Combined #100 and #139 plus equivalent functionality in main.cpp

[diogomart]

Here we are merging #139, which prevents the Python process from exiting in case a ligand fails reading, as well as adding the equivalent functionality to main.cpp, to skip ligands when using the --batch option, instead of exiting with pdbqt_parse_error.

The code from #100 is not merged (it implements the same idea #139, but with a custom error). It's "merged" simply to keep it in the commit graph.