Документ взят из кэша поисковой машины. Адрес оригинального документа : http://monkey.belozersky.msu.ru/npidb/jmol/CHANGES.txt Дата изменения: Fri Nov 21 00:24:04 2008 Дата индексирования: Mon Oct 1 19:45:04 2012 Кодировка:

# Developers: to add a description of changes you have made,
# add it on a line starting with # below the "version=..." line

version=11.6.6

# bug fix: negative number in range involving ^ still fails
# bug fix: translucency of mapped isosurfaces not saved in state
# bug fix: Dialog look and feel for Mac

# -----------------------------------------------------------------------------

#version=11.6.5

# bug fix: negative number in range involving ^ fails: select 10^P -17^P
# bug fix: goto xxx with trailing white space fails to find xxx
# bug fix: goto with a # comment in the script prior to the target line fails
# bug fix: two //xxx comments in a row breaks script
# code: superfast JVXL compression/decompression
# bug fix: straightness absolute value -- values 0 (not straight) to 1 (straight)
# load =1crn;calculate straightness;color "bwr" range 0 1;color straightness
#
# bug fix: isosurface APBS dx file reader broken (since 4/2007)
# menu: "Minimize" GT

# -----------------------------------------------------------------------------

#version=11.6.4

# bug fix: UFF.txt not included in build
# bug fix: function definitions occurring before prior script commands are executed.
# bug fix: message @{xxxx} in function not picking up function context variables
# bug fix: Some browsers do NOT strip \n from tags, necessitating changes in loadInLine()

# bug fix: "valence" not "valency" in data property_valence
# bug fix: initializeBspf(); missing in setTrajectory()

# -----------------------------------------------------------------------------

#version=11.6.3

# bug fix: set antialiastranslucent false not functional
# bug fix: text color near black with antialiasdisplay becomes white
# bug fix: text antialiasing of near-black text looks very bad when antialiased

# -----------------------------------------------------------------------------

#version=11.6.2

# bug fix: forcefield file UFF.prm --> UFF.txt
# bug fix: better Escape method for strings
# bug fix: connect auto not registered in state
# bug fix: draw point translucent only draws ring
# bug fix: load string inline with multiple models fails
#
# code: FindBugs fixes for Eval, DrawRenderer, Isosurface, ForceFieldUFF
# code: ScriptWindow public: sendConsoleEcho,sendConsoleMessage,notifyScriptStart,notifyScriptTermination

# -----------------------------------------------------------------------------

#version=11.6.1

# bug fix: set labelToggle malfunctioning
# bug fix: missing default background for toggled labels
# bug fix: color {oxygen} translucent blue
# bug fix: color translucent 1 blue 1-8 integer settings off by one
# bug fix: background color +/-1 adjustment removed
# bug fix: spardir within /M... directory
# bug fix: (minor) "set echo xxx display" equivalent to "set echo xxx displayed" missing
# bug fix: (minor) "set echo xxx hide" equivalent to "set echo xxx hidden" missing

# -----------------------------------------------------------------------------

#version=11.6

# bug fix: GIF encoder color / class not found issues
# bug fix: very thin cylinder does not appear at all viewing angles
# bug fix: load "/xxx" with unsigned remote applet loads local file instead of remote root directory
# bug fix: sulfur/sulphur always spelt as in IUPAC Red Book
# bug fix: display of aromaticSingle bond for NEW bond results in dotted bond.
# translation: English language variants no longer ignored

# -----------------------------------------------------------------------------

#version=11.6.RC18

# bug fix: fileName not reset after ZAP
# bug fix: set echo none; color echo green null pointer exception
# bug fix: .x not recognized
# bug fix: set xxxCallback "" does not clear callback ("none" was required unnecessarily)
# bug fix: cartoons ending in helix or strand draw single dot for final amino acid

# -----------------------------------------------------------------------------

#version=11.6.RC17

# bug fix: draw scale not saved in state for arc or xy arrow
# bug fix: drag/drop not enabled on consoles
# bug fix: Jmol state command "calculate surfaceDistance WITHIN ({...})" not passing compiler
# bug fix: Swing antialiasDisplay broken due to setTransparentBackground debugging
# bug fix: trajectories not enabled
# code: if (true...)/ if (false...) code cleanup
# bug fix: select model=_modelNumber didn't differentiate between 2.10 and 2.1
# bug fix: select model=0.0 caused infinite loop

# -----------------------------------------------------------------------------

#version=11.6.RC16

# bug fix: mol2 PDB format better handling of chains and derived element types
# bug fix: save image button/menu interface broken in 11.6.RC15

# -----------------------------------------------------------------------------

#version=11.6.RC15

# new feature: MOL2 reader is PDB-enabled.
# new feature: data() and DATA expanded to allow fixed-column entry
# bug fix: data property_partialcharge does not update atomic partialCharge data itself for MEP
# but instead just creates a data type "property_partialcharge"
# bug fix: CML reader failst to load primitive lattice parameters when no symmetry
# note: CML reader only reads the first structure of a file
# bug fix: CML reader not assigning atom labels
# bug fix: CML files not properly loading symmetry
# bug fix: O- formal charge radius MUCH too large; N+ MUCH too small. -- REMOVED
# code: thread control for Java Swing in applet context
# thread creating Swing objects MUST be event thread
# -- using SwingUtilities.invokeAndWait() from the commandWatcher thread
# new feature: load menu items for signed applet
# new feature: save menu items for signed applet
# bug fix: applet -- setting a jmolScript callback prevents menu updates
# new feature: minimize menu item
# new feature: signed applet allows "load ?" and includes previewer
# bug fix: H-M spacegroup designations specifying nonstandard Hall symbols by default

# new feature: signed applet/application load ?xxx uses load dialog
# webexport help updated to reflect ability to handle files opened with "load append"

# -----------------------------------------------------------------------------

#version=11.6.RC14

# new feature: signed applet may write file, images, scripts, variables to disk. User dialog is required.

# new feature: write GIF
# code: allows for getJpeg(quality,asString) option to return byte array instead of base64.
# bug fix: xxx.split()[3].replace does not do selection first
# bug fix: ramachandran and quaternion derivative not indicating structure due to dropping last atom

# -----------------------------------------------------------------------------

#version=11.6.RC13

# bug fix: set historyLevel recording full scripts, not individual commands
# bug fix: y-offset for echo text and images
# bug fix/new feature: HIDE/DiSPLAY/DELETE/COLOR $*xxx* extended to ECHO
# bug fix: findbugs input stream closure
# translation: add GT.escapeHTML and stricter checking for special characters in file names
# used by web export.

# -----------------------------------------------------------------------------

#version=11.6.RC12

# bug fix: getProperty("atominfo",{atom expression}) not working for "atominfo[0].xxx
# bug fix: getProperty("modelinfo",{atom expression}) not working
# new feature: set atomPicking TRUE/FALSE
# new feature: set bondPicking TRUE/FALSE
# bug fix: draw pointgroup when principalPlane == null
# bug fix: findbugs corrections in minimize.forcefield, modelset.AtomCollection, shapespecial.DrawRenderer
# new feature: applet parameter jmolSetCallback("maximumSize", nnn) -- sets maximum size of applet when resizing to this value
# cml reader fix for not applying symmetry to first model
# translation: added GT._ calls for HTML templates and JS in WebExport

# -----------------------------------------------------------------------------

#version=11.6.RC11

# bug fix: echo IMAGE and antialiasdisplay
# bug fix: super/subscripts with antialiasdisplay
# translation: menu items in console
# bug fix: web export / language
# bug fix: draw pointgroup C2 2 not distinguished from draw pointgroup C2 1
# bug fix: d2 point groups cause null pointer exception due to missing principal axis
# bug fix: {*}.x = .... broken

# -----------------------------------------------------------------------------

#version=11.6.RC10

# bug fix -- set picking spin, also compatibility of set picking spin and doing measurements
# bug fix -- draw pointgroup, write pointgroup draw

# -----------------------------------------------------------------------------

#version=11.6.RC9

# code: more efficient return of point group information and calculation
# new feature: getProperty PointGroupInfo
# bug fix: show pointgroup draw null pointer exception
# bug fix: print $planeA - capital letters in a draw name disallow finding it.

# -----------------------------------------------------------------------------

#version=11.6.RC8

# bug fix: ramachandran / ramachandran r navigation problem
# code: Minor refactoring and pruning.
# --- Core applet now 715K (JmolApplet0.jar + _Core, _Jars, _Main, _Popup, and _Viewer)
# code: Pre-Jmol.js button controls removed, saving about 10K
# new feature: script APPLET appletName "some script"
# --allows direct inter-applet communication independent of set SYNC
# --appletName can be * (all applets), > (other applets), . (this applet),
# or an applet name such as "jmolApplet0" or just the extension "0"
# or a quoted set of applet names separated by commas.
# --for *, the current applet always reports LAST
# new feature: x = script("some script", "appletName")
# --same as above
# --in addition, allows retrieval of information from another applet
# for example:
#
# x = script("print getProperty(\"modelInfo.modelCount\")","B")
#
# gets the number of models loaded in applet jmolAppletB.
#
# x = script("show orientation moveto","jmolApplet2")
#
# gets the current orientation of applet jmolApplet2.
#
# xList = script("print getProperty(\"appletInfo.fullName\").split(\"__\")[1] + \":\" + script(\"show rotation\").trim()","*")
#
# gets a new-line-separated list of rotational quaternions for all applets with applet names.
#
#
# new feature: print getProperty("modelInfo.models[3].file") syntax

# -----------------------------------------------------------------------------

#version=11.6.RC7

# new feature: draw ramachandran includes planes connecting atoms.
# bug fix: refresh for hover
# bug fix: state definition for lcaoCartoons, isosurface with IDs containing spaces
# new feature: $*xx* double wild cards
# new feature: generally for objects (draw,pmesh,isosurface,etc.) use DISPLAY/HIDE rather than ON/OFF
# so as to be consistent with other objects. (OFF was not deleting these)
# new feature: support for application transparent background -- "-b" command switch (testing only)
# and setAppletContext "-b" switch as well.
# bug fix: structure helix|sheet|turn|none {atomExpression} was undocumented and had state issues
# new feature: HIDE $xxx
# new feature: DISPLAY $xxx
# new feature: DELETE $xxx
# bug fix: adaptation for malformed PDB files (HEADER with nothing following it)
# bug fix: more language localization in webexport
# new feature: applet message regarding help and command entry

# -----------------------------------------------------------------------------

#version=11.6.RC6

# code: better navigation refreshing
# bug fix: oops, 11.6.RC5 is totally broken due to missing refreshes
# bug fix: language localization in webexport

# -----------------------------------------------------------------------------

#version=11.6.RC5

# bug fix: set fontscaling with multiple echo texts/images at the same xyz location only scaling the first item
# bug fix: set echo xxxx 30 40
# bug fix: WAY more streamlined refreshing
# bug fix: createImage(), not getImage() in order to allow dynamic file change
# bug fix: halo size for antialiased display
# Addition of translation tags to webexport
# bug fix: write IMAGE broken for 11.6.RC2+
# bug fix: unnecessary refreshes removed from moveto/zoom with time 0
# new feature: background IMAGE "filename"
# code: viewer refactoring to simplify/remove private methods and synchronization

# -----------------------------------------------------------------------------

#version=11.6.RC4

# bug fix: select @m throws an error
# code: refactoring shapespecial into shapespecial and shapesurface
# code: refactoring modelset.CellInfo into symmetry.SymmetryInfo
# code: realignment of applet JAR files
# -- new _ShapeSurface.jar, which now includes org.jmol.jvxl/**
# -- removal of _Jvxl.jar
# -- refactoring reduces preliminary applet Jar file loading to 720K (if English)
# -- should provide faster loading of simple models and more efficient loading of more complex ones
# -- basic minimum load involves just JmolApplet0.jar + _Core, _Jars, _Main, _Popup, and _Viewer

# -----------------------------------------------------------------------------

#version=11.6.RC3

# bug fix: minor error in pointgroup; dimension tied to radius
# new feature: set dotDensity [-3 to 3]
# new feature: draw pointGroup [type] [index] SCALE [x]
# where [type] is one of Cs, Ci, Cn, or Sn, where n is an integer or the character "n"

# -----------------------------------------------------------------------------

#version=11.6.RC2

# bug fix: image background transparency

# new feature: set pointGroupDistanceTolerance (default 0.2 angstroms)
# new feature: set pointGroupLinearTolerance (default 8 degrees)

# bug fix: Cs pointgroup not found
# bug fix: set echo DEPTH/IMAGE
# bug fix: workaround for Java 1.6.0_10 diallowing popup menu
# new feature: in Java 1.6.0_10, right-click activates the console, and the
# console has a menubar menu item "Jmol" that is the pop-up menu.
# new feature: applet console has "help" menu item, which includes several hundred items.

# -----------------------------------------------------------------------------

#version=11.6.RC1

# bug fix: D3h point group
# bug fix: LOAD "..." nn loading of model numbers for PDB files should read real model number, not sequentially.

# new feature: write/show pointgroup gives counts and tab-separated listing;
# new feature: write pointgroup draw delivers draw commands
# new feature: better draw pointgroup
# new feature: no saving of point group -- just recalculated each time
# bug fix: measures were messed up
# new feature: echo myecho IMAGE "filename"
# -- reads a JPG, GIF, or PNG image and displays it the
# same as text is displayed.
# new feature: echo myecho DEPTH xx
# -- sets the depth in percent (0% far back, 100% front) for the placement of the image
# -- note that images can be placed in 3D, just as for text.
# -- setting "background echo xxx" then specifies the color
# that is to be designated as the background color (the color that should be omitted).
# -- using "background echo none" specifies that the first pixel
# of the image specifies the color that should be omitted.

# bug fix: 11.5.52 may have lost "true" as a keyword
# new feature: pointgroups with vibration vectors
# bug fix: more testing with pointgroups
# new feature: spacefill/dots/geosurface/cartoon/trace/etc. ONLY
# -- show only this rendering type
# -- same as restrict not selected; spacefill ON
# bug fix: application rubberband selecting inappropriately selects atoms not visible
# new feature: wildcard at beginning for draw/pmesh/isosurface/etc. *xxx on/off/delete allowed
# bug fix: in draw pointGroup -- height of cylinder was too small
# bug fix: longstanding exception: isosurface fullylit --> isosurface backlit --> isosurface frontlit

# -----------------------------------------------------------------------------

#version=11.5.52

# new feature: calculate pointGroup
# new feature: draw pointGroup
# new feature: write pointGroup
# including x = script("write pointGroup")
# new feature: webexport now compresses data files over 512 MB
# new feature: calculate pointGroup -- preliminary only -- untested

# -----------------------------------------------------------------------------

#version=11.5.51

# bug fix: 11.5.49 and 11.5.50 broken for ".max"

# new feature: PRELIMINARY aniso_beta for cif files -- has not been checked for correct Ortep type -- set to 0 for now
# new feature: application select button reinstated
# new feature: application pick button reinstated
# new feature: application measure button tied to picking style
# new feature: application [>|] button
# bug fix: ramachandran/quaternion "reset" not decoupled from model decouple
# code: model orientation saved with model.
# bug fix: set axesOrientationRasmol finally correctly implemented
# new feature: axes labels change subtly for set axesMolecular and setAxesOrientationRasmol
# bug fix: JmolViewer interface deprecated "rotateTo..." methods changed to "rotate..."
# because that's what they really do.
# bug fix: set defaults jmol/rasmol must do reset().

# new feature: webexport now cleans up scratch files on deletion of instances and program exit.

# -----------------------------------------------------------------------------

#version=11.5.50

# bug fix: vibration thread not closing down for applet destroy when applet is off-screen
# bug fix: was reading server path for local path from history in Webexport
# bug fix: $ptx[2] notation broken in 11.5.49
# code: various cleaning/simplifying
# code: way cleaner quaternion derivative calculation code

# -----------------------------------------------------------------------------

#version=11.5.49

# bug fix: strange "scripted: ?" message with measurements removed
# bug fix: extra values in measure reporting, and wrong format
# bug fix: 11.5.48 is broken for scripts with array definitions such as
# p = array(); p[pt] = ....
# code: simplification/unification of statement length checking AFTER allowing for variable substitution
# code: removal of unnecessary/inflexible compilation step involving color parameters
# code: major refactoring/simplification of Token
# code: refactoring/simplification of Compiler
# code: compiler flags for allowed number of parameters removed (not consistent with Jmol math)
# (defaultON and noArgs remain)
# new feature: dipole/draw/ellipsoid/isosurface/pmesh/mo/lcaocartoon ID keyword optional
# but without ID, one is restricted to words that are simple text and not Jmol entities.
# with ID, the next quantity can be anything.
# new feature: $"xxx" quotations or $@{...} allows variable definition of object id reference
# new feature: draw {point} PLANE [plane def, including xy, yz, x, etc.]

# -----------------------------------------------------------------------------

#version=11.5.48

# new feature: mol file bond type 8 as partial
# code: compiler error reporting improved
# bug fix: PDB site definition does not ignore empty site definitions
# bug fix: DEFINE can cause compiling error, e.g. "[2MO]" in 1tmo
# bug fix: quaternion derivative DRAW arrows placed on residue i+1 instead of residue i
# bug fix: connect aromatic auto; select connected([bond type],...)
# bug fix: queue thread termination when applets are off screen
# bug fix : sheetsmoothing not consistent among structures in multi-chain systems
# bug fix: messages not sent to messageCallback
# code: simpler matrix-->quaternion code
# bug fix: 11.5.47 shows oddly sized arrow for very first rendering
# bug fix: quaternion frame "n" after rotationSelected does not reset NH hydrogen positions
# new feature: // at beginning of a line marks comments

# -----------------------------------------------------------------------------

#version=11.5.47

# bug fix: Removed stray semicolons from header script comments in webexport templates. They
# were causing WYSIWG web editors to corrupt the code scripts.
# bug fix: 11.5.46 broke standard "spin x 30" (b)
# new feature: draw ARC {pt1} {pt2} {ptref} {theta0, nDegrees, fractionalOffset}
# new feature: draw ARROW ARC {pt1} {pt2} {ptref} {theta0, nDegrees, fractionalOffset}
#
# draws a circular arc or arrow around an axis defined by {pt1} and {pt2}
# using {ptref} as a starting point (looking down the axis, angles
# are measured in a clockwise manner, starting with the projected position
# of {ptref} in a plane perpendicular to the axis. This is similar (but opposite)
# to the way dihedral angles are indicated.
# theta0 is the the offset angle from 0
# nDegrees is the number of degrees of arc to draw
# fractionalOffset is the fraction of the distance from {pt1} to {pt2} for the
# plane containing the arc.
#
# new feature: draw RAMACHANDRAN
# draws phi and psi angles in the form of draw ARROW ARC
# new feature: write RAMACHANDRAN draw

# -----------------------------------------------------------------------------

#version=11.5.46

# bug fix: remove the skipping of semicolons if parentheses or braces have been closed. (11.5.43 bug)
# bug fix: set picking on broken in 11.5.39
#
# new feature: measure {atomExpression or point} {atomExpression or point} ...
# measurements to POINTS, including using the mouse (set drawPicking on)
# will persist and can be saved in the state (11.5.38 did not allow this)
# for example:
# measure {0 0 0} {atomno=3} {atomno=5}
# measure $point2 {atomno=3} $line[1]
#
# new feature: rotate branch {atom1} {atom2} ...
# new feature: select within(branch, {atom1}, {atom2})
# new feature: Jmol math within("branch", {atom1}, {atom2})
# code: refactoring of getAtomsWithin() and getAtomBits()
#
# bug fix: array size limited
# new feature: quaternion({atom expression}) -- returns calculated
# frame based on quaternionFrame setting.
# bug fix: drawhover not in state
# bug fix: ramachandran for systems including nucleic acids when quaternionFrame = 'n'
# new feature: isosurface functionXY can be used for mapping.
# new feature: spacegroup/symmetry for CML files with tags
#
# bug fix: 11.5.39 could break isosurface/pmesh save/write state in certain cases.
# bug fix: Popin.png in WebExport replaced, was too large, causing dialog box to default to too big on small screens.
# bug fix: zap 2.1 for quaternion frame causes exception
# bug fix: quaternion r derivative2 nonfunctional in 11.5.45
# bug fix: isosurface functionXY not working
# bug fix for 11.5.45: application not returning echos and status messages to console

# -----------------------------------------------------------------------------

#version=11.5.45

# new feature: show rotation aka show orientation rotation
# new feature: show translation aka show orientation translation

# code: mouse manager refactoring

# bug fix: picking off structure did not clear picking for set picking spin
# bug fix: jmolScriptWait() improperly reporting to applet console
# bug fix: too many messages to applet console
#
# Note: planes, axisAngles, and quaternions are all saved as Token.point4f
# axisAngle() and quaternion() are both processed to quaternion format
# {x y z w} where w = cos(theta/2) and {x y z} = sin(theta/2)*unitNormal
# quaternions are always fixed so that cos(theta/2) > 0 -- that is, so that
# the reported theta (q %-2) is in the range [0, 180]
# This is important. One can also get a directed theta based on a
# specified axis using q % {x y z w}. w is ignored; x y z is the
# axis to dot with the quaternion normal in order to switch the
# sign of theta if that value is negative.
#
# new feature: show atom(s)
# new feature: show group(s)
# new feature: show selected
# new feature: draw {point} {plane}
# new feature: draw vector {point} {plane}
# new feature: draw arrow {point} {plane}
# new feature: q = axisAngle({x y z}, theta)
# new feature: q = axisAngle(x, y, z, theta)
# new feature: q = axisAngle("{x y x theta}")
# new feature: q = quaternion("{x y z w}")
# new feature: rotate @{quaternion(....)}
# new feature: rotate @{axisAngle(....)}
# new feature: rotate quaternion {x y z w}
# new feature: rotate axisAngle {x y z theta}

# new feature: {point1} == {point2} if distance < 0.000001
# new feature: {quaternion} == {quaternion2} if distance < 0.000001
# new feature: float1 == float2 if |float1 - float2| < 0.000001

# code: refactoring and simplification of rotate/spin
# code: threads named

# bug fix: hover will find atom in hidden frame.
# bug fix: ellipsoid translucency not saved in state.
# bug fix: local assignment var x = array() followed by x[n] = ... does not work
# bug fix: f(x[i],x[j]) selects only x[j], not both x[i] and x[j]
# bug fix: quaternion frame "n" recognizes file-based H atoms on N for frame definition

# -----------------------------------------------------------------------------

#version=11.5.44

# bug fix: Java exception with write(quaternion) instead of write("quaternion")
# bug fix: set picking spin did not enable draw spin/picking
# bug fix: _applet variable not initializing properly
# bug fix: math calculation .xyz, .color averages broken in 11.5.42
# bug fix: select @x broken in 11.5.43
# bug fix: integer addition not remaining integer

# -----------------------------------------------------------------------------

#version=11.5.43

# bug fix -- if last helix is last atom, SHOW STRUCTURE fails to identify it.
#
# new feature/feature change:
#
# selectX is no longer necessary. Simply use
#
# select {atomExpression} (property expression)
#
# with no "x." An implied variable "_x" can be used explicitly:
#
# select {*} (straightness < 0.995) # does not round
# select {*.ca} (atomY < atomX)
# select {*.ca} (phi < select(y; {*.ca}; y.resno = _x.resno + 1).phi))
#
# new feature: quaterion % point4f --- "thetaDirected" --
# point4f is {x, y, z, w} (w ignored), where {x y z} is a
# preferred direction.
# Returns a point4f angle-Axis equivalent with x, y, z the normal for the quaternion
# rotation and w = theta for the rotation, where the normal and theta are chosen
# to be directed with a positive dot product between the input {x y z}
# vector and the output {x y z}.
#
# thus, because the negative angle switches the normal:
#
# print quaternion({1 0 0}, -20) % 1 ==> {-1 0 0}; %1 ==> 20
#
# but % {1 0 0 0} forces the angle associated with {1 0 0} to be reported
#
# print quaternion({1 0 0}, -20) % {1 0 0 0} ==> {1 0 0 20}
#
# bug fix: POV-RAY output of quadrilaterals.

# new feature: Ramachandran "r" --- includes third (Z) axis quaternion r difference2 X component equivalent

# bug fix: quaternion definition with dot-product check not effective -- removed
# bug fix: quaternion construction from matrix error
#
# new feature: _applet boolean
#
# new feature: extended quaternion math
#
# q = quaternion({x y z}, angleDegrees)
# q = quaternion(q0, q1, q2,q3)
# q = {qx, qy, qz, qw}
#
# returning component values:
#
# q.x, q.y, q.z, q.w
#
# note that the Point4f equivalent stores w LAST, even though it is "q0"
# because the Java Quat4f() and Point4f() both do that as well. We're just
# being consistent with other Java use.
#
# Modulus operator for extended information retrieval:
#
# (q%0) -- q0 (w)
# (q%1) -- q1 (x)
# (q%2) -- q2 (y)
# (q%3) -- q3 (z)
# (q%-1) -- the vector {q1, q2, q3}
# (q%-2) -- theta
# (q%-3) -- equivalent rotational frame X-axis
# (q%-4) -- equivalent rotational frame Y-axis
# (q%-5) -- equivalent rotational frame Z-axis
# (q%{x y z}) -- rotational transform of a point or vector based on a quaternion
#
# thus, for example, (q%{1 0 0}) is the same as (q%-3)
#
# (!q) -- quaternion inverse
#
#
# Quaternion right division (difference "dq"):
#
# q2 / q1 = q2 * (!q1)
#
# Quaternion left division (relative difference n):
#
# q2 \ q1 = (!q1) * q2
#
# Examples:
#
# q = quaternion({1 1 1},120)
# print "" + (q%{1 0 0}) + " " + (q%{0 1 0}) + " " + (q%{0 0 1})
#
# {0 1.0 0} {0 0 1.0} {1.0 0 0}
#
# new feature: Numerical left division (integer divide)
#
# 3.6 \ 2 = 1
# 3.6 \ 1.3 = 2
#
# new feature: sqrt(x)
#
# bug fix: load trajectory for cases with different atom counts.
#
# experimental: "straightness" defined as 1 - 2 * acos(normal(dq[i]%-1) dot normal(dq[i+1])) / PI
# giving a measure proportional to the difference in local helical axis angle
# and ranging from -1 (opposite direction) to 1 (same direction) for proteins
# -- a work in progress. See
#
# load =1d66
# calculate straightness;color straightness

# -----------------------------------------------------------------------------

#version=11.5.42

# code: modified Jmol encoded PDB data output

# bug fix: color of NaN float values changed from "center of color scheme" to GRAY
# bug fix: connect "_1" was inadvertently dropped in 11.5.26.
# bug fix: state script fails to save data for atoms created using the quaternion command
# bug fix: axes/boundbox/unitcell dotted not working since 11.5.6
# bug fix: spin thread not stopped for applet destroy()
# bug fix: quaternion derivative for i/i+1 assigned to i+1 instead of i; now assigned to i
# bug fix: quaternion calculation using published algorithms was giving inverted quaternions
#
# new feature: set PICKLABEL "xxx" -- allows customized pick reports
#
# for example: set pickLabel "%n x = %x, y = %y, z = %z"
#
# new feature: "quaternion derivative" --> "quaternion difference", which is more
# appropriate, we think, with "absolute" and "relative" qualifiers:
#
# quaternion absolute difference # in the molecular frame
# quaternion relative difference # in the (local) frame of first quaternion:
#
# dq_absolute = q2 * q1_inverse
# dq_relative = q1_inverse * q2
#
# absolute involves un-doing q1's rotation (making it the reference frame), then applying q2.
# relative involves applying q2 (maintaining the original reference frame), then undoing q1.
#
# new feature: quaternion [w|x|y|z|a|r] [difference][2] [draw]
# new feature: draw quaternion [w|x|y|z|a|r] [difference][2]
# new feature: write quaternion [w|x|y|z|a|r] [difference][2] [draw]
# and with that: write("quaternion" [,"w"|"x"|"y"|"z"|"a"|"r"][,"difference"|"difference2"][,"draw"])
#
# new feature: set quaternionFrame "N" -- for solid state NMR PISEMA 15N chemical shift frame
# using alpha = 0 and beta = 17 degrees.
#
# new feature: select whatever; quaternion draw
# draws x,y,z and n vectors for a quaternion center
#
# new feature: straightness, defined as:
#
# straightness = 2*|n(dq1).dot(n(dq2))| - 1
#
# where q1 and q2 are quaternions defined generally as:
#
# q = frame{ vA, (vC x vA), vC }
#
# using quaternionFrame "p", which I define as
#
# protein:
#
# vA = C--CA
# vB = C--N[i+1]
#
# purine:
#
# vA = N9--C4
# vB = N9--C8
#
# pyrimidine:
#
# vA = N1--C2
# vB = N1--C6
#
# Differences dq1 and dq2 are absolute quaternion differences
# on the two sides of a residue:
#
# dq1 === q[i] * q[i-1]_inverse
# dq2 === q[i+1] * q[i]_inverse
#
# and n(dq) = the normal vector associated with this quaternion.
# Range is from -1 to 1
#
# applications (note that CALCULATE must be invoked first):
#
# calculate straightness # must be invoked first;
# color straightness;
# select straightness < 0.70; # rounds to nearest hundredth
# selectX {*} x.straightness < 0.995 # does not round
#
# new feature: "%T" label format for straightness

# -----------------------------------------------------------------------------

#version=11.5.41

# new feature: xyz reader reads partial charge in 5th field
# bug fix: carbohydrate popup menu script incorrect
# new feature: "load" of Jmol state scripts works same as "script" command
# (file recognized as SPT type and read as a script instead)
# bug fix: Jmol Embedded scripts containing script comments /* */
# new feature: getproperty menu current
# bug fix: 11.5.40 cannot read most state scripts.

# -----------------------------------------------------------------------------

#version=11.5.40

# (with corrected 40_dev draw scale)
# new feature: new command:
#
# selectX {atomExpression} booleanEvaluation
#
# same as select() function, but simpler to implement
#
# new feature: full math on individual atom properties using
# a new function:
#
# select(x;{atomexpression};booleanEvaluation)
#
# for example:
#
# x = select(x;{*};x.distance({atomno=3}) / 3 > x.distance({atomno=2}))
# x = select(x;{*.ca};x.phi < select(y; {*.ca}; y.resno = x.resno + 1).phi)
#
# bug fix: H1 and H3 in DNA are NOT backbone
# new feature: quaternion derivative2 (2nd derivative) and quaternion e derivative [experimental]
# new feature: draw Vector [x y] or [x y %] {x' y' z'}
# new feature: draw [x y] or [x y %] can be incorporated into lines, curves, arrows
# bug fix: set picking center should not zoom -- just too annoying
# new feature: set echo myecho [x y] and set echo myecho [x y %]
# new feature: axes position [x y] and axes position [x y %]
# sets the axes to the x y screen position or percent indicated.
# bug fix: echos with active script and a model designation
# and multiple models select even if not displayed because it is not their model
# that is displayed.
# bug fix: missing echocallback, scriptcallback, measurecallback "set"able variables
# bug fix: "set picking identify" should be equivalent to "set picking ident"
# bug fix: popup menu had stereo reversed
#
# new feature: signed applet shows frank "Jmol-S" which is NOT removable.
# possibly to come: signed applet will send confirmation first time it reads a local file?
# bug fix: reading .mmol (biological unit) files such as
# http://pqs.ebi.ac.uk/pqs-doc/macmol/1j7n_1.mmol
# new feature: frank appears RED in signed applet, and popup about menu identifies the applet as signed.
# code: better handling of twin script manager threads
# new feature: /*SPLIT*/ in a command string allows it to be processed by
# the two independent processors. (just to isolate javascript from load commands
# for the signed applet

# -----------------------------------------------------------------------------

#version=11.5.39

# new feature: --threaded option for command processor uses
# a watcher thread to monitor a Vector, allowing the signed applet to open any file
# the signed applet uses this automatically unless there is a
# jmolSetCallback("useCommandThread", "false")
# which overrides the default behavior and disallows reading of files from
# JavaScript.
#
# NOTE a limitation: scripts intended for the signed applet that
# contain both load/script commands or the load() function
# CANNOT be combined with the JAVASCRIPT command. This is because
# in that environment, the JAVASCRIPT command must run on the browser's
# JavaScript thread, and the load command -- if crossing server boundaries --
# must NOT run on that thread. I have configured the ScriptManager to
# detect the presence of the word "javascript" followed by a space (exactly that case)
# and if found, use the JavaScript thread instead of the applet thread.
#
# Because it might be useful to combine LOAD and JAVASCRIPT (for the equivalent of a
# "file loaded" callback (but see set LoadStructCallback), if a script contains
# the phrase /*SPLIT*/ in upper case, exactly like that, it will be split and then run
# correctly as two independent scripts.
#
# new feature: _signedApplet boolean is available:
#
# print _signedApplet
# if(_signedApplet);
# javascript alert("you are using the signed applet");
# end if;
#
# bug fix: JmolSimpleViewer caused null pointer exception -- needed setAppletContext()
# bug fix: model-based drawing in multiple-model mode using an
# array of points to load causes null pointer exception:
# load cyclohexane_movie.xyz;pts = {C5}.split();print pts;draw @{pts.xyz.sub({1 0 0})} "X"
# bug fix: quaternion derivative multiplication order
# bug fix: 3D echo text not centering properly with set ECHO myEcho CENTER
# bug fix: select _Xx; select unknown
# bug fix: better reporting of script commands and comments
# new feature: reading COMPND and HEADER records of PDB file
# new features for Protein Explorer:
# new feature: set messageStyleChime
# -- No atoms selected!
# -- atoms selected!
# -- atom picking:
# Atom: xxx Group: xxx Chain: xxx Model: xxx Coordinates: x y z
# -- script
# -- Chime script completed.
# new features:
# show info
# show residue(s)
# show chain(s)
# show sequence
# show orientation moveto # just the moveTo; no comments
# set pdbGetHeader TRUE # to get the header when loading (for Protein Explorer)
# new feature: jmolSetCallback("evalCallback", "someFunction")
# -- overrides _jmol.noEval
# -- canNOT be set using "set evalCallback"
# -- was necessary for Protein Explorer javascript callbacks

# -----------------------------------------------------------------------------

#version=11.5.38

# bug fix: lcaoCartoon naming for multiple centers
# bug fix: pm rounding to integer value
# bug fix: scaling of draw object for multimodel environment can cause null pointer exception
# bug fix: scaling of VECTOR was from center, not origin
# bug fix: select n-m:c chain selection inappropriately case sensitive
# bug fix: draw ARROW {atom center} {xyz} draws arrow the wrong way
# bug fix: draw CIRCLE for multiple models
# bug fix: application -- "make crystal..." menu item does nothing -- removed
# bug fix: zap of quaternion also zaps model inappropriately
# bug fix: zap to one model assigns -1 to currentModelIndex instead of 0
# new feature: draw CIRCLE [FILL | MESH NOFILL] more intuitive open/filling syntax
# new feature: draw VECTOR {atom center} {dx dy dz}
# new feature: draw with mixed types processes them in order
# (11.4 does {x,y,z}, then $xxx, then {atomExpression}, then @{{atoms}.split()})
# new feature: draw .... ">xxx" first character of title ">" forces title to
# last point, not first
# new feature: set quaternionFrame "c" "p" "q"
# - "c" -- CA-C and CA-N, as per Andy Hanson
# - "q" -- peptide plane CA-C and N'-CA' as per J.R.Quine
# - "p" -- peptide plane CA-C and C-N'
# new feature: random(a), random(a,b) where a is lower bound and b is upper bound
# new feature: cross(a,b)
# new feature: sin(x), cos(x)
# new feature: set pdbSequential (default FALSE) for custom PDB files
# -- bypasses inter-group bonding check when creating polymers
# new feature: set drawPicking now enables measuring among atoms and DRAW points
# -- not saved -- just transient measurements (see 11.5.46)
# new feature: CIF reading of B factors for thermal ellipsoids
# new feature: [draw|pmesh|isosurface] xxx* [on|off|delete]
# -- turns on, turns off, or deletes all objects of the type starting with "xxx"


# code: refactoring of biopolyer resolver

# -----------------------------------------------------------------------------

#version=11.5.37

# code: faster ellipsoid rendering with precalc radius factors
# bug fix: spacefill ADPMIN/ADPMAX using probability ellipsoids
# and ellipsoid size setting (Note -- ellipsoid command
# must be run once prior to setting spacefill
# bug fix: reading output from "set showscript 1"
# bug fix: ellipsoids for Uiso atoms uses simple r = sqrt(value)
# bug fix: ellipsoids for applied symmetry causes odd shapes (s8.cif)
# bug fix: security for no mayscript may cause problem with measure callback
# bug fix: rocket positions after translateselected

# -----------------------------------------------------------------------------

#version=11.5.36

# bug fix: frame titles not positioning correctly for antialiased display
# bug fix: quaternions created with extraneous atom lines
# bug fix: select symop not behaving intuitively
# code: meshrenderer debug line not removed

# new feature: (popup menu) Biomolecules submenu added within title menu

# -----------------------------------------------------------------------------

#version=11.5.35

# bug fix: proper thermal ellipsoid probability measures
# code: better garbage collection in relation to JmolAdapter class
# bug fix: load FILTER not saved in state
# bug fix: application -- undo/redo buttons not disabling
# new feature: ZAP clears undo stack

# -----------------------------------------------------------------------------

#version=11.5.34

# bug fix: biomolecule really works this time!

# -----------------------------------------------------------------------------

#version=11.5.33

# bug fix: modelLoader was assigning too much array space for chains

# new feature: more load FILTER options:
#
# #i a specific BIOMT transformation
# !#i not a specific BIOMT transformation
# [XXX] a specific group ID
# ![XXX] not a specific group ID (e.g. ![HOH])
# *.XX an atom name, such as .CA
# !.XX not a specific atom name
# *:X a chain ID
# !:X not a specific chain ID
#
# Between types, or involving NOT, options are AND'd together
# Within a type not involving NOT, options are OR'd together
# Within a type, a single ! implies all are NOT
# Within a type, a single * implies all are ANY

# new feature: load [file info] FILTER "BIOMOLECULE n;NOSYMMETRY"
# FILTER "BIOMOLECULE 1" by default now reads the symmetry;
# use load FILTER "BIOMOLECULE 1;NOSYMMETRY" to not read symmetry
#
# bug fix: ellipsoids for navigation mode and perspective depth
# bug fix: PDB biomolecule for many-BIOMT system

# -----------------------------------------------------------------------------

#version=11.5.32

# bug fix: load FILTER "BIOMOLECULE 1;APPLY SYMMETRY" does not read second line of chain list
# bug fix: added connections do not save properly in state
#
# application only: command undo disabled automatically if saving takes more than one second
# flag is "set undo TRUE/FALSE"
#
# new feature: load [file info] FILTER "[filter string]"
# new feature: load [file info] FILTER "BIOMOLECULE n"
# new feature: load [file info] FILTER "[filter string];BIOMOLECULE n"
#
# The first format loads only those atoms matching a specific filter or set of
# filter terms -- only a crude filter here, only for PDB and mmCIF files:
#
# *.XX an atom name, such as .CA
# *:X a chain ID
#
# multiple matches are allowed -- implied AND:
#
# load "1sva.pdb" FILTER "*.CA"
#
# the match IS CASE SENSITIVE; * IS required
#
# also, "BIOMOLECULE 1" automatically selects for the chains listed for biomolecule 1
# in REMARK 350, and APPLY SYMMETRY applies the symmetry as described in those REMARKS
#
# new feature: isosurface ELLIPSOID id
# AXES {ix iy iz} {jx jy jz} {kx ky kz}
# CENTER {x y z}
# SCALE n.m
# COLOR [translucent [x.y] |opaque] [color]
# ON|OFF
#
# id is a REQUIRED field. AXES is required if a new ellipsoid is being defined
# these axes must be perpendicular
# all other parameters are optional
#
# bug fix: isosurface ELLIPSOID was disabled
# bug fix: Vector4f in Sphere3D causes applet failure, as it includes
# an implicit Vector4d call
# bug fix: stronger wireframe for antialiased display and generator (POV-ray)
# default change: ellipsoids ball only, no axes
# code: better ellipsoid fill method
# default change: ellipsoids ball only, no axes

# Hungarian translation

# -----------------------------------------------------------------------------

#version=11.5.31

# bug fix: set picking measure distance not doing callback (from 11.5.23)
# bug fix: picking echos not working with set antialiasdisplay
# default change: ellipsoids are so fast now, can use default "set ellipsoidBall true"
# bug fix: set ellipsoidAxisDiameter [int] sets the diameter in milliAngstroms
# bug fix: sequence range for missing sequence numbers returns 0
#
# code: fast ellipsoid ball+fill - axis idea; no luck with POV-ray fill
# code: ellipsoid equation/axes conversion in Sphere3D;
# code: POV-Ray ellipsoid generation
# code: better ellipsoid ball rendering using Shade3D.calcIntensity()
# code: 2-fold improvement in rendering ellipsoids by not using getNormix()
# code: 4-fold improvement in rendering ellipsoids by using Miguel's no-mesh idea
# code: 2-fold improvement in rendering ellipsoids by using 40x40x40 shade cache
# code: overall 20-fold improvement in rendering over mesh/normix;
# code: full POV-ray support for ellipsoids
# code: proper partial derivative normalization of ellipsoid shading
# code: refactoring of static quadric surface methods into their own class

# -----------------------------------------------------------------------------

#version=11.5.30

# bug fix: measurement labels for angles do not appear in slab mode (goes WAY back before 10.0)
# bug fix: U_iso_or_equiv fields not read in CIF
# bug fix: (application) writeTip GT string not defined.
# bug fix: (forwared compatibility) invalid state setting (due to later version) now ignored.
# bug fix: state for draw arrow in multimodel context delivers wrong coordinates
#
# new feature: ellipsoid ball rendering tied to "set wireframerotation" option
# new feature: set ellipsoidAxisDiameter x.y
#
# code: better ellipsoid arc rendering using Hermite fill
# code: CifReader cleanup

# -----------------------------------------------------------------------------

#version=11.5.29

# new features for ellipsoid rendering:
#
# set ellipsoidAxes [true]
# set ellipsoidArcs [true]
# set ellipsoidFill [false]
# set ellipsoidDots [false]
# set ellipsoidBall [false]
# set ellipsoidDotCount [200]
#
# [dots|stars|spacefill] ADPMIN [percent]
# [dots|stars|spacefill] ADPMAX [percent]
#
# /* general logic:
# *
# *
# * 1) octant and DOTS are incompatible; octant preferred over dots
# * 2) If not BALL, ARCS, or DOTS, the rendering defaults to AXES
# * 3) If DOTS, then turn off ARCS and FILL
# *
# * note that FILL serves to provide a cut-out for BALL and a
# * filling for ARCS
# */

# -----------------------------------------------------------------------------

#version=11.5.28

# bug fix: state "set measures angstroms" does not include "select *"
# bug fix: labels can change size in returning from antialiasdisplay=true to antialiasdisplay=false
# ELLIPSOID command -- with symmetry and crude footballs, including PDB files
# note that for now PDB file reading of ANISOU requires using {x y z} in load
# command, but you can use {1 1 0} to load ANISOU without applying symmetry
#
# Italian translation

# -----------------------------------------------------------------------------

#version=11.5.27

# bug fix: data CLEAR command nonfunctional
# bug fix: "....".trim("xyz") function not properly trimming ANY x,y,z
# bug fix: draw OFFSET not working properly
# bug fix: PovRAY output of draw objects -- cylinder end caps not considered
# bug fix: draw width 0.05 {...} {...} -- line does not properly render
# bug fix: data "model"...end "model" saves state without first line if first line is empty
# bug fix: "show data types" putting comma in wrong location
# new feature: DATA "data2d_xxxxx"..... end "data2d_xxxxx"
# new feature: isosurface FunctionXY "data2d_xxxxx" {origin} {ni x 0 0} {nj 0 y 0} {nk 0 0 z}
# allows setting isosurface Z values using a block of data (ni rows by nj columns)
# new feature: isosurface FunctionXY "data2d_xyz_xxxx" {origin} {ni x 0 0} {nj 0 y 0} {nk 0 0 z}
# allows setting isosurface values using a block of x y z data, all points for which should be
# on the surface.
# new feature: GamessUK reader
# new feature: reset VARIABLES (replaces "reset ALL")

# -----------------------------------------------------------------------------

#version=11.5.26

# bug fix: draw adds extra circle in 11.5.25
# bug fix: minimization out-of-plane energy calculation error
# bug fix: better initial minimization parameters
# bug fix: (applet) script termination callback should not be sent to message queue
# bug fix: hover appears when a load script leaves an atom very close to (0,0) in the window
# bug fix: draw width -1 or draw mesh nofill with very short cylinders creates odd jumpy effect
# bug fix: draw CIRCLE for multiple model sets
#
#
# new feature: draw CYLINDER
#
# Korean translation

# -----------------------------------------------------------------------------

#version=11.5.25

# new feature: draw CIRCLE
#
# A circle is a 2D object that behaves like a halo, always appearing circular
#
# draw circle {molecule=1} mesh nofill # around specified atoms
# draw diameter 2.0 circle {atomno=3} mesh nofill # 2.0 angstroms; scales
# draw diameter 100 circle {_O}[1] mesh nofill # 100 pixels (doesn't scale)
# draw circle {*} fill # a solid plane in the shape of a circle

# -----------------------------------------------------------------------------

#version=11.5.24

# new feature: minimization CONSTRAINTS {xx} {xx} [{xx} [{xx}]] x.y
# new feature: minimization FIX {atom expression}
#
# multiple constraints can be present; one per line input
# minimization CLEAR releases constraints and fixed atoms
# also, minimize ENERGY saves a detailed listing, which can be
# displayed using one of the two following commands:
#
# new feature: show minimization
# new feature: x = getProperty("minimizationInfo")
#
# to dump the info to a file:
# minimize
# var x = getProperty("minimizationInfo")
# write VAR x "myfile.out"
#
# new feature: isosurface MAXSET n # removes larger fragment sets
# new feature: isosurface DOWNSAMPLE n # down-factors the number of points in a CUBE file by a factor of n

# -----------------------------------------------------------------------------

#version=11.5.23

# new feature: minimize ENERGY # no stepping
# new feature: minimize STEPS n
# new feature: minimize CRITERION x.y
# new feature: minimize CLEAR # flushes logged info and saved atom info
#
# new feature: echoCallback
# new feature: measureCallback
# new feature: minimizationCallback
# new feature: scriptCallback
# new feature: save/restore coordinates
# new feature: getProperty minimizationInfo
#
# code: more efficient minimize calculation setup; better logging
# code: "notify" methods in JmolStatusListener consolidated
# code: Tokens organized
#

# -----------------------------------------------------------------------------

#version=11.5.22

# bug fix: UFF torsion calculation incorrect
# bug fix: UFF.prm not properly recognizing sp2 N in N-oxides
# bug fix: minimizer for compounds containing isotopes D and T
#
# code: eval/compiler error processing update

# -----------------------------------------------------------------------------

#version=11.5.21

# new feature: minimize command -- mostly untested
#
# set minimizationSteps 100
# set minimizationRefresh true
# set minimizationCriterion 0.001
# set loglevel 4 # for a very minimal report
# set loglevel 5 # for a summary report
# set loglevel 6 # for a detailed report
# minimize
# minimize stop
# minimize cancel
#
#
# for example:
#
# load caffeine.xyz
# minimizationSteps = 80
# minimizationRefresh = true
# set loglevel 4
# select connected(2) or connected(3) or oxygen and connected(1)
# connect aromatic modify
# calculate aromatic
# set measurementunits pm
# measure {_O}[1] {_O}[2]
# color measure red
# minimize
#
# new feature: set loglevel 6 allows a "debugHigh" setting
#
# bug fix: load unitcell {a b c alpha beta gamma} not working (since 11.5.8)

# -----------------------------------------------------------------------------

#version=11.5.20

# bug fix: zap file > 2 multiple models do not properly delete

# -----------------------------------------------------------------------------

#version=11.5.19

# bug fix: null surfaceGenerator causes MO exception
# bug fix: isosurface reading/writing JVXL files having insideout keyword

# -----------------------------------------------------------------------------

#version=11.5.18

# bug fix: zap x.y additional work -- connections, isosurfaces
# bug fix: zap x.y not correcting Eval variables
# bug fix: isosurface user VolumeData not properly loading

# -----------------------------------------------------------------------------

#version=11.5.17

# new feature: delete {atom expression} NEEDS TESTING

# bug fix: zap x.y for dots
# bug fix: zap {atom expression} for not including all atoms in a model in the selection

# -----------------------------------------------------------------------------

#version=11.5.16

# new feature: zap {atom expression} # zaps models associated with given atoms.
# use "show models" to see what models are present, then zap them with their
# file.model number:
#
# zap 1.1,2.1 # these two models deleted
# zap atomIndex=0 # ALL ATOMS IN FIRST MODEL deleted
#
# Note that file.model numbers do not change after this.
# So if initially there were two files loaded
#
# zap 1.1
#
# removes the first model and leaves the second as "2.1"
#
# NEEDS THOROUGH TESTING, particularly in regard to saving/restoring the state

# bug fix: atomChooser not updated for zap
# bug fix: isosurface model keyword does not carry on to saved state
# bug fix: lcaocartoons do not color properly or get restored from state properly
# bug fix: popup menu selection of groups and symmetry operations does not work

# menu: internationalization of "Monomer" and "Shapely"
# bug fix: mol2 reader cannot read files with single-line comments

# -----------------------------------------------------------------------------

#version=11.5.15

# bug fix: CAChe CSF reader not reading partial charges
# bug fix: WebExport with http:// files fails to save file
# bug fix: WebExport with local . directory fails to save JmolApplet.jar and Jmol.js
# code: refactoring of jmol.app.webexport: adding html subdirectory

# bug fix: state saving with rotateSelected spinning spins entire model
# bug fix: getproperty("chaininfo") for non-biological model causes null pointer exception

# -----------------------------------------------------------------------------

#version=11.5.14

# bug fix: rotateSelected INTERNAL not adjusting for internal rotation center
# bug fix: .max/.min not allowed in context: "select resno=@{{visible}.resno.max}"
# bug fix: Parser: "3xxx" read as 3 instead of 0; "3.5xxx" read as 3.5 instead of NaN
# application menu: Write state moved to main export menu; Export PDF to image writing
# new feature: MODEL/ENDMDL records in write PDB (still no TER records)
# bug fix: write PDB format incorrectly writes atoms with 4-length names
# bug fix: Spartan SMOL directory reader doesn't assign bonds
# new feature: Spartan archive reader now reads aromatic bonding

# -----------------------------------------------------------------------------

#version=11.5.13 BROKEN FOR XYZ READER

# bug fix: Parser: "3xxx" read as 3 instead of 0; "3.5xxx" read as 3.5 instead of NaN
# application menu: Write state moved to main export menu; Export PDF to image writing
# new feature: MODEL/ENDMDL records in write PDB (still no TER records)
# bug fix: write PDB format incorrectly writes atoms with 4-length names
# bug fix: Spartan SMOL directory reader doesn't assign bonds
# new feature: Spartan archive reader now reads aromatic bonding

# -----------------------------------------------------------------------------

#version=11.5.12

# new feature: four optional defaults for Van der Waals radii:
#
# set defaultVDW jmol
# set defaultVDW rasmol
# set defaultVDW babel
# set defaultVDW user
#
# To set the user variety, first set one of the other sets as a basis
# Then add a DATA statement to include the specific elements you want to give
# new radii to:
#
# set defaultVDW babel;
# DATA "element_vdw" 6 1.7 END "element_vdw";
# DATA "element_vdw" 6 1.7; 7 1.8 END "element_vdw"; # separate using semicolons or new lines
#
# For full state compatibility, these commands should be given prior to
# model loading, as they affect all calculations involving Van der Waals
# radii -- except default zoom.
#
# Now select the user set:
#
# set defaultVDW user
# spacefill on
#
# To delete all user entries:
#
# reset VDW
#
# If user vdw radii are currently set, then this resets the defaults to Jmol.
#
# new feature: show vdw shows a listing of the currently set VDW radii
#
# new feature: integration of star, halo, and spacefill code so all behave the same.
#
# stars 1.0 # set to a specific angstrom radius
# spacefill 100% # percent of CURRENT vdw set
# stars 100%Jmol # percent of Jmol standard
# stars 50%Babel # percent of Babel standard
# spacefill 5%Rasmol # percent of Rasmol standard
# spacefill 30%User # percent of User-defined values (or CURRENT if not defined)
# spacefill +1.2 # angstroms added to current vdw scheme
# halos 50%Jmol # -- halos also have an added bit to make sure they are visible
# spacefill 250 # RasMol 250 units/Angstrom units still
# spacefill -20 # neg numbers same as percentages: 20% here, using current vdw set
# stars @{x+0.1} # math OK
# spacefill @x% # make sure x comes out integer, otherwise % is ignored
#
# note that dots do not have a %Jmol option:
#
# dots 30 # syntax already assumes percent for dots using an integer
#
#
#
# see src/org/jmol/_documents/vdw_comparison.xls

# -----------------------------------------------------------------------------

#version=11.5.11

# bug fix: save/restore of atom data incorrect when user has set propertyAtomNumberField or propertyDataField
# bug fix: functions, save/restore state were disabled by bug in 1.5.8
# bug fix: command "test()" where test() is a user-defined function causes array-out-of-bounds error
# bug fix: undocumented .vdw atom property was equivalent to .valence
# bug fix: GAMESS reading of F orbital order incorrect

# new feature: settable Van der Waals radius using {carbon}.vanderwaals = 1.7
# or using DATA "property_vanderwaals"
# new feature: DATA "property_x i j" .... END "property_x i j"
# overrides default propertyAtomNumberField (i) and propertyDataField (j)
# new feature: State save of property_xxx now in easily readable Jmol Data Format

# -----------------------------------------------------------------------------

#version=11.5.10

# NOTE: REMOVED FROM SERVICE -- see 11.5.11
# bug fix: ISOSURFACE LIST command requires current isosurface
# bug fix: JVXL writing does not properly save pocket cavities or minsets
# bug fix: DATA command assigning property to last atom in structure fails

# -----------------------------------------------------------------------------

#version=11.5.9

# NOTE: REMOVED FROM SERVICE -- see 11.5.11
# bug fix: Gaussian reader not considering possibility of cartesian D and spherical F
# bug fix: ADF reader not reading coordinates for newer ADF output

# -----------------------------------------------------------------------------

#version=11.5.8

# NOTE: REMOVED FROM SERVICE -- see 11.5.11
# bug fix: lines starting with @{ redefine "{"
# bug fix: echo offsets do not correct for window position
# bug fix: menu reports too many chains
# new feature: menu includes all standard color scheme options
# new feature: inline math @{x+3} extended to all commands
# new feature: .sub(), .add(), .mul(), .div() extended to all operand types

# -----------------------------------------------------------------------------

#version=11.5.7

# bug fix: explicit "SELECT NONE" must be given for label defaults to be set

# bug fix: menu select element missing SELECT command
# bug fix: for delayed font scaling animation using the font command and antialias display

# -----------------------------------------------------------------------------

#version=11.5.6

# bug fix: HETATM atoms not automatically bonded to nearby ATOM atoms
# bug fix: setParameterValue("perspectiveDepth",perspectiveDepth);

# bug fix: sets offset based on imageFontScaling, not overall font scaling
# bug fix: multiline labels not positioned properly with offset 0 0
# bug fix: labels not scaling properly
# new feature: label "scaleReference" if > 5.0 is taken to be a reference zoom setting
# saying "make the font size X at a zoom of Y"
# bug fix: labels not scaling properly when in script with file load
# bug fix: labels not appearing in contrast when given same color as background
# bug fix: fixes applet memory leak in relation to consoles

# -----------------------------------------------------------------------------

#version=11.5.5

# bug fix: fixes applet memory leak due to
# platform objects/delay threads not being destroyed

# new feature -- syncCallback -- intercepts messages that would otherwise go to applets for syncing
# when syncCallback is set to a JavaScript function name, that function
# intercepts the sync message and can pass it on (by returning it),
# consume it (by returning an empty string ""), or modify it as desired.
# this allows, for example, monitoring of orientation information so that
# zoom sliders and such can accurately portray their values

# -----------------------------------------------------------------------------

#version=11.5.4

# bug fixes -- font scaling

# new feature: Spartan input files read as Odyssey format
#
# new feature: set delayMaximumMs sets the maximum delay that scripts will use, primarily for testing scripts
# new feature: set fontScaling TRUE/FALSE
# new feature: font [type] [size] [face] [weight] [scaleReference (Angstroms per pixel)]
# atom labels and 3D echos then scale properly.
# note that the current zoom affects the label size.
# bug fix: image writing does not scale fonts properly.
# bug fix: antialias of images not functionally independent of antialias for display
# bug fix: label offset doubled for multiline labels with left/right/center alignment not specified
# bug fix: default label offsets mangled by default Front/Group

# new feature: getProperty("appletInfo") includes a key "registry" for which
# the value is the static Hashtable htRegistry
# //note that the following JavaScript retrieves the registry:
# var registry = jmolGetPropertyAsJavaObject("appletInfo").get("registry")
# // and the following code then retrieves an array of applets:
# var AppletNames = registry.keySet().toArray()
# // and the following sends commands to an applet in the registry:
# registry.get(AppletNames[0]).script("background white")

# new feature: reading of Spartan spinput files (uses Odyssey reader)

# bug fix: PDB files with missing amino acid carbonyl O cause exception

# -----------------------------------------------------------------------------

#version=11.5.3

# bug fix: check if the file is CIF before PDB
# bug fix: color hbonds translucent
# bug fix: state: calculate hbonds not saved
# bug fix: state: calculate surfaceDistance WITHIN (({....}))
# missing outermost parentheses
# bug fix: state: selection state "end function" missing semicolon
# bug fix: isosurface lcaoCartoon "pz" translucent not setting both lobes translucent
# bug fix: color isosurface when isosurface is an lcaoCartoon only colors one lobe
# bug fix: save state for "color SelectionHalos"

# -----------------------------------------------------------------------------

#version=11.5.2

# Translation update: Estonian

# new feature: "getProperty FILECONTENTS ." in the context of
# a zip directory defaultDirectory
# new feature: zip file reading extended to write FILE
#
# bug fix: unclosed InputStream readers in zip file accessing
#
# new feature: allows zip files to be designated as default directoriesusing
# set defaultDirectory "myfile.zip"
# and then using a filename
# bug fix: unclosed readers in Pmesh, FileManager, Jvxl
# new feature: pmesh BINARY "filename"
# BINARY keyword is optional, but recommended for efficiency
#
# * 4 bytes: P M \1 \0
# * 1 byte: \0 for bigEndian
# * 3 bytes: reserved
# * 4 bytes: (int) vertexCount
# * 4 bytes: (int) polygonCount
# * 64 bytes: reserved
# * ------------------------------
# * float[vertexCount*3]vertices {x,y,z}
# * [polygonCount] polygons
# * --each polygon--
# * 4 bytes: (int)nVertices (1,2,3, or 4)
# * [4 bytes * nVertices] int[nVertices]
# *
# * note that there is NO redundant extra vertex in this format
#
# see little-endian example at http://chemapps.stolaf.edu/jmol/docs/misc/pmesh.bin
# and http://chemapps.stolaf.edu/jmol/docs/misc/pmesh.bin.txt

# -----------------------------------------------------------------------------

#version=11.5.1

# bug fix: quaternion for nucleic acids
# code: inefficiencies in Quaternion code
# new feature: within(structure,atom_expression)
# for proteins, just the helix or turn or sheet containing those atoms;
# for nucleic acids, just the chain

# bug fix: wing vectors for biopolymers
# not containing O improperly drawn for sheets
# and, in the case of set traceAlpha TRUE (the default), helixes
# bug fix: translateSelected/rotateSelected does not move cartoons
# bug fix: tainted occupancy not saved in state
# bug fix: biopolymers have wrong wing vectors (from 11.3.62)
# bug fix: restore of state does not reset user-defined atom properties
# code: refactoring Atom and AtomCollection

# -----------------------------------------------------------------------------

#version=11.3.66

# bug fix: CIF reader not skipping loops with load of a specific model of a model set
# bug fix: explicit format LOAD "XXX::whatever" extended to XML variants
# code: adapter/readers/more/JmolDataReader.java removed.
# code: adapter/smarter/Resolver.java cleaned up in relation to XML and DOM options

# -----------------------------------------------------------------------------

#version=11.3.65

# full run of monster_script.spt

# bug fix: pmesh test1 "inline" "1 {2. 0. 0.} 0" disallowed, but that should be OK
# bug fix: isosurface gridpoints "ch3cl_map.jvxl" -- gridpoints for jvxl files that are already mapped
# bug fix: isosurface lcaoCartoon "type" {atomExpression}

# files: JUnitTest for scripts --
# monster script in run directory tests scripts now uses
# files at http://chemapps.stolaf.edu
# all monster scripts made the same
# tests/scripts/check_performance removed.
#
# bug fix: better checking of scripts involving full run of all scripts
# bug fix: defaultDirectory for Jmol application not usable for http:// protocols
# bug fix: load "files" not properly loading zip files or files involving default directory

# -----------------------------------------------------------------------------

#version=11.3.64

# bug fix: version integer missing sometimes
# bug fix: isosurface with trajectories
# interesting that if 1.1 and 1.2 are trajectories you can do
# frame 1.2; isosurface select(*/1.1) sasurface
# this creates an isosurface for model 1.2 that uses the atomic coordinates of model 1.1!
#
# bug fix: isosurface MEP mapped to plane not exactly reproduced in JVXL
# bug fix: isosurface COLOR RANGE by itself does nothing -- changed to use full range
# new feature: isosurface COLOR RANGE ALL added as an equivalent to COLOR RANGE with no numbers

# -----------------------------------------------------------------------------

#version=11.3.63

# -- all functionality in new.htm, new2.htm, and new0.htm tested --

# bug fix: draw/isosurface/etc. on/off/delete should operate on all objects
# bug fix: display within(plane...)
# bug fix: select site=n broken
# bug fix: quaternion/ramachandran/model can show up together if user issues FRAME ALL
# bug fix: frame 1.2 when file 1 only has one model displaying all files
# bug fix: quaternion x reports wrong frame number
# bug fix: selectionHalo status and color not in state
# bug fix: color selectionHalos none
# bug fix: polyhedra .... translucent 0.3 green
# bug fix: moveto alternative format missing necessary 0 rotationRadius requirement
# moveTo ...... {atomExpression} 0 [zoomOrZoomFactor]
# where [zoomOrZoomFactor] is n, +n, -n, *n, /n, or 0 (to indicate fill screen)
# bug fix: subsets not properly handling restrict
# bug fix: models with turns crash jmol if not first model loaded
# bug fix: quaternion command by itself not switching to most recent quaternion
# bug fix: background color off when not white and ends in "FF"
# bug fix: print {atomSet}.color -- .color returning bounding box!
# bug fix: multiframe draw with labels different for each frame not properly saved in state
# bug fix: within upgrade for boundbox: within(boundbox), within(boundbox,atomExpression)

# -----------------------------------------------------------------------------

#version=11.3.62

# bug fix: calculate hbonds for trajectories
# code: distinction between file-derived or connected hbonds and calculated hydrogen bonds
# bug fix: calculate hbonds broken in 11.3.58 (missing model field in BioPolymer)
# bug fix: Jmol not putting structures in for all models in a PDB file
# bug fix: calculate polymers (never documented) not necessary -- calculate structure suffices
# bug fix: calculate structure updated for ignoring jmolDataFrames and using currently selected atoms
# webexport help instructions fix to be consistent for local testing.

# -----------------------------------------------------------------------------

#version=11.3.61

# bug fix: multifile cartoons improperly rendering in all frames
# bug fix: dipoleScale not saved in state
# bug fix: quaternions broken in 11.3.58
# code: Closest class deleted
# code: Quaternion class moved to modelsetbio
# code: dipoles moved to shapespecial
# bug fix: select 1.5 in trajectory context should switch to that set of coordinates
# bug fix: draw not colored
# bug fix: mousewheel too low power
# bug fix: select */4 when "4" is inappropriate returns all instead of none
# bug fix: memory leak in applet due to mouse/hoverwatcher listeners
# bug fix: applets not self-destroying when window containing them close
# bug fix: rotate commands not sent to other applets when set syncScript if OFF

# -----------------------------------------------------------------------------

#version=11.3.60

# bug fix: more work on trajectories in a multimodel context

# bug fix: quick fix for disabling popup menu under Java 7 where permissions are not granted

# bug fix: load trajectory extended to multifile context
# in which case "select 1.3", if file 1 is a trajectory, not only
# selects that file, but also sets the trajectory to 1.3.
# So a "select" of a trajectory also affects the display.
# This makes "select" in a trajectory context similar to "display"
# but doesn't require listing of all the models.

# -----------------------------------------------------------------------------

#version=11.3.59

# bug fix: load append not saved in state properly
# code: trajectory command (never documented) removed
# bug fix: draw ... nofill mesh properties not processed
# bug fix: draw DIAMETER N not properly functioning for curves or arrows
# new feature: draw DIAMETER X.Y allows setting diameter of points, lines, curves, and arrows to Angstroms

# bug fix: 11.3.58 can't set bond diameters
# bug fix: with set syncMouse, target applet sets syncMouse off inappropriately

# -----------------------------------------------------------------------------

#version=11.3.58

# bug fix: set mouseSync with sync * ON disabling sync but not reenabling it
# bug fix: spin on missing in final state function.
# bug fix: select within (3.3, {-1 1 1}) does not work with negative integer coordinate
# bug fix: trajectories were not fully implemented
# code: refactoring of ModelSet and related classes for trajectories
# code: trajectories implemented as independent models
# code: debug comments in AppletRegistry

# new feature: trajectory command no longer necessary -- deprecated (was in 11.2)

# -----------------------------------------------------------------------------

#version=11.3.57

# bug fix: revised sync commands
# new feature: set syncScript; set syncMouse
# sync ON; set syncMouse false; set syncScript false Tracks orientation only
# sync ON; set syncMouse true; set syncScript false Sends mouse events only
# sync ON; set syncMouse false; set syncScript true Sends script commands only
# sync ON; set syncMouse true; set syncScript true Sends both mouse events and script commands
#
# bug fix: "load trajectory" broken

# -----------------------------------------------------------------------------

#version=11.3.56

# bug fix: isosurface map of properties lost in 11.3.54
# new feature: set c? -- displays all Jmol parameters starting with "c" or "_c"
# set _? -- displays all read-only variables (starting with "_")
# new feature: formatted gOpenMol formatted plt volume data reader.
# new Jmol.js for 11.4

# -----------------------------------------------------------------------------

#version=11.3.55

# bug fix: axes/unitcell improperly slabbing on internal slab
# bug fix: XOR returning OR when not a bitset
# bug fix: unary minus for planes and points
# FEATURE CHANGE: slab REFERENCE removed -- no longer necessary
# new feature: set wireframeRotation
# code: simplified Logger.debugging flag
# bug fix: slab/depth planes not properly constructed
# new feature: _slabPlane, _depthPlane variables
# code: MUCH simpler slab plane code

# bug fix: applet.loadInline(String[] models) messes up
# this involves the fact that Safari will deliver null pointer when it
# mistakenly matches a String[] signature to a String, or vice-versa.
# The solution is to use
#
# applet.loadInlineString(String model, String script, boolean isAppend)
#
# and
#
# applet.loadInlineArray(String[] model_or_models, String script, boolean isAppend)
#
# explicitly
# code: refactoring loadInline and interfaces WrappedApplet and JmolAppletInterface
# bug fix: scroll wheel with synchronization does not track properly

# -----------------------------------------------------------------------------

#version=11.3.54

# bug fix: JVXL writing/reading of simple plane writes precision color flag

# new feature: (isosurface) reading of XPLOR ascii electron density map data

# bug fix: reinstating "insideout" isosurface option
# bug fix: JVXL writing of lobe, sphere, ellipsoid, hydrogenOrbital
# bug fix: loadInline not properly autobonding -- causes null pointer error
# bug fix: data ... end model instead of end "model" causes null pointer exception

# -----------------------------------------------------------------------------

#version=11.3.53

# bug fix: symop=0NNN not returning all atoms with translation NNN
# code: optimization of algorithm used for load RANGE
# modification for load RANGE -x.x (within x.x Angstroms of symop=1555) to be within x.x of the
# box containing symop=1555, not the atoms themselves.
# code: cleanup of readers.

# bug fix: no special atom checks for PDB symmetry files

# bug fix: HallInfo --- Hall term miscalculation OUCH! -- mistken commenting out of code in 11.1.28 March, 29, 2007. revision 7243
# bug fix: set measures 0.1 --- solid line does not move.

# bug fix: completion of set parameter clean up

# -----------------------------------------------------------------------------

#version=11.3.52

# bug fix: set of many more (but not all) parameters can accept mathematical expressions
# bug fix; set strandCount not properly handled
# new feature: set strandCountForStrands
# new feature: set strandCountForMeshRibbon
# note --- set strandCount sets BOTH, but now each is independent

# bug fix: quaternion not including chain designation
# bug fix: default connections include proper PDB CONECT records

# new feature: connect PDB # just does PDB CONECT connections
# new feature: connect PDB AUTO # PDB CONECT and autobonding

# -----------------------------------------------------------------------------

#version=11.3.51

# bug fix: write FILE not handling binary file formats properly

# bug fix: PDB CONECT records not creating bonds for ALL models
# bug fix: load =xxxx broken in 11.3.50
# bug fix: amino not a subset of protein
# bug fix: proteins with just C CA N not recognized as such

# code: minor refactoring in org/jmol/util
# code: minor refactoring in org/jmol/jvxl
# code: minor refactoring in org/jmol/adapter

# -----------------------------------------------------------------------------

#version=11.3.50

# new feature: MOL isotope column read; interpreted for D, T, 11C, 13C, 15N (for now)
# bug fix: WebExport not properly accessing files in more complicated situations (pmesh, isosurface, multiple files, etc.)
# bug fix: WebExport not allowing variety of local location options

# bug fix: return command not allowed in simple context
# bug fix: setting perspective model resets unit cell on
# bug fix: debug comment in TransformManager
# bug fix: hideNotSelected not in state.

# -----------------------------------------------------------------------------

#version=11.3.49

# bug fix: set perspectiveDepth off broken in 11.3.48
# bug fix: set scaleAngstromsPerInch not turning off perspectiveDepth
# bug fix: scaleAngstromsPerInch not in state
# bug fix: _firstFrame/_lastFrame variables mess up state
# bug fix: calculate surfaceDistance broken for 11.3.48

# new feature: direct reading of MAC Spartan06 directories.

# -----------------------------------------------------------------------------

#version=11.3.48

#
# new feature: script "myfile.zip|xxx.spt"
#
# bug fix: scale3D not working
#
# new feature: load "myfile.zip|CH3CL.MOL"
# loads a given named model from within a zip file.
#
# new feature: load "myfile.zip|myfile2.zip|CH3CL.MOL"
# loads a given named model from within a zip file within a zip file.
#
# these selections override any manifest that might be in a ZIP file.

# new feature: print getProperty("fileContents","zipFileName", "subfile", "subFile",...)
# getProperty now allows drilling down through a ZIP file. If no subfile is shown,
# then the directory listing is given:
#
# print getProperty("fileContents", "data/test.zip")
#
# CH3CL.MOL
# CH3CL~1.MOL
# CH3F~1.MOL
# CH3OH~1.MOL
# CH4~1.MOL
# BENZEN~1.ZIP
# ENALSP~1.ZIP
# WATERV~1.ZIP
# JmolManifest
#
# print getProperty("fileContents", "data/test.zip", "BENZEN~1.ZIP")
#
# benzenevib.spardir/
# benzenevib.spardir/_locked
# benzenevib.spardir/_spartandir
# benzenevib.spardir/Document
# benzenevib.spardir/M0001/
# benzenevib.spardir/M0001/_spartan
# benzenevib.spardir/M0001/archive
# ...
# benzenevib.spardir/SpreadSheet/
# benzenevib.spardir/SpreadSheet/SheetData

# print getProperty("fileContents", "data/test.zip", "BENZEN~1.ZIP","benzenevib.spardir/M0001/")
#
# benzenevib.spardir/M0001/
# benzenevib.spardir/M0001/_spartan
# benzenevib.spardir/M0001/archive
# benzenevib.spardir/M0001/Calculations
# benzenevib.spardir/M0001/Commands
# benzenevib.spardir/M0001/Geometry
# benzenevib.spardir/M0001/input
# benzenevib.spardir/M0001/log
# benzenevib.spardir/M0001/Molecule
# benzenevib.spardir/M0001/output
# benzenevib.spardir/M0001/parchive
# benzenevib.spardir/M0001/proparc
# benzenevib.spardir/M0001/ret_code
# benzenevib.spardir/M0001/voutput
#
# print getProperty("fileContents", "data/test.zip", "BENZEN~1.ZIP","benzenevib.spardir/M0001/Commands")
#
# # Verbose Mode: 1
# # version: MacSPARTAN '06 129 129 x86/Darwin
# # rootKeys: 'OPT' 'HF' '3-21G(*)' '' ''
# # new Keys: 'OPT HF 3-21G(*) FREQ '
# # ...etc....

#
# new feature: load "myfile.zip" MANIFEST "...."
# new feature: JmolManifest in a zip file directs which files to load and in what order
# JmolManifest is simply a list of files, one per line.
#
# Rules include:
#
# 1) blank lines and lines beginning with # are ignored.
# 2) file names are case-sensitive and must be complete, with full path within the ZIP file
# 3) files must be on separate lines or separated by vertical bar | marks; no whitespace around names
# 4) files may be ZIP files themselves.
# 5) some comments are special:
# IGNORE_ERRORS --- process the file and do not stop if some files are not valid model files
# IGNORE_MANIFEST --- (on the load command line) indicates that the internal ZIP file manifest should be ignored
# EXCEPT_FILES --- process all files EXCEPT those given
#

# new feature: show spacegroup "X,Y,Z;-X,Y,Z;..." finds space group associated with specific operations

# bug fix: multimodel files could have connected atoms between different models.

# bug fix: application animation frame button reset always goes to frame 1

# new feature: load xxx.zip n # where n is the desired file, starting with 1
# new feature: Spartan06 file format reader
# new feature: ZIP file reading for multiple models

# bug fix: antialiasDisplay changes during spinning (or any rendering) causes null pointer error

# -----------------------------------------------------------------------------

#version=11.3.47

# coding efficiencies in atom iterators

# vast speed up of smoothed isosurface map properties

# deprecated: calculate surface (equates to surfaceDistance WITHIN)
# deprecated: calculate surface {...} (equates to surfaceDistance FROM)

# new feature: calculate surfaceDistance FROM {atomExpression}
# new feature: calculate surfaceDistance WITHIN {atomExpression}

# -----------------------------------------------------------------------------

#version=11.3.46

# new feature: calculate surface {atomExpression}

# new feature: set isosurfacePropertySmoothing # default TRUE
# smooths the coloring for isosurface ... map property ...

# bug fix: "isosurface select() map property xxxx" array out of bounds error
# bug fix: color bonds CPK not working
# new feature: calculate polymers
# allows recalculation of polymers after connections are made/broken

# bug fix: tRNA, rRNA with abnormal distances do not connect biopolymers
# bug fix: Jmol math getProperty() doesn't pass parameter in some cases
# code: refactoring,optimizing Escape.toJSON() and Escape.toReadable()
# bug fix: isosurface CAP not turned off prior to map sasurface
# bug fix: adjustable boundbox in multimodel context not specific to model of selected atoms
# bug fix: Jmol math (x[2])[3] indistinguishable from x[2][3]

# -----------------------------------------------------------------------------

#version=11.3.45

# bug fix: new boundbox command with small numbers of atoms
# bug fix: state not saved for coloring elements
# bug fix: state not properly representing deleted bonds
# bug fix: setColix not clearing shading in certain cases

# new feature: Jmol math {atomset}.boundbox returns list of center, vector, corner0, corner1 for this set of atoms
# code: ModelSet.BoxInfo abstraction/refactoring

# -----------------------------------------------------------------------------

#version=11.3.44

# new feature: Jmol math getProperty() function
# allows FULL math access to ALL getProperty types
#
# syntax: getProperty(propertyType, qualifier, item, item, item,...)
#
# examples:
#
# print getProperty("modelInfo")
# print getProperty("boundboxInfo")
# print getProperty("boundboxInfo", "center")
# print getProperty("boundboxInfo", "vector")
# print getProperty("atomInfo",{atomno=3})
# print getproperty("bondInfo",{*},2,"atom1")
# print getProperty() # displays list of possibilities
# print getproperty("polymerinfo",{*},"models",2,"polymers",1,"monomers",39,"atomIndex2")
#
# For many property types, the qualifier is an atom set
# If the atom set is not given, those properties default to {visible}
# For "stateInfo", the qualifier is string: "fileState", "modelState", etc.
# Items may be integers or string-based keys
# Integer items follow the rules of Jmol math selectors:
# 1 first item, 0 last item, -1 next to last item, etc.

# code: set instead of = in measures and labels state

# bug fix: POVRAY and other buttons aren't enabled when there are no atoms but instead draw objects and isosurfaces
# bug fix: new label fonts not loaded when labels resized

# bug fix: nuisance "render mesh error" console report

# new feature: boundbox {atomExpression} [on|off]
# sets the bound box around the specified atom expression
# default ON/OFF is to NOT change current setting

# new feature: boundbox {point or expression} {vector to corner} [on|off]
# sets the bound box to be centered with a given size based on a vector to a corner

# new feature: boundbox corners {point or expression} {point or expression} [on|off]
# sets the bound box to encompass the two corner points

# strangely enough this allows setting the boundbox to a 2D or 1D box

# new feature: show boundbox gives valid boundbox commands and volume

# bug fix for bioshapes visible outside of current visible frame set

# bug fix for selecting atoms of atomsets using [-n] or [0]

# isosurface POINTSPERANGSTROM synonym for RESOLUTION
# also reported in show isosurface

# bug fix: more natural mouse SHIFT-RIGHT behavior.

# new feature: isosurface CAP [plane definition]

# caps the isosurface at the designated plane.
# Specifically for molecular/solvent-type isosurface.
# [plane definition] can be {x y z w} or any combination of
# three {x y z} points, draw point references, or atom expressions

# -----------------------------------------------------------------------------

#version=11.3.43

# bug fix: select statement comparisons of negative decimal properties to "-1" (not "-1.0") causes none found


# new feature: Back to "SET" for state definitions of Jmol parameters.

# bug fix: Strings too long in state can cause Eclipse "infinite loop" bug
#
# solution is a new feature:

# new feature: "\" at the end of a line marks a continuation of that line

# bug fix: assigning a negative value to a dataAtomNumberField value caused BitSet.set() exception

# bug fix: Jmol parameter setting syntax too loose

# The following statement was allowed:

# pickCallback = myfunction

# OK, so that might look good, but it evaluates to
#
# pickCallback = ""
#
# since the VARIABLE myfunction has not been defined.
#
# Solution: Don't allow the syntax
#
# [jmolParameter] = [Token.identifier]
#
# the following is OK:
#
# [jmolParameter] = "some string"
#
# the following is preferred:
#
# SET [jmolParameter] [value]
#

# bug fix: antialias with translucent but antialiasTranslucent = false; labels, text, echos, hover, picking, out of alignment
# bug fix: negative formal charges

# new feature: set drawPicking TRUE
# then reports picking of draw objects as a JavaScript array:
# [ "draw","[drawID]",[modelIndex],[vertexIndex],[x],[y],[z] ]
# this goes to the pickCallback function as the second parameter,
# with the first parameter (normally the atomIndex) being -2.

# bug fix: write coord mol not working

# new feature: connect (...) (...) aromatic auto
# similar to calculate aromatic, except it's isolated to this set of connections; implicit modifyOnly
# can be used in place of
# select *; calculate aromatic
#
# code: refactoring of BondCollection.makeConnections
#
# bug fix: connect (..) (..) # with implicit "single" causes state to use "partial 0"

# new feature: shadows can be activated again via noShadows parameter in .pov file

# -----------------------------------------------------------------------------

#version=11.3.42

# bug fix: new frame title and state

# new feature: set echo [echoID] MODEL [model number]

# bug fix: select by itself not working; oy. Since at least 11.0

# bug fix: ramachandran/quaternion fix for assignment of structure
# bug fix: isosurfaces not taking their default name properly

# new feature: frame title "this a title for THIS frame only"

# bug fix: small fix for povray cap at back side
# bug fix: overly long titles now again substringed in the popup menu.

# bug fix: memory leak in merge -- models[i].modelSet causes modelSet to not finalize.
# bug fix: quaternion


# bug fix: set xxxCallback not allowed

# new feature: **** Jmol Embedded Script **** recognized in /* ... */ comments and /** ... **/ super-comment blocks
# if found, ONLY this text is processed and all other text in the file is ignored.

# -----------------------------------------------------------------------------

#version=11.3.41

# bug fix: math operations with bond bitsets; % and + operating on arrays
# bug fix: _set variable definition removed

# new feature: .type math function

# new feature: Jmol math allows direct string replacement in select atom expressions:
# x = "atomno=3"
# select @x # or select @{x}
# select @{x + 3} # selects atomno=33
# x = array("atomno<10","atomno>20")
# select @x # OR of the list elements
# select @{x[2]} # just element 2 of x (atomno>20)
# select @x[2] # same as {@x}[2]


# new feature: set atom properties using an array instead of a DATA statement:
# (was introduced in 11.3.29, but not fully articulated)
# {*}.x = array(2,3,4,5,6);
# {atomno<=3}.color = array("red","green","blue")
# {*}.property_mydata = array(1.0,5.5,4.4,3.3);
# {atomno < 4}.xyz = array({3 4 5},{4 5 6},{5 6 7})
# if the array is shorter than the number of atoms selected, then
# only that number of atoms are affected

# new feature: set atom properties from space-separated string:

# {atomno < 5}.property_mydata = "1.0 5.5 4.4 3.3";

# -----------------------------------------------------------------------------

#version=11.3.40

# new feature: Ramachandran/Model commands switch between plot and model
# -- one Ramachandran plot per model
# -- axes labels and special hover label for Ramachandran plots
# -- Ramachandran saved in state

# bug fix: Overlapping CPK at a slab now correct for up to 10.000 clipped atoms.

# bug fix: @{} for within(1.0,point,@{....})

# new feature: set xxxx where xxxx is not a Jmol variable causes ERROR

# code: privatized Token to avoid null value problem in Eval.statementAsString()

# POV-Ray clipping coding minor tweak
# POV-Ray fix for number formatting width > 999

# new feature: model-based parallel array calculations:
# x = {atomno=3}.split() # a list, one element for each model
# draw @{x.xyz.sub({1 0 0})} # a set of points, one per model

# new feature: point3f in array():
# xlist = array({1,2,3}, {1,1,0});print xlist[1]+{1 0 0};
# bug fix: draw @{x - {1 0 0}}
# bug fix: antialias with set picking draw
# bug fix: draw object text not selective for frame
# new feature: draw object title line number corresponds to model number for multi-model draw objects

# new feature: matte finish for isosurfaces
# remark: matte finish replaced by adaptable translucent finish (see below)

# bug fix: noninteger MO occupancies
# bug fix: antialias labels not fully bitmapped
# bug fix: RPN processor too limited in nesting level
# bug fix: MO processing for Gaussian and PSI3 errors

# new feature: MoldenReader (Matthew Zwier )
# new feature: MO calculations for spherical orbital basis (Matthew Zwier )

# bug fix: slabbed atoms are now capped in povray output.
# Note: In CPK mode atoms overlap, but are capped at the same height.
# there is a priority in Jmol, but not yet clear to me which. The current priority
# in povray is based on the signed distance from the slab to the atom center.
# bug fix: povray output of translucent objects now have reduced glare, for
# clarity of the representation and better compatibility with the Jmol viewer.

# -----------------------------------------------------------------------------

#version=11.3.39

# bug fix: antialias causing image to be partial size.
# bug fix: hover state not properly showing specific-atom hover labels.

# new feature: write FILE (text-files only)

#new feature webexport: automatic usage of a different path to the applet for local files to allow testing
# only works for Pop-In template at present. Required updates to JmolPopin.js and templates.
#webexport instruction updated to reflect new feature.


# bug fix: antialias adjustments for hover text and background box
# bug fix: antialias fix for text color same as background and in front of translucent surface appearing transparent
# bug fix: antialias fix for applet

# webexport instruction updates.
# bug fix: webexport scriptbutton template had erroneous script names.

# -----------------------------------------------------------------------------

#version=11.3.38

# bug fix: antialiasing with translucent/POV-ray
# new feature: set antialiasTranslucent TRUE/FALSE
# along with antialiasDisplay and antialiasImages
# determines the extent of antialiasing. Requires
# antialiasDisplay or antialiasimages TRUE.

# -----------------------------------------------------------------------------

#version=11.3.37

# new feature: @{mathExpression} for echos, select, etc. where @x can be used.
# select atomno=@{x*2};
# xlist = array("red", "green", "blue");
# n = 2;
# color atoms @{xlist[n]};

# new feature: {atomExpression}.color = "red" (or "[xff0000]" or {255,0,0}

# new feature: helixes as barrels in cartoons or rockets using
# rocketBarrels = true


# bug fix: -- adds antialiasing for translucent objects
# bug fix: error in state for connect DELETE
# bug fix: 0-diameter atoms displayed as single pixels when perspectiveDepth = false

# -----------------------------------------------------------------------------

#version=11.3.36

# antialias better dots

# bug fix: inline loading not working

# POV-Ray dialog update

# set antialiasDisplay T/F (false by default)
# set antialiasImages T/F (true by default)

# -----------------------------------------------------------------------------

#version=11.3.35

# POV-Ray slab/depth
# POV-Ray text -- ALL text (echos, labels, axes, etc.)

# POV-Ray cleaner for Molecular Orbitals
# bug fix: getproperty atominfo returning string to Integer()
# PDB remediated atom name upgrade -- NEEDS CAREFUL CHECKING

# -----------------------------------------------------------------------------

#version=11.3.34

# write povray [width] [height] filename

# POV-Ray for mapped isosurfaces
# POV-Ray embeds Jmol script
# POV-Ray .pov files created by Jmol can be loaded as scripts


# code: cleaning of JmolConstants specialAtomNames
# code: cleaning of TextFormat.simpleReplace
# bug fix: select [SET] or [2MO] or [DB']
# bug fix: app -c flag errors not going to Logger.Error
# bug fix: no partial charges!
# bug fix: 11.3.14+ does not write colormapped JVXL files
# bug fix: Using isosurface within 1.0 @pt1 where pt1 is a draw point save state cannot be restored

# -----------------------------------------------------------------------------

#version=11.3.33

# code: PovRay tweaks -- multiple bonds
# code: PovRay output uses BufferedWriter

# adds support for "xx'" atom designations in PDB and variable names

# bug fix: insertion codes stored incorrectly in 11.3.32

# new feature: inline scripting allows math
#
# script INLINE "select " + site_list[2]


# new feature: site_ support for PDB and CIF
#
# loading of PDB and CIF files containing site information
# automatically defines variables site_xxx and defines selections site_xxx and site_n
# where xxx is the site identifier and n is the site number.
# These settings are reset each time a file is loaded.
# They do not carry over from one file to the next.

# adds "OP1" and "OP2" as backbone designators (new PDB designation)


# _PovrayExporter adds draw, halos, stars, dipoles, vectors, polyhedra,
# backbone, cartoons, meshRibbon, ribbon, rockets, strands, trace,
# dots, geosurface, molecular orbitals, LCAO cartoons, pmesh,
# single-color isosurfaces

# Web Export Dialog changes: new intro tab, new minilog at bottom, instructions converted to
# buttons which open the info in the standard Jmol Help Dialog.


# bug fix: rockets color incorrect for head groups

# -----------------------------------------------------------------------------

#version=11.3.32

# bug fix: vibration disabled in 11.3.31
# bug fix: zoomto cancels slabbing
# bug fix: zoomto (atomExpression) 0 # zooms to 2x

# new feature: getproperty stateinfo TYPE
# where TYPE is one of:
#
# colorState
# dataState
# fileState
# frameState
# modelState
# perspectiveState
# selectionState
# variableState
# windowState
#
# bug fix: backbone not in state

# code(I): Mmset merged into ModelSet;
# Viewer accesses ModelSet methods directly
# ModelManager streamlined substantially
#
# This basically removes two full layers of abstraction.
# All the atoms, bonds, and models are now in ModelSet.
#
# code(II): ModelSet extends ModelCollection extends BondCollection extends AtomCollection
#
# bug fix: dipoles moved back into shape from shapespecial
# bug fix: semi missing in show orientation message, second part (zyz text)
# bug fix: select 0 selects all instead of PDB group 0
# bug fix: write t.xxx

# -----------------------------------------------------------------------------

#version=11.3.31

# bug fix: calculate aromatic for N and O refined

# new feature: valence -- sum of bond orders
# print {atomno=3}.valence
# {atomno=1}.valence = 3
# select (carbon and valence != 4)

# new feature: settable atom properties (preliminary):
# .x, .y. .z, .xyz,
# .fx, .fy, .fz, .fxyz,
# .vx, .vy, .vz, .vxyz,
# .formalcharge, .occupancy, .partialcharge
# .temperature, .valence
# for example:
# a = {atomno=30}
# a.xyz = {1.0, 2.0, 2.3}
# a.temperature = 3.0
# a.formalcharge = 2

# new feature: set atom properties using {xxxx}.x =
#
# {atomno=3}.x = 3
# {(*)[2]}.xyz = {1 2 3}
# for(var i = 1; i < 3; i = i + 1); {(*)[i]}.x = 5;end for;
# {atomno=3}.property_whatever = 2.0

# new feature: set atom properties using an array instead of a DATA statement:

# {*}.property_mydata = array(1.0,5.5,4.4,3.3);
# {*}.property_mydata = "3 4 5 6 7 8";
# {atomno < 4}.xyz = array({3 4 5},{4 5 6},{5 6 7})

# code optimization for within() and setAtomBits()

# more export generator classes

# bug fix: unitcell missing some lines when axes turned off

# -----------------------------------------------------------------------------

#version=11.3.30

# new feature: adds H/Br/Cl/I/C logic to aromatic bond assignments
# new feature: adds Oxygen/Sulfur logic to aromatic bond assignments
# new feature: adds Nitrogen logic to aromatic bond assignments
# bug fix: menu for UNITCELL

# new feature: PovrayExporter (pim schravendijk )

# -----------------------------------------------------------------------------

#version=11.3.29

# new feature: aromaticSingle and aromaticDouble bond order options
# new feature: "smartaromatic" bonds # turned off with "smartAromatic = false"
# new feature: calculate aromatic # calculates reasonable aromatic double/single alternation.
# new feature: reset aromatic # sets all aromaticDouble and aromaticSingle back to aromatic
# new feature: select ISAROMATIC # selects aromatic atoms
# new feature: MOL reader recognizes bond types 4,5,6,7

# new feature: isosurface/mo "squared"

# new feature: fully generalized bond order "partial n.m"
# n = number of lines, up to 5
# m = binary mask for dottedness, up to 31 (0x1F)
# 00001 first line of bond dotted
# 00010 second line of bond dotted
# 00011 first and second line of bond dotted, etc.

# new feature: connect may use numeric bond orders, including "partial n.m"

# new feature: preliminary work on functionalized state
# new feature: global/local functions (to applet, for instance
# in general, functions are global -- common to all applets.
# first-character "_" indicates this function is a LOCAL function, private to this applet.

# -----------------------------------------------------------------------------

#version=11.3.28

# critical bug fix for color command not coloring objects properly
# new feature: bondOrders 2.5 and -2.5 PartialTriple and partialTriple2

# -----------------------------------------------------------------------------

#version=11.3.27

# critical bug fix for functions not returning values
# bug fix for atomarray[i] not selecting properly
# bug fix for write not working with VAR
# bug fix for application not accepting pastes into the
# console consisting of multiple lines
# bug fix for bondOrder command not properly treating 4.0 or 0.5
# bug fix for decimals not represented properly in error messages

# -----------------------------------------------------------------------------

#version=11.3.26

# new feature: _1 parameter for "first atom" in second expression of connect:
# connect 3.0 (_H and connected(_N) (_O and not within(chain,_1)) hbond
# new feature: better reporting of PMESH file format errors

# code cleanup: pmesh moved to shapespecial; privatized

# bug fix within(chain,xxx) not working
# bug fix for() as first command in script or line
# bug fix we were not exporting error free xhtml 1.1.
# bug fix for WebPageMaker not writing files
# bug fix for PAUSE causes app to hang -- this is a reversion of use of SwingUtilities.invokeLater(),
# which actually will not work in ScriptWindow. We need the direct execution in
# order to avoid the event queue from stopping itself.

# -----------------------------------------------------------------------------

#version=11.3.25

# bug fix compiler not recognizing "axes =" or "measures = "
# bug fix for WebPageMaker creating uncompressed PNG
# bug fix for WebPageMaker not stripping \ in load file names

# -----------------------------------------------------------------------------

#version=11.3.24

# critical bug fix for 11.3.23 compiler not recognizing line endings
# bug fix for show state for draw in multi-model environment
# bug fix? for background model not available for multiple frame range (e.g. frame 2.0) or after invalid frame number
#
# new feature: within(distance,isWithinAllModels,atomExpression)
#
# allows finding atoms within a specified distance of other atoms in OTHER models:
#
# select within(5.0,true,model=2.1) # TRUE indicates we should check all models
# select within(5.0,false,model=2.1) # FALSE -- only model 2.1
# select within(5.0,model=2.1) # default is FALSE

# -----------------------------------------------------------------------------

#version=11.3.23

# VERSION full script flow control support:

# if / else if / else / end if
# for / end for
# while / end while
#
# var i = 4
# if (i = 3)
# print "i=3"
# else if (i = 4)
# print "i=4"
# else if (i = 5)
# print "i=5"
# end if
#
# var i = 5
# while ( i > 0)
# print "atom " + i + " " + {atomno=i}.ident + " is at " + {atomno=i}.xyz
# i = i - 1
# end while
#
# n = {*}.size
# for (i = 1; i <= n; i = i + 1)
# for (j = i + 1;j <= n; j = j + 1)
#
# var dist = {atomno=i}.distance({atomno=j})
#
# if (dist < 1.77)
# print "i-j: " + i + "," + j + " " + dist%2
# measure {atomno=i} {atomno=j}
# endif
#
# end for
# end for
#
# var i = 4
# while ( i > 0)
# print "in while: i="+i
# if (i = 2);print "i is 2";endif
# i = i - 1
# end while
#
#

# -----------------------------------------------------------------------------

#version=11.3.22

# Changes to webexport package only
# New Features: textboxes for entry of author name and title for browser window
# persistence across launches of authorname and applet size
# automatic gzip of large structure/quantum files.
# Bug? fix: update the page templates to XHTML 1.1
# Minor fixes to instruction .html files.

# tweak: using "var" keyword prevents display of global variable value

# -----------------------------------------------------------------------------

#version=11.3.21

#
# bug fix: isosurface of MOs not properly displaying color in saved state
# bug fix: state saving of @ definitions has extra = sign.
#
# new feature: fully functional user-defined functions:
#
# MACROS (no parameters)
#
# function mymacro
# background red
# color atoms blue
# end function
#
# function mymacro2
# background black
# color atoms cpk
# end function
#
# background white
# delay 2
#
# mymacro
#
# delay 2
#
# mymacro2
#
#
# SUBROUTINES (parameters, but no return)
#
# function drawline(id,a,b)
# var x = script("draw line"+ id + " {atomno=" + a + "} {atomno=" + b + "}")
# end function
#
# drawline(1,3,5)
# drawline(2,10,12)
#
#
# FUNCTIONS (parameters and returns)
#
# function d(a,b)
# return a.distance(b)
# end function
#
# x = d({atomno=3},{atomno=4})
# print x
#
# SHOW AND WRITE:
#
# show functions
#
# write functions macros.spt
#

# -----------------------------------------------------------------------------

#version=11.3.20

# bug fix for arrows way too fat (introduced in 11.3.19) :(

# -----------------------------------------------------------------------------

#version=11.3.19

# bug fix: critical arrow fix of 11.3.17 for 2-point arrows
# bug fix: write PNG default was 0 compression. -q flag was OK for setting 0-9
# bug fix: ragged arrow tip

# -----------------------------------------------------------------------------

#version=11.3.18

# critical bug fix for 11.3.17 in regard to serialization of arrays
# also introduces
#
# reset ALL # resets all user-created variables
#
# also "exitJmol" typed into the script window for the application does that.
#

# -----------------------------------------------------------------------------

#version=11.3.17

# bug fix: problem with unescaping comma-separated point strings "{1,2,3}" as a point.
# bug fix: drawn arrows scale improperly when zooming; arrow heads off-kilter

# new feature: set defaultDrawArrowScale # 0.5 initially
# Drawn arrows now have a head size that can be set and a dimension that
# scales with the model, so arrow head:atom size ratio remains constant

#
# new feature: setting Jmol,Rasmol,Shapely,Amino,Roygb,Rwb
# color schemes makes those colors the default colors for these schemes.

# rename byResidue_jmol --> byResidue_shapely
# rename byResidue_rasmol --> byResidue_amino

# new feature: array variables saved as arrays
# prior to 11.3.17, you could not do:
#
# x = "this is a test".split(" ")
# y = x[3]
#
# because x was only saved as a string, not an array
# now x is saved as an array, so this is no problem.
#
# new feature Jmol math point(x,y,z) function
#
# point(a,b,c) or point("{x,y,z}")
#
# x = point(y[3], y[6], y[2])
# x = point("{2,3,5}")
#
# needed because, with simple numbers, just
#
# x = {3.0,4.0,5.0}
#
# works, but
#
# x = {r,g,b}
#
# does(did) not.
#
# new feature: Jmol math array element assignment:
#
# a = "2,3,4,5".split(",")
#
# a[3] = "now the 4 becomes this phrase"
# a[a[2]] = "not any more; now it's this"
# a[0] = "setting the final element"
# a[6] = "expanding the array"
# print a
#
# 2
# 3
# not any more; now it's this
# setting the final element
#
# expanding the array
#
# works with strings as well:
#
# a = "this is a test"
# a[8] = " not"
# print a
# >> a = "this is not a test"
#
# new feature: Jmol math x = array(a,b,,,,)
#
# x = array(3,4,5,6)
# print x[3]
# >> 5
#

# new feature: Jmol math plane(x,y,z,w) function
#
# plane(a,b,c,d) or plane("{x,y,z,w}")
# or through three points:
# plane({atomExprOrPoint},{atomExprOrPoint},{atomExprOrPoint})
# or through three points with a reference point
# plane({atomExprOrPoint},{atomExprOrPoint},{atomExprOrPoint},{atomExprOrPoint})
#
# x = plane(y[3], y[6], y[2], 3.0)
# x = plane("{2,3,5,4}")
# x = plane({_H}[1],{_H}[2],{_H}[3],{_C}[1])
# new feature: print command prints a variable expression
#
# print x
# print x * 3
# print x[4] + x[3]
# print x.split(" ")[2][0]

# new feature: aPlane.distance({some atoms})

# new feature: someArray.add("string") adds string to right of each item
# new feature: someArray.sub("string") adds string to left of each item

# colorManager clean-up

# -----------------------------------------------------------------------------

#version=11.3.16

# bug fix: Eval RPN processor for list[n] addition operator not doing selection

# new feature: MOPAC mgf file UHF orbital reading -- preliminary only

# new feature: byElement and byResidue color schemes allow
# customized element and residue coloring schemes.
# built-in include: byElement_Jmol, byElement_Rasmol,
# byResidue_Jmol (shapely) and byResidue_Rasmol (amino)
# with abbreviations byElement == byElementJmol; byResidue == byResidue_Jmol
# color atoms "byresidue_Jmol"
#
# Users can set up their own byElement and byResidue color schemes
# simply by preficing a name with "byElement" or "byResidue":
#
# color "byElement_Mine=[x......] [x......] [x......] ..."
# 0(unknown) 1(H) 2(He) ...
#
# then:
#
# color atoms "byElement_Mine"
#
# RANGE min and max are ignored for byElement and byResidue schemes,
# and there is no scaling done ever, so effectively these prefixes
# make the correlated value a simple index into the array.
# This is what one would want for something that should be a given
# for a specific element or residue
#
# Residue indexes in order correspond to the groupID of an atom:
#
# 0 noGroup,
# 1 ALA, ARG, ASN, ASP, CYS,
# 6 GLN, GLU, GLY, HIS, ILE,
# 11 LEU, LYS, MET, PHE, PRO,
# 16 SER, THR, TRP, TYR, VAL,
# 21 ASX, GLX, UNK,
# 24 A, +A, G, +G, I, +I,
# 30 C, +C, T, +T, U, +U
#
# so this opens the door to user-created residue coloring schemes.
#
# color "byResidue_Mine=[x......] [x......]..."
# nogroup ALA ...
#
# then
#
# color cartoons "byResidue_Mine"

# -----------------------------------------------------------------------------

#version=11.3.15

# new feature: fully customizable popup menu -- see file jmol.mnu
#
# load menu jmol.mnu
#
# applet parameter param=menuFile value="jmol.mnu"
#
# application parameter -m filename
#
# mostly untested
#
# new feature: show menu
# new feature: getProperty menu
#
# These deliver the current menu (as translated) in jmol.mnu format

# -----------------------------------------------------------------------------

#version=11.3.14

# new feature: fully customizable popup menu -- see file jmol.mnu
#
# load menu jmol.mnu
#
# applet parameter param=menuFile value="jmol.mnu"
#
# largely untested


# bug fix: HDO not recognized as "water"
# bug fix: rotateSelected MOLECULAR not around {0 0 0}
# bug fix: -g ignored on -n option, even if -w is present
# bug fix: unknown color palette could cause error

# new feature: %l atomic element number

# new feature: APPLICATION -q (quality) option
# new feature: lcaoCartoon, mo, isosurface, pmesh: color [translucent [n]|opaque] [colors...]

# adjustment: setting JPG default quality to 75, not 100

# new feature: {r,g,b} can be used in place of [r,g,b] for indicating color,
# allowing programmatic color definition:
#
# r = 255; g = 255; b = 0;
# background {@r,@g,@b}

# new feature: expanded color command for properties
#
# color atoms property partialcharge "rwb" range -1.0 1.0
#
# and reverse with range inverted:
#
# color atoms property partialcharge "rwb" range 1.0 -1.0

# new feature: unlimited user-defined color schemes:
#
# select none;
# color "myname=[xff00ff] [xffff00] [xff00ff]"
#
# colors must be [xRRGGBB] format for this one

# new feature: fully remappable isosurface using COLOR command:
#
# isosurface s1 molecular map mep
# color $s1 "bwr"
# color $s1 "rwb" range -0.2 0.2


# APPLICATION adjustment to console window scaling/size

# -----------------------------------------------------------------------------

#version=11.3.13

# this version introduces fully customizable color schemes
#
# new feature: .color for numbers and points delivers the
# color associated with a given value in the current
# coloring or propertyColorScheme.
# (some number).color gives a color triple as a point {x y z}
# {x y z}.color gives a hexadecimal string [xRRGGBB]
#
#
# select atomno=3;color yellow
# x = {atomno=3}.color # gives {255.0, 255.0, 0.0}
# x = {atomno=3}.color.color # gives "[xFFFF00]"
#
# set propertyColorScheme "bwr"
# x = {atomno=3}.partialcharge.color
#

# new feature: color ["schemeName"] RANGE [min] [max]
# allows setting of color range and scheme so that color
# values can be determined. This would be used for making
# a color key using positionable ECHO text boxes:
#
# color "bwr" absolute -0.1 0.1
# x = (0.01).color # gives the point-color associated with that number
# set echo myecho 100 100 # position
# echo " " # just some space
# color echo @x; background echo @x # color this bar the color of 0.01
#
# new feature: show colorscheme "schemeName"
# delivers "colorscheme = " followed by a string of color values.
# without the scheme name, returns the current colorscheme listing
# For example: show colorscheme "low" delivers:
#
# colorscheme = [xff0000] [xff2000] [xff4000] [xff6000] [xff8000] [xffa000] [xffc000] [xffe000] [xfff000] [xffff00] [xf0f000]
#
# setting an array variable to the color values:
#
# list = script("show colorscheme \"low\"")[15][0].split(" ")
#
# new feature: set userColorScheme [list of color names]
# creates a colorscheme referred to as "user" and its reverse, "resu"
# based on a list of color values:
#
# set userColorScheme red green [x00FFFF] blue
# color atoms property partialcharge "user" range -1.0 1.0

# -----------------------------------------------------------------------------

#version=11.3.12

# bug fix: zoomTo 100%
# bug fix: set language fr needs quotes but should not
# bug fix: load multiple files inline causes null pointer exception
#
# new feature: APPLICATION: File|Export...|Export to Web Page

# -----------------------------------------------------------------------------

#version=11.3.11

# bug fix: lcaoCartoon for sp center requires "sp2" not "sp"
# bug fix: mo not showing titles
#
# new feature: lcaoCartoon rotate [x|y|z] degrees create "px"
# new feature: adds Jaguar PLT plot file reader for isosurface
# isosurface sign red blue "myfile.plt"

# -----------------------------------------------------------------------------

#version=11.3.10

# bug fix: script window using swing thread start not from event queue
# bug fix: state of multi-polymer protein cannot be restored
# bug fix: dots nn% not operational
# bug fix: molecular dipole and multiple frames
#
# new feature: molecular dipole for Gaussian files
#
# new feature: simple calculation of approximate dipole moment from charge distributions.
# dipole molecular # from file value if provided
# dipole calculate molecular # from "center of gravity" of charges calculation
#
# new feature: show frame # based on models in the current frame set, displays information about frames
#
# new feature: application option for web page export
#
# new feature: write JPG n "filename" # where n is the quality (<=100)

# -----------------------------------------------------------------------------

#version=11.3.9

# bug fix for isosurface mapping of planes by MEP (see 11.3.2)

# new feature: symmetryRange: load "someFile" {mmm nnn 1|0} range x.x where x.x is a maximum distance away from closest atom in the base cell
# new feature: synchronization of applets using JavaScript
# new feature: synchronization of applets using Jmol scripts:
#
# synchronize .|>|*|appletId[syncId] ON|OFF|SLAVE|command
#
# The synchronize (sync) command allows two or more applets to be synchronized in
# terms of orientation. Move one with the mouse, and the other moves as well.
# In addition, the sync command allows ANY command to be sent to one or more
# other applets directly, without the intervention of JavaScript.
#
# Applets are identified by appletId (jmolApplet0, for instance)
# along with an optional bracketed sync group identifier -- generally a random
# number that identifies the page containing the controlling applet. If the
# syncId is not given, then the ID for the page containing the controlling applet
# is used. This feature is important for cross-frame synchronization only.
#
#
# . this applet only
# > all applets except this one
# * all applets
# appletId id of a specific applet
# [syncId] (optional) a unique string of digits -- brackets included
#
# ON sync as driver (default)
# OFF turn sync off
# SLAVE turn sync on, but not as driver
# command command to send
#
# for example:
#
# sync * # synchronize all applets as drivers
# sync jmolApplet1 #syncs this applet with jmolApplet1 both as drivers
# sync > "set echo top left;echo OK" # sends OK to top left of all OTHER applets
# sync jmolApplet2[254678942] OFF # turns sync off for an applet ON A DIFFERENT PAGE
# # or in a different FRAME
# sync . OFF # turns sync off for this applet
#
# new Jmol.js feature: jmolGetSyncId(); jmolSetSyncId(id);
# allows control over the sync ID via javascript. jmolSetSyncId(id)
# should be called prior to jmolApplet() and should incorporate some sort of
# random digits and no space characters. (A number is good.)
# This should only be necessary for multi-frame pages.

# -----------------------------------------------------------------------------

#version=11.3.8

# bug fix: isosurface color -- not operating for some isosurface types
# bug fix: isosurface "xxxx.cube" -- not assigning proper default colors
# bug fix: gamess reader MO fix
# bug fix: state save of STRUCTURE misplaced

# feature: adds adjustable scale for unitcell axes

# -----------------------------------------------------------------------------

#version=11.3.7

# bug fix: reading of JVXL files for orbitals loses phase information
# bug fix: ACD/Labs nonstandard cml "builtin" property reader
# bug fix: isosurface interior cavity was not setting meshdata surfaceSet null
# bug fix: select dna can select rna if chain is mixed hybrid dna+rna

# -----------------------------------------------------------------------------

#version=11.3.6

# bug fix: inappropriate draw pick spinning for single point
# bug fix: dots not available in multimodel mode
# bug fix: multiple isosurface cavities incorrect in a multimodel environment
# bug fix: isosurface cavity not filled completely
# bug fix: nested ifs can cause last endif to throw error
# bug fix: compiler bug working with very small real numbers
# bug fix: Support for mol2 files with blank line after comments.

# -----------------------------------------------------------------------------

#version=11.3.5

# bug fix: ACD/Labs nonstandard cml "builtin" property reader
# note that xmlReader (SAX reader) is now set to ignore all DOCTYPE declarations
# bug fix: odydata fix for files with \r\n for line ending
# bug fix for PDB remediated T/DT difference of C5M/C7
# bug fix: set spin X was case-selective
# bug fix: echo text not re-orienting on resize of applet or application
# bug fix: multiple isosurface cavities in a multimodel environment
# bug fix: missing set picking ident in popup window
# bug fix: popup menu set picking label not working

# -----------------------------------------------------------------------------

#version=11.3.4

# rough export of VRML using
#
# write VRML "myfile.wrl"
#
# includes colored balls and sticks; uncolored isosurfaces

# -----------------------------------------------------------------------------

#version=11.3.3

# bug fix pmesh not working
# bug fix for state after calculate surface, calculate hbonds, configuration, dynamic variable definition in multimodel environment (ModelSet::addStateScript)

# NEW FEATURES from the 2007 Gordon Research Conference on Visualization in Science and Education:
#
# internal dataFrame concept
#
# new command: ramachandran
#
# new command: quaternion [w x y z] [derivative]
#
# TODO: frame menu
# TODO: write VMRL

# preliminary Maya export -- sets the stage for any number of export frameworks.

# -----------------------------------------------------------------------------

#version=11.3.2

# bug fix: set picking label
# bug fix: minus-sign "fix" in 11.3.1 broke all {x -y z} notation
# bug fix: state for phased atomic orbitals does not preserve red/blue color
# bug fix: mo opaque causing "invalid argument" when no MOs
# bug fix: isosurface cavity molecular caused exception
# feature: adds isosurface capability to map MO and MEP data onto planes

# -----------------------------------------------------------------------------

#version=11.3.1

# bug fix: debugscript on;center 3-5; "-" missing
# bug fix: zoomTo (5-7) read as "5 to -7"
# bug fix: move with time < 0.03 seconds causes molecule to disappear
# bug fix: hover interruption
# bug fix: image offsets in creating JPG image if model has been moved by CTRL-ALT-LEFT drag

# -----------------------------------------------------------------------------

#version=11.3.0

# perspectiveModel 11 default
# bug fix for 3D text echo staying in window
# bug fix for draw text+translucency
# bug fix for draw text not hovering for points
# bug fix for multiple draw objects in show state
# bug fix for spin save reversed direction
# bug fix for CdkAdapter not having auxiliaryInfo data
#
# adds the ability to find the coordinate of a specific
# draw object vertex using $objName[vertexId] as in
# draw p perp plane (atomno=1) (atomno=2)
# x = $p[3]
# draw pt1 $p[1]


# -----------------------------------------------------------------------------

#version=11.1.49

# bug fix for Gaussian file reader fix for very large negative MO coefficients
# bug fix for move not releasing isInMotion
# bug fix for x = "testing"[0], x = "testing"[-1], "testing".split("t")[0], and "testing".split("t")[-1]
# bug fix for select {*}[0], {*}[-1], etc., which now counts from the end back
# adds proper indents on debugscript for if/else/endif
# allows "jmolscript:" for embedded scripts and callbacks

# -----------------------------------------------------------------------------

#version=11.1.48

# bug fix for gamess reader MO fix
# bug fix for mopac GRAPHF file fix (resolver thought MOL)
# bug fix for lcaocartoon "lp" fix for AX3E and AX2E

# -----------------------------------------------------------------------------

#version=11.1.47

# bug fix for compound document reader not reading enough short segment pointers
# bug fix for Spartan reader not recognizing 5D orbital problem
# bug fix for animation skipping frames

# -----------------------------------------------------------------------------

#version=11.1.46

# bug fix for Jvxl.jar standalone application not having complete set of class files (jvxl)
# adds inline help support for Jmol application running under Java 6 (Java 1.6.xx)
# bug fix for inappropriate pre-JVM12 menu items not disabled

# -----------------------------------------------------------------------------

#version=11.1.45

# bug fix for animFrameCallback not indicating animation direction
# bug fix for help not working and help URL not displaying (app)
# bug fix for app not writing state from File...Export menu (app)
# bug fix for retaining the last-saved file type selected for Image export (app)
# bug fix for "wait" not recognizing if it is just a syntax check (app)

# -----------------------------------------------------------------------------

#version=11.1.44

# bug fix for inability to specify fractional coordinates: adds fx, fy, fz as
# select fx < 0.5 and fy < 0.5 and fz < 0.5
# aveFracX = {molecule=1}.fx
# bug fix for inability to use x,y,z,fx,fy,fz with cartesian points
# bug fix for select BONDS ({...}) not preserved in state
# bug fix for geosurface not always restored from saved state
# bug fix for strandcount saved explicitly forces bioshape load

# -----------------------------------------------------------------------------

#version=11.1.43

# bug fix for labels mysteriously disappearing. Also probably taking up HUGE amounts of hashtable space.
# bug fix for hydrogen bond calculation with incomplete nucleic acid definitions.
# bug fix for "set picking draw" crashing Jmol
# bug fix for strandCount not carrying over to meshRibbon
# bug fix for geosurface/dots save/restore state exception
# bug fix for save state using "measurements off" instead of "set measurements off"

# -----------------------------------------------------------------------------

#version=11.1.42

# bug fix for lack of updating of certain variable predefined expressions
# bug fix for smiles nonfunctional

# bug fix for load append and structure commands
# bug fix for load files losing structure and cartoons
# bug fix for multiple frames displayed does not show Select...Elements menu
# bug fix for select @x not functioning where x = {atom expression} or x = "atom expression"
# bug fix for {atom expression}.ident nonfunctional

# code refactoring Frame --> ModelSet and ModelLoader
# code refactoring modelframe --> modelset package
# code refactoring shapebio --> shapebio + molsetbio packages
# code refactoring dissociates Mps.MpsShape from Mps as BioShape
# code refactoring removes Mps.Mpsmodel
# code refactoring Mps --> BioShapeCollection
# code refactoring greatly simplifies BioShapeCollection subclasses

# -----------------------------------------------------------------------------

#version=11.1.41

# bug fix for load with explicit spacegroup not respecting normalization choice
# bug fix for symop=nijk selecting base atoms when not appropriate
# bug fix for select specialposition non-functional
# bug fix for adding atoms but mads[] going stale
# slight redefinition of "special position"
# bug fix for structure loss on load append. (structure is supposed to be recalculated).
# adds language switching for Open / Save dialog boxes and full menuing system in Jmol application
# adds "structure" command -- structure [helix|sheet|turn|none] (atom expression)
# adds "save/restore structure" command

# -----------------------------------------------------------------------------

#version=11.1.40

# bug fix for backgroundModel and save state
# bug fix for load append with spacegroups causing atoms to be repositioned
# bug fix for anim playrev in loop mode causing animation to stall

# -----------------------------------------------------------------------------

#version=11.1.39

# several bug fixes:
#
# bug fix for mo data misreading in smol files
# bug fix for lcaoCartoon "s" giving incomplete spheres
# bug fix for select symop=3555 not giving proper atoms when load "" {444 666 0}
# bug fix for PDB files not supplying information about residues for the popup menu.
# bug fix in frame range 1.0 when file 1 has only one model.

# -----------------------------------------------------------------------------

#version=11.1.38

# bug fix for opaque triangles missing one pixel on right side when translucent objects are present.
# bug fix for label alignments sometimes not being saved properly in the state
# bug fix for animFrameCallback giving multiple callbacks -- still there, but identified now
# in terms of whether animation is on or not in the 7th parameter being 1 or 0:
#
# function animFrameCallback(app,frame,fileno,modelno,firstno,lastno,isRunning){...}

# -----------------------------------------------------------------------------

#version=11.1.37

# fixes bugs in draw and unicode label state definitions
# adds simplistic to text, including echo, label, hover, etc.
# fixes popup menu to better deal with multiple file context
# update of Turkish translation

# -----------------------------------------------------------------------------

#version=11.1.36

# build: renames applet files JmolApplet0*.jar and JmolAppletSigned0*.jar
#
# bug fixes for isosurface in multi-file environment
#
# bug fix and additional work in relation to translations
#
# zoomTo (atom expression) 0
#
# with options
#
# zoomTo (atom expression) 0+n
# zoomTo (atom expression) 0-n
# zoomTo (atom expression) 0*n
# zoomTo (atom expression) 0/n
#
# also
#
# moveTo timeSec {x y z w} (atom expression) 0 [zoom factor]
# and
# moveTo timeSec {x y z w} 0 transX transY (atom expression) 0 [zoom factor]
#
# where [zoom factor] is x, where x > 0
# or
# [0] [[+ | - | * | /] x]
#
#
# app fix for Edit...preferences not properly refreshing for axes and boundbox

# -----------------------------------------------------------------------------

#version=11.1.35

# fix for x = {...}.resno and {...}.groupID
# fix for select resno=-1
# first version of pt_BR translation

# -----------------------------------------------------------------------------

#version=11.1.34

# language submenu

# -----------------------------------------------------------------------------

#version=11.1.33

# bug fixes -- draw state, menu not updating, language submenu

# -----------------------------------------------------------------------------

#version=11.1.32

# adds capability to define a property for selected atoms:
#
# select xxx
# property_x = n.m

# -----------------------------------------------------------------------------

#version=11.1.31

# adds capability to read data from selected fields (white-space delimited columns) in a file
#
# propertyDataField = 0 # no fields -- just read tokens
# propertyDataField = 2 # data are in field 2 (second from the left)
# propertyAtomNumberField = 1 # data must match atomNo in field 1 and will be in
# the field specified by propertyDataField

# -----------------------------------------------------------------------------

#version=11.1.30

# full support for switching languages, including a new "language" menu item
#
# Jmol.js:
#
# jmolSetCallback("language", "de")
#
# Jmol scripting:
#
# language = "de"
#
# Menu:
#
# new language submenu with checkboxes.
#
# allows for efficient specific file reader options for the applet (particularly)
#
# adds _spinning variable
#
# adds LOAD xxx::myfile xxx indicating file type xyz, mol, etc.
#
# not important generally.
#
# adds PQR reader option, at least for PDB2PQR generated output
#
# better spin control during zoomTo and moveTo
# spinning now detects that a zoomTo or moveTo operation is occurring
# or the user is manipulating the model with the mouse, and pauses 1 second
# for that operation to complete before resuming spinning
#
# hover now is turned off during spinning or user manipulation of the model
#
# zoomTo and moveTo the same location changed to no time delay

# -----------------------------------------------------------------------------

#version=11.1.29

# code: totally reorganized isosurface code; new org/jmol/jvxl packages
#
# adds (1) isosurface functionxy "file:data.dat" ...
# adds (2) isosurface functionxy "functionName" {x0 y0 z0} {-ni ...} ...
# adds (3) isosurface functionxy "functionName" {x0 y0 z0} {-ni ...}{-nj ...} ...
#
# (1) "file:" allows reading of xy data from files for graphing f(x,y)
# (2) ni<0 indicates JavaScript functionName will return a single string that
# should be parsed for numeric data.
# (3) ni<0, nj<0 indicates that JavaScript will fill the fourth parameter
# of the function with an array of f[nX][nY] data values:
#
# Jmol:
#
# isosurface s1 functionXY "xyData" {-2 -2 -2} {21 0.1 0 0} {21 0 0.1 0} {21 0 0 0.1}
#
# JavaScript: (slow)
#
# function xyData(app, x, y) {
# return func(x, y)
# }
#
# Jmol:
#
# isosurface s2 functionXY "xyDataAsString" {-2 -2 -2} {-21 0.1 0 0} {21 0 0.1 0} {21 0 0 0.1}
#
# JavaScript: (much faster)
#
# function xyDataAsString(app, nX, nY) {
# var s
# for (var i = 0; i < nX; i++)
# for (var j = 0; j < nY; j++)
# s += "x_"+i+"\ty_"+j+"\t"+func(i,j)+"\n"
#
# //non-numeric formatting allowed but not necessary
#
# return s
# }
#
# Jmol:
#
# isosurface s3 functionXY "xyDataAsArray" {-2 -2 -2} {-21 0.1 0 0} {-21 0 0.1 0} {21 0 0 0.1}
#
# JavaScript: (very fast)
#
# function xyDataAsArray(app, nX, nY, fxy) {
# for (var i = 0; i < nX; i++)
# for (var j = 0; j < nY; j++)
# fxy[i][j] = func(i,j)
# }
#
# (2) and (3) are very fast; (1) is the original method, but it is slow.
#
# MAYSCRIPT expanded
#
# for the Wiki or any application where absolutely no JavaScript
# is to be allowed, simply remove the MAYSCRIPT parameter, which
# now covers all aspects of JavaScript interaction from within Jmol
#
#
# adds applySymmetryToBonds (default: FALSE)
#
# applySymmetryToBonds
#
# When set TRUE, this flag instructs Jmol when applying symmetry
# to atoms, as in "load xxx.cif {1 1 1}", to also apply symmetry
# to the bonds indicated in the file. The flag is useful when
# normal Jmol autobonding would not properly connect atoms, but
# the model is "molecular" -- the base atom coordinates are correct
# for whole molecules. The flag should NOT be used in cases where
# the application of symmetry operations creates new bonds that
# were not present in the original set, as for quartz.cif, where
# there is only one bond initially, and after applying symmetry
# new bonds are created that are between atoms that were created
# using two different symmetry operations.
#
# adds isosurface HOMO/LUMO [+/- n]
#
# better isosurface plane rendering, especially in regard to meshes
# bug fix in isosurface contour -n going WAY back to before 10.9.60
# refactoring of all isosurface-related classes
# support for Spartan MO HOMO
#
# adds isosurface POCKET [cavity] sasurface
# adds isosurface INTERIOR [cavity] sasurface
#
# adds load TRAJECTORY -- for a single file with multiple models all with
# the same number of atoms. Atom locations can also be updated on the
# fly using the data statement.
#
# adds TRAJECTORY n command -- like FRAME or MODEL, but never more
# than one model at a time displayed, because there is only one set
# of atoms.
#
# adds script: option for callbacks set from within Jmol. That is, callbacks
# can either be to host page JavaScript functions or to Jmol scripts. This
# will allow interactive sessions without external JavaScript.
#
# set pickcallback "script: script doCallback.spt"
#
# adds resizeCallback because certain positioning of echos and sizing of the
# structure may require method intervention after the resizing
#
# adds translucency for echo and hover, both text and backgrounds
#
# adds echo script to defined state
#
# adds hourglass cursor during MO/Isosurface operations
#
# fixes inoperative "set pickingstyle measures on"

# -----------------------------------------------------------------------------

#version=11.1.28

# adds
#
# a = script("some script command")
# a = javascript("some javascript")
#
# putting output into a from commands such as "show" or "getProperty", for instance.
#
# reinstates tempManager properly.
#
# adds support for CAChe CSF files with MOPAC (AM1, PM3, etc.),
# Density Functional, and Extended Huckel Gaussian/Slater-based molecular orbitals.
#
# CHANGES DEFAULT RENDERING FOR MOLECULAR ORBITALS TO: MESH NOFILL FRONTONLY
#
# adds MOPAC 2007 graphf output reader (gpt2 files, MOPAC molecular orbitals)
# based on the VERY latest version (not released yet), which includes
# "MOPAC-Graphical data" on the first line, character index 6.
#
# adds
#
# mo HOMO [+/- n]
# mo LUMO [+/- n]
#
# fixes bugs found by FindBugs:
#
# labels: default z setting for labels (set labelFront, set labelGroup, set labelAtom)
# was not being recorded properly
# move: with slab or zoom was doing integer math
# GhemicalMMReader -- was incorrectly assigning aromatic to bond type 4 via fall-through of switch
#
# adds xodydata reading of "boundary" as unitcell
# enhances default axis rendering for axes unitcell
#
# adds expanded isosurface-related commands:
#
# draw list
# isosurface list
# lcaocartoon list
# (mo list) -- not particularly useful
# pmesh list
#
# Listing gives id, number of vertices, number of polygons, visibility,
# and title (usually the command that was given that created this isosurface)
#
# CHANGED BEHAVIOR FOR ISOSURFACE COMMAND WITHOUT ID INDICATED:
#
# Now if no ID is indicated, the previous ID is used for all commands
# EXCEPT "isosurface delete", which deletes all isosurfaces.
#
# This is a change from Jmol 10.2 and 11.0, where if you leave
# off the ID, a new isosurface is created.
#
# This was a needed change to prevent unwanted multiple isosurfaces.
#
# CHANGED BEHAVIOR FOR ISOSURFACE DEFAULT COLOR
#
# The default isosurface color no longer changes shade among 5 possible shades.
# That was necessary only because it was easy to mistakenly make multiple
# isosurfaces that otherwise would look the same.

# -----------------------------------------------------------------------------

#version=11.1.27

# fixes two state bugs:
# 1) dots/geosurface not being saved properly in state
# 2) animation parameters not being saved properly in state

# -----------------------------------------------------------------------------

#version=11.1.26

# fixes two nasty bugs relating to isosurfaces and JVXL files.
# -- JVXL files created from molecular orbitals will show up with no color
# in 11.1.0 - 11.1.25 because of a missing number in the definition line :(
# -- JVXL files created from molecular orbitals will show unwanted cross-over
# surfaces from + to -.

# -----------------------------------------------------------------------------

#version=11.1.25

# --fully dissociates geosurface from dots;
# --allows coloring and transparency of geosurface
# similarly to the way stars are colored

# -----------------------------------------------------------------------------

#version=11.1.24

# refactored Geodesic3D, Dots, DotsRenderer
# independent dots/geosurface
#
# isosurface CAVITY

# -----------------------------------------------------------------------------

#version=11.1.23

# fixes a number of bugs, some critical
#
# adds isosurface CAVITY x.xx -- a new way to depict the cavities of
# a molecule in terms of color.

# -----------------------------------------------------------------------------

#version=11.1.21/22

# adds
#
# load file "=xxxx" and set loadFormat "http://....../%FILE.....
# load files ..... # just a cleaner version of loading multiple files.
# load append ..... # APPENDS the file(s) or model(s) as new frames onto the current set.
# data append ..... # same thing, but inline
#
# isosurface MODEL n
# pmesh MODEL n
# isosurface within x.x (what)
#
# Introduces "real" color translucency
#
# color xxxx translucent N
#
# where N is -1 to 9.
#
# OR OR
# translucent -1 same as Jmol 10.2
# translucent 0.0 opaque
# through
# translucent 1.0 transparent (invisible)
#
# translucent 2 0.125 32 1/8 translucency (slightly translucent)
# translucent 3 0.25 64 2/8 translucency
# translucent 4 0.375 96 3/8 translucency
# translucent 5 0.5 128 4/8 translucency (default)
# translucent 6 0.625 160 5/8 translucency
# translucent 7 0.75 192 6/8 translucency
# translucent 8 0.825 224 7/8 translucency (very sheer)
# translucent 9 1.00 255 8/8 transparent (invisible)

# -----------------------------------------------------------------------------

#version=11.1.20

# cleans up axes/boundbox/unitcell business
#
# allows for individually colored axes:
#
# color axis1 ...
# color axis2 ...
# color axis3 ...
# color axes ... (of course)
#
# and these objects are considered more like background --
# colors and sizes persist past file load
#
# to turn on and off without messing with size, just use
#
# showAxes = true
# showBoundBox = true
#
# etc.

# -----------------------------------------------------------------------------

#version=11.1.19

# allows comparison of user-defined atom properties in SELECT:
#
# select property_myprop < 1e-5;
#
# and
#
# x = {carbon}[5].property_test
# x = {carbon}.property_test.min
# x = {carbon}.property_test.max
#
# etc.
#
# This is it! :)

# -----------------------------------------------------------------------------

#version=11.1.18

# introduces user-definable atom properties that can be used
# to color isosurfaces:
#
# x = load("file.dat");
# isosurface variable x # simple 100% vdw radius mapping
#
# select 1.3
# data "property_myprop @x"
# isosurface property_myprop
#
# allows isosurface mapping of general atom properties:
#
# isosurface sasurface colorscheme bwr map property temperature
#
# adds "bwr" colorscheme as opposed to "rwb", which I think is backward.
#
# isosurface -- now supports APBS ( )
# molecular electrostatic potential output files
#
# write -- modified to allow unquoted filename in
# write isosurface file.name
#
# jvxl 1.0 -- adds ANGSTROMS flag on line with # of atoms (line 3)

# -----------------------------------------------------------------------------

#version=11.1.17

# deprecation of SET
# ------------------
#
# The "SET" command is no longer necessary. Anything that could have
# been set using "SET x .... " can now be set using
#
# x = ....
#
# This allows for a much cleaner interface because we simply make
# settings in a normal sort of way:
#
# axes on
# axes = molecular
#
# measures = angstroms
#
# It will take a bit more to make it all consistent, but the idea
# is that there are then some special reserved variables that
# mean something special when set, like "bondmode"
#
# This build allows for the applet to be "bare-bones" -- only the
# essential classes included in the Jar file; others never included
# or possibly in accompanying jar files, such as, perhaps, JmolPopupMenu.jar,
# JmolNavigation.jar, JmolBio.jar, Jm olSurface.jar, JmolXtal.jar, etc.
#
# Then a developer can slim down the download. The minimum is 697K,
# about 58% of the full package. All that gets you is atoms, bonds,
# and measures.

# -----------------------------------------------------------------------------

#version=11.1.16:

# First incompatibility found:
#
# set echo myecho (atomno=3) or (atomno=5)
# 1) adds two new modifiers:
# .min
# .max
#
# as in:
#
# x = {*}.bonds.length.max #the longest bond length
# x = {*}.atoms.max #the last atom
#
# 2) extends find() to sets of lines. For example:
#
# longLine={*}.bonds.label("%=, %LENGTH").lines.find({*}.bonds.length.max)
# message @longLine
# longest = longLine%(longLine.find(",")-1)
# b = {*}.bonds[longest]
# select b_set;color bonds yellow
#
# NOTE: _set removed in 11.3.41:
# select @b;color bonds yellow
#
# -----------------------------------------------------------------------------

#version=11.1.15:

# APPLICATION: adds undo/redo to a fixed depth of 50 commands
#
# TYPE CONVERSION
#
# We have eight different variable types now:
# boolean True/False
# integer 0, 1, 2, ....
# decimal 3.5, 3.25E-3
# string "test" "3.5"
# point {2.3 3.4 5.6} {0 1/2 1}
# plane {0 1 1 0}
# atomset {oxygen}
# bondset {oxygen}.bonds

# plane and bondset are new; arithmetic operations are not fully developed.

# These can be mixed and matched to good effect. Certain relatively
# intuitive rules apply. Usually the operand on the left sets
# the overall type, allowing for easy type conversion depending upon
# operand order:
# int + float:
# 0 + 3.6 ==> 3 (int on left rounds float on right)
# 3.6 + 0 ==> 3.6 (float on left sets result)
#
# int/float + string:
# 0.0 + "3.5" ==> 3.5 (string converted to float)
# 0 + "3.5" ==> 3 (string converted to float, then int)
# "3.5" + 0 ==> "3.50" (integer converted to string)
# "3.5" + 0.0 ==> "3.50.0" (float converted to string)
#
# 1.0 + {carbon}.xyz ==> 1 + distance from {0 0 0} to {carbon} center
# {carbon}.xyz + 1 ==> {carbon} center point offset by {1 1 1}
#
# x = {carbon}.xyz * {1 0 0} ==> (dot product)
#
# Now x is the average x coordinate of carbon
#
# Boolean expressions are a bit different in that the operators
# AND, OR, XOR, and NOT all require conversion to boolean UNLESS both
# operands are atom expressions, in which case these operate directly on the
# atom sets and return a new atom set, just like in SELECT.
#
# 3 and 0.5 ==> TRUE (both are nonzero)
# false OR 2.0 ==> true (2.0 is not 0, so it is TRUE)
# {oxygen} and {molecule=1} ==> all oxygen atoms in the first molecule
#
# x = ({oxygen} and {molecule=1}).xyz
#
# x is now the center point of all oxygen atoms in the first molecule
#
# In standard math, boolean TRUE evaluates to 1.0; FALSE evaluates to 0.0
#
# true + 2.0 ==> 3.0 ("TRUE" evaluates to 1.0 in math operations)
# 2 + true ==> 3 ("TRUE" evaluates to 1.0 and is then turned into an integer)
#
#
# ATOM EXPRESSION AUTOMATIC DEFINE
#
# When you set a variable to a value, and that value is a point, plane, or atom expression,
# then Jmol automatically registers the result as follows:
#
# points:
# x = "{x y z}"
#
# planes:
# x = "{x y z w}"
#
# atom expressions:
# x = n
# x_set = "({i j k ...})"
#
# NOTE: "set x" removed in 11.3.40:
# NOTE: _set removed in 11.3.41:
#
# x = {oxygen}.xyz
# y = {carbon}.xyz
# draw @x
# draw @y
# draw line1 @x @y
#
# and
#
# x = {carbon}[3][5]
# select @x
# color green

# x = {carbon}[3][5]
# select @x
# color green

#
# x = {carbon or oxygen}.bonds
# select BONDS @x
# color bonds green

#
# DATA() function and variable option for DATA command
#
# x = data({atomno < 10},"xyz")
# x = data({atomno < 10},"mol")
# x = data({atomno < 10},"pdb")
#
# data "model @x"
#
# write data t.xyz
# write data t.mol
# write data t.pdb
#
#
# Better BITSET implementation
#
# CHANGE: default string value for a bitset is now the ({n:m})
# string format, which can be used in numerous commands.
#
# To get the count within a string context, just use .size:
#
# x = "number selected is " + {selected}.size
#
# or force integer math:
#
# x = "number selected is " + (0 + {selected})
#
# merges math functions within(), connected(), substructure() into molecular math
#
# adds connected() both for finding atoms and for identifying bonds:
# xAtoms = connected(3, {carbon})
# xBonds = connected(1.3,2.5,"single", {carbon} {oxygen})
#
# adds
# x.atoms
# to go along with x.bonds
#
# adds distance({carbon},{oxygen})
# adds angle({carbon}[4],{oxygen}[3], {nitrogen}[2])
#
# angle function accepts from three or four
# atom expressions or XYZ coordinates and returns a decimal number for
# the distance, angle, or dihedral relating these points.
# When more than one atom is involved, average positions are used.
#
# Note that when more than one atom is involved in a set,
# the following are different:
#
# x1 = {molecule=1}.distance{molecule=2}
# x2 = {molecule=1}.xyz - {molecule=2}.xyz
#
# x1 is a NUMBER that is the "average distance measured
# from each molecule 1 atom to the average molecule 2 position"
# x2 is a point representing the VECTOR from the "average position of molecule 2"
# to the "average position of molecule 1"
#
# The following are all equivalent:
#
# x3 = {molecule=1}.xyz.distance{molecule=2}
# x4 = 0.0 + ({molecule=1}.xyz - {molecule=2}.xyz)
# x5 = ({molecule=1}.xyz - {molecule=2}.xyz).distance{0 0 0}
# x6 = distance({molecule=1} {molecule=2})
#
# They are all the distance from the center of molecule 1
# to the center of molecule 2
#
#
# x = load("filename")
#
# The string data in the file are loaded into the string.
# If the file does not exist, then the string contains the error message.
#
#
# Implements ({i j:k m n}) bitset option across all commands
#
# RESET varName
#
# reset varName # clears that variable definition
#
#
# "UNSPECIFIED" and "QUADRUPLE" BOND TYPES
#
# An additional bond type is now avaiable: "UNSPECIFIED".
# This shows up in the MOL2 reader and may be selected for and modified using, for example:
#
# select connected(unspecified)
# color bonds red
#
# or
#
# select connected(unspecified)
# connect (selected) single modify
#
# In addition, we now can depict quadruple bonds.

# -----------------------------------------------------------------------------

#version=11.1.14:

# DYNAMIC MEASUREMENTS
#
# Now that we can move atoms so easily, we don't want those measurements getting stale.
#
# set dynamicMeasurements
#
# allows measurements to be recalculated on the fly.
#
#
# MEASUREMENT FORMAT STRINGS
#
# Measurement format strings can be set using
#
# measure "format string..."
#
# where the format string may have the following keys:
#
# %= 1-based index
# %VALUE the value of the measurement
# %UNITS the units for the measurement
# %x1 atom property "x" for atom 1
# %x2 atom property "x" for atom 2
# %x3 atom property "x" for atom 3
# %x4 atom property "x" for atom 4
#
# for example:
#
# measure "%a1 -- %VALUE %UNITS --- %a2"
#
#
# MATH OPERATOR PRECEDENCE AND PARENTHESES
#
# Jmol 11.1.14 supports full standard operator precedence and parentheses
# in IF, SET, and %{} expressions
#
# degUnsat = ({carbon} * 2 + {nitrogen} + 2 - {hydrogen}) / 2
#
#
# BRACES INDICATE ATOM EXPRESSIONS
#
# Use {} in IF, SET and %{} for designating atom expressions.
# We are still using () for "embedded expressions" in all other commands.
#
# nOxygen = {oxygen}
# xOxygen = {oxygen}.x
# ptOxygen = {oxygen.xyz}
#
# a = {oxygen}.temperature
# message %{{carbon}.x}
# if {O22}.bondCount > 2;goto ...
#
# but
#
# draw line1 (atomno=2) (atomno=3)
#
#
# ATOM EXPRESSION ITEM SELECTOR [n]
#
# In SET, IF, and %{ } in MESSAGE and ECHO you can now specify a subset of the
# atom expression.
#
# x = {carbon}[3] # the third carbon atom
# x = {carbon}[3][5] # the third through fifth carbon atoms
# x = {carbon}[3][0] # the third through last carbon atoms
#
# This also works in standard select expressions, but using () instead:
#
# select (carbon)[3] # the third carbon atom
#
# and anywhere an embedded expression might be found:
#
# measure ((_C)[1]) ((_C)[2])
#
#
# POINTS IN IF, SET, and %{}
#
# Points in IF, SET, and %{} can be designated using the standard {x y z}
# notation WITHOUT commas. This is because we have to distinguish between
# atom expressions {1,2,3} and coordinates {x y z}, and this seems to me the
# simplest way to do it. (Comma means "or" in atom expressions.) In all other
# instances, the commas are fine, including "SET UNITCELL" and "SET DEFAULTLATTICE".
#
# x = {1 1 0} + {oxygen}.xyz
#
# { }.distance ATOM PROPERTY FOR SET, IF, and %{}
#
# d = {oxygen and * /1}.distance{oxygen and * /2}
# set echo top left
# echo the O-O distance is %{{oxygen and * /1}.distance{oxygen and * /2}}
#
# message %{{atomno=3}.distance{atomno=4}}
# message %{{atomno=3}.distance{1/2 1/2 1/2}}
#
#
# { }.label "xxxx" ATOM PROPERTY FOR IF, SET, and %{}
#
# The .label format provides a convenient means of delivering a wide range of
# atom-based data back to the user with whatever formatting is desired.
#
# x2 = {atomno=3).label("atom %a\t" + (atomno=3).xyz)
# xyzFile = "" + {selected}.size + "\n\n" + {selected}.label("%a %x %y %z")
#
#
# "....".lines
#
# The .lines operator splits a string into an array based on line termination.
#
# WRITE VAR "filename" (application only)
#
# pdbAtomData = {selected and not hetero}.label("ATOM %5i %-4a%1A%3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e%2C")
# pdbHeteroData = {selected and hetero}.label("HETATM%5i %-4a%1A%3n %1c%4R%1E %8.3x%8.3y%8.3z%6.2Q%6.2b %2e%2C")
# pdbFile = pdbAtomData + pdbHeteroData
# write VAR pdbFile "test.pdb"
#
# molFileData = "line1\nline2\nline3\n"+(""+{selected}.size)%-3+(""+{selected}.bonds.size)%-3+" 0 0 0\n"+{selected}.labels("%-10.4x%-10.4y%-10.4z %2e 0 0 0 0 0")+{selected}.bonds.labels("%3D1%3D2%3ORDER 0 0 0")
#
#
# GETPROPERTY "evaluate"
#
# You can now use getProperty to get expression information directly:
#
# getproperty "evaluate" "{*}.xyz"
#
# or on a web page the following returns a valid XYZ file for molecule 1:
#
# var info = jmolGetPropertyAsJavaObject("evaluate", '"" + {molecule=1} + "\n\n" + {molecule=1}.label("%a %x %y %z")')
#
#
# SELECTED ATOMS FROM ATOM EXPRESSIONS
#
# You can select atoms from an atom expression using [n].
# "[0]" means "and everything after".
#
# x = {atom expression}[3].ident
# x = {atom expression}[3][0].xyz # 3 and after (average position)
# x = {atom expression}[3][5].x # 3-5 (average x)
#
#
# SELECTED BONDS FROM EXPRESSIONS
#
# You can select bonds from an atom expression
#
# x = {atom expression}.bonds.ident
# x = {atom expression}.bonds[3].ident
#
#
# BOND INFORMATION
#
# You can specify how to label a set of bonds using format strings.
# Numbers are currently in Angstroms. Keys are
#
# %# sequential number
# %= file 1-based index
# %ORDER the bond order
# %TYPE the bond type
# %LENGTH the bond length
# %x1 atom property "x" for atom 1
# %x2 atom property "x" for atom 2
#
# The special atom properties %D1 and %D2 give sequential numbers for the
# atoms FOR THIS SET OF BONDS. This is so that a proper subfile of type MOL
# could be generated.
#
# x = {atom expression}.bonds[3].label("%# %3ORDER %TYPE %a1 %a2 %6.3LENGTH")
#
#
# EXPANDED MODULUS % OPERATOR IN IF, SET, AND %{}
#
# Usually modulus is reserved for integer math, so we
# extend that here to add some useful "modulus-like" capability:
#
# string modulus for trimming and padding
# "test" %3 ==> left trim: "tes"
# "test" %6 ==> right pad: "test "
# "test" %-3 ==> right trim: "est"
# "test" %-6 ==> left pad: " test"
#
# float modulus for rounding and scientific notation
# 3.5456 %3 ==> "3.546" (STRING!)
# 3545.6 %-3 ==> "3.55E+3" (STRING!)
#
# 0.0 + 3.5456 %3 ==> 3.546 (float)
# 0.0 + 3545.6 %-3 ==> 3550.0
#
# point modulus for getting base unit cell equivalent position
# {3/2 1/2 1/1} % 0 ==> {1/2 1/2 0}

# -----------------------------------------------------------------------------

#version=11.1.13:

# DATA "coord set"
# invertSelected POINT ....
# invertSelected PLANE ....
# invertSelected HKL ......
# rotateSelected ....
# rotateSelected spin ....
# full state support for "tainting" atom positions using translateSelected or invertSelected
#
# set allowRotateSelected # then use ALT-LEFT for rotating just the selected molecule
#
# this all definitely needs some work and discussion in terms of user interface via mouse
#
#
# write coords xxxx.spt
# load xxxx.spt # minimal -- just coord.
# script xxxx.spt # this is the full state load
#
# x = (some atom expression).atomProperty -- takes an average if more than one atom
# for example:
#
# x = (* /1).temperature
# x = (C5).bondcount
#
# note that you can even say:
# set echo top left
# echo average position= {%{(selected).x},%{(selected).y},%{(selected).z}}
#
# and it will AUTOMATICALLY update with new values as you select different atoms.

# -----------------------------------------------------------------------------

#version=11.1.12:

# app fix for console entry messing up cursor position;
# allows for scripting during pause or interrupt of running script using ! as first character of script
# new: within(x.x,plane,$plane1)
# fix for "draw off" not recorded in save state
# fix for within(integer,...) bug using RasMol units
# fix for _modelnumber showing up as 2001
# reconfigures _modelNumber as x.y for single models; x.x - y.y for range
# adds _currentFileNumber
# adds _currentModelNumberInFile
# disallows user setting of variables with _ as first character
# adds @variableName in any command
# adds frame x.x - y.y
# adds frame 0.0
# adds frame range x.x - y.y
# adds file command
# adds select file=
# tunes select model=