Welcome to the club, ChemDraw Mobile

Yesterday’s buzz in the chemistry software scene revolved around the release of ChemDraw Mobile for iPad (but not iPhone). This is exciting news, even if only for the name: the flagship chemical drawing software from CambridgeSoft has been the go-to brand for creating diagrams for manuscripts for something like a quarter century (give or take). It’s hard to argue that working with chemical structures on mobile devices is an irrelevant hobby when the biggest player in the industry has made the effort to join in, and is giving it top billing with its promotional efforts.

I gave in to the temptation and bought a copy of the app to see what it could do. Long story short, it’s a decent app. I could fill a long review with all the things that could be better, but it’s at version 1.0, and it is terribly bad form to build a weighty critique of a minimum viable product, so we should give the company a few months and a few revisions before getting too pedantic. The laundry list can wait until a few more loads have gone through the washing machine.

The important parts are two: first of all, the sketcher is fairly easy to figure out. I’m fairly sure I understood 100% of its capabilities after about fifteen minutes of attention, although my expertise in the area is extensive to say the least, so mileage may vary. As expected, the app takes the approach of mirroring the core concepts of the desktop version as closely as possible, in order to avoid forcing the user to learn. The advantage of this is obvious, but the disadvantage is that it is actually not possible to draw publication quality structures, unless they are comprised entirely of simple rings and 120° bond angles. The built-in clean functionality can be used to patch up rough drafts, but if the result of the algorithm is not what you want, there isn’t any recourse. This is in marked contrast to the approach taken by the Mobile Molecular DataSheet (MMDS), with its basic primitives rethink of the traditional sketcher paradigms. The MMDS sketcher (also used by most other products from Molecular Materials Informatics) provides a way to draw complicated structures perfectly, the first time around, and is optimised from the ground up to work with tiny touch-based devices like iPhones, and it is also very fast. The catch (there always is one) is that there are new concepts involved, and they need to be learned. And not everyone has the time or motivation to learn new things, which means that there is a sweet spot for apps like ChemDraw Mobile. That being said, you should do some due diligence before you go out and buy it: ChemDoodle Mobile has a similar simplicity-based approach, and it’s free. And there are other options on the market, like Chirys Draw, ChemWriter, TouchMol, among others. And you should also check out the SciMobileApps page for a starting point for the mobile chemistry ecosystem.

Speaking of ecosystems, back to ChemDraw Mobile: for purposes of sharing or using content, the app is very limited. There are 3 things you can do with it:

  1. Download structures in ChemDraw XML (.cdxml) format (from websites or mail attachments) into the ChemDraw Mobile app.
  2. Send structures as email attachments in ChemDraw XML format.
  3. Share with some proprietary new cloud service called Flick-to-Share which requires registration (I haven’t tried it out).

Notice the lack of any kind of graphics output; no clipboard access; no way to send data to other apps; no access to useful services like property prediction or searching. These restrictions should make you ask the question: what’s the point of the app? About all you can do with it is sketch out structures, then transfer them (by email, for most people) to a platform that is capable of reading ChemDraw XML files (e.g. the desktop software, which happens to be rather expensive). Apps with comparable sketching capabilities have been around for more than 3 years, so it’s hard to argue that the new product has really brought anything to the table.

That being said, there’s plenty of time to add capabilities, so if anyone from CambridgeSoft/PerkinElmer ends up reading this blog, I will describe my first feature request: ChemDraw Mobile needs to be able to play in the chemistry mobile app ecosystem in order to provide value, so…

One of the features that has been in the Mobile Molecular DataSheet (MMDS) app for awhile now is the ability to read binary ChemDraw files. Yesterday, I added serverside support for ChemDraw XML files (the only format used by the app), and added file header recognition to MMDS. That means if you use the iOS platform to open a .cdxml file, whether that be from a website (e.g. binary version from ChemSpider Synthetic Pages) or an email attachment, one of the choices of destination is MMDS, which has the power to unpack molecules and reactions. This will be available when the next version of MMDS (1.4.5) gets through the iTunes review process, which typically takes about a week.

This is best illustrated graphically:

chemdraw_mmds

(1) Use the ChemDraw Mobile app to draw something, in this case a 2-step reaction, using my iPad. (2) After using the app to mail the attachment to myself, tapping on the attached .cdxml file, using my iPhone. (3) Launching the attachment in MMDS causes the content to be unpacked, in this case being parsed out into a 2-step reaction. (4) Inserting a new reaction datasheet into the main collection, which shows the reactions contained within.

The ChemDraw XML format is one of the saner ones in use in the cheminformatics industry, and it is reasonably easy to parse out, despite the fact that it is fundamentally a graphical page layout format, with some cheminformatics layered on top, while MMDS uses formats which are pure cheminformatics. The degree of interoperability is nonetheless quite good.

Once the molecules or reactions are loaded into MMDS, there are all kinds of things you can do with them: create graphics for use in manuscripts, including vector graphics and MS Office documents; use them to search databases like ChemSpider, SPRESI, PubChem and ChEBI; use them for property calculations; share them on the open internet, or push out to Twitter with machine readable content intact; store collections in Dropbox to collaborate with coworkers; and most importantly, gain access to the growing ecosystem of mobile chemistry apps via numerous interprocess communication options.

So the feature request: CambridgeSoft, please add one very simple feature in the Export menu:

chemdraw_mmds_x1

Call it “Open-in”, and make it call the operating system to offer any other app the chance to open a .cdxml file. It’s really easy, just a few lines of Objective-C:

    NSString *tmpFN=[NSString stringWithFormat:@"%@/temporary.cdxml",documentDir];
    [self writeCurrentThingToFile:tmpFN];
    NSURL *url=[NSURL fileURLWithPath:tmpFN];
    UIDocumentInteractionController *doc=[UIDocumentInteractionController interactionControllerWithURL:url];
    CGRect fr=[self convertRect:exportButton.bounds fromView:exportButton];
    [doc presentOpenInMenuFromRect:fr inView:self animated:YES];

Similar code used in MMDS and various other apps provides a menu like this:

chemdraw_mmds_x2

To to conclude: welcome to the mobile club, ChemDraw. Now with just a few more very simple enhancements, you can be a fully active member, and play nice with other apps, so people can have more ways to get real, serious work done on their mobile devices.

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  1. #1 by Dan on 6-Jun-2013 - 2:02 am

    Hi,

    No mention of Elemental? It has had over 30K downloads so far.

    https://itunes.apple.com/gb/app/elemental/id518655328?mt=8

    Cheers,
    Dan.

  2. #3 by Dr. Alex M. Clark on 7-Jun-2013 - 2:23 pm

    Apple approved the latest version of MMDS faster than usual, 1.4.5 is available on the AppStore:

    http://itunes.apple.com/app/mobile-molecular-datasheet/id383661863

    … it can read CDXML files. Right now you can only import them from the ChemDraw Mobile app after emailing the data to yourself; so anytime, CambridgeSoft, feel free to support the standard Open With functionality.

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