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Several apps, including the Mobile Molecular DataSheet, MolSync and SAR Table, make use of a remotely situated server to provide additional functionality, such as creating output data, parsing input formats, or producing rendering with a variety of graphics formats. |
log P (octanol/water partition coefficient)
TPSA (topological polar surface area)
Overview
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. Similarly the, MolSync and SAR Table apps rely on remote procedure calls to provide additional functionality.
Services
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.
Output formats
| Name | Ext | Description |
|---|---|---|
| .mol, .sdf | Reading and writing of standard MDL file formats is supported internally, but it is also possible to create MDL MOL (molecules) and MDL SDF (datasheets) using non-standard extensions, which correct for some of the limitations of these formats, and decrease the potential for data loss. | |
| SVG | .svg | SVG stands for Scalable Vector Graphics, which is an open standard XML format used to encode high quality vector graphics. Application support for SVG varies considerably, but the format itself has no rival in terms of quality, and a complete implementation of a rendering engine leaves nothing to be desired as far as chemical graphics are concerned. Most modern web browsers support all of the SVG primitives used by the MolSync service. SVG output applies to single molecules or reactions. |
| HTML + SVG | .html | Since most browsers can render embedded SVG diagrams, the MolSync service offers the ability to create an HTML document containing a table of text and SVG objects that express the contents of the datasheet. The result has the benefit of being contained in a single file. |
| SVG ZIP | _svg.zip | SVG output can also be created for datasheets that contain molecules and/or reactions. Because one file is used for each discrete graphical diagram, they are packaged into a single ZIP archive. |
| PNG ZIP | _png.zip | Single PNG (Portable Network Graphic) raster images for molecules or reactions can be created within the app itself, but for datasheets that can contain multiple graphics, a collection can be obtained as a ZIP archive. |
| SMILES, CurlySMILES | .txt | SMILES is a popular line-notation for encoding molecular structures. The MolSync service can generate a very crude SMILES string (non-canonical, no stereochemistry), which is often sufficient for coarse structure-searching purposes. It can also generate CurlySMILES strings, which is an extension of SMILES which incorporates features relevant to materials. |
| Chemical Markup Language | .cml | The Chemical Markup Language is a schema for describing chemical data, and can be used to encode molecules, reactions and collections thereof. The MolSync service can both read and write the CML format. |
| Microsoft Office | .docx, .xlsx | The varieties of the Office Open XML (OOXML) format used by Microsoft Word and Excel are supported. Molecules, reactions and datasheets can be rendered as a single document, in which molecule/reaction diagrams are rendered as vector graphics, and auxiliary data is presented as text. |
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.
Calculations
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:
Stereochemistry
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.
Tautomers
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.
Configuration
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.
Summary
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.
See Also
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| © 2010-2012 Molecular Materials Informatics Inc. All rights reserved. Last modified 21-Apr-2012 |
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