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Would it be possible to make the OBDotNet (C#) DLL(s) targetting Silverlight or make the C# code public?
The C# code is automatically generated by SWIG. Like the other language bindings it simply calls the native C++ OpenBabel library. As a result, it can not be used in Silverlight.
You might want to check out webel instead, which is running on Silverlight at http://baoilleach.webfactional.com/site_media/webel/ (some functionality is missing at the moment due to maintainence upgrade).