Dear all, I'm really happy to announce that this morning I tagged the Q3 2008 release candidate: https://rdkit.svn.sourceforge.net/svnroot/rdkit/tags/Release_Q32008_1RC1 (browseable at: http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_Q32008_1RC1)
Source and binary distributions (for windows and python 2.5) are available from the google code download page: http://code.google.com/p/rdkit/downloads/list If nothing major comes up, I will plan on doing the actual release one week from today. Note that the build instructions on linux have changed a bit: http://code.google.com/p/rdkit/wiki/BuildingOnLinux_Q32008 If you have time to try out the release candidate, I will be very happy to hear suggestions, problem reports, or compliments. :-) FYI: In the interests of not constantly duplicating messages, future release candidate announcements will be sent only to the devel list. Here's an excerpt from the release notes (which still need to be completed): ****** Release_Q32008_1 ******* (Changes relative to Release_May2008_1) Acknowledgements: - Noel O'Boyle, Igor Filippov, Evgueni Kolossov, Greg Magoon Bug Fixes - A memory leak in the ToBase64 and FromBase64 wrapper functions was fixed. - The UFF atom typer has been made more permissive: it now will pick "close" atom types for things it does not recognize. (issue 2094445) - The handling of molecules containing radicals has been greatly improved (issues 2091839, 2091890, 2093420) - Iterative (or secondary, or dependent) chirality is now supported, see this page for more information: http://code.google.com/p/rdkit/wiki/IterativeChirality (issue 1931470) - Isotope handling has been changed, this allows correct matching of SMARTS with specified isotopes. (issue 1968930) - Some problems with the MACCS key definitions have been fixed. (issue 2027446) - Molecules with multiple fragments can now be correctly embedded. (issue 1989539) - Adding multiple bonds between the same atoms in a molecule now produces an error. (issue 1993296) - The chemical reaction code now handles chiral atoms correctly in when applying reactions with no stereochem information provided. (issue 2050085) - A problem with single-atom cores in TemplateExpand.py has been fixed. (issue 2091304) - A problem causing bicyclobutane containing molecules to not be embeddable has been fixed. (issue 2091864) - The default parameters for embedding are now molecule-size dependent. This should help with the embedding of large, and crowded molecules. (issue 2091974) - The codebase can now be built with boost 1.36. (issue 2071168) - A problem with serialization of bond directions was fixed. (issue 2113433) New Features - The RDKit can now be built under Darwin (Mac OS/X). - Tversky similarity can now be calculated. (request 2015633) - Many of the core datastructures now support equality comparison (operator==). (request 1997439) - Chirality information can now be assigned based on the 3D coordinates of a molecule using MolOps::assignChiralTypesFrom3D(). (request 1973062) Other - the pointers returned from Base64Encode/Decode are now allocated using new instead of malloc or calloc. the memory should be released with delete[]. - the generation of invariants for chirality testing is now quite a bit faster; this results in faster parsing of molecules. - The use of C include files instead of their C++ replacements has been dramatically reduced. - The new (as of May2008) hashing algorithm for fingerprints is now the default in the python fingerprinting code (Chem.Fingerprints.FingerprintMols). - The functions MolOps::assignAtomChiralCodes() and MolOps::assignBondStereoCodes() are deprecated. Use MolOps::assignStereochemistry() instead. - The RDKit no longer uses the old numeric python library. It now uses numpy, which is actively supported. - By default Lapack++ is no longer used. The replacement is the boost numeric bindings: http://mathema.tician.de/software/boost-bindings. Best Regards, -greg
