Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.

Packages

 Alpha_complexes_extensions
 Data structures and algorithms enriching the $ \alpha $-complex data structure of CGAL
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Betti_numbers
 Algorithms for computing Betti numbers from graphs and $ \alpha $-complex
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Cluster_engines
 A package providing classical clustering algorithms within a unified framework
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Morse_Smale_Witten_chain_complex
 Data structure and algorithms for building the Morse Smale Witten Chain Complex from an elevated graph
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus and C. Roth

 
 Morse_theory_based_analyzer
 Algorithms for analyzing an elevated graph using Morse theory tools
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus and C. Roth

 
 Nearest_neighbors_graph_builder
 Algorithms building Nearest Neighbor Graphs (NNG) using spatial search engines.
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus and C. Roth

 
 Point_cloud_rigid_registration_3
 Algorithm superimposing two 3D points' clouds by rotating and translating them.
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Spatial_search
 Data structures and algorithms to search the nearest neighbors of an input point in a data base of points.
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Spherical_kernel_extension_3
 Supplemental predicates and constructions for the CGAL Spherical_kernel_3
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Triangulations_extensions_3
 Data structures and algorithms enriching the 3D Triangulations of CGAL
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Union_of_balls_boundary_3
 Data structure and algorithms to compute the boundary of the union of 3D balls.
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Union_of_balls_boundary_patch_shelling_3
 Data structure and algorithm to compute the depth of 3D balls in a patch at the surface of the union of 3D balls.
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Union_of_balls_medial_axis_3
 Data structure and algorithm to compute the medial-axis of the union of a family of 3D balls.
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Union_of_balls_mesh_3
 Algorithm for meshing and sampling the boundary of the union of a family of 3D balls
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Union_of_balls_surface_volume_3
 Data structure and algorithm to compute the surface area and the volume of the union of a family of 3D balls.
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus and S. Loriot

 

Description

Geometry and Topology.

The molecular geometric models manipulated in the SBL have a geometric representation, either as a collection of balls (van der Waals models or solvent accessible models), or based upon internal coordinates. The GT group of packages provides geometric and topological operations on these representations, with in particular extensions of Delaunay triangulations and relatives (spherical kernel, alpha-shapes), operations on union of balls (medial axis, boundary of the union), and elementary topological operations.