2014_03_1 beta release 1

Beta of the Q1 2014 release.

****** Release_2014.03.1 *******
(Changes relative to Release_2013.09.2)

!!!!!! IMPORTANT !!!!!!

• Due to a bug fix in the rotatable bonds definition, the default
  rotatable bond calculation returns different values than before.
  This also affects MQN descriptor #18.

Acknowledgements:
Paul Czodrowski, Markus Elfring, Nikolas Fechner, Jan Holst Jensen, Christos Kannas, Sereina Riniker, Roger Sayle, Paolo Tosco, Samo Turk, Riccardo Vianello, Maciej Wójcikowski, Toby Wright

Bug Fixes:

• Dict::DataType declaration causing problems with C++11 std::lib
  (github issue 144)
• Pre-condition Violation in AllChem.Compute2DCoords
  (github issue 146)
• GetSimilarityMapForFingerprint() fails when similarity is zero
  (github issue 148)
• PatternFingerprint failure for substructure matching
  (github issue 151)
• query atoms don't match ring queries
  (github issue 153)
• Incorrect SMILES generated after calling MMFF parameterization
  (github issue 162)
• Problems with Xe from SDF
  (github issue 164)
• Radicals not being used in atom--atom matches
  (github issue 165)
• Cannot skip sanitization while reading PDB
  (github issue 166)
• Distance Geometry embedding not thread safe
  (github issue 167)
• O3A::align() and O3A::trans() now return "true" RMSD value
  (github pull 173)
• RangeError when pre-incrementing or decrementing AtomIterators
  (github issue 180)
• ctabs do not contain wedged bonds for chiral s
  (github issue 186)
• ctabs do not contain "A" when appropriate
  (github issue 187)
• Problems round-tripping Al2Cl6 via CTAB
  (github issue 189)
• Don't merge Hs onto dummies
  (github issue 190)
• Wavy bonds to Hs in CTABs should affect the stereochemistry of attached double bonds
  (github issue 191)
• Rendering binary compounds as ClH, FH, BrH or IH rather than putting H first.
  (github issue 199)
• Fixed data race condition in Code/GraphMol/MolAlign/testMolAlign.cpp
  (github pull 202)
• Re-prepared SDF/SMILES files of the MMFF validation suite + a fix
  (github pull 205)
• Problems round-tripping P with non-default valence.
  (github issue 206)
• Added a stricter definition of rotatable bonds as a new function in the ...
  (github pull 211)
• Code/GraphMol/AddHs patch proposal
  (github pull 212)
• Fix: Changed getNumReactantTemplates to GetNumReactantTemplates.
  (github pull 219)
• aromatic B ("b") causes errors from SMARTS parser
  (github issue 220)
• Segmentation fault for MMFF optimization with dummy atoms
  (github issue 224)
• isMoleculeReactantOfReaction() and isMoleculeProductOfReaction() not useable from SWIG wrappers
  (github issue 228)
• cartridge: mol_from_ctab() ignores argument about keeping conformers
  (github issue 229)
• Reaction not correctly preserving chirality on unmapped atoms.
  (github issue 233)
• AllChem.AssignBondOrdersFromTemplate() fails with nitro groups
  (github issue 235)
• Fix molecule dataframe rendering in pandas 0.13.x
  (github pull 236)
• Dummy labels copied improperly into products
  (github issue 243)
• Two bugfixes in MMFF code
  (github pull 248)
• seg fault when trying to construct pharmacophore with no conformation
  (github issue 252)

New Features:

• Expose gasteiger charge calculation to SWIG
  (github issue 152)
• Added additional functionality to PandasTools
  (github pull 155)
• Add MMFFHasAllMoleculeParams() to SWIG interface
  (github issue 157)
• O3A code should throw an exception if the parameterization is not complete.
  (github issue 158)
• Support zero order bonds
  (github issue 168)
• Add attachmentPoint argument to ReplaceSubstructs
  (github issue 171)
• Forcefield constraints (distances, angles, torsions, positions)
  (github pull 172)
• Add kekulize flag to SDWriter
  (github issue 174)
• Support operator= for RWMol
  (github issue 175)
• Get GetAromaticAtoms() and GetQueryAtoms() working from python
  (github issue 181)
• Support richer QueryAtom options in Python
  (github issue 183)
• Support writing V3000 mol blocks
  (github issue 184)
• Allow disabling the building of tests
  (github issue 185)
• Expand DbCLI to allow updating databases
  (github issue 197)
• Code refactoring and enhancement to allow for O3A alignment according to atom-based Crippen logP contribs
  (github pull 201)
• call MolOps::assignStereochemistry() with flagPossibleStereoCenters true from within the molecule parsers.
  (github issue 210)
• Support passing of file-like PandasTools.LoadSDF
  (github pull 221)
• Reaction SMARTS parser should support agents
  (github issue 222)
• Add function to MolOps to allow a molecule to be split into fragments based on a query function
  (github issue 234)
• Adding option useCounts for Morgan fingerprints
  (github pull 238)
• support SimpleEnum functionality for adding recursive queries to reactions
  (github issue 242)
• Additional functions for bit vectors
  (github pull 244)
• Support of RDK fingerprints added to SimilarityMaps
  (github pull 246)
• support 3D distances in the atom pair finerprints
  (github issue 251)

New Database Cartridge Features:

• Support configuration of fingerprint sizes in cartridge.
  (github issue 216)
• Add mol_to_ctab(mol, bool default true) to Postgres cartridge.
  (github pull 230)
• Adds sum formula function to PG cartridge.
  (github pull 232)

New Java Wrapper Features:

Deprecated modules (to be removed in next release):

Removed modules:

• The CMIM integration (previously available to python in the rdkit.ML.FeatureSelect package)
  has been removed due to license incompatibility.

Contrib updates:

• Added Contribution to train ChEMBL-based models
  (github pull 213)
• ConformerParser functionality
  (github pull 245)

Other:

• The Open3DAlign code is considerably faster.
• The SMILES parsing code is faster.
• Fix Bison 3.x incompabtility
  (github pull 226)
• Add Travis support
  (github pull 227)
• port of rdkit.ML bindings from Python/C API to boost::python
  (github pull 237)
• The code now builds more easily using the Anaconda python distribution's
  conda package manager
  (github pull 247)