Thanks for the tip Bob.
Yes, the access to caffeine.bonds.length would be done every time the loop
repeats, which is very inefficient. The most inefficient part of Javascript is
namespace calls, so when doing a.b.c, Javascript would have to find a, then
find b, then find c. The reason this is
I think this question got lost in the lower reaches of my response. It's
fine if the answer is, You can't do that, at least not yet.
My point is that the power of Jmol isn't the twiddle factor; it's the
scriptability (by people who are chemists, not JavaScript or Java experts).
I don't see any
I'm not with you Bob. I checked the ChemDoodle demos (quite nice really) and I
see the same kind of functionality as I see on many Jmol sites, radio buttons
and such to control the appearance or behavior of a molecule. Are you saying
you think this is easier to create using Jmol scripting
I wasn't necessarily trying to say anything. But I'm interested in what
those controls can do. Is it limited to a few standard operations like
changing overall rendering? I think maybe it's limited to just a few simple
operations being simple to implement. At least now. For example, I haven't
Charles, I got headless image generation going. The current release of
Jmol, specifically JmolData.jar does it for PNG creation. There was a minor
snafu with JPG creation, so that will be in Jmol 12.2.20/12.3.20.
I can send you the PHP file I used if you want.
Bob
--
Robert M. Hanson
@Paul
We do not currently have a querying function, and this is a great idea to add.
We have SMARTS support that we can pipe through, however, it will take some
work before we can deal with proteins in such a way. The script is irrelevant
to this functionality though, as the script in itself
OK, I'm catching on. Just takes me a while. It still might be nice to
develop a general set of JavaScript functions that would be particularly
handy. A select() function would be very nice, for example. I guess that's
what you are doing
By the way, is this to prevent the repetitive access to
for Jmol,
but I appreciate that it is both big and a challenge.
Craig Martin
Message: 2
Date: Fri, 30 Mar 2012 08:53:35 -0500
From: Robert Hanson hans...@stolaf.edu
Subject: Re: [Jmol-users] Jmol for iPads?
Absolutely.
On Fri, Mar 30, 2012 at 8:01 AM, Craig T Martin cmar
OK, there are really three threads here:
1) Jmol app for the iPad
2) Jmol export of iPad-ready model twiddles that can be embedded in iBooks
3) Jmol applet-equivalent for browsers running in Java-challenged platforms
(1) was the discussion I was starting. But now I think that's off track. I
I think these are all good points. In order to create a Jmol app for iPads, one
would need to completely port the project to Objective-C, no easy task. To
publish in Apple's App Store also costs money (99$/year), is very, very
complicated and requires constant attention. And regardless of
On Mon, Apr 2, 2012 at 12:35 PM, Kevin Theisen ke...@ichemlabs.com wrote:
I think these are all good points. In order to create a Jmol app for
iPads, one would need to completely port the project to Objective-C, no
easy task. To publish in Apple's App Store also costs money (99$/year), is
Marching cubes in JavaScript. Now there's a challenge! Kevin, I think if you
want something like that, use JmolData.jar. That's headless and can run any
script not involving image creation or font use. So creation of isosurfaces
is fine. Jmol's marching cubes algorithm is highly efficient,
Jmol has, in fact, been factored into all of these areas. That was the
Android project. So all Jmol is entirely independent of platform except for
calls to a specific platform class that inserts whatever
platform-specific aspects are required, such as images, fonts, and
graphics.
So that's not
On Thu, Mar 29, 2012 at 3:08 PM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote:
1. Do you want a QA controlled (by Apple) environment, or the more
advertising-oriented environment of Android?
I do have several Android apps installed without advertisement... I do
not think the above choice is
I find it very disturbing that educators are even considering creating
a learning environment where students are restricted in their
learning! That is just another step back to the middle ages... Henry,
I very much appreciate that people use the platform on which they can
perform their work
Dear Henry,
On Fri, Mar 30, 2012 at 11:01 AM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote:
I find it very disturbing that educators are even considering creating
a learning environment where students are restricted in their
learning! That is just another step back to the middle ages... Henry,
All,
On Fri, Mar 30, 2012 at 10:29 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
I find it very disturbing that educators are even considering creating
a learning environment where students are restricted in their
learning! That is just another step back to the middle ages... Henry,
Wow. I've stepped into (and probably added fuel to) a firestorm.
I'd like to suggest that this is not the forum for arguing the merits of iOS vs
Android. Some of us are a bit fanatical about iOS (OK, I'm one of them), and
some fanatical about Android. But we're all unified in being fanatical
Absolutely.
On Fri, Mar 30, 2012 at 8:01 AM, Craig T Martin cmar...@chem.umass.eduwrote:
The challenge of open source is who's going to fix this and how? Perhaps
our discussion should move in that direction?
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Maybe the first question is what needs to be fixed?
Let's assume for the sake of discussion that there is a port of Jmol to iPads
to address the need for image updating performance. Let's also assume that
Jmol has been factored into UI, scripting, parsing raw source, image
calculation, and
On 29 Mar 2012, at 03:19, Craig T Martin wrote:
Bob,
I wouldn't be so dismissive of the iPad/iPhone revolution. Clearly the
latter looks to be dominating the smart phone market, despite it's higher
price tag. It wasn't that long ago that experts were dismissive of Apple
overall (or
El 29 de març de 2012 4:19, Craig T Martin cmar...@chem.umass.edu ha
escrit:
I wouldn't be so dismissive of the iPad/iPhone revolution. Clearly the
latter looks to be dominating the smart phone market, despite it's higher
price tag.
That may be true in the USA, but not in Europe or the rest
On Wed, Mar 28, 2012 at 9:19 PM, Craig T Martin cmar...@chem.umass.eduwrote:
Bob,
I wouldn't be so dismissive of the iPad/iPhone revolution. Clearly the
latter looks to be dominating the smart phone market, despite it's higher
price tag. It wasn't that long ago that experts were
On 29 Mar 2012, at 13:41, Robert Hanson wrote:
On Wed, Mar 28, 2012 at 9:19 PM, Craig T Martin cmar...@chem.umass.eduwrote:
Bob,
I wouldn't be so dismissive of the iPad/iPhone revolution. Clearly the
latter looks to be dominating the smart phone market, despite it's higher
price tag.
Not quite. I think we're mostly in agreement.
I'm saying that one solution, if you want to implement Jmol on a tablet,
is to to Android. I'm not interested in getting into a debate here of
Apple vs. Android. People have their passions. I was just reacting to
Craig's urge to go out and get an
On 29 Mar 2012, at 14:39, Robert Hanson wrote:
Not quite. I think we're mostly in agreement.
You are right there Bob!
I'm saying that one solution, if you want to implement Jmol on a tablet,
is to to Android. I'm not interested in getting into a debate here of
Apple vs. Android. People
I think we are all missing the underlying point in this discussion. Maybe I'm
ideological, but developing open source is a method to contribute the community
and allow others to contribute back. It is not about competition, and it
disappoints me that we sometimes enter into these discussions of
discussions
Jonathan
On Mar 29, 2012, at 7:41 AM, jmol-users-requ...@lists.sourceforge.net wrote:
Message: 6
Date: Thu, 29 Mar 2012 07:41:47 -0500
From: Robert Hanson hans...@stolaf.edu
Subject: Re: [Jmol-users] Jmol for iPads?
To: jmol-users@lists.sourceforge.net
Message-ID:
caf_yuvwu2s
I'm saddened by the fact that for the foreseeable future this is dragging us
back to the see the pretty molecule spin age. In the cases where this is
useful (pretty molecules spinning), I agree with Jonathan that there are
textbook like presentation options. I would add to Jonathan's
Hi Johathan,
Could you say more about what latest version means, how to run JmolData.jar
headless on the server, and how it works as an image generator? This might be
a very nice way for me to get the iPad functionality I'm looking for.
Thanks,
--Chuck
On Mar 29, 2012, at 10:08 AM, Gutow,
I'll let Jonathan explain JmolData. latest version means in this context
12.2.19 or 12.3.19, which I've scheduled for imminent release. We just
recently realized that one could produce images within this headless mode,
so that's why you need the latest version, whether it is 12.2 or 12.3.
On
Chuck,
As Bob said, latest version means literally the bleeding edge releases 12.2.19
and 12.3.19. I had been using the full-fledged Jmol on as server to generate
images and realized that I could lose the server-side GUI if we could figure
out how to generate images using a GUI free version
Uh..Oh...Now I'm embarrassed...this was workingI apologize to anybody who
tried this. The server side generation of images seems to be broken again. I
hope to have time to chase this over the weekend. However, this means one more
problem has been found and can be rectified. I will post
On Thu, Mar 29, 2012 at 4:19 AM, Craig T Martin cmar...@chem.umass.edu wrote:
I don't yet have an iPad personally, but it's on my list of things to buy
next and I have a number of colleagues who are absolutely fanatical.
Tomorrow we go to the Dean to pitch an idea that will involve the purchase
I just heard a segment on NPR about hundreds of high schools that are
abandoning textbooks and giving every student an iPad instead. As we
all know, iPads will not run java and so will not run Jmol. What are
people's thoughts on porting Jmol to a non-java language that would
run on a wider
On Fri, Mar 23, 2012 at 8:33 PM, Eric Martz ema...@microbio.umass.edu wrote:
I just heard a segment on NPR about hundreds of high schools that are
abandoning textbooks and giving every student an iPad instead.
This is so sad... we're not even over the MS vendor lock-in, and ready
to buy into
Buzzwords... and politics. Who will be putting the cash for all those iPads?
And how soon will
they be obsolete?
I wonder how many (text)books are available for the iPad platform.
Regarding the reprogramming of Jmol, the task is not trivial (as Miguel and Bob
will know),
and who would do it?
At the ACS meeting last fall, someone was showing a version of Spartan on the
iPad. It was merely the builder and viewer. The idea, as I remember it, was
to be able to submit computations to a server and retrieve and display the
results. I do not know whether that is being pursued, and if so
On Mar 23, 2012, at 3:33 PM, Eric Martz wrote:
I just heard a segment on NPR about hundreds of high schools that are
abandoning textbooks and giving every student an iPad instead. As we
all know, iPads will not run java and so will not run Jmol. What are
people's thoughts on porting Jmol
openSoft's IMolView for ipad - pretty fast and responsive
http://www.molsoft.com/iMolview.html
From: Philip Bays pb...@saintmarys.edu
To: jmol-users@lists.sourceforge.net
Sent: Friday, March 23, 2012 4:41 PM
Subject: Re: [Jmol-users] Jmol for iPads
There is also a version of Cuemol for the iphone and iPad
http://itunes.apple.com/us/app/cuemol/id496236710?mt=8
It is a viewer for content developed on a workstation with an authoring
version of the program.
It still has a ways to go, but seems to have potential
On Fri, Mar 23, 2012 at 12:33
Jmol is now portable to the iPad. In principle, at least. The Android port
shows that. But really, developing for the iPad is to develop something
very different in behavior to what you have now, and I think there are
different solutions, then, for that. You can't just take something like
Jmol and
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