The example files did not make it through to the mailing list. With SMILES it is probably safe to just copy them in to the text. (Don't do this for SDF files!)
The -e option enables obabel to continue with the next molecule after an error, so if the crash is not too severe you may be able to get some useful results even with this bug. Chris On 16/04/2012 11:12, green69 wrote: > Hi all, > > I'm using Open Babel 2.3.1 running on a GNU/Linux OS. > > I used to work with molecules DB in SMILES format. Normally with obabel you > can remove counter-ions (with the flag '-r', which remove all but the > largest contiguous fragment) with the following command: > > /obabel -ismi file.smi -r -osmi -O file_out.smi/ > > Unfortunately I found that obabel crashes when try to remove counter-ions > from certain molecules. I attached 2 files each containing 2 molecules > /smilesPROBLEM.smi/& /smilesOK.smi/. The first molecule of > /smilesPROBLEM.smi/ is that which cause the problem. > > I don't know why that molecule is problematic to obabel, while the first > molecule of /smilesOK.smi/ (which is similar), is not problematic. Anyway > here *the real problem is that the program crashes* on that molecule. This > means that a part from the problematic molecule itself, *in the output file > you will miss all those compounds which follow a certain problematic > molecule.* So if you're processing a DB of 1,000 molecules of which the > third is problematic, you will obtain just 2 molecules, missing the rest > 997! > > Please, does anybody know a way to circumvent this problem without write an > ad-hoc external script? Bypassing the problematic molecules and making > obabel converting the rest of compounds, will be fine. ------------------------------------------------------------------------------ For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
