Re: [Rdkit-devel] 2012.06 (Q2 2012) RDKit release

[Eddie C. <cao...@gm...>]

Hi,

For those Mac users using the tappable Homebrew formulae, the formulae has been updated to use the new release. To upgrade, simply run:

$ brew update
$ brew upgrade rdkit

Have fun!

Eddie


On Jul 10, 2012, at 9:11 PM, Greg Landrum wrote:

> I'm very happy to announce that the next version of the RDKit --
> 2012.06 (a.k.a Q2 2012) -- is released.
> 
> The release notes are below.
> 
> The source release is on the sourceforge downloads page:
> http://sourceforge.net/projects/rdkit/files/rdkit/Q2_2012/
> 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, have also been uploaded.
> 
> The online version of the documentation at rdkit.org has been updated.
> 
> 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_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.
> - Due to changes in the cartridge, indexes on molecule and bitvector
>   fingerprint columns will need to be rebuilt.
> 
> 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.
> - AvalonTools bug with coordinate generation for mols with no
>   conformers 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:
> - The functions mol_from_smiles(), mol_from_smarts(), and
>   mol_from_ctab() now return a null value instead of generating an
>   error when the molecule processing fails. This allows molecule
>   tables to be constructed faster.
> - The functions mol_to_smiles() and mol_to_smarts() have been added.
> - Creating gist indices on bit-vector fingerprint columns is faster.
> - The indexing fingerprint for molecular substructures has been changed.
>   The new fingerprint is a bit slower to generate, but is
>   considerably better at screening. More information here:
>   http://code.google.com/p/rdkit/wiki/ImprovingTheSubstructureFingerprint
> 
> New Java Wrapper Features:
> 
> Deprecated modules (to be removed in next release):
> - Support for older (pre9.1) postgresql versions.
> 
> Removed modules:
> - rdkit.Excel
> - the code in $RDBASE/Code/PgSQL/RDLib
> - rdkit.Chem.AvailDescriptors : the same functionality is now available
>   in a more useable manner from rdkit.Chem.Descriptors
> 
> 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.
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel