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Affine coordinate transformation

Christian Blau requested to merge cblau-affine-transformation into master

Introduce a class that performs affine coordinate transformations of the form A*x+t with an input matrix A and a shift vector t.

This greatly facilitates implementation of affine coordinate transformations in density-guided simulations which are needed, e.g., for density-fitting of membrane systems.

See also the planned release notes

  • Density guided simulations can be run against user-translated and transformed input densities
  • Affine transformation of trajectory tool
  • Rigid-body fitting to density tool

Part of #3581

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