On Thu, Dec 22, 2016 at 5:37 PM, Brian Cole <col...@gmail.com> wrote:

> RMSD with auto-morph symmetries with hydrogens are crazy expensive to
> calculate. Symmetry should be on by default, but without hydrogens. Would
> even love to see the RMSD auto-morph symmetry code ignore trifluro type of
> groups too as they dramatically increase the cost of the computation with
> little added value.

Ignoring the Hs with "getBestRMS" is certainly a must. The CF3s are also a
good idea.
Maybe it would make sense to have an option to ignore isomorphisms that
only differ by swapping degree 1 atoms.

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