Re: [Jmol-users] sorting by atom properties

[Robert H. <ha...@st...>]

Yes, x.sort(1) is the way to go.

x = [ ]
Var atoms = {*}
for (var i = atoms.size; i > 0; --i) { x[i] =
[atoms[i].atomIndex,atoms[i].vdw] }
x = x.sort(2)


On Fri, Jun 22, 2012 at 9:10 AM, Alexander Rose <ale...@we...
> wrote:

> Hi,
>
> I would like to sort an atom selection by some atom property. I can do
> 'var x = {1}.vdw.all; x.sort; print x;' but then I loose the link to actual
> atoms. I know what the 3rd smallest vdw radius is but not to which atom(s)
> it belongs.
>
> I know that I could use a loop in Jmol-script but that takes too long for
> proteins or ribosomes, try e.g. the tests at the end. Wait... I tried a 2nd
> implementation that reuses a large enough array and also gets the
> properties at once. So my ideas below for new functions are not that
> pressing. But I still think them a valuable addition. What is your opinion?
>
>
Sounds useful. Can you think of a reasonable syntax?


> -----
>
> If there is no way to do it, I would suggest the following. There is
> already fast way to sort an array of arrays with
> 'array.sort(columnIndexOfNestedArray)'. So how to get an array of arrays
> like 'x = [[vdw1, atomindex1], [vdw2, atomindex2], ...]' which could be
> sorted with 'x.sort(1)'. Then, how to get an array of the sorted (by the
> vdw radius) atomindex. I suggest two variations of the array methods
> add/sub: 'array.add(APPEND, array2)' and 'array.sub(PLUCK, columnIndex)'.
> Array.add(APPEND, array) would do: 'a1 = [1,2,3]; a2 = [4,5,6]; a3 =
> a1.add(APPEND, a2); print a3 => [[1,4],[2,5],[3,6]]' and 'print
> a3.add(APPEND, a1) => [[1,4,1],[2,5,2],[3,6,3]]'. Array.sub(PLUCK,
> columnIndex) would do 'print a3.sub(PLUCK, 2) => [4,5,6]'.
>
> @Bob I'm thinking about adding these myself, would you second the syntax I
> outlined above? Alternatively we could add new functions 'array.append' and
> 'array.pluck'. Is it sufficient to add the new tokens to script.Token.java
> and handle the occurrence of the new tokens in
> script.ScriptMathProcessor.java::evaluateList()?
>
>
> Best
> Alexander
>
>
>
>
> 1VQK.pdb (91602 atoms)
>
> load =1vqk;
> var x = {*}.vdw.all; x.sort; print "sort done"; # instantly done
>
> # very slow
> function property_list(sele){
>        var arr = [];
>        for( a in sele ){
>                arr |= [[ a.atomindex, a.vdw ]];
>        }
>        print "done";
> }
> #property_list( {*} );
>
>
> # much faster, ok for most structures
> function property_list2(sele){
>        var arr = sele.atomindex.all;
>        var prop = sele.vdw.all
>        var n = arr.length
>        for( var i=1; i<=n; ++i ){
>                arr[i] = [ arr[i], prop[i] ];
>        }
>        print "done2";
>        #print arr;
> }
> property_list2( {*} );
>
>
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-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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