On Wed, Nov 4, 2009 at 9:53 AM, Vincent Le Guilloux <vincent.le-guill...@univ-orleans.fr> wrote: > In such cases, the bond order should be set to 'aromatic' instead of > single, even if it's not really a bond order, strictly speaking. As > you said, methods working on bond types should then check for > aromaticity.
Originally, the CDK has a bond order aromatic... but that gave too many problems. However, when that was changed to have an 'aromatic' flag, we 'forgot' to accomodate that some input may not have set bond orders... your query-flavored MDL molfile is such input (though arguably false input), but we see the same problem with SMILES, such as 'c1ccccc1', where no bond order information is given... We really need to add the IBond.Order.UNKNOWN ASAP, and fix all available readers accordingly. >> After doing aromaticity detection, aromatic bonds are marked as such. >> I'm not sure I understand what you mean hear. > > I'm talking about SDF output: We must also fix the MDLWriter to not use query functionality in its output, and it should likely throw an exception when unsupported bond orders are found in the IMolecule passed, including IBond.Order.QUADRUPLE and the future IBond.Order.UNKNOWN... > If the user gives an aromatic structure as input, with aromatic bonds > defined using the aromatic flag (4) instead of single/double bonds, as > there is currently no satisfying way to "dearomatize" a molecule, What is your experience with the DeduceBondOrder tool? Not so good, it seems... ? > the > SDF output should define the output aromatic bonds with this same > flag, instead of single order bond, which, as illustrated, transforms > the input structure to another one at SDF output. See above. The MDL Writer is not supporting queries, and we it should not be writing bond order 4. > This is, I think, a much better solution than setting all bonds to single. Yes, the current way it works is severely hampered by limitations in our data model. Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ 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
