Geoff, Attached is the original example.sdf from Vinay in which bonding is properly defined. As per my notes, when this is converted to canonical SMILES and then back to SDF, the bonding is incorrect. Also, some properties are different for the original SDF and the Babel-generated canonical SMILES.
If you need any other files post-conversion, please let me know and I'll send them. I assume that you'll be able to reproduce the problem but just in case a version difference leads to different results, I'm happy to supply additional files should you need them. -Kirk On Thu, Feb 4, 2010 at 1:00 PM, Geoffrey Hutchison <[email protected] > wrote: > > On Jan 26, 2010, at 12:20 PM, Robert DeLisle wrote: > > > you get a different bonding pattern. See attached. It appears that > babel is having issues with the bonding pattern (due to aromaticity > detection?) of the tricycle. > > This is clear. I'm sorry, since I'm a bit late coming into this. Can > someone send me the actual SDF file, so I can see why the aromaticity/kekule > assignment is failing. Craig did a lot of work for v2.2.3 to make sure this > is right. Both Craig and I have been hunting down problems like this, and > this looks very familiar to a number of test cases. > > Thanks, > -Geoff
example.sdf
Description: Binary data
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