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This script reorders the geometry.

If used without parameters, the order of atoms is the unique order based on topology described in [1]. parameter -t / --template allows to specify a template geometry (must have the same topology for meaningful result), and the geometry is reordered to the order of the template (by matching the topologies).


[1] David Weininger, Arthur Weininger and Joseph L. Wieninger, J. Chem. Inf. Comput. Sci. 29, 97-101, 1989.