Allow selection based on atom indices

[awvwgk]

In case only a subset of the geometries should be compared, like a ligand in a protein, it would be useful to set an index mask from the command line.

Currently only a selection via a filter is possible, which is limited to element symbols. Instead of having to change the element symbols and create a one-time use filter, the index mask could be provided directly from the command-line. Also, such mask can be combined with any filter.