Hi, On Thu, Jun 28, 2012 at 11:25 PM, Jeff Janes <jeff.ja...@gmail.com> wrote: > >From page 35 of the pdf docs for 2.3.1, it has: > ===== > The parameter of the -s option in these examples is actually SMARTS, > which allows a richer matching specification, > if required. It does mean that the aromaticity of atoms and bonds is > significant; use [#6] rather than C to match both > aliphatic and aromatic carbon. > > The -s option’s parameter can also be a file name with an extension. > The file must contain a molecule, which means > only substructure matching is possible (rather than full SMARTS). The > matching is also slightly more relaxed with > respect to aromaticity. > ====== > > > Is there some way to get this treatment as SMILES rather than SMARTS > (like the more relaxed aromaticity) without having to create temporary > files?
AFAIK this is not possible, if the SMARTS/SMILES is provided on the command line, the SMARTS matching algorithm is used. If a file name is provided, the OBIsomorphismMapper class is used. But there is no way to specify to use the latter algorithm if a SMILES is provided on the command line. Perhaps an option could be added for this or we could try to parse the SMARTS to check if it is a valid SMARTS but I'm not sure this would be a good idea since the SMILES parser usually expects valid SMILES and I don't know how well it handles SMARTS (i.e. does it crash?). Others might know more about this. Tim > Thanks, > > Jeff > > ------------------------------------------------------------------------------ > 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-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ 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-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
