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Add orientations-based collective variables #134

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Add orientations-based collective variables #134

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Collective variables that measure orientation respect a reference using quaternions.

Supersedes #132

@pabloferz pabloferz changed the title Create orientation.py for collective variables Add orientations-based collective variables May 25, 2022
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  1. Barycenter functions imported from coordinates.py are ok.
  2. Add weights as input to used weigthed definitions of the CVs.

gustavor101
gustavor101 previously approved these changes May 31, 2022
The reference system for calculating the radius of gyration is respect
to the barycenter or weighted barycenter in case of weighted radius of
gyration. Also its value is the square root of previous values.
Collective variables that measure orientation respect a reference using quaternions
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