On 12/12/2012 18:15, Tim Vandermeersch wrote: > Hi, > > On Wed, Dec 12, 2012 at 5:55 PM, Geoffrey Hutchison <geo...@pitt.edu > <mailto:geo...@pitt.edu>> wrote: > > > 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. > > > Yes, while working on Smiley I've come across several SMILES that are > not valid according to Daylight but OB accepts them. > > Examples: > > n1cccc1 invalid > [n]1cccc1 invalid > [nH]1cccc1 valid > [n-]1cccc1 valid > > OpenBabel currently outputs: > > [nH]1cccc1 > [n]1cccc1 > [nH]1cccc1 > [n-]1cccc1 > > The first is converted to a valid SMILES, not following the Daylight > approach. The second remains invalid without warning. I haven't come > across the second though. Another interpretation for the first would be > [n-]1cccc1 and although this follows the zero implicit hydrogens rule, > OB's solution is what is usually intended I think.
In spite of failing in Daylight's Depict, I would have thought that the second above, [n]1cccc1, was a valid radical; OB depicts it as such. Smiley does not seem set up to handle any radicals at present. Chris ------------------------------------------------------------------------------ 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
