Lines Matching refs:x
3 # NOTE: New features should be introduced in the trunk version 11.9.x
149 # bug fix: label %vx giving x coord, not vibration x component
193 # bug fix: x = {255,0,0}; select color=x; #did not work
232 # new feature: draw ID xxx SYMOP [n or "-x,y,z"] [optional {atom or position}]
305 # bug fix: zap x.y when have measures to draw objects causes exception
310 # rotate x 10
323 # new feature: [x,y,z].sum2 or {xx}.someProperty.sum2 -- sum of squares
434 # given x = C-alpha, C-carbonyl, or N (depending upon set quaternionFrame)
436 # "point" -- nearest point to x on local helix axis
439 # "radius" -- vector normal from local helix point to x
506 # x = 'testing'
522 # bug fix: select(x;{xxx};...) or for(x;{xxx};...) when {xxx} is empty returns incorrect result
557 # new feature: set or x = command no longer restricted to single lines.
569 # new feature: support for extended inline if: x = (a ? this : b ? that : theother)
713 # for (var x = 1; x < {*}; x = x + 1)
714 # if ({*}[x].temperature < 10)
715 # ({*}[x]).radius = 1
717 # ({*}[x]).radius = 0
723 # for (var x = 1; x < {*}; x = x + 1){
724 # if ({*}[x].temperature < 10) {
725 # ({*}[x]).radius = 1
727 # ({*}[x]).radius = 0
733 # for (var x = 1; x < {*}; x = x + 1){
734 # {{*}[x]}.radius = ({*}[x].temperature < 10 ? 1 : 0)
739 # for (var x = 1; x < {*}; x = x + 1){{{*}[x]}.radius = ({*}[x].temperature < 10 ? 1 : 0)}
745 # new feature: load "@x" -- inline load of data contained in variable x.
759 # new feature: .length alias for .size except for x.bonds - so it can be
769 # ans = for(x;{*.ca};x.resno)
775 # ans = for(x;{*.ca};x.bonds.length).all.add()
779 # ans = if (x.resno < 5 ; "low resno"; "high resno")
784 # print for(x;{*.ca};if (x.bonds.length < )
788 # bug fix: x = array();x[1] = "testing" not working
832 # "label %x"
844 # yes yes x yes atomX Cartesian X coordinate
900 # W yes PDB residue designator with x, y, z included: [%n]%r %x %y %z (Jmol 11.3.41)
930 # %[atomX] %x
1002 # new feature: load PARTIALCHARGE ... float ~[-3.4 x 10^38 to 3.4 x 10^38]
1021 # new feature: load {a b -c} packs a x b x c cells
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
1028 # new feature: {x y z}.ux, .uy, .uz similar to .fx, .fy, .fz
1029 # new feature: {x y z}.xyz -- returns cartesian from fractional
1030 # note that .x .y .z does NOT do this conversion. If that is
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)
1123 # bug fix: rotate -x n rotates wrong direction
1197 # draws x,y,z coordinates for the frame defined by the specified quaternion at the specified cente…
1308 # new feature: translate x|y|z x.x nm|angstroms|%
1535 # return _x.x + _x.y + _x.z
1604 # new feature: Jmol math simple array definitions using brackets: x = [3,4,5,6]
1645 # new feature: x = file("some file name") or x = file("?") -- returns full path to file
1706 # new feature: x = quaternion({center_or_point}, {atomX_or_point}, {atomXY_or_point})
1711 # new feature: x = quaternion(q, "id", {center})
1713 # -- creates DRAW sequence to draw quaternion q as three arrows red(x), green(y), blue(z)
1733 # bug fix: .x not recognized
1828 # bug fix: {*}.x = .... broken
1863 # new feature: x = script("some script", "appletName")
1868 # x = script("print getProperty(\"modelInfo.modelCount\")","B")
1872 # x = script("show orientation moveto","jmolApplet2")
1946 # new feature: draw pointGroup [type] [index] SCALE [x]
2006 # including x = script("write pointGroup")
2059 # new feature: draw {point} PLANE [plane def, including xy, yz, x, etc.]
2085 # bug fix: 11.5.46 broke standard "spin x 30" (b)
2152 # {x y z w} where w = cos(theta/2) and {x y z} = sin(theta/2)*unitNormal
2156 # specified axis using q % {x y z w}. w is ignored; x y z is the
2166 # new feature: q = axisAngle({x y z}, theta)
2167 # new feature: q = axisAngle(x, y, z, theta)
2168 # new feature: q = axisAngle("{x y x theta}")
2169 # new feature: q = quaternion("{x y z w}")
2172 # new feature: rotate quaternion {x y z w}
2173 # new feature: rotate axisAngle {x y z theta}
2184 # bug fix: local assignment var x = array() followed by x[n] = ... does not work
2185 # bug fix: f(x[i],x[j]) selects only x[j], not both x[i] and x[j]
2196 # bug fix: select @x broken in 11.5.43
2211 # with no "x." An implied variable "_x" can be used explicitly:
2218 # point4f is {x, y, z, w} (w ignored), where {x y z} is a
2220 # Returns a point4f angle-Axis equivalent with x, y, z the normal for the quaternion
2222 # to be directed with a positive dot product between the input {x y z}
2223 # vector and the output {x y z}.
2244 # q = quaternion({x y z}, angleDegrees)
2250 # q.x, q.y, q.z, q.w
2259 # (q%1) -- q1 (x)
2267 # (q%{x y z}) -- rotational transform of a point or vector based on a quaternion
2294 # new feature: sqrt(x)
2322 # for example: set pickLabel "%n x = %x, y = %y, z = %z"
2336 # new feature: quaternion [w|x|y|z|a|r] [difference][2] [draw]
2337 # new feature: draw quaternion [w|x|y|z|a|r] [difference][2]
2338 # new feature: write quaternion [w|x|y|z|a|r] [difference][2] [draw]
2339 # and with that: write("quaternion" [,"w"|"x"|"y"|"z"|"a"|"r"][,"difference"|"difference2"][,"dra…
2345 # draws x,y,z and n vectors for a quaternion center
2353 # q = frame{ vA, (vC x vA), vC }
2386 # selectX {*} x.straightness < 0.995 # does not round
2416 # select(x;{atomexpression};booleanEvaluation)
2420 # x = select(x;{*};x.distance({atomno=3}) / 3 > x.distance({atomno=2}))
2421 # x = select(x;{*.ca};x.phi < select(y; {*.ca}; y.resno = x.resno + 1).phi)
2425 # new feature: draw Vector [x y] or [x y %] {x' y' z'}
2426 # new feature: draw [x y] or [x y %] can be incorporated into lines, curves, arrows
2428 # new feature: set echo myecho [x y] and set echo myecho [x y %]
2429 # new feature: axes position [x y] and axes position [x y %]
2430 # sets the axes to the x y screen position or percent indicated.
2494 # Atom: xxx Group: xxx Chain: xxx Model: xxx Coordinates: x y z
2526 # (11.4 does {x,y,z}, then $xxx, then {atomExpression}, then @{{atoms}.split()})
2535 # new feature: sin(x), cos(x)
2648 # CENTER {x y z}
2650 # COLOR [translucent [x.y] |opaque] [color]
2700 # new feature: set ellipsoidAxisDiameter x.y
2739 # note that for now PDB file reading of ANISOU requires using {x y z} in load
2749 # bug fix: "....".trim("xyz") function not properly trimming ANY x,y,z
2756 # new feature: isosurface FunctionXY "data2d_xxxxx" {origin} {ni x 0 0} {nj 0 y 0} {nk 0 0 z}
2758 # new feature: isosurface FunctionXY "data2d_xyz_xxxx" {origin} {ni x 0 0} {nj 0 y 0} {nk 0 0 z}
2759 # allows setting isosurface values using a block of x y z data, all points for which should be
2798 # new feature: minimization CONSTRAINTS {xx} {xx} [{xx} [{xx}]] x.y
2807 # new feature: x = getProperty("minimizationInfo")
2811 # var x = getProperty("minimizationInfo")
2812 # write VAR x "myfile.out"
2823 # new feature: minimize CRITERION x.y
2900 # bug fix: zap x.y additional work -- connections, isosurfaces
2901 # bug fix: zap x.y not correcting Eval variables
2910 # bug fix: zap x.y for dots
3025 # stars @{x+0.1} # math OK
3026 # spacefill @x% # make sure x comes out integer, otherwise % is ignored
3078 # new feature: inline math @{x+3} extended to all commands
3191 # * float[vertexCount*3]vertices {x,y,z}
3275 # bug fix: quaternion x reports wrong frame number
3433 # modification for load RANGE -x.x (within x.x Angstroms of symop=1555) to be within x.x of the
3633 # bug fix: Jmol math (x[2])[3] indistinguishable from x[2][3]
3708 # [plane definition] can be {x y z w} or any combination of
3709 # three {x y z} points, draw point references, or atom expressions
3758 # [ "draw","[drawID]",[modelIndex],[vertexIndex],[x],[y],[z] ]
3812 # x = "atomno=3"
3813 # select @x # or select @{x}
3814 # select @{x + 3} # selects atomno=33
3815 # x = array("atomno<10","atomno>20")
3816 # select @x # OR of the list elements
3817 # select @{x[2]} # just element 2 of x (atomno>20)
3818 # select @x[2] # same as {@x}[2]
3823 # {*}.x = array(2,3,4,5,6);
3855 # x = {atomno=3}.split() # a list, one element for each model
3856 # draw @{x.xyz.sub({1 0 0})} # a set of points, one per model
3860 # bug fix: draw @{x - {1 0 0}}
3918 # new feature: @{mathExpression} for echos, select, etc. where @x can be used.
3919 # select atomno=@{x*2};
4021 # bug fix: zoomto (atomExpression) 0 # zooms to 2x
4064 # .x, .y. .z, .xyz,
4075 # new feature: set atom properties using {xxxx}.x =
4077 # {atomno=3}.x = 3
4079 # for(var i = 1; i < 3; i = i + 1); {(*)[i]}.x = 5;end for;
4289 # var x = script("draw line"+ id + " {atomno=" + a + "} {atomno=" + b + "}")
4302 # x = d({atomno=3},{atomno=4})
4303 # print x
4359 # x = "this is a test".split(" ")
4360 # y = x[3]
4362 # because x was only saved as a string, not an array
4363 # now x is saved as an array, so this is no problem.
4365 # new feature Jmol math point(x,y,z) function
4367 # point(a,b,c) or point("{x,y,z}")
4369 # x = point(y[3], y[6], y[2])
4370 # x = point("{2,3,5}")
4374 # x = {3.0,4.0,5.0}
4378 # x = {r,g,b}
4406 # new feature: Jmol math x = array(a,b,,,,)
4408 # x = array(3,4,5,6)
4409 # print x[3]
4413 # new feature: Jmol math plane(x,y,z,w) function
4415 # plane(a,b,c,d) or plane("{x,y,z,w}")
4421 # x = plane(y[3], y[6], y[2], 3.0)
4422 # x = plane("{2,3,5,4}")
4423 # x = plane({_H}[1],{_H}[2],{_H}[3],{_C}[1])
4426 # print x
4427 # print x * 3
4428 # print x[4] + x[3]
4429 # print x.split(" ")[2][0]
4456 # color "byElement_Mine=[x......] [x......] [x......] ..."
4482 # color "byResidue_Mine=[x......] [x......]..."
4572 # (some number).color gives a color triple as a point {x y z}
4573 # {x y z}.color gives a hexadecimal string [xRRGGBB]
4577 # x = {atomno=3}.color # gives {255.0, 255.0, 0.0}
4578 # x = {atomno=3}.color.color # gives "[xFFFF00]"
4581 # x = {atomno=3}.partialcharge.color
4590 # x = (0.01).color # gives the point-color associated with that number
4593 # color echo @x; background echo @x # color this bar the color of 0.01
4630 # new feature: lcaoCartoon rotate [x|y|z] degrees create "px"
4661 # new feature: symmetryRange: load "someFile" {mmm nnn 1|0} range x.x where x.x is a maximum dist…
4774 # new command: quaternion [w x y z] [derivative]
4786 # bug fix: minus-sign "fix" in 11.3.1 broke all {x -y z} notation
4817 # x = $p[3]
4827 # bug fix for x = "testing"[0], x = "testing"[-1], "testing".split("t")[0], and "testing".split("t"…
4873 # bug fix for inability to use x,y,z,fx,fy,fz with cartesian points
4899 # bug fix for select @x not functioning where x = {atom expression} or x = "atom expression"
4985 # moveTo timeSec {x y z w} (atom expression) 0 [zoom factor]
4987 # moveTo timeSec {x y z w} 0 transX transY (atom expression) 0 [zoom factor]
4989 # where [zoom factor] is x, where x > 0
4991 # [0] [[+ | - | * | /] x]
5000 # fix for x = {...}.resno and {...}.groupID
5083 # (1) "file:" allows reading of xy data from files for graphing f(x,y)
5095 # function xyData(app, x, y) {
5096 # return func(x, y)
5293 # adds isosurface CAVITY x.xx -- a new way to depict the cavities of
5309 # isosurface within x.x (what)
5365 # x = {carbon}[5].property_test
5366 # x = {carbon}.property_test.min
5367 # x = {carbon}.property_test.max
5380 # x = load("file.dat");
5381 # isosurface variable x # simple 100% vdw radius mapping
5384 # data "property_myprop @x"
5409 # been set using "SET x .... " can now be set using
5411 # x = ....
5447 # x = {*}.bonds.length.max #the longest bond length
5448 # x = {*}.atoms.max #the last atom
5498 # x = {carbon}.xyz * {1 0 0} ==> (dot product)
5500 # Now x is the average x coordinate of carbon
5511 # x = ({oxygen} and {molecule=1}).xyz
5513 # x is now the center point of all oxygen atoms in the first molecule
5527 # x = "{x y z}"
5530 # x = "{x y z w}"
5533 # x = n
5536 # NOTE: "set x" removed in 11.3.40:
5539 # x = {oxygen}.xyz
5541 # draw @x
5543 # draw line1 @x @y
5547 # x = {carbon}[3][5]
5548 # select @x
5551 # x = {carbon}[3][5]
5552 # select @x
5556 # x = {carbon or oxygen}.bonds
5557 # select BONDS @x
5563 # x = data({atomno < 10},"xyz")
5564 # x = data({atomno < 10},"mol")
5565 # x = data({atomno < 10},"pdb")
5567 # data "model @x"
5581 # x = "number selected is " + {selected}.size
5585 # x = "number selected is " + (0 + {selected})
5594 # x.atoms
5595 # to go along with x.bonds
5627 # x = load("filename")
5679 # %x1 atom property "x" for atom 1
5680 # %x2 atom property "x" for atom 2
5681 # %x3 atom property "x" for atom 3
5682 # %x4 atom property "x" for atom 4
5703 # xOxygen = {oxygen}.x
5707 # message %{{carbon}.x}
5720 # x = {carbon}[3] # the third carbon atom
5721 # x = {carbon}[3][5] # the third through fifth carbon atoms
5722 # x = {carbon}[3][0] # the third through last carbon atoms
5735 # Points in IF, SET, and %{} can be designated using the standard {x y z}
5737 # atom expressions {1,2,3} and coordinates {x y z}, and this seems to me the
5741 # x = {1 1 0} + {oxygen}.xyz
5759 # xyzFile = "" + {selected}.size + "\n\n" + {selected}.label("%a %x %y %z")
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 …ze)%-3+(""+{selected}.bonds.size)%-3+" 0 0 0\n"+{selected}.labels("%-10.4x%-10.4y%-10.4z %2e 0…
5784 …tPropertyAsJavaObject("evaluate", '"" + {molecule=1} + "\n\n" + {molecule=1}.label("%a %x %y %z")')
5792 # x = {atom expression}[3].ident
5793 # x = {atom expression}[3][0].xyz # 3 and after (average position)
5794 # x = {atom expression}[3][5].x # 3-5 (average x)
5801 # x = {atom expression}.bonds.ident
5802 # x = {atom expression}.bonds[3].ident
5815 # %x1 atom property "x" for atom 1
5816 # %x2 atom property "x" for atom 2
5822 # x = {atom expression}.bonds[3].label("%# %3ORDER %TYPE %a1 %a2 %6.3LENGTH")
5867 # x = (some atom expression).atomProperty -- takes an average if more than one atom
5870 # x = (* /1).temperature
5871 # x = (C5).bondcount
5875 # echo average position= {%{(selected).x},%{(selected).y},%{(selected).z}}
5885 # new: within(x.x,plane,$plane1)
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