maybe that version is one behind this fix.
snpInfo = {"rs1229984": [resno: 48,
from: "R",
to: "H"],
"rs1041969": [resno: 57,
from: "N",
to: "K"]
};
print "=== Case 1 ====";
print snpInfo.array("id").select("id,from,to WHERE
to='H'").array("id").format("JSON");
print "=== Case 2 ====";
print snpInfo.array("id").select("(resno) WHERE to='H'").format("JSON");
works in 2015.10.01.
As for memory, I don't doubt that what you are doing is pushing the limits.
To reduce the memory load, you can use
set preservestate false
set undo off
This will prevent state saving between commands in the console. Try one or
both.
Bob
On Fri, Oct 2, 2015 at 11:55 AM, Rolf Huehne <rhue...@fli-leibniz.de> wrote:
> On 10/01/2015 06:12 AM, Robert Hanson wrote:
> > Then map.array("id") is perfect for you. It turns that map into an actual
> > array (temporarily), and you can then use WHERE and WHEREIN on that next
> > level of maps. After you do that, using array("id") again returns your
> > top-level map. The result was identical to what you requested.
> >
> I couldn't test it yet (see below) but I fear the memory footprint might
> be quite high if data has to be copied for it.
>
> The memory footprint of multi-level data constructs in Jmol generally
> seems to be quite high. If I load for example about 15 megabyte of
> annotation data for about 200,000 atoms, calculate coordinates, add
> bonds and then actually load the atoms about 900 megabyte of memory seem
> to be needed. Saved on disk with 'write var...' it takes about 300
> megabytes (and about 200 megabytes after removing whitespace).
>
> In Perl my rule of thumb is a factor of 10-20 to load data into a
> multi-level data structure. The numbers above sound like a factor of 40
> in Jmol.
>
> But maybe this is related also to the observation I mentioned today in
> the thread "Jmol reads a structure file from a pipe or system input":
>
> "In the application there are shown two numbers about the memory used by
> Jmol at the bottom right. The amount of memory used increases about
> 20-30 megabytes for each command I enter into the script console,
> seemingly independent of the command itself."
>
> > I think what you are missing is that Jmol is treating an array or array
> of
> > arrays totally differently from a map. The array is passed through, and
> > WHERE or WHEREIN operate directly on the map itself, no matter how many
> > levels deep it is in the array. So it makes no sense to refer to the
> array
> > itself and its subarrays as the "first level." The first map that is
> found
> > -- that is the level for WHERE; if the values in that map are also maps,
> > those are what are tested for WHEREIN.
> >
> I don't know anything about the Jmol's internals, so what I get here is
> that it would be more complicated than I thought to implement my proposal.
>
> > It's not more complicated than that.
> >
> > snpInfo = {"rs1229984": [resno: 48,
> > from: "R",
> > to: "H"],
> > "rs1041969": [resno: 57,
> > from: "N",
> > to: "K"]
> > };
> >
> > print "=== Case 1 ====";
> > print snpInfo.array("id").select("id,from,to WHERE
> > to='H'").array("id").format("JSON");
> >
> > print "=== Case 2 ====";
> > print snpInfo.array("id").select("(resno) WHERE to='H'").format("JSON");
> >
> > === Case 1 ====
> > { "rs1229984": { "to": "H","from": "R" } }
> > === Case 2 ====
> > [ 48 ]
> >
> This example doesn't work for me in Jmol 14.3.16_2015.09.28:
>
> ------------------------------------------
> $ print snpInfo.array("id").select("id,from,to WHERE
> to='H'").array("id").format("JSON");
> script ERROR: invalid argument
> ----
> print snpInfo . array ( "id" ) . select ( "id,from,to WHERE
> to='H'" ) . array ( "id" ) . format ( "JSON" <<<<)
> $ print snpInfo.array("id").select("(resno) WHERE to='H'").format("JSON");
> script ERROR: invalid argument
> ----
> print snpInfo . array ( "id" ) . select ( "(resno) WHERE
> to='H'" ) . format ( "JSON" <<<<)
> -------------------------------------------
>
> Regards,
> Rolf
>
> --
>
> Rolf Huehne
> Postdoc
>
> Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
> Beutenbergstrasse 11
> 07745 Jena, Germany
>
> Phone: +49 3641 65 6205
> Fax: +49 3641 65 6210
> E-Mail: rhue...@fli-leibniz.de
> Website: http://www.fli-leibniz.de
>
> Scientific Director: Prof. Dr. K. Lenhard Rudolph
> Head of Administration: Dr. Daniele Barthel
> Chairman of Board of Trustees: Dennys Klein
>
> VAT No: DE 153 925 464
> Register of Associations: No. 230296, Amtsgericht Jena
> Tax Number: 162/141/08228
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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
------------------------------------------------------------------------------
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
