User:Remig/plico/remap - Revision history

Remig at 17:17, 12 April 2016

2016-04-12T17:17:38Z

Remig at 14:38, 11 September 2015

2015-09-11T14:38:38Z

Remig: Add menu toggle

2015-07-24T18:38:49Z

Add menu toggle

Remig at 18:44, 13 July 2015

2015-07-13T18:44:40Z

Remig at 19:03, 26 August 2014

2014-08-26T19:03:29Z

Remig: Handle multiple frames

2014-07-17T15:13:50Z

Handle multiple frames

Show changes

Remig: lc all functions

2014-05-16T15:18:34Z

lc all functions

Remig: Do not var globals

2014-04-03T15:41:49Z

Do not var globals

Remig at 13:43, 18 March 2014

2014-03-18T13:43:23Z

Show changes

Remig at 00:15, 16 February 2014

2014-02-16T00:15:00Z

@@ Line 13: / Line 13: @@
 Copy and paste the following to a text editor and save to your scripts directory as remap.spt:
 <pre>#   remap - Jmol script by Ron Mignery
-#   v1.9 beta    9/11/2015 -use thisModel
+#   v1.10 beta    4/12/2016 -require latest common includes
+#
 #   Calculate or change polypeptide chain, atom number, residue names and/or residue
@@ Line 90: / Line 90: @@
          # Prompt for new designators
-         f = {atomIndex=n0idx}.file
+         var f = {atomIndex=n0idx}.file
-         m = {atomIndex=n0idx}.model
+         var m = {atomIndex=n0idx}.model
          var iResno = {atomIndex=n0idx}.resno
          var iChain = {atomIndex=n0idx}.chain
@@ Line 521: / Line 521: @@
      # 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 13: / Line 13: @@
 Copy and paste the following to a text editor and save to your scripts directory as remap.spt:
 <pre>#   remap - Jmol script by Ron Mignery
-#   v1.8 beta    7/24/2015 -add menu toggle
+#   v1.9 beta    9/11/2015 -use thisModel
+#
 #   Calculate or change polypeptide chain, atom number, residue names and/or residue
@@ Line 49: / Line 49: @@
      select {atomIndex=aIdx}
-     var cSet = {selected}
+     var sSet = {selected}
-     while (cSet.size > 0) {
+     while (sSet) {
-         for (var i = 1; i <= cSet.size; i++) {
+         for (var i = 1; i <= sSet.size; i++) {
-             var idx = cSet[i].atomIndex
+             var idx = sSet[i].atomIndex
              var caIdx = get_bb_nward_ca_idx(idx)
              if (caIdx >= 0) {
-                 if ({connected({atomIndex=idx}) and not {hydrogen}}.size < 2) {
+                 var cset = connected({atomIndex=idx}) and not {hydrogen}
-                     return idx
+                var ccset = connected(cset) and not {hydrogen}
+                 }
+             }
+         } # endfor
-         cSet = connected({selected}) and not {selected} and not {hydrogen}
-         select {selected} or cset
+        sSet = connected({selected}) and not {selected} and not {hydrogen}
+         select {selected} or sSet
      return -1
+}
@@ Line 68: / Line 75: @@
 # Bound to ALT-LEFT-CLICK by plico_remap
 function remap_cargo_mb() {
      var idx =_atomPicked
@@ Line 90: / Line 95: @@
          var iChain = {atomIndex=n0idx}.chain
          var iNo = {atomIndex=n0idx}.atomno
-         select {(file=f) and (model=m)}
+         select {thisModel}
          color {selected} @gScheme
-         select {(chain=iChain) and (file=f) and (model=m)}
+         select {(chain=iChain) and thisModel}
          color {selected} @gAltScheme
          refresh
@@ Line 120: / Line 125: @@
      if (isValid) {
-         delete {hydrogen and (file=f) and (model=m)}
+         delete {hydrogen and thisModel}
-         delete {hoh and (file=f) and (model=m)}
+         delete {hoh and thisModel}
-         delete %B and (file=f) and (model=m)
+         delete %B and thisModel
          ssbonds off
@@ Line 141: / Line 146: @@
          var proDidx = -1
          var oxtIdx = -1
-         while ((nIdx >= n0idx) or (cSet.size > 0)) {
+         while ((nIdx >= n0idx) or (cSet)) {
              var s = array(1, 2, 3)
              var pTrp = 0
@@ Line 334: / Line 339: @@
                  else if (newAtomName == "XD") { # LEU ASP ASN
                      var cTrp = (connected(cSet[2]) and not {selected})
-                     var sTrp = ((trp.size > 0) ? (trp[1].element=="N") : false)
+                     var sTrp = ((trp) ? (trp[1].element=="N") : false)
                      if ((cSet[2].element != "C") or sTrp
                          or ((connected(cSet[1]) and not {selected}).size == 0)) {
@@ Line 515: / Line 520: @@
 function plico_remap() {
-     # Push selected
+     # Load common functions if not already
-     gSelSaves = {selected}
+     if (kCommon < 6) {
-     gScheme = defaultColorScheme
+     gPlico = "Remap"
-     gAltScheme = ((gScheme == "Jmol") ? "Rasmol" : "Jmol")
+     plico_prelim(false, true)
-     set echo TOP LEFT
-    background ECHO yellow
+     gEcho = "_______REMAP_______|ALT-CLICK=select chain|SHIFT-DOUBLE-CLICK=exit"
      echo @gEcho
      set picking ON
      bind "ALT-LEFT-CLICK" "_pickAtom";
      bind "ALT-LEFT-CLICK" "+:remap_cargo_mb";
-     bind "DOUBLE" "remap_exit";
+     bind "SHIFT-DOUBLE" "plico_exit(true)";
      bind "LEFT-CLICK" "+:plico_menu_toggle";
+}
 # End of REMAP.SPT</pre>

@@ Line 13: / Line 13: @@
 Copy and paste the following to a text editor and save to your scripts directory as remap.spt:
 <pre>#   remap - Jmol script by Ron Mignery
-#   v1.7 beta    1/23/2015 -set appendNew only while inline
+#   v1.8 beta    7/24/2015 -add menu toggle
+#
 #   Calculate or change polypeptide chain, atom number, residue names and/or residue
@@ Line 525: / Line 525: @@
      echo @gEcho
      gChain = ""
      unbind
@@ Line 531: / Line 532: @@
      bind "ALT-LEFT-CLICK" "+:remap_cargo_mb";
      bind "DOUBLE" "remap_exit";
+}

@@ Line 13: / Line 13: @@
 Copy and paste the following to a text editor and save to your scripts directory as remap.spt:
 <pre>#   remap - Jmol script by Ron Mignery
-#   v1.6 beta    7/26/2014 -.file not .frame
+#   v1.7 beta    1/23/2015 -set appendNew only while inline
+#
 #   Calculate or change polypeptide chain, atom number, residue names and/or residue
@@ Line 492: / Line 492: @@
          delete {selected}
          ls += "end \"append remap\""
          script inline @{ls}
          var xx = {element="Xx"}
          for (var i = 1; i <= xx.size; i++) {
@@ Line 515: / Line 518: @@
      gSelSaves = {selected}
      gScheme = defaultColorScheme
      gAltScheme = ((gScheme == "Jmol") ? "Rasmol" : "Jmol")
@@ Line 542: / Line 543: @@
      color {selected} @gScheme
      gBusy = false
      # Pop selected

@@ Line 13: / Line 13: @@
 Copy and paste the following to a text editor and save to your scripts directory as remap.spt:
 <pre>#   remap - Jmol script by Ron Mignery
-#   v1.5 beta    6/17/2014 -handle multiple frames
+#   v1.6 beta    7/26/2014 -.file not .frame
+#
 #   Calculate or change polypeptide chain, atom number, residue names and/or residue
 #    numbers and print the resultant 1 char string
+#
-gAppendNew = FALSE
+gAppendNew = false
-gBusy = FALSE
+gBusy = false
 # Search for N-C-C-0
@@ Line 78: / Line 78: @@
      # If n-terminal N can be found
      var n0idx = find_n0_idx(idx)
-     var isValid = FALSE
+     var isValid = false
      var newResno = 1
      var newChain = "A"
@@ Line 85: / Line 85: @@
          # Prompt for new designators
          var iResno = {atomIndex=n0idx}.resno
          var iChain = {atomIndex=n0idx}.chain
          var iNo = {atomIndex=n0idx}.atomno
          select {(chain=iChain) and (file=f) and (model=m)}
          color {selected} @gAltScheme
@@ Line 108: / Line 112: @@
                          and (newChain.size == 1)
                          and (newAtomno > 0)) {
-                             isValid = TRUE
+                             isValid = true
+                     }
+                 }
@@ Line 133: / Line 137: @@
          var newGreek = ""
          var newCount = ""
-         var isCB = FALSE
+         var isCB = false
          var nIdx = n0idx
          var proDidx = -1
@@ Line 150: / Line 154: @@
                      s1 = "X"
                      newAtomName = "N"
-                     isCB = FALSE
+                     isCB = false
+             }
              else if (cSet.size == 1) {
@@ Line 250: / Line 254: @@
                          else {
                              proDidx = cSet[i].atomIndex
-                             cSet[i].selected = FALSE
+                             cSet[i].selected = false
+                         }
+                     }
@@ Line 277: / Line 281: @@
+                         }
                          else { # CB
-                             isCB = TRUE
+                             isCB = true
-                             cSet[i].selected = FALSE
+                             cSet[i].selected = false
                              cSet = (cSet and not cSet[i])
                              continue
@@ Line 293: / Line 297: @@
                                  nIdx = cSet[i].atomIndex
+                             }
-                             cSet[i].selected = FALSE
+                             cSet[i].selected = false
+                         }
                          else {
@@ Line 309: / Line 313: @@
                          if (cSet[i].element != "C") {
                              nIdx = cSet[i].atomIndex
-                             cSet[i].selected = FALSE
+                             cSet[i].selected = false
                              continue
+                         }
@@ Line 330: / Line 334: @@
                  else if (newAtomName == "XD") { # LEU ASP ASN
                      var cTrp = (connected(cSet[2]) and not {selected})
-                     var sTrp = ((trp.size > 0) ? (trp[1].element=="N") : FALSE)
+                     var sTrp = ((trp.size > 0) ? (trp[1].element=="N") : false)
                      if ((cSet[2].element != "C") or sTrp
                          or ((connected(cSet[1]) and not {selected}).size == 0)) {
-                         bRev = TRUE
+                         bRev = true
+                     }
                      if ((cSet[2].element == "O") or (cSet[1].element == "N")
                          or ((cSet[1].element == "C") and (cSet[2].element != "C"))) {
-                         bRev = TRUE
+                         bRev = true
+                     }
                      if (hasN) {
@@ Line 365: / Line 369: @@
                      if ((cSet[2].element == "O") or (cSet[1].element == "N")
                          or ((cSet[1].element == "C") and (cSet[2].element != "C"))) {
-                         bRev = TRUE
+                         bRev = true
+                     }
                      if (hasO) {
@@ Line 410: / Line 414: @@
                                  nIdx = cSet[i].atomIndex
+                             }
-                             cSet[i].selected = FALSE
+                             cSet[i].selected = false
+                         }
                          else {
@@ Line 499: / Line 503: @@
          print ls1
+     }
+}
@@ Line 509: / Line 516: @@
      gAppendNew = appendNew
-     set appendNew FALSE
+     set appendNew false
      gScheme = defaultColorScheme
      gAltScheme = ((gScheme == "Jmol") ? "Rasmol" : "Jmol")
@@ Line 534: / Line 541: @@
      select ((file=f) and (model=m))
      color {selected} @gScheme
-     gBusy = FALSE
+     gBusy = false
      set appendNew gAppendNew

@@ Line 1: / Line 1: @@
 '''Remap''' allows you to change the chain ID, atom numbers and/or residue numbers of a polypeptide chain by mouse actions.  It also calculates group values [amino acid names (GLY, THR, etc.)].  Finally it prints the 1 char resultant string to the console.
 Note that it will also remove all waters, hydrogens and %B alternates when any chain is updated.
@@ Line 6: / Line 8: @@
 <pre>Title=PLICO Remap
-Script=script <path to your scripts folder>/remap.spt;plicoRemap
+Script=script <path to your scripts folder>/remap.spt;plico_remap
 </pre>saved as plicoRemap.macro in your .jmol/macros folder as described in [[Macro]].
 Copy and paste the following to a text editor and save to your scripts folder as remap.spt:
 <pre>#   remap - Jmol script by Ron Mignery
-#   v1.3 beta    4/3/2014 for Jmol 14 -do not var globals for Jmol 14.0.13+
+#   v1.3 beta    5/16/2014 -lc all functions
+#
 #   Calculate or change polypeptide chain, atom number, residue names and/or residue
 #    numbers and print the resultant 1 char string
+#
-gAppendNew = TRUE
+var gAppendNew = TRUE
 # Search for N-C-C-0
-function getBBnCAidx(idx) {
+function get_bb_nward_ca_idx(idx) {
      if ({atomIndex=idx}.element == "N") {
          var c1 = (connected({atomIndex=idx}) and not {hydrogen})
@@ Line 43: / Line 45: @@
 # Find N-terminal N
-function findN0idx(aIdx) {
+function find_n0_idx(aIdx) {
      select {atomIndex=aIdx}
@@ Line 50: / Line 52: @@
          for (var i = 1; i <= cSet.size; i++) {
              var idx = cSet[i].atomIndex
-             var caIdx = getBBnCAidx(idx)
+             var caIdx = get_bb_nward_ca_idx(idx)
              if (caIdx >= 0) {
                  if ({connected({atomIndex=idx}) and not {hydrogen}}.size < 2) {
@@ Line 63: / Line 65: @@
+}
-# Bound to ALT-LEFT-CLICK by plicoRemap
+# Bound to ALT-LEFT-CLICK by plico_remap
-function remapCargoMB() {
+function remap_cargo_mb() {
      var idx =_atomPicked
@@ Line 72: / Line 74: @@
      # If n-terminal N can be found
-     var n0idx = findN0idx(idx)
+     var n0idx = find_n0_idx(idx)
      var isValid = FALSE
      var newResno = 1
@@ Line 491: / Line 493: @@
 # Top level of Remap
-function plicoRemap() {
+function plico_remap() {
      # Push selected
@@ Line 509: / Line 511: @@
      set picking ON
      bind "ALT-LEFT-CLICK" "_pickAtom";
-     bind "ALT-LEFT-CLICK" "+:remapCargoMB";
+     bind "ALT-LEFT-CLICK" "+:remap_cargo_mb";
-     bind "DOUBLE" "remapExit";
+     bind "DOUBLE" "remap_exit";
+}
-# Bound to DOUBLE by plicoRemap
+# Bound to DOUBLE by plico_remap
-function remapExit() {
+function remap_exit() {
      unbind
      halo off