{"id":5881,"date":"2011-12-11T13:07:39","date_gmt":"2011-12-11T13:07:39","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=5881"},"modified":"2012-08-15T21:39:09","modified_gmt":"2012-08-15T20:39:09","slug":"mobile-friendly-solutions-for-viewing-wordpress-blogs-with-embedded-3d-molecular-coordinates","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5881","title":{"rendered":"Mobile-friendly solutions for viewing (WordPress) Blogs with embedded  3D molecular coordinates."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"5881\">\n<p>My <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=8\" target=\"_blank\">very first post<\/a> on this blog, in 2008, was to describe how Jmol could be used to illustrate chemical themes by adding 3D models to posts. Many of my subsequent efforts have indeed invoked Jmol. I thought I might review progress since then, with a particular focus on using the new generations of mobile device that have subsequently emerged.<\/p>\n<ol>\n<li>Jmol is based on Java, which has been adopted by Google&#8217;s Android mobile operating system, but not by Apple&#8217;s IOS.\n<ul>\n<li>An Android version of Jmol was <a href=\"https:\/\/market.android.com\/search?q=jmol&amp;so=1\" target=\"_blank\">recently released<\/a>, to rave reviews! I do not know however whether the Jmol on these posts can be viewed via Android. Perhaps someone can post a comment here on that aspect?<\/li>\n<li>HP has <a href=\"http:\/\/www.hp.com\/hpinfo\/newsroom\/press\/2011\/111209xa.html\" target=\"_blank\">just announced<\/a> it will open source WebOS, but it seems Java <a href=\"http:\/\/www.webos-internals.org\/wiki\/Java_Support_in_webOS\" target=\"_blank\">will not be supported<\/a>\u00a0so probably no Jmol there then.<\/li>\n<li>Windows 8 Mobile (Metro) also seems <a href=\"http:\/\/icewalker2g.wordpress.com\/2011\/09\/15\/java-and-the-windows-8-metroverse\/\" target=\"_blank\">unlikely to support it <\/a>either.<\/li>\n<\/ul>\n<\/li>\n<li>Apple has been prominent in touting HTML5 as a Java replacement. In practice, this means that any molecular viewer would be based on a combination of Javascript and WebGL technologies.\u00a0 Whereas Java is a compiled language, Javascript is interpreted on-the-fly by the browser. Its viability has been greatly increased by very large improvements in the speeds that browsers interpret Javascript nowadays, but this speed is unlikely to ever match that of Java. The real issue is whether that matters. The other difference is that whereas a signed Java applet allows data to escape from the security Sandbox (and into eg a file system), Javascript is likely to be much more restrictive. These two properties mean that Javascript\/HTML5 implementations make a lot of use of server-side functionality; in other words a lot of bytes may have to flow between server and mobile device to achieve a desired effect (and the user may have to pay for these bytes via their data plan).\n<ul>\n<li>One early adopter of the Javascript\/WebGL HTML5 model has been ChemDoodle, which I <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=3183\" target=\"_blank\">illustrated on this blog<\/a> about a year ago. I have tidied up the recipe for invoking it since then, and this is given below for anyone interested in implementing it. As of this moment, one essential component, WebGL, is only available to developers of Apple&#8217;s IOS system, but I expect this to become generally available soon. When that happens, ChemDoodle components on this blog will start working.<\/li>\n<li>A new entrant is <a href=\"http:\/\/webglmol.sourceforge.jp\/index-en.html\" target=\"_blank\">GLmol<\/a>, an open source molecular viewer for Apple&#8217;s IOS. A version is also <a href=\"http:\/\/webglmol.sourceforge.jp\/android-en.html\" target=\"_blank\">available for Android<\/a>. I may give a try at embedding this into the blog.<\/li>\n<\/ul>\n<\/li>\n<\/ol>\n<div>It seems that the 3D molecular viewing options are certainly increasing, but at the moment there is some uncertainty in performance, compatibility and the ability to extract molecular data from the &#8220;<em>sandboxes<\/em>&#8220;. This last comment relates to the <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=3154\" target=\"_blank\">re-usability<\/a>\u00a0of data, which I particularly value.<\/div>\n<div>\n<p>Although this post has focussed on embedding and rendering molecular data into a blog post, the same principle in fact applies to other expressions. Perhaps the most interesting is the epub3 e-book format, which also supports Javascript\/HTML5, and which seems likely to be adopted for future interactive e-books. Indeed, it should be possible to fully convert an interactive blog created using this technology to a e-book with relatively little effort. I have also <a href=\"http:\/\/www.ch.imperial.ac.uk\/local\/organic\/pericyclic\/epub3_test.html\" target=\"_blank\">illustrated here<\/a> how lecture notes can be so converted.<\/p>\n<\/div>\n<div>\n<p>If you get the impression that the task of a modern communicator of science and chemistry is not merely that of penning well chosen words to describe their topic, but of having to program their effort, then you may not be mistaken.<\/p>\n<\/div>\n<hr \/>\n<h3>Procedure for creating a 3D model in a WordPress blog post using ChemDoodle.<\/h3>\n<ol>\n<li>As administrator, go to\n<pre>wp-content\/themes\/default<\/pre>\n<p>(or whatever theme you use) and in the file header.php, paste the following<\/p>\n<pre>&lt;link rel=\"stylesheet\" href=\"..\/ChemDoodle\/ChemDoodleWeb.css\" type=\"text\/css\"&gt;\r\n  &lt;script type=\"text\/javascript\" src=\"..\/ChemDoodle\/ChemDoodleWeb-libs.js\"&gt;&lt;\/script&gt;\r\n  &lt;script type=\"text\/javascript\" src=\"..\/ChemDoodle\/ChemDoodleWeb.js\"&gt;&lt;\/script&gt;\r\n   &lt;script type=\"text\/javascript\" language=\"JavaScript\"&gt;\r\n  function httpGet(theUrl)\r\n   {var xmlHttp = null;\r\n   xmlHttp = new XMLHttpRequest();\r\n   xmlHttp.open( \"GET\", theUrl, false );\r\n   xmlHttp.send( );\r\n   return xmlHttp.responseText;}\r\n   &lt;\/script&gt;<\/pre>\n<\/li>\n<li>From<a href=\"http:\/\/web.chemdoodle.com\/installation\" target=\"_blank\"> here,<\/a> get the ChemDoodle components and put them into the directory immediately above the WordPress installation. They are there referenced by the path ..\/ChemDoodle as in the script above. You can put the folder elsewhere if you modify the path in the script accordingly.<\/li>\n<li>Invoke an instance of a molecule thus;\n<pre>&lt;script type=\"text\/javascript\"&gt;\/\/ &lt;![CDATA[\r\nvar transformBallAndStick2 = new ChemDoodle.TransformCanvas3D('transformBallAndStick2', 190, 190);transformBallAndStick2.specs.set3DRepresentation('Ball and Stick');         transformBallAndStick2.specs.backgroundColor = 'white';var molFile = httpGet( 'wp-content\/uploads\/2011\/12\/85-trans.mol' );var molecule = ChemDoodle.readMOL(molFile, 2);         transformBallAndStick2.loadMolecule(molecule);\r\n\/\/ ]]&gt;&lt;\/script&gt;<\/pre>\n<\/li>\n<li>The key requirement is that the body of the script (starting with var) must not contain any line breaks; it must be a single wide line. So that you can see the whole line here, I show it in wrapped form (which you must not use);\n<pre>var transformBallAndStick2 = new\r\nChemDoodle.TransformCanvas3D('\r\ntransformBallAndStick2', 190,\r\n190);transformBallAndStick2.specs.\r\nset3DRepresentation('Ball and Stick');\r\ntransformBallAndStick2.specs.\r\nbackgroundColor = 'white';var molFile =\r\nhttpGet('wp-content\/uploads\/2011\/12\/85-trans.mol');\r\nvar molecule =ChemDoodle.readMOL(molFile, 2);\r\ntransformBallAndStick2.loadMolecule(molecule);<\/pre>\n<\/li>\n<li>The key data will be located in the path <tt>wp-content\/uploads\/2011\/12\/85-trans.mol\u00a0<\/tt>which you should upload. Note that only the MDL molfile is supported in this mode (which makes no server-side requests). One can use eg CML, but this must be as a server request.<\/li>\n<li>If you want multiple instances, then you must change each occurrence of the name of the variable, e.g.\u00a0<strong>transformBallAndStick2<\/strong> to be unique for each.<\/li>\n<li>If you want to annotate the resulting display, server-side requests are again needed. I do not illustrate these here, but there is an <a href=\"http:\/\/web.chemdoodle.com\/tutorial\" target=\"_blank\">excellent tutorial.<\/a><\/li>\n<\/ol>\n<hr \/>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 5881 -->","protected":false},"excerpt":{"rendered":"<p>My very first post on this blog, in 2008, was to describe how Jmol could be used to illustrate chemical themes by adding 3D models to posts. Many of my subsequent efforts have indeed invoked Jmol. I thought I might review progress since then, with a particular focus on using the new generations of mobile [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":5,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[2],"tags":[791,344,790,783,785,786,521,59,784,487,490,343,788,611,789,894,373,787],"ppma_author":[2661],"class_list":["post-5881","post","type-post","status-publish","format-standard","hentry","category-chemical-it","tag-administrator","tag-android","tag-android-mobile-operating-system","tag-ball","tag-chemical-themes","tag-e-book","tag-e-books","tag-google","tag-hp","tag-java","tag-javascript","tag-microsoft-windows","tag-mobile-device","tag-operating-system","tag-php","tag-skolnik","tag-tutorial-material","tag-webgl-technologies"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Mobile-friendly solutions for viewing (Wordpress) Blogs with embedded 3D molecular coordinates. - Henry Rzepa&#039;s Blog<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5881\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Mobile-friendly solutions for viewing (Wordpress) Blogs with embedded 3D molecular coordinates. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"My very first post on this blog, in 2008, was to describe how Jmol could be used to illustrate chemical themes by adding 3D models to posts. 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The code used to obtain the above was: <script src=\"..\/Jmol\/Jmol.js\" type=\"text\/javascript\" \/> This line is best added to the theme header by editing the file \/wp-content\/themes\/default\/header.php to add the following line in the header: <script src=\"..\/Jmol\/Jmol.js\" type=\"text\/javascript\"><\/script> <img onclick=\"jmolInitialize('..\/Jmol\/','JmolAppletSigned.jar');jmolSetAppletColor('yellow'); jmolApplet([450,450],'load\u2026","rel":"","context":"In &quot;Chemical IT&quot;","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/07\/a80.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":1930,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1930","url_meta":{"origin":5881,"position":1},"title":"WebCite and Jmol","author":"Henry Rzepa","date":"April 18, 2010","format":false,"excerpt":"Since I have gotten into the habit of quoting some of my posts in other contexts, I have started to also archive them using WebCite. One can quote the resulting archive as: Rzepa, Henry. Quintuple bonds. \u00a02010-04-18. URL:http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1722. Accessed: 2010-04-18.\u00a0(Archived by WebCite\u00ae at http:\/\/www.webcitation.org\/5p5BtuzSH) There is one issue though. \u00a0Many\u2026","rel":"","context":"In &quot;Chemical IT&quot;","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":11895,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11895","url_meta":{"origin":5881,"position":2},"title":"3D-rendered molecular models on this blog: an update.","author":"Henry Rzepa","date":"January 16, 2014","format":false,"excerpt":"So much to do, so little time to do it. That is my excuse at least. Right from my first post on this blog in 2008\u00a0I have tried to enhance it using Jmol, a Java-based applet (normally indicated with the caption Click for 3D). This has been pretty stable for\u2026","rel":"","context":"In &quot;General&quot;","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":19697,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19697","url_meta":{"origin":5881,"position":3},"title":"Ten years on: Jmol and WordPress.","author":"Henry Rzepa","date":"May 16, 2018","format":false,"excerpt":"Ten years are a long time when it comes to (recent) technologies. The first post on this blog was on the topic of how to present chemistry with three intact dimensions. I had in mind molecular models, molecular isosurfaces and molecular vibrations (arguably a further dimension). Here I reflect on\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":3183,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=3183","url_meta":{"origin":5881,"position":4},"title":"Embedding molecules in blogs: ChemDoodle, WebGL and SVG","author":"Henry Rzepa","date":"December 24, 2010","format":false,"excerpt":"If you get a small rotatable molecule below, then ChemDoodle\/HTML5\/WebGL is working. Why might this be important? Well, the future is mobile, in other words, devices that rely on batteries or other sources of built-in power. This means the power guzzling GPU cards of the past (some reach ~400 Watts!)\u2026","rel":"","context":"In &quot;Chemical IT&quot;","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":12607,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12607","url_meta":{"origin":5881,"position":5},"title":"Test of JSmol in WordPress: the background story.","author":"Henry Rzepa","date":"June 8, 2014","format":false,"excerpt":"A word of explanation about this test page for experimenting with JSmol. Many moons ago I posted about how to include a generated 3D molecular model in a blog post, and have used that method on many posts here ever since. 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