The reason I ask this question is this setting appears to be why some
files come up with too many hydrogens in the molecular formula delivered
as part of moleculeinfo.
The issue is most evident with quantum output files where double bonds
are not explicitly listed. It also shows up in pdb files where atom
connectivity does not indicate double bonds. What happens is that extra
hydrogens that are not in the molecule are added for aromatic carbons
and other atoms that would formally have double bonds too them. The
boolean includeMissingHydrogens is hard-coded to True in the call to
getMolecularFormula made when the command getProperty moleculeinfo is
issued.
I would argue this is not appropriate unless we know that all formal
bonds are provided.
What do others think?
Jonathan
--
Dr. Jonathan H. Gutow
Chemistry Department [email protected]
UW-Oshkosh Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow/
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