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
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