122 lines
5.2 KiB
Plaintext
122 lines
5.2 KiB
Plaintext
=== JSmol2WP ===
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Contributors: Jim Hu
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Tags: shortcodes, JSmol, Jmol, molecular graphics, PDB
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Requires at least: 3.0
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Tested up to: 4.9.4
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Donate link:http://biochemistry.tamu.edu/index.php/alum/giving/
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Stable tag: 1.07
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License: GPLv2 or later
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License URI: http://www.gnu.org/licenses/gpl-2.0.html
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Text domain:jsmol2wp
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Domain path:/languages/
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Plugin to place JSmol molecular graphics applets in Wordpress posts or pages.
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== Description ==
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This shortcode plugin places JSmol applets in WordPress posts and pages.
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Use [jsmol pdb='accession'] for a minimal version. jsmol2wp will look to see if a pdb file has been uploaded to your wordpress and it will use that file if it can find it. If it can't find a matching post for an uploaded attachement, it will try <a href='http://rcsb.org/pdb'>http://rcsb.org/pdb</a>. If it can't find a match there either, you'll get an error message in the JSmol window. Additional information on optional parameters are at the About/Help link in the applets.
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This plugin was developed for use on the website for the Department of Biochemistry and Biophysics
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at Texas A&M University (http://biochemistry.tamu.edu).
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== Installation ==
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Place in the plugins directory and activate. No additional files or configurations are needed.
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Thanks to Bob Hanson and the JMol team for making the javascript code for jsmol available. See:
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http://chemapps.stolaf.edu/jmol/jsmol
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http://wiki.jmol.org/index.php/Jmol_JavaScript_Object
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This plugin also benefited from using Jaime Prilusky's mediawiki extension for inspiration
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http://proteopedia.org/support/JSmolExtension/
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== Upgrade Notice ==
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Version 1.03 updates the Jmol libraries and fixes a bug with the load parameter
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== Frequently Asked Questions ==
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= Is there an example of an installation? =
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See http://jimhu.org/jsmol2wp-plugin-released-at-wordpress-org/
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= Where can I learn more about what JSmol can do? =
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Jmol documentation can be found at http://jmol.sourceforge.net/#Learn%20to%20use%20Jmol and http://jmol.sourceforge.net/docs/JmolUserGuide/
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== Screenshots ==
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1. Applet for a protein.
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2. Applet for a small molecule.
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== Changelog ==
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= 1.07 =
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fix extremely stupid svn error where needed files from the j2s directory were not in the repo
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= 1.06 =
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change rcsb file path to avoid redirect
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= 1.05 =
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load rcsb pdb files via https instead of http
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= 1.04 =
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* updated jsmol package from Jmol sourceforge
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* first attempt at internationalization
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** Added idioma directory from jsMol distributions
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** Added set language directive based on wordpress get_locale()
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= 1.03 =
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* updated jsmol package from Jmol sourceforge
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* Remove beta from help.htm
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* fix bug where load param was not working
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= 1.02 =
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* fixes to this readme.txt file to improve the display at the wordpress.org plugin repository
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= 1.01 =
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* tweaks for wordpress.org deposition
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= 1.0 =
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* update JSmol code to 14.3.12_2015.01.28
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* prepare for release to wordpress.org plugin repository
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= 0.94 beta =
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* add isosurface support
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* rewrite the code to set up structure loading
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* replace WP get_page_by_title with a function that matches the filename
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* add jvxl to file types
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* fixed bug where caption nonmatching required casting match as a string.
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* move the help demo page to a more stable URL.
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= 0.93 beta =
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* set default type based on fileurl extension if present
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* fix bug where reset button failed with data from fileurl
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= 0.92 beta =
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* change appletID to not require $acc.
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= 0.9 beta =
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* improve help page
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* improve uniqueness identifiers for multiple Jmolapplets on the same post/page; add the option to hand code instances
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* improve debug messages (or at least change them)
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* make reset button standard and have it remember the load commands
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* standard buttons depend on the type of molecule loaded.
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* add some semicolons to the template to try to fix lint warnings: http://www.javascriptlint.com/online_lint.php
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= 0.8 beta =
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* removed data directory
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* changed system for counting instances of the shorttag so we don't need preg_match
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* removed whitespace from template hoping that solves the problem of themes adding markup
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* simplified load script as suggested by Bob Hansen
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* made applet IDs more unique by appending post id
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= 0.7 beta =
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* update jsmol libraries to 4.1.7_2014.06.09
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* add dependencies for jquery-ui-core and jquery-ui-menu fixes popup problem in some themes
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* refactor to support additional file types (in progress)
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* fix multiline regex bug
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* fix bug that caused failure to load when permalinks used ?p=post_number format
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* debug constructor
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* debug view
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..* add path to uploaded file
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..* add test for get_page_by_title
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= 0.6 alpha =
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* register script before enqueueing it.
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* added ability to add Jmol.script commands
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* added the ability to add jmolCommandInput
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= 0.5 alpha =
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* added wrap and debug options
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= 0.4 alpha =
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* changed to nojq.
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* modified command processing to not split on allowed characters in Jmol syntax.
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= 0.3 alpha =
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* changed default to spin off in order to save client cpu
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* custom command buttons working.
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= 0.2 alpha =
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* changed system to use a template based on the distro file simple1.htm.
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* added captioning
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* works with local or remote pdb files from rcsb.org/pdb
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= 0.1 pre-alpha =
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* basic shortcode working with uploaded pdb file
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* adds .pdb chemical/pdb mime type to allowed mime types
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* handles multiple shortcodes on the same page
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