RDKit Files

******  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, James Davidson, 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)
- EmbedMolecule() should not create a conformer for molecules that have zero atoms
 (github issue 256)
- cartridge: dice similarity calculation does not use USE_BUILTIN_POPCOUNT flag
 (github issue 259)
- cartridge: similarity calculations wrong for maccs fps when USE_BUILTIN_POPCOUNT flag is set
 (github issue 260)

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
  This is useable from python as Chem.SplitMolByPDBResidues() and Chem.SplitMolByPDBChainId()
 (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)
- add get3DDistance
- support 3D distances in the atom pair fingerprints
 (github issue 251)
- added MolOps::get3DDistanceMat() (Chem.Get3DDistanceMatrix() from python)

 
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)