rdkit/rdkit: 2018_09_1 (Q3 2018) Release

Release_2018.09.1 (Changes relative to Release_2018.03.1) Deprecations As part of the changes and cleaning up done for #1836 many of the #defines used in the RDKit have been renamed. USE_BUILTIN_POPCOUNT -> RDK_OPTIMIZE_NATIVE RDK_THREADSAFE_SSS -> RDK_BUILD_THREADSAFE_SSS BUILD_COORDGEN_SUPPORT -> RDK_BUILD_COORDGEN_SUPPORT BUILD_AVALON_SUPPORT -> RDK_BUILD_AVALON_SUPPORT BUILD_INCHI_SUPPORT -> RDK_BUILD_INCHI_SUPPORT BUILD_SLN_SUPPORT -> RDK_BUILD_SLN_SUPPORT RDK_CAIRO_BUILD -> RDK_BUILD_CAIRO_SUPPORT Documentation updates We have moved to using Sphinx's autodoc to create the Python API documentation. epydoc, the tool we used to use, is no longer actively developed and only supports Python2. There will undoubtedly be problems associated with the change; if you notice anything missing in the documetation or something that's really badly formatted, please either let us know or submit a PR with a fix. Backwards incompatible changes This release includes a set of changes to make the default arguments to common functions less error prone (github #1679). GetAtomSmiles() now generates isomeric SMILES by default. The ringMatchesRingOnly option to the FindMCS() function now applies to atom-atom matches as well as bond-bond matches. The Python functions EmbedMolecule() and EmbedMultipleConfs() now use the ETKDG algorithm by default instead of standard distance geometry. Highlights: This release includes two contributions from the Google Summer of Code: A new generalized fingerprint generator. An integration/port of MolVS to the core RDKit. The API on both of these may change a bit with future releases. The rdkit.Chem.Draw module now includes functions for depicting fingerprint bits. Morgan and RDKit fingerprints are currently supported. Acknowledgements: Boran Adas, Francois Berenger, Thomas Blaschke, Brian Cole, Andrew Dalke, Guillaume Godin, Brice Hoff, Brian Kelley, Karl Leswing, Susan Leung, Pat Lorton, Josh Meyers, Hirotomo Moriwaki, Dan Nealschneider, Noel O'Boyle, Pavel Raiskup, Sereina Riniker, Ricardo Rodriguez Schmidt, Stephen Roughley, Roger Sayle, Takayuki Serizawa, Rim Shayakhmetov, Gregory Simm, Jon Sorenson, Matt Swain, Kiran Telukunta, Paulo Tosco, Alain Vaucher, Maciej Wójcikowski, '0xDECAFC0FFEE', 'jaechanglim', 'paconius' Contrib updates: The FastCluster code has been updated. New Features and Enhancements: expose MolChemicalFeature.{get,set}ActiveConformer() to python (github issue #1636 from greglandrum) added Scripts/create_deb_packages.sh (github pull #1655 from UnixJunkie) Start to use Catch2 for new tests (github pull #1732 from greglandrum) Switch DbCLI scripts from optparse to argparse (github issue #1778 from greglandrum) Add EEM partial charges (github pull #1828 from greglandrum) Add header file providing access to RDKit compile time flags (github issue #1836 from greglandrum) add control over the coordinate precision to coordgen (github pull #1847 from greglandrum) Add Properties interface to ChemicalReactions (github pull #1848 from greglandrum) Switch Python API documentation generation over to Sphinx autodoc (github pull #1849 from greglandrum) expose MolOps::assignStereochemistryFrom3D() to Python (github issue #1850 from greglandrum) bivariate_normal deprecation in mlab.py of matplotlib (github issue #1851 from telukir) Expose minAtomRingSize() and minBondRingSize() to Python wrappers (github pull #1859 from mwojcikowski) enable building DLLs on Windows (github pull #1861 from ptosco) Fix compatibility with Boost 1.67+ (github pull #1864 from mcs07) Don't manually set RDConfig paths in conda env (github pull #1865 from mcs07) Make svg xmlns prefix use more consistent (github pull #1866 from mcs07) Add custom 3D Descriptors (github pull #1867 from greglandrum) Add initial Maestro format Supplier using maeparser library (github pull #1872 from lorton) add queryAtomNonHydrogenDegree() query operation (github issue #1873 from greglandrum) Add an auto-populated file with cmake config options (github pull #1874 from greglandrum) Custom property VSA (github pull #1884 from sriniker) Swap maeparser and coordgen dependencies to use releases (github issue #1887 from greglandrum) expose MolDraw2DSVG.tagAtoms() to python (github pull #1897 from greglandrum) allow the cleanup step of Mol2 parsing to be disabled (github pull #1898 from greglandrum) Allow Atom.GetAtomSmarts() to return isomeric SMILES (github pull #1902 from greglandrum) Allow coordgen and maeparser to be built as static libraries (github pull #1909 from ptosco) Support reaction_to_svg() in cartridge (github issue #1916 from greglandrum) Addresses several minor warning messages during the build (github pull #1935 from d-b-w) Some optimization of the queries constructed from SMARTS (github pull #1940 from greglandrum) Add ring/chain match constraints options to AdjustQueryParameters() (github issue #1943 from greglandrum) roc calculation naming problem (github pull #1975 from 0xDECAFC0FFEE) Fingerprinting functions should call assignStereochemistry() when necessary (github issue #1993 from bricehoff) Dev/GSOC2018_MolVS_Integration (github pull #2002 from susanhleung) GSoC 2018 - Fingerprints (github pull #2005 from Boranadas) port fingerprint bit rendering code from CheTo (github pull #2008 from greglandrum) PgSQL: add support for PostgreSQL_CONFIG cmake var (github pull #2014 from praiskup) Add missing boost header for v1.64 (github pull #2016 from gncs) Enhanced stereo read/write support in SDF files. (github pull #2022 from d-b-w) IPythonConsole hooks should copy the original docstring (github issue #2025 from adalke) Allow dumping interchange information into SVG files (github pull #2030 from greglandrum) MCS: add test for ring--non-ring matches at the atom level (github issue #2034 from greglandrum) Ability to generate a list of possible smiles representation for a given molecule (github issue #2042 from thegodone) add scoring test (relevant to #1975) (github pull #2064 from greglandrum) actually run the SmilesWriterNoNames() test (github pull #2067 from greglandrum) Add a default for maximum products generated by a reaction (maxProduc… (github pull #2069 from bp-kelley) Add user-defined literals for parsing SMILES and SMARTS (github pull #2070 from greglandrum) move rdInfoLog to stderr (github pull #2073 from greglandrum) add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() (github issue #2077 from greglandrum) Expose a CMake flag to build RDKit with -rpath (github pull #2084 from coleb) Dev/expose setquery to python (github pull #2088 from bp-kelley) Updated .gitignore with files generated outside of build directory. (github pull #2095 from ricrogz) Address compile warnings & trivial improvements (github pull #2097 from ricrogz) Coordgen: stop printing Templates location (github pull #2102 from greglandrum) Update Docs For CalcBEDROC (github pull #2103 from lilleswing) Bug Fixes: Cannot find rings for ChEBI 50252 (github issue #299 from greglandrum) Feature request: #defines to test RDKit version (github issue #1454 from baoilleach) Atoms in residue read from pdb lose their AtomPDBResidueInfo after reaction (Bug) (github issue #1632 from hjuinj) SMARTS parse failure for some queries involving Hs (github issue #1719 from greglandrum) Conformer indexing bug in RDFreeSASA.cpp? (github issue #1786 from paconius) allow libs to not be installed (github pull #1832 from greglandrum) RWMol::addAtom(Atom,bool) missing from Java wrappers (github issue #1837 from greglandrum) RWMol::clear now calls ROMol::initMol (github pull #1844 from bp-kelley) Allow types.h to be included in applications that use /D_USE_MATH_DEFINES (github pull #1846 from d-b-w) Fixes failing Python tests on Windows (github pull #1855 from ptosco) Allow building on cygwin using -std=c++11 (github pull #1856 from greglandrum) Stop using the cmake Boost:: targets (github pull #1858 from greglandrum) R-group Decomposition: allow H replacements when matchOnlyAtRgroups is set (github pull #1871 from bp-kelley) Mark cartridge functions as being parallel safe (github issue #1886 from greglandrum) Fixes locale handling on Windows (github pull #1892 from ptosco) get the pandas tests working with pandas 0.23 (github pull #1896 from greglandrum) "make install" appears to miss RDBoost/export.h (github issue #1903 from baoilleach) Fix curl fallback for downloading files (github pull #1904 from d-b-w) Bond stereo information not output to SMARTS (github issue #1906 from greglandrum) Library .so names missing RDKit? (github issue #1913 from baoilleach) Negated atom number queries in SMARTS should not set atomic number of query atom (github issue #1920 from greglandrum) memory leak in Get3DDistanceMatrix (github issue #1924 from jaechanglim) Atom with bond to itself is accepted by the SMILES parser. (github issue #1925 from tblaschke) Possibly incorrect aromatic SMILES generated for structure (github issue #1928 from baoilleach) Using the coordgen library seems to cause a seg fault (github issue #1929 from JoshuaMeyers) Aromaticity failure in 7-ring with charged radical carbon (github issue #1936 from bp-kelley) Fix embarassing bug, check the counter each iteration (github pull #1939 from bp-kelley) RuntimeError when importing rdkit.Chem.Descriptors with Python 3.7 (github issue #1948 from drkeoni) Query features in products of rxn files not properly handled (github issue #1950 from greglandrum) ReactionToSmarts broken for multi-component templates (github issue #1955 from bp-kelley) update knime urls in overview.md (github pull #1966 from greglandrum) CXN extended SMILES labels are not applied to the correct atom in SMILES with explicit H (github issue #1968 from baoilleach) MolFromSmarts MolToSmarts fails to roundtrip on patterns with chirality (github issue #1985 from bp-kelley) QueryAtoms with atom list queries should not have the atomic number set (github issue #1988 from greglandrum) RemoveHs not properly updating double bond stereoatoms (github issue #1990 from shayakhmetov) Error while parsing empty atom list in Mol files. (github issue #2000 from drkeoni) Cleanup step of sanitization sometimes sets undesired formal charges (github issue #2020 from avaucher) GetBondSmiles() returns nothing for wedged bonds when allBondsExplicit is true (github issue #2029 from greglandrum) PMIs and NPRs return same value between different conformer (github issue #2037 from philopon) Failure to parse V3K mol file with bonds to multi-center linkage points (github issue #2040 from greglandrum) patch a memory allocation problem in the maeparser v1.0.0 (github pull #2044 from greglandrum) CIPRank values from JSONDataToMols are not unsigned (github issue #2046 from greglandrum) switch to v1.0.1 of the maeparser (github pull #2048 from greglandrum) Update fastcluster code (github pull #2051 from greglandrum) Fix memory leak in Dict operator= (github pull #2061 from bp-kelley) Atom mapping lost after call to MergeQueryHs() (github issue #2062 from greglandrum) Drawing racemic bond stereo as crossed bonds should be the default (github issue #2063 from coleb) Moved test.h from RDBoost to RDGeneral for consistency with export.h (github pull #2074 from ptosco) CTABs behave differently than before regarding stereo (github issue #2082 from bp-kelley) BitInfo not complete for RDKFingerprint (github issue #2115 from greglandrum) Removed code: Remove the deprecated MolDrawing code (github pull #2111 from greglandrum