Programmatically adding hydrogen and remove water to multiple PDB files

Question

[gundalav]

I'm trying to dock a ligand to several hundred PDB file (receptors). I thus need to prepare the those PDB files like removing water and adding hydrogen.

I can do that manually using Autodock or Pymol. But it's too troublesome. Is there a way to do it programmatically with Python or R or any command line procedure?