Re: [Jmol-developers] Jmol statistics
On Sun, Oct 30, 2011 at 4:04 AM, Robert Hanson hans...@stolaf.edu wrote: Can that be real? The CDK is at around 1800 a month, and Jmol has a much wider audience; so, those numbers look comparable. Or is mostly robots? That is a good question. 20% has an unknown OS, so that could very well be robots... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World#153; now supports Android#153; Apps for the BlackBerryreg; PlayBook#153;. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] Project idea: Jmol-Python API -- Jmol.py
What do you think of writing a Python interface to Jmol? It seems to me a lot of people like to use Python. It's the programming language of the average scientist. Now that we have Jmol set up with a sockets interface (Molecular Playground), why not write an interface that would be the entire JmolViewer interface, but via sockets? And then write a Python (or whatever language) API to go along with it? The Python developer would simply add the Jmol.py toolkit along with Jmol.jar and have instant access to (any number of) viewers, a POV-ray generator, a molecular structure analysis engine, structure and surface file readers, callback mechanisms, a customizable interface (possibly even using the signed applet with a local HTML page), the option to run headless with no visible viewer, etc., etc. From a Python viewpoint, it would be just another package. Jmol.py would work something like a database -- you make a connection, configure the connection, make function calls (queries), get results -- and the API would handle all the connectivity via sockets. From a Jmol viewpoint, it would look like Jmol just turned into a Python version. In effect, rather than writing a PyMol plug-in, what Python developer/user would be doing would be writing a Python program with a Jmol plug-in. Heck, we might even be able to write a PyMol-Jmol API that would enable PyMol plug-ins to be directly adaptable to Jmol, but of course with all the added power, breadth, and flexibility of Jmol. Sort of like the way we were able to port virtually all of Rasmol/Chime capability to Jmol and extend that immensely. (But I would consider that a secondary goal.) Good idea? Anyone want to work on this? I would definitely want to assemble a team to do this -- I personally have no experience at all with Python. Might even be fundable. :) Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World#153; now supports Android#153; Apps for the BlackBerryreg; PlayBook#153;. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Project idea: Jmol-Python API -- Jmol.py
Bob, This looks like a good idea to me. As I've been working with Sage, which is python based, I have some ideas about how that might work. It might also change the way Jmol can be used by Sage, although I'm not sure there is too much they would want to change about the way it is used as a 3-D viewer. This is something I would like to work on. However, because of the way the Univ. of Wisc. System is going, the only way I am going to get to devote adequate time to it, is if I can get funded to work on it. I also think this is a project which I could get some of my CS colleagues interested in. I'm game, but as you've said, we would have to assemble a team and a pretty careful plan about how we would start this. Maybe the first step is to assemble a team to write a grant proposal or proposals? We could target national funding agencies (maybe the international collaboration angle as well?) and maybe Google Summer of Code grants to fund some students? Jonathan On Oct 30, 2011, at 5:27 AM, Robert Hanson wrote: What do you think of writing a Python interface to Jmol? It seems to me a lot of people like to use Python. It's the programming language of the average scientist. Now that we have Jmol set up with a sockets interface (Molecular Playground), why not write an interface that would be the entire JmolViewer interface, but via sockets? And then write a Python (or whatever language) API to go along with it? The Python developer would simply add the Jmol.py toolkit along with Jmol.jar and have instant access to (any number of) viewers, a POV-ray generator, a molecular structure analysis engine, structure and surface file readers, callback mechanisms, a customizable interface (possibly even using the signed applet with a local HTML page), the option to run headless with no visible viewer, etc., etc. From a Python viewpoint, it would be just another package. Jmol.py would work something like a database -- you make a connection, configure the connection, make function calls (queries), get results -- and the API would handle all the connectivity via sockets. From a Jmol viewpoint, it would look like Jmol just turned into a Python version. In effect, rather than writing a PyMol plug-in, what Python developer/user would be doing would be writing a Python program with a Jmol plug-in. Heck, we might even be able to write a PyMol-Jmol API that would enable PyMol plug-ins to be directly adaptable to Jmol, but of course with all the added power, breadth, and flexibility of Jmol. Sort of like the way we were able to port virtually all of Rasmol/Chime capability to Jmol and extend that immensely. (But I would consider that a secondary goal.) Good idea? Anyone want to work on this? I would definitely want to assemble a team to do this -- I personally have no experience at all with Python. Might even be fundable. :) Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World#153; now supports Android#153; Apps for the BlackBerryreg; PlayBook#153;. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World#153; now supports Android#153; Apps for the BlackBerryreg; PlayBook#153;. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Packaging 12.2 for Debian/Ubuntu, disabling naga
Michael, I think you now have to wait on NAGA, if this is a hold up. As anybody can download Jmol and run or develop it on Ubuntu as it now stands, I don't see this as a pressing issue for the Jmol development team. Presently, I do most of my developing on an Ubuntu machine. You've done the correct thing by filing a report with NAGA. Regards, Jonathan On Oct 30, 2011, at 2:44 PM, Michael Banck wrote: Hi, I took a look at packaging 12.2 (congrats!) for Debian/Ubuntu, and realized it now requires the naga NIO asynchronous sockets implementation. I know you bundle the jar in your release tarball, but we have to remove all binary jars and repackage the tarball prior to build as per Debian policy and in order to comply with the Debian Free Software Guidelines. Naga has not yet been packaged for Debian, and as neither their subversion repository nor their release jarfiles have any copyright/license information (the website says MIT), this will likely not be accepted into the Debian/Ubuntu repositories for now. I have filed issue http://code.google.com/p/naga/issues/detail?id=12 to that effect. In the meantime, is there maybe a way to disable the need for having naga around while building jmol? Best regards, Michael -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World#153; now supports Android#153; Apps for the BlackBerryreg; PlayBook#153;. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World#153; now supports Android#153; Apps for the BlackBerryreg; PlayBook#153;. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Packaging 12.2 for Debian/Ubuntu, disabling naga
I'd have to build an interface, which I can do. The website is clear and the MIT license is fully compatible with LGPL from my reading http://www.opensource.org/licenses/mit-license.php So what's the problem exactly? Bob On Sun, Oct 30, 2011 at 2:44 PM, Michael Banck mba...@debian.org wrote: Hi, I took a look at packaging 12.2 (congrats!) for Debian/Ubuntu, and realized it now requires the naga NIO asynchronous sockets implementation. I know you bundle the jar in your release tarball, but we have to remove all binary jars and repackage the tarball prior to build as per Debian policy and in order to comply with the Debian Free Software Guidelines. Naga has not yet been packaged for Debian, and as neither their subversion repository nor their release jarfiles have any copyright/license information (the website says MIT), this will likely not be accepted into the Debian/Ubuntu repositories for now. I have filed issue http://code.google.com/p/naga/issues/detail?id=12 to that effect. In the meantime, is there maybe a way to disable the need for having naga around while building jmol? Best regards, Michael -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World#153; now supports Android#153; Apps for the BlackBerryreg; PlayBook#153;. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World#153; now supports Android#153; Apps for the BlackBerryreg; PlayBook#153;. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Packaging 12.2 for Debian/Ubuntu, disabling naga
That's checked in. See if it works to just leave out the Naga classes in the build. On Sun, Oct 30, 2011 at 5:32 PM, Robert Hanson hans...@stolaf.edu wrote: I'd have to build an interface, which I can do. The website is clear and the MIT license is fully compatible with LGPL from my reading http://www.opensource.org/licenses/mit-license.php So what's the problem exactly? Bob On Sun, Oct 30, 2011 at 2:44 PM, Michael Banck mba...@debian.org wrote: Hi, I took a look at packaging 12.2 (congrats!) for Debian/Ubuntu, and realized it now requires the naga NIO asynchronous sockets implementation. I know you bundle the jar in your release tarball, but we have to remove all binary jars and repackage the tarball prior to build as per Debian policy and in order to comply with the Debian Free Software Guidelines. Naga has not yet been packaged for Debian, and as neither their subversion repository nor their release jarfiles have any copyright/license information (the website says MIT), this will likely not be accepted into the Debian/Ubuntu repositories for now. I have filed issue http://code.google.com/p/naga/issues/detail?id=12 to that effect. In the meantime, is there maybe a way to disable the need for having naga around while building jmol? Best regards, Michael -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World#153; now supports Android#153; Apps for the BlackBerryreg; PlayBook#153;. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World#153; now supports Android#153; Apps for the BlackBerryreg; PlayBook#153;. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Packaging 12.2 for Debian/Ubuntu, disabling naga
Hi, On Sun, Oct 30, 2011 at 06:31:08PM -0500, Robert Hanson wrote: That's checked in. See if it works to just leave out the Naga classes in the build. Thanks a lot for the effort. I tried to backport it to the stable branch, but without success so far; the code has changed quite a bit. I'll see whether I manage over the next days. Michael -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World#153; now supports Android#153; Apps for the BlackBerryreg; PlayBook#153;. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Packaging 12.2 for Debian/Ubuntu, disabling naga
I'll check when I get to work tomorrow, I may have made a mistake there, but I don't think so. You would have to do the build, then simply remove all naga package files. There is no direct reference to them in the code anymore except in org.openscience.jmol.app.jsonkiosk.JsonNioService, which is only accessed via reflection and so can be completely removed. On Sunday, October 30, 2011, Michael Banck mba...@debian.org wrote: Hi, On Sun, Oct 30, 2011 at 06:31:08PM -0500, Robert Hanson wrote: That's checked in. See if it works to just leave out the Naga classes in the build. Thanks a lot for the effort. I tried to backport it to the stable branch, but without success so far; the code has changed quite a bit. I'll see whether I manage over the next days. Michael -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World#153; now supports Android#153; Apps for the BlackBerryreg; PlayBook#153;. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 -- Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World#153; now supports Android#153; Apps for the BlackBerryreg; PlayBook#153;. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
