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.
On Thu, Dec 22, 2016 at 10:27 AM, Greg Landrum <greg.land...@gmail.com>
wrote:
>
> On Thu, Dec 22, 2016 at 4:06 PM, JW Feng <f...@dnli.com> wrote:
>
>>
>> Thanks for confirming the bug. I also vote for changing the code to use
>> only heavy atoms. Is symmetry taken into consideration when calculating
>> RMS during the pruning step?
>>
>
> Symmetry is not taken into account, once the code to do that is available
> in C++ (Peter Gedeck is working on this), we'll add that option too.
>
> -greg
>
>
>
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