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

#  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!
#   -- <n> atoms selected!
#   -- atom picking:
#        Atom: xxx Group: xxx Chain: xxx Model: xxx Coordinates: x y z
#   -- script <exiting>
#   -- 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")

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