Friday, 24 April 2009  Broken symmetry - Can SMILES and InChI
ensure canonicalisation?  I've been working on the SMILES code
in OpenBabel over the last while. The longer I've spent on it,
the more impressed I've been with how it has been handled in the
code and also with what a great idea SMILES was in the first
place. The same goes for InChI, which has a slightly different
goal, but which goes the extra mile and solves normalisation
problems which I didn't even know existed.  But do they work?
Can their canonicalisation procedures ensure that two identical
molecular graphs result in the same canonical SMILES or InChI?
The InChI canonicalisation procedure is summarised in Rich's
post. The Daylight algorithm is in Weininger*3, JCICS, 1989, 29,
97. And the review of the field that throws both into question
is Ivanciuc's review of Processing Constitutional Information in
Gasteiger's Handbook of Cheminformatics.  The key question here
is whether the SMILES and InChI algorithms are capable of
identifying automorp