rdkit: 2014_09_1 (Q3 2014) Release

****** Release_2014.09.1 ******* (Changes relative to Release_2014.03.1) Acknowledgements: Andrew Dalke, James Davidson, Jan Domanski, Patrick Fuller, Seiji Matsuoka, Noel O'Boyle, Sereina Riniker, Alexander Savelyev, Roger Sayle, Nadine Schneider, Matt Swain, Paolo Tosco, Riccardo Vianello, Richard West 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) Hydrogens in mol blocks have a valence value set (github issue #357) Computed props on non-sanitized molecule interfering with substructure matching (github issue #360) 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) Update URLs to InChI API after inchi-trust.org website redesign. (github pull #341 from rwest) 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 add Chem.Draw.MolToQPixmap (github pull #355 from mojaie) New Database Cartridge Features: NOTE: the configuration variable rdkit.ss_fp_size has been renamed to rdkit.sss_fp_size 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): Projects/SDView4 rdkit/utils/ GUIDs.py GenLicense.py Licensing.py PiddleTools.py PilTools.py REFile.py SliceTools.py rdkit/Logger 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