The OpenSMILES spec doesn't fully describe the Daylight valence model. I'll get the full details from Roger, but in the meanwhile here's some bullet points from a talk of his:
"Daylight’s valence model for SMILES is that all aromatic nitrogens have no implicit hydrogens by default. If a hydrogen is present, it has to be specified as “[nH]”. This means that “[n]” should never occur in a generated/canonical SMILES string." Not sure if this helps... - Noel On 22 November 2012 20:50, Tim Vandermeersch <tim.vandermeer...@gmail.com> wrote: > Hi, > > I'm working on an OBFormat for parsing SMILES using my new Smiley parser. > The initial tests look good but there is a specific problem regarding > aromatic nitrogens. When I read a molecule using the new format and write > out the caonical smiles, all aromatic nitrogens are written out as "[nH]". > Does anyone know how the original SMILES parser handles this or how I should > fix this issue? > > Thanks, > Tim > > > > ------------------------------------------------------------------------------ > Monitor your physical, virtual and cloud infrastructure from a single > web console. Get in-depth insight into apps, servers, databases, vmware, > SAP, cloud infrastructure, etc. Download 30-day Free Trial. > Pricing starts from $795 for 25 servers or applications! > http://p.sf.net/sfu/zoho_dev2dev_nov > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
