Title: PCAViz Author: durrantlab Published: August 1, 2019 Last modified: August 2, 2019 --- Search plugins This plugin **hasn’t been tested with the latest 3 major releases of WordPress**. It may no longer be maintained or supported and may have compatibility issues when used with more recent versions of WordPress. ![](https://s.w.org/plugins/geopattern-icon/pcaviz.svg) # PCAViz By [durrantlab](https://profiles.wordpress.org/durrantlab/) [Download](https://downloads.wordpress.org/plugin/pcaviz.zip) * [Details](https://wordpress.org/plugins/pcaviz/#description) * [Reviews](https://wordpress.org/plugins/pcaviz/#reviews) * [Installation](https://wordpress.org/plugins/pcaviz/#installation) * [Development](https://wordpress.org/plugins/pcaviz/#developers) [Support](https://wordpress.org/support/plugin/pcaviz/) ## Description PCAViz is a tool for displaying molecular dynamics simulations in the browser. To encourage use, an easy-to-install PCAViz-powered WordPress plugin enables “plug- and-play” trajectory visualization. The PCAViz download also provides examples showing how to use PCAViz in any webpage. ### Examples of Use The PCAViz WordPress Plugin uses shortcodes that can be inserted into any WordPress post or page. ### Major Attributes 1. If you use the plugin without any attributes, it will allow your site visitors to select from any of the compressed JSON files you’ve uploaded to your WordPress media library. Note that these files must end in `.compressed.json` to be recognized.`[ pcaviz]` 2. If you want to show your site visitors a specific simulation present in your media library, simplify specify the name of the simulation. PCAViz will search through your media library and will choose the first JSON file ending in `.compressed.json` that includes your specified text in its title, URL, or file name. `[pcaviz file ="larp1"]` 3. You can also control the molecular styles. The WordPress plugin uses [3DMol.js](https://3dmol.csb.pitt.edu) to render molecules. Passing the plugin a [3DMol.js AtomStyleSpec](https://3dmol.csb.pitt.edu/doc/types.html#AtomStyleSpec) JSON string changes the way the molecules are displayed. `[pcaviz visStyle='{"cartoon":{" style": "trace", "color": "grey", "opacity": 0.75}}']` 4. Note that the [3DMol.js documentation](https://3dmol.csb.pitt.edu/doc/$3Dmol.GLViewer.html#setStyle) shows AtomStyleSpec examples as JavaScript objects. PCAViz accepts only JSON strings. The two look similar, but with important differences (e.g., keys in JSON strings must always be quoted). We recommend using a [JSON validator](https://jsonformatter.curiousconcept.com) to check your AtomStyleSpec strings. ### Minor Attributes 1. To explicitly specify the height and width of the viewer, in pixels: `[pcaviz height=150 width=150]` 2. To align the viewer to the left, center, or right, and to optionally add a caption:`[ pcaviz align="right" caption="My molecule in motion!"]` 3. To instead use the caption associated with the `.compressed.json` file in your media library: `[pcaviz mediaLibraryCaption="true"]` 4. (Note that this option is automatically set to true when no `file` attribute is specified.) 5. To hide the playback buttons: `[pcaviz playback_buttons="false"]` 6. To prevent the plugin from looping the animation: `[pcaviz loop="false"]` 7. The plugin starts playing the simulation automatically by default. To deactivate autoplay: `[pcaviz autoplay="false"]` 8. To specify the duration of the animation and how frequently the atomic positions are updated: `[pcaviz durationInMilliseconds=10000 updateFreqInMilliseconds=50]` 9. To smooth the animation by averaging the atomic coordinates over multiple frames:`[ pcaviz windowAverageSize=25]` 10. To control how the plugin caches calculated coordinates: `[pcaviz caching="continuous"]` 11. Acceptable values are “none” (no caching), “continuous” (cache each frame’s coordinates after they are first calculated), and “pre” (calculate and cache all frame coordinates before starting the animation). ## Installation You can install the PCAViz WordPress plugin via the official WordPress Plugin Directory. Search for **PCAViz**. The [wordpress.org](https://wordpress.org/support/article/managing-plugins/#automatic-plugin-installation) site provides useful instructions detailing how to install plugins from their directory. You can also install the plugin using this repository’s `pcaviz-wordpress/` directory. Either copy `pcaviz-wordpress/` directly to your server’s `wp-content/plugins/` directory ([instructions](https://wordpress.org/support/article/managing-plugins/#manual-plugin-installation)), or create a ZIP file of the `pcaviz-wordpress/` directory and upload it via your WordPress admin screen ([instructions](https://wordpress.org/support/article/managing-plugins/#manual-upload-via-wordpress-admin)). ## FAQ How can I compress my MD trajectories to use with this plugin? Download the [PCAViz Compressor](http://git.durrantlab.com/jdurrant/pcaviz) to compress your trajectories. ## Reviews There are no reviews for this plugin. ## Contributors & Developers “PCAViz” is open source software. The following people have contributed to this plugin. Contributors * [ durrantlab ](https://profiles.wordpress.org/durrantlab/) [Translate “PCAViz” into your language.](https://translate.wordpress.org/projects/wp-plugins/pcaviz) ### Interested in development? [Browse the code](https://plugins.trac.wordpress.org/browser/pcaviz/), check out the [SVN repository](https://plugins.svn.wordpress.org/pcaviz/), or subscribe to the [development log](https://plugins.trac.wordpress.org/log/pcaviz/) by [RSS](https://plugins.trac.wordpress.org/log/pcaviz/?limit=100&mode=stop_on_copy&format=rss). ## Changelog #### 1.0 * The original version. ## Meta * Version **1.0.0** * Last updated **7 years ago** * Active installations **10+** * WordPress version ** 5.2.2 or higher ** * Tested up to **5.2.24** * PHP version ** 7.3.3 or higher ** * [Advanced View](https://wordpress.org/plugins/pcaviz/advanced/) ## Ratings No reviews have been submitted yet. [Your review](https://wordpress.org/support/plugin/pcaviz/reviews/#new-post) [See all reviews](https://wordpress.org/support/plugin/pcaviz/reviews/) ## Contributors * [ durrantlab ](https://profiles.wordpress.org/durrantlab/) ## Support Got something to say? Need help? [View support forum](https://wordpress.org/support/plugin/pcaviz/) ## Donate Would you like to support the advancement of this plugin? [ Donate to this plugin ](http://durrantlab.com/pcaviz/)