Angel, that got me thinking Jmol 11.5.40 will include a new feature:
full math on individual atom properties using a new function:
select(dummyVariable;{atomexpression};booleanEvaluation)
I've installed the latest applet Jar files at
http://Jmol.ProteinExplorer.org in the subdirectory
http://Jmol.ProteinExplorer.org/molview
in case you are interested in experimenting with this.
for example:
x = select(x;{*};x.atomIndex%427 = 397)
color @x blue;
select ! @x
or
print select(x;{*};x.atomIndex / 50 = 397);
The idea is this:
--choose a dummy variable -- x in this case
--identify a set of atoms to be included in the calculation -- {*} here
--give an expression in terms of atom properties that you want
satisfied. This expression will be looped through for each atom in the
set and tested for being TRUE or FALSE.
While you cannot mix standard select syntax with this:
select select(.) # NOT
you can define a variable and then select it:
var x = select(x;{..};...); select @x
or you can do the math inline with the @{...} syntax:
select @{ select(x;{..};...) }
You just have to be careful to distinguish Jmol math from the original
Rasmol syntax. So you can do this:
select @{ select(x;{*};x.atomno 3) } and model=1
But in this case it would be more efficient to use:
select @{ select(x;{model=1};x.atomno 3) }
because there would be only one loop instead of two.
Note that the variable name chosen as the first parameter of the select
function is local to it -- it's just a dummy variable that needs to be
there so that Jmol can refer to individual atoms when it evaluates that
expression. If you have already defined x, then using select(x;...)
will not change its value -- and, likewise, within the select()
evaluation, your x will not be used if the dummy variable is given the
name x. I think this is fair.
In principal you could replace just about any select of the form:
select atomno 3 or
with:
x = select(x;{*};x.atomno 3 or)
It actually might be more efficient this way. But I'm not sure. The new
way is pretty efficient and fewer loops are involved than the old way.
Because in the old way, each term such as atomno 3 or model=2
required a full scan of all atoms, whereas here there is just one
overall loop. Maybe someone could run some timing tests and tell us what
the difference is.
Notice that the select syntax, with its two semicolons, is similar to
the FOR command syntax:
for (var i; i 3; i = i + 1)
In fact, having that already in Jmol explains why it was easy to
implement this so fast. It was a nice challenge getting this to work.
And, believe it or not, it only took about 40 lines of code (and about
5 hours of my time!).
Thanks, Angel, for posting your need. This should be quite generally useful.
By the way, in preparing Jmol Protein Explorer, I'm amazed at all the
comments in the code about how SLOW Chime was to select atoms for large
systems. I guess I only used it for small molecules. Was it really that
slow? One hardly notices any delay in Jmol selecting 50,000 atoms. I
wonder what in the world Chime was doing
Bob
Angel Herraez wrote:
Hi
I have a complex loading of several models and I need to select a
combination of atoms based on their atomIndex property and the
mathematical MODULUS operator.
I have tried
select (atomIndex % 427) = 397;
but a get an error, a comparison operator was expected
It seems that the limitation is in operating with atomIndex before
the comparison, since
select (atomIndex / 50) = 397;
gives the same error, while
select atomIndex = 397;
works OK
What is the way to achieve this?
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Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
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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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