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Automated Drawing of Structural Molecular Formulas under Constraints

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Fraunhofer-Institut für Algorithmen und Wissenschaftliches Rechnen (SCAI), Schloss Birlinghoven, 53757 Sankt Augustin, Germany
BioSolveIT GmbH, An der Ziegelei 75, 53757 Sankt Augustin, Germany
Center for Bioinformatics (ZBH), University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
Cite this: J. Chem. Inf. Comput. Sci. 2004, 44, 3, 1065–1078
Publication Date (Web):April 15, 2004
Copyright © 2004 American Chemical Society

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In this paper, we present a new algorithm for automated drawing of 2D structural formulas of molecules. The algorithm is based on the classical scheme of a drawing queue placing the molecular fragments in a sequential way. We extend the concept of so-called prefabricated units developed for complex ring systems to automatically created drawing units for chains and rings which will then be assembled in a sequential fashion. The approach is fast and can be naturally extended to the problem of drawing molecules with common core structures. Further on, we present an algorithm that allows the drawing of 2D structural formulas under directional constraints assigned to a subset of bonds. Since no numerical optimization is necessary, the algorithm creates drawings of small organic molecules on the order of 500 structures per second. The new algorithm is relevant for all kinds of prediction and analysis software presenting a large number of probably similar molecular structures to the user of the software.

 Current address:  Center for Bioinformatics (ZBH), University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany.


 Corresponding author phone:  +49 40 42838 7351; fax:  +49 40 42838 7352; e-mail:  [email protected]

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