The release schedule for ODDT is currently slightly backed up with the AppStore review process, but with any luck this new feature will be available soon.

The 3D molecule viewing widget is very new, and doesn’t provide much in the way of interactivity – viewing and rotating is all it does, but as a “minimum viable feature” is want to do, this will grow, e.g. more gestures (pinch-zoom, rotate, translate, etc.) and more file formats that can be parsed (currently only MDL and native formats can have their Z-coordinate extracted).

A new feature will be making its way to the Mobile Molecular DataSheet, and other apps, soon: tweeting out chemical data (molecules, reactions, datasheets) without having to login to a repository for storing the source data. All that’s required is authorisation of your Twitter account, as configured within iOS.

To see a preview of how it works, click on the image to the right, to watch a short screencast.

This is not the first foray by Molecular Materials Informatics into the twitterverse: the MolSync app can tweet out chemical data, too, but only when you have already uploaded the raw data to the /Public folder of your Dropbox account. The Open Drug Discovery Teams app makes heavy use of Twitter, but only emits tweets in order to modify content, rather than creating it.

The core technical issue for tweeting chemical data is that Twitter itself allows just 140 characters of data, but this space can include shortened links, so a tweet can redirect the reader to a valuable payload. But that content has to be stored someplace else – and you can’t store something on a mobile app and make it available to the world, hence the need for a service to provide this function. There are many services for storing certain types of data, such as pictures, but this is unhelpful for chemistry: while it’s great for someone to see a bitmapped rendition of a molecule, its true value is unlocked only if the source data, in a machine readable format, is available.

Hence the storage service needs to be able to manufacture a graphical representation, for the benefit of people reading the tweet with a standard client, and also able to make the core data available, so people can integrate it into their cheminformatics workflow. This problem is now solved by using a third party service – pastebin.com – and having it store the raw chemical data (i.e. the molecule/reaction/datasheet, as machine-readable text). This service generates a public link that is accessible from any connected dervice, and it is combined with the molsync.com data sharing service, which wraps the raw data, and produces a freshly rendered HTML5 page that displays the content. The chemical data content comes with calculated properties, and can be downloaded in a variety of formats, both cheminformatics and graphics.

To see it in action, try this link:

http://molsync.com/share/?src=http://pastebin.com/raw.php?i=S3ZPKCA4

So back to mobile apps: MMDS now makes use of pastebin.com + molsync.com to host and serve up the data, so with the latest version you can tweet out anything you want, and the only logging in you have to do is with Twitter, which involves tapping the “Allow” button, as long as you have configured it within iOS.

The new version will be submitted to the AppStore soon, so it ought to be available in a week or two.

While it can’t be seen in the screencast version, the static rendering scene makes full use of the iPad3 retina screen and 4x multi-sampled anti-aliasing. This means that the spheres and cylinders are rendered in full 2048×1536 glory (3.1 mega-dots) not just once, but four times, in order to obtain a composite that has nicely alpha-blended edges, instead of ugly “jaggies”. Which is another way of saying that it looks really great, all the more so on a retina-class screen.

At the current state of optimisation, it takes about a half-second to draw this scene, for a 3D molecule with 60-something atoms. Under some circumstances this is an acceptable time lag for rendering a nice static picture, but not for interactive updates such as drag-to-rotate, and so the widget uses the time honoured trick of switching to wireframe mode in order to ensure real time updating.

3D visualisation capabilities will be added to some of the apps from Molecular Materials Informatics. But it’s not yet decided which ones, so that’ll have to count as a surprise.

Integration with iCloud within a mobile app is seemless. If you have enabled iCloud support in the setup of your iOS device, it will be available immediately, without any fuss. The MolSync app defines its own document storage area, within which you can upload and download files. This document storage area is automagically synchronised with Apple’s cloud hosting, and is updated between all of the devices that make use of it.

MolSync implements it as an ordinary directory, which behaves analogously to the Dropbox repositories. The directory can be browsed with a file manager style interface, and the files can be viewed, manipulated and synchronised with MMDS.

At the current time, iCloud is primarily used for keeping files synchronised between devices, which is helpful if you own more than one device, or anytime you upgrade to a new one. Options for accessing files from the desktop (e.g. web or from a Mac) are quite limited – we don’t quite know where exactly Apple is going with this one, so it’s not necessarily a replacement for the functionality of Dropbox. But it’s nice to have both.

Another improvement is the addition of configuration settings within the standard housing for iOS apps. MMDS has its own configuration dialog within the app itself, but most iOS users are accustomed to using the system app called Settings to configure their apps. Some of the most common settings, such as Expert Mode, are now mirrored to the general settings editor, i.e. they can be updated within the general settings mechanism, or they can be specified within MMDS itself.

These improvements will come through for MMDS 1.3.13, which has been submitted to the AppStore. The rest of the apps will follow suit as they are updated.

The new feature is in its early stages, and the visual feng shui will certainly mutate before the next release, but the core functionality is operational. Stay tuned for the next major version.

EPS is a vector graphics format that has been a mainstay of the publishing industry for a long time, but it has never been well supported by the dominant software, i.e. Microsoft Office. Adoption of the format has been severely compromised by the ability to include a low resolution bitmapped preview of the vector graphic drawing. This made sense at the time for technical reasons, but it means that many graphics packages simply display the preview from the graphic, rather than actually rendering it properly. When printing to a PostScript printer, everything is fine, since the graphic can be passed along in its native format, but to any other kind of printer, or alternate format, the lack of a proper renderer means that the output just uses the preview bitmap. Long story short, if you use a .eps file in your document, chances are it will come out the other end looking like garbage.

Not so – however – of Apple’s line of products, such as Keynote. These render EPS files in their true glory, providing print-quality, regardless of device. Graphics can be resized to any resolution, and still render perfectly. Output options, such as PDF, do not suffer in the slighest.

The vector graphics exporting features offered by Molecular Materials Informatics now provide strong coverage for all the platforms: for Windows, export as Microsoft Word or Excel documents (.docx, .xlsx); for Mac, export as Encapsulated PostScript (.eps); for open ecosystems, such as most Linux software, use Scalable Vector Graphics (.svg).

Other than the quantity, one little anecdote stands out: MolSync was initially rejected, on account of violating an AppStore guideline. The given reason seemed to be either incorrect, or the victim of a recent change in policy, since the app hadn’t started doing anything differently. After typing in a polite response, the app was approved a few minutes later. That kind of service is hard to beat.

Maybe I’m just living on borrowed time, but my interactions thus far with Apple have been uniformly positive. Maybe it’s from responding to the negative press that they were getting several years back, or maybe they had always been nice most of the time, but I have yet to find anything to complain about.

The calculation of these properties is done by a back-end server, specifically using the MolSync RPC calculation API. The app displays R/S and E/Z stereochemistry labels as a static overlay on the displayed structure. Tautomers, on the other hand, are interactive.

For the given structure, each of the possible tautomer transforms is indicated by a dotted outline around the affected atoms. Selecting/tapping the atom group applies the transform: the structure interconverts to the tautomer. The new tautomer has all of its possible transforms outlines, which means that tapping on various parts of the molecule allows the entire tautomer graph to be navigated.