Thanks for pointing that out. I will take a look and see if I can figure out what's going on.
-greg On Fri, Oct 25, 2019 at 9:53 AM Hongbin Yang <yanyangh...@163.com> wrote: > Hi Greg, > > Great to know the release! > > But the docs for Python API does not work in my browser. It is empty for > every page such as http://rdkit.org/docs/source/rdkit.Chem.AllChem.html > > Am I the only one? > > Best, > > Hongbin Yang 杨弘宾, Ph.D. > Research: Toxicophore and Chemoinformatics > On 10/25/2019 15:20，Greg Landrum<greg.land...@gmail.com> > <greg.land...@gmail.com> wrote： > > Dear all, > > I'm pleased to announce that the next version of the RDKit - 2019.09 - is > released. The release notes are below. > > The release files are on the github release page: > https://github.com/rdkit/rdkit/releases/tag/Release_2019_09_1 > > Binaries have been uploaded to anaconda.org (https://anaconda.org/rdkit). > The available conda binaries for this release are: > Linux 64bit: python 3.6, 3.7 > Mac OS 64bit: python 3.6, 3.7 > Windows 64bit: python 3.6, 3.7 > > Conda builds of the PostgreSQL cartridge are also available: > Linux 64bit: postgresql 9.6, 10, 11 > Mac OS 64bit: postgresql 9.6, 10, 11 > > I believe that conda-forge will also switch to the new version in the near > future. > > The online version of the documentation at rdkit.org ( > http://rdkit.org/docs/index.html) has been updated. > > Some things that will be finished over the next couple of days: > - The conda build scripts will be updated to reflect the new version > - The homebrew script > > Thanks to everyone who submitted code, bug reports, and suggestions for > this release! > > Please let me know if you find any problems with the release or have > suggestions for the next one, which is scheduled for March/April 2020. > > Best Regards, > -greg > > # Release_2019.09.1 > (Changes relative to Release_2019.03.1) > > ## Important > - The atomic van der Waals radii used by the RDKit were corrected/updated > in #2154. > This leads to different results when generating conformations, molecular > volumes, > and molecular shapes. > > ## Backwards incompatible changes > - See the note about atomic van der Waals radii above. > - As part of the enhancements to the MolDraw2D class, we changed the type > of > DrawColour from a tuple to be an actual struct. We also added a 4th > element to > capture alpha values. This should have no affect on Python code (the > alpha > value is optional when providing color tuples), but will require changes > to C++ > and Java/C# code that is using DrawColour. > - When reading Mol blocks, atoms with the symbol "R" are now converted into > queries that match any atom when doing a substructure search (analogous > to "*" > in SMARTS). The previous behavior was to only match other dummy atoms > - When loading SDF files using PandasTools.LoadSDF(), we now default to > producing isomeric smiles in pandas tables. To reproduce the original > behavior, use isomericSmiles=False in the call to the function. > - The SMARTS generated by the RDKit no longer contains redundant wildcard > queries. This means the SMARTS strings generated by this release will > generally > be different from that in previous releases, although the results > produced by > the queries should not change. > - The RGroupDecomposition code now removes Hs from output R groups by > default. > To restore the old behavior create an RGroupDecompositionParameters > object and > set removeHydrogensPostMatch to false. > - The default values for some of the new fingerprint generators have been > changed so > that they more closely resemble the original fingerprinting code. In > particular most fingerprinters no longer do count simulation by default > and > the RDKit fingerprint now sets two bits per feature by default. > - The SMARTS generated for MCS results using the ringMatchesRingOnly or > completeRingsOnly options now includes ring-membership queries. > > ## Highlights: > - The substructure matching code is now about 30% faster. This also > improves the > speed of reaction matching and the FMCS code. (#2500) > - A minimal JavaScript wrapper has been added as part of the core release. > (#2444) > - It's now possible to get information about why molecule sanitization > failed. (#2587) > - A flexible new molecular hashing scheme has been added. (#2636) > > ## Acknowledgements: > Patricia Bento, Francois Berenger, Jason Biggs, David Cosgrove, Andrew > Dalke, > Thomas Duigou, Eloy Felix, Guillaume Godin, Lester Hedges, Anne Hersey, > Christoph Hillisch, Christopher Ing, Jan Holst Jensen, Gareth Jones, Eisuke > Kawashima, Brian Kelley, Alan Kerstjens, Karl Leswing, Pat Lorton, John > Mayfield, Mike Mazanetz, Dan Nealschneider, Noel O'Boyle, Stephen Roughley, > Roger Sayle, Ricardo Rodriguez Schmidt, Paula Schmiel, Peter St. John, > Marvin > Steijaert, Matt Swain, Amol Thakkar Paolo Tosco, Yi-Shu Tu, Ricardo > Vianello, > Marc Wittke, '7FeiW', 'c56pony', 'sirbiscuit' > > > ## Bug Fixes: > - MCS returning partial rings with completeRingsOnly=True > (github issue #945 from greglandrum) > - Alternating canonical SMILES for fused ring with N > (github issue #1028 from greglandrum) > - Atom index out of range error > (github issue #1868 from A-Thakkar) > - Incorrect cis/trans stereo symbol for conjugated ring > (github issue #2023 from baoilleach) > - Hardcoded max length of SMARTs string cut of input query for FragCatlog > (github issue #2163 from 7FeiW) > - VSA_EState {1, ..., 10} calculated by rdkit doesn't seem correct. > (github issue #2372 from c56pony) > - MolStandardize: FragmentRemover should not sanitize fragments > (github issue #2411 from greglandrum) > - MolStandardize: combinatorial explosion in Normalizer > (github issue #2414 from greglandrum) > - MCS code doesn't return envelope MCS if CompleteRingsOnly is true > (github issue #2420 from greglandrum) > - RemoveHs() does not remove all hydrogens. > (github issue #2422 from paulaju) > - Incorrect assignment of explicit Hs to Al+3 read from mol block > (github issue #2423 from greglandrum) > - Cannot set maxProducts > 1000 in RunReactants > (github issue #2427 from tduigou) > - Chem.MolStandardize.standardize.Standardizer drops molecular properties > (github pull #2431 from lilleswing) > - Canon::rankMolAtoms results in crossed double bonds in rings > (github issue #2437 from greglandrum) > - make boost::iostreams optional > (github pull #2440 from greglandrum) > - Fix/rgroup sdf isotope > (github pull #2449 from bp-kelley) > - Uncharger incorrectly removing charge from boron anions > (github issue #2452 from greglandrum) > - Add java builds to azure devops > (github pull #2460 from greglandrum) > - Cart fixes > (github pull #2462 from jones-gareth) > - Negative atom map values cause depickling to fail > (github issue #2465 from greglandrum) > - Deserialization failures crash Java wrapper > (github issue #2466 from greglandrum) > - rdkit.six fix and cleanup > (github pull #2469 from rvianello) > - dummy atom queries are flagged as complex > (github issue #2471 from greglandrum) > - 3D structure display broken in jupyter notebook > (github issue #2473 from greglandrum) > - Inconsistent defaults for nonBondedThresh in MMFF optimization > (github issue #2475 from greglandrum) > - Fix/rgroup multiple labels > (github pull #2481 from bp-kelley) > - 2D Depiction clipped atom highlighting > (github issue #2486 from DavidACosgrove) > - BRICSBuild now passes scrambleReagents to children > (github pull #2488 from greglandrum) > - Pattern Fingerprint Issues > (github issue #2501 from jones-gareth) > - CMake Error: Wrap directories being used when python build is turned > off > (github issue #2516 from jasondbiggs) > - - fixes ResonanceMolSupplier bug in perceiving conjugated groups > (github pull #2517 from ptosco) > - Fix/mmff threadsafety issues > (github pull #2518 from bp-kelley) > - update expected SVG output in cartridge tests > (github pull #2520 from greglandrum) > - fix to SDWriter docs > (github pull #2521 from pstjohn) > - Fix the azure pipelines builds > (github pull #2522 from greglandrum) > - Code cleanups from PVS/Studio > (github pull #2531 from greglandrum) > - getAtomNeighbors() and getAtomBonds() not in SWIG wrappers. > (github issue #2532 from greglandrum) > - Default sanitizerxn doesn't aromatize if possible > (github issue #2547 from bp-kelley) > - Add RDKIT_FILEPARSERS_EXPORT to finishMolProcessing > (github pull #2551 from d-b-w) > - Chem.rdFMCS.FindMCS hangs for certain ligand pairs > (github issue #2581 from lohedges) > - fix the inclusion path for the targets file (#2584) > (github pull #2589 from rvianello) > - Fix inocuous typo/bug in Dative bond matching > (github pull #2593 from ricrogz) > - E/Z and CIS/TRANS stereo bonds are incorrectly matched > (github pull #2596 from ricrogz) > - Uncharger ignores dications > (github issue #2602 from greglandrum) > - Possible Garbage Collection Bug in Pharmacophore Generation > (github issue #2603 from cing) > - Uncharger incorrectly neutralizes cations when non-neutralizable > anions are present. > (github issue #2605 from greglandrum) > - Bad valence corrections on Pb, Sn > (github issue #2606 from greglandrum) > - Pb and Sn should support valence 2 > (github issue #2607 from greglandrum) > - Uncharger incorrectly modifying a zwitterion > (github issue #2610 from greglandrum) > - CanonicalRankAtomsInFragment breakTies doesn't > (github issue #2611 from bp-kelley) > - Pattern fingerprint failing substructure condition in very large > molecules > (github issue #2614 from greglandrum) > - Memory leak with Chem.Atom() constructor > (github issue #2639 from AlanKerstjens) > - Fixes: Atoms in non-standard valences not being properly written to > mol blocks > (github pull #2646 from greglandrum) > - C++ MCS code returns a null MCS between methylcyclopentane and > methylcyclohexane > (github issue #2662 from ptosco) > - CXSMILES writer has error if mol comes from v3000 molfile > (github issue #2666 from d-b-w) > - MolToCXSmiles generates error for empty molecule > (github issue #2667 from greglandrum) > - fix a problem with normalize, ringinfo, and fragments > (github pull #2685 from greglandrum) > - Error when a squiggle bond is in an aromatic ring > (github issue #2695 from greglandrum) > - Cannot combine multiple range queries on a single atom. > (github issue #2709 from greglandrum) > - setBondStereoFromDirections() returning incorrect results. > (github issue #2712 from greglandrum) > - update supplier documentation to reflect python 3 iterator syntax > (github pull #2719 from greglandrum) > - removeHs messing up double bond stereo in partially sanitized molecules > (github issue #2721 from greglandrum) > - seg fault in ReactionRunner > (github issue #2722 from greglandrum) > - Intermittent test failures for JavaDistanceGeometryTests > (github issue #2727 from greglandrum) > - Fixes a bug in TorsionConstraint > (github pull #2732 from ptosco) > - Apply fix for #1592 to _MolsToGridSVG > (github pull #2737 from yishutu) > > ## New Features and Enhancements: > - Added rankAtoms to ROMol wrapper and added Java test case > (github pull #1540 from sroughley) > - Use van der Waals radii from blue obelisk > (github pull #2154 from UnixJunkie) > - add generateDepictionMatching2DStructure() to SWIG wrappers > (github issue #2239 from greglandrum) > - Added OptimizeMoleculeConfs with pre-generated force-field > (github pull #2401 from ptosco) > - FreeSASA improvements > (github pull #2402 from ptosco) > - Speed up symmetrizeSSSR > (github issue #2403 from d-b-w) > - Trim whitespace from mol fragment SMARTS and check SMARTS presence > (github pull #2406 from ricrogz) > - Run clang-tidy over the entire codebase > (github pull #2408 from greglandrum) > - Enable Azure Pipelines builds for CI > (github pull #2409 from ricrogz) > - Add RDProps interface to Conformers > (github issue #2441 from greglandrum) > - Add minimal JavaScript wrapper > (github pull #2444 from greglandrum) > - Fixes annoying warnings on MSVC > (github pull #2454 from ptosco) > - add prepareMolsBeforeDrawing option for drawMols > (github pull #2455 from greglandrum) > - computeGasteigerCharges quality of life improvement for python api > (github issue #2480 from bp-kelley) > - Preserve bond direction in fragmentOnBonds > (github pull #2484 from greglandrum) > - SanitizeRxn code and docstring cleanup > (github pull #2491 from greglandrum) > - Support XYZ format for output > (github pull #2498 from e-kwsm) > - vf2 optimisations > (github pull #2500 from johnmay) > - Python wrap enhanced stereo setters > (github pull #2509 from d-b-w) > - Fix the azure pipelines builds > (github pull #2522 from greglandrum) > - add a script for benchmarking fingerprint screenout and substructure > performance > (github pull #2523 from greglandrum) > - make "R" in CTABs an AtomNull query > (github pull #2528 from greglandrum) > - Expose SDF loading options to LoadSDF > (github pull #2534 from bp-kelley) > - Remove unused ctest: testCanon > (github pull #2541 from ricrogz) > - Update maeparser and coordgen versions > (github pull #2542 from ricrogz) > - Improved handling of bond stereo in reactions > (github pull #2553 from ricrogz) > - Code simplification for fingerprints to np array > (github pull #2557 from ChrisHill8) > - Integrate Unique Ring Families from RingDecomposerLib > (github pull #2558 from greglandrum) > - Allow providing a bounds matrix to EmbedMol > (github pull #2560 from greglandrum) > - Enable SimilarityMaps in C++ > (github pull #2562 from greglandrum) > - Do not run UnitTestMCS.py::TestTimeout in debug builds > (github pull #2569 from ricrogz) > - Expose more drawing methods to Python > (github issue #2571 from greglandrum) > - Allow Point2D to be constructed from Point3D > (github pull #2572 from greglandrum) > - Allows dative bonds to be drawn > (github pull #2573 from greglandrum) > - Allow identification of chemistry problems > (github pull #2587 from greglandrum) > - Adds MolFragmentToSmarts to generate smarts for a subset of a Molecule > (github pull #2594 from d-b-w) > - Removal of redundant wildcards in SMARTS (Null Atom/Bond Query > combination) > (github pull #2595 from ricrogz) > - Support range-based charge queries from SMARTS > (github issue #2604 from greglandrum) > - Keep PDB info from Maestro files if available > (github pull #2619 from lorton) > - optimization of the MolStandardize code > (github pull #2621 from greglandrum) > - Assign stereo bond labels in molecules read from SMARTS > (github pull #2623 from ricrogz) > - Automatically load the ipython extensions running in Jupyter > (github pull #2626 from bp-kelley) > - draw zero-order bonds > (github pull #2630 from greglandrum) > - Updated cartridge documentation > (github pull #2635 from msteijaert) > - Add new mol hashing code > (github pull #2636 from greglandrum) > - emolecules link updated > (github pull #2638 from marcwittke) > - Update maeparser to 1.2.1 and coorgen to 1.3.1 > (github pull #2652 from ricrogz) > - Get numpy include dir programmatically > (github pull #2653 from sirbiscuit) > - Fix long columns pandas > (github pull #2655 from sirbiscuit) > - Added AtomComparator.AtomCompareAnyHeavyAtom and test cases to FMCS > code > (github pull #2656 from sroughley) > - The C++ MCS code generates ambiguous SMARTS strings > (github issue #2663 from ptosco) > - add bond-selector info to SVGs > (github pull #2664 from greglandrum) > - support writing CXSMILES from the cartridge > (github issue #2668 from greglandrum) > - support the new hashing code in the cartridge > (github pull #2671 from greglandrum) > - Adds additional capabilities to the minimal JS wrapper > (github pull #2676 from greglandrum) > - Add MolHash to Java Wrappers > (github issue #2677 from sroughley) > - A bunch of changes to the new fingerprinter code > (github pull #2679 from greglandrum) > - Add viewBox to default SVG output > (github issue #2680 from bp-kelley) > - Allow Java to see RGroup labels in the std::map wrapper. > (github pull #2681 from bp-kelley) > - Update maeparser to v1.2.2. > (github pull #2682 from ricrogz) > - Update coordgen to v1.3.2 > (github pull #2686 from ricrogz) > - Add a drawOptions object to IPythonConsole > (github pull #2691 from greglandrum) > - Make StructureGroups editable from Python > (github pull #2692 from greglandrum) > - Update documentation > (github pull #2697 from greglandrum) > - Make removeHydrogensPostMatch=true the default for RGD > (github pull #2701 from greglandrum) > - Eat our own dogfood, Clone is deprecated so use copy > (github pull #2711 from bp-kelley) > - The MCS smartsString may still be ambiguous > (github issue #2714 from ptosco) > - Add threaded runner for the filter catalog > (github pull #2718 from bp-kelley) > - Add Leader picker implementation > (github pull #2724 from greglandrum) > - Add consideration of ring fusion to the MCS algorithm > (github pull #2731 from ptosco) > > > ## Deprecated code (to be removed in a future release): > > - The old MolHash code should be considered deprecated. This release > introduces > a more flexible alternative. Specifically the following pieces will be > removed in a future release: > - The python functionality > `rdkit.Chem.rdMolHash.GenerateMoleculeHashString()` > - The C++ functionality directly present in the header file > `GraphMol/MolHash/MolHash.h` > >
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
