ligands.dict charge assignment for xyz files

[gianmarco-terrones]

When using molSimplify from the command line, the generated terachem_input files do not have the correct charge if the ligand is not neutral and uses an xyz file as its geometry in ligands.dict.

[adityanandy]

@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...

[gianmarco-terrones]

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.

[gianmarco-terrones]

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]))