Jmol Code

Fah

OK, a new idea for applet synchronization.
test is at
http://www.stolaf.edu/people/hansonr/jmol/test/json/sync.htm

It's not fully articulated, but the basic idea being tested
here is direct applet-applet communication via a static appletRegistry

Implementation, using Jmol-new.js:

function jmolSync(mode, targetSuffix) {
_jmolCheckBrowser();
if (targetSuffix == "all") {
with (_jmol) {
for (var i = 0; i < appletSuffixes.length; ++i) {
var applet = _jmolGetApplet(appletSuffixes[i]);
if (applet) applet.syncScript(mode);
}
}
} else {
var applet=_jmolGetApplet(targetSuffix);
if (applet) applet.syncScript(mode);
}
}

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.

Just a start. All I have time for today.

fixing compiler not trapping errors. Adds tokenNext(int aToken)

friendlier file read when amino group atoms are WAY out of order.

fixed error in RasMol HBond calculation.
(N-H bond was being calculated 25% too long
as the C-O distance instead of the RasMol
1.0 Angstroms).

fix for too long hydrogen bonds

(1) adding range to monitor/measure command:

monitor <min_dist> <max_dist> ALL (atom set) (atom set)....

This allows for better control over measurements.

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:

monitor 1.2 2.0 (carbon) (oxygen)
monitor ALL (atomno=1) (atomno=2)

Note that unless otherwise specified, all matching
criteria in ALL frames are generated, thus allowing
for "animated" measures.

(2) added "nm" and "pm" to list for set measurement

Fah

Fah

Fah