Lines Matching +full:- +full:- +full:-
7 # bug fix: (not really) -- " " character in VRML export added to accomodate AutoDesk 3D MAX import …
15 # bug fix: MO export to cartesian exporters (VRML/X3D/Maya) should not do front-only
20 # -----------------------------------------------------------------------------
27 # -----------------------------------------------------------------------------
33 # utilizing user-defined functions of the form @{xxx({n})}
40 # -----------------------------------------------------------------------------
50 # bug fix: labels given text after containing an image have incorrect y-displacement
53 # -----------------------------------------------------------------------------
58 # bug fix: Jmol 11.8.10-11.8.13 will not read state orientation correctly
60 # -----------------------------------------------------------------------------
71 # -----------------------------------------------------------------------------
77 # bug fix: NWChem reader not reading files with lower-case-only atom names
78 # bug fix: code - viewer.getDisplayModelIndex() not used properly when background model is present
82 # -----------------------------------------------------------------------------
94 # code: JmolFrameExportJmolAdapter abandoned -- hasn't been implemented since 11.0
96 # -----------------------------------------------------------------------------
100 # bug fix: MSIE mouse-wheel malfunction due to Jmol not consuming the wheel motion
102 # bug fix: Hall name translator can incorrectly assign matrix for F m -3 m group
113 # -----------------------------------------------------------------------------
124 # -- MOLECULAR keyword added
128 # -----------------------------------------------------------------------------
137 # causing applet-applet interference.
143 # bug fix: jmol -ionxs with a script that includes measurement tries to update a nonexistant measur…
153 # bug fix: zshade now working correctly (almost -- see 11.8.11)
154 # bug fix: setting spacefill to a large user-defined VDW radius incorrect
158 # -----------------------------------------------------------------------------
164 # bug fix: Hall symbol translation generates incorrect Jones-Faithful operation (missing translatio…
165 # (broken by 11.8.4 9/5/2009) -- Thank you, Sarah Mattler, WUSTL!
167 # -----------------------------------------------------------------------------
180 # -----------------------------------------------------------------------------
188 # -----------------------------------------------------------------------------
194 # bug fix: symop() -- can now be used without "all."
197 # -----------------------------------------------------------------------------
205 # bug fix: compiler error for literal -0 or -0.0
210 # bug fix: animation direction -1 not functional
211 # bug fix: script lines 1-3 not functional
213 # -----------------------------------------------------------------------------
220 # bug fix for MOReaders * NBO: --- note, "-" can be in column with " " causing tokenization failure
222 # -----------------------------------------------------------------------------
232 # new feature: draw ID xxx SYMOP [n or "-x,y,z"] [optional {atom or position}]
234 # see http://chemapps.stolaf.edu/jmol/docs/examples-11/showsym.htm
265 # -----------------------------------------------------------------------------
277 # * IDTFConverter.exe -input t.idtf -output t.u3d
281 # * see http://www.ecma-international.org/publications/standards/Ecma-363.htm
285 # bug fix: gaussian reader may fail to read MOs from Gaussian 03: AM64L-G03RevC.01 3-Apr-2004
287 # -----------------------------------------------------------------------------
292 # bug fix: DRAW point size 6 pixels (an even number) sets it just one pixel off center -- 7 is bett…
293 # new feature (TODO): 4D extension (that's right -- FOUR dimensions)
295 # new feature: lone pairs and radicals -- extension of lcaoCartoon:
303 # TODO: load 1crn.pdb;quaternion;quaternion diff;zap 2.1 -- leaves blank model 2.1 and destroys sta…
304 # TODO: what to do about deleting models prior to current -- why statescript removed?
316 # new feature: set quaternionFrame "a" -- alpha-carbon-ONLY straightness. see 1JGQ
320 # new feature: set helixStep 0 -- relates a quaternion to the standard reference frame
323 # new feature: [x,y,z].sum2 or {xx}.someProperty.sum2 -- sum of squares
325 # -- includes draw, ellipsoids, dots, isosurface, cartoons, stars, halos,
327 # -- no background labels
328 # -- labels are not exactly the right size
329 # -- no background image
330 # -- no ellipsoid quadrant cutouts
331 # -- slightly irregular trace when very small diameter
335 # -----------------------------------------------------------------------------
340 # new feature: set helixStep 1,2,3,... sets step for quaternion-based analysis of structure -- see…
341 # bug fix: 1C4D has [FOR] -- not accepted
347 # new feature: isosurface area for subsets -- use
351 # -----------------------------------------------------------------------------
355 # bug fix: mouse-picked measurements broken in 11.8.RC1
357 # -----------------------------------------------------------------------------
362 # -- note, bug fixes in .RCx versions will not be fixed in 11.6
364 # -----------------------------------------------------------------------------
368 # new feature: set quaternionFrame "RC" or "RP" -- ramachandran-derived straightness
375 # new feature: NAVIGATION STOP -- sets navX, navY, navZ to 0
391 # return a value -- any value, not just an array:
399 # bug fix: spacegroup "-- [--]" displayed when load command option SPACEGROUP is used
406 # new feature: within("HELIX"), within("SHEET") -- helix and sheet, but not ends
407 # new feature: all.bin(f0, f1, df) -- binning of data to give an integer array of counts
421 # -----------------------------------------------------------------------------
427 # This application completely disallows any display -- it is totally formless
429 # no display, no shapes, no labels, no echos -- just the model data.
431 # bug fix: command-line jmol scripts not exiting jmol upon an error condition
434 # given x = C-alpha, C-carbonyl, or N (depending upon set quaternionFrame)
436 # "point" -- nearest point to x on local helix axis
437 # "axis" -- quaternion derivative vector normal indicating local helix axis
438 # "angle" -- rotation around local heix axis for resno i --> i+1
439 # "radius" -- vector normal from local helix point to x
440 # "draw" -- draw command for the local helix vector
450 # -----------------------------------------------------------------------------
455 # bug fix: load trajectory {0 -1 1} not loading any models if first model has 0 atoms
469 # TODO script editor -- search? argh... I knew this would be a can of worms...
470 # script editor -- undo/redo works (CTRL-Z, then SHIFT-CTRL-Z or CTRL-Y)
472 # new feature: drag/drop and file menu-open scripts directly into editor, from where they can be ch…
476 # scripts (and changing values during the pauses) - preliminary only
484 # new feature: SHOW TRACE -- reports stack trace
489 # script, do anything you want -- even within functions -- change variables,
490 # set parameters, anything -- and then resume with RESUME. Some of us
511 # as an equivalent of double quotes cannot break existing scripts. -- BH 06/2009
515 # -----------------------------------------------------------------------------
525 # new feature: merging of label() and format() functions -- same in all respects.
528 # -----------------------------------------------------------------------------
537 # new feature: a = [] note that a+=2 then produces [2] -- "a+=" similar to JavaScript a.push(2)
541 # -----------------------------------------------------------------------------
562 # new feature: -p Jmol application command line option --printOnly silent operation with only prin…
564 # java -Xmx512m -jar "Jmol.jar" -pions "myscript.spt"
570 …yfile.top" COORD {first,last,stride} "mdcrd::myfile.trj" defaults to last = -1 ("load all trajecto…
571 # bug fix: gzipped gzip file not read properly. (Jmol-FAH files)
576 # new feature: load ("filename", nBytesMax) --- and returns "java.io.FileNotFoundException" if file
580 # new feature: print {xxx}.label.all("xxxx") -- forces array even if only one atom (like "{xxx}.lab…
584 # code: refactored classes -- next best thing to a separate package (they aren't really public)
586 # CompilationTokenParser --> ScriptCompilationTokenParser
587 # Compiler --> ScriptCompiler
588 # Eval -> ScriptEvaluator
589 # FlowContext --> ScriptFlowContext
590 # Function -> ScriptFunction
591 # Variable -> ScriptVariable
607 # -----------------------------------------------------------------------------
611 # bug fix -- bitsets not copied: m1 = {m and selected} changes m to "m and selected"
618 # --Jmol scripting now supports ++, --, +=, -=, *=, /=, \=, |=, &=
619 # --The if, for, while, and function constructs are all about the same, using braces.
627 # --A relatively free typing of variables. Jmol is going to save variables as strings
631 # --Commands separated by semicolons or line breaks
632 # --Object-like methods and fields such as {*}.xyz.all.join(" ") and {atomno=3}.radius
633 # --On-the-fly compilation.
637 # --A broarder range of variable types, including boolean, integer, decimal,
638 # string, point, axis-angle/plane/quaternion, atom bitset, bond bitset,
639 # and one-dimensional array.
640 # --No case-sensitivity for variable names.
641 # --1-based rather than 0-based arrays. (ONLY because that's the way models are numbered.)
642 # --Array indexing from the back to the front using n <= 0: A[0] A[-1] A[-2].
643 # --Array ranges [n][m], for example A[-3][0]
644 # --Core commands do not use commas or parentheses.
645 # --Visual-Basic-like IF / ELSEIF /END IF, FOR/END FOR, WHILE /END WHILE, and GOTO options.
646 # --A broad range of mathematical operations
647 # --Of course, a whole suite of methods that relate to molecular structure.
661 # -----------------------------------------------------------------------------
679 # Jmol scripting now supports ++, --, +=, -=, *=, /=, \=, |=, &=
695 # plus some more -- no line breaks necessary for for/if/while:
710 # new feature: complete freedom from lines and "end if, end for, end while" --
745 # new feature: load "@x" -- inline load of data contained in variable x.
749 …ture: An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/
759 # new feature: .length alias for .size except for x.bonds - so it can be
789 # -----------------------------------------------------------------------------
806 # display insertion = "?" // single-character wildcard here
840 # yes D yes atomIndex atom 0-based index; a unique number for each atom regardless of the number …
843 # yes yes B yes atomType atom type (mol2, AMBER files) or atom name (other file types) -- Jmol 11.…
860 # yes n yes group 3-letter residue code
861 # yes m yes group1 single-letter residue code (amino acids only)
862 …-5 |ALA, ARG, ASN, ASP, CYS|| 6-10| GLN, GLU, GLY, HIS, ILE|| 11-15| LEU, LYS, MET, PHE, PRO|| …
864 … as [%[group]]%[sequence]:%[chain] %%%[altloc]/%[model] #%[atomno]. For non-PDB data, same as %[a…
869 # yes yes Q yes occupancy occupancy 0.00 - 1.00
875 # yes yes I yes radius currently displayed radius -- in SELECT command comparisons ("select radius…
880 …-derived straightness (second derivative of the quaternion describing the orientation of the resid…
886 # yes yes t yes temperature temperature factor (B-factor)
899 # q yes occupancy (0-100%)
990 # new feature: application flag -L --nosplash no splash screen (For Jmol in Sun Wonderland dev. 5)
993 # --NMR files where you want just one model at a time and, once loaded, want to save the positions
994 # --basically anywhere you want a "trajectory" but don't want to save all that data
997 # -----------------------------------------------------------------------------
1002 # new feature: load PARTIALCHARGE ... float ~[-3.4 x 10^38 to 3.4 x 10^38]
1003 # new feature: load TEMPERATURE ... float [-327.68 to 327.67], with 0.01 precision (stored as sho…
1008 # -----------------------------------------------------------------------------
1013 # --all features of the load command, but only loads the vibrational information
1014 # --applies {within(loadAtomDataTolerance,xyzcoord)}.vxyz = vibcoord, so to all unit cells
1015 # --optional n is just as for any load -- optional nth model
1016 # --operates on previously selected atoms only
1017 # --allows embedded jmolscript, just as for any load
1018 # --sets _vibrationName from file's atom set collection name
1021 # new feature: load {a b -c} packs a x b x c cells
1022 # new feature: select within(-0.1, {1/2 1/2 1/2}) -- negative distance within selects atoms based o…
1023 # new feature: select within(-0.1, atomno=3) -- negative distance within selects atoms based on uni…
1024 # new feature: select within(-0.1, true, atomno=3) -- negative distance within model selects atoms …
1025 # new feature: select ux|uy|uz < x.x -- selection based on unit coordinates
1026 # new feature: {x y z}.fxyz -- returns fractional from cartesian
1027 # new feature: {x y z}.uxyz -- returns unitcell from cartesian
1029 # new feature: {x y z}.xyz -- returns cartesian from fractional
1034 # new feature: {atomExpression}.uxyz, .ux, .uy, .uz -- unit cell coordinate
1039 # then {x}.uxyz will be in the range {-1,-1,-1/1} (inclusive) to {0,0,0/1} (exclusive)
1051 # -----------------------------------------------------------------------------
1055 # code: better treatment of user-defined space group
1059 # "v" (reverse -- "true" if a string does NOT match; nonmatching elements for list)
1067 # Hall symbol: -P 1
1077 # -P 1
1084 # bug fix: unitCell normalization error could miss some atoms in multi-unit cell visualizations
1088 # -----------------------------------------------------------------------------
1094 # new feature: label %G -- group index, like atom index, 0-based for entire collection
1095 # new feature: ramachandran DRAW -- draws dihedral planes and angles
1100 # -----------------------------------------------------------------------------
1105 # new feature: application -s - reads input from System.in (untested)
1109 # new feature: isosurface FunctionXYZ -- same as FunctionXY, but must return float[][][]
1110 # -- note, this involves an additional required function in interface JmolStatusListener
1113 # -----------------------------------------------------------------------------
1123 # bug fix: rotate -x n rotates wrong direction
1131 # -----------------------------------------------------------------------------
1145 # -----------------------------------------------------------------------------
1150 # bug fix -- Spartan reader adding " in front of atom label
1151 # new feature: frame ALIGN {atoms} -- aligns frames around designated atoms in each frame
1152 # for example: frame ALIGN {C2} -- align each frame on C2/n where n is a frame number
1153 # for example: frame ALIGN {*} -- align all frames on center for that frame
1154 # new feature: Spartan MO-Animation files can be read
1155 # bug fix -- animation/spin while script is rendering can cause Exception
1163 # bug fix -- trajectories with files having bonds can be a problem
1164 # bug fix -- animation/spinning while connections are being made can cause exception
1165 # code -- more documentation and somewhat reorganized adapter section.
1175 # will generate highest-occupied MO for all models and run through them quickly
1179 # -----------------------------------------------------------------------------
1186 # new feature: restore orientation DEFAULT -- resets orientation to file's default orientation or s…
1191 # -----------------------------------------------------------------------------
1201 # -----------------------------------------------------------------------------
1207 # -----------------------------------------------------------------------------
1221 # code: polygonColixes[] to define polygon colors rather than vertex-based colors (as in OBJ file)
1242 # bug fix: picked atoms automatically selected -- bug in 11.7.24
1247 # -----------------------------------------------------------------------------
1259 # -----------------------------------------------------------------------------
1265 # new feature: CTRL-K toggles keystrokes with display; ALT-K or CTRL_ALT_K same without display
1266 # color of frank displays condition -- blue (unsigned) or orange (signed) indicates ke…
1272 # -- streamlined methods for converting CUBE data to JVXL files
1274 # -----------------------------------------------------------------------------
1292 # -----------------------------------------------------------------------------
1296 # new feature: load "myfile.cif" {ijk i'j'k' -1}
1299 # same as {555 555 -1}
1301 # bug fix: {*}.formalCharge = 1 after {*}.formalCharge = -1 sets formal charge to -7 and exception
1304 # -----------------------------------------------------------------------------
1312 # new feature: u3d exporter template only -- no actual output
1314 # -----------------------------------------------------------------------------
1323 # -----------------------------------------------------------------------------
1327 # bug fix: protein-protein hydrogen bonds not calculated across biopolymer boundaries
1329 # -----------------------------------------------------------------------------
1335 # bug fix: application -i option still gives message from "set xxxx"
1336 # bug fix: recent application changes do not work with -w option
1338 # -----------------------------------------------------------------------------
1345 # new feature: new command "exitJmol" does just that -- application only;
1348 # new feature: application -d --debug sets loglevel to 5
1349 # new feature: application -J --jmolscript1 Jmol script BEFORE -s
1350 # new feature: application -j --jmolscript2 Jmol script AFTER -s not accepting values
1362 # of a specific quality (-1 indicates default)
1363 # 0 to 100 for JPG (-1 = default of 75)
1364 # 0-9 for PNG (-1 = default of 2)
1391 # -----------------------------------------------------------------------------
1398 # q = quaternion({1 2 -2}, {2 1 2}) = {0.57735026 0.57735026 0.0 0.57735026} (xyzw format)
1400 # bug fix: ignoreError -- need not get error string
1433 # -----------------------------------------------------------------------------
1437 # new feature: set errorCallback -- cannot be a Jmol script!
1442 # bug fix: app -j "xxx" option not properly implemented
1445 # readers: MOLDEN reader update contributed by Albert DeFusco - adefusco
1446 # readers: GAMESS reader update contributed by Albert DeFusco - adefusco
1448 # -----------------------------------------------------------------------------
1461 # -----------------------------------------------------------------------------
1468 # new feature: out-of-memory "Java heap error" trapping in scripts and image creation
1479 # -----------------------------------------------------------------------------
1490 # bug fix: negative number in range involving ^ fails: select 10^P -17^P
1493 # -----------------------------------------------------------------------------
1503 # new feature: isosurface INLINE "--pmesh data--"
1514 # bug fix: straightness absolute value -- values 0 (not straight) to 1 (straight)
1516 # new feature: efvet file reader (http://ef-site.hgc.jp/eF-site)
1521 # -----------------------------------------------------------------------------
1526 # new feature: user-definable atom selector for extended select:
1530 # new feature: user-definable atom selector functions.
1546 # -----------------------------------------------------------------------------
1552 # new feature: set fontCaching false -- for testing of font caching issues
1556 # -----------------------------------------------------------------------------
1566 # for any atoms A--X- - -Y where A is attached to X,
1569 # maximum distance for X---Y. (default 3.25 ?)
1579 # -----------------------------------------------------------------------------
1585 # bug fix: text antialiasing of near-black text looks very bad when antialiased
1590 # note -- this will reset the atom color to its standard CPK value.
1596 # -----------------------------------------------------------------------------
1600 # bug fix: forcefield file UFF.prm --> UFF.txt
1608 # code: faster loading -- no "pre" definition of atom sets
1611 # -----------------------------------------------------------------------------
1621 # -----------------------------------------------------------------------------
1629 # bug fix: color translucent 1 blue 1-8 integer settings off by one
1630 # bug fix: background color +/-1 adjustment removed
1632 # -----------------------------------------------------------------------------
1638 # new feature: (Application) -c option checks without loading files; -C option checks with loading …
1639 # code: LOAD command ignores all nonrecognized pre-filename keywords
1641 # -----------------------------------------------------------------------------
1645 # new feature: x = file("some file name") or x = file("?") -- returns full path to file
1647 # new feature: (Application) command line option -j --jmolscript "script commands"
1655 # -----------------------------------------------------------------------------
1667 # matching is case-sensitive.
1678 # -----------------------------------------------------------------------------
1694 # load files "u.mdtop" FILTER "![WAT],![URE]" COORD {0 -1 1} "mdcrd::u.mdcrd" ;
1696 # -- mdtop file must have %FLAG and %FORMAT comments
1697 # -- FILTER is optional
1698 # -- COORD {first,last,step} is optional for each coordinate file loaded
1699 # first,last,step same as in VMD -- 0 for very first trajectory, last -1 meaning "all"
1701 # -- explicit format "mdcrd::" is required, because these files have no identifying characteristics
1702 # -- as many COORD keywords/coordinate files as desired can be included:
1704 # load files "u.mdtop" FILTER "![WAT],![URE]" COORD {0 -1 1} "mdcrd::u1.mdcrd" "mdcrd::u2.mdcrd"…
1708 # -- quaternion is created based on three atoms or coordinates
1709 # -- such that X = atomX - center, Z = cross(atomXY - center, atomX), Y = cross(Z, X)
1713 # -- creates DRAW sequence to draw quaternion q as three arrows red(x), green(y), blue(z)
1715 # -----------------------------------------------------------------------------
1722 # -- this change represents a difference in behavior between the unsigned applet and other code (s…
1727 # -----------------------------------------------------------------------------
1736 # -----------------------------------------------------------------------------
1749 # -----------------------------------------------------------------------------
1756 # -----------------------------------------------------------------------------
1760 # new feature: MOL2 reader is PDB-enabled.
1761 # new feature: data() and DATA expanded to allow fixed-column entry
1768 # bug fix: O- formal charge radius MUCH too large; N+ MUCH too small. -- REMOVED
1771 # -- using SwingUtilities.invokeAndWait() from the commandWatcher thread
1774 # bug fix: applet -- setting a jmolScript callback prevents menu updates
1777 # bug fix: H-M spacegroup designations specifying nonstandard Hall symbols by default
1782 # -----------------------------------------------------------------------------
1793 # -----------------------------------------------------------------------------
1798 # bug fix: y-offset for echo text and images
1804 # -----------------------------------------------------------------------------
1814 # new feature: applet parameter jmolSetCallback("maximumSize", nnn) -- sets maximum size of applet …
1818 # -----------------------------------------------------------------------------
1830 # -----------------------------------------------------------------------------
1837 # bug fix -- set picking spin, also compatibility of set picking spin and doing measurements
1838 # bug fix -- draw pointgroup, write pointgroup draw
1840 # -----------------------------------------------------------------------------
1847 # bug fix: print $planeA - capital letters in a draw name disallow finding it.
1849 # -----------------------------------------------------------------------------
1855 # --- Core applet now 715K (JmolApplet0.jar + _Core, _Jars, _Main, _Popup, and _Viewer)
1856 # code: Pre-Jmol.js button controls removed, saving about 10K
1858 # --allows direct inter-applet communication independent of set SYNC
1859 # --appletName can be * (all applets), > (other applets), . (this applet),
1862 # --for *, the current applet always reports LAST
1864 # --same as above
1865 # --in addition, allows retrieval of information from another applet
1878 # gets a new-line-separated list of rotational quaternions for all applets with applet names.
1883 # -----------------------------------------------------------------------------
1893 # new feature: support for application transparent background -- "-b" command switch (testing only)
1894 # and setAppletContext "-b" switch as well.
1903 # -----------------------------------------------------------------------------
1911 # -----------------------------------------------------------------------------
1926 # -----------------------------------------------------------------------------
1934 # -- new _ShapeSurface.jar, which now includes org.jmol.jvxl/**
1935 # -- removal of _Jvxl.jar
1936 # -- refactoring reduces preliminary applet Jar file loading to 720K (if English)
1937 # -- should provide faster loading of simple models and more efficient loading of more complex ones
1938 # -- basic minimum load involves just JmolApplet0.jar + _Core, _Jars, _Main, _Popup, and _Viewer
1940 # -----------------------------------------------------------------------------
1945 # new feature: set dotDensity [-3 to 3]
1949 # -----------------------------------------------------------------------------
1961 # new feature: in Java 1.6.0_10, right-click activates the console, and the
1962 # console has a menubar menu item "Jmol" that is the pop-up menu.
1965 # -----------------------------------------------------------------------------
1972 # new feature: write/show pointgroup gives counts and tab-separated listing;
1975 # new feature: no saving of point group -- just recalculated each time
1978 # -- reads a JPG, GIF, or PNG image and displays it the
1981 # -- sets the depth in percent (0% far back, 100% front) for the placement of the image
1982 # -- note that images can be placed in 3D, just as for text.
1983 # -- setting "background echo xxx" then specifies the color
1985 # -- using "background echo none" specifies that the first pixel
1992 # -- show only this rendering type
1993 # -- same as restrict not selected; spacefill ON
1996 # bug fix: in draw pointGroup -- height of cylinder was too small
1997 # bug fix: longstanding exception: isosurface fullylit --> isosurface backlit --> isosurface frontl…
1999 # -----------------------------------------------------------------------------
2008 # new feature: calculate pointGroup -- preliminary only -- untested
2010 # -----------------------------------------------------------------------------
2016 # new feature: PRELIMINARY aniso_beta for cif files -- has not been checked for correct Ortep type …
2031 # -----------------------------------------------------------------------------
2035 # bug fix: vibration thread not closing down for applet destroy when applet is off-screen
2041 # -----------------------------------------------------------------------------
2061 # -----------------------------------------------------------------------------
2072 # bug fix : sheetsmoothing not consistent among structures in multi-chain systems
2074 # code: simpler matrix-->quaternion code
2079 # -----------------------------------------------------------------------------
2103 # -----------------------------------------------------------------------------
2123 # new feature: quaternion({atom expression}) -- returns calculated
2137 # -----------------------------------------------------------------------------
2153 # quaternions are always fixed so that cos(theta/2) > 0 -- that is, so that
2154 # the reported theta (q %-2) is in the range [0, 180]
2177 # new feature: float1 == float2 if |float1 - float2| < 0.000001
2186 # bug fix: quaternion frame "n" recognizes file-based H atoms on N for frame definition
2188 # -----------------------------------------------------------------------------
2199 # -----------------------------------------------------------------------------
2203 # bug fix -- if last helix is last atom, SHOW STRUCTURE fails to identify it.
2217 # new feature: quaterion % point4f --- "thetaDirected" --
2220 # Returns a point4f angle-Axis equivalent with x, y, z the normal for the quaternion
2227 # print quaternion({1 0 0}, -20) % 1 ==> {-1 0 0}; %1 ==> 20
2231 # print quaternion({1 0 0}, -20) % {1 0 0 0} ==> {1 0 0 20}
2233 # bug fix: POV-RAY output of quadrilaterals.
2235 # new feature: Ramachandran "r" --- includes third (Z) axis quaternion r difference2 X component eq…
2237 # bug fix: quaternion definition with dot-product check not effective -- removed
2258 # (q%0) -- q0 (w)
2259 # (q%1) -- q1 (x)
2260 # (q%2) -- q2 (y)
2261 # (q%3) -- q3 (z)
2262 # (q%-1) -- the vector {q1, q2, q3}
2263 # (q%-2) -- theta
2264 # (q%-3) -- equivalent rotational frame X-axis
2265 # (q%-4) -- equivalent rotational frame Y-axis
2266 # (q%-5) -- equivalent rotational frame Z-axis
2267 # (q%{x y z}) -- rotational transform of a point or vector based on a quaternion
2269 # thus, for example, (q%{1 0 0}) is the same as (q%-3)
2271 # (!q) -- quaternion inverse
2298 # experimental: "straightness" defined as 1 - 2 * acos(normal(dq[i]%-1) dot normal(dq[i+1])) / PI
2300 # and ranging from -1 (opposite direction) to 1 (same direction) for proteins
2301 # -- a work in progress. See
2306 # -----------------------------------------------------------------------------
2320 # new feature: set PICKLABEL "xxx" -- allows customized pick reports
2324 # new feature: "quaternion derivative" --> "quaternion difference", which is more
2333 # absolute involves un-doing q1's rotation (making it the reference frame), then applying q2.
2341 # new feature: set quaternionFrame "N" -- for solid state NMR PISEMA 15N chemical shift frame
2349 # straightness = 2*|n(dq1).dot(n(dq2))| - 1
2359 # vA = C--CA
2360 # vB = C--N[i+1]
2364 # vA = N9--C4
2365 # vB = N9--C8
2369 # vA = N1--C2
2370 # vB = N1--C6
2375 # dq1 === q[i] * q[i-1]_inverse
2379 # Range is from -1 to 1
2390 # -----------------------------------------------------------------------------
2402 # -----------------------------------------------------------------------------
2427 # bug fix: set picking center should not zoom -- just too annoying
2438 # new feature: signed applet shows frank "Jmol-S" which is NOT removable.
2441 # http://pqs.ebi.ac.uk/pqs-doc/macmol/1j7n_1.mmol
2448 # -----------------------------------------------------------------------------
2452 # new feature: --threaded option for command processor uses
2463 # JavaScript thread, and the load command -- if crossing server boundaries --
2480 # bug fix: JmolSimpleViewer caused null pointer exception -- needed setAppletContext()
2481 # bug fix: model-based drawing in multiple-model mode using an
2491 # -- No atoms selected!
2492 # -- <n> atoms selected!
2493 # -- atom picking:
2495 # -- script <exiting>
2496 # -- Chime script completed.
2505 # -- overrides _jmol.noEval
2506 # -- canNOT be set using "set evalCallback"
2507 # -- was necessary for Protein Explorer javascript callbacks
2509 # -----------------------------------------------------------------------------
2517 # bug fix: select n-m:c chain selection inappropriately case sensitive
2520 # bug fix: application -- "make crystal..." menu item does nothing -- removed
2522 # bug fix: zap to one model assigns -1 to currentModelIndex instead of 0
2530 # - "c" -- CA-C and CA-N, as per Andy Hanson
2531 # - "q" -- peptide plane CA-C and N'-CA' as per J.R.Quine
2532 # - "p" -- peptide plane CA-C and C-N'
2537 # -- bypasses inter-group bonding check when creating polymers
2539 # -- not saved -- just transient measurements (see 11.5.46)
2542 # -- turns on, turns off, or deletes all objects of the type starting with "xxx"
2547 # -----------------------------------------------------------------------------
2553 # and ellipsoid size setting (Note -- ellipsoid command
2561 # -----------------------------------------------------------------------------
2572 # -----------------------------------------------------------------------------
2579 # bug fix: application -- undo/redo buttons not disabling
2582 # -----------------------------------------------------------------------------
2588 # -----------------------------------------------------------------------------
2615 # bug fix: PDB biomolecule for many-BIOMT system
2617 # -----------------------------------------------------------------------------
2632 # filter terms -- only a crude filter here, only for PDB and mmCIF files:
2637 # multiple matches are allowed -- implied AND:
2660 # bug fix: stronger wireframe for antialiased display and generator (POV-ray)
2667 # -----------------------------------------------------------------------------
2677 # code: fast ellipsoid ball+fill - axis idea; no luck with POV-ray fill
2679 # code: POV-Ray ellipsoid generation
2681 # code: 2-fold improvement in rendering ellipsoids by not using getNormix()
2682 # code: 4-fold improvement in rendering ellipsoids by using Miguel's no-mesh idea
2683 # code: 2-fold improvement in rendering ellipsoids by using 40x40x40 shade cache
2684 # code: overall 20-fold improvement in rendering over mesh/normix;
2685 # code: full POV-ray support for ellipsoids
2689 # -----------------------------------------------------------------------------
2705 # -----------------------------------------------------------------------------
2728 # * note that FILL serves to provide a cut-out for BALL and a
2732 # -----------------------------------------------------------------------------
2738 # ELLIPSOID command -- with symmetry and crude footballs, including PDB files
2744 # -----------------------------------------------------------------------------
2751 # bug fix: PovRAY output of draw objects -- cylinder end caps not considered
2752 # bug fix: draw width 0.05 {...} {...} -- line does not properly render
2764 # -----------------------------------------------------------------------------
2769 # bug fix: minimization out-of-plane energy calculation error
2773 # bug fix: draw width -1 or draw mesh nofill with very short cylinders creates odd jumpy effect
2781 # -----------------------------------------------------------------------------
2794 # -----------------------------------------------------------------------------
2815 # new feature: isosurface DOWNSAMPLE n # down-factors the number of points in a CUBE file by a fact…
2817 # -----------------------------------------------------------------------------
2838 # -----------------------------------------------------------------------------
2843 # bug fix: UFF.prm not properly recognizing sp2 N in N-oxides
2848 # -----------------------------------------------------------------------------
2852 # new feature: minimize command -- mostly untested
2883 # -----------------------------------------------------------------------------
2889 # -----------------------------------------------------------------------------
2896 # -----------------------------------------------------------------------------
2900 # bug fix: zap x.y additional work -- connections, isosurfaces
2904 # -----------------------------------------------------------------------------
2913 # -----------------------------------------------------------------------------
2939 # bug fix: mol2 reader cannot read files with single-line comments
2941 # -----------------------------------------------------------------------------
2951 # bug fix: getproperty("chaininfo") for non-biological model causes null pointer exception
2953 # -----------------------------------------------------------------------------
2962 # bug fix: write PDB format incorrectly writes atoms with 4-length names
2966 # -----------------------------------------------------------------------------
2973 # bug fix: write PDB format incorrectly writes atoms with 4-length names
2977 # -----------------------------------------------------------------------------
2998 # radii -- except default zoom.
3020 # spacefill 30%User # percent of User-defined values (or CURRENT if not defined)
3022 # halos 50%Jmol # -- halos also have an added bit to make sure they are visible
3024 # spacefill -20 # neg numbers same as percentages: 20% here, using current vdw set
3036 # -----------------------------------------------------------------------------
3042 # bug fix: command "test()" where test() is a user-defined function causes array-out-of-bounds error
3052 # -----------------------------------------------------------------------------
3056 # NOTE: REMOVED FROM SERVICE -- see 11.5.11
3061 # -----------------------------------------------------------------------------
3065 # NOTE: REMOVED FROM SERVICE -- see 11.5.11
3069 # -----------------------------------------------------------------------------
3073 # NOTE: REMOVED FROM SERVICE -- see 11.5.11
3081 # -----------------------------------------------------------------------------
3090 # -----------------------------------------------------------------------------
3106 # -----------------------------------------------------------------------------
3113 # new feature -- syncCallback -- intercepts messages that would otherwise go to applets for syncing
3120 # -----------------------------------------------------------------------------
3124 # bug fixes -- font scaling
3151 # -----------------------------------------------------------------------------
3165 # -----------------------------------------------------------------------------
3190 # * ------------------------------
3193 # * --each polygon--
3199 # see little-endian example at http://chemapps.stolaf.edu/jmol/docs/misc/pmesh.bin
3202 # -----------------------------------------------------------------------------
3218 # bug fix: restore of state does not reset user-defined atom properties
3221 # -----------------------------------------------------------------------------
3230 # -----------------------------------------------------------------------------
3237 # bug fix: isosurface gridpoints "ch3cl_map.jvxl" -- gridpoints for jvxl files that are already map…
3240 # files: JUnitTest for scripts --
3250 # -----------------------------------------------------------------------------
3261 # bug fix: isosurface COLOR RANGE by itself does nothing -- changed to use full range
3264 # -----------------------------------------------------------------------------
3268 # -- all functionality in new.htm, new2.htm, and new0.htm tested --
3281 # where [zoomOrZoomFactor] is n, +n, -n, *n, /n, or 0 (to indicate fill screen)
3286 # bug fix: print {atomSet}.color -- .color returning bounding box!
3290 # -----------------------------------------------------------------------------
3295 # code: distinction between file-derived or connected hbonds and calculated hydrogen bonds
3298 # bug fix: calculate polymers (never documented) not necessary -- calculate structure suffices
3302 # -----------------------------------------------------------------------------
3317 # bug fix: applets not self-destroying when window containing them close
3320 # -----------------------------------------------------------------------------
3335 # -----------------------------------------------------------------------------
3348 # -----------------------------------------------------------------------------
3354 # bug fix: select within (3.3, {-1 1 1}) does not work with negative integer coordinate
3360 # new feature: trajectory command no longer necessary -- deprecated (was in 11.2)
3362 # -----------------------------------------------------------------------------
3375 # -----------------------------------------------------------------------------
3380 # new feature: set c? -- displays all Jmol parameters starting with "c" or "_c"
3381 # set _? -- displays all read-only variables (starting with "_")
3385 # -----------------------------------------------------------------------------
3392 # FEATURE CHANGE: slab REFERENCE removed -- no longer necessary
3401 # mistakenly matches a String[] signature to a String, or vice-versa.
3414 # -----------------------------------------------------------------------------
3424 # bug fix: loadInline not properly autobonding -- causes null pointer error
3427 # -----------------------------------------------------------------------------
3433 # modification for load RANGE -x.x (within x.x Angstroms of symop=1555) to be within x.x of the
3439 # bug fix: HallInfo --- Hall term miscalculation OUCH! -- mistken commenting out of code in 11.1.28…
3440 # bug fix: set measures 0.1 --- solid line does not move.
3444 # -----------------------------------------------------------------------------
3452 # note --- set strandCount sets BOTH, but now each is independent
3460 # -----------------------------------------------------------------------------
3475 # -----------------------------------------------------------------------------
3488 # -----------------------------------------------------------------------------
3500 # -----------------------------------------------------------------------------
3567 # # rootKeys: 'OPT' 'HF' '3-21G(*)' '' ''
3568 # # new Keys: 'OPT HF 3-21G(*) FREQ '
3579 # 2) file names are case-sensitive and must be complete, with full path within the ZIP file
3583 # IGNORE_ERRORS --- process the file and do not stop if some files are not valid model files
3584 # IGNORE_MANIFEST --- (on the load command line) indicates that the internal ZIP file manifest…
3585 # EXCEPT_FILES --- process all files EXCEPT those given
3588 # new feature: show spacegroup "X,Y,Z;-X,Y,Z;..." finds space group associated with specific operat…
3600 # -----------------------------------------------------------------------------
3614 # -----------------------------------------------------------------------------
3635 # -----------------------------------------------------------------------------
3647 # -----------------------------------------------------------------------------
3670 # Items may be integers or string-based keys
3672 # 1 first item, 0 last item, -1 next to last item, etc.
3697 # bug fix for selecting atoms of atomsets using [-n] or [0]
3702 # bug fix: more natural mouse SHIFT-RIGHT behavior.
3707 # Specifically for molecular/solvent-type isosurface.
3711 # -----------------------------------------------------------------------------
3715 # bug fix: select statement comparisons of negative decimal properties to "-1" (not "-1.0") causes …
3760 # with the first parameter (normally the atomIndex) being -2.
3775 # -----------------------------------------------------------------------------
3793 # bug fix: memory leak in merge -- models[i].modelSet causes modelSet to not finalize.
3799 …*** Jmol Embedded Script **** recognized in /* ... */ comments and /** ... **/ super-comment blocks
3802 # -----------------------------------------------------------------------------
3830 # new feature: set atom properties from space-separated string:
3834 # -----------------------------------------------------------------------------
3839 # -- one Ramachandran plot per model
3840 # -- axes labels and special hover label for Ramachandran plots
3841 # -- Ramachandran saved in state
3851 # POV-Ray clipping coding minor tweak
3852 # POV-Ray fix for number formatting width > 999
3854 # new feature: model-based parallel array calculations:
3860 # bug fix: draw @{x - {1 0 0}}
3863 # new feature: draw object title line number corresponds to model number for multi-model draw objec…
3883 # -----------------------------------------------------------------------------
3888 # bug fix: hover state not properly showing specific-atom hover labels.
3890 # new feature: write FILE (text-files only)
3893 # only works for Pop-In template at present. Required updates to JmolPopin.js and templates.
3904 # -----------------------------------------------------------------------------
3908 # bug fix: antialiasing with translucent/POV-ray
3914 # -----------------------------------------------------------------------------
3930 # bug fix: -- adds antialiasing for translucent objects
3932 # bug fix: 0-diameter atoms displayed as single pixels when perspectiveDepth = false
3934 # -----------------------------------------------------------------------------
3942 # POV-Ray dialog update
3947 # -----------------------------------------------------------------------------
3951 # POV-Ray slab/depth
3952 # POV-Ray text -- ALL text (echos, labels, axes, etc.)
3954 # POV-Ray cleaner for Molecular Orbitals
3956 # PDB remediated atom name upgrade -- NEEDS CAREFUL CHECKING
3958 # -----------------------------------------------------------------------------
3964 # POV-Ray for mapped isosurfaces
3965 # POV-Ray embeds Jmol script
3966 # POV-Ray .pov files created by Jmol can be loaded as scripts
3972 # bug fix: app -c flag errors not going to Logger.Error
3977 # -----------------------------------------------------------------------------
3981 # code: PovRay tweaks -- multiple bonds
4007 # single-color isosurfaces
4015 # -----------------------------------------------------------------------------
4052 # -----------------------------------------------------------------------------
4058 # new feature: valence -- sum of bond orders
4094 # -----------------------------------------------------------------------------
4105 # -----------------------------------------------------------------------------
4129 # in general, functions are global -- common to all applets.
4130 # first-character "_" indicates this function is a LOCAL function, private to this applet.
4132 # -----------------------------------------------------------------------------
4137 # new feature: bondOrders 2.5 and -2.5 PartialTriple and partialTriple2
4139 # -----------------------------------------------------------------------------
4151 # -----------------------------------------------------------------------------
4165 # bug fix for PAUSE causes app to hang -- this is a reversion of use of SwingUtilities.invokeLater(…
4169 # -----------------------------------------------------------------------------
4177 # -----------------------------------------------------------------------------
4182 # bug fix for show state for draw in multi-model environment
4190 # select within(5.0,false,model=2.1) # FALSE -- only model 2.1
4193 # -----------------------------------------------------------------------------
4215 # i = i - 1
4225 # print "i-j: " + i + "," + j + " " + dist%2
4236 # i = i - 1
4241 # -----------------------------------------------------------------------------
4254 # -----------------------------------------------------------------------------
4262 # new feature: fully functional user-defined functions:
4312 # -----------------------------------------------------------------------------
4318 # -----------------------------------------------------------------------------
4322 # bug fix: critical arrow fix of 11.3.17 for 2-point arrows
4323 # bug fix: write PNG default was 0 compression. -q flag was OK for setting 0-9
4326 # -----------------------------------------------------------------------------
4333 # reset ALL # resets all user-created variables
4338 # -----------------------------------------------------------------------------
4342 # bug fix: problem with unescaping comma-separated point strings "{1,2,3}" as a point.
4343 # bug fix: drawn arrows scale improperly when zooming; arrow heads off-kilter
4353 # rename byResidue_jmol --> byResidue_shapely
4354 # rename byResidue_rasmol --> byResidue_amino
4436 # colorManager clean-up
4438 # -----------------------------------------------------------------------------
4444 # new feature: MOPAC mgf file UHF orbital reading -- preliminary only
4448 # built-in include: byElement_Jmol, byElement_Rasmol,
4480 # so this opens the door to user-created residue coloring schemes.
4489 # -----------------------------------------------------------------------------
4493 # new feature: fully customizable popup menu -- see file jmol.mnu
4499 # application parameter -m filename
4508 # -----------------------------------------------------------------------------
4512 # new feature: fully customizable popup menu -- see file jmol.mnu
4523 # bug fix: -g ignored on -n option, even if -w is present
4528 # new feature: APPLICATION -q (quality) option
4541 # color atoms property partialcharge "rwb" range -1.0 1.0
4545 # color atoms property partialcharge "rwb" range 1.0 -1.0
4547 # new feature: unlimited user-defined color schemes:
4558 # color $s1 "rwb" range -0.2 0.2
4563 # -----------------------------------------------------------------------------
4589 # color "bwr" absolute -0.1 0.1
4590 # x = (0.01).color # gives the point-color associated with that number
4611 # color atoms property partialcharge "user" range -1.0 1.0
4613 # -----------------------------------------------------------------------------
4623 # -----------------------------------------------------------------------------
4634 # -----------------------------------------------------------------------------
4639 # bug fix: state of multi-polymer protein cannot be restored
4655 # -----------------------------------------------------------------------------
4673 # along with an optional bracketed sync group identifier -- generally a random
4676 # is used. This feature is important for cross-frame synchronization only.
4683 # [syncId] (optional) a unique string of digits -- brackets included
4703 # This should only be necessary for multi-frame pages.
4705 # -----------------------------------------------------------------------------
4709 # bug fix: isosurface color -- not operating for some isosurface types
4710 # bug fix: isosurface "xxxx.cube" -- not assigning proper default colors
4716 # -----------------------------------------------------------------------------
4725 # -----------------------------------------------------------------------------
4737 # -----------------------------------------------------------------------------
4745 # bug fix: set spin X was case-selective
4746 # bug fix: echo text not re-orienting on resize of applet or application
4751 # -----------------------------------------------------------------------------
4761 # -----------------------------------------------------------------------------
4779 # preliminary Maya export -- sets the stage for any number of export frameworks.
4781 # -----------------------------------------------------------------------------
4786 # bug fix: minus-sign "fix" in 11.3.1 broke all {x -y z} notation
4792 # -----------------------------------------------------------------------------
4796 # bug fix: debugscript on;center 3-5; "-" missing
4797 # bug fix: zoomTo (5-7) read as "5 to -7"
4800 # bug fix: image offsets in creating JPG image if model has been moved by CTRL-ALT-LEFT drag
4802 # -----------------------------------------------------------------------------
4821 # -----------------------------------------------------------------------------
4827 # bug fix for x = "testing"[0], x = "testing"[-1], "testing".split("t")[0], and "testing".split("t"…
4828 # bug fix for select {*}[0], {*}[-1], etc., which now counts from the end back
4832 # -----------------------------------------------------------------------------
4840 # -----------------------------------------------------------------------------
4848 # -----------------------------------------------------------------------------
4854 # bug fix for inappropriate pre-JVM12 menu items not disabled
4856 # -----------------------------------------------------------------------------
4863 # bug fix for retaining the last-saved file type selected for Image export (app)
4866 # -----------------------------------------------------------------------------
4878 # -----------------------------------------------------------------------------
4889 # -----------------------------------------------------------------------------
4902 # code refactoring Frame --> ModelSet and ModelLoader
4903 # code refactoring modelframe --> modelset package
4904 # code refactoring shapebio --> shapebio + molsetbio packages
4907 # code refactoring Mps --> BioShapeCollection
4910 # -----------------------------------------------------------------------------
4916 # bug fix for select specialposition non-functional
4921 # adds "structure" command -- structure [helix|sheet|turn|none] (atom expression)
4924 # -----------------------------------------------------------------------------
4932 # -----------------------------------------------------------------------------
4944 # -----------------------------------------------------------------------------
4950 # bug fix for animFrameCallback giving multiple callbacks -- still there, but identified now
4955 # -----------------------------------------------------------------------------
4964 # -----------------------------------------------------------------------------
4970 # bug fixes for isosurface in multi-file environment
4979 # zoomTo (atom expression) 0-n
4991 # [0] [[+ | - | * | /] x]
4996 # -----------------------------------------------------------------------------
5001 # fix for select resno=-1
5004 # -----------------------------------------------------------------------------
5010 # -----------------------------------------------------------------------------
5014 # bug fixes -- draw state, menu not updating, language submenu
5016 # -----------------------------------------------------------------------------
5025 # -----------------------------------------------------------------------------
5029 # adds capability to read data from selected fields (white-space delimited columns) in a file
5031 # propertyDataField = 0 # no fields -- just read tokens
5036 # -----------------------------------------------------------------------------
5073 # -----------------------------------------------------------------------------
5080 # adds (2) isosurface functionxy "functionName" {x0 y0 z0} {-ni ...} ...
5081 # adds (3) isosurface functionxy "functionName" {x0 y0 z0} {-ni ...}{-nj ...} ...
5091 # isosurface s1 functionXY "xyData" {-2 -2 -2} {21 0.1 0 0} {21 0 0.1 0} {21 0 0 0.1}
5101 # isosurface s2 functionXY "xyDataAsString" {-2 -2 -2} {-21 0.1 0 0} {21 0 0.1 0} {21 0 0 0.1}
5111 # //non-numeric formatting allowed but not necessary
5118 # isosurface s3 functionXY "xyDataAsArray" {-2 -2 -2} {-21 0.1 0 0} {-21 0 0.1 0} {21 0 0 0.1}
5145 # the model is "molecular" -- the base atom coordinates are correct
5153 # adds isosurface HOMO/LUMO [+/- n]
5156 # bug fix in isosurface contour -n going WAY back to before 10.9.60
5157 # refactoring of all isosurface-related classes
5163 # adds load TRAJECTORY -- for a single file with multiple models all with
5167 # adds TRAJECTORY n command -- like FRAME or MODEL, but never more
5188 # -----------------------------------------------------------------------------
5202 # Density Functional, and Extended Huckel Gaussian/Slater-based molecular orbitals.
5208 # "MOPAC-Graphical data" on the first line, character index 6.
5212 # mo HOMO [+/- n]
5213 # mo LUMO [+/- n]
5220 # GhemicalMMReader -- was incorrectly assigning aromatic to bond type 4 via fall-through of switch
5225 # adds expanded isosurface-related commands:
5230 # (mo list) -- not particularly useful
5252 # -----------------------------------------------------------------------------
5260 # -----------------------------------------------------------------------------
5265 # -- JVXL files created from molecular orbitals will show up with no color
5266 # in 11.1.0 - 11.1.25 because of a missing number in the definition line :(
5267 # -- JVXL files created from molecular orbitals will show unwanted cross-over
5268 # surfaces from + to -.
5270 # -----------------------------------------------------------------------------
5274 # --fully dissociates geosurface from dots;
5275 # --allows coloring and transparency of geosurface
5278 # -----------------------------------------------------------------------------
5287 # -----------------------------------------------------------------------------
5293 # adds isosurface CAVITY x.xx -- a new way to depict the cavities of
5296 # -----------------------------------------------------------------------------
5315 # where N is -1 to 9.
5318 # translucent -1 same as Jmol 10.2
5332 # -----------------------------------------------------------------------------
5345 # and these objects are considered more like background --
5355 # -----------------------------------------------------------------------------
5359 # allows comparison of user-defined atom properties in SELECT:
5361 # select property_myprop < 1e-5;
5373 # -----------------------------------------------------------------------------
5377 # introduces user-definable atom properties that can be used
5393 # isosurface -- now supports APBS ( )
5396 # write -- modified to allow unquoted filename in
5399 # jvxl 1.0 -- adds ANGSTROMS flag on line with # of atoms (line 3)
5401 # -----------------------------------------------------------------------------
5406 # ------------------
5425 # This build allows for the applet to be "bare-bones" -- only the
5434 # -----------------------------------------------------------------------------
5454 # longest = longLine%(longLine.find(",")-1)
5461 # -----------------------------------------------------------------------------
5472 # decimal 3.5, 3.25E-3
5609 # x2 = {molecule=1}.xyz - {molecule=2}.xyz
5619 # x4 = 0.0 + ({molecule=1}.xyz - {molecule=2}.xyz)
5620 # x5 = ({molecule=1}.xyz - {molecule=2}.xyz).distance{0 0 0}
5655 # -----------------------------------------------------------------------------
5676 # %= 1-based index
5686 # measure "%a1 -- %VALUE %UNITS --- %a2"
5694 # degUnsat = ({carbon} * 2 + {nitrogen} + 2 - {hydrogen}) / 2
5747 # echo the O-O distance is %{{oxygen and * /1}.distance{oxygen and * /2}}
5756 # atom-based data back to the user with whatever formatting is desired.
5768 # pdbAtomData = {selected and not hetero}.label("ATOM %5i %-4a%1A%3n %1c%4R%1E %8.3x%8.3y%8.3z%6…
5769 # pdbHeteroData = {selected and hetero}.label("HETATM%5i %-4a%1A%3n %1c%4R%1E %8.3x%8.3y%8.3z%6…
5773 …ne2\nline3\n"+(""+{selected}.size)%-3+(""+{selected}.bonds.size)%-3+" 0 0 0\n"+{selected}.label…
5794 # x = {atom expression}[3][5].x # 3-5 (average x)
5811 # %= file 1-based index
5828 # extend that here to add some useful "modulus-like" capability:
5833 # "test" %-3 ==> right trim: "est"
5834 # "test" %-6 ==> left pad: " test"
5838 # 3545.6 %-3 ==> "3.55E+3" (STRING!)
5841 # 0.0 + 3545.6 %-3 ==> 3550.0
5846 # -----------------------------------------------------------------------------
5858 # set allowRotateSelected # then use ALT-LEFT for rotating just the selected molecule
5864 # load xxxx.spt # minimal -- just coord.
5867 # x = (some atom expression).atomProperty -- takes an average if more than one atom
5879 # -----------------------------------------------------------------------------
5889 # reconfigures _modelNumber as x.y for single models; x.x - y.y for range
5894 # adds frame x.x - y.y
5896 # adds frame range x.x - y.y