Version 0.31 (7. January 1996), Tomi Engel

This nice guy is trying to provide a basic framework for chemical visualization. BeakerBoy serves as the center of a possible collection of many different chemistry tools that should be able to cooperate across a network and different hardware platforms. As a main goal I want to create a flexible app design that is very simple to extend via additional bundles and able to interoperate with other applications or the SciTools project from the EMBL-Heidelberg.

Feature Check

Version 0.31 still has to be considered as an alpha version that is under development and might change a lot. To get a little impression of the things I have in mind for the releases yet to come read the second chapter of this documentation. I would like to get any kind of feedback from other programmers or chemist to make this app more intuitive, flexible and maybe find some better solutions.

All you can do with the current version is:

1. Load some sample molecules.
2. Create new regions by grouping either atoms or bonds.
3. Use the Inspector to adjust the graphical parameters (color, styles, etc.).
4. Double-click any collection of selected regions to show them.
5. Rotate the molecules using the RotatorPanel or the 3DDeviceServer.
6. Print the views.

Every view you see will be drawn using the settings valid at the moment of creation! Later changes won't affect any already visible view. Right now you might consider this a feature because you might open the same region with as many different settings as you like. if this all sounds a little fuzzy just go ahead and play with the BeakerBoy and see how it works. However, the current behavior definitely will change in the future.

Check out the release notes for more details on feature creep.

Vision

I am trying to make this app as NeXTSTEP'ish as possible. Full drag & drop, object links etc. will definitely be added someday. There will be APIs for any kind of loadable bundle or service link. DOs will find their way into this project too. It is almost ideal for creating server based number crunching analysis tools. And once the SciTools project gets going I will try to make BeakerBoy compatible or what ever might be necessary to allow easy coexistence.

As said before. This app wants to provide a well defined API, reusable objects and a flexible concept. It is not designed to squeeze the last bit out of memory or CPU performance. The basic idea is to provide useful working speed with almost any molecule size on any hardware. This will need a wide variety of QRenderMan settings. For really impressive pictures I might add some kind of link to solidModeller, intuitiv3D, etc. (some basic shading code will be included in BeakerBoy too).

If you are interested in chemistry on NeXTSTEP checkout MolViewer by Steve Ludtke. Not as pretty as my app :-) but a lot more useful (at the moment). Georg Tuparev from the EMBL-Heidelberg is writing a front-end to MolScript, porting WHATIF and working on the SciTools. Maybe those projects are interesting to you too.

Package Download

The application is available for download in the following packages:

Example Molecules for Download

It might be boring to have a 3D visualization tool and no data to visualize we are providing a set of "handmade" example molecules:

Since our server might not be the fastest, we encourage you to search for the files in some of the well known archives if necessary. We recommend: www.peanuts.org (Germany), ftp.beng.org (Germany) and next-ftp.peak.edu (USA). In addition to that we would like to point you to the stepwise softrak service which can direct you to other interesting applications.

Credits

• The guys at NeXT for this amazing OS + development tools. This was my first NeXTSTEP/Obj-C application and the code was written within 76 days (see the Release Notes). I would have never believed that this was possible. And it was fun too.
• Steve Ludtke for the 3DKit code inside MolViewer that gave me a quick start. Although I don't find his code very readable ... but it works.
• Greg Burd's swapView saved me a lot of time and helped me with all the swapping. But it needed a complete rewrite to meet the apps needs.
• Mike Ferris for the MOKit. Very nice and useful objects for everybody. His String object helped me to get going. But now it merged with the MiscKit and so I'm not using his good kit anymore
• H. Scott Roy for the IconKit. A very well designed object collection for the basic drag&drop stuff. You can find it on every NeXTSTEP ftp site.
• Georg Tuparev for providing access to NeXTSTEP for HP and Sparc at the EMBL-Heidelberg.
• Everybody writing nice objects like the guys from the MiscKit (Don don't get tired of keeping it all together. Misc is cool)
• My brother for all the nice images and chemistry background info I might not remember in detail anymore.

Future development

When you take a look at our original (old) road map it will be easy to spot that we are way behind schedule (if there ever was one) and this academic project has not seen an update in the past few years. It is questionable if we will or can revive it under Mac OS X.

Currently we are lacking a true 3D library. So if there should be a revival we first need to pick up the FarmersOsprey project and finish our 3DKit. Since that is quite unlikely on its own the future is a little dark for the BeakerBoy and its refreshing smile.