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 faster