Tag: chemical structure diagrams

Chemistry data round-tripping. Has there been ANY progress?

This is one of those topics that seems to crop up every three years or so. Since then, new versions of operating systems, new versions of programs, mobile devices and perhaps some progress?

Right, I will briefly recapitulate. Chemical structure diagrams are special; they contain chemical semantics (what an atom is, what a bond is, stereochemistry, charges, etc). One needs special programs to represent this. Take two well-known ones. ChemBioDraw V 13 is the latest in a long line dating back to 1985 or so. A newcomer is ChemDoodle, just updated to version 6. The idea is you express your molecule, and capture some of its semantics using one of these programs. And then paste the data into another veritable word processor, Word (also dating back to around 1984). Then send the Word document to a colleague. Who might want to copy the structure back out, and put it back into ChemBioDraw/ChemDoodle. And put those semantics to good use, by editing it, or re-purposing the information. This is round-tripping the data. Its been almost 30 years, surely the process should be seamless by now? Wrong!

One problem is that the “exchange-particle” is the clipboard, yet another ancient and presumed mature technology. Its invisible of course, we rarely get to see it. And very operating system specific! So what is the current state of play? Round tripping ChemBiodraw structures across a single operating system might work. Well, it currently does for just one of the two most common desktop operating systems (remember, Word is provided by the originator of one of these operating systems). The other program, ChemDoodle round trips within both operating systems.

But, here is the key point, not across operating systems. Paste either a ChemBioDraw or a Chemdoodle structure into Word on one of these OS, and try re-editing that diagram on the version of Word on the other OS. The data is lost unless you have the “right” operating system.

An experiment I have not tried, but regarding which I would welcome any feedback is to factor in the two newest operating systems, this time for mobile devices such as tablets and phones. Lets not even worry whether different flavours of one of these mobile OSs are compatible. Apps for drawing chemical structures are available for both of these. Here, the amazing clipboard still exists. One now has four OS to consider, and four homogenous permutations and a minimum of six heterogenous round trips the data could try to take for any given app. We do not even consider app2app transfers not involving discrete intermediate documents. I would predict that only a few of these permutations preserve round-tripped data and its semantics.

Perhaps we need to look at it in a different way? One simply avoids putting data from one program into another. Chemical data is kept in its own files, never mixed with data from other programs, but always kept/sent separately. Pre-1984 and the clipboard, this might have made sense. But in an era when XML was invented around 17 years ago to allow data to fully retain semantic information in any environment it finds itself in, it seems surprising that we still have this situation.

I mention all of this, since there is a current refocusing on the importance of data; “emancipating data” is now important. But the reality is that much current software destroys the semantics in data at almost every turn. Thirty years of no progress then. But what of Chem4Word, a combination of differently namespaced XML in which the chemistry is expressed in CML (it is only available for a single operating system!). I will perhaps devote a separate post to that one; first I have to try a few experiments!

December 2, 2013
Blogbooks, e-books and future proofing chemical diagrams.
Most of the chemical structure diagrams in this blog originate from Chemdraw, which seems to have been around since the dawn of personal computers! I have tended to use this program to produce JPG bitmaps for the blog, writing them out in 4x magnification, so that they can be scaled down for display whilst retaining some measure of higher resolution if needed for other purposes. These other purposes might be for e.g. the production of e-books (using Calibre), the interesting Blog(e)book format offered as a service by Feedfabrik, or display on mobile tablets where the touch-zoom metaphor to magnify works particularly well. But bitmap images are not really well future proofed for such new uses. Here I explore one solution to this issue.

I have previously mentioned scalable vector graphics (SVG) as an alternative, and fortunately the production of such has become routine.³ The diagram above² is indeed SVG (and if you cannot see it, then try a modern SVG-capable browser¹). It was produced thus:
1. Drawn in Chemdraw
2. Exported as Encapsulated postscript
3. Imported into Scribus, an Open Source desktop publishing program (where it can be annotated/edited if need be)
  - This program will also need Ghostscript installed to handle the EPS
4. and exported from Scribus to SVG.
5. Notice how the diagram above automatically scales to fill the width of the page. If you click on it, you get the diagram on its own. If you zoom the browser window, it should scale perfectly.
6. I note that these SVG diagrams work well in e-books or blogbooks.
There seem to be many other (open) programs out there which support SVG, so the above combination is not necessary the only one, or indeed the best. There is one other aspect which might be mentioned. The old GIF or JPG bitmap formats do have good meta-data support, such as EXIF, GPS or XMP. These invisible data have often been used to embed a molecular connection table into a GIF or JPG file, such that the original molecular data can be reconstituted from the image file. Unfortunately, there are no real standards for doing this, and so round-tripping the data is probably a closed process within a specific software environment. However, because SVG is an XML format, it can be readily made to carry such information in a fully inter-operable manner. For example, one could easily embed a CML description of the molecule into its own container (namespace) in the SVG file. For the purposes of rendering an on-screen image, this extra information is of course ignored.

¹ I notice that Internet Explorer 9 (both 32- and 64-bit versions) will display (and save) the above diagram if you click on it, but it cannot (yet) be inlined into the post, although the documentation implies it should.
² The version below is the conventional JPG form (click on it to see the original 4x version).

Diagram displayed using JPG.

³. Historical note. Peter Murray-Rust and I have been promoting SVG for use in chemistry for 11+ years now. For one ancient page, see here. The syntax has decayed somewhat, but some of the diagrams still work!
October 31, 2011

Tag: chemical structure diagrams

Chemistry data round-tripping. Has there been ANY progress?

Blogbooks, e-books and future proofing chemical diagrams.