Bugs item #3090342, was opened at 2010-10-19 10:57 Message generated for change (Tracker Item Submitted) made by pascalmuller You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3090342&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: 2.3.x Status: Open Resolution: None Priority: 5 Private: No Submitted By: Pascal Muller (pascalmuller) Assigned to: Nobody/Anonymous (nobody) Summary: Ionization problem Initial Comment: Ionization can raise hybridization error Eg O=C1COC=C1 is converted (2.2.99 and 2.3.0, -p7.4) in: [O-]C1=CC=[O]C1 Or there is ionization error, 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 which are ionized in: C[O]=C1C=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 In my opinion, these molecules should not be ionized. Only ZINC00001233 with +1 charge is correct. Pascal pascal.jm.mul...@gmail.com Scientific Linux 5.5 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3090342&group_id=40728 ------------------------------------------------------------------------------ Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
