On Tue, Nov 3, 2009 at 5:06 PM, Vincent Le Guilloux <vincent.le-guill...@univ-orleans.fr> wrote: > When I load the same molecule but with all bond types defined at 4 > (aromatic)
Bond order 4 in MDL molfiles are only meant to be used for SSS queries, not for storage of chemical graphs... The CDK must not write those, nor do the current MDL readers actually read queries... the fact that they read 4 as aromatic flag = 1 is actually incorrect... > the CDK will directly set the aromatic flag to 1, but will define all bonds > as SINGLE bonds. The latter is because the IBond.Order structure does not have the concept of an unknown bond order (yet)... SINGLE is used to indicate bonding, but is clearly imprecise too... This is a problem and must be fixed: * support for unknown bond orders * warn about query content in MDL molfiles (RELAXED mode) * fail on query conent in MDL molfiles (STRICT mode) 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
