Add option to keep the existing b-factor in the input PDB

[amjjbonvin]

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Adds the option to keep the existing b-factor in the input PDB files by setting set_bfactor=false in topoaa. b-factors of unknown atoms are assigned the average b-factor of the known atoms per residue

[amjjbonvin]

Looks like I made a mess of those pull requests….

[amjjbonvin]

Should now be fine - please review