This isn't a bug. "Si" isn't a legal SMILES string. Any element not in the "organic subset" of C, N, O, P, S, B and the halogens must be inside brackets, like your second example. See the SMILES specification here:
http://opensmiles.org/spec/open-smiles-3-input.html#3.1.5 Cheers, Craig On 5/13/11 2:07 PM, SourceForge.net wrote: > Bugs item #3301767, was opened at 2011-05-13 17:07 > Message generated for change (Tracker Item Submitted) made by mirari > You can respond by visiting: > https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3301767&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: File Translation > Group: 2.2.x > Status: Open > Resolution: None > Priority: 5 > Private: No > Submitted By: Marat Talipov (mirari) > Assigned to: Nobody/Anonymous (nobody) > Summary: babel does not read 'Si' element name from Smiles > > Initial Comment: > Open Babel tool does not read name 'Si' element name from the smiles notation: >> echo "Si" | babel -i smi -o xyz > 0 molecules converted > 5 audit log messages > > However everything works fine if 'Si' is brackteted: >> echo "[Si]" | babel -i smi -o xyz > 1 > > Si 0.00000 0.00000 0.00000 > 1 molecule converted > 6 audit log messages > > Seems that babel reads 'Si' name as two elements, 'S' and aromatic 'I', which > is wrong. > > Open Babel 2.2.3 -- Feb 18 2011 -- 13:16:37 > Darwin Marat-Talipovs-iMac.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan > 29 15:17:16 PST 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386 i386 iMac11,3 > Darwin > > Marat Talipov, > talip...@gmail.com > > ---------------------------------------------------------------------- > > You can respond by visiting: > https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3301767&group_id=40728 > > ------------------------------------------------------------------------------ > Achieve unprecedented app performance and reliability > What every C/C++ and Fortran developer should know. > Learn how Intel has extended the reach of its next-generation tools > to help boost performance applications - inlcuding clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
