On Nov 17, 2009, at 7:34 AM, Dmitry Pavlov wrote: > 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]) > > 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.
It might be that the Daylight spec refers to the fact that the bond is implicit. If an explicit bond is specified then it seems that the ring closure number can come after the bond. For the above case, Daylight Depict will accept the SMILES. Another example is C1CC2C1CCC2C C1CC-2C1CCC-2C which Daylight will also accept as valid SMILES. I can't find mention of this behavior in the spec - does anybody know if this behavior is specified somewhere? ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- A motion to adjourn is always in order. ------------------------------------------------------------------------------ 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 Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
