Bob,
To answer your questions:
This is really an argument of semantics, with the ChemDoodle Web Components, we
would do something like the following.
var selected = myCanvas.select(10, 20);
myCanvas.center(selected);
myCanvas.repaint();
Instead of using Jmol script and the Jmol compiler, it would just be pure
Javascript with the ChemDoodle Web Components API.
But let me describe a little more about what the ChemDoodle Web Components
library is. It was devised as a portable API to build scientific interfaces.
This may include structures, reactions, spectra and 3D. It may also include
other things that we have not done yet, such as graphs and vector maps. It was
not created to compete with Jmol. The ChemDoodle Web Components library is also
a framework, which is different from most graphical solutions like Jmol, which
are applications. Jmol and other applications are prebuilt to define how a user
uses them. They can be incorporated into other projects readily, but if you
want to do significant modification, then it is a much more difficult task. The
ChemDoodle Web Components, on the other hand, provide an API to build
scientific applications and products. We provide all the tools to define the
graphics, and interfaces and how the user will interact with the interface. We
also created an assortment of predefined components to show common use cases,
but really anything can be made with them. If the developer wants a pinch
gesture on Android to send an email to friends, that can be done. If a
developer wants to render a simulation of a bus moving through traffic, that
can be done. If a developer wants to build benzene pong, that can be done!
http://web.chemdoodle.com/demos/benzene-pong
Ok, moving on, let's discuss WebGL. WebGL has been the biggest restraint for
our development of advanced 3D scientific graphics. It is a very powerful
technology, but its support across browsers (both mobile and web) have
progressed at a snail's pace. We first started working with WebGL in 2009. In
early 2011, Chrome and Firefox both enabled it. Further support has remained
stagnant until last week when it was announced WebGL is coming to Android (
http://blog.tojicode.com/2013/01/get-webgl-working-on-android-chrome-beta.html
). I would have to bet that WebGL is coming to iOS this year as well. With that
being said, WebGL is supported in all desktop browsers today. Firefox and
Chrome support it by default, you can turn it on in Safari and Opera, and for
IE6-9, there is Google Chrome Frame. That brings us to the second restraint
with WebGL, hardware support. As with all hardware accelerated technologies,
you have to take into account the hardware. This is especially important with a
web technology, because security is infinitely harder. So there are blacklists
from the browser vendors to restrict WebGL for given graphics cards. Browser
vendors are working through these issues though, and last we checked, the
blacklists are shrinking. This is a good thing, because the browser vendors are
ensuring that WebGL is a safe technology.
So let us now talk about ChemDoodle Web Components adoption. The ChemDoodle Web
Components library is very popular, used all over the place, especially our
top-quality and industry leading HTML5 sketcher (
http://web.chemdoodle.com/demos/sketcher ). But we really are focused on the 3D
components in this discussion, so I will limit the examples to the following.
Also keep in mind, that the 3D ChemDoodle Web Components are a WebGL
technology, and support for WebGL is limited, so adoption is affected as
expected. Also, do not forget our two other WebGL demos:
http://web.chemdoodle.com/demos/2d-to-3d-coordinates
http://web.chemdoodle.com/demos/iza-zeolite-explorer
I don't keep track of all the open projects on the internet, we don't know all
of those that exist, but here are some that caught my attention:
From the Polymer Science Learning Foundation -
http://chemsrv1.uwsp.edu/advanced/index.html
Seqcrawler - http://www.biomedcentral.com/1471-2105/13/175/abstract
UCLA Multimodal Connectivity Database, this one is interesting because they use
our 3D API to render maps, not chemicals -
http://umcd.humanconnectomeproject.org/technical_specification
In many blogs and teaching sites (I only list 3):
http://doctorbrookschemistry.net/
http://www.ch.imperial.ac.uk/rzepa/blog/?p=5881
http://molecularmodelingbasics.blogspot.com/2011/05/interactive-chemistry-ebooks.html
And of course, one of our proudest collaborations, Jmol -
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object
The 3D ChemDoodle Web Components are also used by dozens of pharmaceutical
companies and in other industry applications, however all of them (so far) are
internal projects and I am not able to comment on them.
We have also partnered with many industry leaders to use 3D ChemDoodle Web
Components to create products. I can only forward you to relevant press
releases:
http://www.prweb.com/releases/2012/3/prweb9281945.htm
http://news.cengage.com/higher-education/cengage-learning-and-ichemlabs-deliver-chemical-information-in-2d-and-3d/
Of course, this list is not inclusive and due to non-disclosure agreements, I
cannot comment on them further.
As for the future, let me answer your last two questions and wrap up. As for
searching for "ChemDoodle", you will find many different products. That is
because ChemDoodle is a brand for our chemical graphics software, and not any
specific product. We provide ChemDoodle desktop (commercial), which is used in
thousands of institutions in over 70 countries. We provide ChemDoodle Mobile,
which is a very popular and free mobile application that has close to 50,000
installs on both iOS and Android each. And of course, we provide the ChemDoodle
Web Components. Those that have read this far, a lot of our revenue is
reinvested back into our open source projects to benefit the community. If you
would like to support us and the open source community, please consider
purchasing ChemDoodle or convincing your department to get a site license for
ChemDoodle ( http://www.chemdoodle.com ). It is very affordable and
high-quality and you can get a little something for yourself as well as support
our open source work!
As for the psuedo-3D <canvas> components that we provide, they are a great
fallback on platforms that don't support WebGL, but due to the recent news
about mobile WebGL support, I think it is a better decision to be fully
invested in WebGL development. WebGL is hardware accelerated after all, so it
will be significantly faster than <canvas> 2D. Watch us over the next year to
see the many new features.
Again, I am a supporter of JSmol. There is nothing stopping a ChemDoodle Web
Components supporter from being a JSmol supporter and vice versa. We are all
open source advocates here. As always Bob, I welcome your feedback and I do
hope that at some point we again work together.
Sincerely,
Kevin Theisen
President, iChemLabs
On Jan 14, 2013, at 7:54 PM, Robert Hanson wrote:
> Where we cross in the night, Kevin, is in what we imagine people wanting to
> do with "scripting" I think. While people could tap into the core of JSmol
> and learn how to manipulate the model directly, writing something that, say,
> allowed the selection of atoms and then centered the display on them, it's a
> lot easier to write:
>
> Jmol.script(jmolApplet0, "select 10-20;center selected;display selected")
>
> Right? My apologies to developers who would prefer to access the model
> directly and not utilize these higher level scripting features.
>
> I'm truly very interested in seeing actual pages that have been developed
> using ChemDoodle 3D tools. All I can find are your two pages, Kevin:
>
> http://web.chemdoodle.com/demos/pdb-ribbons
> http://web.chemdoodle.com/demos/molgrabber-3d
>
> Please point us to pages that others have developed that utilize some sort of
> nontrivial manipulation of the model to good effect. I for one would be very
> interested in what people have done with this tool. My problem is that when I
> search for "ChemDoodle" I find only 2D drawing sites. What keywords should I
> be using for that?
>
> Another question: I'm struggling to understand how you envision the
> HTML5-only and the WebGL versions of ChemDoodle 3D being used. How do you see
> that working? Do you see the WebGL version as being at all usable at this
> point -- based on the limited availability of WebGL? Is it still just a
> proof-of-concept for a future when WebGL is ubiquitous? (Can the same be said
> for HTML5?) What are the advantages to using one over the other?
>
> Bob
>
>
>
>
>
>
>
>
>
>
>
> On Mon, Jan 14, 2013 at 7:45 AM, Kevin Theisen <ke...@ichemlabs.com> wrote:
> Hi Bob,
>
> I get it, you are biased towards JSmol as I am biased towards the ChemDoodle
> Web Components. Certainly you are an authority on Jmol, but when it comes to
> the ChemDoodle Web Components and to WebGL your knowledge is lacking at best.
>
> I'm not interested in starting a flame war here, I only responded to correct
> the biased statement about our product.
>
> Jmol provides a tried and tested scripting language that many here are used
> to using. This is a good thing. But it is not the only way. The ChemDoodle
> Web Components use Javascript. You are always stating that you need to be a
> programming wizard to use even basic Javascript tools. I would be surprised
> if your users didn't find that a bit insulting. Everyone here is very smart
> and probably already knows how to use Javascript. With our tutorial the
> majority of the ChemDoodle Web Components API can be mastered within a few
> hours, allowing users significant control over the software and a very
> sophisticated and flexible ability to mold their HTML5 interfaces.
>
> I am glad our developments in the HTML5 space over the last 4 years have
> inspired you to create JSmol. The open source community benefits from having
> access to many options. As I said before, regardless of our opinions, the
> community wins here, which is the real goal behind open source solutions. I
> am happy to contribute!
>
> Sincerely,
> Kevin Theisen
> President, iChemLabs
>
>
>
>
>
>
> On Jan 13, 2013, at 8:12 PM, Robert Hanson wrote:
>
>>
>>
>>
>> On Sun, Jan 13, 2013 at 4:59 PM, Kevin Theisen <ke...@ichemlabs.com> wrote:
>> Thanks for the analysis Bob, I need to add in my thoughts.
>>
>> First, as far as open source goes, I don't really believe there is any sense
>> of some "competition". Open source provides tools to the community, each is
>> unique and will be used in unique ways by the community. Some will even use
>> multiple solutions to craft the type of product they are trying to create.
>> Open source solutions are all great. In the open source world, if a tool is
>> not necessary, people will not use it and it will not be developed further.
>> But an open source developer that believes he/she is in some sort of
>> competition with another open source solution has already lost.
>>
>>
>> I hope I didn't make that sound competitive. I was remarking about the tools
>> that are out there that I know of. I'm very happy to see ChemDoodle continue
>> to develop, and if what we have done helps in that, that's terrific. I'm
>> just saying that right now it has such a long way to go to get to Jmol's
>> level of sophistication, operability, and flexibility, whereas JSmol is
>> there right now.
>>
>>
>> And this is the only pointed question I have for you Bob, how do you see the
>> J(S)mol code being sustainable as time goes on? There will be users that
>> want offline desktop support, <canvas> support and WebGL support. Each time
>> you develop a feature, you have to re-implement it twice more or very soon
>> users will get confused as to which version to use. What is your advice on
>> this?
>>
>> Well, actually, that's the beauty of it, Kevin. JSmol is Jmol. The codebase
>> is the same, so new features are new features, that's all. It is highly
>> sustainable. Not sure what you mean by "reimplementing". I push one button,
>> and it becomes the Jmol Java application and the Jmol applet; I push
>> another, and it becomes JavaScript. It's not as if I am developing these
>> independently. I have not been developing JSmol as a new product; I have
>> been adapting Jmol to be able to be compiled directly into either Java or
>> JavaScript, that's all.
>>
>> The WebGL support is minimal simply because I have been reluctant to produce
>> something that is only an approximation of the "real thing" so far. In
>> contrast, the HTML5 version is an exact pixel-for-pixel reproduction of Jmol
>> in JavaScript. It's the same code. I think the WebGL aspects will develop,
>> if there is really interest in that, but I don't see it as a high priority
>> right now. There is still just too little of a base for WebGL. For example,
>> I just got a new Windows 8 computer, and both Chrome and MSIE refuse to view
>> http://web.chemdoodle.com/demos/molgrabber-3d . Since iPads also don't have
>> WebGL enabled, that's just not a workable solution. Maybe Apple will enable
>> full HTML5 functionality, but I'm not interested in waiting for that.
>>
>> I'm not sure about your comment in relation to Jmol needing a server. What
>> is that all about?Are you saying ChemDoodle is pulling files successfully
>> off a hard drive without a server in MSIE and Chrome? Desktop Jmol is in the
>> form of the Jmol application. Java is not disappearing from computers -- the
>> issue isn't Java per se, it's Java as a plug-in to a browser.
>>
>> Kevin, a few questions for you:
>>
>> What is the platform base for ChemDoodle 3D now? I still can't find much
>> that will run it.
>>
>> Is http://web.chemdoodle.com/demos/molgrabber-3d still a working page? (I
>> can't get that to work, personally.)
>>
>> Do you have plans to support MSIE?
>>
>> Can you please point us to the page you had that lists web sites using
>> ChemDoodle? I'm very interested in seeing what people are doing iw
>>
>> Bob
>>
>>
>>
>> --
>> 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
>>
>> ------------------------------------------------------------------------------
>> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
>> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
>> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
>> MVPs and experts. SALE $99.99 this month only -- learn more at:
>> http://p.sf.net/sfu/learnmore_122412_______________________________________________
>>
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> ------------------------------------------------------------------------------
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. SALE $99.99 this month only -- learn more at:
> http://p.sf.net/sfu/learnmore_122412
> _______________________________________________
> 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, 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
>
> ------------------------------------------------------------------------------
> Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS
> and more. Get SQL Server skills now (including 2012) with LearnDevNow -
> 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts.
> SALE $99.99 this month only - learn more at:
> http://p.sf.net/sfu/learnmore_122512_______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
------------------------------------------------------------------------------
Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS
and more. Get SQL Server skills now (including 2012) with LearnDevNow -
200+ hours of step-by-step video tutorials by Microsoft MVPs and experts.
SALE $99.99 this month only - learn more at:
http://p.sf.net/sfu/learnmore_122512
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
