Improved Implementation of Point Location in General Two-Dimensional Subdivisions

We present a major revamp of the point-location data structure for general two-dimensional subdivisions via randomized incremental construction, implemented in CGAL, the Computational Geometry Algorithms Library. We can now guarantee that the constructed directed acyclic graph G is of linear size and provides logarithmic query time. Via the construction of the Voronoi diagram for a given point set S of size n, this also enables nearest-neighbor queries in guaranteed O(log n) time. Another major innovation is the support of general unbounded subdivisions as well as subdivisions of two-dimensional parametric surfaces such as spheres, tori, cylinders. The implementation is exact, complete, and general, i.e., it can also handle non-linear subdivisions. Like the previous version, the data structure supports modifications of the subdivision, such as insertions and deletions of edges, after the initial preprocessing. A major challenge is to retain the expected O(n log n) preprocessing time while providing the above (deterministic) space and query-time guarantees. We describe an efficient preprocessing algorithm, which explicitly verifies the length L of the longest query path in O(n log n) time. However, instead of using L, our implementation is based on the depth D of G. Although we prove that the worst case ratio of D and L is Theta(n/log n), we conjecture, based on our experimental results, that this solution achieves expected O(n log n) preprocessing time.Comment: 21 page

Spanning trees crossing few barriers

We consider the problem of finding low-cost spanning trees for sets of n points in the plane, where the cost of a spanning tree is defined as the total number of intersections of tree edges with a given set of m barriers. We obtain the following results: (i) if the barriers are possibly intersecting line segments, then there is always a spanning tree of cost O(min(m2,m SQRT(n))); (ii) if the barriers are disjoint line segments, then there is always a spanning tree of cost O(m); (iii) if the barriers are disjoint convex objects, then there is always a spanning tree of cost O(n + m). All our bounds are worst-case optimal

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu