On Thursday 20 April 2006 23:45, Sun, Hongmei* wrote: > Thanks for quick response. > > I used jchempaint 2.2.1 actually. > > BTW, what cause the strange molecule structure in jchempaint(smiles: > Nc6ccc(N=Nc1ccc(cc1)c2ccc(cc2)N=Nc3c(N)c5c(cc3S(=O)(=O)O)cc(c(N=Nc4ccccc4)c >5 (O))S(=O)(=O)O)c(N)c6)?
The lack of a good saturation method. Using lower case carbons in SMILES indicate that they are sp2 carbons. This will leave the delocalized bond systems with just single bonds. CDK attempts to 'saturate' these bonds, by assigning double bond orders, but this is a non-trivial task. Parsing SMILES with implicit bond orders is known to be broken. Use SMILES like c1=cc=cc=c1 (with explicit bond orders) to be save. Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ ------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
