A new option which keeps stereochemistry.
A new option which keeps stereochemistry.

Here is a jupyter notebook for the illustration: https://github.com/xg590/miscellaneous/blob/master/charnley_rmsd_proof.ipynb
$ time (for i in {1..10} ;do python rmsd/calculate_rmsd.py tests/c6h7-int1-a.xyz tests/c6h7-int1-xz.xyz --use-reflections;done)
$ time (for i in {1..10} ;do python rmsd/calculate_rmsd.py tests/c6h7-int1-a.xyz tests/c6h7-int1-xz.xyz --use-reflections-keep-stereo;done)
charnley/rmsd