Commit by hansonr :: r17211 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties:

version=12.3.27

# new feature: [menu] vibration [*,/] 2
# new feature: XSF isosurface reader
# new feature: load CENTROID (only complete molecules having cenroid in unit cell)

# bug fix: write PNGJ broken in 12.3.26
# bug fix: 12.3.26 breaks Jmol/JspecView connection
# bug fix: draw pointgroup scale x.x -- changing x.x does not revise point group
# bug fix: reading of JVXL-version 1 (nonXML) files does not display colors
# bug fix: translate y 10 works, but translate Y 10 does not

Commit by hansonr :: r17210 /branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties:

version=12.2.27

# bug fix: draw pointgroup scale x.x -- changing x.x does not revise point group
# bug fix: reading of JVXL-version 1 (nonXML) files does not display colors
# bug fix: translate y 10 works, but translate Y 10 does not

Commit by hansonr :: r17209 /branches/v12_2/Jmol/src/org/jmol/ (3 files in 2 dirs):

version=12.2.27_dev

# bug fix: draw pointgroup scale x.x -- changing x.x does not revise point group

Commit by hansonr :: r17208 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs):

version=12.3.27_dev

# bug fix: draw pointgroup scale x.x -- changing x.x does not revise point group

Commit by hansonr :: r17206 /trunk/Jmol/src/org/jmol/ (16 files in 8 dirs):

version=12.3.27_dev

# new feature: [menu] vibration [*,/] 2
# new feature: XSF isosurface reader
# new feature: load CENTROID (only complete molecules having cenroid in unit cell)
# bug fix: write PNGJ broken in 12.3.26

Commit by hansonr :: r17203 /trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java:

Castep reader H:xxx atom names

Commit by hansonr :: r17202 /trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java:

version=12.3.27_dev

# bug fix: reading of JVXL-version 1 (nonXML) files does not display colors

Commit by hansonr :: r17201 /branches/v12_2/Jmol/src/org/jmol/ (2 files in 2 dirs):

version=12.2.27_dev

# bug fix: reading of JVXL-version 1 (nonXML) files does not display colors

Commit by hansonr :: r17200 /trunk/Jmol/src/org/jmol/viewer/ (Jmol.properties Viewer.java):

version=12.3.27_dev

# bug fix: translate y 10 works, but translate Y 10 does not

Commit by hansonr :: r17199 /branches/v12_2/Jmol/src/org/jmol/viewer/ (Jmol.properties Viewer.java):

version=12.2.27_dev

# bug fix: translate y 10 works, but translate Y 10 does not

Commit by hansonr :: r17198 /trunk/Jmol/src/org/jmol/viewer/ (Jmol.properties Viewer.java):

version=12.3.27_dev

# bug fix: 12.3.26 breaks Jmol/JspecView connection

Commit by hansonr :: r17194 /trunk/Jmol/src/org/jmol/smiles/package.html:

No log message

Commit by hansonr :: r17193 /branches/v12_2/Jmol/src/org/jmol/viewer/Jmol.properties:

for release

Commit by hansonr :: r17192 /trunk/Jmol/src/org/jmol/ (2 files in 2 dirs):

version=12.3.26

# bug fix: select 1.0 fails
# bug fix: COMPARE broken
# bug fix: Writing file into .jmol file after reading it from another results in the whole
# zip file being copied into the new .jmol file.
# new feature: Jmol SMARTS searching can include full Jmol selection syntax within
# an atom primitive using the "atomType" option and "select:":
#
# load caffeine.xyz
# print {*}.find('{c}$(select _N and connected(2, _C))')
#
# new feature: model ID "xxx" (or frame ID....)
# -- sets the model's ID to "xxx"
# -- can be used to switch to that model using model "xxx"
# -- can be targeted file-specifically using "filename#xxx"
# -- if two models have the same ID and no filename is given,
# then the first model found becomes the current model
# -- used for correlating non-Jmol synced applets
# new feature: script "t.spt"(...variables...)
# -- quotes are optional if file name does not include " " or "("
# -- "script" is optional if file name is quoted or ends with ".spt"
# -- allows passing variables to a script much like a function call
# -- variables will be in VAR named "_arguments" within that script (like JavaScript)
# -- _arguments, like all arrays in Jmol, is 1-based, 0-terminated (unlike JavaScript)
# -- _arguments is unsettable by the user
# -- for standard script functions, _arguments will be []
#
# -- for example, if test.spt is simply "show _arguments", then
# load $caffeine
# test.spt({*}, {*}.xyz ,35, [1,2,3,4])
#
# will output:
#
# _arguments = [({0:23}),{-0.086670786 -0.02787502 5.6667876E-4},35,[1,2,3,4]]
#
# new feature: set forcefield "UFF" or "MMFF"
# -- default is MMFF
# -- automatically switches to UFF if atom types cannot be set
# -- minimizationCallback reports actual force field used
#
# new feature: set energyUnits kJ|kcal
# new feature: set DOTSCALE (default 1) also allows isosurface/mo mesh scaling
# new feature: antialiased display and image creation uses larger mesh scaling for cleaner look
#
# code: adding empirical rules to MMFF94 calculation
#
# checkmm.spt;checkAllEnergies
#
# checking calculated energies for 761 models
# 1 COMKAQ E= -7.3250003 Eref= -7.6177 diff= 0.2926998
# 2 DUVHUX10 E= 64.759995 Eref= 64.082855 diff= 0.6771393
# 3 FORJIF E= 35.978 Eref= 35.833878 diff= 0.14412308
# 4 JADLIJ E= 25.104 Eref= 24.7038 diff= 0.4001999
# 5 PHOSLA10 E= 111.232994 Eref= 112.07078 diff= 0.8377838
# 6 PHOSLB10 E= -93.479004 Eref= -92.64081 diff= 0.8381958
#
# for 761 atoms, 6 have energy differences outside the range -0.1 to 0.1
# with a standard deviation of 0.05309403
#
# bug fix: nested SMARTS strings can give incorrect response
# load data "mol"
# C:/jmol-dev/bobtest/t6.mol
# __Jmol-12_05191218593D 1 1.00000 0.00000 0
# Jmol version 12.3.26 2012-05-19 18:34 EXTRACT: ({0 3 4})
# 3 2 0 0 0 0 1 V2000
# 2.89480 4.81990 0.01710 N 0 0 0 0 0 0
# 3.52580 2.75730 -0.17290 N 0 0 0 0 0 0
# 3.94370 4.03730 -0.25710 C 0 0 0 0 0 0
# 1 3 2 0 0 0
# 2 3 1 0 0 0
# M END
# end "mol"
# select search("$([#7][#6]([#7&!$([#7][O])])=[#7])")
# show selected
# was returning 1 atom, but should be 0 (because there are only two N atoms!)
# bug fix: measurementUnits = "au" does not work

Commit by hansonr :: r17191 /branches/v12_2/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java:

version=12.2.26

# bug fix: select 1.0 fails

Commit by hansonr :: r17190 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties:

hold for model 1.0

Commit by hansonr :: r17189 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs):

No log message

Commit by hansonr :: r17188 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs):

load caffeine.xyz
print {*}.find('{c}$(select:_N and connected(2, _C))')

Commit by hansonr :: r17187 /branches/v12_2/Jmol/src/org/jmol/ (2 files in 2 dirs):

version=12.2.26

# bug fix: COMPARE broken
# bug fix: nested SMARTS strings can give incorrect response
# checkmm.spt
# checkmm("FOVRAJ")
# select search("/aromaticstrict aromaticdouble/$([#7v3][#6]([#7D3v3&!$([#7][O])])=[#7v4])") # no
# show selected
# was returning 1 atom, but should be 0
# bug fix: measurementUnits = "au" does not work

Commit by hansonr :: r17186 /trunk/Jmol/src/org/jmol/ (2 files in 2 dirs):

No log message