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...? - Noel ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
