ Line 204: / Line 204: @@
                          gChain = {atomIndex=idx}.chain
                          select {chain=gChain}
-                         handleCollisions2( idx)
+                         handle_collisions( idx)
+                     }
+                 }
@@ Line 228: / Line 228: @@
      gChain = ""
      unbind
+}
@@ Line 240: / Line 251: @@
              echo Tug session undone
              if (gPlicoRecord != "") {
-                 plicoRecord("load tugsave.pdb;")
+                 plico_record("load tugsave.pdb;")
+             }
+         }