[Rdkit-devel] some nice performance improvements

2012-06-28 Thread Greg Landrum
Dear all, I've been making some changes to the SMILES canonicalization code (more on this later) that have also led to some nice (IMO) performance improvements. Here are the numbers. My usual benchmarking operations (http://code.google.com/p/rdkit/wiki/Benchmarking) don't really help here: 1000 m

[Rdkit-devel] Changes in the canonicalization algorithm and tests thereof

2012-06-28 Thread Greg Landrum
Dear all, I've been making some changes to the SMILES canonicalization code. My original intent was to get the code to efficiently and correctly generate SMILES for fragments of molecules (demo of this below). Along the way I realized that I could make the canonicalization faster and, I think, mor