Algorithms for depicting two-dimensional structures (Daylight depict, Bernd Rohde's depict, cactvs smi2mol) compute an atom and bond layout for each molecule. When depicting a set of related molecules, say from reaction product enumeration or a substructure search, each structure is depicted independently. The result is usually a page in which the reaction core or common substructure is aligned differently for each structure. This makes it difficult to compare structures, or to quickly recognize related structures, especially if you have a favorite way of viewing that substructure. MolAlign is a program which reads a molfile of related structures, along with a SMARTS substructure definition and produces a molfile in which each structure is rotated so that the common substructures are aligned with each other. I will show examples of the use of this program and a display of the results.
I will discuss limitations of this approach and ways in which it can be improved. This program will be made available in the Daylight contrib directory.