Bugs item #3542290, was opened at 2012-07-10 17:05 Message generated for change (Tracker Item Submitted) made by cjames53 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3542290&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: Craig (cjames53) Assigned to: Nobody/Anonymous (nobody) Summary: SDF round-trip error with explicit H atoms Initial Comment: An explicit H in a SMILES produces an explicit H when exported as an SDF. If this same SDF is then parsed and printed as a SMILES, the wrong SMILES is printed. echo "[H]NC" | babel -i smi -o smi NC echo "[H]NC" | babel -i smi -o sdf | babel -i sdf -o can C[NH] The problem seems to be that the explicit H in the SMILES is converted into an explicit H in the OBMol object. This yields an OBAtom with some explicit and some implicit H neighbors. The SMILES writer handles this correctly. But for this same OBMol object, the SDF writer assumes that you want these hydrogens written out, but then when it reads them back in, the SDF parser makes a different assumption about the atom's valence. In other words, the OBMol object that the SDF writer generates is different than the OBMol object that it reads back in. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3542290&group_id=40728 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
