User:Remig/plico/plicoCommonNT - Revision history

Remig: Avoid "axis," a newly reserved word

2016-04-12T17:11:07Z

Avoid "axis," a newly reserved word

Remig at 14:30, 11 September 2015

2015-09-11T14:30:41Z

Show changes

Remig: Support fold_trna.spt

2015-07-24T18:27:10Z

Support fold_trna.spt

Remig: Add support for fold_trna.spt

2015-07-13T18:35:23Z

Add support for fold_trna.spt

Show changes

Remig: Faster A-B conversion

2014-11-18T21:31:49Z

Faster A-B conversion

Show changes

Remig: better A-B conversion

2014-08-18T17:30:21Z

better A-B conversion

Show changes

Remig: Handle multiple frames

2014-07-16T14:50:46Z

Handle multiple frames

Show changes

Remig at 12:46, 11 June 2014

2014-06-11T12:46:32Z

Remig: Add stuff

2014-06-10T20:48:22Z

Add stuff

Show changes

Remig: lc all functions

2014-05-16T15:01:49Z

lc all functions

Show changes

@@ Line 3: / Line 3: @@
 Copy and paste the following into a text editor and save in your scripts folder as plicoNTcommon.spt.
 <pre>#   plicoNTcommon - Jmol script by Ron Mignery
-#   v1.9 beta    9/11/2015 -use thisModel
+#   v1.10 beta    4/12/2016 -axis is now a reserved word
+#
 #   Routines and values common to Plico suite scripts that work with nucleotides
 #   Must be present in the same directory as other Plico scripts that use them
-kNTcommon = 5
+kNTcommon = 6
 kC5O5PO3B = -71.0
 kO5PO3C3B = -107.0
@@ Line 1,188: / Line 1,188: @@
 # Select mobile before calling
 function pivot_to_close_atoms( aMov, aStat, aPivot, dist) {
-     var axis = cross(aStat.xyz, aMov.xyz) - aPivot.xyz
+     var caxis = cross(aStat.xyz, aMov.xyz) - aPivot.xyz
      var dir = 1
      var d = distance(aMov, aStat)
      if (d > dist) {
          while (d > dist) {
-             rotateSelected @aPivot @axis @dir
+             rotateSelected @aPivot @caxis @dir
              var nd = distance(aMov, aStat)
              if (nd > d) {
-                 rotateSelected @aPivot @axis @{-dir}
+                 rotateSelected @aPivot @caxis @{-dir}
                  if (dir == 1) {
-                     rotateSelected @aPivot @axis @{-dir}
+                     rotateSelected @aPivot @caxis @{-dir}
                      dir = -1
                      continue
@@ Line 1,211: / Line 1,211: @@
      else {
          while (d < dist) {
-             rotateSelected @aPivot @axis @dir
+             rotateSelected @aPivot @caxis @dir
              var nd = distance(aMov, aStat)
              if (nd < d) {
-                 rotateSelected @aPivot @axis @{-dir}
+                 rotateSelected @aPivot @caxis @{-dir}
                  if (dir == 1) {
-                     rotateSelected @aPivot @axis @{-dir}
+                     rotateSelected @aPivot @caxis @{-dir}
                      dir = -1
                      continue

@@ Line 3: / Line 3: @@
 Copy and paste the following into a text editor and save in your scripts folder as plicoNTcommon.spt.
 <pre>#   plicoNTcommon - Jmol script by Ron Mignery
-#   v1.8 beta    7/13/2015 -suport fold_trna.spt
+#   v1.8 beta    7/13/2015 -support fold_trna.spt
+#
 #   Routines and values common to Plico suite scripts that work with nucleotides
@@ Line 85: / Line 85: @@
          aOP2.xyz = get_tet_idx(aO3p.atomIndex, aP.atomIndex, aO5.atomIndex, 1.73)
          aOP1.xyz = get_tet_idx(aO5.atomIndex, aP.atomIndex, aO3p.atomIndex, 1.73)
-         var ms = minimizationSilent
+         plico_minimize( {(connected(aP) or aP) and not aO3p})
          select selsave
+     }
@@ Line 177: / Line 174: @@
              aOP1.xyz = get_tet_idx(aO5.atomIndex, aP.atomIndex, aO3p.atomIndex, 1.73)
              if (force) {
-                 var savemt = useMinimizationThread
+                 plico_minimize ({(connected(aP) or aP) and not aO3p})
+             }
          }   # endfor i
@@ Line 198: / Line 189: @@
 function fix_all_nt_collisions( iChain) {
      var selsave = {selected}
      chset = count_collisions(true)
      for (var i = 1; i <= chset.size; i++) {
@@ Line 214: / Line 201: @@
          if ({c and cset and not base}.size > 0) {
              select {@{rset} and base}
-             minimize {selected}
+             plico_minimize( {selected})
+         }
          else if (c.atomname[1][2] == "OP") {
@@ Line 220: / Line 207: @@
+         }
          else {
-             select {@{rset}}
+             plico_minimize(rset)
+         }
+     }
      measure off
      select selsave
+}
@@ Line 489: / Line 473: @@
      select {((resno=res5) or (resno=@{res5+1}))
          and (chain=iChain) and (file=f) and (model=m)}
-     minimize {selected}
+     plico_minimize( {selected})
      fix_p_res(res5+1, iChain, true)
+}
@@ Line 522: / Line 506: @@
      select {((resno=res5) or (resno=@{res5+1}))
       and (chain=iChain) and (file=f) and (model=m)}
-     minimize {selected}
+     plico_minimize( {selected})
      fix_p_res(res5+1, iChain, true)
      fix_p_res(res5, iChain, true)
@@ Line 895: / Line 879: @@
 function adjust_nts(res5, res3, iChain, toab, a, s) {
      # Collect any pairing
@@ Line 934: / Line 916: @@
+         }
+     }
+}
@@ Line 957: / Line 938: @@
 function repair_p_res(res, iChain) {
      var aP = get_atom_rcn( res, iChain, "P")
-     var ms = minimizationSilent
+     plico_minimize( {connected(aP) or aP})
+}
@@ Line 1,002: / Line 980: @@
              var pyang = abs(angle(aC6or4, near[i], aN1or3))
              var dihedral = abs(angle(aC2p, near[i], aN1or3, aC2))
              if ((puang > 110) and (pyang > 110) and (dihedral < 40)) {
                  return [near[i].resno, near[i].chain, dist, puang]
@@ Line 1,493: / Line 1,470: @@
          connected({resno=r}) and {(chain=iChain) and (file=f) and (model=m)})
      if (cset.size > 0) {
          for (var i = 0; i < cset.size; i++) {
-             minimize {(resno=r) or (resno=@{cset[i].resno})}
+             plico_minimize( {(resno=r) or (resno=@{cset[i].resno})})
+         }
+     }
@@ Line 1,509: / Line 1,480: @@
          and {(chain=iChain) and (file=f) and (model=m)})
      if (cset.size > 0) {
          for (var i = 0; i < cset.size; i++) {
-             minimize {(resno=r) or (resno=@{cset[i].resno})}
+             plico_minimize( {(resno=r) or (resno=@{cset[i].resno})})
+         }
+     }
+}
@@ Line 1,579: / Line 1,544: @@
 function replane_bases(iChain) {
      for (var i = {chain=iChain}.resno.min; i <= {chain=iChain}.resno.max; i++) {
-         minimize {resno=i and base}
+         plico_minimize( {resno=i and base})
+     }
+}

@@ Line 3: / Line 3: @@
 Copy and paste the following into a text editor and save in your scripts folder as plicoNTcommon.spt.
 <pre>#   plicoNTcommon - Jmol script by Ron Mignery
-#   v1.2 beta    6/9/2014 -add stuff
+#   v1.3 beta    6/11/2014 -bug fix
+#
 #   Routines and values common to Plico suite scripts that work with nucleotides
@@ Line 479: / Line 479: @@
+         }
+     }
-     return [-1, aC1.chain]
+     return [-1, aC4or6.chain]
+}
 # end of plicoNTcommon.spt
 </pre>