feat: added the --reduce option to protonate using Reduce with pdb4amber

[PabloNA97]

Support option to add hydrogens with Reduce. From the AMBER manual:

  usage: pdb4amber [-h] [-i FILE]  ...
  ...
  --reduce Run Reduce first to add hydrogens. (default: no)
  ...
  Reduce is a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. It was developed by J. Michael Word at Duke University in the lab of David and Jane Richardson. Reduce is described
  in: Word, et. al. (1999) Asparagine and Glutamine: Using Hydrogen Atom Contacts in the Choice of Side-chain
  Amide Orientation...