Molecules

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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.

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Yet another update for Molecules is now live on the App Store, this time version 2.02. The focus of this update is performance, and the new version greatly improves the speed of the new rendering engine. The 3-D models are now rendered at 3-6 times the speed that they were in the previous version, which should make previously choppy framerates on the iPad 1 much smoother. If you're interested in how this significant optimization was achieved, check out my question about it on Stack Overflow. Thanks go out to Tommy and Pivot for pointing me in the right direction on this.

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A minor update to Molecules, version 2.01, is now on the App Store. This new version fixes some slight bugs with the new rendering engine in 2.0, including a case where the ambient occlusion shading for a model would sometimes appear too dark, as well as some odd glitches when using pinch zooming on a model.

I've also reenabled panning across the model using two fingers, which wasn't working well for 2.0 so I had left it out of the initial release. The way that the panning works has also been tweaked to have zooming and rotation always occur from the center of the screen.

Finally, rendering performance on the iPad 2 has been slightly improved.

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The 2.0 version of Molecules brings with it a brand new rendering engine that utilizes OpenGL ES 2.0 to deliver realistic 3-D representations of molecular structures. This is a long way from the original OpenGL ES 1.1 renderer that I first wrote about here, so I want to describe in detail how this new version works. The source code for Molecules is available under the BSD license, so you are free to download the project from the main application page and follow along as I walk through the process.

Read on for a detailed breakdown of the new Molecules renderer.

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A major new update to Molecules, version 2.0, is now live on the App Store. This version brings an all-new renderer for newer iOS devices, one that is capable of beautiful, realistic 3-D graphics. You are now able to search the NCBI PubChem database of small molecule compounds, something people have been asking for since the launch of the application. In addition to this, the interface of the application has been streamlined and particularly improved on the iPad. As always, the latest source code of Molecules is available for download.

Read on for more about the new version of Molecules.

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A new version of Molecules is now available on the App Store. This adds iOS 4.0 multitasking and Retina display support, and fixes a number of issues that users have identified.

Read on for more about this update.

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A new version of Molecules is now available on the App Store, and the available source code has also been updated.  The new version fixes a potential crash in iPhone OS 4.0 and adds a new means of directly installing molecular structures in the application.

On the iPad (and soon the iPhone), you can now drag and drop molecular structures into (and out of) Molecules using iTunes.  When your device is connected, you can go to the Apps tab and scroll down until the File Sharing section is visible.  Within that section, click on Molecules to display all currently loaded molecular structure files.  To add a new structure, simply drag it into the list of files.  On the next startup of Molecules, it will be parsed and added to the application's internal database.

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You might have noticed that I updated Molecules to make it version 1.4, which adds some rendering enhancements and bug fixes for PDB searches. However, the highlight of this release is the addition of an iPad-specific interface. Additionally, now that iPhone OS 3.2 is publicly available, I have released the source code to the universal iPhone / iPad version of Molecules.

Read on for more about this version.

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After a long hiatus, I've finally updated Molecules. Version 1.3.2 is an update focused on performance, with few new features (much like a certain OS version). Rendering speed has been nearly doubled, larger structures can be displayed due to memory optimizations, and a faster search interface is used when communicating with the Protein Data Bank. As usual, the source code for this version is available.

Read on for more about what's new in this version.

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Even though the vast majority of the visitors to my site seem to be stopping by for the Cocoa / Amazon EC2 writeups, I thought I should let those of a scientific persuasion know about a molecular modeling blog I came across. The Macromolecular Modeling Blog caught my eye when they mentioned Molecules recently, so I figured I should return the favor. For any molecular biologists / bioinformaticists out there, this looks to be a very solid resource.

Also, anyone with an interest in nanotechnology needs to start reading K. Eric Drexler's blog. I've stated before how much of a fan I am of his work.

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