{"id":34271,"date":"2015-02-01T00:58:18","date_gmt":"2015-02-01T00:58:18","guid":{"rendered":"https:\/\/wordpress.org\/plugins-wp\/jsmol2wp\/"},"modified":"2018-03-09T10:28:45","modified_gmt":"2018-03-09T10:28:45","slug":"jsmol2wp","status":"closed","type":"plugin","link":"https:\/\/wordpress.org\/plugins\/jsmol2wp\/","author":426620,"comment_status":"closed","ping_status":"closed","template":"","meta":{"version":"1.07","stable_tag":"trunk","tested":"4.9.29","requires":"3.0","requires_php":"","requires_plugins":"","header_name":"jsmol2wp","header_author":"JimHu","header_description":"","assets_banners_color":"ffffff","last_updated":"2018-03-09 10:28:45","external_support_url":"","external_repository_url":"","donate_link":"http:\/\/biochemistry.tamu.edu\/index.php\/alum\/giving\/","header_plugin_uri":"","header_author_uri":"http:\/\/jimhu.org","rating":4,"author_block_rating":0,"active_installs":10,"downloads":1322,"num_ratings":0,"support_threads":0,"support_threads_resolved":0,"author_block_count":0,"sections":["description","installation","faq","changelog"],"tags":[],"upgrade_notice":{"":"<p>Version 1.03 updates the Jmol libraries and fixes a bug with the load parameter<\/p>"},"ratings":{"1":0,"2":0,"3":0,"4":"1","5":0},"assets_icons":[],"assets_banners":{"banner-772x250.png":{"filename":"banner-772x250.png","revision":"1081065","resolution":"772x250","location":"assets"}},"assets_blueprints":{},"all_blocks":[],"tagged_versions":["1.01","1.02","1.03","1.04","1.05","1.06"],"block_files":[],"assets_screenshots":[],"screenshots":{"1":"Applet for a protein.","2":"Applet for a small molecule."}},"plugin_section":[],"plugin_tags":[38642,38641,38643,38644,357],"plugin_category":[43],"plugin_contributors":[],"plugin_business_model":[],"class_list":["post-34271","plugin","type-plugin","status-closed","hentry","plugin_tags-jmol","plugin_tags-jsmol","plugin_tags-molecular-graphics","plugin_tags-pdb","plugin_tags-shortcodes","plugin_category-customization","plugin_committers-jimhu"],"banners":[],"icons":{"svg":false,"icon":"https:\/\/s.w.org\/plugins\/geopattern-icon\/jsmol2wp_ffffff.svg","icon_2x":false,"generated":true},"screenshots":[],"raw_content":"<!--section=description-->\n<p>This shortcode plugin places JSmol applets in WordPress posts and pages.<\/p>\n\n<p>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.<\/p>\n\n<p>This plugin was developed for use on the website for the Department of Biochemistry and Biophysics\nat Texas A&amp;M University (http:\/\/biochemistry.tamu.edu).<\/p>\n\n<!--section=installation-->\n<p>Place in the plugins directory and activate. No additional files or configurations are needed.<\/p>\n\n<p>Thanks to Bob Hanson and the JMol team for making the javascript code for jsmol available. See:<\/p>\n\n<p>http:\/\/chemapps.stolaf.edu\/jmol\/jsmol\nhttp:\/\/wiki.jmol.org\/index.php\/Jmol_JavaScript_Object<\/p>\n\n<p>This plugin also benefited from using Jaime Prilusky's mediawiki extension for inspiration\nhttp:\/\/proteopedia.org\/support\/JSmolExtension\/<\/p>\n\n<!--section=faq-->\n<dl>\n<dt>Installation Instructions<\/dt>\n<dd><p>Place in the plugins directory and activate. No additional files or configurations are needed.<\/p>\n\n<p>Thanks to Bob Hanson and the JMol team for making the javascript code for jsmol available. See:<\/p>\n\n<p>http:\/\/chemapps.stolaf.edu\/jmol\/jsmol\nhttp:\/\/wiki.jmol.org\/index.php\/Jmol_JavaScript_Object<\/p>\n\n<p>This plugin also benefited from using Jaime Prilusky's mediawiki extension for inspiration\nhttp:\/\/proteopedia.org\/support\/JSmolExtension\/<\/p><\/dd>\n<dt>Is there an example of an installation?<\/dt>\n<dd><p>See http:\/\/jimhu.org\/jsmol2wp-plugin-released-at-wordpress-org\/<\/p><\/dd>\n<dt>Where can I learn more about what JSmol can do?<\/dt>\n<dd><p>Jmol documentation can be found at http:\/\/jmol.sourceforge.net\/#Learn%20to%20use%20Jmol and http:\/\/jmol.sourceforge.net\/docs\/JmolUserGuide\/<\/p><\/dd>\n\n<\/dl>\n\n<!--section=changelog-->\n<h4>1.07<\/h4>\n\n<p>fix extremely stupid svn error where needed files from the j2s directory were not in the repo<\/p>\n\n<h4>1.06<\/h4>\n\n<p>change rcsb file path to avoid redirect<\/p>\n\n<h4>1.05<\/h4>\n\n<p>load rcsb pdb files via https instead of http<\/p>\n\n<h4>1.04<\/h4>\n\n<ul>\n<li>updated jsmol package from Jmol sourceforge<\/li>\n<li>first attempt at internationalization\n** Added idioma directory from jsMol distributions\n** Added set language directive based on wordpress get_locale()<\/li>\n<\/ul>\n\n<h4>1.03<\/h4>\n\n<ul>\n<li>updated jsmol package from Jmol sourceforge<\/li>\n<li>Remove beta from help.htm<\/li>\n<li>fix bug where load param was not working<\/li>\n<\/ul>\n\n<h4>1.02<\/h4>\n\n<ul>\n<li>fixes to this readme.txt file to improve the display at the wordpress.org plugin repository<\/li>\n<\/ul>\n\n<h4>1.01<\/h4>\n\n<ul>\n<li>tweaks for wordpress.org deposition<\/li>\n<\/ul>\n\n<h4>1.0<\/h4>\n\n<ul>\n<li>update JSmol code to 14.3.12_2015.01.28<\/li>\n<li>prepare for release to wordpress.org plugin repository<\/li>\n<\/ul>\n\n<h4>0.94 beta<\/h4>\n\n<ul>\n<li>add isosurface support<\/li>\n<li>rewrite the code to set up structure loading<\/li>\n<li>replace WP get_page_by_title with a function that matches the filename<\/li>\n<li>add jvxl to file types<\/li>\n<li>fixed bug where caption nonmatching required casting match as a string.<\/li>\n<li>move the help demo page to a more stable URL.<\/li>\n<\/ul>\n\n<h4>0.93 beta<\/h4>\n\n<ul>\n<li>set default type based on fileurl extension if present<\/li>\n<li>fix bug where reset button failed with data from fileurl<\/li>\n<\/ul>\n\n<h4>0.92 beta<\/h4>\n\n<ul>\n<li>change appletID to not require $acc.<\/li>\n<\/ul>\n\n<h4>0.9 beta<\/h4>\n\n<ul>\n<li>improve help page<\/li>\n<li>improve uniqueness identifiers for multiple Jmolapplets on the same post\/page; add the option to hand code instances<\/li>\n<li>improve debug messages (or at least change them)<\/li>\n<li>make reset button standard and have it remember the load commands<\/li>\n<li>standard buttons depend on the type of molecule loaded.<\/li>\n<li>add some semicolons to the template to try to fix lint warnings: http:\/\/www.javascriptlint.com\/online_lint.php<\/li>\n<\/ul>\n\n<h4>0.8 beta<\/h4>\n\n<ul>\n<li>removed data directory<\/li>\n<li>changed system for counting instances of the shorttag so we don't need preg_match<\/li>\n<li>removed whitespace from template hoping that solves the problem of themes adding markup<\/li>\n<li>simplified load script as suggested by Bob Hansen<\/li>\n<li>made applet IDs more unique by appending post id<\/li>\n<\/ul>\n\n<h4>0.7 beta<\/h4>\n\n<ul>\n<li>update jsmol libraries to 4.1.7_2014.06.09<\/li>\n<li>add dependencies for jquery-ui-core and jquery-ui-menu fixes popup problem in some themes<\/li>\n<li>refactor to support additional file types (in progress)<\/li>\n<li>fix multiline regex bug<\/li>\n<li>fix bug that caused failure to load when permalinks used ?p=post_number format<\/li>\n<li>debug constructor<\/li>\n<li>debug view\n..* add path to uploaded file\n..* add test for get_page_by_title<\/li>\n<\/ul>\n\n<h4>0.6 alpha<\/h4>\n\n<ul>\n<li>register script before enqueueing it.<\/li>\n<li>added ability to add Jmol.script commands<\/li>\n<li>added the ability to add jmolCommandInput<\/li>\n<\/ul>\n\n<h4>0.5 alpha<\/h4>\n\n<ul>\n<li>added wrap and debug options<\/li>\n<\/ul>\n\n<h4>0.4 alpha<\/h4>\n\n<ul>\n<li>changed to nojq.<\/li>\n<li>modified command processing to not split on allowed characters in Jmol syntax.<\/li>\n<\/ul>\n\n<h4>0.3 alpha<\/h4>\n\n<ul>\n<li>changed default to spin off in order to save client cpu<\/li>\n<li>custom command buttons working.<\/li>\n<\/ul>\n\n<h4>0.2 alpha<\/h4>\n\n<ul>\n<li>changed system to use a template based on the distro file simple1.htm. <\/li>\n<li>added captioning<\/li>\n<li>works with local or remote pdb files from rcsb.org\/pdb<\/li>\n<\/ul>\n\n<h4>0.1 pre-alpha<\/h4>\n\n<ul>\n<li>basic shortcode working with uploaded pdb file<\/li>\n<li>adds .pdb chemical\/pdb mime type to allowed mime types<\/li>\n<li>handles multiple shortcodes on the same page<\/li>\n<\/ul>","raw_excerpt":"Plugin to place JSmol molecular graphics applets in Wordpress posts or pages.","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/wordpress.org\/plugins\/wp-json\/wp\/v2\/plugin\/34271","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wordpress.org\/plugins\/wp-json\/wp\/v2\/plugin"}],"about":[{"href":"https:\/\/wordpress.org\/plugins\/wp-json\/wp\/v2\/types\/plugin"}],"replies":[{"embeddable":true,"href":"https:\/\/wordpress.org\/plugins\/wp-json\/wp\/v2\/comments?post=34271"}],"author":[{"embeddable":true,"href":"https:\/\/wordpress.org\/plugins\/wp-json\/wporg\/v1\/users\/jimhu"}],"wp:attachment":[{"href":"https:\/\/wordpress.org\/plugins\/wp-json\/wp\/v2\/media?parent=34271"}],"wp:term":[{"taxonomy":"plugin_section","embeddable":true,"href":"https:\/\/wordpress.org\/plugins\/wp-json\/wp\/v2\/plugin_section?post=34271"},{"taxonomy":"plugin_tags","embeddable":true,"href":"https:\/\/wordpress.org\/plugins\/wp-json\/wp\/v2\/plugin_tags?post=34271"},{"taxonomy":"plugin_category","embeddable":true,"href":"https:\/\/wordpress.org\/plugins\/wp-json\/wp\/v2\/plugin_category?post=34271"},{"taxonomy":"plugin_contributors","embeddable":true,"href":"https:\/\/wordpress.org\/plugins\/wp-json\/wp\/v2\/plugin_contributors?post=34271"},{"taxonomy":"plugin_business_model","embeddable":true,"href":"https:\/\/wordpress.org\/plugins\/wp-json\/wp\/v2\/plugin_business_model?post=34271"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}