Dear all,
Today I tagged the beta for the 2012.12 release in svn:
http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2012_12_1beta1/<http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2012_09_1beta2/>
and uploaded a source distribution to the google code site:
*http://rdkit.googlecode.com/files/RDKit_2012_12_1beta1.tgz*
If no show-stopper bugs appear, I will do the release itself at the
end of next week.
Excerpts from the updated release notes are below.
Best Regards,
-greg
****** Release_2012.12.1 *******
(Changes relative to Release_2012.09.1)
!!!!!! IMPORTANT !!!!!!
Acknowledgements:
Andrew Dalke, James Davidson, Robert Feinstein, Nikolas Fechner,
Nicholas Firth, Markus Hartenfeller, Jameed Hussain, Thorsten Meinl,
Sereina Riniker, Roger Sayle, Pat Walters, Bernd Wiswedel
Bug Fixes:
- Using parentheses for zero-level grouping now works in reaction
SMARTS. This allows intramolecular reactions to be expressed.
- SMILES generated for molecules with ring stereochemistry
(e.g. N[C@H]1CC[C@H](CC1)C(O)=O) are now canonical. (issue 40)
- SKP lines in a CTAB property block are now properly handled. (issue
255)
- The molecular drawing code now shows dotted lines for Any bonds.
(issue 260)
- ROMol::debugMol() (ROMol.DebugMol() in Python) now reports isotope
information. (issue 261)
- The molecular drawing code now correctly highlights wedged bonds.
(issue 262)
- RWMol::addAtom() now adds atoms to conformers.
(issue 264)
- TDT files with atomic coordinates now have those coordinates in the
correct order. (issue 265)
- A ring-finding error/crash has been fixed. (issue 266)
- Dummy atoms now have a default valence of 0 and no maximim
valence. (issue 267)
- The Python code no longer throws string exceptions. (issue 268)
- Invalid/unrecognized atom symbols in CTABs are no longer
accepted. (issue 269)
- Chem.RDKFingerprint now accepts atom invariants with values larger
than the number of atoms. (issue 270)
- The code should now all work when the locale (LANG) is set to
values other than "C" or one of the English locales. (issue 271)
- Two-coordinate Hs are no longer removed by
MolOps::removeHs(). (issue 272)
- R groups read from CTABs are now marked using setIsotope() instead
of setMass(). (issue 273)
- Hs present in the molecule graph no longer incorrectly impact
substructure matches. (issue 274)
- Murcko decomposition of molecules with chiral ring atoms now
works. (issue 275)
- Methane now shows up in molecular drawings. (issue 276)
- '&' in SLN properties is now correctly handled. (issue 277)
- Molecules with string-valued molAtomMapNumber atomic properties can
now be serialized. (issue 280)
- SMARTS strings containing a dot in a recursive piece are now
properly parsed. (issue 281)
- The SMILES and SLN parsers no longer leak memory when sanitization
of the result molecule fails. (issue 282)
New Features:
- RDKit ExplicitBitVects and DiscreteValueVects can now be directly
converted into numpy arrays.
- Rogot-Goldberg similarity has been added.
- C++: BitVects and SparseIntVects now support a size() method.
- C++: DiscreteValueVects now support operator[].
- An initial version of a SWIG wrapper for C# has been added.
- Support for easily adding recursive queries to molecules and
reactions has been added. More documentation is required for this
feature.
- To allow more control over the reaction, it is possible to flag reactant
atoms as being protected by setting the "_protected" property on those
atoms. Flagged atoms will not be altered in the reaction.
- Atoms and Bonds now support a ClearProp() method from python.
- The new Python module rdkit.ML.Scoring.Scoring includes a number of
standard tools for evaluating virtual screening experiments: ROC
curve generation, AUC, RIE, BEDROC, and Enrichment,
New Database Cartridge Features:
- The Chi and Kappa descriptors are now available
New Java Wrapper Features:
- The Chi and Kappa descriptors are now available
Deprecated modules (to be removed in next release):
Removed modules:
- The old SWIG wrapper code in $RDBASE/Code/Demos/SWIG has been
removed. The SWIG wrappers are now in $RDBASE/Code/JavaWrappers
Other:
- The C++ code for drawing molecules previously found in
$RDBASE/Code/Demos/RDKit/Draw has been moved to
$RDBASE/Code/GraphMol/MolDrawing
- Calculation of the Chi and Kappa descriptors has been moved into
C++.
- To make builds easier, the thread-safety of the recursive-smarts
matcher has been made optional. The build option is
RDK_BUILD_THREADSAFE_SSS.
- There are two new entries in the Contrib directory:
* Contrib/PBF : An implementation of the Plane of Best Fit
contributed by Nicholas Firth.
* Contrib/mmpa : An implementation of GSK's matched molecular pairs
algorithm contributed by Jameed Hussain
- A new "Cookbook" has been added to the documentation to provide
a collection of recipes for how to do useful tasks.
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