Subject: OpenGL library for Scientific Research; Genetic Algorithms; Gaussian Curve Regression in Force Fields

From: "Jason L. Douglas" <[email-masked]>
Date: Wed, 14 Jul 1999 01:30:03 -0500

I have just posted two new products free to anyone who wishes to download and use them; both compiled binaries and source is included. The first is an MS-DOS program which finds protein tertiary conformations using a very extensive genetic algorithm, with many features such as quantitative inheritance and implementation of Fischer's theorem (which balances exploration versus exploitation). The force field used is a new method, using the classical Coulumb expression of nuclear energy coupled with an electronic energy term calculated using Gaussian curves regressed to quantum mechanics calculations on dielectronic species. The term also attempts to take into account electron-electron repulsion and shielding effects. In tests, it seems to have done a well job predicting hydrogen-bonding distances as well as London dispersion forces, though the total energy curve is not quite shaped right at very far distances (this can be dealt with in several ways). A paper in PDF format is also available, to help you understand the theory and methodology behind these methods. The program is available both as a compiled DOS executable, and also contains complete C source code.
The second product is an OpenGL library for scientific researchers to implement in their programs. This can save a great amount of time in reducing your graphics code to a minimum, off-loading everything to this library. The full code is included so you can modify it as you wish. It is tailored for Windows 95/98/NT platforms, but can be easily modified to work on other operating systems (XWindows, Mac OS, OS/2, etc.) that support OpenGL. It does, of course, support hardware acceleration, which can help give more processor time to CPU-intensive calculations while still providing real-time graphics. The code is in C++, and is thus only of use to C++ programmers. An example, both in source code and compiled, is also provided to demonstrate the capabilities of this library. The library can also be interfaced with PC-GAMESS (or other versions of GAMESS) to render Connolly surfaces, geodesic surfaces, electron density contours, electrostatic potential contours, and full electron density plots, all with complete control over alpha-blending! You can also display your molecular models in vector, tube, ball-and-stick, and CPK models, and control wire-frame rendering or semi-transparency values, add dynamic lighting, and varying levels of rendering quality. Support for protein models will hopefully be added soon.

All of these are available through my website at:

http://home.fuse.net/douglas/index.htm

NOTE: All downloads must come through this website for informational tracking purposes.

You can contact me at:
Jason Douglas
[email-masked]