Dear all,
Today I tagged the beta for the 2013.09 release in git:
https://github.com/rdkit/rdkit/releases/tag/Release_2013_09_1beta1
Here's the github download link:
https://github.com/rdkit/rdkit/archive/Release_2013_09_1beta1.tar.gz
Python 2.7 binaries for win32 and win64 are also available as part of that
github release.
If no show-stopper bugs appear, I will do the release itself next week.
Excerpts from the partially updated release notes are below. You can also
view these online here:
https://raw.github.com/rdkit/rdkit/master/ReleaseNotes.txt
Best Regards,
-greg
****** Release_2013.09.1 *******
(Changes relative to Release_2013.06.1)
Acknowledgements:
James Davidson, JP Ebejer, Nikolas Fechner, Gregory 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:
- 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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