2017_09_3 (Q3 2017) Release

Release_2017.09.3

(Changes relative to Release_2017.09.2)

Acknowledgements:

Jason Biggs, Brian Kelley, Noel O'Boyle, Paolo Tosco

Bug Fixes:

• Missed symmetrization in R-Group decomposition
  (github issue #1659 from bp-kelley)
• 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)
• bonds that are STEREOCIS or STEREOTRANS cannot be depickled
  (github issue #1710 from greglandrum)
• Added dependency from Boost headers to PgSQL CMakeLists.txt
  (github pull #1717 from ptosco)

2017_09_2 (Q3 2017) Release

Release_2017.09.2

(Changes relative to Release_2017.09.1)

Acknowledgements:

Brian Cole, Brian Kelley, Noel O'Boyle, Pavel Polishchuk, Matt Swain,
Paolo Tosco, Hsiao Yi

Bug Fixes:

• 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)
• Make sure EmbedMultipleConfs is deterministic for very large seeds and a seed of 0
  (github pull #1635 from coleb)
• 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)
• Add 2017 UGM into README.md
  (github pull #1660 from hsiaoyi0504)
• 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)

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)

2017_09_1b1 (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

Acknowledgements:

Brian Cole, Peter Gedeck, Guillaume Godin, 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, 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 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)
• • 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)

2017_03_3 (Q1 2017) Release

Release_2017.03.3

(Changes relative to Release_2017.03.2)

Acknowledgements:

Francois Berenger, Brian Cole, Brian Kelley, John Mayfield, Noel O'Boyle,
Matt Swain

Bug Fixes:

• Fix cxsmiles parse on VS2008
  (github pull #1415 from mcs07)
• 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)
• MolToSmarts does not include atom-map or isotope info for molecules built from SMILES
  (github issue #1472 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)
• Unicode problem with pidPS tests on Mac
  (github issue #1490 from greglandrum)

2017_03_2 (Q1 2017) Release

Release_2017.03.2

(Changes relative to Release_2017.03.1)

Acknowledgements:

Peter Gedeck, Jameed Hussain, Brian Kelley, Matthew O'Meara, Steve Wilkins

Bug Fixes:

• 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)
• 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)
• fix a couple failing windows tests related to temp file removal
  (github issue #1446 from greglandrum)

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

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 <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)
• 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 instead

2016_09_4 (Q3 2016) Release

Release_2016.09.4

(Changes relative to Release_2016.09.3)

Acknowledgements:

Chris Earnshaw, Peter Gedeck, Brian Kelley, Paolo Tosco, 'i-tub'

Bug Fixes:

• 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)
• - fixed build failure on Windows due to missing link to library
  (github pull #1241 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)

2016_09_3 (Q3 2016) Release

Release_2016.09.3

(Changes relative to Release_2016.09.2)

Acknowledgements:

Peter Gedeck, Brian Kelley, Matt Swain, Paolo Tosco, Hsiao Yi

Bug Fixes:

• Fixes #1162 (resMolSupplierTest failing with boost 1.62)
  (github pull #1166 from ptosco)
• Add Contrib dir to RDPaths
  (github pull #1176 from mcs07)
• 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)