Molecules

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.

I've been doing a lot of work with Core Animation lately during development of my next iPhone application, and I came across an interesting way to optimize OpenGL ES rendering that I thought I'd share. This small improvement yielded a 14-25% increase in the triangles per second I was able to push in Molecules.

Read on for more about this optimization.

Now that I'm back from the holidays, all immediate issues are taken care of here at work, and iTunes Connect is back up, I've submitted version 1.3.1 of Molecules for review (and updated the source code. This is a bugfix version, addressing the recent crashes when trying to search the Protein Data Bank. The PDB servers stopped responding to one half of the search query I was sending, which was a condition I had not anticipated, and Molecules would crash as a result. Unfortunately, until they fix the server response, the search results will no longer list the titles of molecules.

I apologize for any problems this has caused. I was stupid not to anticipate this kind of response.

I thought I should let you know about a new application that recently appeared in the iTunes App Store called iMoleBuilder (iTunes link). It is a $12.99 molecular visualizer that also lets you construct molecules and save them to the device or an available FTP site.

Read on for more of my impressions of this application.

Earlier today, I submitted version 1.3 of Molecules for review in the iTunes App Store. The major new feature that this version adds is the ability to download custom molecular structures. For those of you who can't wait, the source code has been updated .

Again, I apologize for the delay in providing a new version. I'm working on a new iPhone application that I hope to unveil within the next couple weeks and it is taking most of my available time.

Read on for more information about this version.

Recently, I was given the opportunity to write an article about the educational applications of Molecules for the RCSB Protein Data Bank's fall newsletter. That article is now online, and I think it came out well. It's worth reading if you're interested in my thoughts about the scientific and educational applications of the iPhone / iPod Touch.

With the lifting of the Nondisclosure Agreement on the iPhone SDK, I'm pleased to finally make available the source code to Molecules. If you go to the main page for the application, you should now find a link to download the latest source tarball (for version 1.2) on the right-hand side. You can also download the source code here. I am working on migrating my personal Subversion setup so that you can check out the latest code and so that I can authorize contributors to commit fixes and additions.

Read on for a description of the internal structure of Molecules.

I just submitted Molecules 1.2 for review in the App Store. Sorry it's taken me so long to get a new version out to you, but this version required a complete rewrite of a portion of the core code. I also have been distracted by a few things at my day job and some shiny new technology that I've been playing with.

Read on for more information on this release.

This might be jumping the gun a bit, but I wanted to let you know that a new version of Molecules, 1.1, has been submitted for review for the iTunes App Store. Even though it will take a bit of time to be approved, I thought you might be interested in a preview of some of the new features in this version.

This version adds two new visualization modes, as well as integrated keyword searching of the Protein Data Bank.

Read on for more details.

I had a great time at the satellite iPhoneDevCamp in Chicago, where I was surprised with the number of well-known (to me, at least) developers who are located in the area. Although the San Francisco outpost may have had more attendees, I'd argue that we had as good a technical and business discussion going. We certainly had better shirts (courtesy of Stand Alone).

Anyway, I was allowed to give a talk on some of the lessons that I'd learned in implementing the 3-D graphics in Molecules using OpenGL ES. It was well-received, so I figured that I should create a written guide based on my talk.

Read on for my lengthy writeup about OpenGL-based 3-D graphics on the iPhone.