Biomedical Engineering Reference
In-Depth Information
PyMOL
http://www.pymol.org/
A python based molecular visualization environment, offering functionalities simi-
lar to those of VMD.
1.5.2.4 Methodology
The Computational Geometry Algorithms Library (CGAL)
http://www.cgal.org
Developing geometric applications in general and computational structural biology
applications in particular is a difficult endeavor for two reasons. First, the numerical
rounding errors inherent to any floating point representation must be controlled, in
order for the program to follow to correct decision tree. Second, the code design
itself must be flexible enough to accommodate various numerical strategies but also
combinatorial structures. These two constraints underpin the C++ library CGAL,
which has become the reference library for efficient and robust geometric software.
The Ipe extensible drawing editor
http://ipe7.sourceforge.net/
IPE is a vector graphics editor, which carries two main advantages over competitors
such as xfig or inkscape for figures involving mathematical formulae and/or
ellaborate geometric constructions: first, it directly allow typing LaTeX formulae;
second, it is coupled to CGAL for constructions such as Delaunay and Voronoı
diagram.
1.5.2.5 Atomic Resolution Models
A number of programs have been made available to analysis protein—protein
interactions [
65
]. In the sequel, we focus on the software implementing the recent
developments presented in this chapter.
Intervor
http://cgal.inria.fr/abs/Intervor
Intervor is the application implementing the Voronoı interface model presented in
Sect.
1.2.4
.
Vo r l u m e
http://cgal.inria.fr/abs/Vorlume
Vorlume is a program (the only one to the best of our knowledge), computing a
certified estimate of the surface area and volume of a union of balls. See Sect.
1.2.3
.
vorpatch
http://cgal.inria.fr/abs/vorpatch
vorpatch is the application computing a topological encoding of a binding patch
based on the shelling tree presented in Sect.
1.2.5
.
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