Dear all, I have tagged a beta of the next RDKit release here: https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_1b1
The relevant section of the release notes is below. Note that the list of people in the acknowledgement section was mostly created automatically from github. If you feel like I missed you, or if I got your name wrong, please let me know so that I can update the release notes before the actual release. Unless someone specifically requests them, I don't plan to do binaries for the beta. Unless major problems are found, I plan to do the actual release late next week. Between now and then I hope to get a few more bugs crushed, but there shouldn't be any additional feature additions. Best, -greg # Release_2016.03.1 (Changes relative to Release_2015.09.2) ## Important In order to build the RDKit, it is now necessary to have at least v1.7 of numpy installed. ## Acknowledgements: Note: The RDKit has the wonderful "problem" that there are a lot of contributors and it's tough for me to capture them all to put together release notes. I don't even know many of the contributors (which is *awesome!*) The names here come largely from what I pull in an automated way from github. In cases where there's no real name listed in github, I either guessed or used just the github alias in quotes. If I got it wrong, please let me know! Josep Arus, Nik Bates-Haus, Andrew Dalke, 'DoliathGavid', 'elcaceres', Peter Gedeck, James Jeffryes, Brian Kelley, Rich Lewis, Daniel Lowe, 'maddogcz', Kozo Nishida, Michal Nowotka, Axel Pahl, Steven Roughley, Alexander Savelyev, Nadine Schneider, Teague Sterling, Nik Stiefl, Matt Swain, Eric Ting, Paolo Tosco, Samo Turk, JL Varjo, Riccardo Vianello ## Highlights: - Improvements to the build system: it's now much easier to build with InChI and/or Avalon support since cmake now knows how to fetch the appropriate source code for you. Building the PostgreSQL cartridge is now integrated into normal build process. - Some improvements to molecule rendering and Jupyter notebook integration: The new `Draw.PrepareMolForDrawing()` function takes care of standard tasks like wedging bonds, kekulization, and adding chiral Hs. `Draw.MolsToGridImage()` can generate SVGs and uses the new molecular drawing code for PNGs when possible. The Jupyter notebook integration uses the new drawing code when possible. - Error and warning messages from the C++ core can now be displayed in the Jupyter notebook ## Bug Fixes: - Sanitizer rejects higher valency halides (github issue #115 from dan2097) - Bad E/Z assignment from ctab (github issue #188 from greglandrum) - bad E/Z assignment from ctab (github issue #192 from greglandrum) - Documentation is still python2 specific. (github issue #374 from greglandrum) - SVG export - Python 3 support (github issue #398 from maddogcz) - FragmentOnBonds() producing incorrect chirality (github issue #511 from greglandrum) - Rings containing all dummy atoms with single bonds are flagged as aromatic (github issue #518 from greglandrum) - IPython integration broken with latest Jupyter (github issue #666 from samoturk) - Added missing include/forward declarations (github pull #668 from ptosco) - Fixes a memory leak in fragmentMol (github pull #669 from bp-kelley) - resetVect option being ignored by reaccsToFingerprint() (github issue #671 from greglandrum) - failure in AddHs when addCoords is true and coords are all zero (github issue #678 from greglandrum) - 404 error for the link to Installation instructions (github issue #679 from EricTing) - Fix java8 build (github pull #681 from greglandrum) - Smiles containing "[as]" do not parse. (github issue #682 from greglandrum) - SMARTS reaction triggers invariant violation on chiral compounds (github issue #685 from JamesJeffryes) - partially specified chiral substructure queries don't work properly (github issue #688 from bp-kelley) - ExactMolWt ignoring the mass of the electron (github issue #694 from greglandrum) - Bad 1-4 bounds matrix elements in highly constrained system (github issue #696 from greglandrum) - More ChEMBL molecules that fail bounds smoothing (github issue #697 from greglandrum) - Molecule serialization doesn't read/write atomic numbers above 128 (github issue #713 from greglandrum) - AddHs cip rank is declared <int> should be unsigned int? (github issue #717 from bp-kelley) - ensure line endings are handled consistently for all users (github pull #729 from rvianello) - Fixes return type of operator[] (fails on later clangs) (github pull #733 from bp-kelley) - Fix/thread safe localeswitcher line endings (github pull #743 from bp-kelley) - Fixes Boost 1.46 issues with type traits (github pull #748 from bp-kelley) - PR #749 causes seg faults on windows (github issue #750 from greglandrum) - Fixes notebook problems with newer jupyter installs (github pull #753 from bp-kelley) - Double bond geometry loss on calling removeHs (github issue #754 from sroughley) - Bug fix to getShortestPath (github pull #757 from JLVarjo) - reversed stereochemistry with sulfoxides and ring closures (github issue #760 from greglandrum) - libRDBoost.so.1: undefined symbol (github issue #762 from kozo2) - Removed -Xdoclint:none flag when packing org.RDKitDoc.jar (github pull #763 from undeadpixel) - AnyBond specification treated as single when joining rings in SMARTS (github issue #766 from teaguesterling) - CanonicalRankAtomsInFragment() leaks when called from Python (github issue #769 from greglandrum) - MolCanvas2D drawing upside down (github issue #774 from greglandrum) - Drawing single-atom molecules hangs. (github issue #781 from greglandrum) - chiral lexical order for ring closure after branch (github issue #786 from adalke) - surface -> self.surface (github pull #787 from mnowotka) - Chem.MolToSmarts param misnomer (github issue #792 from elcaceres) - Fixes MolToSmarts python docs (github pull #793 from bp-kelley) - npscorer.py: Py3 compat and importable from other locations (github #801 from apahl) - Pre-condition Violation: bad bond type (github issue #805 from nbateshaus) - rooted atom fingerprint non identical for the same molecules (github issue #811 from nisti74) - test60RunSingleReactant() not being run (github issue #825 from greglandrum) - PostgreSQL bug fixes (github pull #835 from ptosco) - Return value of NumRadicalElectrons and NumValenceElectrons should be integer (github issue #846 from gedeck) ## New Features and Enhancements: - switch to using new version of avalon toolkit (github issue #382 from greglandrum) - MolDraw2D: Expand basic drawing api (github issue #417 from greglandrum) - MolDraw2D: add options (github issue #424 from greglandrum) - fixed FutureWarning in PeriodicTable.py (github pull #665 from richlewis42) - first pass, using google style (github pull #672 from greglandrum) - Use sets instead of and map. Minor comments cleanup. (github pull #675 from DoliathGavid) - Dev/squash msvc14 warnings (github pull #684 from bp-kelley) - Fix/stop unnecessary filtercatalog updates (github pull #690 from bp-kelley) - Add RDK_USE_BOOST_SERIALIZATION configure option (On by default) (github pull #691 from bp-kelley) - Minor optimizations of the force field minimization code, fix for issue 696 (github pull #693 from greglandrum) - Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints (github issue #695 from greglandrum) - Fixed a couple of compilation warnings in Resonance.cpp/Resonance.h (github pull #701 from ptosco) - Dev/run single reactant (github pull #705 from bp-kelley) - Updates CMAKE_SOURCE_DIR to CMAKE_CURRENT_SOURCE_DIR (github pull #707 from bp-kelley) - Make LocaleSwitcher threadsafe (github issue #710 from greglandrum) - Exposes Get/Set Double, Int, Uint and bool props to molecules (github pull #711 from bp-kelley) - Speed up molblock generation (github pull #712 from greglandrum) - Expose generateOneProductSet? (github issue #721 from DoliathGavid) - Add a reader for FPB files (still experimental) (github pull #724 from greglandrum) - replace std::map::at with std::map::operator[] (github pull #730 from rvianello) - Fix/get double prop get props asdict (github pull #734 from bp-kelley) - Add support for Tversky similarity to the FPB reader (github pull #735 from greglandrum) - Fix ConformerParser to use const std::string & (github pull #737 from mcs07) - Fix/expose invariant exception (github pull #740 from bp-kelley) - Support CTABs where the second letter in atom symbols is capitalized (github issue #741 from greglandrum) - Adds support for capturing RDLogs in Python StdErr streams (github pull #749 from bp-kelley) - Allow adding Hs only to atoms matching a query operator (github issue #758 from greglandrum) - Add argument to addHs allowing only certain Hs to be considered (github pull #759 from greglandrum) - avoid the multiple definition of rdkitVersion/boostVersion (github pull #761 from rvianello) - cleanup possible pythonObjectToVect leaks in python wrappers (github issue #764 from greglandrum) - Stop possible core leaks in pythonObjectToVect() (github pull #770 from greglandrum) - Add C++ function to prepare mol for rendering (github issue #771 from greglandrum) - Prefer wedging bonds to Hs (github issue #772 from greglandrum) - Add prepareMolForDrawing() function to C++ (github pull #775 from greglandrum) - Support blanks in MolsToGridImage() (github issue #776 from greglandrum) - A number of small additions and features to the drawing code (github pull #802 from greglandrum) - Support larger isotope deltas in the chirality assignment (github issue #803 from greglandrum) - Adds option RDK_USE_COMPLEX_ROTOR_DEFINITION (github pull #810 from bp-kelley) - add Draw.MolsToSVGGrid() (github pull #817 from greglandrum) - make Hs black instead of gray (github pull #819 from greglandrum) - Fix alignMols so that it takes into account of QueryAtoms and QueryBonds (github pull #821 from DoliathGavid) - feat/github831: Add getText() static method. (github pull #832 from greglandrum) - Add an unfolded count-based version of the RDKFingerprint (github pull #838 from NadineSchneider) - Add some utils functions to ChemReactions (github pull #840 from NadineSchneider) - Autodetect boost c++ library and compile with matching one (github pull #845 from bp-kelley) ## New Database Cartridge Features: - support providing InChI (or InChI key) generation options in cartridge (github pull #755 from greglandrum) - building the cartridge is now integrated with the cmake build system (github pull #785 from ptosco) ## New Java Wrapper Features: - Add a bit more control over the lazy MaxMin picker to the java layer (github pull #791 from greglandrum) - Ensure reduceProductToSideChains exposed in Java/Swig (github issue #744 from bp-kelley) ## Deprecated code (to be removed in next release): ## Removed code: ## Contrib updates: ## Other:
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