Jesper Foldager

Fix three issues for n-term proline. I) Add both H2 and H3 to proline. II) Fix crash related to H2 dihedral being defined by side-chain atom CD, which is not initially added in the initialisation of the chain. III) Handle that initialisation from pdb file, without --init-from-pdb, set the n-term phi angle to NAN. Both II) and III) resulted phaistos crashing.

Fixed sirious bug in simulated annealing. This mc was approximately doing greedy optimization due to inheritance from Optimization instead of Simulation, providing the wrong acceptance_criterion method.

Ensure the method hbpotential is const

Fix problem with binary characters in pdb outpu...

fix term rmsd-constraint copy constructor and i...

Add option to calculate rmsd on heavy atoms (sk...

Add atom iterator that skips hydrogen

Fix rmsd calculation when ca-only=false for rms...