Disambiguate multiple matches with connectivity and formal charge

[Yoshanuikabundi]

At present, a residue definition is matched to a residue in a PDB file by atom names, and then once the entire PDB file is loaded a check is made for any stray CONECT records. If there are multiple atom name based matches to a residue, we should use CONECT records and formal charges to help disambiguate them. However, if this filters out all residues, it should be ignored so that incorrect formal charges do not prevent a PDB file from being loaded.