[Rdkit-announce] 2017.03 (Q1 2017) RDKit Release

[Greg L. <gre...@gm...>]

I'm pleased to announce that the next version of the RDKit -- 2017.03
(a.k.a. Q1 2017) -- is released. The release notes are below.

The release files are on the github release page:
*https://github.com/rdkit/rdkit/releases/tag/Release_2017_03_1
<https://github.com/rdkit/rdkit/releases/tag/Release_2017_03_1>*

We are in the process of updating the conda build scripts to reflect the
new version and uploading the binaries to anaconda.org (https://anaconda
.org/rdkit).
The plan for conda binaries for this release is:
Linux 64bit: python 2.7, 3.5, 3.6
Mac OS 64bit: python 2.7, 3.5, 3.6
Windows 64bit: python 2.7, 3.5, 3.6
Windows 32bit: python 2.7

Some things that will be finished over the next couple of days:
- The conda build scripts will be updated to reflect the new version and
new conda builds will be available in the RDKit channel at anaconda.org (
https://anaconda.org/rdkit).
- The homebrew script
- The online version of the documentation at rdkit.org

Thanks to everyone who submitted bug reports and suggestions for this
release!

Please let me know if you find any problems with the release or have
suggestions for the next one, which is scheduled for September 2017.

Best Regards,
-greg

# 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