ToyChem Package

Description

The ToyChem Package implements a realistic artificial chemistry model. Molecules are represented by their molecular graphs. The properties of the molecules are completely determined by the orbital graph, which can be unambiguously constracted from the structural formula of a molecule by applying the VSEPR rules.

The core of the package consists of a collection of routines for the prediction of physico-chemical properties of molecular graphs. These routines can be accessed through stand-alone programs, such as ToyChemEnergy which should be sufficient for most users. For those who wish to develop their own programs a library is provided which can be linked to your own code.

Web Service

Follow the link to try out the program ToyChemEnergy from the ToyChem Package . (currently not available).

Download

A prerelease v1.0.0pre source code (some documentation is missing) of the ToyChem Package . (currently not available)

Bug Reports

Please send bug reports to <xtof@tbi.univie.ac.at>

Literature

"Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry"
Gil Benkö, Christoph Flamm and Peter F. Stadler
In: Proceedings of the 8th European Conference on Artifical Life
(ECAL 2005) M. Capcarrere et al. (Eds.); Springer-Verlag Berlin Heidelberg, LNAI 3630, pp. 725-733, 2005
(doi:10.1007/11553090_73 )
[Abstract] [Postscript] [PDF]

"The ToyChem Package: A Computational Toolkit Implementing a Realistic Artificial Chemistry Model"
Gil Benkö, Christoph Flamm, Peter F. Stadler
unpublished Technical Note
[abstract] [Postscript] [PDF]

Gil Benkö,Christoph Flamm, Peter F. Stadler
"Multi-Phase Artificial Chemistry"
In: The Logic of Artificial Life - Proceedings of the 6th German Workshop on Artificial Life (GWAL 2004)
H. Schaub, F. Detje, U. Brüggemann (Eds.)
Akademische Verlagsgesellschaft Aka GmbH, Berlin, 2004, pp. 16-22.
[abstract] [Postscript] [PDF]

Gil Benkö, Christoph Flamm, Peter F. Stadler
"Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting"
In: Advances in Artificial Life - Proceedings of the 7th European Conference
on Artificial Life (ECAL 2003)
W. Banzhaf, T. Christaller, P. Dittrich, J. T. Kim, J. Ziegler (Eds.)
Springer Verlag, 2003, pp. 10-19.
[abstract] [Postscript] [PDF]

Gil Benkö, Christoph Flamm, Peter F. Stadler
"A Graph-Based Toy Model of Chemistry"
J. Chem. Inf. Comput. Sci., 43, 1085-1093 (2003)
[abstract] [Postscript] [PDF]

Contact

<xtof@tbi.univie.ac.at> or <gil@bioinf.uni-leipzig.de>

Useful Links

	PerlMol - Perl Modules for Molecular Chemistry
	SMILES Home Page