rdkit/rdkit: 2016_09_1 (Q3 2016) Release

Release_2016.09.1 (Changes relative to Release_2016.03.1) Important The adjustQueryParameters structure has been rewritten. If you were using this in your code, you'll need to update your code. Acknowledgements: Brian Cole, Piotr Dabrowski, Jan Domanski, Peter Gedeck, Richard Hall, Brian Kelley, Joos Kiener, 'maddogcz', John Mayfield, 'michalsta', Michal Nowotka, 'philopon', Nico Pulver, Sereina Riniker, Stephen Roughley, Roger Sayle, Nadine Schneider, Gianluca Sforna, Peter Shenkin, Paolo Tosco, David Turbert, Riccardo Vianello, Maciek Wojcikowski Highlights: New AdjustQueryProperties() (adjustQueryProperties() in C++) for fine-tuning substructure queries. ReactionEnum functionality adds significant new capabilities for doing library enumeration Similarity searches with the PostgreSQL cartridge are substantially faster New 3D descriptors (requires Eigen3 if you are building them yourself) New Features and Enhancements: Trajectory/Snapshot objects (github pull #863 from ptosco) Adds Avalon fingerprints to default set (github pull #871 from bp-kelley) Adds the default index to the building block templates (github pull #873 from bp-kelley) Pandas: Allow reading just the properties from SDF file (github pull #883 from mwojcikowski) Dev/filtercatalog functional groups (github pull #885 from bp-kelley) Dev/preprocessrxn cpp (github pull #892 from bp-kelley) Rollup of warning squashing (with some tests diagnostics thrown in) (github pull #895 from bp-kelley) Adds RDAny (smaller generic holder) Updates all used dictionaries (github pull #896 from bp-kelley) expose FPS functions to SWIG (github pull #897 from greglandrum) Add SaveFile method to the PyMol wrapper (github pull #898 from greglandrum) Add a MultiFPBReader class (github pull #909 from greglandrum) Improved Python doc strings for Trajectory/Snapshot objects (github pull #912 from ptosco) Added support for building the gzip'd stream test (github pull #914 from ptosco) Improved Trajectory Python doc strings (github pull #915 from ptosco) improve error reporting for kekulization failures (github pull #919 from greglandrum) Feat/github934 (github pull #939 from greglandrum) Add support for a simplified aromaticity model. (github pull #942 from greglandrum) Dev/moldescriptors callables (github pull #944 from bp-kelley) Dev/cleanup warnings (github pull #948 from greglandrum) Modifications to enable building with MinGW compilers (github pull #960 from ptosco) Made DistGeomHelpers test robust against small 3D coordinate variations (github pull #961 from ptosco) Adds aromatization and reaction options to AdjustQuery (github pull #965 from bp-kelley) Improved planarity for ETKDG (github pull #967 from sriniker) Fixes built-in popcount in PgSQL cartridge on Windows (github pull #978 from ptosco) A variety of drawing-related changes (github pull #986 from greglandrum) Get pango 2D depiction to work with cairocffi (github pull #998 from ptosco) Adds Atom atom map and rlabel apis (github pull #1004 from bp-kelley) Dev/chemtransforms chirality (github pull #1006 from bp-kelley) Added the option to label deuterium and tritium as D and T (github pull #1011 from ptosco) Adds replaceCore function that takes a matchVect (github pull #1013 from bp-kelley) Add an initial version of wavy bonds (github pull #1014 from greglandrum) remove a compiler warning (github pull #1019 from greglandrum) Make the Contrib directory available in RDConfig (github pull #1024 from NadineSchneider) Adds some additional canned atom and bond query definitions (github pull #1047 from greglandrum) Draw crossed bonds (github pull #1052 from greglandrum) Alex/struct checker apr15 (github pull #1054 from bp-kelley) MolDraw2D: allow the amount of padding around atom labels to be adjusted. (github issue #1056 from greglandrum) Add multiple molecule drawing to the C++ interface (github pull #1059 from greglandrum) add pickle support to FilterCatalog (github pull #1063 from greglandrum) Issue #1066: Improved .gitignore file (github pull #1068 from gedeck) Cleanup of Scaffolds Python code (github pull #1069 from gedeck) Consistent formatting of Python code (github issue #1071 from gedeck) Improved test coverage of Python code (github pull #1081 from gedeck) Improved test coverage of rdkit.DataStructs (github pull #1083 from gedeck) Add some 3D molecular descriptors (requires Eigen3) (github pull #1084 from greglandrum) Conformer GetPos returns a numpy array rather than a tuple of tuples (github pull #1087 from jandom) make the 3D descriptors available in the Descriptors module (github pull #1097 from greglandrum) Documentation update. (github pull #1100 from greglandrum) Provide SVG output from the cartridge (github pull #1109 from greglandrum) Allow the output of ROMol::debugMol() to show up in jupyter (github pull #1110 from greglandrum) Dev/reaction enumeration (github pull #1111 from bp-kelley) yapf formatting of recent changes to Python code in rdkit and Code (github pull #1120 from gedeck) Add a parameters structure for controlling the embedding options. (github pull #1121 from greglandrum) add more detailed error reporting when python tests fail in TestRunner.py (github pull #1122 from greglandrum) add support for a default constructor to the python-exposed RWMol class (github pull #1129 from greglandrum) The RunStruchk function is not exposed in pyAvalonTools (github issue #1130 from pulveni1) SSSR performance improvements to support larger systems (github pull #1131 from coleb) Script PythonFormat.py will test the RDkit python code for conformance with the agreed format using yapf (github pull #1133 from gedeck) support additional trans-uranic elements (github pull #1134 from greglandrum) Expanded sequence support (github pull #1140 from greglandrum) add UGM link to documentation (github pull #1142 from David-Turbert) Remove iPythonConsole configuration for normal Draw tests (github pull #1146 from gedeck) Wrap DetectBondStereoChemistry in python (github pull #1156 from coleb) New Database Cartridge Features: Provide SVG output from the cartridge (github pull #1109 from greglandrum) Add cartridge support for adjustQueryProperties() (github pull #949 from greglandrum) refactoring of the postgresql cartridge (github pull #992 from rvianello) New Java Wrapper Features: Expose filtermatch to swig (github pull #1117 from bp-kelley) adjustQueryProperties() Java wrappers for Trajectory/Snapshot objects (github pull #977 from ptosco) Added getAlignmentTransform to ROMol.i to expose in Java SWIG wrapper (github pull #1155 from sroughley) Bug Fixes: initialization of the PeriodicTable object should be made thread-safe (github issue #381 from greglandrum) AssignAtomChiralTagsFromStructure() not recognizing chiral S (github issue #607 from greglandrum) Fixed a few typos in Code/PgSQL/rdkit/CMakeLists.txt (github pull #867 from ptosco) MergeQueryHs explicit H warning when no explicit Hs were actually used (github issue #868 from bp-kelley) Fixes regression in python api CalcNumRotatableBonds (github pull #870 from bp-kelley) Single atoms setting radius 1 bits in Morgan fingerprints (github issue #874 from greglandrum) Providing subImgSize argument to MolsToGridImage() causes drawing failure (github issue #876 from greglandrum) javadoc failure on CentOS 7 (github pull #878 from ptosco) adjust cartridge tests after the fix for #874 (github pull #884 from greglandrum) bugreport: invalid handling of negation of aromaticity when parsing SMARTS (github issue #893 from michalsta) Fixes depictor problem with empty fragments (github pull #894 from greglandrum) Fix building with G++ on Mac OS X (github pull #900 from johnmay) linked additional libs to fix a build failure on Windows (github pull #901 from ptosco) Rdkit 2016_03_1 generate SVG typo in Python bindings (github issue #903 from maddogcz) PAINS filters update fails when old Python is installed (github issue #904 from greglandrum) rdMolDraw2D.PrepareMolForDrawing() should not default to forceCoords=True (github issue #906 from greglandrum) AddHs() using 3D coordinates with 2D conformations (github issue #908 from greglandrum) ugly coordinates generated for peptide chains (github issue #910 from greglandrum) Cartridge: makefile not using -O2 for C code. (github issue #920 from greglandrum) Removes incorrect setting of hasNonPodData (github pull #923 from bp-kelley) cleanups of RDLog's tee behavior (github pull #926 from greglandrum) initialize boost::once_flag properly (github pull #927 from greglandrum) sys not imported in IPythonConsole.py (github issue #928 from greglandrum) AddTee is now SetTee (github pull #930 from bp-kelley) mistake in SVG generated for wedged bonds (github issue #932 from greglandrum) PandasTools AttributeError with pandas-0.18.1 (github issue #933 from philopon) Jupyter Notebooks: Issue with PyMol.MolViewer on Windows (github issue #936 from kienerj) Subshape module: Not Python 3 compatible (github issue #937 from kienerj) property dictionaries leaking memory (github issue #940 from greglandrum) Bug when removing stereo info? (github pull #946 from mnowotka) Distorted aromatic rings from ETKDG (github issue #952 from greglandrum) MolDraw2D: default color should not be cyan (github issue #953 from greglandrum) GetPropNames() no longer working on Atoms or Bonds (github issue #955 from greglandrum) Kekulization issues post successful smiles parsing (github issue #962 from bp-kelley) Fixes includes for older boost/gcc (github pull #966 from bp-kelley) ugly conformations can be generated for highly constrained ring systems (github issue #971 from greglandrum) Cleanup bad conformations (github pull #973 from greglandrum) Unnecessary warnings in rxn.validate() (github issue #975 from greglandrum) Minor fix to Code/GraphMol/Wrap/testTrajectory.py (github pull #979 from ptosco) prepareMolForDrawing(): Do not add Hs to some three-coordinate Cs (github issue #982 from greglandrum) MolDraw2D: wedged bonds between chiral centers drawn improperly (github issue #983 from greglandrum) Fix format-security GCC warning (github pull #984 from giallu) MolDraw2D scaling problems (github issue #985 from greglandrum) RIght-justified elements in RCSB SDF files can now be parsed (github pull #994 from ptosco) Right-justified elements in RCSB SDF files raise an exception (github issue #995 from ptosco) ChemReactions: Bugfix in copy constructor (github pull #996 from NadineSchneider) PgSQL README typos (github pull #997 from ptosco) Fixes rounding errors in test (github pull #1001 from bp-kelley) Fixes middle-justified symbols in sd files, adds M_CHG tests (github pull #1002 from bp-kelley) fix compatibility issues with postgres < 9.5 (#1000) (github pull #1005 from rvianello) Fixes MMFF94 aromaticity perception and ChemicalForceFields.MMFFHasAllMoleculeParams() (github pull #1007 from ptosco) fixes typo which breaks the PostgreSQL cartridge build on Windows (github pull #1008 from ptosco) Fix Inchi being hardcoded into PostgreSQL (github pull #1009 from ptosco) Support ETKDG from within the SWIG wrappers (github pull #1010 from greglandrum) move definition of computedPropName to namespace RDKit::detail (github issue #1017 from greglandrum) fix non-inchi build (github pull #1018 from greglandrum) Fixes #1018 (github pull #1020 from ptosco) GetSSSR interrupts by segmentation fault (github issue #1023 from PiotrDabr) FMCS fix for Windows DLLs (github pull #1030 from ptosco) Cause ImportError from failed dlopen of the rdBase.so shared library to propagate. (github pull #1032 from coleb) typos in MMPA hash code (github issue #1044 from greglandrum) MolOps::cleanUp() being called by CTAB parser even when sanitization isn't on (github issue #1049 from greglandrum) Bond::BondDir::EITHERDOUBLE not exposed to python (github issue #1051 from greglandrum) add python3 compatibility (github pull #1057 from greglandrum) doc updates from Dave Cosgrove (github pull #1060 from greglandrum) Fix leak with renumberAtoms() in the SWIG wrappers (github pull #1064 from greglandrum) Timings on Windows with Python 3 (github pull #1067 from ptosco) computeInitialCoords() should call the SSSR code before it calls assignStereochemistry() (github issue #1073 from greglandrum) Remove duplicates doesn't work on first column in rdkit.Dbase.DbUtils.GetData (github issue #1082 from gedeck) clear up a bunch of windows warnings (github pull #1086 from greglandrum) MolsToGridImage barfs on '&' in labels, at least with useSVG=True (github issue #1090 from shenkin) Fixes csharp build for 64 bit systems (github pull #1098 from bp-kelley) Cartridge: some C++ functions returning pointers to local storage (github issue #1106 from greglandrum) Check for doubles after other integer types when reporting properties (github pull #1115 from bp-kelley) Replace has_key use in Python (#issue1042) (github pull #1132 from gedeck) fix moldraw2d headers installation path (github pull #1143 from giallu) Remove iPythonConsole configuration for normal Draw tests (github pull #1146 from gedeck) Adds SWIGWIN definition in WIN32 if not 32bit (github pull #1158 from bp-kelley) Fix/java win64 memoryleak (github pull #1159 from bp-kelley) Deprecated code (to be removed in a future release): rdkit.VLib python module Removed code: Contrib updates: added an implementation of the Gobbi Atom-Atom-Path (AAP) similarity (github pull #1015 from Richard-Hall) Other