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=11.5.26

# 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 f