Miguel, here is the list of commits I have performed organized by topic:
Jmol Scripting
rendering
file loading
miscellaneous
JavaScript public applet methods
Jmol-new.js
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Jmol scripting
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connect <min distance> <max distance> <bond type> <radius> (source
atom selection) (target atom selection) with options NEW and EXISTS
measure <min distance> <max distance> (atom expr) (atom expr) ....
with ALL option (default is FIRST)
parameters are optional, but the ALL keyword is necessary if
the distances are omitted in order to designate that all
occurances within the atom sets are depicted. Examples:
measure 1.2 2.0 (carbon) (oxygen)
measure ALL (atomno=1) (atomno=2)
Note that unless otherwise specified, all matching
criteria in ALL frames are generated, thus allowing
for "animated" measures.
set measurement -- added "nm" and "pm" as equivalents to "nanometers"
and "picometers"
more frame/model/animation features, including:
frame next
frame prev
frame playrev
frame pause
frame play
frame play [start]
frame play [start] [end]
frame resume
frame range [start] [end]
animation play
animation pause
animation resume
These allow "tape-recorder" type action, with the ability to designate
a particular subset of the frames over which to iterate. Start and end
frames can be designated in either order. Richard Spinney suggested this.
[now we need a little tape recorder control applet to coordinate with!]
examples:
frame play 3
start from frame 3
frame play 3 10
start from frame 3 and play through frame 10
frame play 10 3
start from frame 10 and play through frame 3
frame pause
animation pause
pause animation
frame play
animation resume
start animation from current frame
define command change: Specifically in 'define' commands, the user may
redefine terms, but we throw up a clear warning as to possible effects
-- some commands (in this case frame) may not work properly after this
definition.
select visible
where "visible" defined as
(a) atom is displayed as spacefill, wireframe, star, dots, halo, or
vibration vector, or
(b) a RasMol group containing that atom is displayed in some form --
cartoon, trace, ribbon, rockets, meshribbon, backbone
pmesh augmented such that if the fileName is given as the string
"inline", then the next string is taken to be the equivalent of a
pmesh file contents. Optionally, \n can be replaced by | if desired.
e.g.
allows for some interesting capability, including the scripted
construction of points, lines, triangles, and rectangles at specific
coordinates. See
http://www.stolaf.edu/people/hansonr/jmol/test/json/pmesh.htm
load command now allows for multiple files; first parameter is any
string; next strings are taken as file names to load; considered
preliminary; not fully tested.
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rendering
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fixed /modelNumber display for non-PDB files
fixed restrict with backbone not behaving correctly
fixed %m error in label formats
fix for too long hydrogen bonds.
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file loading
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load allows for multiple files; first parameter is any string; next
strings are taken as file names to load; not fully tested.
embedded in a data file you can specify a "default" script to run by
having in the second line of either a MOL file or an XYZ file contain
(at any position) "#jmolscript:" followed by a valid script.
friendlier file read when amino group atoms are WAY out of order.
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miscellaneous
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fixed scripting from menu not calling callback functions;
fixed script compiler not trapping errors
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JavaScript public applet methods
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applet.getProperty()
applet.getPropertyAsString()
applet.getPropertyAsJSON()
applet.scriptCheck()
applet.scriptWait(), which returns all status messages as a JSON
string after running the script synchronously. Now one could combine
.scriptWait() and .getProperty() for some pretty interesting effects.
applet.loadInline(strModel,script)
polling option instead of callbacks. See
http://www.stolaf.edu/people/hansonr/jmol/test/json/callbacks.htm
applet.syncScript(mode, targetSuffix)
not fully articulated, but the basic idea being tested
here is direct applet-applet communication
where <mode> is one of:
"ON" --driver of synchronizations
"SYNC" --turn on and sync, but not as a driver
"OFF" --not synced (not quite working yet)
This uses a new public applet method, syncScript(), which
allows control of synchronization and passing of a reorientation script.
The method uses NO JavaScript -- the applets identify themselves
within a common registry and then talk directly to each other.
Part of the idea here is to experiment with this sort of direct
communication -- calling functions in a different applet.
I suspect there will be browser/platform issues.
-----------
Jmol-new.js
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new public Javascript functions:
void loadInlineScript(strModel,script,targetSuffix)
JSArray jmolGetStatus(strStatus,targetSuffix)
JSArray jmolGetPropertyAsArray(sKey,sValue,targetSuffix)
String jmolGetPropertyAsString(sKey,sValue,targetSuffix)
String jmolGetPropertyAsJSON(sKey,sValue,targetSuffix)
JavaObject jmolGetPropertyAsJavaObject(sKey,sValue,targetSuffix)
String jmolScriptWait(script, targetSuffix)
void jmolSync(mode, targetSuffix)
see http://www.stolaf.edu/people/hansonr/jmol/test/json/Jmol-new.js
---------------------------------------------------------------
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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