Bioinformatics Preprint 05-002
The ToyChem Package: A Computational Toolkit Implementing a Realistic Articial Chemistry Model
Gil Benkö, Christoph Flamm, Peter F. Stadler
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Most models of artificial chemistries are far away from the "look-and-feel" of a real-world chemistry. Usually, abstract algebraic entities are used that do not lend themselves to a natural definition of reaction enthalpies or to the incorporation of the crucial conservation properties of mass and atom types. In this short contribution we describe an improved version of an artificial chemistry model that stays close enough to a quantum-chemical description to be recognizable as an approximation to organic chemistry while at the same time allowing for a computationally endcient implementation that makes large-scale simulation feasible. Molecules are represented by their molecular graphs whose energy is defined via a simplified Extended uckel Theory approach based on the orbital graphs. The model is implemented as an Ansi C++ library, as a stand alone executable, and as a simple webserver. The software is distributed free of charge under the GNU Public License.
extended Hückel MO theory, chemistry toy model, artificial chemistry
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