Lines Matching refs:is
1 # NOTE: This is not the development trunk. It is the release branch.
17 # bug fix: message this is a @{test} fails
78 # bug fix: code - viewer.getDisplayModelIndex() not used properly when background model is present
80 # bug fix: Export uses incorrect width/height parameters when size is not window size
144 # bug fix: select xxx when xxx is an array fails to do lookup of defined values
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
292 # bug fix: DRAW point size 6 pixels (an even number) sets it just one pixel off center -- 7 is bett…
312 # is the same as
344 # where n is an integer 1,2,3... that selects which set is to be displayed and
346 # bug fix: spacegroup reading when center of molecule is not in unit cell can cause bonding errors
349 # bug fix: draw OFF in state script is not selective
389 # bug fix: arrays passed to functions by reference do not update if size is increased
399 # bug fix: spacegroup "-- [--]" displayed when load command option SPACEGROUP is used
409 # bug fix: WRITE MO does not work when no current MO is present
427 # This application completely disallows any display -- it is totally formless
441 # note that the axis length is the rise, radius length is the radius,
442 # and 360 / angle is the pitch of the helix
459 # code: refactored scriptEvaluator and Jmol.java. Now it is much simpler
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
522 # bug fix: select(x;{xxx};...) or for(x;{xxx};...) when {xxx} is empty returns incorrect result
534 # bug fix: set xxxx n where n is an integer fails.
577 # does not exist when nBytesMax == 0, so is a simple test for "Local File Exists"
627 # --A relatively free typing of variables. Jmol is going to save variables as strings
669 # bug fix: in certain APPEND cases, binary space partitioning forest initialization is not complete
696 # the braces really aren't necessary; there is no ambiguity here:
756 # note that an outer set of {} is required when setting a property
866 # yes I yes ionic radius used for bonding (<b>i</b>onic radius when a formal charge is defined)
880 …), "P" (carbonyl-carbon based), or "N" (amide-nitrogen based). The default is alpha-carbon based, …
924 # new feature: label %[....] where .... is one of:
1015 # --optional n is just as for any load -- optional nth model
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,
1152 # for example: frame ALIGN {C2} -- align each frame on C2/n where n is a frame number
1155 # bug fix -- animation/spin while script is rendering can cause Exception
1161 # process is rendering
1226 # where n is an optional pointer to a specific group (starting with 1)
1232 # [n] is optional; defaults to 9
1236 # CONTOUR keyword is CONTOURLINES NOFILL
1255 # bug fix: Spartan reader reads MOs improperly when only a partials set of MOs is included in the f…
1270 # because there is no need for voxelData = float[nx][ny][nz].
1370 # return can be String if there is an error.
1382 # primarily, this is for writing to an OutputStream directly, but
1428 # new feature: when errorCallback or scriptCallback is enabled, messages are translated
1431 # bug fix: translation not disabled when messageCallback is present
1473 …lect {*.ca} (phi < select(y; {*.ca}; y.resno = _x.resno + 1).phi) fails when atomExpression is ({})
1500 # all pmesh command does is guarantee that if the pmesh data is standard pmesh ASCII data,
1531 # _x is used for the selected atom (not _atom) as for
1565 # if hbondsAngleMinimum is set > 0 (default 90 ?), then that angle is checked
1566 # for any atoms A--X- - -Y where A is attached to X,
1667 # matching is case-sensitive.
1697 # -- FILTER is optional
1698 # -- COORD {first,last,step} is optional for each coordinate file loaded
1700 # default {0 0 1} so that just one trajectory is loaded from each file
1701 # -- explicit format "mdcrd::" is required, because these files have no identifying characteristics
1708 # -- quaternion is created based on three atoms or coordinates
1760 # new feature: MOL2 reader is PDB-enabled.
1786 # new feature: signed applet may write file, images, scripts, variables to disk. User dialog is req…
1908 # bug fix: oops, 11.6.RC5 is totally broken due to missing refreshes
1947 # where [type] is one of Cs, Ci, Cn, or Sn, where n is an integer or the character "n"
1962 # console has a menubar menu item "Jmol" that is the pop-up menu.
1979 # same as text is displayed.
1984 # that is to be designated as the background color (the color that should be omitted).
2035 # bug fix: vibration thread not closing down for applet destroy when applet is off-screen
2047 # bug fix: 11.5.48 is broken for scripts with array definitions such as
2056 # but without ID, one is restricted to words that are simple text and not Jmol entities.
2092 # of {ptref} in a plane perpendicular to the axis. This is similar (but opposite)
2094 # theta0 is the the offset angle from 0
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
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]
2155 # This is important. One can also get a directed theta based on a
2156 # specified axis using q % {x y z w}. w is ignored; x y z is the
2158 # sign of theta if that value is negative.
2203 # bug fix -- if last helix is last atom, SHOW STRUCTURE fails to identify it.
2207 # selectX is no longer necessary. Simply use
2218 # point4f is {x, y, z, w} (w ignored), where {x y z} is a
2252 # note that the Point4f equivalent stores w LAST, even though it is "q0"
2269 # thus, for example, (q%{1 0 0}) is the same as (q%-3)
2324 # new feature: "quaternion derivative" --> "quaternion difference", which is more
2379 # Range is from -1 to 1
2432 # and multiple models select even if not displayed because it is not their model
2433 # that is displayed.
2438 # new feature: signed applet shows frank "Jmol-S" which is NOT removable.
2454 # the signed applet uses this automatically unless there is a
2461 # CANNOT be combined with the JAVASCRIPT command. This is because
2473 # new feature: _signedApplet boolean is available:
2533 # new feature: random(a), random(a,b) where a is lower bound and b is upper bound
2625 # flag is "set undo TRUE/FALSE"
2653 # id is a REQUIRED field. AXES is required if a new ellipsoid is being defined
2753 # bug fix: data "model"...end "model" saves state without first line if first line is empty
2787 # A circle is a 2D object that behaves like a halo, always appearing circular
3026 # spacefill @x% # make sure x comes out integer, otherwise % is ignored
3042 # bug fix: command "test()" where test() is a user-defined function causes array-out-of-bounds error
3100 # new feature: label "scaleReference" if > 5.0 is taken to be a reference zoom setting
3114 # when syncCallback is set to a JavaScript function name, that function
3139 # the value is the static Hashtable htRegistry
3155 # bug fix: check if the file is CIF before PDB
3162 # bug fix: color isosurface when isosurface is an lcaoCartoon only colors one lobe
3182 # BINARY keyword is optional, but recommended for efficiency
3197 # * note that there is NO redundant extra vertex in this format
3281 # where [zoomOrZoomFactor] is n, +n, -n, *n, /n, or 0 (to indicate fill screen)
3315 # bug fix: select */4 when "4" is inappropriate returns all instead of none
3329 # in which case "select 1.3", if file 1 is a trajectory, not only
3402 # The solution is to use
3452 # note --- set strandCount sets BOTH, but now each is independent
3518 # getProperty now allows drilling down through a ZIP file. If no subfile is shown,
3519 # then the directory listing is given:
3574 # JmolManifest is simply a list of files, one per line.
3594 # new feature: load xxx.zip n # where n is the desired file, starting with 1
3667 # For many property types, the qualifier is an atom set
3668 # If the atom set is not given, those properties default to {visible}
3669 # For "stateInfo", the qualifier is string: "fileState", "modelState", etc.
3683 # default ON/OFF is to NOT change current setting
3722 # solution is a new feature:
3744 # the following is OK:
3748 # the following is preferred:
3800 # if found, ONLY this text is processed and all other text in the file is ignored.
3827 # if the array is shorter than the number of atoms selected, then
3847 # new feature: set xxxx where xxxx is not a Jmol variable causes ERROR
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.
3975 # bug fix: Using isosurface within 1.0 @pt1 where pt1 is a draw point save state cannot be restored…
3997 # where xxx is the site identifier and n is the site number.
3998 # These settings are reset each time a file is loaded.
4024 # where TYPE is one of:
4130 # first-character "_" indicates this function is a LOCAL function, private to this applet.
4165 # bug fix for PAUSE causes app to hang -- this is a reversion of use of SwingUtilities.invokeLater(…
4191 # select within(5.0,model=2.1) # default is FALSE
4214 # print "atom " + i + " " + {atomno=i}.ident + " is at " + {atomno=i}.xyz
4235 # if (i = 2);print "i is 2";endif
4359 # x = "this is a test".split(" ")
4363 # now x is saved as an array, so this is no problem.
4401 # a = "this is a test"
4404 # >> a = "this is not a test"
4464 # and there is no scaling done ever, so effectively these prefixes
4466 # This is what one would want for something that should be a given
4523 # bug fix: -g ignored on -n option, even if -w is present
4653 # new feature: write JPG n "filename" # where n is the quality (<=100)
4661 # new feature: symmetryRange: load "someFile" {mmm nnn 1|0} range x.x where x.x is a maximum dist…
4675 # syncId is not given, then the ID for the page containing the controlling applet
4676 # is used. This feature is important for cross-frame synchronization only.
4702 # random digits and no space characters. (A number is good.)
4723 # bug fix: select dna can select rna if chain is mixed hybrid dna+rna
4742 # note that xmlReader (SAX reader) is now set to ignore all DOCTYPE declarations
4864 # bug fix for "wait" not recognizing if it is just a syntax check (app)
4919 # bug fix for structure loss on load append. (structure is supposed to be recalculated).
4951 # in terms of whether animation is on or not in the 7th parameter being 1 or 0:
4989 # where [zoom factor] is x, where x > 0
5065 # spinning now detects that a zoomTo or moveTo operation is occurring
5066 # or the user is manipulating the model with the mouse, and pauses 1 second
5069 # hover now is turned off during spinning or user manipulation of the model
5128 # (2) and (3) are very fast; (1) is the original method, but it is slow.
5133 # is to be allowed, simply remove the MAYSCRIPT parameter, which
5143 # to the bonds indicated in the file. The flag is useful when
5145 # the model is "molecular" -- the base atom coordinates are correct
5149 # there is only one bond initially, and after applying symmetry
5168 # than one model at a time displayed, because there is only one set
5171 # adds script: option for callbacks set from within Jmol. That is, callbacks
5238 # Now if no ID is indicated, the previous ID is used for all commands
5241 # This is a change from Jmol 10.2 and 11.0, where if you leave
5242 # off the ID, a new isosurface is created.
5315 # where N is -1 to 9.
5371 # This is it! :)
5391 # adds "bwr" colorscheme as opposed to "rwb", which I think is backward.
5408 # The "SET" command is no longer necessary. Anything that could have
5422 # is that there are then some special reserved variables that
5430 # Then a developer can slim down the download. The minimum is 697K,
5431 # about 58% of the full package. All that gets you is atoms, bonds,
5500 # Now x is the average x coordinate of carbon
5508 # false OR 2.0 ==> true (2.0 is not 0, so it is TRUE)
5513 # x is now the center point of all oxygen atoms in the first molecule
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,
5576 # CHANGE: default string value for a bitset is now the ({n:m})
5581 # x = "number selected is " + {selected}.size
5585 # x = "number selected is " + (0 + {selected})
5603 # When more than one atom is involved, average positions are used.
5605 # Note that when more than one atom is involved in a set,
5611 # x1 is a NUMBER that is the "average distance measured
5613 # x2 is a point representing the VECTOR from the "average position of molecule 2"
5642 # An additional bond type is now avaiable: "UNSPECIFIED".
5736 # notation WITHOUT commas. This is because we have to distinguish between
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.
5819 # atoms FOR THIS SET OF BONDS. This is so that a proper subfile of type MOL
5827 # Usually modulus is reserved for integer math, so we
5865 # script xxxx.spt # this is the full state load