I find it difficult to work out the PI electron count for these sorts of systems. Can you confirm that this is a real molecule, and that the 5-membered ring is uncharged?
- Noel 2010/1/7 Andreas Maunz <[email protected]>: > Hi all, > > In my simple world, a molecule is just a graph with nodes corresponding > to atomic numbers, while the edges are either single, double, or triple > (no aromatic bindings). My graph miner reads in molecules as > > OBAtomIterator atom; > mol.BeginAtom(atom); > do { > InputNodeLabel inputnodelabel = (*atom)->GetAtomicNum(); > } while (mol.NextAtom(atom)); > > Similar for the edges, i.e. bondorder = (*bond)->GetBondOrder(); It then > computes all fragments from the graphs that adhere to certain > conditions, such as minimum frequency. > > Now, I want to match the found fragments back to (a subset of) the > molecules, e.g.: > m: n1(c2ccccc2)n(c(C)cc1=O)C > f: [#6]-[#6](=[#6]-[#6]-[#7]-[#6])(-[#7]) > The example above won't match back to the molecule, although my graph > mining application has found f as a subgraph of m. I use this code (in > ruby) to match back: > > c=OpenBabel::OBConversion.new > c.set_in_format 'smi' > m=OpenBabel::OBMol.new > c.read_string m, "n1(c2ccccc2)n(c(C)cc1=O)C" > m.set_aromatic_perceived # seems necessary: Without > m.set_aromatic_perceived, even such simple examples as m = c1ccccc1 and > f = [#6]=[#6] won't match. > p=OpenBabel::OBSmartsPattern.new > if !p.init("[#6]-[#6](=[#6]-[#6]-[#7]-[#6])(-[#7])") > puts "Error! Smarts pattern invalid." > exit > end > p.match(m) > > My problem is: the last line returns 'false'. What is the problem here? > > Greetings > Andreas > > Here is a depiction of the molecule: > http://www.daylight.com/daycgi/depict?6e31286332636363636332296e28632843296363313d4f2943 > > -- > http://www.maunz.de > OpenPGP key: http://www.maunz.de/[email protected]_pub.asc > > Warning: dates in calendar are closer than they appear > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > OpenBabel-Devel mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev _______________________________________________ OpenBabel-Devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-devel
