[Rdkit-devel] Beta of Q2 2012 release available

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

Today I tagged the beta for the 2012.06 (Q3 2012 in the old
numbering) release in svn:
http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2012_06_1beta1/

and uploaded a source distribution to the google code site:
http://code.google.com/p/rdkit/downloads/detail?name=RDKit_2012_06_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.

This release has a relatively small number of new features, but a
large number of bug fixes and some performance enhancements.
Excerpts from the release notes are below.

Best Regards,
-greg

******  Release_2012.06.1 *******
(Changes relative to Release_2012.03.1)

!!!!!! IMPORTANT !!!!!!
 - Some of the bug fixes affect the generation of SMILES. Canonical
   SMILES generated with this version of the RDKit will be different
   from previous versions.

Acknowledgements:
Andrew Dalke, JP Ebejer, Igor Filippov, Peter Gedeck, Jan Holst
Jensen, Adrian Jasiński, George Papadatos, Andrey Paramonov, Adrian
Schreyer, James Swetnam

Bug Fixes:
 - Radicals are now indicated in molecular depictions. (Issue 3516995)
 - Calling .next() on an SDMolSupplier at eof no longer results in an
   infinite loop. (Issue 3524949)
 - Chirality perception no longer fails in large molecules.
   (Issue 3524984)
 - problem creating molblock for atom with four chiral nbrs
   (Issue 3525000)
 - A second sanitization leads to a different molecule.
   (Issue 3525076)
 - can't parse Rf atom in SMILES
   (Issue 3525668)
 - generates [HH2-] but can't parse it
   (Issue 3525669)
 - improper (re)perception of 1H-phosphole
   (Issue 3525671)
 - ForwardSDMolSupplier not skipping forward on some errors
   (Issue 3525673)
 - SMILES/SMARTS parsers don't recognize 0 atom maps
   (Issue 3525776)
 - R group handling in SMILES
   (Issue 3525799)
 - Canonical smiles failure in symmetric heterocycles
   (Issue 3526810)
 - Canonical smiles failure with "extreme" isotopes
   (Issue 3526814)
 - Canonical smiles failure with many symmetric fragments
   (Issue 3526815)
 - Canonical smiles failure with dependent double bonds
   (Issue 3526831)
 - Build Fails Due to Missing include in Code/RDBoost/Wrap.h
   (Issue 3527061)
 - Incorrect template parameter use in std::make_pair
   (Issue 3528136)
 - Canonicalization failure in cycle
   (Issue 3528556)
 - incorrect values reported in ML analysis
   (Issue 3528817)
 - Cartridge does not work on 32bit ubuntu 12.04
   (Issue 3531232)
 - Murcko Decomposition generates unuseable molecule.
   (Issue 3537675)
 - A few memory leaks were fixed in the Java Wrappers
 - The exact mass of molecules with non-standard isotopes is now
   calculated correctly.
 - The default (Euclidean) distance metric should now work with Butina
   clustering.
 - Some bugs in the depictor were fixed.

New Features:
 - ChemicalFeatures now support an optional id
 - Isotope handling has been greatly improved. Atoms now have a
   getIsotope() (GetIsotope() in Python) method that returns zero if
   no isotope has been set, the isotope number otherwise.
 - The function MolFragmentToSmiles can be used to generate canonical
   SMILES for pieces of molecules.
 - The function getHashedMorganFingerprint (GetHashedMorganFingerprint
   in Python) has been added.

New Database Cartridge Features:

New Java Wrapper Features:

Deprecated modules (to be removed in next release):

Removed modules:
 - rdkit.Excel
 - the code in $RDBASE/Code/PgSQL/RDLib

Other:
 - Similarity calculations on ExplicitBitVectors should now be much faster
 - Use of [Xa], [Xb], etc. for dummy atoms in SMILES is no longer
   possible. Use the "*" notation and either isotopes (i.e. [1*],
   [2*]) or atom maps (i.e. [*:1], [*:2]) instead.
 - Initial work was done towards make the RDKit work on big endian
   hardware (mainly changes to the way pickles are handled)
 - Canonical SMILES generation is now substantially faster.