Hi Noel, thanks for the reply. Actually, the mol is taken from the Blood-Brain-Barrier dataset from Rueckert and Kramer: "Optimizing Feature Sets for Structured Data". (http://www.springerlink.com/content/x22202075j328w46/), so it should be a real molecule. Since, unfortunately, I am not a chemist, I can't tell you about the charge.
Here is another example from the same dataset that doesn't work, although it should: f: [#7]-[#6]=[#6]-[#6]=[#6]-[#6]-[#6]-[#6] m: c1cc(CCNC)ncc1 It is even more confusing since the different linear fragments occuring in benzene are found w/o problems: "[#6]-[#6]" Found 3 instances. Here are the atom indices: Hit 0: [ 1 6 ] Hit 1: [ 2 3 ] Hit 2: [ 4 5 ] "[#6]=[#6]" Found 3 instances. Here are the atom indices: Hit 0: [ 1 2 ] Hit 1: [ 3 4 ] Hit 2: [ 5 6 ] "[#6]-[#6]=[#6]" Found 6 instances. Here are the atom indices: Hit 0: [ 1 6 5 ] Hit 1: [ 2 3 4 ] Hit 2: [ 3 2 1 ] Hit 3: [ 4 5 6 ] Hit 4: [ 5 4 3 ] Hit 5: [ 6 1 2 ] "[#6]=[#6]-[#6]" Found 6 instances. Here are the atom indices: Hit 0: [ 1 2 3 ] Hit 1: [ 2 1 6 ] Hit 2: [ 3 4 5 ] Hit 3: [ 4 3 2 ] Hit 4: [ 5 6 1 ] Hit 5: [ 6 5 4 ] "[#6]=[#6]-[#6]=[#6]" Found 3 instances. Here are the atom indices: Hit 0: [ 1 2 3 4 ] Hit 1: [ 2 1 6 5 ] Hit 2: [ 3 4 5 6 ] "[#6]=[#6]-[#6]=[#6]" Found 3 instances. Here are the atom indices: Hit 0: [ 1 2 3 4 ] Hit 1: [ 2 1 6 5 ] Hit 2: [ 3 4 5 6 ] ... and so on. Andreas Noel O'Boyle wrote on 01/07/2010 01:09 PM: > > 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 >> >> > > -- http://www.maunz.de OpenPGP key: http://www.maunz.de/[email protected]_pub.asc I do know everything, just not all at once. It's a virtual memory problem. ------------------------------------------------------------------------------ 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
