Molecules 2.1 now on the App Store

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It's been a little while since the last update, but version 2.1 of Molecules just went live on the App Store. 2.1 adds full support for the new Retina iPad, and has an enhanced rendering engine to support the detail on that newer device. I've also improved the contrast slightly on newer devices.

For iPad users, I've also added an atomic color key, which I know has been a highly requested feature. I've yet to rework the iPhone / iPod touch interface to support this, so this is not present on those devices.



Really love your application. The atomic color key is a nice feature.

Is there any way to organize molecules in folders on the device (iPad or iPhone)? When you have more than a dozen structures stored--tends to get lengthy to scroll.

Lastly, on my iPhone I could used .sdf files from PubChem. I tried loading them directly on the iPad through iTunes but they don't show up in the application. Are they still supported?

SDF files are supported from PubChem, but I forgot to fix the file sharing support for them. The file format is supported, but the application is not seeing those files properly when you place them in its Documents directory. I'll fix this in the next update.

Placing molecules in folders will require a rework of the underlying data model I use, but it's something I've been planning for a while. I just need to find time to implement that.

Thanks for your quick response. If I'm understanding you, to import .sdf files I should use the in-app Add Molecules features directly from PubChem. I haven't tried that yet. Definitely not a big problem to use that.



Sorry to "reply" to this comment, but I'm trying to enter the forum of Molecules but I dont know where to register and obtain a Username/pass. I've searched in the entire web page without success.


Edgar Fernandes

Hi, this is a fantastic app, one can download data from NCBI and visualize even the ribosome without any problem! It is a great tool for my students. You have also the wonderful colorcode of the atoms. What I miss is the measurements that you can do for example in jmol. The angles and the distances between atoms are very important for molecular chemistry and reactions mechanisms.
All the best..

Hi Brad,
I happened to come across your website to find out the work you did. You did a very good job. I am an engineer myself and writing iPhone/ipad app is my hobby. I and my partner started Hidden Creek Software last April and we've developed two apps since and they are iMathGenius and Graycode. iMathGenius is and Graycode is

I have a question related to iPhone development. Currently I am thinking to develop an app to display a text/drawing onto a live video and then capture an image when a user chooses to do it. The book "Beginning iOS5 Development" has a demo project to capture live video, but I do not know how to overlay a drawing onto the video and also when a user captures the image, I want the drawing/text is displayed along with the video. Any thought? Thanks in advance.

If you think I should send such question privately to you, please let me know your private email address. Thanks.


Take a look at my GPUImage framework:

In particular, look at the FilterShowcase example's "UI element" example to see how to blend text with incoming camera images or video. From there, it's easy to use the framework to grab images of these composited scenes.

I took a quick look at the GPUImage and found it is too powerful for the application I need to do. Do you have a strip-down version which does not require the big overhead? A simple demo can display a live video and overlay a text title like "hello world" and when you move your phone, the "hello world" is moving around the screen. A "capture" button is fixed onto the screen and when the user click "capture" button, a photo is displayed with "hello world" title in it.

Sorry, am I asking too much from you? I really appreciate your help. Thanks.

Wonderful app! Is there any way to download a space filling model to a 3D printer?

Not from this application. I actually use some tricks here to provide these renderings, and 3-D coordinates would not be generated for all surface points from this. I also don't have any way to export rendered coordinates in a format that a 3-D printer would understand.


can we change the color of each molecule?

Dear Dr,

Thank you for sharing the source code it is a great job
Can we use a part of your code as a viewer for simple educational structure in my main application.

Thank you in advance

Sure, it's available under the BSD license. Others have done this, such as the Inkling electronic textbook application.

Thank you for your very kind and quick answer,

After copying all methods and properties called in moleculesDelegate to my appDelegate
I considered the class : SLSMoleculeRootViewController and linked it with a view controller in my storyboard to be called using the segue via :

if ([segue.identifier isEqualToString:@"GoMol2D"]){

SLSMoleculeRootViewController *MolViewController = [segue destinationViewController];

ReactionDelegate *AppDelegate = (ReactionDelegate *)[[UIApplication sharedApplication] delegate];
[AppDelegate connectToDatabase];
[AppDelegate loadInitialMoleculesFromDisk];
[AppDelegate loadMissingMoleculesIntoDatabase];
[AppDelegate.SLSMrootViewController loadInitialMolecule];
//[AppDelegate showDownloadIndicator];


NSLog(@"[ MolViewController.molecules count]=%d", (int)[ MolViewController.molecules count]);


I got: [ MolViewController.molecules count]=0 ?

What was wrong with that?

Thanks in advance.

I solved it,
it was the initilalization of database issue

This looks like a cool app. But I downloaded a new molecule and went to its description screen in the app. There is no obvious way to leave this screen. So I'm stuck in it. Help please.

Clicking on the back arrow at the upper left of the screen doesn't take you back?

Hey Brad - not sure if you noticed there is a version of molecules being sold on the app store today for $.99.
Just thought you should know.
(wed dec 11th)

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