added aliases and fixed some groups

[keitaroyam]

Using https://github.com/MRC-LMB-ComputationalStructuralBiology/Ligand-Tools/tree/main/fix-groups, all monomers that needed group remediation or alias addition have been updated.

The alias mechanism is supported by gemmi, and can be used by Refmac through servalcat ("refmacat"). The paper will be published soon hopefully..

• group changes (without alias addition) happened to 121 monomers
• aliases added to 1520 monomers
  • peptide: 957
  • M-peptide: 166
  • P-peptide: 52
  • DNA/RNA: 348

[keitaroyam]

Updated a script to 1) not make group changes between RNA and DNA, 2) fix H/H2/H3 order in alias (that was random before).

• group changes (without alias addition) happened to 99 monomers
• aliases added to 1520 monomers
  • peptide: 957
  • M-peptide: 166
  • P-peptide: 52
  • DNA/RNA: 348

[GaribMurshudov]

I think they can be merged.