Hello all,
We (developers of Indigo cheminformatics toolkit) recently received a bug report on Dingo rendering library by Charlie Zhu. He claims that the following SMILES string was produced by CDK and fails to load in Indigo: [H]OC2=NN(C(=O)C=3C(=O)c1c([H])c([H])c(c([H])c1N([H])C2=3)Cl)C([H])([H])C#Cc4c([H])nc([H])c([H])c4([H]) As a developer of SMILES parser in Indigo, I can not see how this SMILES string can be correct. Probably my understanding of SMILES format is incomplete, so I ask you for explanation. The problem is the "=3" fragment, which occurs twice, first on symbols 17-18. "3" must be a ring closure index which, as Daylight site (http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) says, are designated "by a digit immediately following the atomic symbol at each ring closure". In this SMILES string, "3" never follows any atomic symbol (it actually follows the double bond symbol twice), and this is why our SMILES parser rejects this string, and then Dingo raises an error. Could you please explain this "=3" thing to me? Thanks a lot in advance. With best regards, Dmitry ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
