I recently came across this brilliant collection of software from Michel Petitjean

• ARMS: Spatial Alignment with the RMS (Root Mean Square) method. (fixed pairwise correspondence)
• ASV: Analytical calculation of van der Waals surfaces and volumes. (or any union of spheres)
• CCCPP: Computes Cavites, Channels, Pores and Pockets in proteins.
• CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules. (pairwise correspondence computed)
• CYL: Minimal radius enclosing cylinder. Minimal radius circumscribed cylinder.
• DIVCF: Selects by clustering major conformations of a molecule in a set of its conformers.
• DOG: Docking Geometrically two molecules. (fixed pairwise correspondence)
• GRD: Computation of the Radius and Diameter of a molecular graph. (computes also the topological shape index)
• MCG: Optimal Partition (classification): numerical variables and non-euclidean spaces. The number of classes is computed.
• POP: Optimal Partition (classification): categorical variables. The number of classes is computed.
• POSE: Computes the RMSD between two ligand poses. No rotation translation is performed.
• QCM: Quantitative Chirality Measure of a conformer (graph automorphisms enumeration included)
• RADI: Computation of the Radius and Diameter of a spatial set. (computes also various other geometrical parameters)
• VIRAPOPS: A forward simulator dedicated to rapidly evolved viral populations.

Binaries are available for MacOSX and Linux.