doi abstract bibtex

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.

@article{Fricker:2004aa, Abstract = {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.}, Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, Author = {Fricker, PC and Gastreich, M and Rarey, M}, Date = {MAY-JUN 2004}, Date-Added = {2008-09-14 16:44:27 -0400}, Date-Modified = {2008-09-14 16:45:25 -0400}, Doi = {10.1021/ci049958u}, Isi = {000221608000033}, Isi-Recid = {134777911}, Isi-Ref-Recids = {134777912 134777913 116319080 88182467 134777914 132390134 73418769 112718168 86265660 134777915 63655121 129147746 128009080 117048205 120351179 107954946 128945519 75424890 93575150 134777916 134777917}, Journal = {J.~Chem.~Inf.~Comput.~Sci.}, Keywords = {depiction; 2d; drawing}, Number = {3}, Pages = {1065--1078}, Publisher = {AMER CHEMICAL SOC}, Timescited = {7}, Title = {Automated Drawing of Structural Molecular Formulas under Constraints}, Volume = {44}, Year = {2004}, Bdsk-File-1 = {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}, Bdsk-Url-1 = {http://dx.doi.org/10.1021/ci049958u}}

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