I take a break from political economy and talk computer science.

Blair Fix

Today I’m going to take a break from political economy and talk about computer science. The reason? Nowadays a large part of doing science involves writing code. Scientists write code to collect data, to analyze it, to plot it and to run models that explain it. Suffice it to say that modern scientists (myself included) spend a lot of time coding. Computing is, in many ways, about repetition. It’s about doing a task over and over.

In the Beginning … There Were Loops

Imperial College London

Henry Rzepa

Ten years are a long time when it comes to (recent) technologies. The
[first post on this blog](https://www.ch.imperial.ac.uk/rzepa/blog/?p=8)
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
how ten years of progress in technology has required changes and the
challenge of how any necessary changes might be kept "under the hood" of
this blog.

That first post described how the Java-based applet Jmol could be used
to present 3D models and animations. Gradually over this decade, use of
the [Java technology](https://www.ch.imperial.ac.uk/rzepa/blog/?p=18365)
has become more challenging, largely in an effort to make Web-page
security higher. Java was implemented into web browsers via something
called Netscape Plugin Application Programming Interface 
or [NPAPI,](https://en.wikipedia.org/wiki/NPAPI) dating from around
1995. NPAPI has now been withdrawn from pretty much all modern
browsers.^‡^ Modern replacements are based on JavaScript, and the
standard tool for presenting molecular models, Jmol has been totally
refactored into
[JSmol](https://sourceforge.net/projects/jmol/files/Jmol/){rel="noopener"
target="_blank"}.^†^ Now the challenge becomes how to replace Jmol by
JSmol, whilst retaining the original Jmol Java-based syntax (as
described in the [original
post](https://www.ch.imperial.ac.uk/rzepa/blog/?p=8)). Modern JSmol uses
its own improved syntax, but fortunately one can use a syntax converter
script Jmol2.js which interprets the old syntax for you. Well, almost
all syntax, but not in fact the variation I had used throughout this
blog, which took the form:

[\[caption\]\<img onclick="jmolApplet(\[450,450\],'load
*a-data-file*;spin 3;');" src="static-image-file" width="450″ /\> Click
for 3D structure\[/caption\]]{.small}

This design was originally intended to allow browsers which did not have
the Java plugin installed to default to a static image, but that
clicking on the image would allow browsers that did support Java to
replace (in a new window) the static image with a 3D model generated
from the contents of *a-data-file.* The `Jmol2.js` converter script had
not been coded to detect such invocations. Fortunately Angel came to my
rescue and wrote a 39 line Javascript file that does just that (my
Javascript coding skills do not extend that far!). Thanks Angel!!

In fact I did have to make one unavoidable change, to;

[\[caption\]\<img onclick="jmolApplet(\[450,450\],'load
*a-data-file*;spin 3;'**[,'c1′]{style="color: #ff0000;"}**);"
src="image-file" width="450″ /\> Click for 3D
structure\[/caption\]]{.small}

to correct an error present in the original. It manifests when one has
more than one such model present in the same document, and this
necessitates that each instance has a unique name/identifier (*e.g.*
c1). So now, in the WordPress header for the theme used here (in fact
the default theme), the following script requests are added to the top
of each page, the third of which is the new script.

\<script type="text/javascript" src="JSmol.min.js"\>\</script\>  
\<script type="text/javascript" src="js/Jmol2.js"\>\</script\>  
\<script type="text/javascript" src="JmolAppletNew.js"\>\</script\>

The result is *e.g.*  

::: {#attachment_14274 .wp-caption .aligncenter style="width: 450px"}
![Click for
3D](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/07/GAVFIS.jpg){.size-full
.wp-image-14274 decoding="async"
aria-describedby="caption-attachment-14274"
onclick="jmolApplet([450,450],'load wp-content/uploads/2015/07/GAVFIS-lattice.mol2;spin 3;','c1');"
width="440"
srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/07/GAVFIS.jpg 1660w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/07/GAVFIS-300x252.jpg 300w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/07/GAVFIS-1024x859.jpg 1024w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/07/GAVFIS-900x755.jpg 900w"
sizes="(max-width: 1660px) 100vw, 1660px"}

Click for 3D structure of GAVFIS
:::

::: {#attachment_14280 .wp-caption .aligncenter style="width: 450px"}
![Click for
3D](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/07/GAVFIS-SOMO.jpg){.size-full
.wp-image-14280 decoding="async"
aria-describedby="caption-attachment-14280"
onclick="jmolInitialize('../Jmol/','JmolAppletSigned.jar');jmolSetAppletColor('white');jmolApplet([450,450],'load wp-content/uploads/2015/07/GAVFIS_gp_mo113.cub.xyz;isosurface wp-content/uploads/2015/07/GAVFIS_gp_mo113.cub.jvxl translucent;zoom 70;spin 3;','c3');"
width="440"
srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/07/GAVFIS-SOMO.jpg 872w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2015/07/GAVFIS-SOMO-300x282.jpg 300w"
sizes="(max-width: 872px) 100vw, 872px"}

Click for 3D interaction
:::

This solution unfortunately is also likely to be unstable over the
longer term. As standards (and security) evolve, so invocations such as
`onclick=` have become considered "bad practice" (and may even become
unsupported). Even more complex procedures will have to be devised to
keep up with the changes in web browser behaviour and so I may have to
again rescue the 3D models in this blog at some stage!^¶^ Once upon a
time, the expected usable lifetime of *e.g.* a Scientific Journal
(print!) was a very long period (\>300 years). Since \~1998 when most
journals went online, that lifetime has considerably shortened (or at
least requires periodic, very expensive, maintenance). For more
ambitious types of content such as the 3D models discussed here, it
might be judged to be \<10 years, perhaps much less before the
maintenance becomes again necessary. Sigh!

------------------------------------------------------------------------

^‡^ At the time of writing,
[WaterFox](https://blog.waterfoxproject.org/) is one of the few browsers
to still support it. ^†^An early issue with using Javascript instead of
Java was performance. For some tasks, the former was often 10-50 times
slower. Improvements in both hardware and software have now largely
eliminated this issue. ^¶^Thus using
[Jquery](https://stackoverflow.com/questions/35970987/js-onclick-mobile-alternative-onclick-deprecated-on-ios-and-android-too?utm_medium=organic&utm_source=google_rich_qa&utm_campaign=google_rich_qa).

::: {.wp_orcid_field}
[https://orcid.org/0000-0002-8635-8390](https://orcid.org/0000-0002-8635-8390){target="_blank"
rel="author"}
:::


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.

Messaggi di Rogue Scholar

In the Beginning … There Were Loops

Ten years on: Jmol and WordPress.