This PR introduces a new Calculator and Optimizer:
the RmsdMappedCalculator calculates the RMSD between two molecules with different num. atoms and/or atom order by calculating the displacement based on the nearest atom of the same atom type.
the Aligner optimizer runs Spindry where the host and guest are molecules to be aligned. A new AlignmentPotential has been introduced that defines the cost of a configuration based on pair distances with atoms of matching atom type and only the nearest for each pair.
Examples have been added to examples/ showing both in action.
This PR introduces a new Calculator and Optimizer:
RmsdMappedCalculatorcalculates the RMSD between two molecules with different num. atoms and/or atom order by calculating the displacement based on the nearest atom of the same atom type.Aligneroptimizer runs Spindry where the host and guest are molecules to be aligned. A newAlignmentPotentialhas been introduced that defines the cost of a configuration based on pair distances with atoms of matching atom type and only the nearest for each pair.examples/showing both in action.