Bugs item #3089597, was opened at 2010-10-18 09:26 Message generated for change (Tracker Item Submitted) made by baoilleach You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3089597&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: Library Functions Group: 2.3.x Status: Open Resolution: None Priority: 3 Private: No Submitted By: Noel O'Boyle (baoilleach) Assigned to: Noel O'Boyle (baoilleach) Summary: Geminal diols have incorrect implicit Hs detected Initial Comment: (This bug is fixed...I just want to record the details here in case it needs to be revisited.) >From the mailing list: "I went through a large dataset of PubChem 3D structures looking for implicit H failures (removing, then adding Hs). 1/3 of the failures are due to the following in atomtyp.txt: INTHYB [$([#6]([#8D1])[#8D1])] 2 #sp2 carbon This makes any C attached to two Os turn into sp2...even in geminal diols , for example, ClC(Cl)(Cl)C(O)O. According to wikipedia, these don't tend to last long but they are in PubChem (whether errors or not, I can't say). If it's commented out, then it works fine for these cases. Is there any reason for this rule (it seems to date from the early days)? Perhaps it's to correct ligand structures from the PDB where all examples of this indicate COO-? If so, maybe the PDB cases are better handled in the code using the molecular geometry...?" The solution is to comment out the offending line in the file. If it turns out that there are subsequent problems with interpreting PDBs, we deal with it as follows: "You're suggesting to add a method to pdbformat for "correctCarboxylateHybridization" correct? That shouldn't be too hard -- make sure hybridization is assigned already, then go through the SMARTS match and check for a real COO-." ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3089597&group_id=40728 ------------------------------------------------------------------------------ Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
