Jmol Code

FollowSymLinks added for the wiki

adding detail to getProperty("shapeInfo") and getProperty("ModelInfo")

(1) augmenting pmesh "inline" and draw to allow a friendlier
flow of data -- [x,y,z] -- really anywhere [,] are ignored.

(2) allowing for identifier access to draw objects as
[point1], [line1], etc., in square brackets. It's a simple,
clean method that doesn't require anything in the compiler.

examples:

http://www.stolaf.edu/people/hansonr/jmol/test/json/pmesh.htm

pmesh test1 "inline" "1 [0. 0. .5] 0";color pmesh white;pmesh test1 dots
pmesh test2 "inline" "2 [0. 0. 0.] [1. 0. 0.] 1 [3 0 1 0]";color pmesh orange
pmesh test3 "inline" "3 [-0.49, -2.8, -1.2] [-2.2, 0.80, 1.09] [1.89, 2.12, 0.42] 1 [4 0 1 2 0]";color pmesh yellow
pmesh test4 "inline" "4 [0., 0., 0.] [0., 2., 0.] [2., 2., 0.] [2., 0., 0.] 1 [5 0 1 2 3 0]";color pmesh translucent red
load caffeine2.xyz;draw triangle1 150 (atomno=1) (atomno=14) (atomno=15);draw line2 200 [triangle1] (atomno=9) (atomno=11);color draw translucent green
draw line1 120 (atomno=1) (atomno=2);color draw white
draw line1 300 (oxygen) (nitrogen)
draw triangle1 400
draw line1 100;draw triangle1 100
draw triangle1;color draw red;draw line1;color draw blue
draw line2 200 [triangle1] (atomno=9) (atomno=11);color pmesh green
draw square1 [1.0 1.0 1.0] [1.0 0.0 1.0] [0.0 0.0 1.0] [0.0 1.0 1.0]

just removing dangling debug comment I had forgotten to remove

fixes select resno < nnn problem.
created Atom.getResno() and Group.getResno()
as distinct from Group.getSeqcode().
Involves returning seqcode >> 8 instead of seqcode

Fah

adjustments to new "draw" command
oh, and I see I didn't commit Draw or DrawRenderer last time.

adds drawing support for points, lines, and planes (triangles and quadralaterals).

(1) new classes Draw and DrawRenderer

(2) new script command "draw" based on pmesh

draw line1 (atomno=1) (atomno=2)
#a line from atom 1 to atom 2

draw line1 120 (atomno=1) (atomno=2)
#a line from atom 1 to atom 2, scaled to 120%

draw point1 (all)
#geometric center of the model

draw point2 (oxygen)
#center of all oxygens

draw line2 1.0 1.0 1.0 3.0 3.0 3.0
#draw a line from (1,1,1) to (3,3,3)

just a start....

Bob Hanson

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.