aRMSD: A Comprehensive Tool for Structural Analysis.

A new free tool for structural comparison is presented that combines existing and new features into a single software package. aRMSD incorporates the functions of establishing a pairwise correlation between the atoms of two molecular structures and the calculation of the optimal rotation matrix that minimizes the root-mean-square deviation (RMSD) between the molecules. The complexity of the Hungarian assignation problem is reduced by decomposing molecules into different subsets based on different atom or group types allowing for an efficient and robust treatment of large molecules while tolerating different substituents. Various weighting functions can be used for the calculation of RMSD values and similarity descriptors, and the utilization of coordinate uncertainties allows for the calculation of standard deviations for all calculated properties through error propagation. A new three-dimensional (3D) graphical representation that combines multiple aspects of structural information is presented which is useful in the analysis of structural similarity and diversity. The capabilities of aRMSD are demonstrated by selected examples that show how the program can be utilized in the analysis of structural changes and in the correlation of structure and activity in molecules. The source code of the program can be downloaded at https://github.com/armsd/aRMSD .