RMSD is now calculated by a homemade function linked with numba for f…

…ast calculation.

It is still a little slower than MDTraj but MDTraj's RMSD function re-align no matter what, which is problematique when we want to cluster after an alignment on another part of the protein.

environment.yml

@@ -12,3 +12,4 @@ dependencies:
 - conda-forge::mdtraj
 - scikit-learn
 - conda-forge::prettytable
+- numba

examples/backbone/RMSD_between_clusters.csv

@@ -1,14 +1,5 @@
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