ligands.dict charge assignment for xyz files about molsimplify HOT 3 CLOSED

@gianmarco-terrones as a comment on this --> ligands should generally not be stored in the ligands dict as XYZs, but rather as .mol files, which store charge. But I agree this is worth adjusting...

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Resolved! Now using xyz files in ligands.dict works even if the ligands that use the xyz files as geometries are not neutral. Verified that the terachem_input generated has the correct charge by running molsimplify -core iron -geometry oct -lig ooh -oxstate 2 -spin 1. Before, this had the line charge 2. Now, it gives the correct charge of charge -4. ooh uses an xyz as its geometry in ligands.dict and has a charge of -1.

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I should add, the key was @ralf-meyer 's change in molSimplify/Scripts/io.py in the function lig_load. The xyz files were not being given a charge when read by OpenBabel. Ralf fixed this by including the lines

    # Set charge to last entry in ligands.dict
    lig.OBMol.SetTotalCharge(int(dbentry[-1][0]))

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