Dear all,
I'm pleased to announce that the next version of the RDKit -- 2013.06
(a.k.a Q2 2013) -- is released. This one is "a bit" late due to my travel
schedule. Better late than never.
The release notes are below.
The source release is on the sourceforge downloads page:
http://sourceforge.net/projects/rdkit/files/rdkit/Q2_2013/<http://sourceforge.net/projects/rdkit/files/rdkit/Q1_2013/>
The files can also be downloaded from the google project page:
http://code.google.com/p/rdkit/downloads/list
I will be uploading 32-bit and 64-bit Windows binaries for Python 2.7
later today.
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.
Best Regards,
-greg
****** Release_2013.06.1 *******
(Changes relative to Release_2013.03.2)
Administrivia note:
In the course of this release cycle, development was moved over
entirely to github. The sourceforge svn repository no longer contains
an up-to-date version of the code.
Acknowledgements:
Andrew Dalke, JP Ebejer, Nikolas Fechner, Roger Sayle, Riccardo Vianello,
Yingfeng Wang, Dan Warner
Bug Fixes:
- The docs for Descriptors.MolWt are now correct (GitHub #38)
- Molecules coming from InChi now have the correct molecular
weight. (GitHub #40)
- RemoveAtoms() no longer leads to problems in canonical SMILES
generation when chiral ring atoms are present. (GitHub #42)
- Atom invariants higher than the number of atoms in the molecule can
now be provided to the atom pairs and topological torsions
fingerprinters. (GitHub #43)
- A typo with the handling of log levels was fixed in the python
wrapper code for InChI generation. (GitHub #44)
- Stereochemistry no longer affects canonical SMILES generation if
non-stereo SMILES is being generated. (GitHub #45)
- The ExactMolWt of [H+] is no longer zero. (GitHub #56)
- The MPL canvas now has an addCanvasDashedWedge() method. (GitHub
#57)
- RWMol::insertMol() now copies atom coordinates (if
present). (GitHub #59)
- The "h" primitive in SMARTS strings now uses the method
getTotalNumHs(false) instead of getImplicitValence().
(GitHub #60)
- bzip2 files now work better with the SDWriter class. (GitHub #63)
- a crashing bug in InChI generation was fixed. (GitHub #67)
New Features:
- Sanitization can now be disabled when calling GetMolFrags() from
Python (GitHub #39)
- Bond.GetBondTypeAsDouble() has been added to the python
wrapper. (GitHub #48)
- The fmcs code now includes a threshold argument allowing the MCS
that hits a certain fraction of the input molecules (instead of all
of them) to be found. The code has also been synced with the most
recent version of Andrew Dalke's version.
- Atoms now have a getTotalValence() (GetTotalValence() from Python)
method. (GitHub #61)
- R labels from Mol files now can go from 0-99
- chiral flags in CTABs are now handled on both reading and writing.
The property "_MolFileChiralFlag" is used.
New Database Cartridge Features:
New Java Wrapper Features:
- {Get,Set}Prop() methods are now available for both Atoms and
Bonds. (GitHub #32)
Deprecated modules (to be removed in next release):
Removed modules:
- rdkit.utils.pydoc_local
Other:
- the handling of flex/bison output files as dependencies has been
improved (GitHub #33)
- the molecule drawing code should now also work with pillow (a fork of
PIL)
- the PANDAS integration has been improved.
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