Molalign

Introduction

Algorithms for depicting two-dimensional structures, such as Daylight depict, Bernd Rohde's depict, cactvs gifcreator or the algorithms of C. Shelley (J. Chem. Inf. Comput. Sci. 23 (1983), 61-65) compute atom and bond layout for each molecule. When depicting a set of related molecules, say from a 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 even to quickly recognize the structure, especially if you have a favorite way of viewing that substructure. At MUG99, David Wild presented a paper, VisualiSAR: A Web-based SAR Tool, which included a description of an algoritm for improved alignment of depcitions. I present here a different algorithm and describe how I have incorporated it into a program, molalign, using Jeremy Yang's and Jack Delaney's du_mol2smi utility functions.