Thank you, Nico, for releasing Jmol 11.3.21.
Jmol 11.3.21 represents a quantum leap in scripting and a couple of bug
fixes for problems introduced in recent versions:
# bug fix: isosurface of MOs not properly displaying color in saved state
# bug fix: state saving of @ definitions has extra = sign.
new feature: fully functional user-defined functions
----------------------------------------------------
This is really something. There are three new scripting capabilities in
Jmol that as far as I know were not possible at all in Chime scripting
or RasMol. (Correct me if I am wrong.) Basically, this enhancement turns
Jmol math into a fledging computing language. The three features include:
macros -- you can now create single-word commands that can be called to
execute sequences of commands, much like "script somefile.spt" but
without the file.
subroutines -- you can pass variables to a script in the form of a
subroutine.
functions -- you can create scripts that have return values that can be
used in Jmol math calculations and expressions.
All three of these features use the same new mechanism -- a pair of
statements ("function" and "end function") with statements in between.
Variables introduced with the "var" keyword, as in JavaScript, are local
to the function in which they are contained. Localization with "var"
also works for file-based scripts, which are in all ways identical to
script-based macros.
The advantage of using functions over individual script files is obvious
-- faster loading and faster execution, cleaner coding, and more
extensible "library"-like capabilities.
Functions may or may not have parameters and may or may not have return
values.
So, for example:
MACROS (no parameters)
function mymacro
background red
color atoms blue
end function
function mymacro2
background black
color atoms cpk
end function
background white
delay 2
mymacro
delay 2
mymacro2
SUBROUTINES (parameters, but no return)
function drawline(id,a,b)
var x = script("draw line"+ id + " {atomno=" + a + "} {atomno=" + b +
"}")
end function
drawline(1,3,5)
drawline(2,10,12)
Note that if x is defined outside the function, it is unchanged by this
call, because we have "var x". If the "var" were not there, then x is a
global variable that is saved in the state. Variables preceeded by "var"
are not saved in the state.
FUNCTIONS (parameters and returns)
function d(a,b)
return a.distance(b)
end function
x = d({atomno=3},{atomno=4})
print x
Functions of all types may be nested -- macros can call other macros;
functions can call subroutines, subroutines can call functions, etc. The
overall depth, including script file levels is arbitrarily set at 10 for
now. But there is no particular reason it has to be that small.
SHOW, WRITE, and RESET
----------------------
Along with these capabilities are extensions of the three commands SHOW,
WRITE, and RESET to allow for easier development.
show functions # list functions in the console window
write functions macros.spt # dump functions to a file
reset x # "undefine" a variable
reset all # delete all user-defined variables
reset functions # delete all functions
Of course, there will be a few things to shake out here; I'm hoping some
users will be interested enough to give this a try and let us know what
problems arise and what sort of uses this functionality might have.
I suppose the next thing we need is "for" and "while" just to make
looping a bit easier. That's coming -- it's really a very simple
addition at this point, though maybe not this week.
Bob Hanson
--
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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