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)

2013_09_2 Release

****** 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)

2013_09_1 Release

****** 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.

2013_09_1 beta release 1

Beta of the Q3 2013 release.

2013_09_1pre

An early version of the Q3 2013 release created to allow a binary for the RDKit UGM