This is the README for BeakerBoy.0.31.s.tar.gz [Download] [Browse] [Up]
Release 0.31, 7.1.1995 by Thomas Engel (tomi@shinto.nbg.sub.org)
The BeakerBoy Application
ATTENTION..you need gnutar and gzip to unpack this package.
This nice guy is trying to provide a basic framework for chemical
vizualization. It 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.
The current Release
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. Doubleclick 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 as a feature because you
might open the same region with as many different settings as you
like. But this definitly will change in the future.
The Package
This release come with the following resources. They are split in
seperate packages to give you the freedom of only downloading the
parts you are interested in.
- BeakerBoy.app & Documentation.
The BeakerBoy.0.31.NIHS.bd.tar.gz archive contains a plug'n'play
binary for NeXT, Intel, HP and Sparc hardware that was compiled
under NeXTSTEP 3.3. It also includes the documentation.
- Source.
In BeakerBoy.0.31.s.tar.gz you can find the complete source code
for this project. More details on compiling are included below.
- LookMolecules.
If you want an example molecule collection get the M-1 since
BeakerBoy v0.2 still unchangedM-1 BeakerBoy-LookMolecules.0.1.d.tar.gz
archive. This package has its seperate version number.
The latest release should be available in the /Science/Chemistry area
of the following NeXT ftp servers:
ftp.nmr.embl-heidelberg.de
ftp.informatik.uni-muenchen.de
ftp.cs.orst.edu
You might also check out the projects section of my WWW homepage. It
can be found at:
http://wwwcip.informatik.uni-erlangen.de/user/tsengel/
All it does
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.
v0.31 - Better 3DDeviceServer support.
- A basic PDB filefilter.
- Compiles on HP and Sparc hardware just fine...out of the box.
v0.3 - 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.
v0.2 - 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
CPK)
- Show a nice interface with no function at all...hold on for
a while to see a lot of thing get implemented and improved.
Bright Future
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)
- Helppages.
- Using Bundles.
- Simple stereo-camera.
- Molecule construction from basic fragments. (atoms,
bonds, molecules)
- 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.
More Details
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.
Compiling
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
above.
In Case of Trouble
If you have any questions you might contact me.
Thomas Engel
Netpunstr. 9
D-90522 Oberasbach
Germany
E-mail: tsengel@cip.informatik.uni-erlangen.de
tomi@shinto.nbg.sub.org
(NeXTMail welcome)
Warranty and copyright
Copyleft
Source code that is not part of the MiscKit project - and therefore
underlies the MiscKit distribution and copyright rules - is
distributed under the GNUpublic license.
No Warranty
This software is provided 'as is' and the programmer is not
responsible for any harm this program may cause. You - the user - are
responsible for everything that may happen to your business,
hardware, software, car, CD collection or what ever may be worth your
attention or money. Using this product is at your own risk and
your private fun.
There should be no serious bugs inside but remember that a
carbon-based unit did the coding.
TravelWare
Like all my projects this app is free and should be considered as
travel-ware.
1. Let it travel to as many people as you know.
2. Send me a postcard or E-mail if you use it. I will try to
keep you informed about new releases.
3. If you have a free bed or some free space on your floor... give
me a hint. I might come and visit you on my trip to the US
(locations on Hawaii, near Seattle or WhistlerMnt. (Canada)
preferred)
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.
Enjoy it.
Tomi
These are the contents of the former NiCE NeXT User Group NeXTSTEP/OpenStep software archive, currently hosted by Netfuture.ch.