Hello Robert,
> What is a Jenkins plug-in?
It is an extension to Jenkins. Jenkins is a build server, used mainly for
building software, but that can be used for general automation, systems
integration and grid computing (see Apache Mesos). Our goal in BioUno is
automate research pipelines with Jenkins. Writing plug-ins for Jenkins, it took
me 3 hours to run jmol and write this plug-in.
> What was the question about accessing a remote database?
At the moment the plug-in needs a file (pdb, mol) in the job workspace. But I
believe downloading it from places like RCSB PDB protein bank, web servers or
other public data sources would be doable too. But I'm only starting to learn
about jmol :^)
> <script src="/plugin/jmol/js/JSmol.min.js"></script>
I get these errors in chrome when I replace those JS's by JSmol.min.js.
1. Uncaught ReferenceError: jmolApplet is not defined (index):47
1. Uncaught TypeError: undefined is not a function prototype.js:5798
1. Uncaught TypeError: undefined is not a function
Thank you!
Bruno
>________________________________
> From: Robert Hanson <hans...@stolaf.edu>
>To: Bruno P. Kinoshita <brunodepau...@yahoo.com.br>; Jmol Developers
><jmol-developers@lists.sourceforge.net>
>Sent: Tuesday, June 3, 2014 1:48 AM
>Subject: Re: [Jmol-developers] Using Jmol in Jenkins jobs
>
>
>
>Looks very nice. What is a Jenkins plug-in? What was the question about
>accessing a remote database? You should be able to replace
>
><script src="/plugin/jmol/js/JSmoljQueryExt.js"></script><script
>src="/plugin/jmol/js/JSmolCore.js"></script><script
>src="/plugin/jmol/js/JSmolApplet.js"></script><script
>src="/plugin/jmol/js/JSmolApi.js"></script><script
>src="/plugin/jmol/js/j2sjmol.js"></script><script
>src="/plugin/jmol/js/JSmolThree.js"></script><script
>src="/plugin/jmol/js/JSmolGLmol.js"></script><script
>src="/plugin/jmol/js/JSmol.nojq.js"></script><script
>src="/plugin/jmol/js/Jmol2.js">
>
>with
>
><script src="/plugin/jmol/js/JSmol.min.js"></script>
>
>
>
>I think.
>
>
>Bob Hanson
>
>
>On Mon, Jun 2, 2014 at 8:41 PM, Bruno P. Kinoshita
><brunodepau...@yahoo.com.br> wrote:
>
>Hi all!
>>
>>
>>
>>I had some spare time this weekend and as project of the day I wrote a
>>Jenkins plug-in that uses Jmol to display molecules in builds [1]. This can
>>be useful for automated pipelines that retrieve data from API's or version
>>control like Git.
>>
>>
>>It all started while I was learning more about BioJava. One of its first
>>tutorials uses Jmol to display proteins and I thought it would be nice to
>>start by integrating Jmol and Jenkins. A future version of this plug-in could
>>use BioJava to retrieve the protein from a remote database.
>>
>>
>>For a live version you can go to
>>http://builds.tupilabs.com/view/BioUno/job/jmol-sample/1/
>>
>>
>>Let me know if you find it useful, and kudos for all the work in Jmol. It was
>>my first time using it, but there was good documentation and examples, and
>>the Javascript library worked very well too.
>>
>>
>>Cheers
>>Bruno
>>
>>
>>[1] https://github.com/biouno/jmol-plugin
>>------------------------------------------------------------------------------
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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
>
>
>
>------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
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