Tuesday, December 28, 2010

Reordering SMILES atom order

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.


greg landrum said...

The RDKit smiles parser bug was fixed in rev1586 (http://rdkit.svn.sourceforge.net/viewvc/rdkit?view=revision&revision=1586).

The fix will be in the Q4 2010 release.

Andrew Dalke said...

Thanks for the quick fix! I've updated the text to say that it's been fixed for anybody using Q4 2010 or newer.

baoilleach said...

Thanks Andrew. Very nice. Maybe you'll see this in a future OB.