2015_09_1 (Q3 2015) Release

Release_2015.09.1

(Changes relative to Release_2015.03.1)

Acknowledgements:

Pierre Bhoorasingh, Gungor Budak, Andrew Dalke, JP Ebejer, Peter Ertl,
Jan Holst Jensen, Brian Kelley, Joos Kiener, Noel O'Boyle, Axel Pahl,
Sereina Riniker, Alexander Savelyev, Roger Sayle, Nadine Schneider,
Andrew Stretton, Paolo Tosco, Samo Turk, JL Varjo, Riccardo Vanello,
Maciek Wojcikowski

Highlights:

• Addition of parsers/writers for sequence notation, FASTA, and basic HELM
• Improved conformation generation based on experimental torsional parameters
• Much better filtering of generated conformations to ensure they
  match the chirality of the input structure
• New method for enumerating molecular resonance structures
• Addition of a molecular FilterCatalog data structure

Bug Fixes:

• Draw.MolToImage(mol) does not work for Python 3, because cairo for Python 3 has not yet implemented Surface.create_for_data
  (github issue #460 from apahl)
• SDWriter.close() fails when the underlying stream has an error
  (github issue #498 from greglandrum)
• Hexafluorophosphate cannot be handled
  (github issue #510 from greglandrum)
• Labels of highlighted atoms are invisible
  (github issue #519 from NadineSchneider)
• MolDraw2D: Fix in highlighting atoms
  (github pull #521 from NadineSchneider)
• Cartridge: index failing for molecular equality in some circumstances
  (github issue #525 from greglandrum)
• Bad ring finding in a complex fused ring
  (github issue #526 from greglandrum)
• Fixed crash upon closing a gzip/bzip2 stream opened in binary mode for use with SDWriter under Python3
  (github pull #531 from ptosco)
• Regression: _smilesAtomOutputOrder incorrect for dot disconnected molecules
  (github issue #532 from baoilleach)
• Fix #532 - smilesAtomOutputOrder incorrect
  (github pull #535 from baoilleach)
• Fix Python3 encoding for FilterCatalog/Entry serialization
  (github pull #537 from bp-kelley)
• Catalog::setCatalogParams needs to be virtual now
  (github pull #538 from bp-kelley)
• Bonds in allyl cation are not conjugated
  (github issue #539 from greglandrum)
• Fixes GitHub issue 539
  (github pull #540 from ptosco)
• SaltBuilder._initPatterns incorrectly handles SMARTS errors
  (github issue #541 from adalke)
• merging query Hs failing on recursive SMARTS
  (github issue #544 from greglandrum)
• Crash in O3A alignment when running multi-threaded
  (github issue #546 from greglandrum)
• PyMol.py: changed xmlrpc import to have Python2/Python3 compatibility
  (github pull #547 from apahl)
• fix MMPA bugs for some tests
  (github pull #548 from AlexanderSavelyev)
• TFD fix for single bonds adjacent to triple bonds
  (github pull #550 from sriniker)
• Canonicalization paper Aug2015
  (github pull #552 from NadineSchneider)
• Chirality not affected by atom-map index
  (github issue #553 from adalke)
• Implicit Hs should not appear in depictions for query atoms.
  (github issue #556 from greglandrum)
• Fix issue with invalid reactions throwing NameError
  (github pull #559 from bp-kelley)
• InChI radicals not properly converted
  (github issue #562 from pierrelb)
• MMPA code not python3 compatible
  (github issue #564 from greglandrum)
• mmpa: fix bug with num_of_cuts > 2 case
  (github pull #566 from AlexanderSavelyev)
• Incorrect stereochemistry after embedding
  (github issue #568 from greglandrum)
• changed FrameToGridImage() so that the dataframe index can be used as legend
  (github pull #570 from apahl)
• MolDraw2DCairo.GetDrawingText() doesn't work with Python3
  (github issue #571 from greglandrum)
• addBond return value
  (github issue #572 from JLVarjo)
• Process aborts during ForwardSDMolSupplier gc when the file object is closed
  (github issue #579 from adalke)
• Fix/update pains filter catalog
  (github pull #581 from bp-kelley)
• Importing PandasTools on Windows fails due to Salts.txt
  (github issue #583 from baoilleach)
• renumberAtoms() not setting conformer dimensionality properly
  (github issue #584 from greglandrum)
• stereo atoms property on double bonds not being updated properly with insertMol
  (github issue #608 from greglandrum)
• UFF Atom type not properly assigned to lanthanides
  (github issue #613 from greglandrum)
• segfault from MolToInchi when bad bond stereochem info is present
  (github issue #614 from greglandrum)
• MQN12 (heavy atom count) seems to be always 0.
  (github issue #623 from kienerj)
• fmcs: fix issue with initial seed for PR 580
  (github pull #624 from AlexanderSavelyev)
• fmcs: fixes #631 with chiralirty
  (github pull #634 from AlexanderSavelyev)
• Fixes sprintf not found on some gcc compiles
  (github pull #635 from bp-kelley)
• Fix AppVeyor and Travis UnitTests
  (github pull #636 from bp-kelley)
• Fixes #629 - python GetSubstructureMatch thread safety
  (github pull #637 from bp-kelley)
• Fix regressions occurring when building with msvc9
  (github pull #638 from rvianello)
• Fix/python gil release on rdkit threadsafe sss only
  (github pull #639 from bp-kelley)
• ctest not running some of the python tests.
  (github issue #643 from greglandrum)
• Issue643
  (github pull #646 from greglandrum)
• Fix/various bug fixes filtercatalog and bad operator
  (github pull #648 from bp-kelley)
• unlocking or destroying a locked mutex in the substructure matcher
  (github issue #653 from greglandrum)
• MMPA compile error with Microsoft Visual C++ Compiler for Python 2.7
  (github issue #655 from rvianello)
• new canon: fix in special symmetry invariant
  (github pull #663 from NadineSchneider)

New Features and Enhancements:

• enable popcount by default for cartridge
  (github issue #428 from greglandrum)
• Added the RSMD calculation over N molecules in the cookbook.
  (github pull #495 from malteseunderdog)
• Modified force field constraint tests to be more robust
  (github pull #503 from ptosco)
• Fix mol drawing on Python3 (issue #460)
  (github pull #504 from apahl)
• mmpa first version was added
  (github pull #505 from AlexanderSavelyev)
• Forcefield tests now use RDKit::feq() instead of RDKit::round()
  (github pull #506 from ptosco)
• SDMolSupplier(), setData() and strictParsing
  (github pull #507 from ptosco)
• Improvements to LoadSDF and WriteSDF
  (github pull #513 from samoturk)
• updates to mmpa. reduce number of smiles parsing
  (github pull #515 from AlexanderSavelyev)
• Some enhancements for the new canonicalization
  (github pull #520 from NadineSchneider)
• mmpa: remove boost_regex dependency at all. Add new test references
  (github pull #527 from AlexanderSavelyev)
• Support getting atoms involved in Pharm2D bits
  (github issue #530 from greglandrum)
• Optimized MMFF::MMFFOptimizeMoleculeConfs()
  (github pull #534 from ptosco)
• RDKit learns how to filter PAINS/BRENK/ZINC/NIH via FilterCatalog
  (github pull #536 from bp-kelley)
• Expose Conformer's copy constructor to Python
  (github issue #545 from greglandrum)
• PyMol.py: changed xmlrpc import to have Python2/Python3 compatibility
  (github pull #547 from apahl)
• Update PAINS smarts to validated set. Always use mergeQueryHs when reading Smarts
  (github pull #549 from bp-kelley)
• Add a curated set of PAINS filters to the RDKit
  (github issue #555 from greglandrum)
• Update pains from wehi_pains.csv
  (github pull #560 from bp-kelley)
• Change MMPA to use CanonicalRankAtoms instead of _CIPRank
  (github issue #561 from adalke)
• Add adjustQuery() function to make substructure queries more specific.
  (github issue #567 from greglandrum)
• changed sascorer.py to enable import from different location
  (github pull #569 from apahl)
• add export_values() to enums in the python wrapper where it's sensible to do so
  (github issue #573 from greglandrum)
• Support Sheridan's BT and BP fingerprints
  (github issue #574 from greglandrum)
• Locale dependent float for _GasteigerCharge
  (github issue #577 from adalke)
• fmcs: implement adding an initial seed structure
  (github pull #580 from AlexanderSavelyev)
• Where possible convert docs from RST to MD
  (github issue #585 from greglandrum)
• [UGM2015] Autodetection of numThreads
  (github issue #586 from mwojcikowski)
• Generating SVG Images with Transparent Background
  (github issue #587 from gungorbudak)
• updates to PandasTools.LoadSDF
  (github pull #599 from adalke)
• Can control mol depiction size with PandasTools.molSize = (200,200).
  (github pull #600 from samoturk)
• pandas performance and functionality improvements
  (github pull #601 from adalke)
• Adding documentation for installation with conda.
  (github pull #602 from strets123)
• Automatic atom reordering in TorsionFingerprints
  (github pull #603 from sriniker)
• remove bare excepts
  (github pull #606 from adalke)
• Added option to use SVG rendering in pandas data frames
  (github pull #609 from samoturk)
• Handle inserting molecules with conformers into molecules without conformers
  (github issue #610 from greglandrum)
• If wedged bonds are already present, write them to mol blocks
  (github issue #611 from greglandrum)
• Dev/filter catalog java wrapper
  (github pull #612 from bp-kelley)
• Support extended reduced graphs
  (github issue #615 from greglandrum)
• port NumSpiroCenters and NumBridgeheadAtoms descriptors to C++
  (github issue #617 from greglandrum)
• Add parser/writer for peptide sequences
  (github issue #620 from greglandrum)
• Add parser/writer for FASTA
  (github issue #621 from greglandrum)
• Add parser/writer for HELM
  (github issue #622 from greglandrum)
• Migrate std::string APIs to const std::string &
  (github pull #627 from bp-kelley)
• Chirality tests
  (github pull #628 from sriniker)
• Improvements of TFD
  (github pull #630 from sriniker)
• Added ResonanceMolSupplier
  (github pull #632 from ptosco)
• Image tostring/fromstring methods replaced by tobytes/frombytes
  (github pull #644 from rvianello)
• ET(K)DG implementation
  (github pull #647 from sriniker)
• Build multithreading support by default when boost::threads is present
  (gith...

2015_09_1 (Q3 2015) Beta Release 1

Release_2015.09.1

(Changes relative to Release_2015.03.1)

Acknowledgements:

Pierre Bhoorasingh, Gungor Budak, Andrew Dalke, JP Ebejer, Peter Ertl,
Jan Holst Jensen, Brian Kelley, Joos Kiener, Noel O'Boyle, Axel Pahl,
Sereina Riniker, Alexander Savelyev, Roger Sayle, Nadine Schneider,
Andrew Stretton, Paolo Tosco, Samo Turk, JL Varjo, Riccardo Vanello,
Maciek Wojcikowski

Highlights:

• Addition of parsers/writers for sequence notation, FASTA, and basic HELM
• Improved conformation generation based on experimental torsional parameters
• New method for enumerating molecular resonance structures
• Addition of a molecular FilterCatalog data structure

Bug Fixes:

• Draw.MolToImage(mol) does not work for Python 3, because cairo for Python 3 has not yet implemented Surface.create_for_data
  (github issue #460 from apahl)
• SDWriter.close() fails when the underlying stream has an error
  (github issue #498 from greglandrum)
• Hexafluorophosphate cannot be handled
  (github issue #510 from greglandrum)
• Labels of highlighted atoms are invisible
  (github issue #519 from NadineSchneider)
• MolDraw2D: Fix in highlighting atoms
  (github pull #521 from NadineSchneider)
• Bad ring finding in a complex fused ring
  (github issue #526 from greglandrum)
• Fixed crash upon closing a gzip/bzip2 stream opened in binary mode for use with SDWriter under Python3
  (github pull #531 from ptosco)
• Regression: _smilesAtomOutputOrder incorrect for dot disconnected molecules
  (github issue #532 from baoilleach)
• Fix #532 - smilesAtomOutputOrder incorrect
  (github pull #535 from baoilleach)
• Fix Python3 encoding for FilterCatalog/Entry serialization
  (github pull #537 from bp-kelley)
• Catalog::setCatalogParams needs to be virtual now
  (github pull #538 from bp-kelley)
• Bonds in allyl cation are not conjugated
  (github issue #539 from greglandrum)
• Fixes GitHub issue 539
  (github pull #540 from ptosco)
• SaltBuilder._initPatterns incorrectly handles SMARTS errors
  (github issue #541 from adalke)
• merging query Hs failing on recursive SMARTS
  (github issue #544 from greglandrum)
• Crash in O3A alignment when running multi-threaded
  (github issue #546 from greglandrum)
• PyMol.py: changed xmlrpc import to have Python2/Python3 compatibility
  (github pull #547 from apahl)
• fix MMPA bugs for some tests
  (github pull #548 from AlexanderSavelyev)
• TFD fix for single bonds adjacent to triple bonds
  (github pull #550 from sriniker)
• Canonicalization paper Aug2015
  (github pull #552 from NadineSchneider)
• Chirality not affected by atom-map index
  (github issue #553 from adalke)
• Implicit Hs should not appear in depictions for query atoms.
  (github issue #556 from greglandrum)
• Fix issue with invalid reactions throwing NameError
  (github pull #559 from bp-kelley)
• InChI radicals not properly converted
  (github issue #562 from pierrelb)
• MMPA code not python3 compatible
  (github issue #564 from greglandrum)
• mmpa: fix bug with num_of_cuts > 2 case
  (github pull #566 from AlexanderSavelyev)
• Incorrect stereochemistry after embedding
  (github issue #568 from greglandrum)
• changed FrameToGridImage() so that the dataframe index can be used as legend
  (github pull #570 from apahl)
• MolDraw2DCairo.GetDrawingText() doesn't work with Python3
  (github issue #571 from greglandrum)
• addBond return value
  (github issue #572 from JLVarjo)
• Process aborts during ForwardSDMolSupplier gc when the file object is closed
  (github issue #579 from adalke)
• Fix/update pains filter catalog
  (github pull #581 from bp-kelley)
• Importing PandasTools on Windows fails due to Salts.txt
  (github issue #583 from baoilleach)
• renumberAtoms() not setting conformer dimensionality properly
  (github issue #584 from greglandrum)
• stereo atoms property on double bonds not being updated properly with insertMol
  (github issue #608 from greglandrum)
• UFF Atom type not properly assigned to lanthanides
  (github issue #613 from greglandrum)
• segfault from MolToInchi when bad bond stereochem info is present
  (github issue #614 from greglandrum)
• MQN12 (heavy atom count) seems to be always 0.
  (github issue #623 from kienerj)
• fmcs: fix issue with initial seed for PR 580
  (github pull #624 from AlexanderSavelyev)
• fmcs: fixes #631 with chiralirty
  (github pull #634 from AlexanderSavelyev)
• Fixes sprintf not found on some gcc compiles
  (github pull #635 from bp-kelley)
• Fix AppVeyor and Travis UnitTests
  (github pull #636 from bp-kelley)
• Fixes #629 - python GetSubstructureMatch thread safety
  (github pull #637 from bp-kelley)
• Fix regressions occurring when building with msvc9
  (github pull #638 from rvianello)
• Fix/python gil release on rdkit threadsafe sss only
  (github pull #639 from bp-kelley)
• ctest not running some of the python tests.
  (github issue #643 from greglandrum)
• Issue643
  (github pull #646 from greglandrum)
• Fix/various bug fixes filtercatalog and bad operator
  (github pull #648 from bp-kelley)

New Features and Enhancements:

• Added the RSMD calculation over N molecules in the cookbook.
  (github pull #495 from malteseunderdog)
• Modified force field constraint tests to be more robust
  (github pull #503 from ptosco)
• Fix mol drawing on Python3 (issue #460)
  (github pull #504 from apahl)
• Forcefield tests now use RDKit::feq() instead of RDKit::round()
  (github pull #506 from ptosco)
• SDMolSupplier(), setData() and strictParsing
  (github pull #507 from ptosco)
• Improvements to LoadSDF and WriteSDF
  (github pull #513 from samoturk)
• updates to mmpa. reduce number of smiles parsing
  (github pull #515 from AlexanderSavelyev)
• Some enhancements for the new canonicalization
  (github pull #520 from NadineSchneider)
• mmpa: remove boost_regex dependency at all. Add new test references
  (github pull #527 from AlexanderSavelyev)
• Support getting atoms involved in Pharm2D bits
  (github issue #530 from greglandrum)
• Optimized MMFF::MMFFOptimizeMoleculeConfs()
  (github pull #534 from ptosco)
• RDKit learns how to filter PAINS/BRENK/ZINC/NIH via FilterCatalog
  (github pull #536 from bp-kelley)
• Expose Conformer's copy constructor to Python
  (github issue #545 from greglandrum)
• PyMol.py: changed xmlrpc import to have Python2/Python3 compatibility
  (github pull #547 from apahl)
• Update PAINS smarts to validated set. Always use mergeQueryHs when reading Smarts
  (github pull #549 from bp-kelley)
• Add a curated set of PAINS filters to the RDKit
  (github issue #555 from greglandrum)
• Update pains from wehi_pains.csv
  (github pull #560 from bp-kelley)
• Change MMPA to use CanonicalRankAtoms instead of _CIPRank
  (github issue #561 from adalke)
• Add adjustQuery() function to make substructure queries more specific.
  (github issue #567 from greglandrum)
• changed sascorer.py to enable import from different location
  (github pull #569 from apahl)
• add export_values() to enums in the python wrapper where it's sensible to do so
  (github issue #573 from greglandrum)
• Support Sheridan's BT and BP fingerprints
  (github issue #574 from greglandrum)
• Locale dependent float for _GasteigerCharge
  (github issue #577 from adalke)
• fmcs: implement adding an initial seed structure
  (github pull #580 from AlexanderSavelyev)
• Where possible convert docs from RST to MD
  (github issue #585 from greglandrum)
• [UGM2015] Autodetection of numThreads
  (github issue #586 from mwojcikowski)
• Generating SVG Images with Transparent Background
  (github issue #587 from gungorbudak)
• updates to PandasTools.LoadSDF
  (github pull #599 from adalke)
• Can control mol depiction size with PandasTools.molSize = (200,200).
  (github pull #600 from samoturk)
• pandas performance and functionality improvements
  (github pull #601 from adalke)
• Adding documentation for installation with conda.
  (github pull #602 from strets123)
• Automatic atom reordering in TorsionFingerprints
  (github pull #603 from sriniker)
• Added option to use SVG rendering in pandas data frames
  (github pull #609 from samoturk)
• Handle inserting molecules with conformers into molecules without conformers
  (github issue #610 from greglandrum)
• If wedged bonds are already present, write them to mol blocks
  (github issue #611 from greglandrum)
• Dev/filter catalog java wrapper
  (github pull #612 from bp-kelley)
• Support extended reduced graphs
  (github issue #615 from greglandrum)
• port NumSpiroCenters and NumBridgeheadAtoms descriptors to C++
  (github issue #617 from greglandrum)
• Add parser/writer for peptide sequences
  (github issue #620 from greglandrum)
• Add parser/writer for FASTA
  (github issue #621 from greglandrum)
• Add parser/writer for HELM
  (github issue #622 from greglandrum)
• Migrate std::string APIs to const std::string &
  (github pull #627 from bp-kelley)
• Chirality tests
  (github pull #628 from sriniker)
• Improvements of TFD
  (github pull #630 from sriniker)
• Added ResonanceMolSupplier
  (github pull #632 from ptosco)
• Image tostring/fromstring methods replaced by tobytes/frombytes
  (github pull #644 from rvianello)
• ET(K)DG implementation
  (github pull #647 from sriniker)
• Build multithreading support by default when boost::threads is present
  (github issue #649 from greglandrum)

New Database Cartridge Features:

• Support for PostgreSQL v8.x has been removed
• NumSpiroCenters and NumBridgeheadAtoms added

New Java Wrapper Features:

• Support for FilterCatalogs

Deprecated code (to be removed in next release):

Removed code:

• rdkit/DataStructs/BitVect.py : a C++ version is used, this was only present for historical reasons
• rdkit/DataStructs/SparseIntVect.py : a C++ version is used, this was only present for historical reasons

Contrib updates:

• Addition of Peter Ertl's Natural Product Likeness score.

Other:

• Much of the documentation has been translated from RST to MD

CanonicalizationPaper_Aug2015

Branch with the state of the code that corresponds to the submitted canonicalization paper.

2015_03_1 (Q1 2015) Release

****** Release_2015.03.1 *******
(Changes relative to Release_2014.09.2)

!!!!!! IMPORTANT !!!!!!

• This release has a new algorithm for canonical atom ordering. This
  means that canonical SMILES generated with the new version will be
  different from those generated with previous versions.

Acknowledgements:
David Cosgrove, Andrew Dalke, JP Ebejer, Niko Fechner, Igor Filippov,
Patrick Fuller, David Hall, J Bach Hardie, Jan Holst Jensen, Brian
Kelley, Rich Lewis, John May, Michael Reutlinger, Sereina Riniker,
Alexander Savelyev, Roger Sayle, Nadine Schneider, Paolo Tosco, Samo
Turk, JL Varjo, Riccardo Vianello

Highlights:

• A new algorithm for generating canonical atom orders. The new
  algorithm is faster and more robust than the old one.
• C++-based molecule drawing code, allows consistent molecule
  renderings from C++, Java, and Python. This will become the
  default renderer in the next release.
• General performance improvements and reduction of memory usage.
• Torsion Fingerprints for comparing 3D conformations to each other
• MCS code now available from the PostgreSQL cartridge

Bug Fixes:

• fmcs: use the zero bond type instead of other
  (github issue #368 from AlexanderSavelyev)
• bug fixed in TorsionFingerprints.GetTFDMatrix
  (github issue #376 from sriniker)
• rdkit.Chem.MolDb.Loader_sa does not work with python3.4
  (github issue #390)
• ChemReactions: Bugfix/Memleak-fix in runReactants
  (github issue #394 from NadineSchneider)
• TorsionConstraint bug fix
  (github issue #395 from ptosco)
• Fixed LoadSDF to keep 3D info
  (github pull #401 from samoturk)
• Incorrect expected absolute stereochemistries in a test
  (github issue #407)
• GetSubstructMatches() consumes all available memory
  (github issue #409)
• Bugfix in the chirality handling of chemical reactions
  (github pull #410 from NadineSchneider)
• fixed two minor bugs in MMFF code
  (github issue #416 from ptosco)
• Varied sanitise rejection with hydrogen representation
  (github issue #418)
• Fixed two trivial bugs
  (github issue #419 from ptosco)
• RDKit learns how to roundtrip MOLFile values.
  (github issue #420 from bp-kelley)
• cairoCanvas.py python3 compatibility
  (github issue #426 from bach-hardie)
• Chem.FragmentOnSomeBonds() should update implicit H count on aromatic heteroatoms when addDummies is False
  (github issue #429)
• Chem.FragmentOnSomeBonds() crashes if the bond list is empty
  (github issue #430)
• Increase limit for smallest ring size
  (github issue #431 from cowsandmilk)
• Problems caused by heteroatoms with radicals in aromatic rings.
  (github issue #432)
• Conversion from mol to InChI getting ring stereo wrong
  (github issue #437)
• Metals in mol2 blocks handled incorrectly
  (github issue #438)
• Fixed a few tests failing when the Windows git client is used
  (github pull #439 from ptosco)
• Fixed tests failing on Windows when retrieving sources through the Windows git client
  (github pull #440 from ptosco)
• Conformers not copied correctly in renumberAtoms
  (github issue #441)
• Radicals are not correctly assigned when reading from SMILES
  (github issue #447)
• moving RDBoost/Exceptions.h to RDGeneral
  (github pull #458 from rvianello)
• Add code to accept blank SMILES input.
  (github issue #468 from janholstjensen)
• Accept empty SMILES and SMARTS
  (github issue #470)
• Fix MolFile Atom Line List Writer
  (github issue #471 from bp-kelley)
• Moved 3D ipython renderer to dependency
  (github pull #472 from patrickfuller)
• Windows build/test failure fixes
  (github issue #473 from ptosco)
• install missing FMCS/Graph.h header file
  (github pull #478 from rvianello)
• added const qualifiers to some methods of Atom/Bond iterator classes
  (github pull #479 from rvianello)
• Bugfix in SmilesWrite and some additional tests for getMolFrags function
  (github issue #482 from NadineSchneider)
• Removed a while(1) {} in BFGSOpt.h which might result in an infinite loop
  (github issue #484 from ptosco)
• Gasteiger charge calculation fails with hexavalent sulfur #485
  (github issue #485)
• SmilesWriter not creating automatic name values for molecules read from CTABs
  (github issue #488)
• Fix StringType access, remove unused imports
  (github issue #494 from bp-kelley)

New Features:

• Isomeric fix in PandasTools
  (github issue #369 from samoturk)
• added SaveXlsxFromFrame - first version
  (github issue #371 from samoturk)
• New feature: Torsion fingerprints
  (github issue #372 from sriniker)
• Add function to extract a molecule with a single (particular) conformer from a multiconf mol
  (github issue #384)
• Added C++ and Python helpers to retrieve force-field parameters
  (github issue #387 from ptosco)
• Support providing all options to SWIG-wrapped FMCS
  (github issue #397)
• Add function to request if calling UpdatePropertyCache is necessary
  (github issue #399)
• Add function to test if UpdatePropertyCache is necessary
  (github issue #400 from NadineSchneider)
• Substructure highlighting in pandas dataframe (fixes #362)
  (github issue #403 from nhfechner)
• Added SDF Export to PandasTools and adjusted SDF Import
  (github issue #404 from nhfechner)
• support count-based avalon fingerprint
  (github issue #408)
• New C++ drawing code
  (github issue #412 from greglandrum)
• RDKit learns how to compute code coverage for tests
  (github issue #413 from bp-kelley)
• Dictionary access is saniztized and optimized.
  (github issue #414 from bp-kelley)
• expose MolOps::rankAtoms() and MolOps::rankAtomsInFragment() to python
  (github issue #421)
• Dev/expose rank atoms to python
  (github issue #422 from bp-kelley)
• rdkit learns how to wrap a proper RWMol in python
  (github issue #423 from bp-kelley)
• Docs: document "magic" property values that are used throughout the code
  (github issue #425)
• MolDraw2D: expose class to Python
  (github issue #433)
• RDKit learns how to query properties on Atoms
  (github issue #442 from bp-kelley)
• Issue445: provide helper functions for multithreaded evaluation of some expensive functions
  (github issue #448 from greglandrum)
• RDKit learns how to release the GIL in python
  (github pull #449 from bp-kelley)
• Dev/property queries
  (github pull #450 from bp-kelley)
• Support a confId argument to the atom pair fingerprinting code
  (github issue #453)
• Save the atom bookmarks so we can deconvolute reaction products.
  (github pull #454 from bp-kelley)
• Cartridge: Support converting no structs to InChI
  (github issue #455)
• RDKit learns how to expose ChemicalReaction copy constructor to python
  (github pull #456 from bp-kelley)
• chirality flag was implemented for fmcs() function
  (github pull #466 from AlexanderSavelyev)
• Support copy and deepcopy properly for at least Mol and RWMol
  (github issue #467)
• Cartridge: add qmol_from_smiles() and qmol_from_ctab()
  (github issue #469)
• restore java and python wrappers. New parameter (matchChiralTag)
  (github issue #477 from AlexanderSavelyev)
• Added a Python wrapper for getShortestPath()
  (github issue #487 from ptosco)
• Dev/merge query hs no unmapped atoms
  (github issue #490 from bp-kelley)

New Database Cartridge Features:

• The MCS code is now available within the cartridge
• The functions qmol_from_smiles() and qmol_from_ctab()

New Java Wrapper Features:

• The new molecule rendering code is accessible from the SWIG wrappers.

Deprecated code (to be removed in next release):

• C++: The functionality in $RDBASE/Code/GraphMol/MolDrawing has been
  superseded by the new drawing code in $RDBASE/Code/GraphMol and will
  be removed in the next release.
• Python:
  • rdkit/Dbase/Pubmed
  • rdkit/Chem/fmcs (this has been superseded by the C++ implementation)
• Cartridge: support for v8.x of PostgreSQL (v8.4 is no longer
  supported by the PostgreSQL project team as of July 2014)

Removed code:

• the method Atom::setMass() has been removed. Please use setIsotope()
  instead.
• the methods involving an atom's dativeFlag have been removed.

Contrib updates:

Other:

• Python 2.6 support is deprecated. Starting with the next RDKit
  release, we will only support python 2.7 and python 3.4 and
  higher. Python 2.6 has not been supported since October 2013. If you
  believe that you are stuck with python 2.6 because of the version of
  RHEL you are running, please read this post to learn about your
  options:
  http://www.curiousefficiency.org/posts/2015/04/stop-supporting-python26.html
• The RDKit molecule objects (ROMol and RWMol) now require about 15%
  less memory to store

2015_03_1 (Q1 2015) Beta Release 1

****** Release_2015.03.1 *******
(Changes relative to Release_2014.09.2)

!!!!!! IMPORTANT !!!!!!

• This release has a new algorithm for canonical atom ordering. This
  means that canonical SMILES generated with the new version will be
  different from those generated with previous versions.

Acknowledgements:
David Cosgrove, Andrew Dalke, JP Ebejer, Niko Fechner, Igor Filippov,
Patrick Fuller, David Hall, J Bach Hardie, Jan Holst Jensen, Brian
Kelley, Rich Lewis, John May, Sereina Riniker, Alexander Savelyev,
Roger Sayle, Nadine Schneider, Paolo Tosco, Samo Turk, JL Varjo,
Riccardo Vianello

Highlights:

• A new algorithm for generating canonical atom orders. The new
  algorithm is faster and more robust than the old one.
• C++-based molecule drawing code, allows consistent molecule
  renderings from C++, Java, and Python. This will become the
  default renderer in the next release.
• General performance improvements and reduction of memory usage.
• Torsion Fingerprints for comparing 3D conformations to each other
• MCS code now available from the PostgreSQL cartridge

Bug Fixes:

• fmcs: use the zero bond type instead of other
  (github issue #368 from AlexanderSavelyev)
• bug fixed in TorsionFingerprints.GetTFDMatrix
  (github issue #376 from sriniker)
• rdkit.Chem.MolDb.Loader_sa does not work with python3.4
  (github issue #390)
• ChemReactions: Bugfix/Memleak-fix in runReactants
  (github issue #394 from NadineSchneider)
• TorsionConstraint bug fix
  (github issue #395 from ptosco)
• Fixed LoadSDF to keep 3D info
  (github pull #401 from samoturk)
• Incorrect expected absolute stereochemistries in a test
  (github issue #407)
• GetSubstructMatches() consumes all available memory
  (github issue #409)
• Bugfix in the chirality handling of chemical reactions
  (github pull #410 from NadineSchneider)
• fixed two minor bugs in MMFF code
  (github issue #416 from ptosco)
• Varied sanitise rejection with hydrogen representation
  (github issue #418)
• Fixed two trivial bugs
  (github issue #419 from ptosco)
• RDKit learns how to roundtrip MOLFile values.
  (github issue #420 from bp-kelley)
• cairoCanvas.py python3 compatibility
  (github issue #426 from bach-hardie)
• Chem.FragmentOnSomeBonds() should update implicit H count on aromatic heteroatoms when addDummies is False
  (github issue #429)
• Chem.FragmentOnSomeBonds() crashes if the bond list is empty
  (github issue #430)
• Increase limit for smallest ring size
  (github issue #431 from cowsandmilk)
• Problems caused by heteroatoms with radicals in aromatic rings.
  (github issue #432)
• Metals in mol2 blocks handled incorrectly
  (github issue #438)
• Fixed a few tests failing when the Windows git client is used
  (github pull #439 from ptosco)
• Fixed tests failing on Windows when retrieving sources through the Windows git client
  (github pull #440 from ptosco)
• Conformers not copied correctly in renumberAtoms
  (github issue #441)
• Radicals are not correctly assigned when reading from SMILES
  (github issue #447)
• moving RDBoost/Exceptions.h to RDGeneral
  (github pull #458 from rvianello)
• Add code to accept blank SMILES input.
  (github issue #468 from janholstjensen)
• Accept empty SMILES and SMARTS
  (github issue #470)
• Fix MolFile Atom Line List Writer
  (github issue #471 from bp-kelley)
• Moved 3D ipython renderer to dependency
  (github pull #472 from patrickfuller)
• Windows build/test failure fixes
  (github issue #473 from ptosco)

New Features:

• Isomeric fix in PandasTools
  (github issue #369 from samoturk)
• added SaveXlsxFromFrame - first version
  (github issue #371 from samoturk)
• New feature: Torsion fingerprints
  (github issue #372 from sriniker)
• Add function to extract a molecule with a single (particular) conformer from a multiconf mol
  (github issue #384)
• Added C++ and Python helpers to retrieve force-field parameters
  (github issue #387 from ptosco)
• Support providing all options to SWIG-wrapped FMCS
  (github issue #397)
• Add function to request if calling UpdatePropertyCache is necessary
  (github issue #399)
• Add function to test if UpdatePropertyCache is necessary
  (github issue #400 from NadineSchneider)
• Substructure highlighting in pandas dataframe (fixes #362)
  (github issue #403 from nhfechner)
• Added SDF Export to PandasTools and adjusted SDF Import
  (github issue #404 from nhfechner)
• support count-based avalon fingerprint
  (github issue #408)
• New C++ drawing code
  (github issue #412 from greglandrum)
• RDKit learns how to compute code coverage for tests
  (github issue #413 from bp-kelley)
• Dictionary access is saniztized and optimized.
  (github issue #414 from bp-kelley)
• expose MolOps::rankAtoms() and MolOps::rankAtomsInFragment() to python
  (github issue #421)
• Dev/expose rank atoms to python
  (github issue #422 from bp-kelley)
• rdkit learns how to wrap a proper RWMol in python
  (github issue #423 from bp-kelley)
• Docs: document "magic" property values that are used throughout the code
  (github issue #425)
• MolDraw2D: expose class to Python
  (github issue #433)
• RDKit learns how to query properties on Atoms
  (github issue #442 from bp-kelley)
• Issue445: provide helper functions for multithreaded evaluation of some expensive functions
  (github issue #448 from greglandrum)
• RDKit learns how to release the GIL in python
  (github pull #449 from bp-kelley)
• Dev/property queries
  (github pull #450 from bp-kelley)
• Support a confId argument to the atom pair fingerprinting code
  (github issue #453)
• Save the atom bookmarks so we can deconvolute reaction products.
  (github pull #454 from bp-kelley)
• Cartridge: Support converting no structs to InChI
  (github issue #455)
• RDKit learns how to expose ChemicalReaction copy constructor to python
  (github pull #456 from bp-kelley)
• chirality flag was implemented for fmcs() function. NOTE: as of the beta release,
  there is a known order-dependency bug in this functionality.
  (github pull #466 from AlexanderSavelyev)
• Support copy and deepcopy properly for at least Mol and RWMol
  (github issue #467)
• Cartridge: add qmol_from_smiles() and qmol_from_ctab()
  (github issue #469)
• restore java and python wrappers. New parameter (matchChiralTag)
  (github issue #477 from AlexanderSavelyev)

New Database Cartridge Features:

• The MCS code is now available within the cartridge
• The functions qmol_from_smiles() and qmol_from_ctab()

New Java Wrapper Features:

• The new molecule rendering code is accessible from the SWIG wrappers.

Deprecated code (to be removed in next release):

• C++: The functionality in $RDBASE/Code/GraphMol/MolDrawing has been
  superseded by the new drawing code in $RDBASE/Code/GraphMol and will
  be removed in the next release.
• Python:
  • rdkit/Dbase/Pubmed
  • rdkit/Chem/fmcs (this has been superseded by the C++ implementation)
• Cartridge: support for v8.x of PostgreSQL (v8.4 is no longer
  supported by the PostgreSQL project team as of July 2014)

Removed code:

• the method Atom::setMass() has been removed. Please use setIsotope()
  instead.
• the methods involving an atom's dativeFlag have been removed.

Contrib updates:

Other:

• Python 2.6 support is deprecated. Starting with the next RDKit
  release, we will only support python 2.7 and python 3.4 and
  higher. Python 2.6 has not been supported since October 2013. If you
  believe that you are stuck with python 2.6 because of the version of
  RHEL you are running, please read this post to learn about your
  options:
  http://www.curiousefficiency.org/posts/2015/04/stop-supporting-python26.html
• The RDKit molecule objects (ROMol and RWMol) now require about 15%
  less memory to store

2014_09_2 (Q3 2014) Patch Release

****** Release_2014.09.2 *******
(Changes relative to Release_2014.09.1)

Acknowledgements:
Sereina Riniker, Nadine Schneider, Paolo Tosco

Bug Fixes:

• SMILES parser doing the wrong thing for odd dot-disconnected construct
  (github issue #378)
• O3A code generating incorrect results for multiconformer molecules
  (github issue #385)
• Suppliers probably not safe to read really large files
  (github issue #392)
• Torsion constraints not worrking properly for negative torsions
  (github issue #393)
• Core leak in reactions
  (github issue #396)

2014_09_1 (Q3 2014) Release

****** Release_2014.09.1 *******
(Changes relative to Release_2014.03.1)

Acknowledgements:
Andrew Dalke, James Davidson, Jan Domanski, Patrick Fuller, Seiji
Matsuoka, Noel O'Boyle, Sereina Riniker, Alexander Savelyev, Roger
Sayle, Nadine Schneider, Matt Swain, Paolo Tosco, Riccardo Vianello,
Richard West

Bug Fixes:

• Bond query information not written to CTAB
  (github issue #266)
• Bond topology queries not written to CTABs
  (github issue #268)
• Combined bond query + topology query not correctly parsed from CTAB
  (github issue #269)
• SWIG wrapped suppliers leak memory on .next()
  (github issue #270)
• SWIG wrappers don't build with SWIG 3.0.x
  (github issue #277)
• core leak from DataStructs.ConvertToNumpyArray
  (github issue #281)
• MolTransforms not exposed to Java wrapper
  (github issue #285)
• Seg fault in ReactionFromRxnBlock
  (github issue #290)
• BitInfo from GetHashedMorganFingerprint() has non-folded values
  (github issue #295)
• bad inchi for chiral S when the molecule is sanitized
  (github issue #296)
• Cannot generate smiles for ChEBI 50252
  (github issue #298)
• Either molecule-molecule substruct matching is wrong OR the docs for Atom::Match incorrect
  (github issue #304)
• fluorine F-F gives segmentation fault with MMFF forcefield
  (github issue #308)
• cartridge: MACCS similarity wrong when using the builtin popcount and the index
  (github issue #311)
• Substructure Search via SMARTS implicit hydrogens
  (github issue #313)
• SMARTS output for [x] is wrong
  (github issue #314)
• Bonds not being set up properly in renumberAtoms
  (github issue #317)
• Python 2 code in python 3 branch
  (github issue #326)
• Linking error with ICC 15.0 on Linux
  (github issue #327)
• Using explicit hydrogens in the SMILES lead to the same AP FP for two different molecules
  (github issue #334)
• memory leaks when smiles/smarts parsers fail
  (github issue #335)
• No double bond stereo perception from CTABs when sanitization is turned off
  (github issue #337)
• missing MACCS key 44 might be found
  (github issue #352)
• Hydrogens in mol blocks have a valence value set
  (github issue #357)
• Computed props on non-sanitized molecule interfering with substructure matching
  (github issue #360)
• Fixed a weakness in the angular restraint code
  (github pull #261 from ptosco)
• A few fixes to improve MMFF/UFF robustness
  (github pull #274 from ptosco)
• Static webGL rendering fix
  (github pull #287 from patrickfuller)
• Revert #include ordering in SmilesMolSupplier.cpp
  (github pull #297 from mcs07)
• Add missing include for RDDepict::compute2DCoords
  (github pull #301 from baoilleach)
• Herschbach-Laurie fallback implemented to fix GitHub 308
  (github pull #312 from ptosco)
• Issue #320 Making GetBestRMS more idiot-proof
  (github pull #322 from jandom)
• Update URLs to InChI API after inchi-trust.org website redesign.
  (github pull #341 from rwest)

New Features:

• Should be able to do intramolecular bond breaking in reactions.
  (github issue #58)
• Support reactions in cartridge
  (github issue #223)
• Documentation of Inchi methods
  (github issue #240)
• add DescribeQuery() to Bond python wrapper
  (github issue #267)
• support avalon fingerprint in cartridge
  (github issue #286)
• support partial fragmentation with fragmentOnSomeBonds
  (github issue #288)
• Add calcNumHeterocycles() descriptor
  (github issue #351)
• C++ implementation of FMCS algorithm
• Reordering feature for Butina clustering
  (github pull #302 from sriniker)
• Changes and new functions for the calculation of RMS values between conformers of a molecule
  (github pull #306 from sriniker)
• Extended chemical reaction functionality and add chemical reactions to cartridge
  (github pull #315 from NadineSchneider)
• Custom color to highlight atoms in Mol2Image
  (github pull #316 from jandom)
• Several different fingerprint algorithms for chemical reactions are now available
• add Chem.Draw.MolToQPixmap
  (github pull #355 from mojaie)

New Database Cartridge Features:

• NOTE: the configuration variable rdkit.ss_fp_size has been renamed to rdkit.sss_fp_size
• Chemical reactions and several operations on them are now supported
• Avalon fingerprints now supported (when support has been compiled in)

New Java Wrapper Features:

• FMCS implementation exposed
• Fingerprints for chemical reactions
• Possible core leak in some of the MolSuppliers was fixed

Deprecated modules (to be removed in next release):

• Projects/SDView4
• rdkit/utils/
  • GUIDs.py
  • GenLicense.py
  • Licensing.py
  • PiddleTools.py
  • PilTools.py
  • REFile.py
  • SliceTools.py
• rdkit/Logger

Removed modules:

Contrib updates:

Other:

• The RDKit now supports both python3 and python2.
• There is now conda integration for the RDKit.
• SMILES generation is substantially faster

2014_09_1 (Q3 2014) Beta Release

****** Release_2014.09.1 *******
(Changes relative to Release_2014.03.1)

Acknowledgements:
Andrew Dalke, Jan Domanski, Patrick Fuller, Noel O'Boyle, Sereina
Riniker, Alexander Savelyev, Roger Sayle, Nadine Schneider, Matt
Swain, Paolo Tosco, Riccardo Vianello

Bug Fixes:

• Bond query information not written to CTAB
  (github issue 266)
• Bond topology queries not written to CTABs
  (github issue 268)
• Combined bond query + topology query not correctly parsed from CTAB
  (github issue 269)
• SWIG wrapped suppliers leak memory on .next()
  (github issue 270)
• SWIG wrappers don't build with SWIG 3.0.x
  (github issue 277)
• core leak from DataStructs.ConvertToNumpyArray
  (github issue 281)
• MolTransforms not exposed to Java wrapper
  (github issue 285)
• Seg fault in ReactionFromRxnBlock
  (github issue 290)
• BitInfo from GetHashedMorganFingerprint() has non-folded values
  (github issue 295)
• bad inchi for chiral S when the molecule is sanitized
  (github issue 296)
• Cannot generate smiles for ChEBI 50252
  (github issue 298)
• Either molecule-molecule substruct matching is wrong OR the docs for Atom::Match incorrect
  (github issue 304)
• fluorine F-F gives segmentation fault with MMFF forcefield
  (github issue 308)
• cartridge: MACCS similarity wrong when using the builtin popcount and the index
  (github issue 311)
• Substructure Search via SMARTS implicit hydrogens
  (github issue 313)
• SMARTS output for [x] is wrong
  (github issue 314)
• Bonds not being set up properly in renumberAtoms
  (github issue 317)
• Python 2 code in python 3 branch
  (github issue 326)
• Linking error with ICC 15.0 on Linux
  (github issue 327)
• Using explicit hydrogens in the SMILES lead to the same AP FP for two different molecules
  (github issue 334)
• memory leaks when smiles/smarts parsers fail
  (github issue 335)
• No double bond stereo perception from CTABs when sanitization is turned off
  (github issue 337)
• missing MACCS key 44 might be found
  (github issue 352)
• Fixed a weakness in the angular restraint code
  (github pull 261 from ptosco)
• A few fixes to improve MMFF/UFF robustness
  (github pull 274 from ptosco)
• Static webGL rendering fix
  (github pull 287 from patrickfuller)
• Revert #include ordering in SmilesMolSupplier.cpp
  (github pull 297 from mcs07)
• Add missing include for RDDepict::compute2DCoords
  (github pull 301 from baoilleach)
• Herschbach-Laurie fallback implemented to fix GitHub 308
  (github pull 312 from ptosco)
• Issue #320 Making GetBestRMS more idiot-proof
  (github pull 322 from jandom)

New Features:

• Should be able to do intramolecular bond breaking in reactions.
  (github issue 58)
• Support reactions in cartridge
  (github issue 223)
• Documentation of Inchi methods
  (github issue 240)
• add DescribeQuery() to Bond python wrapper
  (github issue 267)
• support avalon fingerprint in cartridge
  (github issue 286)
• support partial fragmentation with fragmentOnSomeBonds
  (github issue 288)
• Add calcNumHeterocycles() descriptor
  (github issue 351)
• C++ implementation of FMCS algorithm
• Reordering feature for Butina clustering
  (github pull 302 from sriniker)
• Changes and new functions for the calculation of RMS values between conformers of a molecule
  (github pull 306 from sriniker)
• Extended chemical reaction functionality and add chemical reactions to cartridge
  (github pull 315 from NadineSchneider)
• Custom color to highlight atoms in Mol2Image
  (github pull 316 from jandom)
• Several different fingerprint algorithms for chemical reactions are now available

New Database Cartridge Features:

• Chemical reactions and several operations on them are now supported
• Avalon fingerprints now supported (when support has been compiled in)

New Java Wrapper Features:

• FMCS implementation exposed
• Fingerprints for chemical reactions
• Possible core leak in some of the MolSuppliers was fixed

Deprecated modules (to be removed in next release):

Removed modules:

Contrib updates:

Other:

• The RDKit now supports both python3 and python2.
• There is now conda integration for the RDKit.
• SMILES generation is substantially faster

Release_test_for_zenodo

Just a test to see if the zenodo integration is working

2014_03_1 (Q1 2014) Release

****** Release_2014.03.1 *******
(Changes relative to Release_2013.09.2)

!!!!!! IMPORTANT !!!!!!

• Due to a bug fix in the rotatable bonds definition, the default
  rotatable bond calculation returns different values than before.
  This also affects MQN descriptor #18.

Acknowledgements:
Paul Czodrowski, James Davidson, Markus Elfring, Nikolas Fechner, Jan Holst Jensen, Christos Kannas, Sereina Riniker, Roger Sayle, Paolo Tosco, Samo Turk, Riccardo Vianello, Maciej Wójcikowski, Toby Wright

Bug Fixes:

• Dict::DataType declaration causing problems with C++11 std::lib
  (github issue 144)
• Pre-condition Violation in AllChem.Compute2DCoords
  (github issue 146)
• GetSimilarityMapForFingerprint() fails when similarity is zero
  (github issue 148)
• PatternFingerprint failure for substructure matching
  (github issue 151)
• query atoms don't match ring queries
  (github issue 153)
• Incorrect SMILES generated after calling MMFF parameterization
  (github issue 162)
• Problems with Xe from SDF
  (github issue 164)
• Radicals not being used in atom--atom matches
  (github issue 165)
• Cannot skip sanitization while reading PDB
  (github issue 166)
• Distance Geometry embedding not thread safe
  (github issue 167)
• O3A::align() and O3A::trans() now return "true" RMSD value
  (github pull 173)
• RangeError when pre-incrementing or decrementing AtomIterators
  (github issue 180)
• ctabs do not contain wedged bonds for chiral s
  (github issue 186)
• ctabs do not contain "A" when appropriate
  (github issue 187)
• Problems round-tripping Al2Cl6 via CTAB
  (github issue 189)
• Don't merge Hs onto dummies
  (github issue 190)
• Wavy bonds to Hs in CTABs should affect the stereochemistry of attached double bonds
  (github issue 191)
• Rendering binary compounds as ClH, FH, BrH or IH rather than putting H first.
  (github issue 199)
• Fixed data race condition in Code/GraphMol/MolAlign/testMolAlign.cpp
  (github pull 202)
• Re-prepared SDF/SMILES files of the MMFF validation suite + a fix
  (github pull 205)
• Problems round-tripping P with non-default valence.
  (github issue 206)
• Added a stricter definition of rotatable bonds as a new function in the ...
  (github pull 211)
• Code/GraphMol/AddHs patch proposal
  (github pull 212)
• Fix: Changed getNumReactantTemplates to GetNumReactantTemplates.
  (github pull 219)
• aromatic B ("b") causes errors from SMARTS parser
  (github issue 220)
• Segmentation fault for MMFF optimization with dummy atoms
  (github issue 224)
• isMoleculeReactantOfReaction() and isMoleculeProductOfReaction() not useable from SWIG wrappers
  (github issue 228)
• cartridge: mol_from_ctab() ignores argument about keeping conformers
  (github issue 229)
• Reaction not correctly preserving chirality on unmapped atoms.
  (github issue 233)
• AllChem.AssignBondOrdersFromTemplate() fails with nitro groups
  (github issue 235)
• Fix molecule dataframe rendering in pandas 0.13.x
  (github pull 236)
• Dummy labels copied improperly into products
  (github issue 243)
• Two bugfixes in MMFF code
  (github pull 248)
• seg fault when trying to construct pharmacophore with no conformation
  (github issue 252)
• EmbedMolecule() should not create a conformer for molecules that have zero atoms
  (github issue 256)
• cartridge: dice similarity calculation does not use USE_BUILTIN_POPCOUNT flag
  (github issue 259)
• cartridge: similarity calculations wrong for maccs fps when USE_BUILTIN_POPCOUNT flag is set
  (github issue 260)

New Features:

• Expose gasteiger charge calculation to SWIG
  (github issue 152)
• Added additional functionality to PandasTools
  (github pull 155)
• Add MMFFHasAllMoleculeParams() to SWIG interface
  (github issue 157)
• O3A code should throw an exception if the parameterization is not complete.
  (github issue 158)
• Support zero order bonds
  (github issue 168)
• Add attachmentPoint argument to ReplaceSubstructs
  (github issue 171)
• Forcefield constraints (distances, angles, torsions, positions)
  (github pull 172)
• Add kekulize flag to SDWriter
  (github issue 174)
• Support operator= for RWMol
  (github issue 175)
• Get GetAromaticAtoms() and GetQueryAtoms() working from python
  (github issue 181)
• Support richer QueryAtom options in Python
  (github issue 183)
• Support writing V3000 mol blocks
  (github issue 184)
• Allow disabling the building of tests
  (github issue 185)
• Expand DbCLI to allow updating databases
  (github issue 197)
• Code refactoring and enhancement to allow for O3A alignment according to atom-based Crippen logP contribs
  (github pull 201)
• call MolOps::assignStereochemistry() with flagPossibleStereoCenters true from within the molecule parsers.
  (github issue 210)
• Support passing of file-like PandasTools.LoadSDF
  (github pull 221)
• Reaction SMARTS parser should support agents
  (github issue 222)
• Add function to MolOps to allow a molecule to be split into fragments based on a query function
  This is useable from python as Chem.SplitMolByPDBResidues() and Chem.SplitMolByPDBChainId()
  (github issue 234)
• Adding option useCounts for Morgan fingerprints
  (github pull 238)
• support SimpleEnum functionality for adding recursive queries to reactions
  (github issue 242)
• Additional functions for bit vectors
  (github pull 244)
• Support of RDK fingerprints added to SimilarityMaps
  (github pull 246)
• add get3DDistance
• support 3D distances in the atom pair fingerprints
  (github issue 251)
• added MolOps::get3DDistanceMat() (Chem.Get3DDistanceMatrix() from python)

New Database Cartridge Features:

• Support configuration of fingerprint sizes in cartridge.
  (github issue 216)
• Add mol_to_ctab(mol, bool default true) to Postgres cartridge.
  (github pull 230)
• Adds sum formula function to PG cartridge.
  (github pull 232)

New Java Wrapper Features:

Deprecated modules (to be removed in next release):

Removed modules:

• The CMIM integration (previously available to python in the rdkit.ML.FeatureSelect package)
  has been removed due to license incompatibility.

Contrib updates:

• Added Contribution to train ChEMBL-based models
  (github pull 213)
• ConformerParser functionality
  (github pull 245)

Other:

• The Open3DAlign code is considerably faster.
• The SMILES parsing code is faster.
• Fix Bison 3.x incompabtility
  (github pull 226)
• Add Travis support
  (github pull 227)
• port of rdkit.ML bindings from Python/C API to boost::python
  (github pull 237)
• The code now builds more easily using the Anaconda python distribution's
  conda package manager
  (github pull 247)