With the American Chemical Society San Diego meeting coming up next month, and a year’s worth of new products and new features to cram into a 30 minute talk, now is as good a time as any to review some of the upandcoming developments that are on the roadmap for Molecular Materials Informatics.
These projects include some of the improvements that are intended for the near future. This planning ahead is just a snapshot in time, so entries will be added, deleted or reprioritised as necessary.
The Mobile Molecular DataSheet (MMDS) is still the flagship product, and the iOS version is the primary delivery tool for core functionality such as molecular structure drawing, reaction editing, datasheet management, communications and access to webservices and remote procedure calls. Some of the more advanced capabilities remain specific to the app itself, which is somewhat of a swiss army knife, but a large portion of the functionality added to MMDS is also part of the core technology library, MMDSLib, and hence the rest of the apps produced by Molecular Materials Informatics, and several apps produced by third parties, also inherit the new improvements.
The basic sketching primitives on which the mobile structure editor is based were worked out and implemented almost two years ago, and have been steadily refined as the product matured. Seldom has a month gone by without a new feature, ergonomic tweak, or bug fix. The very first version was powerful enough to draw very complex chemical structures well, but in many cases the operation sequences necessary to achieve the desired results were not always obvious, and when they were known, not necessarily as convenient as they could be. Time, practice and exposure to real world use has a tendency to highlight these kinds of issues, and the following improvements are planned, in order to streamline some of the edge cases.
Switch substituents: often there are two terminal substituents hanging off an atom that are just the wrong way around. A common example is carboxylic acid: often you realise after the fact that switching the two oxygens (=O and -OH) would result in a diagram that looks better. This case is easy to fix manually, but sometimes it’s much more of a pain (e.g. nitro & benzyl). At times like this it would be great to be able to press a button to make the switch.
Rotate around a bond: it is common for drawing operations to need to flip parts of a structure, e.g. vertical or horizontal, but sometimes the operation would be much more helpful if it were not limited to the X- and Y-axes. Being able to pick a bond and rotate one substituent by 180° can short circuit quite a bit of drawing surgery.
Bond reconnect: while the drawing primitives are designed for creating structure diagrams from scratch, such that each step is carried out with precision, there are plenty of cases where this ideal does not apply. A semi-automated approach to fixing up bad structures can be implemented by leveraging the advanced template placement algorithms that are already a part of the sketcher: by selecting a chain bond in the middle of a trouble area, breaking it, then re-placing one side using the advanced template fusion algorithms, the localised geometry can be fixed up. This can currently be done manually using cut’n’paste, but a specialised operation that collapses the intermediate steps will make it more convenient to fixup structures.
Structure cleaning: some initial work has already been put in toward implementing a structure-cleanup algorithm, which will take an imperfectly drawn structure, and try to fix it up, while making use of the starting geometry to assist the layout procedure, keep the general orientation, and generally try not to make it any worse. The algorithm is being developed and validated in a serverside environment, so it may be offered to the app via remote procedure call (RPC), or it may be ported to run on the device itself.
Formula abbreviations: the sketcher can represent terminal substituents as inline abbreviations, and while this feature has been available for some time, the interface for creating new abbreviations could use some improvement. One additional common use case for abbreviations is to collapse some substituent into its molecular formula, e.g. C6H5, which most chemists have little difficulty recognising as phenyl. The new feature here is a single action button that converts selected atoms into an inline-abbreviation with its molecular formula as a label. This will also conveniently address another common feature request: the ability to draw methyl groups as CH3, rather than just a single bond line.
Freeform move/rotate: the whole idea of the drawing primitive approach to sketching molecules is to avoid the need to manually position atoms, and so the philosophy has been to leave this manual positioning capability out as a way to force all of these goals to be accomplished by other means. But having achieved this, the fact of the matter is that sometimes you just want to drag some atoms around the screen with your finger. Particularly when there are multiple components, e.g. adjunct ions. And to rotate them, too. There are some smart tricks that can be implemented here, like making existing bonds snap into position at computed angles and distances, so there’s more to this feature than just coming up with a gesture based interface.
Atom/bond geometry editor: while it is possible to accomplish a great deal using the primitive sketching operations, sometimes the easiest way to position an atom, or a bond, or a torsion angle, is to open a dialog box and type in a number. This feature has been on the MMDS roadmap for a long time, but sooner or later it will actually get implemented.
The MolSync app is positioned as a centralised hub for mobile access to chemical data, because it stores its content on a cloud-hosted repository rather than the local storage of the device.
Other repositories: at the present time MolSync only integrates with Dropbox, but the app was designed from the ground up to work with any number of cloud storage technologies. The next storage device on the roadmap is WebDAV. Adding support for this open standard for file storage will free the app from being associated with a single provider, and also make the app much more compelling for using within a company intranet.
Enhanced file browsing: the file browsing view is currently fairly basic. The app has access to the filename, and can make a guess as to the type. It is kept simple in order to avoid wasting too much bandwidth, and inflating users’ data transmission bills. But the user experience sure would be nicer if the app background-downloaded each of the files, investigated their types, and drew a thumbnail image of the content.
Direct integration with SAR Table: the SAR Table app can share data with MolSync, but only by using generic interprocess communication. Tighter integration, whereby the apps are explicitly aware of each other, is planned.
Tweeting improvements: it is currently possible to tweet-out chemical data from MolSync, but the catch is that for tweeting to be a useful thing to do, the data has to be accessible via a URL. Since Dropbox accounts come with a public folder, this can be accomplished, but right now you have to copy the data into /Public prior to tweeting. It would be nice if this could be done automatically. Other possibilities include uploading data to a third party server that serves it up publicly. Furthermore, the MolSync tweeting capabilities will improved so that it is easy to provide data to the ODDT project. This will be described in more detail with imminent blog posts.
The SAR Table app is a young product, with an exciting life ahead of it. Keep an eye on this one, because planned new features are mainly of the major variety, rather than iterative refinement.
Expanded scope of scaffold matching: the introduction of scaffold matching features is recent, and is essentially a minimum viable product. Scaffold matching can only be done one row at a time, and the use-case workflow scenarios are fairly narrow. Expect the feature to take on additional nuances for more diverse use, e.g. re-matching substituents when the possibilities are degenerate, and also improved exploratory features, e.g. matching batches of compounds. These improvements will be fed in incrementally, since scaffold matching is a delicate art.
Better importing: the first release of the app concentrated on creating new tables from scratch, which matches the original two workflow scenarios (creating figures for manuscripts, and re-entering data from already published figures). But there are many cases where datasheets with structures are already available, and the importing process could use some attention.
Colour-coding schemes for properties: numerical data is often easier to reconcile when colours are used to encode certain ranges. With structure-activity data, it is common to use a “traffic light” scheme: green for actives, red for inactives, yellow for intermediate cases. There is no one-size-fits-all colour scheme, so they will be configurable with a scheme editor. Displaying activity/property data colour coding in the row-based table view is handy, but this is intended to be a waypoint on the path toward additional visualisation techniques. This will be genuinely exciting, but too soon for details.
Not to be confused with the MolSync app, molsync.com refers to an original software stack that is deployed at http://molsync.com, and provides cheminformatics support capabilities for most of the apps produced by Molecular Materials Informatics. Currently this includes generation of publication quality graphics, advanced format interconversions, property calculations, scaffold matching, and a web front end for previewing raw chemical data. The software is a 100% original cheminformatics toolkit written in Java. The project is maturing at a healthy pace, as it evolves to provide an increasing range of support functionality.
Additional property calculations: recently the service was extended to provide log P and molar refractivity calculations for MolPrime+. Some more workhorse calculations, e.g. TPSA, will likely be added.
Enhanced webservices: the MMDS app has provided a front end for generic webservices features for quite some time. The protocol is open and documented, and there are code examples in PHP to encourage the creation of custom services. With new calculations being added to the molsync.com software stack, it makes sense to provide a new range of services through this API, by first assembling a new serverside framework. Improvements to the front end in MMDS, and extensions to the protocol, will allow the feature to become more useful. Once this project gets underway, expect webservice access to be integrated more closely into the molecule, reaction and datasheet editing workflow of MMDS, and possibly other apps as well.
Intranet deployment: these features are currently publicly available via the molsync.com server which is provided by Molecular Materials Informatics, as the default remote procedure call server. While the server does not actually store any of the structures or data that users submit, it is still a generally bad idea to submit confidential information across the open internet, or without a contractual guarantee at the other end. Fortunately, the software has always been intended as a product that can be deployed by an organisation, within the firewalled intranet. Some preliminary steps have been made toward producing a deployable product, although a pricing model has yet to be established. It is a proprietary product, and will not be free.
The most recent project, which is short for Open Drug Discovery Teams, is currently in full-speed-ahead mode. It has been described in several blog posts already, and will be followed up by many more, so there’s no need to go into detail here.
Hopefully these plans are interesting to current and future users of mobile chemistry apps. And if there’s anything you think should be added or moved up a few notches, let us know. We’re always interested to hear from you.