MolSync is available as an iOS app (iPhone, iPod, iPad) which allows access to chemical data within a Dropbox repository. Molecular diagrams, reactions and datasheets can be browsed, viewed, downloaded, converted to other formats, rendered as graphics, or opened with other apps, such as the Mobile Molecular DataSheet (MMDS).

Overview

Getting Started

Dropbox account

Setting up

First upload

Folders

Files

Viewing files

Converting formats

Generating graphics

Uploading

Integration with MMDS

Linking from MMDS

Linking from MolSync

Updating from MMDS

Updating from MolSync

Collaboration

Summary

Overview


The MolSync iOS app runs on all of the Apple touchscreen devices (iPhone, iPod and iPad). It is used with a Dropbox account. Much of the functionality of MolSync is standalone, but it is designed to be used in conjunction with the Mobile Molecular DataSheet (MMDS). The app is available on the Apple iTunes AppStore.

MolSync allows chemical data to be managed on a remote file repository. Chemical data, which consists of molecular structure diagrams, reactions and datasheets, can be browsed and viewed using this app. Files with a recognised filetype can be downloaded for viewing. Data can be converted to other formats, and also used to generate graphics. Data can also be used to send to other apps which recognise the datatypes.

The following video clips provide introductory material for using MolSync:

Getting Started


Getting MolSync working involves several steps: it needs to be purchased from the iTunes AppStore, then once it is installed it needs to be connected to a valid Dropbox account.

Dropbox account


The current version of MolSync supports access to Dropbox. You need to have a Dropbox account in order to use MolSync. If you do not have one yet, see:

Create a Dropbox account: www.dropbox.com.

Dropbox is free to use for entry-level functionality.

Setting up


When MolSync is run for the first time, it shows a home page with two icons:

Double-tap the Settings icon:

The Dropbox account can now be configured. The default name for the repository is Dropbox. It is necessary to enter the login email address associated with your Dropbox account. Dismiss the dialog box by tapping Accept, and note that an icon for the repository has been added to the home page:

Double-tap on the Dropbox icon. The first time it is opened, it will be necessary to login to the account, which requires a password:

First upload


If you are already using your Dropbox account to store chemical data, then the functionality of MolSync can be explored right away. If it does not have any chemical data files, you can use another app in conjunction with MolSync to upload them.

Integration with the Mobile Molecular DataSheet is described in more detail later in this article.

Mobile Molecular DataSheet

The Mobile Molecular DataSheet (MMDS) is the preferred app for use in conjunction with MolSync. It provides editing capabilities, tight integration, and many other features. It is available from the iTunes AppStore.

Run the MMDS app. Select a datasheet, such as the collection of Src inhibitors shown below, and open the datasheet menu: select the Link to MolSync entry:

MMDS will pass the datasheet to MolSync via interprocess communication, and the MolSync app will activate, and initiate the import process. A preview of the datasheet will be shown. Press the Import button to continue:

Select a filename, and pick a folder to upload the datasheet into. The filename is derived from the datasheet title, but it may be modified. Press the Upload button to send the file to Dropbox. Once the upload is complete, the file will be available to any software that is capable of browsing your Dropbox account.

MolPrime

While MMDS has the most powerful features for integrating with MolSync, it is not free. There are other apps that are capable of passing chemical data to MolSync, and one of these is MolPrime. MolPrime is free, and can be downloaded from iTunes AppStore.

To use MolPrime to upload a molecular structure to your Dropbox account via MolSync, run the app, and draw a molecule, e.g. caffeine:

Change to the Launch tab, and activate the Open with option:

Select MolSync, and the app will be opened, and the import process will be initiated. This time the incoming data is single molecular structure rather than a datasheet:

Uploading the molecular structure to a folder follows the same steps as for uploading a datasheet.

Folders


Whenever a folder is opened from the main menu, and login credentials have been established, a folder will be displayed. For example, the root Dropbox folder:

The scrollable list shows subfolders at the top, and individual files at the bottom. All files are shown. Sub-folders are indicated by a shaded background and a forward-slash ("/") character:

Double-tapping on a sub-folder will open it up and make it the current folder. The list of files will be downloaded and displayed:

In this case, a folder called Uploads has been made the current folder. It contains one file, caffeine.mol. Note that the first entry in the list is a folder with the label: "../". Double-tapping on this entry will return to the parent folder.

For convenience, folders that are likely to be used often can be pinned to the home page. To pin a folder, tap the menu icon (top left), then select Pin:

Next time the home page is seen, it will include all of the subfolders that have been pinned:

Files


Files that are recognised by type are annotated by an icon. These include:

SuffixFile type
.elMolecular structure (native format)
.dsDataSheet (XML format)
.molMDL molecule
.sdfMDL SDfile (multiple molecules)
.rxnMDL RXN (one reaction)
.rdfMDL RDF (multiple reactions)

For example, the selected file, caffeine.el, is a representation of the chemical structure of caffeine, using the SketchEl format:

Viewing files


Double-tapping on a recognised file type downloads the file, and brings up the viewer. In this case, the molecular structure is shown:

File formats that are equivalent to datasheets or reactions are previewed using the datasheet viewer:

Some of these formats can store multiple rows and provide auxiliary data, which can be browsed and scrolled as necessary.

Converting formats


To convert a file into a compatible format, or to create a new copy of the file using the same format, either open the file in preview mode and press the Convert button, or select the file in the browser and use the Convert to... menu entry.

A dialog will appear which allows selection of the format. The options present depend on the file type:

Hit the Generate button to initiate the conversion. When it is complete, a new dialog will be presented, requesting the filename and location of the new file:

The default filename is the same as the source filename, with its extension replaced with one appropriate for the new type. A folder must be selected. The list shown above includes the Dropbox repository, and 3 subfolders that have been pinned. The selected folder is Public, which is a Dropbox feature that allows data to be shared.

Press the Upload button to add the file to the repository:

Generating graphics


Generating graphics files is similar to the process of converting to a different file format. Either open the file in preview mode and press the Graphics button, or select the file in the browser and use the Graphics... menu entry.

The setup dialog that appears shows a list of available graphics formats, and also provides an opportunity to specify how the graphics will be rendered:

The graphics formats differ depending on the file type. For molecules and reactions, the options include PNG (portable network graphics), which is the gold standard for bitmapped graphics files, and SVG (scalable vector graphics), which is an open vector graphics format. For datasheets, which typically contain multiple molecules or reactions, the options include zipped versions of these formats. Within the resulting zip file will be included one graphic image for each renderable datum.

The colour scheme can be selected from one of 4 options, which cover light background vs dark background, and colour vs monochrome. Graphics for publication are usually black-on-white, while other types of presentation, e.g. slides or web pages, often favour the use of coloured heteroatoms. Note that the actual background of the resulting graphics is always transparent.

The resolution is provided in terms of pixels-per-angstrom. Structure and reaction diagrams use Angstrom units for (X,Y) coordinates of atom locations. Even though 2D diagrams are not physical models, model-like units are used, for convenience. When producing bitmaps, the resolution is an important consideration. When producing graphics for low resolution purposes, such as web pages or presentation slides, a smaller number of pixels is preferable, because the files will be smaller, and may not need to be downsized during the display process. For printing purposes, use of raster graphics should be avoided if possible, but when it must be done, a high resolution is necessary for good results. For vector graphics such as SVG, the resolution is much less important, and serves only as a sizing hint.

As with conversion to other file formats, graphics generation is followed by a dialog box requesting a folder and name for uploading the newly-created file:

Interoperability

Individual files can be opened with other apps that are installed on the device. To access this functionality, select the file in the folder browser, open the menu by tapping the button at the top left, and selecting the Open with... entry:

The file will be downloaded. If there are any other apps that recognise the file type, they will be displayed. The iPhone/iPod and iPad display the open with functionality slightly differently, but the effect is the same:

In this example, there are two other apps installed on the device which are capable of handling molecules with the SketchEl format: MMDS and MolPrime. Selecting the MMDS option downloads the data from the repository, then launches the Mobile Molecular DataSheet, providing it with the content:

The open with functionality is generic, and can be used with any iOS app that registers itself as being capable of processing the corresponding filetype. MolSync also provides tight integration with the Mobile Molecular DataSheet, which is described later.

Uploading


MolSync can launch other apps with downloaded data, and it can also be launched by other apps, including the built in email client and mobile browser.

For example, when downloading a chemical data type from a website, a list of apps is presented:

Select MolSync, and the app will be launched, and open in preview mode:

Selecting the Convert or Graphics buttons allows the data to be uploaded to a selected folder, using the selected file format/rendering options.

Integration with MMDS


While MolSync provides basic viewing and conversion functionality for chemical data files stored on a Dropbox account, it does not provide editing capabilities. This capability is provided by another app, the Mobile Molecular DataSheet (MMDS), which is also available on the iTunes AppStore.

As described previously, MolSync supports opening of generic files, using any apps registered to receive the filetypes, and can receive chemical data from other apps. This mechanism can be used to pass data back and forth between MolSync and MMDS, and any other compatible apps, but it does not create any special association between the file stored on the Dropbox repository and the other app. While apps such as MMDS can pass the data back to MolSync, it is up to you to keep track of filenames, folders and versions.

To address this issue, the two apps - MolSync and MMDS - have a technique for associating a datasheet stored on a Dropbox account with a datasheet stored on the device by the MMDS app.

Linking datasheets

There are two ways two initiate the linking of an MMDS datasheet with a MolSync file:

  1. Start with a datasheet within MMDS, and link it to MolSync by uploading it to a repository.
  2. Start with a file in a MolSync repository, download it, and add it to the MMDS datasheet collection.

Linking from MMDS


Run the MMDS app, and select a datasheet of choice, e.g. Hydrocarbons in the example below. Open the datasheet menu, and select Link to MolSync:

The MolSync app will open, and you will be prompted to import the datasheet, which involves uploading it to a repository. In the following example, the MMDS subfolder is selected:

When the upload is complete, the datasheet will be modified to include a repository log, and then it will be sent back to MMDS:

Note that the datasheet is now annotated with a MolSync logo on the right hand side of the banner. This signifies that the datasheet is annotated in such a way that it can be traced back to its location within a MolSync repository.

Returning to the MolSync app, viewing the contents of the /MMDS subfolder shows the recently-uploaded file:

Linking from MolSync


When a datasheet is already present in a MolSync repository, it can be explicitly linked to MMDS, which allows it to be edited and updated, both locally and on the cloud-based repository. Consider the file named Aspirin-like molecules.ds, which has been independently uploaded:

To associate the datasheet with MMDS, open the file menu, and select Link to MMDS:

The file will be downloaded, and sent to the MMDS app, which will add the datasheet to its collection:

The datasheet that has been added to the MMDS collection is annotated with a MolSync logo on the right hand side of the title banner. This signifies that the datasheet has information that links it to a MolSync file.

Note that only XML-formatted datasheets, with the file extension .ds, can be linked to MMDS. Individual molecules, and other datasheet-like formats such as MDL SD files cannot be linked: they must first be converted into XML datasheet files, which can be done within MolSync, or by using Open with... to send to MMDS, which will trigger the conversion automatically.

Updating from MMDS


The point of linking a MolSync file to an MMDS datasheet is to allow updates to either copy to be conveniently synchronised. MMDS provides powerful viewing and editing tools for datasheets, and it is also very straightforward to update these changes by sending the datasheet back to MolSync.

Consider the datasheet entitled Hydrocarbons, which initially contained the first four straight chain hydrocarbons. After adding the next entry in the series - pentane - it may be appropriate to update the file stored on the cloud-hosted repository. To do this, tap the MolSync logo on the banner:

Upon confirmation, the new version of the datasheet will be transmitted to MolSync.

Because the datasheet contains information about the file that it corresponds to, and the file is still present, MolSync is able to match them up, and so it shows the resynchronisation dialog:

Information about the file and its location are shown. The View New button allows the incoming replacement datasheet to be viewed, while the View Current displays the datasheet that is currently stored in the repository.

Other than Cancel, there are three actions that can be taken with the incoming datasheet. Use the Replace button to overwrite the existing file, or use the Backup button for a safer strategy, which will rename the existing file before uploading its replacement. The Rename button provides the option to select a different filename (or location) to upload the file to.

The above screenshot shows the result of having pressed the Backup button. The file Hydrocarbons.ds contains the latest version with 5 hydrocarbons, while Hydrocarbons_backup1.ds contains the original version with only 4.

Updating from MolSync


Updates can go the other way, too. If a new version of a datasheet is uploaded to a repository, e.g. by using the Dropbox app or web portal, the new version can be sent to MMDS for an update.

For example, if the file Aspirin-like molecules.ds was modified, open the file menu and select Link to MMDS:

MMDS will be opened, and it will respond with a dialog for resychronising the file. It is similar in form to the dialog that MolSync shows when an update is received:

Both the new datasheet and the current datasheet can be viewed. The new datasheet contains an extra entry at the beginning:

Opting to Replace the datasheet will overwrite the local copy:

Using the bidirectional update mechanisms, files can be edited and synchronised in a variety of different ways.

Collaboration


It is possible to share files with colleagues using features that are intrinsic to Dropbox, for instance explicit folder sharing. Dropbox also has another built in feature: files stored in the /Public folder can be browsed by anyone, without having to provide login credentials.

MolSync makes use of this public availability by adding an extra menu option for files stored in the Public folder:

Upon selecting the Open in Browser option, the URL for accessing the file publicly will be composed with a sharing service provided by http://molsync.com:

The web page provides a graphical rendition of the chemical data, and a variety of additional services, e.g. downloading the content in selected cheminformatics or graphics formats, and sharing the content via social media.

The service provided by http://molsync.com allows access to a number of social network sharing options via the website itself. However, there is also a convenience feature for sharing chemical data on Twitter:

For more information about Twitter integration, see: Tweeting Chemical Data with MolSync.

Summary


The MolSync app brings remote file management options to iOS devices, and adds a variety of features for chemical data formats. It is closely integrated with the Mobile Molecular DataSheet, which allows local files to be synchronised with cloud-based storage solutions.

See Also


Annotated Screens (iPhone, iPad), Demonstration Videos, Drawing with Templates (iPhone), Introduction to Drawing (iPhone), Introduction to Reactions (iPhone), Introduction to SAR Table (iOS), Mobile Molecular DataSheet (iOS), MolSync Remote Procedure Calls, Output to a Projector (iPhone), Overview of Drawing Gestures (iPhone), Products, Sharing Data with MolSync: Case Study 1, Sharing Data with MolSync: Case Study 2, Tweeting Chemical Data with MolSync