Hi, (Open Babel 2.2.3)
The following smiles O=C1COC=C1 has a charge of -5 when ionized as follow: babel -p 7.4 file.smi out.smi The smiles output is: [O-][C-]1=[C-][C-]=[O-]C1 With babel 2.2.99 I just build: [O-]C1=CC=[O]C1 better but not OK, IMHO. I found this with C[C@@]1(C(=O)C=C(O1)C(=O)[O-])c1ccccc1 ZINC00000010 which gives with -p 7.4 C[C@@]1([C-](=[C-][C-](=[O-]1)C(=O)[O-])[O-])c1ccccc1 More than 400 molecules seems to be problematic, out of my test set of 20 thousands, like COC1=CC(=O)O[C@@H](C1)/C=C/c2ccccc2 ZINC00001102 CC1(N=C(N=C(N1c2ccc(cc2)Cl)N)N)C ZINC00001233 CC1([NH+]=C(N=C(N1c2ccc(cc2)Cl)N)N)C ZINC00001233 ionized (2.2.3, didn't try with 2.2.99): C[O-]=[C-]1[C-]=[C-]([O-])O[C@@H](C1)/C=C/c1ccccc1 ZINC00001102 CC1(N=[C+](N=[C+](N1c1ccc(cc1)Cl)N)N)C ZINC00001233 CC1([N+]=[C+](N=[C+](N1c1ccc(cc1)Cl)N)N)C ZINC00001233 Is it a bug? Regards, Pascal ------------------------------------------------------------------------------ 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-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
