changes.txt

Jmol是一个使用java语言编写的开源的免费三维分子显示工具,用于分子模型的浏览和编辑

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

#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 <module> 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