On Dec 12, 2012, at 11:44 AM, Noel O'Boyle wrote: > I can't find it on the Daylight website, or in the OpenSMILES spec, > but Roger has told me (the classic "appeal to authority" argument) ... > Certainly Daylight's Depict (http://www.daylight.com/daycgi/depict) > does not accept c1nncc1, but is happy with c1n[nH]cc1.
The problem is not the appeal to authority or whether or not Daylight depict accepts certain things. What we know from experience is that SMILES collections exist, which include such non-standard patterns. IIRC, there are a few such things in PubChem and ZINC. I remember them bitterly in the efforts in 2.2 and 2.3 to make the canonical SMILES round-trip. I’m sure you remember them -- I always complain about aromatic compounds with lots of nitrogens -- this is the reason. Now, our stated intent with OB has long been “accept quirks, but warn”. Certainly the PDB parser does this. Several threads exist on the mailing list on how the SMILES parser is too silent. -Geoff ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
