Overview

Front page

Edit

Rename

Delete

Copy

Life

Email

Move

Properties

Open in

Drawing structures

Casual mode

Novice mode

Expert mode

Conclusion

Overview

MolPrime provides the powerful drawing capabilities of the Mobile Molecular DataSheet in a smaller and more accessible app. MolPrime is available for free, and is outwardly similar to MolPrime⁺, which adds additional functionality.

The app runs on iPhone, iPod and iPad devices:

Front page

The opening page displays a collection of structures, each of which has its own icon and label. These are editable, and can be added to, deleted or moved. Icons can be selected by tapping on them, and a long-press or double-tap activates the icon.

The first two icons have a special function: the Introduction icon brings up the about view, while the Create New allows a new structure to be drawn from scratch.

Activating any of the structure buttons (by touch-and-hold or selecting with one tap, then tapping again) brings up a menu bank, which consists of icons, as shown below:

Edit Rename Delete Copy Life Email Move Properties Open in

For a reminder of the function of any of these icons, touch the icon and hold on it for a couple of seconds, and an explanation tip will be shown.

Edit

Structure editing is explained below. Editing can also be activated by double-tapping on the structure icon.

Rename

The name of the structure can be modified using the in-app keyboard:

Delete

Structures can be deleted. Note that there is no undo function, so deletion is permanent.

Copy

Structures can be copied onto the clipboard using several formats:

The native format is SketchEl, which is a concise, minimalistic structure format that is compatible with a broader range of chemistry than most sketch formats. When the objective is to paste the structure into another app from Molecular Materials Informatics, this format should always be used, as it is guaranteed to be lossless. For interacting with other software, it is often useful to copy the structure using the industry standard MDL Molfile format. In some cases it is also useful to be able to create a SMILES string, especially for pasting into search engines that do not have a mobile-compatible structure editor.

Life

The selected structure can be used to play the cellular automaton classic game of life:

The selected structure is converted into a coarse grid in order to seed the cellular population.

Email

One of the most effective ways to utilise a structure is to send it by email. A new email message is composed, which automatically includes a variety of information about the molecule, including name, molecular weight and formula in the subject and body of the email:

The structure representation is also included using two attachments: structure.el, which uses the native SketchEl format that is preferred by all products from Molecular Materials Informatics, and structure.mol, which uses the MDL Molfile format that is understood by almost all cheminformatics software.

The last attachment is a picture of the molecule (structure.png). Before initiating the outgoing email, the user is prompted to select the dimensions of the picture:

Several colour schemes are available, as well as resolutions. The default 90 dpi resolution is suitable for viewing onscreen, but for any kind of publication quality output, a higher resolution should be used.

Move

Newly added structures are inserted at the beginning of the list. They can be subsequently rearranged by entering move mode:

Pressing one of the directional arrows moves the structure. Deselecting the structure ends the moving operation.

Properties

Some simple properties can be calculated for structures:

Note that for the example shown on the right, one of the nitrogen atoms has an incorrect valence, which is highlighted in red.

Open in

If there is more than one chemistry app installed, it is possible to transmit the structure to another app:

The operating system compiles a list of apps that understand the native structure format, and presents each of them as a possible destination. Selecting an app launches it with the selected structure.

Drawing structures

Drawing chemical structures on a mobile device is a different proposition from using a desktop PC. An ideally touchscreen interface requires a number of redesigned concepts, and these can be daunting at first. Most of the apps produced by Molecular Materials Informatics use the powerful gesture-based sketching interfaced pioneered by the Mobile Molecular DataSheet app.

Because many users of MolPrime are new to mobile chemistry software, the app provides three levels, in order to ease the culture shock. The first time the editor is invoked, the following choice will be presented:

As the dialog explains, the Casual mode provides a very simple sketcher interface that is familiar to anyone who has drawn a chemical structure using computer software. The Novice and Expert modes provide access to the full power of the gesture-based sketcher.

The choice of sketcher can easily be changed at any time by opening the Settings app and selecting MolPrime:

Casual mode

The interface for the Casual mode is very simple:

The available tools are shown in the button bank on the bottom, and function in a way that is similar to most conventional sketchers designed for use on PCs. This is a good way to become acquainted quickly with using chemical structures on a mobile device, but it is limited in functionality. Drawing or modifying complex structures, to produce publication quality results, is much better accomplished by using the gesture-based modes.

Novice mode

The Novice has 3 button banks:

The left hand bank provides tools that are somewhat familiar to users of conventional sketchers, which provide a bridge toward using the more ergonomic methods. The right hand bank provides quick access to common ring structures.

On the top right is the tooltips icon. Tapping on this button brings up a prompt to preview various sketcher operations, which are animated in order to demonstrate tasks.

Expert mode

The Expert mode has a sparser layout, with just one command bank:

All functionality is made available through the command bank, the context bank, and various gesture operations. These are explained in the introductory tutorial.

For both Novice and Expert mode, creating a new structure is preempted by a startup dialog:

The new structure can be blank, or seeded with the contents of the clipboard (if any), or started out with one of the template groups.

Conclusion

MolPrime is a simple app that introduces chemical structure drawing, and structure interoperability, to the iOS platform. It is free to use, and is a good starting point for exploring chemistry apps on mobile devices.

Once you have become accustomed to using MolPrime, you should consider these apps, among others:

MolPrime+	The more powerful upgrade of MolPrime provides more advanced features such as calculating physical properties, mass distributions, tautomers and stereocentres; searching public databases by structure directly from the app; and exporting Microsoft Word documents with embedded vector graphics for use in publication quality manuscripts.
MMDS	The Mobile Molecular DataSheet (MMDS) is a powerful tool that allows management of datasheets, containing structures, reactions and auxiliary data. The app is loaded with functionality, including property calculation, numerous exporting and graphics creation capabilities, access to generic webservices and structure searches, and more.
SAR Table	Create tables of scaffolds, R-groups and activities. Create tables for manuscript preparation, or conveniently recreate tables from papers, or perform structure-activity analysis by scaffold assignment and model building.
MolSync	Access your chemical data on Dropbox or iCloud using this chemically aware file browser. Link datasheets to MMDS for syncing between multiple collaborators.

See Also

Mobile Molecular DataSheet (iOS), MolPrime+, MolPrime+ Property Calculation, Products