2019_03_1b1 (Q1 2019) Release

Release_2019.03.1

(Changes relative to Release_2018.09.1)

REALLY IMPORTANT ANNOUNCEMENT

• As of this realease (2019.03.1) the RDKit no longer supports Python 2. Please
  read this rdkit-discuss post to learn what your options are if you need to
  keep using Python 2:
  https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg08354.html

Backwards incompatible changes

• The fix for github #2245 means that the default behavior of the MaxMinPicker
  is now truly random. If you would like to reproduce the previous behavior,
  provide a seed value of 42.
• The uncharging method in the MolStandardizer now attempts to generate
  canonical results for a given molecule. This may result in different output
  for some molecules.

Highlights:

• There's now a Japanese translation of large parts of the RDKit documentation
• SGroup data can now be read from and written to Mol/SDF files
• The enhanced stereo handling has been improved: the information is now
  accessible from Python, EnumerateStereoisomers takes advantage of it, and it
  can be read from and written to CXSmiles

Acknowledgements:

Michael Banck, Francois Berenger, Thomas Blaschke, Brian Cole, Andrew Dalke,
Bakary N'tji Diallo, Guillaume Godin, Jan Holst Jensen, Sunhwan Jo, Brian
Kelley, Petr Kubat, Karl Leswing, Susan Leung, John Mayfield, Adam Moyer, Dan
Nealschneider, Noel O'Boyle, Stephen Roughley, Takayuki Serizawa, Gianluca
Sforna, Ricardo Rodriguez Schmidt, Matt Swain, Paolo Tosco, Ricardo Vianello,
'John-Videogames', 'magattaca', 'msteijaert', 'paconius', 'sirbiscuit'

Bug Fixes:

• PgSQL: fix boolean definitions for Postgresql 11
  (github pull #2129 from pkubatrh)
• update fingerprint tutorial notebook
  (github pull #2130 from greglandrum)
• Fix typo in RecapHierarchyNode destructor
  (github pull #2137 from iwatobipen)
• SMARTS roundtrip failure
  (github issue #2142 from mcs07)
• Error thrown in rdMolStandardize.ChargeParent
  (github issue #2144 from paconius)
• SMILES parsing inconsistency based on input order
  (github issue #2148 from coleb)
• MolDraw2D: line width not in python wrapper
  (github issue #2149 from greglandrum)
• Missing Python API Documentation
  (github issue #2158 from greglandrum)
• PgSQL: mol_to_svg() changes input molecule.
  (github issue #2174 from janholstjensen)
• Remove Unicode From AcidBasePair Name
  (github pull #2185 from lilleswing)
• Inconsistent treatment of [as] in SMILES and SMARTS
  (github issue #2197 from greglandrum)
• RGroupDecomposition fixes, keep userLabels more robust onlyMatchAtRGroups
  (github pull #2202 from bp-kelley)
• Fix TautomerTransform in operator=
  (github pull #2203 from bp-kelley)
• testEnumeration hangs/takes where long on 32bit architectures
  (github issue #2209 from mbanck)
• Silencing some Python 3 warning messages
  (github pull #2223 from coleb)
• removeHs shouldn't remove atom lists
  (github issue #2224 from rvianello)
• failure round-tripping mol block with Q atom
  (github issue #2225 from rvianello)
• problem round-tripping mol files that include bond topology info
  (github issue #2229 from rvianello)
• aromatic main-group atoms written to SMARTS incorrectly
  (github issue #2237 from greglandrum)
• findPotentialStereoBonds() stopping too early
  (github issue #2244 from greglandrum)
• MinMax Diversity picker seeding shows deterministic / non-random behaviour
  (github issue #2245 from sroughley)
• Fix to serialize binary strings
  (github pull #2264 from bp-kelley)
• Recognize N in three-membered rings as potentially chiral
  (github issue #2268 from greglandrum)
• Failure when parsing mol block with M PXA
  (github issue #2277 from greglandrum)
• query-query matching failing for atoms constructed from SMARTS
  (github issue #2299 from greglandrum)
• SMILES parsing fails for dative ring closures
  (github issue #2303 from greglandrum)
• Missing Dict.h overload: std::string Dict::getValstd::string
  (github issue #2308 from greglandrum)
• fix a problem with the random pickers test
  (github pull #2310 from greglandrum)
• AddHs() using 3D coordinates with 2D conformations
  (github pull #2328 from greglandrum)
• change to make the SWIG builds work on windows
  (github pull #2340 from greglandrum)
• uncharger behaves differently on molecules constructed from mol blocks and SMILES
  (github issue #2346 from greglandrum)
• Memory Error When Writing ToBinary With "AllProps"
  (github issue #2352 from atom-moyer)
• Seg fault on init if RDBASE is not set
  (github issue #2368 from greglandrum)
• PandasTools.FrameToGridImage() fails with SVG output
  (github issue #2380 from greglandrum)
• ClusterMols.GetDistanceMatrix throws a type error in Python 3
  (github issue #2387 from John-Videogames)

New Features and Enhancements:

• Allow access to Enhanced Stereochemistry information from Python
  (github issue #2108 from d-b-w)
• Adopt EnumerateStereoisomers to use extended stereo
  (github issue #2109 from greglandrum)
• Enable ctest -T memcheck
  (github pull #2113 from ricrogz)
• Support for parsing/writing SGroups in SD Mol files
  (github pull #2138 from ricrogz)
• Rename the #define _DEBUG to MMPA_DEBUG in mmpa.cpp
  (github pull #2140 from baoilleach)
• MolDraw2D: line width should be controlled by MolDrawOptions
  (github issue #2151 from greglandrum)
• Some refactoring of the distance geometry code
  (github pull #2153 from greglandrum)
• Less warnings
  (github pull #2155 from UnixJunkie)
• ShapeTverskyIndex python function
  (github pull #2156 from susanhleung)
• Skip compound if smiles conversion fails
  (github pull #2168 from msteijaert)
• Fix #2176: InChI functions should return NULL on un-InChI-able input molecules.
  (github pull #2177 from janholstjensen)
• Update installation instructions for Linux
  (github pull #2181 from sirbiscuit)
• Update CMake rules to find external coorgen & maeparser libs
  (github pull #2184 from ricrogz)
• Update to use the travis Xenial environment
  (github pull #2200 from greglandrum)
• Do not allow PandasTools to overwrite pandas settings
  (github pull #2206 from sirbiscuit)
• re-enable (and update) the file parser tests
  (github pull #2208 from greglandrum)
• Added documentation files written in Japanese into Book directory
  (github pull #2210 from magattaca)
• Add C++ convenience function for drawing ROMols
  (github issue #2220 from greglandrum)
• Change boost int types to std types
  (github pull #2233 from bp-kelley)
• Added exports for SGroup functions
  (github pull #2242 from ricrogz)
• Use coordMap when starting embedding from random coords
  (github issue #2246 from greglandrum)
• Improve interactivity of output SVG
  (github pull #2253 from greglandrum)
• Add options for substructure searching
  (github pull #2254 from greglandrum)
• keep extra information about bonds from Mol files
  (github pull #2260 from greglandrum)
• Allow converting mol blocks directly to InChI
  (github pull #2262 from greglandrum)
• Patch/pains updates
  (github pull #2272 from johnmay)
• add warning for 2D conformations flagged as 3D
  (github pull #2273 from greglandrum)
• Store extra CXSMILES data as a property
  (github pull #2281 from ricrogz)
• Parse enhanced stereo information from CXSMILES
  (github pull #2282 from ricrogz)
• Robustify parsing of CTABs and SGROUPs
  (github pull #2283 from greglandrum)
• Write enhanced stereo to cxsmiles
  (github pull #2290 from greglandrum)
• Allow custom type-handlers in the RDProps interface
  (github pull #2293 from bp-kelley)
• Add serialization to SubstructLibrary
  (github pull #2295 from bp-kelley)
• support reading/writing atom props from SD files
  (github pull #2297 from greglandrum)
• Add test for issue #2285, fix molbundle test
  (github pull #2301 from bp-kelley)
• Update maeparser & coordgen libraries
  (github pull #2302 from ricrogz)
• Mem errors clean up
  (github pull #2305 from ricrogz)
• Add definition of MolFragmentToCXSmiles
  (github pull #2307 from greglandrum)
• Doc update
  (github pull #2312 from greglandrum)
• Adds gzstream stream, exposes to swig
  (github pull #2314 from bp-kelley)
• Remove a bunch of Python2-related warts
  (github pull #2315 from greglandrum)
• some much-needed optimization work on the new property lists
  (github pull #2317 from greglandrum)
• Build warnings revisited
  (github pull #2318 from ricrogz)
• change bogus "3D" to "2D" in a test file
  (github pull #2319 from greglandrum)
• Allow copying atoms in Python
  (github pull #2322 from d-b-w)
• fixes an r-group symmetrization problem
  (github pull #2324 from greglandrum)
• simple docstring fix
  (github pull #2326 from sunhwan)
• allow using system's catch2 for tests
  (github pull #2327 from giallu)
• Python wrap DetectAtomStereoChemistry from MolFileStereochem.h
  (github issue #2329 from d-b-w)
• switch to using cmake to handle the C++ spec
  (github pull #2334 from greglandrum)
• WIP: optional integration with YAeHMOP
  (github pull #2335 from greglandrum)
• Exposes substructlibrary to swig
  (github pull #2337 from bp-kelley)
• Add a skip_all_if_match option to the FragmentRemover
  (github pull #2338 from greglandrum)
• Dev/general csharp fixes
  (github pull #2341 from bp-kelley)
• Add a read-only Python wrapper for SGroups
  (github pull #2343 from greglandrum)
• Expose RGroupDecomposition to SWIG
  (github pull #2345 from greglandrum)
• update debian build script to python3
  (github pull #2350 from UnixJunkie)
• add GetStereoIsomerCount() function to EnumerateStereoisomers
  (github pull #2354 from greglandrum)
• Update coordgenlibs to v1.2.2
  (github pull #2355 from ricrogz)
• Small fixes to get DLLs to build on Windows
  (github p...

2018_09_3 (Q3 2018) Release

Release_2018.09.3

(Changes relative to Release_2018.09.2)

Acknowledgements:

Michael Banck, Brian Cole, Brian Kelley, Adam Moyer

Bug Fixes:

• SMILES parsing inconsistency based on input order
  (github #2148 from coleb)
• RGroupDecomposition fixes, keep userLabels more robust onlyMatchAtRGroups
  (github #2202 from bp-kelley)
• testEnumeration hangs/takes where long on 32bit architectures
  (github #2209 from mbanck)
• findPotentialStereoBonds() stopping too early
  (github #2244 from greglandrum)
• query-query matching failing for atoms constructed from SMARTS
  (github #2299 from greglandrum)
• SMILES parsing fails for dative ring closures
  (github #2303 from greglandrum)
• Missing Dict.h overload: std::string Dict::getValstd::string
  (github #2308 from greglandrum)
• fixes #908
  (github #2328 from greglandrum)
• uncharger behaves differently on molecules constructed from mol blocks and SMILES
  (github #2346 from greglandrum)
• Memory Error When Writing ToBinary With "AllProps"
  (github #2352 from atom-moyer)

2018_09_2 (Q3 2018) Release

Release_2018.09.2

(Changes relative to Release_2018.09.1)

Acknowledgements:

Brian Cole, Jan Holst Jensen, Brian Kelley, Petr Kubat, Takayuki Serizawa,
Matt Swain, Riccardo Vianello, 'paconius'

Bug Fixes:

• PgSQL: fix boolean definitions for Postgresql 11
  (github #2129 from pkubatrh)
• update fingerprint tutorial notebook
  (github #2130 from greglandrum)
• Fix typo in RecapHierarchyNode destructor
  (github #2137 from iwatobipen)
• SMARTS roundtrip failure
  (github #2142 from mcs07)
• Error thrown in rdMolStandardize.ChargeParent
  (github #2144 from paconius)
• MolDraw2D: line width not in python wrapper
  (github #2149 from greglandrum)
• Missing Python API Documentation
  (github #2158 from greglandrum)
• PgSQL: mol_to_svg() changes input molecule.
  (github #2174 from janholstjensen)
• Inconsistent treatment of [as] in SMILES and SMARTS
  (github #2197 from greglandrum)
• Fix TautomerTransform in operator=
  (github #2203 from bp-kelley)
• Silencing some Python 3 warning messages
  (github #2223 from coleb)
• removeHs shouldn't remove atom lists
  (github #2224 from rvianello)
• failure round-tripping mol block with Q atom
  (github #2225 from rvianello)
• problem round-tripping mol files that include bond topology info
  (github #2229 from rvianello)
• aromatic main-group atoms written to SMARTS incorrectly
  (github #2237 from greglandrum)

2018_09_1 (Q3 2018) Release

Release_2018.09.1

(Changes relative to Release_2018.03.1)

Deprecations

• As part of the changes and cleaning up done for #1836 many of the #defines
  used in the RDKit have been renamed.
  • USE_BUILTIN_POPCOUNT -> RDK_OPTIMIZE_NATIVE
  • RDK_THREADSAFE_SSS -> RDK_BUILD_THREADSAFE_SSS
  • BUILD_COORDGEN_SUPPORT -> RDK_BUILD_COORDGEN_SUPPORT
  • BUILD_AVALON_SUPPORT -> RDK_BUILD_AVALON_SUPPORT
  • BUILD_INCHI_SUPPORT -> RDK_BUILD_INCHI_SUPPORT
  • BUILD_SLN_SUPPORT -> RDK_BUILD_SLN_SUPPORT
  • RDK_CAIRO_BUILD -> RDK_BUILD_CAIRO_SUPPORT

Documentation updates

We have moved to using Sphinx's autodoc to create the Python API documentation.
epydoc, the tool we used to use, is no longer actively developed and only supports
Python2. There will undoubtedly be problems associated with the change; if you notice
anything missing in the documetation or something that's really badly formatted,
please either let us know or submit a PR with a fix.

Backwards incompatible changes

This release includes a set of changes to make the default arguments to common
functions less error prone (github #1679).

• GetAtomSmiles() now generates isomeric SMILES by default.
• The ringMatchesRingOnly option to the FindMCS() function now applies to
  atom-atom matches as well as bond-bond matches.
• The Python functions EmbedMolecule() and EmbedMultipleConfs() now use the
  ETKDG algorithm by default instead of standard distance geometry.

Highlights:

• This release includes two contributions from the Google Summer of Code:
  • A new generalized fingerprint generator.
  • An integration/port of MolVS to the core RDKit.
    The API on both of these may change a bit with future releases.
• The rdkit.Chem.Draw module now includes functions for depicting fingerprint
  bits. Morgan and RDKit fingerprints are currently supported.

Acknowledgements:

Boran Adas, Francois Berenger, Thomas Blaschke, Brian Cole, Andrew Dalke, Guillaume Godin,
Brice Hoff, Brian Kelley, Karl Leswing, Susan Leung, Pat Lorton, Josh Meyers, Hirotomo Moriwaki,
Dan Nealschneider, Noel O'Boyle, Pavel Raiskup, Sereina Riniker, Ricardo Rodriguez Schmidt,
Stephen Roughley, Roger Sayle, Takayuki Serizawa, Rim Shayakhmetov, Gregory Simm, Jon Sorenson,
Matt Swain, Kiran Telukunta, Paulo Tosco, Alain Vaucher, Maciej Wójcikowski, '0xDECAFC0FFEE',
'jaechanglim', 'paconius'

Contrib updates:

• The FastCluster code has been updated.

New Features and Enhancements:

• expose MolChemicalFeature.{get,set}ActiveConformer() to python
  (github issue #1636 from greglandrum)
• added Scripts/create_deb_packages.sh
  (github pull #1655 from UnixJunkie)
• Start to use Catch2 for new tests
  (github pull #1732 from greglandrum)
• Switch DbCLI scripts from optparse to argparse
  (github issue #1778 from greglandrum)
• Add EEM partial charges
  (github pull #1828 from greglandrum)
• Add header file providing access to RDKit compile time flags
  (github issue #1836 from greglandrum)
• add control over the coordinate precision to coordgen
  (github pull #1847 from greglandrum)
• Add Properties interface to ChemicalReactions
  (github pull #1848 from greglandrum)
• Switch Python API documentation generation over to Sphinx autodoc
  (github pull #1849 from greglandrum)
• expose MolOps::assignStereochemistryFrom3D() to Python
  (github issue #1850 from greglandrum)
• bivariate_normal deprecation in mlab.py of matplotlib
  (github issue #1851 from telukir)
• Expose minAtomRingSize() and minBondRingSize() to Python wrappers
  (github pull #1859 from mwojcikowski)
• enable building DLLs on Windows
  (github pull #1861 from ptosco)
• Fix compatibility with Boost 1.67+
  (github pull #1864 from mcs07)
• Don't manually set RDConfig paths in conda env
  (github pull #1865 from mcs07)
• Make svg xmlns prefix use more consistent
  (github pull #1866 from mcs07)
• Add custom 3D Descriptors
  (github pull #1867 from greglandrum)
• Add initial Maestro format Supplier using maeparser library
  (github pull #1872 from lorton)
• add queryAtomNonHydrogenDegree() query operation
  (github issue #1873 from greglandrum)
• Add an auto-populated file with cmake config options
  (github pull #1874 from greglandrum)
• Custom property VSA
  (github pull #1884 from sriniker)
• Swap maeparser and coordgen dependencies to use releases
  (github issue #1887 from greglandrum)
• expose MolDraw2DSVG.tagAtoms() to python
  (github pull #1897 from greglandrum)
• allow the cleanup step of Mol2 parsing to be disabled
  (github pull #1898 from greglandrum)
• Allow Atom.GetAtomSmarts() to return isomeric SMILES
  (github pull #1902 from greglandrum)
• Allow coordgen and maeparser to be built as static libraries
  (github pull #1909 from ptosco)
• Support reaction_to_svg() in cartridge
  (github issue #1916 from greglandrum)
• Addresses several minor warning messages during the build
  (github pull #1935 from d-b-w)
• Some optimization of the queries constructed from SMARTS
  (github pull #1940 from greglandrum)
• Add ring/chain match constraints options to AdjustQueryParameters()
  (github issue #1943 from greglandrum)
• roc calculation naming problem
  (github pull #1975 from 0xDECAFC0FFEE)
• Fingerprinting functions should call assignStereochemistry() when necessary
  (github issue #1993 from bricehoff)
• Dev/GSOC2018_MolVS_Integration
  (github pull #2002 from susanhleung)
• GSoC 2018 - Fingerprints
  (github pull #2005 from Boranadas)
• port fingerprint bit rendering code from CheTo
  (github pull #2008 from greglandrum)
• PgSQL: add support for PostgreSQL_CONFIG cmake var
  (github pull #2014 from praiskup)
• Add missing boost header for v1.64
  (github pull #2016 from gncs)
• Enhanced stereo read/write support in SDF files.
  (github pull #2022 from d-b-w)
• IPythonConsole hooks should copy the original docstring
  (github issue #2025 from adalke)
• Allow dumping interchange information into SVG files
  (github pull #2030 from greglandrum)
• MCS: add test for ring--non-ring matches at the atom level
  (github issue #2034 from greglandrum)
• Ability to generate a list of possible smiles representation for a given molecule
  (github issue #2042 from thegodone)
• add scoring test (relevant to #1975)
  (github pull #2064 from greglandrum)
• actually run the SmilesWriterNoNames() test
  (github pull #2067 from greglandrum)
• Add a default for maximum products generated by a reaction (maxProduc…
  (github pull #2069 from bp-kelley)
• Add user-defined literals for parsing SMILES and SMARTS
  (github pull #2070 from greglandrum)
• move rdInfoLog to stderr
  (github pull #2073 from greglandrum)
• add confId argument to MolChemicalFeatureFactor::getFeaturesForMol()
  (github issue #2077 from greglandrum)
• Expose a CMake flag to build RDKit with -rpath
  (github pull #2084 from coleb)
• Dev/expose setquery to python
  (github pull #2088 from bp-kelley)
• Updated .gitignore with files generated outside of build directory.
  (github pull #2095 from ricrogz)
• Address compile warnings & trivial improvements
  (github pull #2097 from ricrogz)
• Coordgen: stop printing Templates location
  (github pull #2102 from greglandrum)
• Update Docs For CalcBEDROC
  (github pull #2103 from lilleswing)

Bug Fixes:

• Cannot find rings for ChEBI 50252
  (github issue #299 from greglandrum)
• Feature request: #defines to test RDKit version
  (github issue #1454 from baoilleach)
• Atoms in residue read from pdb lose their AtomPDBResidueInfo after reaction (Bug)
  (github issue #1632 from hjuinj)
• SMARTS parse failure for some queries involving Hs
  (github issue #1719 from greglandrum)
• Conformer indexing bug in RDFreeSASA.cpp?
  (github issue #1786 from paconius)
• allow libs to not be installed
  (github pull #1832 from greglandrum)
• RWMol::addAtom(Atom,bool) missing from Java wrappers
  (github issue #1837 from greglandrum)
• RWMol::clear now calls ROMol::initMol
  (github pull #1844 from bp-kelley)
• Allow types.h to be included in applications that use /D_USE_MATH_DEFINES
  (github pull #1846 from d-b-w)
• Fixes failing Python tests on Windows
  (github pull #1855 from ptosco)
• Allow building on cygwin using -std=c++11
  (github pull #1856 from greglandrum)
• Stop using the cmake Boost:: targets
  (github pull #1858 from greglandrum)
• R-group Decomposition: allow H replacements when matchOnlyAtRgroups is set
  (github pull #1871 from bp-kelley)
• Mark cartridge functions as being parallel safe
  (github issue #1886 from greglandrum)
• Fixes locale handling on Windows
  (github pull #1892 from ptosco)
• get the pandas tests working with pandas 0.23
  (github pull #1896 from greglandrum)
• "make install" appears to miss RDBoost/export.h
  (github issue #1903 from baoilleach)
• Fix curl fallback for downloading files
  (github pull #1904 from d-b-w)
• Bond stereo information not output to SMARTS
  (github issue #1906 from greglandrum)
• Library .so names missing RDKit?
  (github issue #1913 from baoilleach)
• Negated atom number queries in SMARTS should not set atomic number of query atom
  (github issue #1920 from greglandrum)
• memory leak in Get3DDistanceMatrix
  (github issue #1924 from jaechanglim)
• Atom with bond to itself is accepted by the SMILES parser.
  (github issue #1925 from tblaschke)
• Possibly incorrect aromatic SMILES generated for structure
  (github issue #1928 from baoilleach)
• Using the coordgen library seems to cause a seg fault
  (github issue #1929 from JoshuaMeyers)
• Aromaticity failure in 7-ring with charged radical carbon
  (github issue #1936 from bp-kelley)
• Fix embarassing bug, check the counter each iteration
  (github pull #1939 from bp-kelley)
  -...

2018_09_1b1 (Q3 2018) Release

Release_2018.09.1

(Changes relative to Release_2018.03.1)

Deprecations

• As part of the changes and cleaning up done for #1836 many of the #defines
  used in the RDKit have been renamed.
  • USE_BUILTIN_POPCOUNT -> RDK_OPTIMIZE_NATIVE
  • RDK_THREADSAFE_SSS -> RDK_BUILD_THREADSAFE_SSS
  • BUILD_COORDGEN_SUPPORT -> RDK_BUILD_COORDGEN_SUPPORT
  • BUILD_AVALON_SUPPORT -> RDK_BUILD_AVALON_SUPPORT
  • BUILD_INCHI_SUPPORT -> RDK_BUILD_INCHI_SUPPORT
  • BUILD_SLN_SUPPORT -> RDK_BUILD_SLN_SUPPORT
  • RDK_CAIRO_BUILD -> RDK_BUILD_CAIRO_SUPPORT

Backwards incompatible changes

This release includes a set of changes to make the default arguments to common
functions less error prone (github #1679).

• GetAtomSmiles() now generates isomeric SMILES by default.
• The ringMatchesRingOnly option to the FindMCS() function now applies to
  atom-atom matches as well as bond-bond matches.
• The Python functions EmbedMolecule() and EmbedMultipleConfs() now use the
  ETKDG algorithm by default instead of standard distance geometry.

Highlights:

• This release includes two contributions from the Google Summer of Code:
  • A new generalized fingerprint generator.
  • An integration/port of MolVS to the core RDKit.
    The API on both of these may change a bit with future releases.
• The rdkit.Chem.Draw module now includes functions for depicting fingerprint
  bits. Morgan and RDKit fingerprints are currently supported.

Acknowledgements:

Boran Adas, Francois Berenger, Thomas Blaschke, Brian Cole, Andrew Dalke, Guillaume Godin, Brice Hoff, Brian Kelley, Karl Leswing, Susan Leung, Pat Lorton, Josh Meyers, Hirotomo Moriwaki, Dan Nealschneider, Noel O'Boyle, Pavel Raiskup, Sereina Riniker, Ricardo Rodriguez Schmidt, Stephen Roughley, Roger Sayle, Rim Shayakhmetov, Gregory Simm, Jon Sorenson, Matt Swain, Kiran Telukunta, Paulo Tosco, Alain Vaucher, Maciej Wójcikowski, '0xDECAFC0FFEE', 'jaechanglim', 'paconius'

Contrib updates:

• The FastCluster code has been updated.

New Features and Enhancements:

• expose MolChemicalFeature.{get,set}ActiveConformer() to python
  (github issue #1636 from greglandrum)
• added Scripts/create_deb_packages.sh
  (github pull #1655 from UnixJunkie)
• Start to use Catch2 for new tests
  (github pull #1732 from greglandrum)
• Switch DbCLI scripts from optparse to argparse
  (github issue #1778 from greglandrum)
• Add EEM partial charges
  (github pull #1828 from greglandrum)
• Add header file providing access to RDKit compile time flags
  (github issue #1836 from greglandrum)
• add control over the coordinate precision to coordgen
  (github pull #1847 from greglandrum)
• Add Properties interface to ChemicalReactions
  (github pull #1848 from greglandrum)
• Switch Python API documentation generation over to Sphinx autodoc
  (github pull #1849 from greglandrum)
• expose MolOps::assignStereochemistryFrom3D() to Python
  (github issue #1850 from greglandrum)
• bivariate_normal deprecation in mlab.py of matplotlib
  (github issue #1851 from telukir)
• Expose minAtomRingSize() and minBondRingSize() to Python wrappers
  (github pull #1859 from mwojcikowski)
• enable building DLLs on Windows
  (github pull #1861 from ptosco)
• Fix compatibility with Boost 1.67+
  (github pull #1864 from mcs07)
• Don't manually set RDConfig paths in conda env
  (github pull #1865 from mcs07)
• Make svg xmlns prefix use more consistent
  (github pull #1866 from mcs07)
• Add custom 3D Descriptors
  (github pull #1867 from greglandrum)
• Add initial Maestro format Supplier using maeparser library
  (github pull #1872 from lorton)
• add queryAtomNonHydrogenDegree() query operation
  (github issue #1873 from greglandrum)
• Add an auto-populated file with cmake config options
  (github pull #1874 from greglandrum)
• Custom property VSA
  (github pull #1884 from sriniker)
• Swap maeparser and coordgen dependencies to use releases
  (github issue #1887 from greglandrum)
• expose MolDraw2DSVG.tagAtoms() to python
  (github pull #1897 from greglandrum)
• allow the cleanup step of Mol2 parsing to be disabled
  (github pull #1898 from greglandrum)
• Allow Atom.GetAtomSmarts() to return isomeric SMILES
  (github pull #1902 from greglandrum)
• Allow coordgen and maeparser to be built as static libraries
  (github pull #1909 from ptosco)
• Support reaction_to_svg() in cartridge
  (github issue #1916 from greglandrum)
• Addresses several minor warning messages during the build
  (github pull #1935 from d-b-w)
• Some optimization of the queries constructed from SMARTS
  (github pull #1940 from greglandrum)
• Add ring/chain match constraints options to AdjustQueryParameters()
  (github issue #1943 from greglandrum)
• roc calculation naming problem
  (github pull #1975 from 0xDECAFC0FFEE)
• Fingerprinting functions should call assignStereochemistry() when necessary
  (github issue #1993 from bricehoff)
• Dev/GSOC2018_MolVS_Integration
  (github pull #2002 from susanhleung)
• GSoC 2018 - Fingerprints
  (github pull #2005 from Boranadas)
• port fingerprint bit rendering code from CheTo
  (github pull #2008 from greglandrum)
• PgSQL: add support for PostgreSQL_CONFIG cmake var
  (github pull #2014 from praiskup)
• Add missing boost header for v1.64
  (github pull #2016 from gncs)
• Enhanced stereo read/write support in SDF files.
  (github pull #2022 from d-b-w)
• IPythonConsole hooks should copy the original docstring
  (github issue #2025 from adalke)
• Allow dumping interchange information into SVG files
  (github pull #2030 from greglandrum)
• MCS: add test for ring--non-ring matches at the atom level
  (github issue #2034 from greglandrum)
• add scoring test (relevant to #1975)
  (github pull #2064 from greglandrum)
• actually run the SmilesWriterNoNames() test
  (github pull #2067 from greglandrum)
• Add a default for maximum products generated by a reaction (maxProduc…
  (github pull #2069 from bp-kelley)
• Add user-defined literals for parsing SMILES and SMARTS
  (github pull #2070 from greglandrum)
• move rdInfoLog to stderr
  (github pull #2073 from greglandrum)
• add confId argument to MolChemicalFeatureFactor::getFeaturesForMol()
  (github issue #2077 from greglandrum)
• Expose a CMake flag to build RDKit with -rpath
  (github pull #2084 from coleb)
• Dev/expose setquery to python
  (github pull #2088 from bp-kelley)
• Updated .gitignore with files generated outside of build directory.
  (github pull #2095 from ricrogz)
• Address compile warnings & trivial improvements
  (github pull #2097 from ricrogz)
• Coordgen: stop printing Templates location
  (github pull #2102 from greglandrum)
• Update Docs For CalcBEDROC
  (github pull #2103 from lilleswing)

Bug Fixes:

• Cannot find rings for ChEBI 50252
  (github issue #299 from greglandrum)
• Feature request: #defines to test RDKit version
  (github issue #1454 from baoilleach)
• Atoms in residue read from pdb lose their AtomPDBResidueInfo after reaction (Bug)
  (github issue #1632 from hjuinj)
• SMARTS parse failure for some queries involving Hs
  (github issue #1719 from greglandrum)
• Conformer indexing bug in RDFreeSASA.cpp?
  (github issue #1786 from paconius)
• allow libs to not be installed
  (github pull #1832 from greglandrum)
• RWMol::addAtom(Atom,bool) missing from Java wrappers
  (github issue #1837 from greglandrum)
• RWMol::clear now calls ROMol::initMol
  (github pull #1844 from bp-kelley)
• Allow types.h to be included in applications that use /D_USE_MATH_DEFINES
  (github pull #1846 from d-b-w)
• Fixes failing Python tests on Windows
  (github pull #1855 from ptosco)
• Allow building on cygwin using -std=c++11
  (github pull #1856 from greglandrum)
• Stop using the cmake Boost:: targets
  (github pull #1858 from greglandrum)
• R-group Decomposition: allow H replacements when matchOnlyAtRgroups is set
  (github pull #1871 from bp-kelley)
• Mark cartridge functions as being parallel safe
  (github issue #1886 from greglandrum)
• Fixes locale handling on Windows
  (github pull #1892 from ptosco)
• get the pandas tests working with pandas 0.23
  (github pull #1896 from greglandrum)
• "make install" appears to miss RDBoost/export.h
  (github issue #1903 from baoilleach)
• Fix curl fallback for downloading files
  (github pull #1904 from d-b-w)
• Bond stereo information not output to SMARTS
  (github issue #1906 from greglandrum)
• Library .so names missing RDKit?
  (github issue #1913 from baoilleach)
• Negated atom number queries in SMARTS should not set atomic number of query atom
  (github issue #1920 from greglandrum)
• memory leak in Get3DDistanceMatrix
  (github issue #1924 from jaechanglim)
• Atom with bond to itself is accepted by the SMILES parser.
  (github issue #1925 from tblaschke)
• Possibly incorrect aromatic SMILES generated for structure
  (github issue #1928 from baoilleach)
• Using the coordgen library seems to cause a seg fault
  (github issue #1929 from JoshuaMeyers)
• Aromaticity failure in 7-ring with charged radical carbon
  (github issue #1936 from bp-kelley)
• Fix embarassing bug, check the counter each iteration
  (github pull #1939 from bp-kelley)
• RuntimeError when importing rdkit.Chem.Descriptors with Python 3.7
  (github issue #1948 from drkeoni)
• Query features in products of rxn files not properly handled
  (github issue #1950 from greglandrum)
• ReactionToSmarts broken for multi-component templates
  (github issue #1955 from bp-kelley)
• update knime urls in overview.md
  (github pull #1966 from greglandrum)
• CXN extended SMILES labels are not applied to the correct atom in SMILES with explicit H
  (github issue #1968 from baoilleach)
• MolFromSmarts MolToSmarts fails to roundtrip on patte...

2018_03_4 (Q1 2018) Release

Release_2018.03.4

(Changes relative to Release_2018.03.3)

Acknowledgements:

Brian Kelley, Noel O'Boyle, Rim Shayakhmetov, Jon Sorenson

Bug Fixes:

• Possibly incorrect aromatic SMILES generated for structure
  (github issue #1928 from baoilleach)
• Update KNIME URLs in overview.md
  (github pull #1966 from greglandrum)
• CXN extended SMILES labels are not applied to the correct atom in SMILES
  with explicit H
  (github issue #1928 from baoilleach)
• MolFromSmarts MolToSmarts fails to roundtrip on patterns with chirality
  (github issue #1985 from bp-kelley)
• RemoveHs not properly updating double bond stereoatoms
  (github issue #1990 from shayakhmetov)
• Error while parsing empty atom list in Mol files.
  (github issue #2000 from drkeoni)

2018_03_3 (Q1 2018) Release

Release_2018.03.3

(Changes relative to Release_2018.03.2)

Acknowledgements:

Thomas Blaschke, Brian Kelley, Josh Meyers, Dan Nealschneider, Noel O'Boyle,
Jon Sorenson, Paulo Tosco, 'jaechanglim'

Bug Fixes:

• R-group Decomposition: allow H replacements when matchOnlyAtRgroups is set
  (github pull #1871 from bp-kelley)
• Fixes locale handling on Windows
  (github pull #1892 from ptosco)
• get the pandas tests working with pandas 0.23
  (github pull #1896 from greglandrum)
• Fix curl fallback for downloading files
  (github pull #1904 from d-b-w)
• Bond stereo information not output to SMARTS
  (github issue #1906 from greglandrum)
• Library .so names missing RDKit?
  (github issue #1913 from baoilleach)
• Negated atom number queries in SMARTS should not set atomic number of query atom
  (github issue #1920 from greglandrum)
• memory leak in Get3DDistanceMatrix
  (github issue #1924 from jaechanglim)
• Atom with bond to itself is accepted by the SMILES parser.
  (github issue #1925 from tblaschke)
• Using the coordgen library seems to cause a seg fault
  (github issue #1929 from JoshuaMeyers)
• Aromaticity failure in 7-ring with charged radical carbon
  (github issue #1936 from bp-kelley)
• Fix embarassing bug, check the counter each iteration
  (github pull #1939 from bp-kelley)
• RuntimeError when importing rdkit.Chem.Descriptors with Python 3.7
  (github issue #1948 from drkeoni)
• Query features in products of rxn files not properly handled
  (github issue #1950 from greglandrum)
• ReactionToSmarts broken for multi-component templates
  (github issue #1955 from bp-kelley)

2018_03_2 (Q1 2018) Release

Release_2018.03.2

(Changes relative to Release_2018.03.1)

Acknowledgements:

Brian Kelley, Dan Nealschneider, Noel O'Boyle, Stephen Roughley, Roger Sayle,
Paulo Tosco

Bug Fixes:

• Feature request: #defines to test RDKit version
  (github issue #1454 from baoilleach)
• SMARTS parse failure for some queries involving Hs
  (github issue #1719 from greglandrum)
• allow libs to not be installed
  (github pull #1832 from greglandrum)
• RWMol::addAtom(Atom,bool) missing from Java wrappers
  (github issue #1837 from greglandrum)
• RWMol::clear now calls ROMol::initMol
  (github pull #1844 from bp-kelley)
• Allow types.h to be included in applications that use /D_USE_MATH_DEFINES
  (github pull #1846 from d-b-w)
• Fixes failing Python tests on Windows
  (github pull #1855 from ptosco)
• Allow building on cygwin using -std=c++11
  (github pull #1856 from greglandrum)
• Stop using the cmake Boost:: targets
  (github pull #1858 from greglandrum)

2018_03_1 (Q1 2018) Release

Release_2018.03.1

(Changes relative to Release_2017.09.1)

C++11 notes

Starting with this release, the RDKit core C++ code is written in modern C++;
for this release that means C++11. This means that the compilers used to build
it cannot be completely ancient. Here are the minimum tested versions:

• g++ v4.8: though note that the SLN parser code cannot be built with v4.8. It
  will automatically be disabled when this older compiler is used.
• clang v3.9: it may be that older versions of the compiler also work, but we
  haven't tested them.
• Visual Studio 2015: it may be that older versions of the compiler also work,
  but we haven't tested them.

Backwards incompatible changes

This release includes a set of changes to make the default arguments to common
functions less error prone (github #1679).

• MolToSmiles() now generates isomeric SMILES by default.
• The embedding code now uses the ETKDG method by default.
• MolToMolBlock() will now by default generate a set of 2D coordinates for
  molecules when the includeStereo option is set to True. The changes are made
  to a copy of the molecule; the molecule itself will not be modified.
• The Mol file (and SDF) parser now determines atomic stereochemisty based on
  the 3D coordinates provided (if 3D coordinates are provided).
• The SMILES parser now supports CXSMILES by default (assuming that additional
  text that looks like CXSMILES extensions is there).

In every case the old behavior can be obtained by providing an optional argument
to the function(s) mentioned.

Acknowledgements:

Boran Adas, José Emilio Sánchez Aparicio, Patrick Avery, Jason Biggs, Brian
Cole, Andrew Dalke, JW Feng, Peter Gedeck, Guillaume Godin, Richard Hall, Thomas
Heavy, Gareth Jones, Brian Kelley, Karl Leswing, Susan Leung, Chris Morris, Dan
Nealschneider, Noel O'Boyle, Axel Pahl, Pavel Polishchuk, Sereina Riniker, Jeff
van Santen, Roger Sayle, Martin Šícho, Matt Swain, Paolo Tosco, Sam Webb, Maciej
Wójcikowski, Nicola Zonta, 'clinntt', 'hjuinj', 'iwatobipen',

Highlights:

• An initial version of an integration with Schrodinger's coordgen library is
  included. This produces much better 2D coordinates for complex molecules.
• Thanks to the move to modern C++ the RDKit is now faster and uses less
  memory
• A number of improvements were made to the PDB reader
• v2 of the ETKDG torsions and potentials is now available

Contrib updates:

• Implementation of Peter Ertl's IFG method for identifying functional groups
  from Guillaume Godin and Richard Hall
  (github pull #1813 from thegodone)

New Features and Enhancements:

• Support InChi 1.05
  (github issue #1533 from greglandrum)
• Update CPack to create .deb files correctly
  (github pull #1580 from psavery)
• Initial commit of EnumerateHeterocycles
  (github pull #1588 from coleb)
• Version 2 of ETKDG
  (github pull #1597 from sriniker)
• GetMolFrags now optionally returns atom indices along with mols
  (github pull #1602 from ptosco)
• NP Likeness with confidence value
  (github pull #1608 from apahl)
• Adding an option to EnumerateStereoisomers to only return unique isomers
  (github pull #1612 from coleb)
• Add function wedgeBond()
  (github issue #1615 from greglandrum)
• Dev/substructlibrary docs
  (github pull #1620 from bp-kelley)
• Turns off exception throwing for certain classes Rlabel sanitization.
  (github pull #1621 from bp-kelley)
• Add an "MDL" aromaticity model
  (github issue #1622 from hjuinj)
• Add support for %(NNN) notation for ring closures
  (github pull #1624 from baoilleach)
• Enable windows build that uses cairo
  (github pull #1628 from greglandrum)
• [MRG] Fix PDB reader + add argument to toggle proximity bonding
  (github pull #1629 from mwojcikowski)
• Improve AddHs for molecules read from PDB
  (github pull #1647 from mwojcikowski)
• Improved regression test for ETKDG version 2
  (github pull #1640 from sriniker)
• RDKit interpretation of atom stereo SMILES is different from 4 other toolkits
  (github issue #1652 from coleb)
• Treat bonds in PDB CONECT records explicitly, but make blacklisted ones zero-order.
  (github pull #1658 from mwojcikowski)
• There is no need to enforce that (i, j) and (k, l) be bonded when setting a i, j, k, l dihedral
  (github pull #1673 from ptosco)
• Make default arguments to common functions less error prone
  (github issue #1679 from greglandrum)
• Add Fast cluster script
  (github pull #1683 from iwatobipen)
• Update embedded InChI to v1.05
  (github pull #1684 from mcs07)
• Add AllChem.MMFFGetMoleculeForceField().CalcGradient() to Python wrappers
  (github issue #1688 from theavey)
• Play nice with naughty MOL blocks
  (github issue #1689 from jw-feng)
• Make the defaults for some functions less error prone.
  (github pull #1690 from greglandrum)
• implemented Python wrappers for computing PMI axes and moments
  (github pull #1700 from ptosco)
• Enable range-based for loops for molecules
  (github pull #1701 from bp-kelley)
• Support some cactvs extensions to SMARTS
  (github pull #1704 from greglandrum)
• Integrate Coordgen
  (github pull #1708 from greglandrum)
• Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
  (github pull #1713 from greglandrum)
• Set atomic properties from SMARTS
  (github pull #1716 from greglandrum)
• Allow installation of Python tests to facilitate testing installations
  (github pull #1724 from greglandrum)
• setAromaticity() should work even if there are aromatic atoms present
  (github issue #1730 from greglandrum)
• Use uint32 atom and bond indices
  (github pull #1742 from greglandrum)
• Switch from boost::thread to std::thread
  (github pull #1745 from greglandrum)
• switch to using std::regex in the SLN parser
  (github pull #1746 from greglandrum)
• replace the usage of rdk_auto_ptr with std::unique_ptr
  (github pull #1752 from greglandrum)
• getMolBoundsMatrix() should do triangle bound smoothing by default
  (github issue #1763 from greglandrum)
• Added Morgan feature fingerprints to Java API
  (github pull #1764 from jones-gareth)
• Reaction fingerprints not exposed in Java wrapper
  (github issue #1776 from webbres)
• add Tversky index calculation for shapes
  (github pull #1777 from susanhleung)
• Add MolToInchiKey function()
  (github pull #1784 from greglandrum)
• speedup the NumBitsInCommon operation
  (github pull #1785 from greglandrum)
• Stop putting brackets around * atoms in SMILES
  (github pull #1788 from greglandrum)
• Support for a JSON-based molecule interchange format
  (github pull #1798 from greglandrum)

Bug Fixes:

• Fixes Java wrapper build error with Boost 1.64
  (github pull #1613 from ptosco)
• AssignStereochemistry cleanIt=True incorrectly removing new CIS/TRANS bond stereo
  (github issue #1614 from coleb)
• switch to using a specific freesasa version
  (github pull #1619 from greglandrum)
• Add support for %(NNN) notation for ring closures
  (github pull #1624 from baoilleach)
• Draw._moltoSVG() raises an exception
  (github issue #1625 from greglandrum)
• MolDrawCairo2D does not build on windows
  (github issue #1627 from greglandrum)
• Enable windows build that uses cairo
  (github pull #1628 from greglandrum)
• don't always download the FreeSASA source
  (github issue #1630 from greglandrum)
• Make sure EmbedMultipleConfs is deterministic for very large seeds and a seed of 0
  (github pull #1635 from coleb)
• from rdkit.Chem import AllChem has grown a six dependency
  (github issue #1637 from bp-kelley)
• Fixing bug in IPythonConsole SVG rendering introduced in 1027d44
  (github pull #1641 from coleb)
• changes required to allow replacing the obsolete conda_version in conda-rdkit
  (github pull #1644 from ptosco)
• GetConformerRMSMatrix does not work if some conformers were removed
  (github issue #1650 from DrrDom)
• EnumerateLibrary with initFromString called twice doesn't clear the reaction
  (github issue #1657 from bp-kelley)
• Missed symmetrization in R-Group decomposition
  (github issue #1659 from greglandrum)
• Use numpy not numeric for boost 1.65+ - fixes #1581
  (github pull #1664 from mcs07)
• Support valence 7 for As, Sb, and Bi
  (github issue #1668 from greglandrum)
• Fix: GetDonor2FeatVects heavy atoms confusion
  (github pull #1676 from josan82)
• Acetylenic hydrogens not given appropriate 2D coordinates
  (github issue #1691 from jasondbiggs)
• Warning on import of rgroup decomposition package
  (github issue #1695 from greglandrum)
• AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required
  (github issue #1702 from baoilleach)
• Dative bonds interfere with kekulization and the perception of aromaticity
  (github issue #1703 from greglandrum)
• Fix/rgroup prefer matching nonhs over hs
  (github pull #1707 from bp-kelley)
• bonds that are STEREOCIS or STEREOTRANS cannot be depickled
  (github issue #1710 from greglandrum)
• Get queries from the new cactvs SMARTS extensions to pickle correctly
  (github pull #1712 from greglandrum)
• fix an irritating cmake problem
  (github pull #1715 from greglandrum)
• Added dependency from Boost headers to PgSQL CMakeLists.txt
  (github pull #1717 from ptosco)
• Updates python test runner to always use sys.executable
  (github pull #1721 from bp-kelley)
• • make bond stereo detection in rings consistent
    (github pull #1727 from ptosco)
• xlocale.h not needed to compile with clang
  (github issue #1728 from adalke)
• BreakBRICSBonds() not preserving stereochemistry
  (github issue #1734 from greglandrum)
• rdmolfiles.CanonicalRankAtoms segfaults on 0 atom molecules
  (github issue #1735 from lilleswing)
• deprecated apply() function causes GetRDKFingerprin...

2018_03_1b1 (Q1 2018) Release

Release_2018.03.1

(Changes relative to Release_2017.09.1)

C++11 notes

Starting with this release, the RDKit core C++ code is written in modern C++; for this release that means C++11.
This means that the compilers used to build it cannot be completely ancient. Here are the minimum tested versions:

• g++ v4.8: though note that the SLN parser code cannot be built with v4.8. It will automatically be disabled when this older compiler is used.
• clang v3.9: it may be that older versions of the compiler also work, but we haven't tested them.
• Visual Studio 2015: it may be that older versions of the compiler also work, but we haven't tested them.

Backwards incompatible changes

This release includes a set of changes to make the default arguments to common functions less error prone (github #1679).

• MolToSmiles() now generates isomeric SMILES by default.
• The embedding code now uses the ETKDG method by default.
• MolToMolBlock() will now by default generate a set of 2D coordinates for molecules when the includeStereo option is set to True. The changes are made to a copy of the molecule; the molecule itself will not be modified.
• The Mol file (and SDF) parser now determines atomic stereochemisty based on the 3D coordinates provided (if 3D coordinates are provided).
• The SMILES parser now supports CXSMILES by default (assuming that additional text that looks like CXSMILES extensions is there).

In every case the old behavior can be obtained by providing an optional argument to the function(s) mentioned.

Acknowledgements:

Boran Adas, José Emilio Sánchez Aparicio, Patrick Avery, Jason Biggs, Brian Cole, Andrew Dalke, JW Feng, Peter Gedeck, Thomas Heavy, Gareth Jones, Brian Kelley, Karl Leswing, Susan Leung, Chris Morris, Noel O'Boyle, Axel Pahl, Pavel Polishchuk, Sereina Riniker, Jeff van Santen, Roger Sayle, Matt Swain, Palo Tosco, Sam Webb, Maciej Wójcikowski, Nicola Zonta, 'clinntt', 'hjuinj', 'iwatobipen',

Highlights:

• A number of improvements were made to the PDB reader
• Thanks to the move to modern C++ the RDKit is now faster and uses less memory

New Features and Enhancements:

• Support InChi 1.05
  (github issue #1533 from greglandrum)
• Update CPack to create .deb files correctly
  (github pull #1580 from psavery)
• Initial commit of EnumerateHeterocycles
  (github pull #1588 from coleb)
• Version 2 of ETKDG
  (github pull #1597 from sriniker)
• GetMolFrags now optionally returns atom indices along with mols
  (github pull #1602 from ptosco)
• NP Likeness with confidence value
  (github pull #1608 from apahl)
• Adding an option to EnumerateStereoisomers to only return unique isomers
  (github pull #1612 from coleb)
• Add function wedgeBond()
  (github issue #1615 from greglandrum)
• Dev/substructlibrary docs
  (github pull #1620 from bp-kelley)
• Turns off exception throwing for certain classes Rlabel sanitization.…
  (github pull #1621 from bp-kelley)
• Add an "MDL" aromaticity model
  (github issue #1622 from hjuinj)
• Add support for %(NNN) notation for ring closures
  (github pull #1624 from baoilleach)
• Enable windows build that uses cairo
  (github pull #1628 from greglandrum)
• [MRG] Fix PDB reader + add argument to toggle proximity bonding
  (github pull #1629 from mwojcikowski)
• Improve AddHs for molecules read from PDB
  (github pull #1647 from mwojcikowski)
• Improved regression test for ETKDG version 2
  (github pull #1640 from sriniker)
• RDKit interpretation of atom stereo SMILES is different from 4 other toolkits
  (github issue #1652 from coleb)
• Treat bonds in PDB CONECT records explicitly, but make blacklisted ones zero-order.
  (github pull #1658 from mwojcikowski)
• There is no need to enforce that (i, j) and (k, l) be bonded when setting a i, j, k, l dihedral
  (github pull #1673 from ptosco)
• Make default arguments to common functions less error prone
  (github issue #1679 from greglandrum)
• Add Fast cluster script
  (github pull #1683 from iwatobipen)
• Update embedded InChI to v1.05
  (github pull #1684 from mcs07)
• Add AllChem.MMFFGetMoleculeForceField().CalcGradient() to Python wrappers
  (github issue #1688 from theavey)
• Play nice with naughty MOL blocks
  (github issue #1689 from jw-feng)
• Make the defaults for some functions less error prone.
  (github pull #1690 from greglandrum)
• implemented Python wrappers for computing PMI axes and moments
  (github pull #1700 from ptosco)
• Enable range-based for loops for molecules
  (github pull #1701 from bp-kelley)
• Support some cactvs extensions to SMARTS
  (github pull #1704 from greglandrum)
• Integrate Coordgen
  (github pull #1708 from greglandrum)
• Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
  (github pull #1713 from greglandrum)
• Set atomic properties from SMARTS
  (github pull #1716 from greglandrum)
• Allow installation of Python tests to facilitate testing installations
  (github pull #1724 from greglandrum)
• setAromaticity() should work even if there are aromatic atoms present
  (github issue #1730 from greglandrum)
• Use uint32 atom and bond indices
  (github pull #1742 from greglandrum)
• Switch from boost::thread to std::thread
  (github pull #1745 from greglandrum)
• switch to using std::regex in the SLN parser
  (github pull #1746 from greglandrum)
• replace the usage of rdk_auto_ptr with std::unique_ptr
  (github pull #1752 from greglandrum)
• getMolBoundsMatrix() should do triangle bound smoothing by default
  (github issue #1763 from greglandrum)
• Added Morgan feature fingerprints to Java API
  (github pull #1764 from jones-gareth)
• Reaction fingerprints not exposed in Java wrapper
  (github issue #1776 from webbres)
• add Tversky index calculation for shapes
  (github pull #1777 from susanhleung)
• Add MolToInchiKey function()
  (github pull #1784 from greglandrum)
• speedup the NumBitsInCommon operation
  (github pull #1785 from greglandrum)
• Stop putting brackets around * atoms in SMILES
  (github pull #1788 from greglandrum)
• Support for a JSON-based molecule interchange format
  (github pull #1798 from greglandrum)

Bug Fixes:

• Fixes Java wrapper build error with Boost 1.64
  (github pull #1613 from ptosco)
• AssignStereochemistry cleanIt=True incorrectly removing new CIS/TRANS bond stereo
  (github issue #1614 from coleb)
• switch to using a specific freesasa version
  (github pull #1619 from greglandrum)
• Add support for %(NNN) notation for ring closures
  (github pull #1624 from baoilleach)
• Draw._moltoSVG() raises an exception
  (github issue #1625 from greglandrum)
• MolDrawCairo2D does not build on windows
  (github issue #1627 from greglandrum)
• Enable windows build that uses cairo
  (github pull #1628 from greglandrum)
• don't always download the FreeSASA source
  (github issue #1630 from greglandrum)
• Make sure EmbedMultipleConfs is deterministic for very large seeds and a seed of 0
  (github pull #1635 from coleb)
• from rdkit.Chem import AllChem has grown a six dependency
  (github issue #1637 from bp-kelley)
• Fixing bug in IPythonConsole SVG rendering introduced in 1027d44
  (github pull #1641 from coleb)
• changes required to allow replacing the obsolete conda_version in conda-rdkit
  (github pull #1644 from ptosco)
• GetConformerRMSMatrix does not work if some conformers were removed
  (github issue #1650 from DrrDom)
• EnumerateLibrary with initFromString called twice doesn't clear the reaction
  (github issue #1657 from bp-kelley)
• Missed symmetrization in R-Group decomposition
  (github issue #1659 from greglandrum)
• Use numpy not numeric for boost 1.65+ - fixes #1581
  (github pull #1664 from mcs07)
• Support valence 7 for As, Sb, and Bi
  (github issue #1668 from greglandrum)
• Fix: GetDonor2FeatVects heavy atoms confusion
  (github pull #1676 from josan82)
• Acetylenic hydrogens not given appropriate 2D coordinates
  (github issue #1691 from jasondbiggs)
• Warning on import of rgroup decomposition package
  (github issue #1695 from greglandrum)
• AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required
  (github issue #1702 from baoilleach)
• Dative bonds interfere with kekulization and the perception of aromaticity
  (github issue #1703 from greglandrum)
• Fix/rgroup prefer matching nonhs over hs
  (github pull #1707 from bp-kelley)
• bonds that are STEREOCIS or STEREOTRANS cannot be depickled
  (github issue #1710 from greglandrum)
• Get queries from the new cactvs SMARTS extensions to pickle correctly
  (github pull #1712 from greglandrum)
• fix an irritating cmake problem
  (github pull #1715 from greglandrum)
• Added dependency from Boost headers to PgSQL CMakeLists.txt
  (github pull #1717 from ptosco)
• Updates python test runner to always use sys.executable
  (github pull #1721 from bp-kelley)
• • make bond stereo detection in rings consistent
    (github pull #1727 from ptosco)
• xlocale.h not needed to compile with clang
  (github issue #1728 from adalke)
• BreakBRICSBonds() not preserving stereochemistry
  (github issue #1734 from greglandrum)
• rdmolfiles.CanonicalRankAtoms segfaults on 0 atom molecules
  (github issue #1735 from lilleswing)
• deprecated apply() function causes GetRDKFingerprint to fail in Python 3
  (github issue #1747 from clinntt)
• Stop dereferencing end() iterators
  (github pull #1748 from greglandrum)
• out of range fromAtom causes GetMorganFingerprintAsBitVect to segfault
  (github issue #1749 from adalke)
• Generated SMARTS does not contain atomic chiral tags
  (github issue #1756 from greglandrum)
• make the build work even if boost::serialization is disabled
  (github pull #1767 from greglandrum)
• Fix typo in GetBoolProp documentation
  (github pul...