[Rdkit-devel] 2011.09 (Q3 2011) RDKit release

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

I'm very happy to announce that the next version of the RDKit --
2011.09 (a.k.a Q3 2011) -- is released.

The release notes are below.

The source release is on the sourceforge downloads page:
http://sourceforge.net/projects/rdkit/files/rdkit/Q3_2011/
The files can also be downloaded from the google project page:
http://code.google.com/p/rdkit/downloads/list
The binaries for Windows, Python 2.6  and Python 2.7 are uploaded already.

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
suggestions for the next one.

-greg


******  Release_2011.09.1 *******
(Changes relative to Release_2011.06.1)

!!!!!! IMPORTANT !!!!!!
 - A bug in the definition of the Lipinski HBD descriptor was fixed in
   this release. The descriptor Lipinski.NHOHCount will return
   different values for molecules containing Ns or Os with more than
   one attached H.

Acknowledgements:
Eddie Cao, Richard Cooper, Paul Czodrowski, James Davidson, George
Papadatos, Riccardo Vianello

Bug Fixes:
 - A problem with interpretation of stereochemistry from mol files was
   fixed (Issue 3374639)
 - Sterochemistry information for exocyclic double bonds in mol blocks
   is no longer lost. (Issue 3375647)
 - linear double bonds from mol files now have their stereochemistry
   set correctly(Issue 3375684)
 - Chirality for phosphates and sulfates is not longer automatically
   removed. (Issue 3376319)
 - A bug with the reading of query information from mol files was
   fixed. (Issue 3392107)
 - Sterochemistry is now cleaned up after processing mol2
   files. (Issue 3399798)
 - mergeQueryHs now correctly handles atoms with multiple Hs (Issue
   3415204)
 - mergeQueryHs now correctly handles atoms without initial query
   information (Issue 3415206)
 - the calcLipinskiHBD() (equivalent to Lipinski.NHOHCount) descriptor
   now correctly handles Ns or Os with multiple Hs. (Issue 3415534)
 - Morgan fingerprints generated using the fromAtoms argument now have
   all bits from those atoms set.(Issue 3415636)
 - A problem with the way MolSuppliers handle the EOF condition when
   built with the most recent versions of g++ was fixed.
 - Translation of RDKit stereochemistry information into InChI
   stereochemistry information is improved.

New Features:

New Database Cartridge Features:
 - molecules can now be built from mol blocks using the function
   mol_from_ctab(). The corresponding is_valid_ctab() function was
   also added.
 - the radius argument is now optional for the functions morganbv_fp,
   morgan_fp, featmorganbv_fp, and featmorgan_fp. The default radius
   for all four functions is 2.

Deprecated modules (to be removed in next release):

Removed modules:

Other:
 - The documentation in $RDBASE/Docs/Book has been migrated to use
   Sphinx instead of OpenOffice.
 - The optional InChI support can now be built using a system
   installation of the InChI library.