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 gu...@uwosh.edu UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow/ ------------------------------------------------------------------------------ Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers