Dear all,
I'm very happy to announce that the next version of the RDKit --
Q32008_1 -- is released.
The release notes are below.
The source release and a windows binary are on the sourceforge downloads page:
https://sourceforge.net/project/showfiles.php?group_id=160139&package_id=180003&release_id=631220
The files can also be downloaded from the google project page:
http://code.google.com/p/rdkit/downloads/list
If you plan to build from source, please read the new build instructions:
1) For Linux: http://code.google.com/p/rdkit/wiki/BuildingOnLinux
2) For Windows: http://code.google.com/p/rdkit/wiki/BuildingOnWindows
I also updated the browseable and downloadable API documentation at rdkit.org:
http://www.rdkit.org/C++_Docs
http://rdkit.org/RDKit_C++_Docs.Q32008.tgz
http://www.rdkit.org/Python_Docs
http://rdkit.org/RDKit_Python_Docs.Q32008.tgz
Note that both the source and binary distributions of the code now
include the API documentation in directory $RDBASE/Docs/Code
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
any suggestions.
-greg
****** Release_Q32008_1 *******
(Changes relative to Release_May2008_1)
Acknowledgements:
- Noel O'Boyle, Igor Filippov, Evgueni Kolossov, Greg Magoon
Bug Fixes
- A memory leak in the ToBase64 and FromBase64 wrapper functions was
fixed.
- The UFF atom typer has been made more permissive: it now will pick
"close" atom types for things it does not recognize. (issue
2094445)
- The handling of molecules containing radicals has been greatly
improved (issues 2091839, 2091890, 2093420)
- Iterative (or secondary, or dependent) chirality is now supported,
see this page for more information:
http://code.google.com/p/rdkit/wiki/IterativeChirality
(issue 1931470)
- Isotope handling has been changed, this allows correct matching of
SMARTS with specified isotopes. (issue 1968930)
- Some problems with the MACCS key definitions have been
fixed. (issue 2027446)
- Molecules with multiple fragments can now be correctly
embedded. (issue 1989539)
- Adding multiple bonds between the same atoms in a molecule now
produces an error. (issue 1993296)
- The chemical reaction code now handles chiral atoms correctly in
when applying reactions with no stereochem information
provided. (issue 2050085)
- A problem with single-atom cores in TemplateExpand.py has been
fixed. (issue 2091304)
- A problem causing bicyclobutane containing molecules to not be
embeddable has been fixed. (issue 2091864)
- The default parameters for embedding are now molecule-size
dependent. This should help with the embedding of large, and
crowded molecules. (issue 2091974)
- The codebase can now be built with boost 1.36. (issue 2071168)
- A problem with serialization of bond directions was fixed.
(issue 2113433)
New Features
- The RDKit can now be built under Darwin (Mac OS/X).
- Tversky similarity can now be calculated. (request 2015633)
- Many of the core datastructures now support equality comparison
(operator==). (request 1997439)
- Chirality information can now be assigned based on the 3D
coordinates of a molecule using
MolOps::assignChiralTypesFrom3D(). (request 1973062)
- MolOps::getMolFrags() can now return a list of split molecules
instead of just a list of atom ids. (request 1992648)
- ROMol::getPropNames() now supports the includePrivate and
includeComputed options. (request 2047386)
Other
- the pointers returned from Base64Encode/Decode are now allocated
using new instead of malloc or calloc. the memory should be
released with delete[].
- the generation of invariants for chirality testing is now quite a
bit faster; this results in faster parsing of molecules.
- The use of C include files instead of their C++ replacements has
been dramatically reduced.
- The new (as of May2008) hashing algorithm for fingerprints is now
the default in the python fingerprinting code
(Chem.Fingerprints.FingerprintMols).
- The functions MolOps::assignAtomChiralCodes() and
MolOps::assignBondStereoCodes() are deprecated. Use
MolOps::assignStereochemistry() instead.
- The RDKit no longer uses the old numeric python library. It now
uses numpy, which is actively supported.
- By default Lapack++ is no longer used. The replacement is the boost
numeric bindings: http://mathema.tician.de/software/boost-bindings.
