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


Authors: F. Cazals and T. Dreyfus


The 3D weighted $\alpha$-complex is intensively used in the SBL library for modeling molecules. This package provides two major tools for:

  • visualizing a 3D weighted $\alpha$-complex using molecular viewers,
  • serializing a 3D weighted $\alpha$-complex.

These functionality are provided for the 3D weighted $\alpha$-complex data structures of the CGAL library, namely CGAL::Alpha_shape_3 and CGAL::Fixed_alpha_shape_3.



It uses the package Molecular_viewers for creating input files of molecular viewers such as PyMOL or VMD for visualizing the simplices of a 3D weighted $\alpha$-complex, except the tetrahedra. The package Molecular_viewers works as follows :

  • (i) open a file,
  • (iii) output the 3D weighted $\alpha$-complex using the output stream operator on the viewer.

There are two ways to output a 3D weighted $\alpha$-complex:

  • by iterating over each simplex, and dumping each simplex; it will output all simplices of the underlying triangulation whatever is the status of the simplex in the $\alpha$-complex.
  • by dumping directly the $\alpha$-complex; it will output only the edges and faces of the underlying triangulation that are in the $\alpha$-complex.

See Visualization with VMD for an example.


It uses the Boost serialization library for serializing the vertices of the $\alpha$-complex. More precisely, each vertex of the $\alpha$-complex can be serialized exactly as the vertex of the underlying triangulation, as defined in the package Triangulations_extensions_3.

See Serializing the vertices for an example.


Visualization with VMD

The following example load a plain text file of 3D spheres, compute the $\alpha$-complex of the input, and save in a visualization state file for VMD the vertices, edges and faces of the $\alpha$-complex. Note that the vertices are represented as 3D transparent red spheres, while the other simplices are represented with opaque red geometric objects.

Serializing the vertices

The following example load a plain text file of 3D spheres, compute the $\alpha$-complex of the input, and save in an archive the vertices of the output $\alpha$-complex.