Bugs item #3014855, was opened at 2010-06-11 15:35 Message generated for change (Tracker Item Submitted) made by dan2097 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3014855&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Daniel Lowe (dan2097) Assigned to: Nobody/Anonymous (nobody) Summary: CML hydrogenCount attribute handling bug Initial Comment: I am trying to output CML corresponding to the resonance form of carbon monoxide, [C]=O As it is not necessarily clear whether hydrogen are implicit or explicit I have added hydrogenCount="0" to the carbon to say explicitly that the carbon has no hydrogens. OpenBabel however appears to ignore hydrogenCount="0" implicitly adding two hydrogens. On a related note OpenBabel's handling of CML's hydrogenCount attribute when explicit hydrogen are present is technically wrong. If you have an atom with hydrogenCount="2" and one explicit hydrogen the number of hydrogens bonded tor the atom should according to the CML spec still actually be 2 , not 3. Taken from http://cml.sourceforge.net/schema/cmlCore/HTMLDOCS/cmlCore.pdf : "hydrogenCount[el.atom.hydrogenCount] The total number of hydrogen atoms bonded to an atom. The total number of hydrogen atoms bonded to an atom, whether explicitly included as atoms or not. It is an error to have hydrogen count less than the explicit hydrogen count. There is no default value and no assumptions about hydrogen Count can be made if it is not given." I have attached a zip file with a CML file demonstrating both cases. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3014855&group_id=40728 ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
