Well, wouldn't you know it? What started out as a simple idea turned into
quite a challenge. But I think I'm done, and I am very interested in
extensive testing. Sorry, Angel -- you may have to rewrite your book!
OK, so there are two major new pieces in Jmol 11.7.40 (see files in
http://chemapps.stolaf.edu/jmol/docs/examples-11)
1. Major clean-up of the code in regard to atom properties. We had three
different sections of code all doing about the same thing - getting atom
properties:
label %x
select atomno > 3
print {*}.atomno.all
Now these are all consolidated, and as I did that I tried to fill out the
matrix shown at
http://chemapps.stolaf.edu/jmol/docs/index.htm?ver=11.8#atomproperties. I
think there is some checking to do of that, but it's pretty complete. I
hadn't realized there were quite so many atom properties! You will see one
very new thing:
label %[atomname] %[occupancy]
in addition to the older
label %a %q
So there's no absolute limit to the number of such parameters. You will see
quite a few new options there that weren't there last week.
2. In line for and if. In Java and JavaScript you can do in-line IF
commands:
x = (something == this ? that : theOtherThing)
And in Excel you can use:
if(a3 > 3, H34, D100)
Well, it's a little different in Jmol, but you can now do it as well -- just
use semicolons to separate the parts. (question marks and colons and commas
are already in use):
ans = if( ifTrue ; thenThis ; elseThis )
When I am working with Jmol I tend to do a lot with lists. My undergraduate
researcher, Steven, and I were finding this morning that there could be a
use for processing sets of atoms in parallel. So rather than
b = [1 2 3]
c = ["red" "green" "blue"]
n = {*}.length
for (var i = 1; i <= n; i = i + 1)
if ({*}[i].x < b[1]);
{*}[i].color = c[1];
else if ({*}[i].x < b[2]);
{*}[i].color = c[2];
else
{*}[i].color = c[3];
endif
end for
Perhaps we could just use and "inline FOR" command:
b = [2 5 8]
c = ["red" "green" "blue"]
pt = {1 1 1}
{*}.color = for (x;{*}; if(x.distance(pt) < b[1];c[1];if(x.distance(pt) <
b[2]; c[2]; c[3] )))
Or, perhaps it would be nice to color atoms based on their minimum bond
length:
{*}.property_minbond = for(x;{*}; x.bonds.length.min)
color property_minbond
label %3.2[property_minbond]
Or to have an atom's radius based on its temperature:
tmax = {*}.temperature.max
tmin = {*}.temperature.min
{*}.radius = for(x;{*};(x.temperature - tmin) / (tmax - tmin))
That mirrors:
myvar = select(x; {*}; x.whatever > x.something)
which was introduced in 11.5.40.
It's a little odd, I realize, but I think it could come in handy. Definitely
a work in progress, so be on the alert for strange behaviors if you start
using Jmol 11.7.40. (I don't recommend it quite yet for general use, but I
would like to see a few others give it a work-out.) I think we're close to
calling this 11.8 now -- there are quite a few additions since 11.6. Maybe
by the end of July? Get those feature requests in!
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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