Dear all, I'm very happy to announce that the next version of the RDKit -- Q42008_1 -- is released.
The release notes are below. The source release and a windows binary are on the sourceforge downloads page: https://sourceforge.net/project/showfiles.php?group_id=160139&package_id=180003&release_id=631220 The files can also be downloaded from the google project page: http://code.google.com/p/rdkit/downloads/list I also updated the browseable and downloadable API documentation at rdkit.org: http://www.rdkit.org/C++_Docs http://rdkit.org/RDKit_C++_Docs.Q42008.tgz http://www.rdkit.org/Python_Docs http://rdkit.org/RDKit_Python_Docs.Q42008.tgz The API documentation is also available as a separate download from the google code or sourceforge pages. Thanks to the everyone who submitted bug reports and suggestions for this release! Please let me know if you find any problems with the release 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
