Jmol just took a quantum leap in the area of scripting.
The following is a valid Jmol script, as of Jmol 11.3.23, which Nico
just released:
load data/caffeine.xyz;color background white;
function d(i,j)
return {atomno=i}.distance({atomno=j})
end function
var n = {*}.size
for (var i = 1; i < n; i = i + 1)
for (var j = i + 1;j <= n; j = j + 1)
var dis = d(i,j);
if (dis < 1.23)
print "short i-j: " + i + "," + j + " " + dis%2
measure {atomno=i} {atomno=j}
continue;
else if (dis < 1.77)
print "medium i-j: " + i + "," + j + " " + dis%2
var line = "line" + i + "_" + j
draw @line {atomno=i} {atomno=j}
break 1;
end if
end for
end for
No, it's not JavaScript. It's not Java. It's Jmol. Take a look and you
will see measure and draw commands in there.
I realize that it's hard to believe this is a Jmol script. But it is.
You get a sense of the ramifications of this when you take a look at
that d(i,j) function and the measure command being used or a bit further
down with:
var line = "line"+i+"_"+j
draw @line {atomno=i} {atomno=j}
Notice the {atomno=i} mixing of selection of atoms based on atomic
properties and math variables. I think this is really where the
interesting part is going to be.
Now we have macros, subroutines, functions, local variables, and several
new capabilities beyond the basic "if/else/endif" or "goto":
if
else if
else
end if
while
end while
for
end for
goto _label
message _label
function
end function
A bit more discussion may be found at
http://chemapps.stolaf.edu/jmol/docs/?ver=1.4
There could very well be a few more bugs to find, so if you go for this sort of
thing,
do look out for it misbehaving.
Looks like a whole new chapter or two in that book we were talking about.
Bob
--
Robert M. Hanson
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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