Hi, I seem to have hit a roundtrip problem, which occurs both in OB-2.2.3 and SVN head (r4132). The molecule in question is http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=10052993 Similarly, http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=10054537 is also affected. Both have a lone Br- or Cl- ion.
Is that a bug, or should I have done some preprocessing, or set an option somewhere ? Yours, Steffen # InChI to SMILES: echo "InChI=1S/C26H26N4O2S.BrH/c1-3-14-27-26(33)29-22-8-4-19(5-9-22)18-30-15-12-21(13-16-30)25-28-17-24(32-25)20-6-10-23(31-2)11-7-20;/h4-13,15-17H,3,14,18H2,1-2H3,(H-,27,29,33);1H" | babel -i inchi - -o smi - # CCCN=C(Nc1ccc(cc1)Cn1ccc(=C2N=CC(=[O+]2)c2ccc(cc2)OC)cc1)[S-].Br # 1 molecule converted # And now to Canonical SMILES is OK: echo 'CCCN=C(Nc1ccc(cc1)Cn1ccc(=C2N=CC(=[O+]2)c2ccc(cc2)OC)cc1)[SH-].Br' | babel -i smi - -o can - # Br.CCCN=C([SH-])Nc1ccc(cc1)Cn1ccc(=C2N=CC(=[O+]2)c2ccc(OC)cc2)cc1 # 1 molecule converted # Now back to InChI gives Error: echo 'CCCN=C(Nc1ccc(cc1)Cn1ccc(=C2N=CC(=[O+]2)c2ccc(cc2)OC)cc1)[SH-].Br' | babel -i smi - -o inchi - # Also InChI key also gives an Error: echo 'CCCN=C(Nc1ccc(cc1)Cn1ccc(=C2N=CC(=[O+]2)c2ccc(cc2)OC)cc1)[SH-].Br' | babel -i smi - -o inchi -xK - # Also not with the canonical SMILES: echo "Br.CCCN=C([SH-])Nc1ccc(cc1)Cn1ccc(=C2N=CC(=[O+]2)c2ccc(OC)cc2)cc1" | babel -i can - -o inchi - -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
