Congratulations on the release, Greg!
I am really a very recent adopter of RDKit, but even in the short time I have
been using it I have been amazed at the quality and depth of functionality!
Please keep up the good work, and I hope I can continue to help a tiny amount
in the only way I know how - by selfishly requesting new features :)
Kind regards
James
-----Original Message-----
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: Wed 30/06/2010 21:16
To: RDKit Discuss; RDKit Developers List; rdkit-annou...@lists.sourceforge.net
Subject: [Rdkit-announce] Q2 2010 Release
Dear all,
I'm very happy to announce that the next version of the RDKit --
Q22010_1 -- is released.
The release notes are below.
The source release and windows binaries (python 2.6 only this time,
please let me know if anyone needs a python 2.5 release) will be on
the sourceforge downloads page:
http://sourceforge.net/projects/rdkit/files/rdkit/Q2_2010/
The files can also be downloaded from the google project page:
http://code.google.com/p/rdkit/downloads/list
I have also updated the online documentation.
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_Q22010_1 *******
(Changes relative to Release_Q12010_1)
!!!!!! IMPORTANT !!!!!!
- There are a couple of refactoring changes that affect people using
the RDKit from C++. Please look in the Other section below for a list.
- If you are building the RDKit yourself, changes made in this
release require that you use a reasonably up-to-date version of
flex to build it. Please look in the Other section below for more
information.
Acknowledgements:
- Andrew Dalke, James Davidson, Kirk DeLisle, Thomas Heller, Peter Gedeck,
Greg Magoon, Noel O'Boyle, Nik Stiefl,
Bug Fixes:
- The depictor no longer generates NaNs for some molecules on
windows (issue 2995724)
- [X] query features work correctly with chiral atoms. (issue
3000399)
- mols will no longer be deleted by python when atoms/bonds returned
from mol.Get{Atom,Bond}WithIdx() are still active. (issue 3007178)
- a problem with force-field construction for five-coordinate atoms
was fixed. (issue 3009337)
- double bonds to terminal atoms are no longer marked as "any" bonds
when writing mol blocks. (issue 3009756)
- a problem with stereochemistry of double bonds linking rings was
fixed. (issue 3009836)
- a problem with R/S assignment was fixed. (issue 3009911)
- error and warning messages are now properly displayed when cmake
builds are used on windows.
- a canonicalization problem with double bonds incident onto aromatic
rings was fixed. (issue 3018558)
- a problem with embedding fused small ring systems was fixed.
(issue 3019283)
New Features:
- RXN files can now be written. (issue 3011399)
- reaction smarts can now be written.
- v3000 RXN files can now be read. (issue 3009807)
- better support for query information in mol blocks is present.
(issue 2942501)
- Depictions of reactions can now be generated.
- Morgan fingerprints can now be calculated as bit vectors (as
opposed to count vectors.
- the method GetFeatureDefs() has been added to
MolChemicalFeatureFactory
- repeated recursive SMARTS queries in a single SMARTS will now be
recognized and matched much faster.
- the SMILES and SMARTS parsers can now be run safely in
multi-threaded code.
Deprecated modules (to be removed in next release):
- rdkit/qtGui
- Projects/SDView
Removed modules:
- SVD code: External/svdlibc External/svdpackc rdkit/PySVD
- rdkit/Chem/CDXMLWriter.py
Other:
- The large scale changes in the handling of stereochemistry were
made for this release. These should make the code more robust.
- If you are building the RDKit yourself, changes made in this
release require that you use a reasonably up-to-date version of
flex to build it. This is likely to be a problem on Redhat, and
redhat-derived systems. Specifically: if your version of flex is
something like 2.5.4 (as opposed to something like 2.5.33, 2.5.34,
etc.), you will need to get a newer version from
http://flex.sourceforge.net in order to build the RDKit.
- Changes only affecting C++ programmers:
- The code for calculating topological-torsion and atom-pair
fingerprints has been moved from $RDBASE/Code/GraphMol/Descriptors
to $RDBASE/Code/GraphMol/Fingerprints.
- The naming convention for methods of ExplicitBitVect and
SparseBitVect have been changed to make it more consistent with
the rest of the RDKit.
- the bjam-based build system should be considered
deprecated. This is the last release it will be actively
maintained.
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