rdkit/rdkit: 2017_09_1 (Q3 2017) Release

Release_2017.09.1 (Changes relative to Release_2017.03.1) Important The fix for bug #1567 changes the way fragment SMILES are canonicalized. MolFragmentToSmiles() and canonicalizeFragment() will now often return different results The fix for bug #1604 changes the behavior of QueryAtom::setQuery(), which now deletes the current query before setting the new value. If you are using QueryAtom::setQuery() from C++ (or possibly Java), be sure that you are not also deleting that memory. Acknowledgements: Brian Cole, Peter Gedeck, Guillaume Godin, Jan Halborg Jensen, Malitha Kabir, Tuomo Kalliokoski, Brian Kelley, Noel O'Boyle, Matthew O'Meara, Pavel Polishchuk, Cameron Pye, Christian Ribeaud, Stephen Roughley, Patrick Savery, Roger Sayle, Nadine Schneider, Gregor Simm, Matt Swain, Paolo Tosco, Alain Vaucher, Sam Webb, 'phenethyl', 'xiaotaw' Highlights: The new R-Group decomposition code provides a flexible and powerful tool for building R-group tables or datasets look in $RDBASE/Docs/Notebooks for example notebooks showing how to use this. Drawing of chemical reactions has been greatly improved and is now done using the C++ rendering code. The MaxMinPicker is dramatically faster. New descriptors: the QED descriptor has been added as have a large collection of new 3D descriptors and implementations of the USR and USRCAT fingerprints. New Features and Enhancements: Bring back USR and USRCAT descriptors (github pull #1417 from greglandrum) Generate a warning for conflicting bond directions (github issue #1423 from greglandrum) expose and test GetDrawCoords() (github pull #1427 from greglandrum) Improvement suggestions for SaltRemover (github issue #1431 from ribeaud) Remove obsolete scripts from Scripts dir (github pull #1440 from greglandrum) Support drawing reactions from C++ (github pull #1444 from greglandrum) QED code with unit test file (github pull #1445 from gedeck) Add support for other datatypes to ConvertToNumpyArray (github issue #1447 from pyeguy) updated FindCairo.cmake (github pull #1455 from ptosco) fixes PgSQL CMakeLists.txt to enable conda build on Windows (github pull #1457 from ptosco) Some cleanups to make Travis builds faster (github pull #1464 from greglandrum) ExplainPairScore does not support includeChirality=True (github issue #1466 from xiaotaw) Add a collection of new 3D descriptors (github pull #1467 from greglandrum) Update cartridge documentation to use ChEMBL 23 (github issue #1491 from greglandrum) First entry of the SubstructLibrary module (github pull #1493 from bp-kelley) assorted fixes to get the current master branch to build on Windows (github pull #1495 from ptosco) Support assignment of stereochemistry tags to bonds from 3D structure (github issue #1497 from gncs) Support black and white molecule drawing (github issue #1510 from greglandrum) Missing def_readwrite for backgroundColour in rdMolDraw2D.cpp (github issue #1519 from goraj) Adds canonicalization of atom maps (github pull #1521 from bp-kelley) Implement stereoisomer enumeration (github pull #1531 from greglandrum) Add a MolBundle class (github pull #1537 from greglandrum) Provide support for color palettes in MolDraw2D (github pull #1546 from greglandrum) A few reaction drawing tweaks (github pull #1549 from greglandrum) R group improvements (github pull #1552 from greglandrum) Add a canned Atom query for heavy atom degree (github issue #1563 from greglandrum) Adds FreeSASA adapter (github pull #1565 from bp-kelley) Added C++ version of getBestRMS() (github pull #1568 from psavery) SMILES lexer optimization/enhancement (github pull #1575 from greglandrum) Update IPythonConsole and PandasTools to use new drawing code (github pull #1577 from greglandrum) Squashes warnings on cygwin (github pull #1578 from bp-kelley) Support continuous highlighting in drawMolecules(). (github pull #1579 from greglandrum) Enhanced Similarity Maps depiction (github pull #1594 from gerebtzoff) Bug Fixes: RDKit gets stuck on PubChem CID 102128817 (github issue #1281 from TuomoKalliokoski) MMP code not including molecules with no cuts (github issue #1406 from greglandrum) Fixes PandasTools to also work with pandas 0.20 (github pull #1410 from bp-kelley) csharp input files out of date (github issue #1413 from greglandrum) Fix cxsmiles parse on VS2008 (github pull #1415 from mcs07) MaxMinPicker picking non-existent element (github issue #1421 from greglandrum) _isCallable clashes with Celery (github issue #1434 from momeara) Impossible to build the RDKit from source without Python installed (github issue #1435 from greglandrum) RemoveHs() removes H atom attached to dummy if it came from AddHs() (github issue #1439 from DrrDom) fix a couple failing windows tests related to temp file removal (github pull #1446 from greglandrum) SanitizeRxn fails with a runtime exception when unused Rlabels are in product (github issue #1448 from bp-kelley) String module conversion bug (github pull #1452 from coleb) GetConformerRMS() documentation is misleading (github pull #1459 from greglandrum) URANGE_CHECK not doing its job in RWMol::addBond (github issue #1461 from baoilleach) ExplainPairScore does not support includeChirality=True (github issue #1466 from xiaotaw) MolToSmarts does not include atom-map or isotope info for molecules built from SMILES (github issue #1472 from greglandrum) AdjustQueryProperties() removing properties from dummy atoms (github issue #1474 from greglandrum) Fixes lookup for HELM Monomer 'D' (github pull #1477 from bp-kelley) Aromatic rings composed solely of dummy atoms should not be kekulized (github issue #1478 from bp-kelley) Directly specify rotor model used in QED. (github pull #1483 from bp-kelley) Unicode problem with pidPS tests on Mac (github issue #1490 from greglandrum) Pattern fingerprint setting bad bits with degree zero atoms (github issue #1496 from greglandrum) Remove xlocale header (github pull #1501 from greglandrum) Fixes atom documentation (github pull #1505 from bp-kelley) TypeError from PandasTools.SaveXlsxFromFrame (github issue #1507 from pyeguy) Removes trailing spaces after \ to fix windows compilation errors (github pull #1516 from bp-kelley) prepareMolForDrawing() not in SWIG wrappers (github issue #1522 from greglandrum) Bond is missing IsInRing methods in Java wrapper (github issue #1535 from sroughley) Fixes blanking of non-query atom data when QueryAtomData was being pi… (github pull #1541 from bp-kelley) ChemicalReaction code not calling setNoImplicit() when H counts are set. (github issue #1544 from greglandrum) Fixes failing build with MSVC (github pull #1547 from ptosco) Kekulization error with cores from R-Group Decomposition (github issue #1550 from greglandrum) Fixes double free for Dict::update (github pull #1571 from bp-kelley) QueryAtom::setQuery() should delete the old query first (github pull #1604 from greglandrum