On 14/10/2010 14:43, Tim Vandermeersch wrote: > On Wed, Oct 13, 2010 at 8:58 PM, Geoffrey Hutchison > <ge...@geoffhutchison.net> wrote: >>> 3429680: [Li+251] 24639246 >>> 3429701: [ClH+276] 24639289 >>> 3429702: CCCC[n+251]1cccc(C)c1 24639291 >> >> These are an easy fix to the SMILES reader. Currently, we only take single >> digits for charge. Now I think the molecule is preposterous (e.g., lithium >> doesn't have 251 electrons to remove!) but I can certainly imagine some >> metals with formal charges of +10 or above. >> >> My feeling is that eMolecules probably wants to add some level of filtering >> to remove species with highly unusual valence. > > Yes, but we should handle this by throwing an error. There are > probably more of these cases though. > >> Also, does the SMILES format have a "continue after error" flag like SDF? >> That seems like a good addition. > > I don't think so but this would be nice since it is a widely used format.
I think this is already present, if I've understood correctly. With the command-line or OBConversion::Convert, the -e option will continue after an error for formats which have a SkipObjects function (smiles, mdl, mol2, xml formats). > It would also be nice to have an option to write all molecules that > produced an error to a file for example. (Gert suggested this) This > could be done from OBConversion I think. This sounds like a good idea, I'll try to write something, unless somebody else does first. Chris ------------------------------------------------------------------------------ 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
