COSMOS (COmparing Small MOlecules for Similarity) is a computer program to compare (small) molecules for 3D similarity by superposition. Given two molecules (as MDL Molfiles) you can compare them for spatial similarity.In an MDL Molfile (.mdl) the 3D-structure of a molecule can be described. The format is standardized by MDL. For detailled information look at the official description by MDL.Runtime and precision of the algorithm can be fine tuned using the parameters explained in the description of the algorithm. For drug-like molecules the standard values are recommended.