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A 3D molecular surface representation supporting neighborhood queries

  • Geo-Algorithms
  • Conference paper
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Advances in Spatial Databases (SSD 1995)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 951))

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Abstract

Applications in molecular biology more and more require geometric data management along with physicochemical data handling. Thus, 3D structures and surfaces of molecules become basic objects in molecular databases. We propose the neighborhood query on graphs such as molecular surfaces as a fundamental query class concerning topological information on patch adjacency. Furthermore, we suggest a patch-based data structure, called the TriEdge structure, first, to efficiently support neighborhood query processing, and second, to save space in comparison to common 2D subdivision data structures such as the quad-edge structure or the doubly-connected edge list. In analogy to the quad-edge structure, the TriEdge structure has an algebraic interface and is implemented via complex pointers. However, we achieve a reduction of the space requirement by a factor of four. Finally, we investigate the time performance of our prototype which is based on an object-oriented database management system.

This research was funded by the German Ministry for Research and Technology (BMFT) under grant no. 01 IB 307 B. The authors are responsible for the content of this paper.

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Authors and Affiliations

  1. Institute for Computer Science, University of Munich, Leopoldstr. 11 B, D-80802, München, Germany

    Thomas Seidl & Hans-Peter Kriegel

Authors
  1. Thomas Seidl
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  2. Hans-Peter Kriegel
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Max J. Egenhofer John R. Herring

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© 1995 Springer-Verlag Berlin Heidelberg

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Seidl, T., Kriegel, HP. (1995). A 3D molecular surface representation supporting neighborhood queries. In: Egenhofer, M.J., Herring, J.R. (eds) Advances in Spatial Databases. SSD 1995. Lecture Notes in Computer Science, vol 951. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-60159-7_15

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  • DOI: https://doi.org/10.1007/3-540-60159-7_15

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-60159-3

  • Online ISBN: 978-3-540-49536-9

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