Lines Matching refs:that
136 # that meant state functions _set... were static
138 # So for this fix I've changed that to be "static_..." for
141 # a state or in "show functions" so that a state does not
143 # bug fix: jmol -ionxs with a script that includes measurement tries to update a nonexistant measur…
243 # dragged in, Jmol recognizes that and loads the state. Very cool.
293 # new feature (TODO): 4D extension (that's right -- FOUR dimensions)
308 # bug fix: undocumented rotate[selected] {pt1} {pt2} ... has pt1/pt2 backward. Should be such that:
344 # where n is an integer 1,2,3... that selects which set is to be displayed and
390 # new feature: by passing an array to a function, you can make that variable
441 # note that the axis length is the rise, radius length is the radius,
463 # script editor behaving properly except for a nasty SWING bug that will
475 # that load scripts into a "script editor" and allow stepping through
486 # bug fix: 2 pixels off in y for labels. Don't know why I thought that was necessary in Text.java::…
537 # new feature: a = [] note that a+=2 then produces [2] -- "a+=" similar to JavaScript a.push(2)
565 # just outputs messages from the print commands in that script
569 # new feature: support for extended inline if: x = (a ? this : b ? that : theother)
628 # in terms of the Jmol "state" but in this version I introduce the Variable class that
641 # --1-based rather than 0-based arrays. (ONLY because that's the way models are numbered.)
647 # --Of course, a whole suite of methods that relate to molecular structure.
671 …eMinimizationThread T/F nec. to be FALSE when running minimizations in scripts that require values
756 # note that an outer set of {} is required when setting a property
760 # used where you would use that in Java, for instance:
994 # --basically anywhere you want a "trajectory" but don't want to save all that data
1030 # note that .x .y .z does NOT do this conversion. If that is
1040 # Note that uxyz is not settable, but fxyz is, so one could, for example,
1125 # note: for NBOs you still need FILTER "NBO" so with charges that would be FILTER "NBO;NBOcharges"
1153 # for example: frame ALIGN {*} -- align all frames on center for that frame
1160 # around code that might be running and deleting atoms or bonds while some other
1185 …LoadOrientation (default: FALSE) automatically sets "reset" orientation to that in file, if present
1345 # new feature: new command "exitJmol" does just that -- application only;
1383 # the rest seemed simple to implement along with that.
1404 # new feature: Jmol.js jmolScriptWaitOutput(script) returns all messages that would
1500 # all pmesh command does is guarantee that if the pmesh data is standard pmesh ASCII data,
1565 # if hbondsAngleMinimum is set > 0 (default 90 ?), then that angle is checked
1672 # cd # reports current directory and sets default directory to that
1700 # default {0 0 1} so that just one trajectory is loaded from each file
1709 # -- such that X = atomX - center, Z = cross(atomXY - center, atomX), Y = cross(Z, X)
1962 # console has a menubar menu item "Jmol" that is the pop-up menu.
1982 # -- note that images can be placed in 3D, just as for text.
1984 # that is to be designated as the background color (the color that should be omitted).
1985 # -- using "background echo none" specifies that the first pixel
1986 # of the image specifies the color that should be omitted.
2026 # because that's what they really do.
2056 # but without ID, one is restricted to words that are simple text and not Jmol entities.
2153 # quaternions are always fixed so that cos(theta/2) > 0 -- that is, so that
2158 # sign of theta if that value is negative.
2252 # note that the Point4f equivalent stores w LAST, even though it is "q0"
2253 # because the Java Quat4f() and Point4f() both do that as well. We're just
2339 # and with that: write("quaternion" [,"w"|"x"|"y"|"z"|"a"|"r"][,"difference"|"difference2"][,"dra…
2381 # applications (note that CALCULATE must be invoked first):
2433 # that is displayed.
2459 # NOTE a limitation: scripts intended for the signed applet that
2462 # in that environment, the JAVASCRIPT command must run on the browser's
2464 # must NOT run on that thread. I have configured the ScriptManager to
2465 # detect the presence of the word "javascript" followed by a space (exactly that case)
2470 # the phrase /*SPLIT*/ in upper case, exactly like that, it will be split and then run
2728 # * note that FILL serves to provide a cut-out for BALL and a
2739 # note that for now PDB file reading of ANISOU requires using {x y z} in load
2787 # A circle is a 2D object that behaves like a halo, always appearing circular
2924 # Note that file.model numbers do not change after this.
3028 # note that dots do not have a %Jmol option:
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
3117 # this allows, for example, monitoring of orientation information so that
3128 # new feature: set delayMaximumMs sets the maximum delay that scripts will use, primarily for test…
3132 # note that the current zoom affects the label size.
3140 # //note that the following JavaScript retrieves the registry:
3197 # * note that there is NO redundant extra vertex in this format
3236 # bug fix: pmesh test1 "inline" "1 {2. 0. 0.} 0" disallowed, but that should be OK
3237 # bug fix: isosurface gridpoints "ch3cl_map.jvxl" -- gridpoints for jvxl files that are already map…
3256 # interesting that if 1.1 and 1.2 are trajectories you can do
3258 # this creates an isosurface for model 1.2 that uses the atomic coordinates of model 1.1!
3312 # bug fix: select 1.5 in trajectory context should switch to that set of coordinates
3330 # selects that file, but also sets the trajectory to 1.3.
3400 # this involves the fact that Safari will deliver null pointer when it
3515 # these selections override any manifest that might be in a ZIP file.
3584 # IGNORE_MANIFEST --- (on the load command line) indicates that the internal ZIP file manifest…
3724 # new feature: "\" at the end of a line marks a continuation of that line
3734 # OK, so that might look good, but it evaluates to
3828 # only that number of atoms are affected
4335 # also "exitJmol" typed into the script window for the application does that.
4346 # Drawn arrows now have a head size that can be set and a dimension that
4466 # This is what one would want for something that should be a given
4585 # allows setting of color range and scheme so that color
4590 # x = (0.01).color # gives the point-color associated with that number
4674 # number that identifies the page containing the controlling applet. If the
4742 # note that xmlReader (SAX reader) is now set to ignore all DOCTYPE declarations
5065 # spinning now detects that a zoomTo or moveTo operation is occurring
5067 # for that operation to complete before resuming spinning
5084 # (2) ni<0 indicates JavaScript functionName will return a single string that
5086 # (3) ni<0, nj<0 indicates that JavaScript will fill the fourth parameter
5147 # the application of symmetry operations creates new bonds that
5150 # new bonds are created that are between atoms that were created
5234 # and title (usually the command that was given that created this isosurface)
5250 # isosurfaces that otherwise would look the same.
5377 # introduces user-definable atom properties that can be used
5408 # The "SET" command is no longer necessary. Anything that could have
5422 # is that there are then some special reserved variables that
5431 # about 58% of the full package. All that gets you is atoms, bonds,
5502 # Boolean expressions are a bit different in that the operators
5523 # When you set a variable to a value, and that value is a point, plane, or atom expression,
5605 # Note that when more than one atom is involved in a set,
5611 # x1 is a NUMBER that is the "average distance measured
5637 # reset varName # clears that variable definition
5661 # Now that we can move atoms so easily, we don't want those measurements getting stale.
5819 # atoms FOR THIS SET OF BONDS. This is so that a proper subfile of type MOL
5828 # extend that here to add some useful "modulus-like" capability:
5873 # note that you can even say: