> The presence of the hydrogen on the pyridinium nitrogen is critical for > aromaticity.
Yes, except there are decidedly users who feel that with SMILES, explicit hydrogens only need to be used in cases of stereochemistry. I remember a thread with Andrew Dalke (now CC'ed) where he argued IIRC, that if a user left an atom in lowercase, they meant to imply aromaticity and software should, unless there are clear issues, respect that. (Andrew, please feel free to reject me.. A quick search through my e-mail isn't finding the conversation.) > in Noel's example. Start with 4n+2 pyridine, n1ccccc1 and lose a (pi) > electron gives > [N+]1=CC=CC=C1 not [n+]1ccccc1. Eh, the problem here is, I think more of a grey area than you're expressing. I think we agree that this is aromatic: c1[n+H]cnc2[nH]cnc12 Now the question is instead, how to interpret: c1[n+]cnc2[nH]cnc12 I'd say "depending on interpretation (with an implicit rather than explicit H) this is possibly aromatic." You seem to be arguing "the H should be explicit, so I'm going to mark that as non-aromatic." My feeling is based on the principal of least surprise.. that a user input a SMILES (possibly non-standard) with aromaticity and it's now not aromatic. I do find benefit in preserving the aromaticity unless it's clearly wrong (e.g. +2, +25, etc.) > The same happens if the electron is lost from one of the carbons, > N1=CC=C[CH+]=C1. > For Noel's example above, OpenBabel now matches Daylight's (and OpenEye's) > behaviour. > http://www.daylight.com/daycgi/depict?43313d5b4e2b5d433d4e63325b6e485d636e633132 That's useful data, and certainly falling more in line with other toolkits is a good thing. I want the discussion because this seems a very fuzzy area, so before I modify the unit test, I want to be sure there's some consensus on "well, that's a non-standard SMILES and you really need an H if it's going to be marked as aromatic." > p.s. I'm not claiming that the revised SMARTS in aromatic.txt are correct, > just that they have fewer bugs than without this patch. Agreed, and that's why I merged the patch — it's clearly better than the previous version. I'm just wondering, since you raised the issue if we've found an edge case or not. Thanks, -Geoff ------------------------------------------------------------------------------ Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
