On 7/21/10 5:39 PM, TJ O'Donnell wrote: > In building a database of pubchem and other publicly available structures, > I'm converting from molfile to isomeric cansmi. In several cases (about > 7 per thousand) > I get one cansmi from the molfile, but another when I ask for the cansmi > of the > resulting cansmi. For database integrity reasons, the cansmi(cansmi) = > cansmi should > be always be true, so this is getting me into trouble for these structures. > > Sometimes it is double-bond stereo flipping, sometimes an aromaticity > problem. > It also seems to have something to do with symmetric structures. > > I've attached an example sdf file with 20 structures, all of which show > this behaviour. > I hope someone can take a look and see if I'm doing something odd or how I > might correct this.
Hi TJ, These are known problems. Mostly it's lack of time to fix them. Tim made some progress recently, but the aromaticity (which always involves nitrogen) is still a problem. Craig > > Below is a sample babel session showing the problem on my linux system > with openbabel 2.2.3 > I haven't tried windows or mac or other babel versions > > Thanks, > TJ O'Donnell > > t...@ubuntu:~/chord/openbabel$ babel -i sdf -o can <cantest.sdf >cantest.smi > 20 molecules converted > 1 info messages 591 audit log messages > t...@ubuntu:~/chord/openbabel$ babel -i smi -o can <cantest.smi >cancan.smi > 20 molecules converted > 6 info messages 646 audit log messages > t...@ubuntu:~/chord/openbabel$ diff -y can*.smi > [Cu].c1ccc2C3=NC4=NC(=NC5=NC(=NC6=NC(=NC(=N3)c2c1)c1ccccc61)c | > [Cu].c1ccc2C3=NC(=NC4=NC(=NC5=NC(=NC6=NC(=N3)c3ccccc63)c3cccc > OC(=O)CCC(=O)c1ccc2C3C=CC=C4C=CC=C(c2c1)C34 10617 | > OC(=O)CCC(=O)c1ccc2c(c1)c1cccc3cccc2c13 10617 > [Cl-].C[NH+](C)CC[n]1c2ccccc2[n](C)c2ccccc2c1=O 9418 | > [Cl-].C[NH+](C)CCn1c2ccccc2n(C)c2ccccc2c1=O 9418 > [Cl-].C[N+](=C1/C=C/C(=C(c2ccccc2)c2ccc(cc2)N(C)C)C=C1)C | > [Cl-].C[N+](=C1\C=C\C(=C(c2ccccc2)c2ccc(cc2)N(C)C)C=C1)C > O=[C]1=[NH]C2=C(N1)[C](=O)=[NH][C](=O)=[N]2C 11804 | > O=c1[nH]c2c([nH]1)c(=O)[nH]c(=O)n2C 11804 > [O-][N+](=O)c1cc2ccc3cccc4ccc(c1)C2C34 13090 | > [O-][N+](=O)c1cc2ccc3cccc4ccc(c1)c2c34 13090 > C[C@@H]1CCCC1C 13197 | cc1cc...@h]1c 13197 > Cl.NC(=N/C(=N/CCc1ccccc1)/N)N 13266 | Cl.NC(=N\C(=N\CCc1ccccc1)\N)N 13266 > [O-][N+](=O)C1=CC=C2c3ccccc3C3=CC=CC1C23 13462 | > [O-][N+](=O)c1ccc2c3ccccc3c3cccc1c23 13462 > CCN(CC)c1ccc(cc1)C(=C1C=CC(=[N+](CC)CC)/C=C/1)c1ccccc1.[O-]S( | > CCN(CC)c1ccc(cc1)C(=C\1C=CC(=[N+](CC)CC)\C=C1)c1ccccc1.[O-]S( > CCN(CC)c1ccc(cc1)C(=C1C=CC(=[N+](CC)CC)/C=C/1)c1ccccc1 12450 | > CCN(CC)c1ccc(cc1)C(=C1\C=C\C(=[N+](CC)CC)C=C1)c1ccccc1 12450 > NC(=N/N=C/c1ccc(o1)[N+](=O)[O-])N 13685 | > NC(=N\N=C\c1ccc(o1)[N+](=O)[O-])N 13685 > O=c1c2CC=CCc2[nH]c2cc3c(cc12)[nH]c1ccccc1c3=O 13976 | > O=c1c2cc3[nH]c4ccccc4c(=O)c3cc2[nH]c2ccccc12 13976 > CN(C)CC[n]1c2ccc(Cl)cc2[nH]c2ccccc2c1=O 14396 | > CN(C)CCn1c2ccc(Cl)cc2[nH]c2ccccc2c1=O 14396 > CN(C)CC[n]1c2ccccc2[nH]c2ccc(Cl)cc2c1=O 14397 | > CN(C)CCn1c2ccccc2[nH]c2ccc(Cl)cc2c1=O 14397 > CN(C)CC[n]1c2cc(C)ccc2[n](C)c2ccccc2c1=O 14405 | > CN(C)CCn1c2cc(C)ccc2n(C)c2ccccc2c1=O 14405 > CN(C)CCC[n]1c2ccc(Cl)cc2[nH]c2ccccc2c1=O 14409 | > CN(C)CCCn1c2ccc(Cl)cc2[nH]c2ccccc2c1=O 14409 > c...@h]1ccc[c@H]1C 14498 | C[C@@H]1CCC[C@@H]1C 14498 > c1ccc2[n](c1)cc[n]1ccccc21 14553 | c1ccc2n(c1)ccn1ccccc21 14553 > NC(=N/C(=N/c1ccc2ccccc2c1)/N)N 14623 | NC(=N\C(=N\c1ccc2ccccc2c1)\N)N 14623 > t...@ubuntu:~/chord/openbabel$ babel --version > No output file or format spec! > Open Babel 2.2.3 -- Mar 7 2010 -- 03:47:42 > Usage: babel [-i<input-type>] <name> [-o<output-type>] <name> > Try -H option for more information. > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > > > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
