[Rdkit-devel] Candidate for the Q4 2008 release

[Greg L. <gre...@gm...>]

Dear all,

I just tagged a release candidate for the Q4 2008 release in svn:
http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_Q42008_1RC1/
I also uploaded a source tarball to the google code project page:
http://rdkit.googlecode.com/files/RDKit_Q42008_RC1.tgz

The release notes are at the end of this message.

If no major problems turn up, I will do the actual release in one
week: on the 13th of January.

Please let me know if you find any problems or have any suggestions.
-greg

******  Release_Q42008_1 *******
(Changes relative to Release_Q32008_1)

!!!!!! IMPORTANT !!!!!!
 - A fix in the handling of stereochemistry in rings means that the
   SMILES generated with this release are different from those in
   previous releases. Note that the canonicalization algorithm does
   not work in cases of pure ring stereochemistry : the SMILES should
   be correct, but it is not canonical. Rings containing chiral
   centers should be fine.

Acknowledgements:
 - Kirk DeLisle, Markus Kossner, George Magoon, Nik Stiefl

Bug Fixes
 - core leaks in learning code (issue 2152622)
 - H-bond acceptor definitions (issue 2183240)
 - handling of aromatic dummies (issue 2196817)
 - errors in variable quantization (issue 2202974)
 - errors in information theory functions on 64 bit machines (issue 2202977)
 - kekulization problems (issue 2202977)
 - infinite loop in getShortestPaths() for disconnected structures
(issue 2219400)
 - error in depictor for double bonds with stereochemistry connected
   to rings (issue 2303566)
 - aromaticity flags not copied to null atoms in reaction products
   (issue 2308128)
 - aromaticity perception in large molecule hangs (issue 2313979)
 - invariant error in canonicalization (issue 2316677)
 - mol file parser handling of bogus bond orders (issue 2337369)
 - UFF optimization not terminating when atoms are on top of each
   other (issue 2378119)
 - incorrect valence errors with 4 coordinate B- (issue 2381580)
 - incorrect parsing of atom-list queries with high-numbered atoms
   (issue 2413431)
 - MolOps::mergeQueryHs() crashing with non-query molecules. (issue
   2414779)

New Features
 - SLN parser (request 2136703).
 - Mol2 parser : Corina atom types (request 2136705).
 - Building under mingw (request 2292153).
 - Null bonds in reaction products are replaced with the corresponding
   bond from the reactants (request 2308123).

Other
 - a bunch of deprecation warnings from numpy have been cleaned up
   (issue 2318431)
 - updated documentation
 - some optimization work on the fingerprinter