RDKit Files

******  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.