rdkit: 2014_09_1 (Q3 2014) Beta Release

****** Release_2014.09.1 ******* (Changes relative to Release_2014.03.1) Acknowledgements: Andrew Dalke, Jan Domanski, Patrick Fuller, Noel O'Boyle, Sereina Riniker, Alexander Savelyev, Roger Sayle, Nadine Schneider, Matt Swain, Paolo Tosco, Riccardo Vianello Bug Fixes: Bond query information not written to CTAB (github issue 266) Bond topology queries not written to CTABs (github issue 268) Combined bond query + topology query not correctly parsed from CTAB (github issue 269) SWIG wrapped suppliers leak memory on .next() (github issue 270) SWIG wrappers don't build with SWIG 3.0.x (github issue 277) core leak from DataStructs.ConvertToNumpyArray (github issue 281) MolTransforms not exposed to Java wrapper (github issue 285) Seg fault in ReactionFromRxnBlock (github issue 290) BitInfo from GetHashedMorganFingerprint() has non-folded values (github issue 295) bad inchi for chiral S when the molecule is sanitized (github issue 296) Cannot generate smiles for ChEBI 50252 (github issue 298) Either molecule-molecule substruct matching is wrong OR the docs for Atom::Match incorrect (github issue 304) fluorine F-F gives segmentation fault with MMFF forcefield (github issue 308) cartridge: MACCS similarity wrong when using the builtin popcount and the index (github issue 311) Substructure Search via SMARTS implicit hydrogens (github issue 313) SMARTS output for [x] is wrong (github issue 314) Bonds not being set up properly in renumberAtoms (github issue 317) Python 2 code in python 3 branch (github issue 326) Linking error with ICC 15.0 on Linux (github issue 327) Using explicit hydrogens in the SMILES lead to the same AP FP for two different molecules (github issue 334) memory leaks when smiles/smarts parsers fail (github issue 335) No double bond stereo perception from CTABs when sanitization is turned off (github issue 337) missing MACCS key 44 might be found (github issue 352) Fixed a weakness in the angular restraint code (github pull 261 from ptosco) A few fixes to improve MMFF/UFF robustness (github pull 274 from ptosco) Static webGL rendering fix (github pull 287 from patrickfuller) Revert #include ordering in SmilesMolSupplier.cpp (github pull 297 from mcs07) Add missing include for RDDepict::compute2DCoords (github pull 301 from baoilleach) Herschbach-Laurie fallback implemented to fix GitHub 308 (github pull 312 from ptosco) Issue #320 Making GetBestRMS more idiot-proof (github pull 322 from jandom) New Features: Should be able to do intramolecular bond breaking in reactions. (github issue 58) Support reactions in cartridge (github issue 223) Documentation of Inchi methods (github issue 240) add DescribeQuery() to Bond python wrapper (github issue 267) support avalon fingerprint in cartridge (github issue 286) support partial fragmentation with fragmentOnSomeBonds (github issue 288) Add calcNumHeterocycles() descriptor (github issue 351) C++ implementation of FMCS algorithm Reordering feature for Butina clustering (github pull 302 from sriniker) Changes and new functions for the calculation of RMS values between conformers of a molecule (github pull 306 from sriniker) Extended chemical reaction functionality and add chemical reactions to cartridge (github pull 315 from NadineSchneider) Custom color to highlight atoms in Mol2Image (github pull 316 from jandom) Several different fingerprint algorithms for chemical reactions are now available New Database Cartridge Features: Chemical reactions and several operations on them are now supported Avalon fingerprints now supported (when support has been compiled in) New Java Wrapper Features: FMCS implementation exposed Fingerprints for chemical reactions Possible core leak in some of the MolSuppliers was fixed Deprecated modules (to be removed in next release): Removed modules: Contrib updates: Other: The RDKit now supports both python3 and python2. There is now conda integration for the RDKit. SMILES generation is substantially faste