rdkit/rdkit: 2017_03_1b1 (Q1 2017) Release

Release_2017.03.1 (Changes relative to Release_2016.09.1) Important The fix for bug #879 requires that all substructure search indices be rebuilt. All C++ library names now start with RDKit (see #1349). Acknowledgements: Brian Cole, David Cosgrove, Berend Huisman, Peter Gedeck, 'i-tub', Jan Holst Jensen, Brian Kelley, Rich Lewis, Brian Mack, Eloy Felix Manzanares, Roger Sayle, Nadine Schneider, Gregor Simm, Matt Swain, Paolo Tosco, Riccardo Vianello, Hsiao Yi Highlights: It's now possible (though not the default) to pickle molecule properties with the molecule There's a new, and still in development, "Getting started in C++" document. A lot of the Python code has been cleaned up New Features and Enhancements: Add removeHs option to MolFromSmiles() (github issue #554 from greglandrum) support a fixed bond length in the MolDraw2D code (github issue #565 from greglandrum) Pattern fingerprint should set bits for single-atom fragments. (github issue #879 from greglandrum) Reviewed unit tests of rdkit.ML - coverage now 63.1% (github pull #1148 from gedeck) Reviewed unit tests of rdkit.VLib - coverage now 67.1% (github pull #1149 from gedeck) Removes exponetial numBonds behavior (github pull #1154 from bp-kelley) Exposes normalize option to GetFlattenedFunctionalGroupHierarchy (github pull #1165 from bp-kelley) Expose RWMol.ReplaceBond to Python (github pull #1174 from coleb) Review of rdkit.Chem.Fraggle code (github pull #1184 from gedeck) Add support for dative bonds. (github pull #1190 from janholstjensen) Python 3 compatibility (issue #398) (github pull #1192 from gedeck) 1194: Review assignments of range in Python code (github pull #1195 from gedeck) Moved GenerateDepictionMatching[23]DStructure from Allchem.py to C++ (github pull #1197 from DavidACosgrove) Review rdkit.Chem.pharm#D modules (github pull #1201 from gedeck) Find potential stereo bonds should return any (github pull #1202 from coleb) Gedeck coverage sim div filters (github pull #1208 from gedeck) Gedeck review unit test inchi (github pull #1209 from gedeck) Coverage rdkit.Dbase (github pull #1210 from gedeck) Coverage rdkit.DataStructs (github pull #1211 from gedeck) UnitTestPandas works on Python3 (github pull #1213 from gedeck) Cleanup and improvement to test coverage of PandasTools (github pull #1215 from gedeck) Cleanup of rdkit.Chem.Fingerprints (github pull #1217 from gedeck) Optimization of UFF and MMFF forcefields (github pull #1218 from ptosco) Support for ChemAxon Extended SMILES/SMARTS (github issue #1226 from greglandrum) Improved test coverage for rdkit.Chem.Fingerprints (github pull #1243 from gedeck) Adding a few tests for coverage utils (github pull #1244 from gedeck) Make Pandastools modifications to generic RDkit functionality more obvious (github pull #1245 from gedeck) Rename test file and cleanup (github pull #1246 from gedeck) Review of rdkit.Chem.MolKey (github pull #1247 from gedeck) Review tests in rdkit.Chem.SimpleEnum (github pull #1248 from gedeck) Move execution of DocTests in rdkit.Chem into a UnitTest file (github pull #1256 from gedeck) Review code in rdkit.Chem.Suppliers (github pull #1258 from gedeck) Add python wraps (github pull #1259 from eloyfelix) Rename file UnitTestDocTests in rdkitChem (github pull #1263 from gedeck) Gedeck rdkit chem unit test surf (github pull #1267 from gedeck) cleanup rdkit.Chem.Lipinski and rdkit.Chem.GraphDescriptors (github pull #1268 from gedeck) Address Issue #1214 (github pull #1275 from gedeck) Dev/pickle properties (github pull #1277 from bp-kelley) Remove unused test boilerplate (github pull #1288 from gedeck) Refactored the script SDFToCSV (github pull #1289 from gedeck) Dev/rdmmpa api update (github pull #1291 from bp-kelley) Fix/rogers fixes (github pull #1293 from bp-kelley) Remove expected (error) output during unit tests (github pull #1298 from gedeck) Refactor FeatFinderCLI and add unittests (github pull #1299 from gedeck) Refactor BuildFragmentCatalog - 1 (github pull #1300 from gedeck) Review of rdkit.Chem code - 1 (github pull #1301 from gedeck) Minor cleanup in rdkit.Chem (github pull #1304 from gedeck) Start using py3Dmol in the notebook (github pull #1308 from greglandrum) Add the option to match formal charges to FMCS (github pull #1311 from greglandrum) Review of rdkit.Chem.Subshape (github pull #1313 from gedeck) Review rdkit.Chem.UnitTestSuppliers (github pull #1315 from gedeck) Add cis/trans tags to double bonds (github pull #1316 from greglandrum) MolDraw2D: make custom atom labels easier (github issue #1322 from greglandrum) MolDraw2D: allow DrawMolecules() to put all molecules in one pane (github issue #1325 from greglandrum) Refactoring rdkit.Chem.SATIS (github pull #1329 from gedeck) Minor cleanup of rdkit.Chem.SaltRemover (github pull #1330 from gedeck) Review rdkit.chem.FunctionalGroups and rdkit.Chem.UnitTestSuppliers (github pull #1331 from gedeck) Get the tests working with python 3.6 (github pull #1332 from greglandrum) add "RDKit" to the beginning of all library names (github pull #1349 from greglandrum) Fix/sanitizerxn merge hs (github pull #1367 from bp-kelley) Update AllChem.py (github pull #1378 from BerendHuisman) New Java Wrapper Features: Bug Fixes: python2 code in python3 install (github issue #1042 from kcamnairb) Fixes #1162 (resMolSupplierTest failing with boost 1.62) (github pull #1166 from ptosco) add missing $RDKLIBS to cartridge build (github pull #1167 from rvianello) Include for uint64_t (github pull #1168 from mcs07) replace std::map::at with std::map::find (github pull #1169 from mcs07) Fix Trajectory GetSnapshot behaviour after Clear (github pull #1172 from mcs07) Add Contrib dir to RDPaths (github pull #1176 from mcs07) RDThreads.h: No such file or directory (github issue #1177 from gncs) this now builds with vs2008 (github pull #1178 from greglandrum) Add information on building RDkit on macOS using conda (github pull #1180 from gedeck) new sequence capabilities not available from either Python or Java (github issue #1181 from greglandrum) Gets the reaction sanitization code working correctly on 32bit systems (github pull #1187 from greglandrum) Adds RDProps to c# wrapper (github pull #1188 from bp-kelley) fix compatibility with PostgreSQL 9.2 (github pull #1189 from greglandrum) Fixes memory leak in closeCheckMolFiles, fixes valgrind read issue in… (github pull #1200 from bp-kelley) Support valences of 4 and 6 for Te (github issue #1204 from hsiaoyi0504) Stereochemistry not output to SMILES when allHsExplicit=True (github issue #1219 from greglandrum) Remove deprecated string module functions (github pull #1223 from gedeck) Turns on -fpermissive for gcc >= 6 and boost < 1.62 (github pull #1225 from bp-kelley) FindPotentialStereoBonds() failure (github issue #1230 from greglandrum) make the Pandas version checking more robust (github pull #1239 from greglandrum) fixed build failure on Windows due to missing link to library (github pull #1241 from ptosco) fixed a test failure on Windows due to CR+LF encoding (github pull #1242 from ptosco) MolFromMolBlock sanitizing when it should not be (github issue #1251 from greglandrum) PMI descriptors incorrect (github issue #1262 from greglandrum) Reactions don't modify isotope unless chemical element is specified for the product (github issue #1266 from i-tub) Do not include the 3D descriptors in rdkit.Chem.Descriptors.descList (github issue #1287 from greglandrum) ring stereochemistry perception failing for spiro centers (github issue #1294 from greglandrum) Property pickling test failing on windows (github issue #1348 from greglandrum) Fixes overflow error in boost when compiler chooses int for enum type (github pull #1351 from bp-kelley) Hybridization type of group 1 metals (github issue #1352 from richlewis42) bad python docs for some distance geometry functions (github issue #1385 from greglandrum) Contrib updates: Chemical reaction role assignment code from Nadine Schneider (github pull #1185 from NadineSchneider) Deprecated code (to be removed in a future release): rdkit.Chem.MCS: please use rdkit.Chem.rdFMCS instea