Add support to PDB ligands on CLI

[pslacerda]

Add support to mk_prepare_ligand.py read PDB files.

They're crystallographic ligands from PDB and PDBBind. Because of this, they have no hydrogen and must be added.

It works on my use case, but maybe someone have also PDB files for micro-molecules with explicit hydrogens already into.

[rwxayheee]

Hello @pslacerda

you might want to take a quick look at #317. We do this in a more rigorous way in a sense that we check the CCD template.

Because of that we’re unlikely to merge this PR. But you’re welcome to explore your preferred ways of preparing ligands!

For future PR and for development please use develop branch as the destination branch :D