[Rdkit-devel] 2011.03 (Q1 2011) RDKit release

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

Dear all,

I'm very happy to announce that the next version of the RDKit --
2011.03 (a.k.a Q1 2011) -- is released.

The release notes are below.

The source release is on the sourceforge downloads page:
http://sourceforge.net/projects/rdkit/files/rdkit/Q1_2011/
The files can also be downloaded from the google project page:
http://code.google.com/p/rdkit/downloads/list
I will upload Windows binaries (python 2.6 only, please let me know if
anyone needs a python 2.7 release) in the next couple of days.

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_2011.03.1 *******
(Changes relative to Release_2010.12.1)

Acknowledgements:
 - Eddie Cao, James Davidson, Kirk DeLisle, Peter Gedeck, George
   Magoon, TJ O'Donnell, Gianluca Sforna, Nik Stiefl, Bernd Wiswedel

Bug Fixes:
 - The performance of SSSR finding for molecules with multiple highly-fused
   ring systems has been improved. (Issue 3185548)
 - Isotope information is now correctly saved when molecules are
   serialized (pickled). (Issue 3205280)
 - Generating SMILES for a molecule no longer changes the
   molecule. This fixes a round-trip bug with certain highly symmetric
   molecules read from SD files. (Issue 3228150)
 - Another bounds-matrix generation bug for highly (con)strained
   systems was fixed. (Issue 3238580)
 - Conformation information is now better handled by deleteSubstructs(),
   replaceSubstructs(), and replaceCore().

New Features:
 - the rdkit.Chem.Draw package has been significantly refactored.
 - Code for doing Murcko decomposition of molecules has been
   added. From Python this is in the module:
   rdkit.Chem.Scaffolds.MurckoScaffold
   It's available in C++ in the GraphMol/ChemTransforms area.
 - rdkit.Chem.AllChem.TransformMol() now takes optional arguments
   allowing the conformation to be transformed to be specified and
   other existing conformations to be preserved.
 - Calculations for most of the descriptors in rdkit.Chem.Lipinski and
   rdkit.Chem.MolSurf have been moved into C++. The python API is the
   same, but the calculations should be somewhat faster.
 - Extensive feature additions to the SWIG-based java wrapper.
 - The Chem.ReplaceCore() function is now better suited for use
   in R-group decomposition.
 - The Morgan fingerprinting code can now return information about
   which atoms set particular bits.
 - The function pathToSubmol() now copies coordinate information
   from conformations (if present). The function is also now available
   from Python
 - The path and subgraph finding code now takes an optional
   rootedAtAtom argument to allow only paths/subgraphs that start at a
   particular atom to be generated.
 - The function findAtomEnvironmentOfRadiusN has been added to allow
   circular atom environments to be located in molecules.
 - MolOps::assignStereochemistry now can also flag potential
   stereocenters that are not specified.

New Database Cartridge Features:
 - the descriptor-calculation functions mol_numrotatablebonds(),
   mol_numheteroatoms(), mol_numrings(), and mol_tpsa() have been
   added.

Deprecated modules (to be removed in next release):

Removed modules:

Other:
 - In C++, the functions CalcCrippenDescriptors and CalcAMW have been
   renamed calcCrippenDescriptors and calcAMW to make them consistent
   with the other descriptor calculators.
 - The molecule serialization (pickling) format has been changed. The
   new format is more compact.