I would suggest implementing Atom, Bond, etc. The getProperty() method is
also very powerful.
On Wed, May 14, 2014 at 2:08 AM, eric henon <eric.he...@univ-reims.fr>wrote:
> Dear all,
>
> In my last email, I was wondering how to
> retrieve variable content of the Jmol environment,
> from a standalone java application.
>
> It seems that methods like *getAtomNumber
> <https://www.cellmicrocosmos.org/download/cm2/doc/org/jmol/api/JmolViewer.html#getAtomNumber(int)>*
> or *getAtomPoint3f
> <https://www.cellmicrocosmos.org/download/cm2/doc/org/jmol/api/JmolViewer.html#getAtomPoint3f(int)>
> of
> the class *
> JmolViewer are able to return some data. But these
> data are specific to objects like atoms, or bonds. However,
> what I need is something slightly different.
>
> In my Jmol application, I display a bound box
> that can be rotated, scaled, translated, and
> I want to get back the final volume, corner
> coordinates ... These data are encapsulated in
> some variables of my Jmol application.
> But how can I get back them ?
>
> Any help will be appreciated.
> Thanks.
>
> Eric
>
>
>
>
> Le 10 mai 2014 à 19:41, eric henon a écrit :
>
> Dear Bob,
>
>
> Thank you for your reply, that works fine !
>
> Just a last question: how to get back jMol variable values into
> the parent java application ?
>
> Thanks in advance for your help.
> Eric
>
>
> Message: 2
>
> Date: Mon, 5 May 2014 17:56:59 -0500
>
> From: Robert Hanson <hans...@stolaf.edu>
>
> Subject: Re: [Jmol-developers] Running Script commands directly from a
>
> Java application
>
> To: Jmol Developers <jmol-developers@lists.sourceforge.net>
>
> Message-ID:
>
> <CAF_YUvU3xKpVN4SSx=vNPLc2_cp=wb-jbq-hxuze0sutjao...@mail.gmail.com>
>
> Content-Type: text/plain; charset="utf-8"
>
>
> Sure. All the menus do this. The toolbar buttons in the Java application,
>
> the surface tool dialog does this. File...Export...Gaussian has buttons. So
>
> check out org.openscience.jmol.app and included classes. The template is
>
> something like this:
>
>
> JButton goButton;
>
> JmolViewer viewer;
>
> ...
>
> goButton = new JButton("Turn the background to red");
>
> goButton.setActionCommand("background red");
>
> goButton.addActionListener(this);
>
> ...
>
>
> @Override
>
> public void actionPerformed(ActionEvent e) {
>
> Object source = e.getSource();
>
> if (source == goButton) {
>
> viewer.script(((JButton)goButton).getActionCommand());
>
> }
>
> }
>
>
>
> Various ways to embellish upon that.
>
>
> Bob
>
>
>
>
>
>
>
> On Mon, May 5, 2014 at 9:21 AM, eric henon <eric.he...@univ-reims.fr>
> wrote:
>
>
> Dear all,
>
>
> Last year, I built an web application using the jmolApplet.
>
> This applet (JBox) allows for embedding a protein in a boundbox,
>
> which can interactively be translated, zoomed in, or
>
> even individually rotated about three axis.
>
>
> I would like now to built my own java application
>
> embedding jmol that would allow for the same possibilities
>
> (rotating, ... boundBox).
>
>
>
> I have already used the Integration.java example
>
> to create a JmolPanel. It works fine. However, instead of using the
>
> "text" AppConsole possibilities, I would like to add buttons
>
> in my own application that would automatically pass script commands
>
> (functions)
>
> directly to jmol. Is this possible ? Are there any example for something
>
> like that ?
>
>
> Thanks in advance.
>
> Eric
>
>
>
>
> ------------------------------------------------------------------------------
>
> Is your legacy SCM system holding you back? Join Perforce May 7 to find
>
> out:
>
> • 3 signs your SCM is hindering your productivity
>
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>
> _______________________________________________
>
> Jmol-developers mailing list
>
> Jmol-developers@lists.sourceforge.net
>
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>
>
>
>
> --
>
> Robert M. Hanson
>
> Larson-Anderson 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
>
> -------------- next part --------------
>
> An HTML attachment was scrubbed...
>
>
> ------------------------------
>
>
> Message: 3
>
> Date: Thu, 8 May 2014 11:50:50 +0200
>
> From: Angel Herr?ez <angel.herr...@uah.es>
>
> Subject: Re: [Jmol-developers] What is the second Canvas2d for that
>
> shows up below the active one when using JSmol?
>
> To: <jmol-developers@lists.sourceforge.net>
>
> Message-ID: <536b537a.7561.2d99d...@angel.herraez.uah.es>
>
> Content-Type: text/plain; charset="US-ASCII"
>
>
> I'm having a similar problem as Jonathan's. Two canvas2d objects are
>
> created.
>
>
> I believe there is something wrong with Jmol.getAppletHtml()
>
> The problem does not happen when I use Jmol.getApplet() directly in the
> div.
>
>
> Note: I am using jquery-1.10.2.min.js plus JSmol.min.nojq.js
>
>
> Symptoms:
>
>
> - The page is taller (scroolbar) than its intended contents.
>
>
> - A square area below the actual JSmol square is sensitive to right-click
>
> opening of the popup menu and also to zoom by mouse wheel.
>
>
> - Firefox Inspector gives this source code:
>
> <div id="JmolOb_appletdiv" style="z-index: 15; width: 100%; height: 100%;
>
> position: absolute; top: 0px; left: 0px; display: block;">
>
> <script type="text/javascript"></script>
>
> <canvas id="JmolOb_canvas2d" style="width: 100%; height: 100%;
>
> z-index: 17;" width="400" height="400"></canvas>
>
> <canvas id="JmolOb_canvas2d" style="width: 100%; height: 100%;"
>
> width="400" height="400"></canvas>
>
> </div>
>
>
>
> This is my code in the page:
>
>
> <head>
>
> <script>
>
> /* viewerMolec is a global object-variable defined before, that holds
> many
>
> parameters for the page.
>
> */
>
> viewerMolec.infoJmol = {
>
> color: '#'+viewerCfg.bkg,
>
> height: '100%',
>
> width: '100%',
>
> j2sPath: viewerMolec.pathJmol + 'j2s',
>
> jarPath: viewerMolec.pathJmol + 'java',
>
> jarFile: 'JmolAppletSigned0.jar',
>
> isSigned: true,
>
> serverURL: viewerMolec.pathJmol + 'php/jsmol.php',
>
> loadstructcallback: 'viewer_OnModelLoad',
>
> pickcallback: 'viewer_OnAtomOrBondPicked',
>
> measureCallback: 'viewer_OnMeasures',
>
> script: 'set frank off; /*etc*/ ',
>
> zIndexBase: 15,
>
> z: 15,
>
> deferUncover:true,
>
> coverImage:'cover.png',
>
> use: 'html5'
>
> };
>
>
> $(document).ready( function() {
>
>
> $('#viewerViewer').html(Jmol.getAppletHtml('JmolOb',viewerMolec.infoJmol))
>
> ;
>
> });
>
> </script>
>
>
> <style>
>
> #viewer { width:800px; height:400px; position:relative; }
>
> #viewerTools { width:49%; height:100%; position:absolute; left:0; top:0;
>
> overflow:hidden; }
>
> #viewerViewer { width:50%; height:100%; position:absolute; left:50%;
> top:0; }
>
> </style>
>
> </head>
>
>
> <body>
>
> <div id="viewer">
>
> <div id="viewerTools">
>
> // etc.
>
> </div>
>
> <div id="viewerViewer"><img src="cover.png">
>
> </div>
>
> </div>
>
> </body>
>
>
>
>
>
>
>
> ------------------------------
>
>
> Message: 4
>
> Date: Thu, 8 May 2014 10:06:54 -0500
>
> From: Robert Hanson <hans...@stolaf.edu>
>
> Subject: Re: [Jmol-developers] What is the second Canvas2d for that
>
> shows up below the active one when using JSmol?
>
> To: Jmol Developers <jmol-developers@lists.sourceforge.net>
>
> Message-ID:
>
> <caf_yuvw+uylr_1egwz601342cj3dd3wakff_8swoaj85hnd...@mail.gmail.com>
>
> Content-Type: text/plain; charset="utf-8"
>
>
> That's not enough to go on. Yes, the applet is creating itself twice. As
>
> described above, we need to check what is happening with
>
>
> proto._createCanvas2d
>
>
> You must determine why it is running twice.
>
>
> Also, correct your <img> tag. It is not closed.
>
>
>
>
>
> On Thu, May 8, 2014 at 4:50 AM, Angel Herr?ez <angel.herr...@uah.es>
> wrote:
>
>
> I'm having a similar problem as Jonathan's. Two canvas2d objects are
>
> created.
>
>
> I believe there is something wrong with Jmol.getAppletHtml()
>
> The problem does not happen when I use Jmol.getApplet() directly in the
>
> div.
>
>
> Note: I am using jquery-1.10.2.min.js plus JSmol.min.nojq.js
>
>
> Symptoms:
>
>
> - The page is taller (scroolbar) than its intended contents.
>
>
> - A square area below the actual JSmol square is sensitive to right-click
>
> opening of the popup menu and also to zoom by mouse wheel.
>
>
> - Firefox Inspector gives this source code:
>
> <div id="JmolOb_appletdiv" style="z-index: 15; width: 100%; height: 100%;
>
> position: absolute; top: 0px; left: 0px; display: block;">
>
> <script type="text/javascript"></script>
>
> <canvas id="JmolOb_canvas2d" style="width: 100%; height: 100%;
>
> z-index: 17;" width="400" height="400"></canvas>
>
> <canvas id="JmolOb_canvas2d" style="width: 100%; height: 100%;"
>
> width="400" height="400"></canvas>
>
> </div>
>
>
>
> This is my code in the page:
>
>
> <head>
>
> <script>
>
> /* viewerMolec is a global object-variable defined before, that holds many
>
> parameters for the page.
>
> */
>
> viewerMolec.infoJmol = {
>
> color: '#'+viewerCfg.bkg,
>
> height: '100%',
>
> width: '100%',
>
> j2sPath: viewerMolec.pathJmol + 'j2s',
>
> jarPath: viewerMolec.pathJmol + 'java',
>
> jarFile: 'JmolAppletSigned0.jar',
>
> isSigned: true,
>
> serverURL: viewerMolec.pathJmol + 'php/jsmol.php',
>
> loadstructcallback: 'viewer_OnModelLoad',
>
> pickcallback: 'viewer_OnAtomOrBondPicked',
>
> measureCallback: 'viewer_OnMeasures',
>
> script: 'set frank off; /*etc*/ ',
>
> zIndexBase: 15,
>
> z: 15,
>
> deferUncover:true,
>
> coverImage:'cover.png',
>
> use: 'html5'
>
> };
>
>
> $(document).ready( function() {
>
>
> $('#viewerViewer').html(Jmol.getAppletHtml('JmolOb',viewerMolec.infoJmol))
>
> ;
>
> });
>
> </script>
>
>
> <style>
>
> #viewer { width:800px; height:400px; position:relative; }
>
> #viewerTools { width:49%; height:100%; position:absolute; left:0; top:0;
>
> overflow:hidden; }
>
> #viewerViewer { width:50%; height:100%; position:absolute; left:50%;
>
> top:0; }
>
> </style>
>
> </head>
>
>
> <body>
>
> <div id="viewer">
>
> <div id="viewerTools">
>
> // etc.
>
> </div>
>
> <div id="viewerViewer"><img src="cover.png">
>
> </div>
>
> </div>
>
> </body>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
>
> Is your legacy SCM system holding you back? Join Perforce May 7 to find
>
> out:
>
> • 3 signs your SCM is hindering your productivity
>
> • Requirements for releasing software faster
>
> • Expert tips and advice for migrating your SCM now
>
> http://p.sf.net/sfu/perforce
>
> _______________________________________________
>
> Jmol-developers mailing list
>
> Jmol-developers@lists.sourceforge.net
>
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>
>
>
>
> --
>
> Robert M. Hanson
>
> Larson-Anderson 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
>
> -------------- next part --------------
>
> An HTML attachment was scrubbed...
>
>
> ------------------------------
>
>
>
> ------------------------------------------------------------------------------
>
> Is your legacy SCM system holding you back? Join Perforce May 7 to find
> out:
>
> • 3 signs your SCM is hindering your productivity
>
> • Requirements for releasing software faster
>
> • Expert tips and advice for migrating your SCM now
>
> http://p.sf.net/sfu/perforce
>
>
> ------------------------------
>
>
> _______________________________________________
>
> Jmol-developers mailing list
>
> Jmol-developers@lists.sourceforge.net
>
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>
>
> End of Jmol-developers Digest, Vol 96, Issue 1
>
> **********************************************
>
>
>
>
>
> ------------------------------------------------------------------------------
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>
>
--
Robert M. Hanson
Larson-Anderson 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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