I wrote a rather long essay about how to generate SMILES strings where the atoms are in arbitrary/user-defined order. The first two implementations use RDKit but in the last I couldn't work around an RDKit bug so I switched over to OpenBabel. (Edit: Greg commented here that the bug has been fixed in version control and will out as part of the Q4 2010 release.)
This is the place to leave questions and comments about what I wrote.
Tuesday, December 28, 2010
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