> Hello Rajarshi, > > > I still do not feel like I have got the idea... > > C1=CC=CC=C1 (another example from Daylight site) > clearly has not implicit single bond between > the first "C" and the "1" following it. In this > example, the first "C" is marked with "1", and > in example you gave (C1CC-2C1CCC-2C),
... the single bonds are marked with "2". > > Is it an option to put the 'ring closure digit' > either after atom or after bond? It is documented > somewhere? > > With best regards, > > Dmitry > > > >>> 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 ------------------------------------------------------------------------------ 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
