Open-source 3D data processing libraries originally developed for computer vision and pattern recognition are used to align and compare molecular shapes and sub-shapes. Here, a shape is represented by a set of points distributed on the van der Waals surface of molecules. Each point is colored by its closest atom, which itself belongs to a user defined class. The strength of this representation is that it allows for comparisons of point clouds of different kind of chemical entities: small molecules, peptides, proteins or cavities (the negative image of the