User Manual

Table of Contents

• Introduction
• Functionality
  • Visualization
  • Serialization
• Examples
  • Visualization with VMD
  • Serializing the vertices

Alpha_complexes_extensions

Authors: F. Cazals and T. Dreyfus

Introduction

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

• visualizing a 3D weighted -complex using molecular viewers,

• serializing a 3D weighted -complex.

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

Functionality

Visualization

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 -complex, except the tetrahedra. The package Molecular_viewers works as follows :

• (i) open a file,

• (ii) create the viewer (e.g SBL::IO::VMD_viewer) on the open file

• (iii) output the 3D weighted -complex using the output stream operator on the viewer.

There are two ways to output a 3D weighted -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 -complex.

• by dumping directly the -complex; it will output only the edges and faces of the underlying triangulation that are in the -complex.

See Visualization with VMD for an example.

Serialization

It uses the Boost serialization library for serializing the vertices of the -complex. More precisely, each vertex of the -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.

Examples

Visualization with VMD

The following example load a plain text file of 3D spheres, compute the -complex of the input, and save in a visualization state file for VMD the vertices, edges and faces of the -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 -complex of the input, and save in an archive the vertices of the output -complex.