Just when you thought we were done....
Thank you, Nico, for releasing Jmol 11.8.3 and Jmol 11.9.2. The first has a
few minor bug fixes; Jmol 11.9.2 has some interesting capability:
The 11.9.2 capability is highlighted at
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
script/write state LOCALPATH/REMOTEPATH (suggested by Christopher King)
Jmol 11.9.2 adds two options to the SCRIPT and WRITE STATE commands. When
reading or writing a script, the LOCALPATH keyword instructs Jmol to strip
all paths beginning with "file:/" down to the indicated path. So, for
example, script LOCALPATH "" "myfile.spt" indicates that all local files
referenced in the state script should be read from the current default
directory. Similarly, REMOTEPATH strips paths from file refrences starting
with "http:", "https:", and "ftp:". LOCALPATH and REMOTEPATH are desigend
specifically to be used with scripts created by Jmol in the process of
defining its state, but the option can be used with scripts you write
yourself. The mechanism is simply looking for instances of
/*file*/"some_file_name". If this construction is found in any script read,
the replacement will be made. script test1.spt #this won't work, because the
script saved was for a state that had a file read from my laptop.
{xxx}.volume("type") (Thanks go to David Brown for this suggestion.)
Jmol 11.9.2 introduces a calculation for molecular volume. This calculation
depends upon what set of Van Der Waals radii one uses. "type" can be one of
"Jmol", "Babel", "Rasmol" or "User". If not provided, "type" defaults to the
default type specified by the command set defaultVanDerWaal. The calculation
is a simple one that just adds up all the Van Der Waals volumes and
subtracts off the overlap of spheres associated with bonds as described by
A. Bondi (J. Phys. Chem. 68, 1964, 441-451.). The built-in Van der Waals set
"Babel" most closely represents this setting.
clickCallback (See demo)
Starting with Jmol 11.9.1, you can detect clicking and dragging within the
applet window, and you can cancel that operation if desired. The callback
function takes the form:
function myClickCallback(app,x,y,modifiers,clickCount,Ret){}
app is the applet identifier, usually "jmolApplet0". x and y are screen
coordinates with [0,0] in the bottom left corner. modifiers is a set of bits
indicating what keys and mouse buttons were pressed: 1(shift), 2(ctrl),
4(right), 8(alt), 16(left). If none of these bits are set, this is a
"mouse-up" event. clickCount is the number of clicks. 0 here indicates the
mouse was pressed (as in the initiation of a drag operation); negative
numbers indicate dragging; positive numbers are standard clicks of the
mouse. Ret is an array with just one element that allows returning a new
modifier. Setting Ret[0]=0 cancels Jmol processing of the event.
acos(x) and q1.dot(q2)
Jmol 11.9.1 adds the acos() function, returning a value in degrees, and
quaternion dot product.
--
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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