[Rdkit-devel] Beta of Q1 2011 Release Available

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

Dear all,

This morning I tagged the beta for the Q1 2011 (2011.03 in the new
numbering) release in svn:
http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2011_03_1beta1/

and uploaded a source distribution to the google code site:
http://code.google.com/p/rdkit/downloads/detail?name=RDKit_2011_03_1beta1.tgz
If there's demand for it, I will also put up a windows binary.

As usual: if no show-stopper bugs appear, I will do the release itself
in about a week.

Excerpts from the release notes are below.

Best Regards,
-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.