How do I provide this setting to the writer? I see a getter for IOSetting's but no setter
On Tue, Aug 16, 2011 at 12:19 AM, Egon Willighagen <[email protected]> wrote: > On Mon, Aug 15, 2011 at 9:44 PM, Rajarshi Guha <[email protected]> > wrote: >> Hi, using the latest CDK when I write out a molecule using the >> SDFWriter I loose all aromaticity (ie no kekule form or aromatic bonds >> in the output). Has anybody seen this? > > Yes, the MDL molfile format does not have a concept for aromaticity, > so this information is indeed lost. People have been (mis)using the > '4' bond order which is used for storing queries, where you indicate a > bond might be single or double. While this is bad practice, if you do > like to do that, use this IO option: > > writeAromaticBondTypes = new BooleanIOSetting( > "WriteAromaticBondTypes", > IOSetting.LOW, > "Should aromatic bonds be written as bond type 4?", > "false" > ); > > Grtz, > > Egon > > > -- > Dr E.L. Willighagen > Postdoctoral Researcher > Institutet för miljömedicin > Karolinska Institutet (http://ki.se/imm) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > -- Rajarshi Guha NIH Chemical Genomics Center ------------------------------------------------------------------------------ uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
