The Mobile Molecular DataSheet app for iOS is able to take advantage of remotely located servers to do some of its calculations. MMDS is largely self-sufficient, insofar as datasheets are stored on the device, and the interface and all of the editing capabilities are baked into the app and will work whether or not there is a network connection. However, it has a number of features designed for data sharing and networking, and some newer, peripheral features are implemented not on the device itself but on a remotely located server.
The following areas of functionality are handled by making remote procedure calls.
Outgoing email with MMDS
MMDS is capable of converting molecules, reactions and datasheets to a number of different formats, and when an outgoing email is composed, these are automatically attached. Additional formats that cannot be generated by MMDS itself, but can be provided by invoking a remote procedure call, are presented as options prior to composing an email:
Upon pressing the Compose button, if any of the optional formats are selected, they are transmitted to the remote procedure call server, and the results are added to the email as an attachment.
File creation with MolSync
The MolSync app can interface with the MolSync service to provide the ability to translate molecules, reactions or datasheets into other cheminformatics formats, or rendered graphics:
Once the translation is complete, the new file will be saved, by uploading it to the file server.
Outgoing email with SAR Table
The SAR Table app makes can call upon the MolSync service for additional graphics formats:
As with MMDS, the rendered graphics can be exported in the form of outgoing email attachments.
File format parsing
When MMDS is installed on a device, it registers itself as an attachment handler for chemical data formats that it is able to parse. While the core formats can be extracted directly from the app itself, others can be extracted with the help of a remote procedure call.
Supported formats include ChemDraw (.cdx) and the Chemical Markup Language (.cml). This capability is most commonly encountered when parsing incoming attachments or browser downloads, e.g.:
If a ChemDraw or CML file is opened as an email attachment, or downloaded using mobile Safari, MMDS will transmit the data to the remote procedure call server in order to extract the content. The result could be a molecule, a reaction, or a datasheet (containing molecules and/or reactions), depending on the composition of the input file.
Several structure-based calculations are available, which predict numeric values or other molecular properties.
log P (octanol/water partition coefficient)
The water/octanol partition coefficient is a physiologically relevant indicator useful to medicinal chemists. The value
is either measured experimentally, or predicted using one of many available structure-based calculation methods. The calculation
method used in this case is commonly referred to as ClogP, which is based on an atom-group contribution approach:
The same method is also used to calculate molar refractivity.
TPSA (topological polar surface area)
The topological polar surface area is an indication of the extent to which the molecule presents polarised atoms to the outer
contact area. The calculation is done using an atom-group contribution approach:
The CIP (Cahn-Ingold-Prelog) designations for chirality (R, S) and restricted rotation double bond isomers (Z, E) can be calculated for an incoming molecule. Chiral atom centres with 4 different substituents, and a resolvable pattern of wedge bonds, are designated as R or S. Alkene-like double bonds with asymmetric substituents are designated as Z or E.
For a given input molecule, a list of tautomeric formats can be enumerated. The resulting set will contain the original molecule,
and any molecules that can be obtained from it by iteratively applying a set of tautomer shifts. The tautomer shift rules are
based on a published set of transforms:
The service also returns a directed graph which shows how each of the tautomers can be mapped onto one another.
By default, remote procedure calls are directed to the server molsync.com, which is hosted by Molecular Materials Informatics, and is based on an all original software stack. This means that all requests are routed to a server on the other side of the internet. The requests are not encrypted, so highly sensitive information should not be transmitted this way.
At a future date, it will be possible to obtain a license to use the software in-house. The MMDS app allows the server to be specified from the main menu, under Configure / Settings...:
The default host URL is http://molsync.com/MolSync, which provides anonymous/stateless services to all users of MMDS.
The MMDS, MolSync and SAR Table apps each have a lot of cheminformatics functionality packed into the respective app, but certain tasks are delegated to a remote procedure call server.