Faster, cleaner, smaler, more capabilities
https://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2013.3/Jmol%2013.3.6/
___JmolVersion="13.3.6"
JmolVersion="13.3.5_dev_2013.09.27"
code: careful attention to core functions yields results in 10% reduction
in core download size:
-- uncompressed(former)
gzipped
-- JSmol.min.nojq.js 134K 38K
-- core.z.js 1586K(1781K) 364K
-- corescript.z.js 378K (436K) 95K
-- TOTAL 2098K(2217K) 497K
(9.5% reduction)
-- JmolApplet0.jar 1038K 1005K
-- Thus, the "real" transfer size -- based on server-side gzipping -- is
half the size of Jmol/Java.
new feature: adds remote logging for applet and app via http:// and via
function for applet using
jmolApplet0._applet.viewer.setLogfile(function(data) {......})
new feature compare {1.1} {2.1} BONDS "smiles"
-- does flexible fit based on dihedrals.
-- does internal rotation even if ROTATION TRANSLATION are not given
(considered a possible bug)
-- concatenation of:
list = compare({1.1},{2.1},"smiles","BONDS")
rotate branch @list 1
compare {1.1} {2.1} SMARTS "smiles" rotate translate
so, for example:
load files "$tyrosine" "$lysergamide"
select 1.1; color bonds red
select 2.1; color bonds yellow
sm = "c1ccccc1CCN"
compare {1.1} {2.1} BONDS @sm rotate translate
new feature: show BEST ROTATION / show BEST VOLUME (better than
undocumented show rotation best, show rotation volume)
new feature: set animationMode "ONCE" "LOOP" "PALINDROME"
new feature: show animationMode; x = animationMode
new feature: CAPTURE command, including ROCK and SPIN
-- application and signed applet only (no JS)
-- creates animated GIF
-- uses ANIMATION FPS to determine play-back rate.
CAPTURE "filename"
-- starts capturing
-- uses ANIMATION MODE to determine looping
-- both PALINDROME and LOOP create looping; ONCE (default) does not
CAPTURE "filename" ROCK x|y|z degrees
-- does a clean rocking of the molecule about one of the three major
axes
-- axis and degrees optional; y 5 assumed
-- based on: rotate Y 10 10;delay 2.0; rotate Y -10 -10; delay
2.0;rotate Y -10 -10; delay 2.0;rotate Y 10 10;delay 2.0
-- uses LOOP mode
CAPTURE "filename" SPIN x|y|z
-- does a full spin of the molecule about one of the three major axes
-- axis optional; y assumed
-- based on: rotate Y 360 30;delay 15.0;
-- uses LOOP mode
CAPTURE off/on
-- temporarily disables/enables capturing
CAPTURE "" or just CAPTURE
-- end capturing
new feature: set drawFontSize // defaults to 14.0
FEATURE CHANGE: added bindings: "drag" and "up" -- may affect power users
who use BIND command
new: _center CTRL+SHIFT+LEFT+click
new: _reset SHIFT+LEFT+double+click
mouse actions include one (each) of:
SINGLE DOUBLE
LEFT MIDDLE RIGHT WHEEL
DOWN DRAG UP CLICK
for example:
SINGLE-RIGHT-CLICK
DOUBLE-LEFT-DRAG
defaults are SINGLE, LEFT, and CLICK
sequence is always:
down
(drag,drag,drag...)
up
(click) (only if no drag)
Any of these actions may be tapped using
bind "<some mouse action>" "<jmol action or script>"
Note that adding "+:" to an action
bind "<some mouse action" "+:<script...>"
does not replace the Jmol action, just supplements it.
$ show mouse
_assignNew LEFT+click assign/new atom or bond
(requires set picking assignAtom_??/assignBond_?)
_center CTRL+SHIFT+LEFT+click center
_clickFrank LEFT+click pop up recent context
menu (click on Jmol frank)
_pickConnect LEFT+click connect atoms (requires
set picking CONNECT)
_deleteAtom LEFT+click delete atom (requires set
picking DELETE ATOM)
_deleteBond LEFT+click delete bond (requires set
picking DELETE BOND)
_depth CTRL+SHIFT+LEFT+double+drag adjust depth (back
plane; requires SLAB ON)
_dragAtom LEFT+drag move atom (requires set
picking DRAGATOM)
_dragDrawObject SHIFT+LEFT+drag move whole DRAW object
(requires set picking DRAW)
_dragDrawPoint ALT+LEFT+drag move specific DRAW point
(requires set picking DRAW)
_dragLabel SHIFT+LEFT+drag move label (requires set
picking LABEL)
_dragMinimize LEFT+drag move atom and minimize
molecule (requires set picking DRAGMINIMIZE)
_dragMinimizeMolecule LEFT+drag move and minimize
molecule (requires set picking DRAGMINIMIZEMOLECULE)
_dragSelected ALT+SHIFT+LEFT+drag move selected atoms
(requires set DRAGSELECTED)
_dragZ SHIFT+LEFT+drag drag atoms in Z direction
(requires set DRAGSELECTED)
_navTranslate LEFT+drag translate navigation
point (requires set NAVIGATIONMODE and set picking NAVIGATE)
_pickAtom LEFT+click pick an atom
_pickIsosurface LEFT+click pick an ISOSURFACE point
(requires set DRAWPICKING
_pickLabel LEFT+click pick a label to toggle it
hidden/displayed (requires set picking LABEL)
_pickMeasure LEFT+click pick an atom to include
it in a measurement (after starting a measurement or after set picking
DISTANCE/ANGLE/TORSION)
_pickNavigate CTRL+SHIFT+LEFT+click pick a point or atom to
navigate to (requires set NAVIGATIONMODE)
_pickPoint LEFT+click pick a DRAW point (for
measurements) (requires set DRAWPICKING
_popupMenu CTRL+LEFT+down, RIGHT+down pop up the full
context menu
_reset SHIFT+LEFT+double+click, MIDDLE+double+click
reset (when clicked off the model)
_rotate LEFT+drag rotate
_rotateBranch SHIFT+LEFT+drag rotate branch around bond
(requires set picking ROTATEBOND)
_rotateSelected ALT+LEFT+drag rotate selected atoms
(requires set DRAGSELECTED)
_rotateZ ALT+LEFT+drag, SHIFT+RIGHT+drag rotate Z
_rotateZorZoom SHIFT+LEFT+drag, MIDDLE+drag rotate Z
(horizontal motion of mouse) or zoom (vertical motion of mouse)
_select LEFT+double+click select an atom (requires
set pickingStyle EXTENDEDSELECT)
_selectToggleOr LEFT+click if all are selected,
unselect all, otherwise add this group of atoms to the set of selected
atoms (requires set pickingStyle DRAG)
_setMeasure LEFT+double+click pick an atom to initiate
or conclude a measurement
_slab CTRL+SHIFT+LEFT+drag adjust slab (front plane;
requires SLAB ON)
_slabAndDepth CTRL+ALT+SHIFT+LEFT+drag move slab/depth
window (both planes; requires SLAB ON)
_slideZoom LEFT+drag zoom (along right edge of
window)
_spinDrawObjectCCW LEFT+drag click on two points to
spin around axis counterclockwise (requires set picking SPIN)
_spinDrawObjectCW SHIFT+LEFT+drag click on two points to
spin around axis clockwise (requires set picking SPIN)
_stopMotion LEFT+double+click stop motion (requires set
waitForMoveTo FALSE)
_swipe LEFT+drag spin model (swipe and
release button and stop motion simultaneously)
_translate CTRL+ALT+LEFT+drag, CTRL+RIGHT+drag,
SHIFT+LEFT+double+drag, MIDDLE+double+drag translate
_wheelZoom WHEEL zoom
bug fix: JSON NIO port SYNC broken
bug fix: print getProperty("image", "width=200;height=300;type=png") not
working
bug fix: write IMAGE "t.png" not working
bug fix: rotate -10 -10 not working
bug fix: mouse bindings not distinguishing DOWN/CLICK/DRAG/UP properly
bug fix: mouse bindings _center and _reset not working
bug fix: show MOUSE not including user-defined mouse bindings
bug fix: chains improperly selected in JSmol/HTML5
bug fix: JSmol/HTML5 not allowing drag-drop or file loading from a local
drive.
bug fix: JSmol/HTML5 not allowing WRITE FILE ?
bug fix: JSmol/HTML5 not allowing WRITE xxx.pdb, xxx.mol, etc
bug fix: platformSpeed persists but appears unreadable after loading a
state
bug fix: JavaScript version InputStreamReader not processing non-UTF data
correctly
bug fix: second reading of older PNG files with embedded script fails
due to improper png file caching
code: overhaul of image creation methods
code: continued refactoring of ScriptEvaluator to ScriptExt
code: refactoring to isolate LabelToken and Labels from core JavaScript load
code: refactoring, simplification of image output and export
-- folders created: org.jmol.image, org.jmol.dialog
-- JpgEncoder, Jpg64Encoder, PngEncoder brought to org.jmol.image
and made subclasses of ImageEncoder
-- PpmEncoder fixed
-- ImageEncoder stripped of all unnecessary ImageConsumer/producer
business
-- org.jmol.export.image.ImageCreator and parts of
org.jmol.viewer.stateCreator reorganized
into org.jmol.OutputManager, org.jmol.OutputManagerAwt, and
org.jmol.OutputManagerJS
-- clipboard functions moved into org.jmol.awt and org.jmol.awtjs2d
-- org.jmol.io.JmolOutputChannel now serves for just about all output
needs.
code: major simplification and consolidation of file I/O methods, including
exporters, using JmolOutputChannel class.
code: only FileOutputStream reference is one reference in org.jmol.awt.
code: code merge between 13.2 and 13.3 18 Sept 2013
code: major clean-up of ActionManager
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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