Throw warning or error for malformed manifest data

[aowen-uwmad]

In parse_molecules, there is

        # Skip this molecule if any required field is missing or empty
        if not mol_type_val or not mol_chain_val or not mol_seq_val:
            idx += 1
            continue

That means if a user has a bad row, it will still silently create an input file, but it's almost certainly not the input file they want.

I think when this happens, the generator should skip writing an input file for this row of data and print a warning that it was skipped. That will require

• changing the parse_molecules function to return an error or exception
• changing the main function to catch the exception: print an error and continue to the next for loop