On 15/10/2010 10:13, Jean-Paul Ebejer wrote: > Hi there, > > I am using Openbabel 2.2.3 (on Ubuntu) and get a dreaded segmentation > fault: > > x...@yyy:~/test/1hvy$ obfit > > "[H]OC(C(C(C(N([H])C(c1sc(N(C([H])([H])[H])C(c2c([H])c([H])c3nc(C([H])([H])[H])n([H])c(=O)c3c2[H])([H])[H])c([H])c1[H])=O)([H])C(O[H])=O)([H])[H])([H])[H])=O" > ligand.mol 50_conformers.sdf > > Segmentation fault > > > The file ligand.mol (1hvy) is taken from the Astex dataset (attached) > and 50_conformers.sdf is a file with some conformers I generated > (using RDkit as a side point). > I've tried similar commands on other compounds in the set and they > work successfully. > > Any reason why I get the segmentation fault? Also, if this has to > fail - shouldn't it fail a little bit more gracefully (with a nice > error message that is). > > Any help will be greatly appreciated!
I am not very familiar with obfit, but nobody else has replied to you. The number of atoms in the SMARTS(54) is greater than in the reference molecule(52) and obfit is failing because the SMARTS parser returns 54 matching atoms when matching the two. This must be a bug in the parser. But am I right in saying that the input data was at fault and should have been rejected? With the hydrogen removed from the SMARTS, obfit runs, although I do not know whether the results are meaningful. Chris ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
