rdkit/rdkit: 2017_03_1 (Q1 2017) Release

Release_2017.03.1

(Changes relative to Release_2016.09.1)

Important

• The fix for bug #879 changes the definition of the layered fingerprint. This means that all database columns using layered fingerprints as well as all substructure search indices should be rebuilt.
• All C++ library names now start with RDKit (see #1349).

Acknowledgements:

Brian Cole, David Cosgrove, JW Feng, Berend Huisman, Peter Gedeck, 'i-tub', Jan Holst Jensen, Brian Kelley, Rich Lewis, Brian Mack, Eloy Felix Manzanares, Stephen Roughley, 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 <boost/cstdint.hpp> 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)
• all-atom RMSD used to prune conformers in embedding code, docs say heavy-atom RMSD is used (github issue #1227 from greglandrum)
  • FindPotentialStereoBonds() failure (github issue #1230 from greglandrum)
• make the Pandas version checking more robust (github pull #1239 from greglandrum)
• Failure to embed larger aromatic rings (github issue #1240 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)
• Bond from reactant not added to product (github issue #1387 from greglandrum)
• int32_t with no namespace in MolPickler.h (github issue #1388 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 instead