Combined #100 and #139 plus equivalent functionality in main.cpp #146
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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--batchoption, instead of exiting withpdbqt_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.