Rajarshi, Noel, Thank you very much for your explanations and examples.
Rajarshi, The OpenSmiles specifications made it clear for me: "If a bond symbol is present between the atom and rnum, it can be present on either or both bonded atoms. However, if it appears on both bonded atoms, the two bond symbols must be the same." (Although they have put the cyclohexane image in place of cyclohexene). Noel, your examples of cis-trans double bond touching the ring also made sense to me, especially G and H. We will adjust SMILES loader in Indigo to support this. With best regards, Dmitry Noel O'Boyle wrote: > BTW, the other more common use of bond symbols at ring closures is to > designate cis/trans stereochemistry at a ring closure. See > http://baoilleach.blogspot.com/2009/04/are-you-on-my-side-or-not-its-ez.html > > - Noel > > 2009/11/17 Noel O'Boyle <[email protected]>: >> 2009/11/17 Rajarshi Guha <[email protected]>: >>> >>> On Tue, Nov 17, 2009 at 7:58 AM, Dmitry Pavlov <[email protected]> wrote: >>>> 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), >>> Hmm, for the benzene case, C=1CC=CC=C1 does not seem to render properly in >>> Daylight, but C-1CCCCC-1 does render >>> >>>> Is it an option to put the 'ring closure digit' >>>> either after atom or after bond? It is documented >>>> somewhere? >>> I haven't seen this described anywhere in the Daylight spec. As I said, my >>> understanding was that ring closures always come just after an atom symbol. >>> >>> However OpenSmiles does address this explicitly: >>> >>> http://www.opensmiles.org/spec/open-smiles-3-input.html#3.4 >>> >>> But it's still not clear why the benzene example fails >> You need to alternate the double bonds: C=1C=CC=CC=1 works >> >>> -- >>> Rajarshi Guha >>> NIH Chemical Genomics Center >>> >>> ------------------------------------------------------------------------------ >>> 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 >>> >>> ------------------------------------------------------------------------------ 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
