On 08/21/2015 04:16 PM, Robert Hanson wrote:
> yes. First use
>
> x = load("test.png", TRUE)
>
> this loads test.png as a binary file, creating an associative array of
> information in the file in the form of binary arrays.
>
> $ x = load("test.png", TRUE)
> $ print x.keys
> $_BINARY_$
> 1deh.pdb.gz
> JmolManifest.txt
> Jmol_version_14.3.16_2015.08.17__2015-08-17_22.19
> _IMAGE_
> state.spt
>
> Now you can inspect these. Caution, though! They are binary arrays. The
> ascii files will look OK, but they are still not strings!
>
> $ print x["JmolManifest.txt"].type
> bytearray
>
> $ print x["JmolManifest.txt"]
> # Jmol Manifest Zip Format 1.1
> # Created Tue Aug 18 18:22:06 CDT 2015
> # JmolVersion 14.3.16_2015.08.17 2015-08-17 22:19
> state.spt
>
> [Note that JmolManifest.txt is not run - Jmol only looks for the first
> ".spt" file in it and runs that.]
>
> # turn the byte array into a string:
>
> s = "" + x["JmolManifest.txt"]
>
> [change s]
>
> # write it back into x
>
> x["JmolManifest.txt"] = s;
>
> # creating more stuff in x
>
> x["testing.spt"] = "background red";
>
> # write a new PNGJ file
>
> write VAR x "test2.png"
>
> UNFORTUNATELY there is a bug there in that very last command. Jmol
> currently writes a ZIP file instead of a PNGJ file.
>
> I've put up at least a Jmol.jar file that corrects that, Rolf.
>
> http://chemapps.stolaf.edu/jmol/zip/Jmol.jar
>
> Jmol.___JmolVersion="14.3.16_2015.08.21"
>
> bug fix: write VAR x "test.png" creates a ZIP file instead of a PNGJ file
> when x is from load("test.png",true)
>
Thank you very much, Bob!
My question aimed at the second task needed for my idea of
storing/restoring custom Jmol extensions with a PNGJ file:
If the custom system is already loaded it should be able to skip
installing itself again in a maybe older version. so it would be
necessary to modify it.
But your answer actually also helped to achieve the first task of
getting the extension into the PNGJ file (see below).
The only thing that seems to be missing for the second task is to be
able to load PNGJ data from a variable:
==== Load PNGJ from variable =========
x = load("test.png", true);
$ load "@x"
script ERROR: io error reading string: java.io.FileNotFoundException:
string (No such file or directory)
======================================
The following example demonstrates the successful integration of a
custom hoverCallback (showing a blue halo) into a PNGJ file, available
(temporarily) at
"http://www.fli-leibniz.de/~rhuehne/jmol/1deh_custom_state.png":
====== Custom PNGJ Creation =======================================
#------ Jmolscript hover callback implementation ---------------
lastAtomIndexHovered = -1;
lastHoverUnfinished = false;
hoverTimeoutId = "";
function hoverAction(action) {
if (hoverTimeoutId != "") {
timeout ID @hoverTimeoutId off;
hoverTimeoutId = "";
}
var switchOff = false;
var currentSelection = {selected};
if (action == "end") {
if (lastHoverUnfinished) {
switchOff = true;
}
} elseif (action == "start") {
if (lastHoverUnfinished) {
if (lastAtomIndexHovered != _atomhovered) {
switchOff = true;
}
}
}
if (switchOff) {
if (lastAtomIndexHovered >= 0) {
select atomindex=@lastAtomIndexHovered;
color halo yellow;
halo off;
}
lastAtomIndexHovered = -1;
lastHoverUnfinished = false;
}
if (_atomhovered >= 0 && action == "start") {
lastAtomIndexHovered = _atomhovered;
select atomindex=@lastAtomIndexHovered;
color halo cyan;
halo on;
lastHoverUnfinished = true;
hoverTimeoutId = "hoverEnd_" + now();
timeout ID @hoverTimeoutId 1.0 "hoverAction('end')";
}
select @currentSelection;
}
set hoverCallback "jmolscript: hoverAction('start');";
#-------------------------------------------------------
function buildCustomStateScript {
var stateVariables = ["lastAtomIndexHovered", "lastHoverUnfinished",
"hoverTimeoutId"];
var stateFunctions = ["hoverAction"];
var stateCommands = ['set hoverCallback "jmolscript: hoverAction(' +
"'start');" + '";'];
var customStateScript = [];
for (var stateVariable IN stateVariables) {
customStateScript.push(script("show " + stateVariable));
}
for (var stateFunction IN stateFunctions) {
customStateScript.push(script("show function " + stateFunction));
}
for (var stateCommand IN stateCommands) {
customStateScript.push(stateCommand);
}
return customStateScript.join();
}
load =1deh;
rotate best;
zoom 600;
customPNGJ = write("PNGJ");
modifiedState = ("" + customPNGJ["state.spt"]).split();
addOn = 'script /*file*/"$SCRIPT_PATH$customState.spt";';
modifiedState.push(addOn);
customPNGJ["state.spt"] = modifiedState.join();
customPNGJ["customState.spt"] = buildCustomStateScript;
write VAR customPNGJ "1deh_custom_state.png";
==========================================================
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
![http://www.fli-leibniz.de/~rhuehne/jmol/1deh_custom_state.png":](http://www.fli-leibniz.de/~rhuehne/jmol/1deh_custom_state.png":){kind=link}