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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
24 # bug fix: revertings changes to cancelRendering
36 # bug fix: write to clipboard not working
67 # bug fix: draw: when only some models are visible, does not properly assign models to drawn object
92 # bug fix: occasional null pointer error during ZAP due to continued rendering by
100 # bug fix: MSIE mouse-wheel malfunction due to Jmol not consuming the wheel motion
117 # bug fix: strand count assignment error in cif/pdb readers causes failure to load 3ovo.cif
121 # bug fix: set toggleLabel inappropriately resets label to default setting
134 # local to the applet, with all other functions being static.
138 # So for this fix I've changed that to be "static_..." for
143 # bug fix: jmol -ionxs with a script that includes measurement tries to update a nonexistant measur…
144 # bug fix: select xxx when xxx is an array fails to do lookup of defined values
154 # bug fix: setting spacefill to a large user-defined VDW radius incorrect
162 # bug fix: incorrect reference to jmolStatusListener for sync callback in StateManager
163 # bug fix: file drop needs zap prior to load for cleaner operation
195 # bug fix: isosurface reading of contoured JVXL files defaults to "nomesh nofill"
219 # bug fix: acos, to be consistent, needs to deliver degrees, not radians
238 # new feature: ho, ho, this is fun. Wouldn't it be nice to just drag a JPG into
242 # The IMAGE option instructs Jmol to add its state to the JPG image, so when it is
245 # also with PNG images; to not do this, use
269 # new feature: Jmol embedded in applications can use WRITE command to create all types of images an…
285 # bug fix: gaussian reader may fail to read MOs from Gaussian 03: AM64L-G03RevC.01 3-Apr-2004
304 # TODO: what to do about deleting models prior to current -- why statescript removed?
305 # bug fix: zap x.y when have measures to draw objects causes exception
320 # new feature: set helixStep 0 -- relates a quaternion to the standard reference frame
342 # bug fix: color isosurface red translucent prior to isosurface command causes null pointer excepti…
344 # where n is an integer 1,2,3... that selects which set is to be displayed and
361 # bug fix: measurements defined using points not restricting to models
375 # new feature: NAVIGATION STOP -- sets navX, navY, navZ to 0
378 # SPACE to stop
379 # LEFT/RIGHT to pan left or right
380 # UP/DN to move forward/back
381 # ALT UP/DN to pitch up/down
382 # CNTL UP/DN to increase/decrease speed in larger amounts
389 # bug fix: arrays passed to functions by reference do not update if size is increased
390 # new feature: by passing an array to a function, you can make that variable
407 # new feature: all.bin(f0, f1, df) -- binning of data to give an integer array of counts
436 # "point" -- nearest point to x on local helix axis
439 # "radius" -- vector normal from local helix point to x
445 # code: findNearestAtomPicked added to JmolViewer
460 # to create a truly "headless" Jmol application, where Jmol is being
481 # sets as well as perturbation, CI and CC calculation methods. This is dumped to
509 # all are implicitly strings. You CAN use "..." but you don't have to,
537 # new feature: a = [] note that a+=2 then produces [2] -- "a+=" similar to JavaScript a.push(2)
554 # new feature: general commands no longer restricted to single lines.
557 # new feature: set or x = command no longer restricted to single lines.
562 …on --printOnly silent operation with only print command output or warnings going to the console
570 …ectory "myfile.top" COORD {first,last,stride} "mdcrd::myfile.trj" defaults to last = -1 ("load all…
575 # "all" equivalent to {*}
584 # code: refactored classes -- next best thing to a separate package (they aren't really public)
611 # bug fix -- bitsets not copied: m1 = {m and selected} changes m to "m and selected"
616 # Similarities to JavaScript:
627 # --A relatively free typing of variables. Jmol is going to save variables as strings
629 # subclasses Token and allows for a more organized approach to variables and sets the
642 # --Array indexing from the back to the front using n <= 0: A[0] A[-1] A[-2].
647 # --Of course, a whole suite of methods that relate to molecular structure.
671 # new feature: set useMinimizationThread T/F nec. to be FALSE when running minimizations in script…
880 …rogen based). The default is alpha-carbon based, which corresponds closely to the following combin…
883 # yes u yes surfacedistance shortest distance to a surface atom
888 # yes yes uX unit cell X coordinate normalized to [0,1)
889 # yes yes uY unit cell Y coordinate normalized to [0,1)
890 # yes yes uZ unit cell Z coordinate normalized to [0,1)
914 # new feature: relaxed limitation on spacefill, halo, star, dots size to 16A.
988 # bug fix: quaternion straightness not setting end points to Float.NaN
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
1001 # new feature: load OCCUPANCY ... int [0 to 255]
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…
1014 # --applies {within(loadAtomDataTolerance,xyzcoord)}.vxyz = vibcoord, so to all unit cells
1028 # new feature: {x y z}.ux, .uy, .uz similar to .fx, .fy, .fz
1031 # intended, you need to use {x y z}.xyz.x
1039 # then {x}.uxyz will be in the range {-1,-1,-1/1} (inclusive) to {0,0,0/1} (exclusive)
1086 # bug fix: possible exception when writing large image with translucency due to caught memory overf…
1127 # bug fix: autoBond option in Preference menu was not writing to properties file in $HOME/.jmol
1142 # load "xxx.gamess" filter "!EIGEN" # to only load NBOs; by default ALL MOs are loaded.
1156 # in general, one needs to use
1169 # new feature: MO no longer restricted to one per model set; rather, one per MODEL
1183 # bug fix: signed applet does not use CD to set dialog default directory
1185 # new feature: set autoLoadOrientation (default: FALSE) automatically sets "reset" orientation to t…
1186 # new feature: restore orientation DEFAULT -- resets orientation to file's default orientation or s…
1199 # bug fix: MO calculations skips d2+ orbital due to integer division.
1215 # bug fix: toolbar icon for pickMeasure tied to tools "measurements..." item
1221 # code: polygonColixes[] to define polygon colors rather than vertex-based colors (as in OBJ file)
1222 # new feature: isosurface points can be retrieved using $id[n] where n=0,1,2,3... similar to $draw[…
1226 # where n is an optional pointer to a specific group (starting with 1)
1232 # [n] is optional; defaults to 9
1272 # -- streamlined methods for converting CUBE data to JVXL files
1280 # new feature: character \0 at the start of an echo does screen echo only, not to callback or conso…
1283 # sets the echo to bottom left and shows the key strokes as they appear
1301 # bug fix: {*}.formalCharge = 1 after {*}.formalCharge = -1 sets formal charge to -7 and exception
1333 # bug fix: vibrationperiod set to 0 if vibration off when state saved
1348 # new feature: application -d --debug sets loglevel to 5
1363 # 0 to 100 for JPG (-1 = default of 75)
1367 # or sent to an output stream (os != null)
1368 # or set to a file (os == null, fileName != null)
1382 # primarily, this is for writing to an OutputStream directly, but
1383 # the rest seemed simple to implement along with that.
1389 # sends image (null parameter) or text to clipboard
1405 # have been sent to the console.
1456 # code: refactoring of method names to remove ambiguities between "openFile" and "createModelSet"
1457 # code: fixing inappropriate calls to getOpenFileError(), which actually creates the model set.
1508 # bug fix: goto xxx with trailing white space fails to find xxx
1509 # bug fix: goto with a # comment in the script prior to the target line fails
1514 # bug fix: straightness absolute value -- values 0 (not straight) to 1 (straight)
1566 # for any atoms A--X- - -Y where A is attached to X,
1588 # {atomno=3}.element = 6 # set atom 3 to carbon
1590 # note -- this will reset the atom color to its standard CPK value.
1609 # code: Eval load conversion of param[] values to htParams entries
1645 # new feature: x = file("some file name") or x = file("?") -- returns full path to file
1665 # NOTE: 11.7.8 changes just "type" to "atomType"
1668 # defaults to atom name if no types are indicated
1672 # cd # reports current directory and sets default directory to that
1675 # cd temp # moves to subdirectory temp
1685 # these fils can then be combined using an external program of user's choice to create
1713 # -- creates DRAW sequence to draw quaternion q as three arrows red(x), green(y), blue(z)
1743 # bug fix: Swing antialiasDisplay broken due to setTransparentBackground debugging
1761 # new feature: data() and DATA expanded to allow fixed-column entry
1764 # bug fix: CML reader failst to load primitive lattice parameters when no symmetry
1780 # webexport help updated to reflect ability to handle files opened with "load append"
1786 # new feature: signed applet may write file, images, scripts, variables to disk. User dialog is req…
1789 # code: allows for getJpeg(quality,asString) option to return byte array instead of base64.
1791 # bug fix: ramachandran and quaternion derivative not indicating structure due to dropping last atom
1799 # bug fix/new feature: HIDE/DiSPLAY/DELETE/COLOR $*xxx* extended to ECHO
1814 …ter jmolSetCallback("maximumSize", nnn) -- sets maximum size of applet when resizing to this value
1815 # cml reader fix for not applying symmetry to first model
1827 # bug fix: d2 point groups cause null pointer exception due to missing principal axis
1892 # so as to be consistent with other objects. (OFF was not deleting these)
1908 # bug fix: oops, 11.6.RC5 is totally broken due to missing refreshes
1918 # bug fix: createImage(), not getImage() in order to allow dynamic file change
1920 # Addition of translation tags to webexport
1924 # code: viewer refactoring to simplify/remove private methods and synchronization
1936 # -- refactoring reduces preliminary applet Jar file loading to 720K (if English)
1944 # bug fix: minor error in pointgroup; dimension tied to radius
1945 # new feature: set dotDensity [-3 to 3]
1984 # that is to be designated as the background color (the color that should be omitted).
2016 …IMINARY aniso_beta for cif files -- has not been checked for correct Ortep type -- set to 0 for now
2019 # new feature: application measure button tied to picking style
2025 # bug fix: JmolViewer interface deprecated "rotateTo..." methods changed to "rotate..."
2056 # but without ID, one is restricted to words that are simple text and not Jmol entities.
2073 # bug fix: messages not sent to messageCallback
2084 # were causing WYSIWG web editors to corrupt the code scripts.
2092 # of {ptref} in a plane perpendicular to the axis. This is similar (but opposite)
2093 # to the way dihedral angles are indicated.
2095 # nDegrees is the number of degrees of arc to draw
2096 # fractionalOffset is the fraction of the distance from {pt1} to {pt2} for the
2111 # measurements to POINTS, including using the mouse (set drawPicking on)
2131 # bug fix: Popin.png in WebExport replaced, was too large, causing dialog box to default to too big…
2135 # bug fix for 11.5.45: application not returning echos and status messages to console
2147 # bug fix: jmolScriptWait() improperly reporting to applet console
2148 # bug fix: too many messages to applet console
2151 # axisAngle() and quaternion() are both processed to quaternion format
2157 # axis to dot with the quaternion normal in order to switch the
2203 # bug fix -- if last helix is last atom, SHOW STRUCTURE fails to identify it.
2222 # to be directed with a positive dot product between the input {x y z}
2229 # but % {1 0 0 0} forces the angle associated with {1 0 0} to be reported
2299 # giving a measure proportional to the difference in local helical axis angle
2300 # and ranging from -1 (opposite direction) to 1 (same direction) for proteins
2312 # bug fix: color of NaN float values changed from "center of color scheme" to GRAY
2314 # bug fix: state script fails to save data for atoms created using the quaternion command
2317 # bug fix: quaternion derivative for i/i+1 assigned to i+1 instead of i; now assigned to i
2379 # Range is from -1 to 1
2385 # select straightness < 0.70; # rounds to nearest hundredth
2411 # same as select() function, but simpler to implement
2430 # sets the axes to the x y screen position or percent indicated.
2435 # bug fix: "set picking identify" should be equivalent to "set picking ident"
2439 # possibly to come: signed applet will send confirmation first time it reads a local file?
2444 # new feature: /*SPLIT*/ in a command string allows it to be processed by
2445 # the two independent processors. (just to isolate javascript from load commands
2453 # a watcher thread to monitor a Vector, allowing the signed applet to open any file
2464 # must NOT run on that thread. I have configured the ScriptManager to
2468 # Because it might be useful to combine LOAD and JAVASCRIPT (for the equivalent of a
2482 # array of points to load causes null pointer exception:
2503 # set pdbGetHeader TRUE # to get the header when loading (for Protein Explorer)
2514 # bug fix: pm rounding to integer value
2522 # bug fix: zap to one model assigns -1 to currentModelIndex instead of 0
2527 # new feature: draw .... ">xxx" first character of title ">" forces title to
2554 # must be run once prior to setting spacefill
2577 # code: better garbage collection in relation to JmolAdapter class
2612 # use load FILTER "BIOMOLECULE 1;NOSYMMETRY" to not read symmetry
2696 # bug fix: (forwared compatibility) invalid state setting (due to later version) now ignored.
2699 # new feature: ellipsoid ball rendering tied to "set wireframerotation" option
2725 # * 2) If not BALL, ARCS, or DOTS, the rendering defaults to AXES
2728 # * note that FILL serves to provide a cut-out for BALL and a
2737 # bug fix: labels can change size in returning from antialiasdisplay=true to antialiasdisplay=false
2740 # command, but you can use {1 1 0} to load ANISOU without applying symmetry
2771 # bug fix: (applet) script termination callback should not be sent to message queue
2772 # bug fix: hover appears when a load script leaves an atom very close to (0,0) in the window
2809 # to dump the info to a file:
2918 # use "show models" to see what models are present, then zap them with their
2931 # NEEDS THOROUGH TESTING, particularly in regard to saving/restoring the state
2934 # bug fix: isosurface model keyword does not carry on to saved state
2946 # bug fix: WebExport with http:// files fails to save file
2947 # bug fix: WebExport with local . directory fails to save JmolApplet.jar and Jmol.js
2960 # application menu: Write state moved to main export menu; Export PDF to image writing
2971 # application menu: Write state moved to main export menu; Export PDF to image writing
2989 # Then add a DATA statement to include the specific elements you want to give
2990 # new radii to:
2996 # For full state compatibility, these commands should be given prior to
3009 # If user vdw radii are currently set, then this resets the defaults to Jmol.
3015 # stars 1.0 # set to a specific angstrom radius
3021 # spacefill +1.2 # angstroms added to current vdw scheme
3022 # halos 50%Jmol # -- halos also have an added bit to make sure they are visible
3043 # bug fix: undocumented .vdw atom property was equivalent to .valence
3059 # bug fix: DATA command assigning property to last atom in structure fails
3078 # new feature: inline math @{x+3} extended to all commands
3079 # new feature: .sub(), .add(), .mul(), .div() extended to all operand types
3085 # bug fix: explicit "SELECT NONE" must be given for label defaults to be set
3094 # bug fix: HETATM atoms not automatically bonded to nearby ATOM atoms
3100 # new feature: label "scaleReference" if > 5.0 is taken to be a reference zoom setting
3104 # bug fix: fixes applet memory leak in relation to consoles
3110 # bug fix: fixes applet memory leak due to
3113 # new feature -- syncCallback -- intercepts messages that would otherwise go to applets for syncing
3114 # when syncCallback is set to a JavaScript function name, that function
3144 # // and the following sends commands to an applet in the registry:
3173 # new feature: zip file reading extended to write FILE
3177 # new feature: allows zip files to be designated as default directoriesusing
3226 # bug fix: explicit format LOAD "XXX::whatever" extended to XML variants
3228 # code: adapter/smarter/Resolver.java cleaned up in relation to XML and DOM options
3260 # bug fix: isosurface MEP mapped to plane not exactly reproduced in JVXL
3261 # bug fix: isosurface COLOR RANGE by itself does nothing -- changed to use full range
3262 # new feature: isosurface COLOR RANGE ALL added as an equivalent to COLOR RANGE with no numbers
3281 # where [zoomOrZoomFactor] is n, +n, -n, *n, /n, or 0 (to indicate fill screen)
3284 # bug fix: quaternion command by itself not switching to most recent quaternion
3300 # webexport help instructions fix to be consistent for local testing.
3310 # code: Quaternion class moved to modelsetbio
3311 # code: dipoles moved to shapespecial
3312 # bug fix: select 1.5 in trajectory context should switch to that set of coordinates
3316 # bug fix: memory leak in applet due to mouse/hoverwatcher listeners
3318 # bug fix: rotate commands not sent to other applets when set syncScript if OFF
3328 # bug fix: load trajectory extended to multifile context
3330 # selects that file, but also sets the trajectory to 1.3.
3332 # This makes "select" in a trajectory context similar to "display"
3343 # new feature: draw DIAMETER X.Y allows setting diameter of points, lines, curves, and arrows to An…
3401 # mistakenly matches a String[] signature to a String, or vice-versa.
3402 # The solution is to use
3433 # modification for load RANGE -x.x (within x.x Angstroms of symop=1555) to be within x.x of the
3573 # new feature: JmolManifest in a zip file directs which files to load and in what order
3592 # bug fix: application animation frame button reset always goes to frame 1
3608 # deprecated: calculate surface (equates to surfaceDistance WITHIN)
3609 # deprecated: calculate surface {...} (equates to surfaceDistance FROM)
3631 # bug fix: isosurface CAP not turned off prior to map sasurface
3632 # bug fix: adjustable boundbox in multimodel context not specific to model of selected atoms
3652 # allows FULL math access to ALL getProperty types
3668 # If the atom set is not given, those properties default to {visible}
3672 # 1 first item, 0 last item, -1 next to last item, etc.
3683 # default ON/OFF is to NOT change current setting
3685 # new feature: boundbox {point or expression} {vector to corner} [on|off]
3686 # sets the bound box to be centered with a given size based on a vector to a corner
3689 # sets the bound box to encompass the two corner points
3691 # strangely enough this allows setting the boundbox to a 2D or 1D box
3715 # bug fix: select statement comparisons of negative decimal properties to "-1" (not "-1.0") causes …
3718 # new feature: Back to "SET" for state definitions of Jmol parameters.
3726 # bug fix: assigning a negative value to a dataAtomNumberField value caused BitSet.set() exception
3734 # OK, so that might look good, but it evaluates to
3759 # this goes to the pickCallback function as the second parameter,
3765 # similar to calculate aromatic, except it's isolated to this set of connections; implicit modifyOn…
3771 # bug fix: connect (..) (..) # with implicit "single" causes state to use "partial 0"
3793 # bug fix: memory leak in merge -- models[i].modelSet causes modelSet to not finalize.
3843 # bug fix: Overlapping CPK at a slab now correct for up to 10.000 clipped atoms.
3849 # code: privatized Token to avoid null value problem in Eval.statementAsString()
3863 # new feature: draw object title line number corresponds to model number for multi-model draw objec…
3878 # there is a priority in Jmol, but not yet clear to me which. The current priority
3879 # in povray is based on the signed distance from the slab to the atom center.
3887 # bug fix: antialias causing image to be partial size.
3892 #new feature webexport: automatic usage of a different path to the applet for local files to allow …
3893 # only works for Pop-In template at present. Required updates to JmolPopin.js and templates.
3894 #webexport instruction updated to reflect new feature.
3955 # bug fix: getproperty atominfo returning string to Integer()
3972 # bug fix: app -c flag errors not going to Logger.Error
3999 # They do not carry over from one file to the next.
4009 # Web Export Dialog changes: new intro tab, new minilog at bottom, instructions converted to
4021 # bug fix: zoomto (atomExpression) 0 # zooms to 2x
4098 # new feature: adds H/Br/Cl/I/C logic to aromatic bond assignments
4099 # new feature: adds Oxygen/Sulfur logic to aromatic bond assignments
4100 # new feature: adds Nitrogen logic to aromatic bond assignments
4112 # new feature: reset aromatic # sets all aromaticDouble and aromaticSingle back to aromatic
4119 # n = number of lines, up to 5
4120 # m = binary mask for dottedness, up to 31 (0x1F)
4128 # new feature: global/local functions (to applet, for instance
4129 # in general, functions are global -- common to all applets.
4130 # first-character "_" indicates this function is a LOCAL function, private to this applet.
4159 # code cleanup: pmesh moved to shapespecial; privatized
4165 # bug fix for PAUSE causes app to hang -- this is a reversion of use of SwingUtilities.invokeLater(…
4167 # order to avoid the event queue from stopping itself.
4245 # Changes to webexport package only
4249 # Bug? fix: update the page templates to XHTML 1.1
4250 # Minor fixes to instruction .html files.
4330 # critical bug fix for 11.3.17 in regard to serialization of arrays
4357 # prior to 11.3.17, you could not do:
4433 # new feature: someArray.add("string") adds string to right of each item
4434 # new feature: someArray.sub("string") adds string to left of each item
4469 # Residue indexes in order correspond to the groupID of an atom:
4480 # so this opens the door to user-created residue coloring schemes.
4531 # adjustment: setting JPG default quality to 75, not 100
4561 # APPLICATION adjustment to console window scaling/size
4602 # setting an array variable to the color values:
4607 # creates a colorscheme referred to as "user" and its reverse, "resu"
4621 # new feature: APPLICATION: File|Export...|Export to Web Page
4667 # The synchronize (sync) command allows two or more applets to be synchronized in
4669 # In addition, the sync command allows ANY command to be sent to one or more
4688 # command command to send
4694 # sync > "set echo top left;echo OK" # sends OK to top left of all OTHER applets
4701 # should be called prior to jmolApplet() and should incorporate some sort of
4733 # bug fix: nested ifs can cause last endif to throw error
4742 # note that xmlReader (SAX reader) is now set to ignore all DOCTYPE declarations
4790 # feature: adds isosurface capability to map MO and MEP data onto planes
4797 # bug fix: zoomTo (5-7) read as "5 to -7"
4798 # bug fix: move with time < 0.03 seconds causes molecule to disappear
4814 # adds the ability to find the coordinate of a specific
4870 # bug fix for inability to specify fractional coordinates: adds fx, fy, fz as
4873 # bug fix for inability to use x,y,z,fx,fy,fz with cartesian points
4885 # bug fix for strandCount not carrying over to meshRibbon
4919 # bug fix for structure loss on load append. (structure is supposed to be recalculated).
4929 # bug fix for load append with spacegroups causing atoms to be repositioned
4930 # bug fix for anim playrev in loop mode causing animation to stall
4960 # adds simplistic <sub></sub> <sup></sup> to text, including echo, label, hover, etc.
4961 # fixes popup menu to better deal with multiple file context
4972 # bug fix and additional work in relation to translations
5020 # adds capability to define a property for selected atoms:
5029 # adds capability to read data from selected fields (white-space delimited columns) in a file
5067 # for that operation to complete before resuming spinning
5071 # zoomTo and moveTo the same location changed to no time delay
5133 # is to be allowed, simply remove the MAYSCRIPT parameter, which
5142 # to atoms, as in "load xxx.cif {1 1 1}", to also apply symmetry
5143 # to the bonds indicated in the file. The flag is useful when
5155 # better isosurface plane rendering, especially in regard to meshes
5156 # bug fix in isosurface contour -n going WAY back to before 10.9.60
5172 # can either be to host page JavaScript functions or to Jmol scripts. This
5182 # adds echo script to defined state
5220 # GhemicalMMReader -- was incorrectly assigning aromatic to bond type 4 via fall-through of switch
5244 # This was a needed change to prevent unwanted multiple isosurfaces.
5249 # That was necessary only because it was easy to mistakenly make multiple
5264 # fixes two nasty bugs relating to isosurfaces and JVXL files.
5268 # surfaces from + to -.
5276 # similarly to the way stars are colored
5293 # adds isosurface CAVITY x.xx -- a new way to depict the cavities of
5315 # where N is -1 to 9.
5348 # to turn on and off without messing with size, just use
5378 # to color isosurfaces:
5391 # adds "bwr" colorscheme as opposed to "rwb", which I think is backward.
5396 # write -- modified to allow unquoted filename in
5421 # It will take a bit more to make it all consistent, but the idea
5425 # This build allows for the applet to be "bare-bones" -- only the
5450 # 2) extends find() to sets of lines. For example:
5465 # APPLICATION: adds undo/redo to a fixed depth of 50 commands
5481 # These can be mixed and matched to good effect. Certain relatively
5490 # 0.0 + "3.5" ==> 3.5 (string converted to float)
5491 # 0 + "3.5" ==> 3 (string converted to float, then int)
5492 # "3.5" + 0 ==> "3.50" (integer converted to string)
5493 # "3.5" + 0.0 ==> "3.50.0" (float converted to string)
5495 # 1.0 + {carbon}.xyz ==> 1 + distance from {0 0 0} to {carbon} center
5503 # AND, OR, XOR, and NOT all require conversion to boolean UNLESS both
5515 # In standard math, boolean TRUE evaluates to 1.0; FALSE evaluates to 0.0
5517 # true + 2.0 ==> 3.0 ("TRUE" evaluates to 1.0 in math operations)
5518 # 2 + true ==> 3 ("TRUE" evaluates to 1.0 and is then turned into an integer)
5523 # When you set a variable to a value, and that value is a point, plane, or atom expression,
5595 # to go along with x.bonds
5612 # from each molecule 1 atom to the average molecule 2 position"
5614 # to the "average position of molecule 1"
5624 # to the center of molecule 2
5665 # allows measurements to be recalculated on the fly.
5736 # notation WITHOUT commas. This is because we have to distinguish between
5737 # atom expressions {1,2,3} and coordinates {x y z}, and this seems to me the
5738 # simplest way to do it. (Comma means "or" in atom expressions.) In all other
5756 # atom-based data back to the user with whatever formatting is desired.
5778 # You can now use getProperty to get expression information directly:
5807 # You can specify how to label a set of bonds using format strings.
5828 # extend that here to add some useful "modulus-like" capability: