Dear all,
I'm pleased to announce that the next version of the RDKit -- 2013.09
(a.k.a Q3 2013) -- is released.
The release notes are below.
The source release is on the sourceforge downloads page:
http://sourceforge.net/projects/rdkit/files/rdkit/Q3_2013/
The files can also be downloaded from the google project page:
http://code.google.com/p/rdkit/downloads/list
I have uploaded 32-bit and 64-bit Windows binaries for Python 2.7 and, in
response to a couple of requests, 32-bit and 64-bit Windows binaries for
Java.
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, which is scheduled for March 2014 (we're
moving to a six-month release cycle).
Best Regards,
-greg
****** Release_2013.09.1 *******
(Changes relative to Release_2013.06.1)
Acknowledgements:
James Davidson, JP Ebejer, Nikolas Fechner, Grégori Gerebtzoff, Michal
Nowotka, Sereina Riniker, Roger
Sayle, Gianluca Sforna, Matthew Szymkiewicz, Paolo Tosco, Dan Warner,
!!!!!! IMPORTANT !!!!!!
- Due to a bug fix in the parameter set, the MolLogP and MolMR
descriptor calculators now return different values for molecules
with pyrrole (or pyrrole-like) Ns.
Bug Fixes:
- The pymol ShowMol method can now handle molecules with more than
999 atoms (they are sent via PDB)
- Various stability improvements to the Pandas integration.
(github issues 129 and 51)
- Some RDKit methods require python lists and don't allow passing
numpy arrays or pandas series directly
(github issue 119)
- mol2 parser not setting E/Z flags on double bonds
(github issue 114)
- Incorrect angle terms in UFF
(github issue 105)
- Problems with stereochemistry flags and PathToSubmol()
(github issue 103)
- Bad Crippen atom type for pyrrole H
(github issue 92)
- PandasTools tests fail with Pandas v0.12
(github issue 91)
- Isotope information not affecting chirality
(github issue 90)
- properties are not read from SDF files with V3000 mol blocks.
(github issue 88)
- assignStereochemistry does not remove bond wedging that shouldn't be
there.
(github issue 87)
- Drawing code modifies wedge bonds in reactions
(github issue 86)
- Stereochemistry not perceived when parsing CTABs unless sanitization is
done.
(github issue 82)
- 2D rendering issue for epoxide ( CAS 70951-83-6)
(github issue 78)
- PandasTools doctests should be failing, but are not
(github issue 75)
- Better handling of radicals to/from mol files
(github issue 73)
- Benzothiazolium structure can be parsed from ctab, but the SMILES
generated cannot be processed.
(github issue 72)
- Chem.MolFromInch hangs on CID 23691477 and CID 23691480
(github issue 68)
- Chem.MolFromInchi on CHEMBL104337 leads to segmentation fault
(github issue 67)
- "Could not embed molecule." (The Anthony Conundrum)
(github issue 55)
New Features:
- Add fragmentOnBonds() to python wrapper
(github issue 142)
- Allow renumbering atoms in a molecule.
(github issue 140)
- MMFF94 and MMFF94S support
- implementation of the Open3DAlign rigid alignment algorithm
- Support for reading and writing PDB files
- The python function AllChem.AssignBondOrdersFromTemplate() can be
used to assign bond orders from a reference molecule to the bonds
in another molecule. This is helpful for getting bond orders
correct for PDB ligands.
(github issue 135)
- Bond lengths, angles, and torsions can now be queries and adjusted.
(github issue 132)
- Implementation of similarity maps
(github issue 94)
- Python implementation of the Fraggle similarity algorithm.
See Jameed Hussain's presentation from the 2013 UGM for details:
https://github.com/rdkit/UGM_2013/blob/master/Presentations/Hussain.Fraggle.pdf?raw=true
- SparseIntVects now support -=, +=, /=, and *= with ints from C++
and Python
- support \\ in SMILES
(github issue 136)
- Support a similarity threshold in DbCLI
(github issue 134)
- Support construction molecules from other molecules in the python wrapper
(github issue 133)
- support tversky similarity in DbCLI
(github issue 130)
- support tversky similarity in cartridge
(github issue 121)
- support reading and writing reactionComponentType and
reactionComponentNumber from ctabs
(github issue 118)
- Add in-place forms of addHs(), removeHs(), and mergeQueryHs()
(github issue 117)
- modify MolOps::cleanUp() to support this azide formulation: C-N=N#N
(github issue 116)
- Dihedral rotation exposed in python
(github issue 113)
- Support for cairocffi (cairo drop-in replacement that plays nicely with
virtualenv)
(github issue 80)
- Grey color for Hydrogens
(github issue 97)
- Improvements to the Dict interface in C++
(github issue 74)
- customizable drawing options
(github issue 71)
- Add method for setting the chiral flag in mol blocks
(github issue 64)
- New descriptors added (Python only for now):
MaxPartialCharge(),MinPartialCharge(),MaxAbsPartialCharge(),MinAbsPartialCharge(),
MaxEStateIndex(),MinEStateIndex(),MaxAbsEStateIndex(),MinAbsEStateIndex()
New Database Cartridge Features:
New Java Wrapper Features:
- MMFF support
- PDB reading and writing
- Open3DAlign support
Deprecated modules (to be removed in next release):
Removed modules:
Contrib updates:
- The MMPA implementation has been updated
See Jameed Hussain's tutorial from the 2013 UGM for details:
https://github.com/rdkit/UGM_2013/tree/master/Tutorials/mmpa_tutorial
[Jameed Hussain]
- An implementation of Ertl and Schuffenhauer's Synthetic
Accessibility score is available in Contrib/SA_Score
[Peter Ertl, Greg Landrum]
- Command line scripts for the Fraggle similarity algorithm
See Jameed Hussain's presentation from the 2013 UGM for details:
https://github.com/rdkit/UGM_2013/blob/master/Presentations/Hussain.Fraggle.pdf?raw=true
[Jameed Hussain]
Other:
- Some of the changes to UFF deviate from the published force
field. Specifics of the changes, and the reasoning behind them, are
in Paolo Tosco's 2013 RDKit UGM presentation:
https://github.com/rdkit/UGM_2013/blob/master/Presentations/Tosco.RDKit_UGM2013.pdf?raw=true
- Reaction drawing has been improved. Support for reaction drawing
has been added to the IPython notebook.
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