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 accross 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.
New features in Version 0.31
This is a quick summary of the features this version offers. A complete history of all the versions, their features and the currently known bugs can be found inside the Release Notes.
- Better 3DDeviceServer support.
- A basic PDB filefilter.
- Compiles on HP and Sparc hardware just fine ... out of the box.
bundles and able to interoperate with other applications or the SciTools project from the EMBL-Heidelberg.
- - 3DDeviceServer support for using 3D mouse devices.
- More filefilters (Look3D, Alchemy, MacMolecule, MVT)
- Uses the IconKit for drag&drop.
- Allows simple grouping which will creat regions.
- Few preferences (background color, and 3DMouse on/off).
- Uses different render settings for rotation and displaying.
- Printing the views.
Load multiple molecules (Look3D format) and show them
with multiple camera views using different styles. The
coordinate system is left-handed (x to the right, y upwards
and z into the screen. The camera is positioned on the
negative z axis). I'm not sure if this is the common
orientation ? If not, please give me a hint.
- Rotate molecules.
- Set different molecule styles and rendering qualities.
(Hollow Sticks, Round Sticks, Balls & Sticks, Spacefilling
- Show a nice interface with no function at all...hold on for
a while to see a lot of thing get implemented and improved.
Here is a rough overview of my privat timetable for this project.
Given the fact that I'm a student it might be possible to make it a
non-vapour project :-) But after all. Time passes on...deadlines
slip...nobody cares. More details can be found in the next chapter:
('95) - Load, save, new, ... basic stuff.
- More and better fileFilters. (PDB high on the list)
- Using Bundles.
- Simple stereo-camera.
- Molecule construction from basic fragments. (atoms,
- A simple German localization.
('96) - Tools executable on remote machines via PDO: HP, Sun,
SGI, DEC servers?
- StructureBoy...a 2D chemistry drawing tool.
- Nice clipping planes. Other drawing styles.
- Protein building tool.
- Energy optimization.
('99) - Direct brain-slot adaptor and other simple extentions.
- ...include here what you like. It might get real ;-)
I am trying to make it as NeXTSTEP' ish as possible. Full Drag&Drop,
Object Links etc. will definitly 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 coexistance.
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 stuff will be
included in BeakerBoy too).
Feel free to send comments on the app, interface, molecule files or
what ever. But please just send messages with useable
information...not something like: "I hate it"...please say why you
hate it ;o)
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
frontend to MolScript, porting WHATIF and working on the SCITools.
Maybe those projects are interesting to you too.
Sorry, you will need the latest versions of the IconKit and MiscKit
to compile the app. Some objects which have been included in v0.3
moved to the MiscKit and are no longer present in this project. If you
are interested in programming you should get those libraries anyway.
There are many good, reusable objects in there.
What is the 3DDeviceServer
To allow the user to rotate and move a molecule BeakerBoy uses the
3DDeviceServer.app. It is a DO based server app that does control the
access to any kind of 3D hardware..as long as there is a driver for
it. It is also available at all the major NeXTSTEP ftp-sites listed
The application is available for download in the following packages:
- 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.
What I really would like to have is something as powerful as the old NoteBook application from Millenium Software. It allowed you to have multiple sections, on-the-fly content indexing and other funky features. If no such app becomes available for Mac OS X in the near future, I would be tempted to write it on my own.