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

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

version=11.6.20

# bug fix: automatic adjustment for 5D (spherical) orbitals, especially for Spartan Smol reader
# bug fix: try/catch needed around rendering
# bug fix: animation/spin while script is rendering can cause Exception
# bug fix: MO rendering with antialiasDisplay information font incorrect
# bug fix: draw arrow/vector slightly overshoots end point

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

#version=11.6.19

# bug fix: isosurface/mo FRONTONLY not operative
# bug fix: MO calculations skips d2+ orbital due to integer division.
# bug fix: (application) measurement tool bar icon not toggling
# bug fix: "color MO" if executed twice can crash Jmol

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

#version=11.6.18

# bug fix: line raster not completing lines
# bug fix: (Application) meaurement table not updating properly
# bug fix: subtle MarchingSquares calculation error produces incorrect contours for mapped plane
# bug fix: isosurface TRIANGLES not turning off when isosurface cleared
# bug fix: remapping colors of translucent isosurface can have incorrect colors
# bug fix: isosurface sphere 1.0 map molecular  not working
# bug fix: MO calculation with selected atoms can fail 
# bug fix: Jmol in other applications not initialized the same way can cause null pointer exception loading file with symmetry

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

#version=11.6.17

# bug fix: Spartan reader reads MOs improperly when only a partials set of MOs is included in the file
# bug fix: Some Spartan files not reading: Compound Document not properly finding root directory block

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

#version=11.6.16

# bug fix: PDB load filter broken for ANISOU
# bug fix: isosurface plane improperly coloring nonmapped planes
# bug fix: Mopac graphf UHF files not read properly for beta orbitals, or can't read file

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

#version=11.6.15

# bug fix: set picking draw can lose focus during drag operation
# bug fix: {*}.formalCharge = 1 after {*}.formalCharge = -1 sets formal charge to -7 and exception
# bug fix: write command does not report full path to file written
# bug fix: Menu File|Open does not honor "start in" directory

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

#version=11.6.14

# bug fix: @~xxx({xxxx}) compiler bug
# bug fix: structure helix ({xx:yy}) compiler bug
# bug fix: user menu write povray/vrml/maya missing quotation marks in command

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

#version=11.6.13

# bug fix: user menu ...Text menus not translated

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

#version=11.6.12

# bug fix: protein-protein hydrogen bonds not calculated across biopolymer boundaries
# bug fix: quaternion straightness update

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

#version=11.6.11

# aargh -- forgot to upload file for 11.6.10

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

#version=11.6.10

# bug fix: vibrationperiod set to 0 if vibration off when state saved

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

#version=11.6.9

# bug fix: application -i option still gives message from "set xxxx"
# bug fix: some quaternions cannot be created from a 3x3, namely:
#   q = quaternion({1 2 -2}, {2 1 2}) = {0.57735026 0.57735026 0.0 0.57735026} (xyzw format)
# bug fix: ignoreError -- need not get error string
# bug fix: write image does not set mustRender
# bug fix: set debugscript and set loglevel do not act in script immediately 
# bug fix: translations of Console not implemented correctly
# bug fix: translation not disabled when messageCallback is present
# bug fix: script error messages not updating when language changed
# bug fix: MO scale
# bug fix: measure allConnected broken

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

#version=11.6.8

# bug fix: write .... @{...} fails
# bug fix: write .... @{...} can fail
# bug fix: write image CLIPBOARD broken
# bug fix: select {*.ca} (phi < select(y; {*.ca}; y.resno = _x.resno + 1).phi) fails when atomExpression is ({})
# bug fix: applet compilation error not sent in termination message
# bug fix: build javax package does not include Matrix4d.class, AxisAngle4d.class
# bug fix: compilation of myfunc({1 2 3}) fails
# bug fix: hover watcher occasional uncaught exception

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

#version=11.6.7

# bug fix: quaternion straightness update
# bug fix: applet improperly reporting status of "quiet" commands
# bug fix: stereo not in state
# bug fix: stereoDegrees parameter not reported correctly

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

#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 <param> 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