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. Thanks in advance for your help! -- View this message in context: http://forums.openbabel.org/obabel-crash-while-removing-salt-removing-counter-ions-tp4561055p4561055.html Sent from the General discussion mailing list archive at Nabble.com. ------------------------------------------------------------------------------ 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
