RDKit Files

******  Release_2013.09.2 *******
(Changes relative to Release_2013.09.2)

Acknowledgements:
Andrew Dalke, JP Ebejer, Daniel Moser, Sereina Riniker, Roger Sayle, Manuel Schwarze, Julia Weber

Bug Fixes:
- cannot pickle unsanitized molecules
  (github issue 149)
- Problems reading PDB files when locale is DE
  (github issue 170)
- calling RWMol::clear() leaves property dict empty
  (github issue 176)
- zero atom molecule generates exception in MolToSmiles when 
  rootedAtAtom is provided
  (github issue 182)
- bond orders not being set when PDB files are read
  (github issue 194)
- GenMACCSKeys() raises an exception with an empty molecule
  (github issue 195)
- left-justified SDF bond topology of "0" raises an unexpected
  exception
  (github issue 196)

******  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.