Should be fixed now. On Fri, Oct 25, 2019 at 9:58 AM Greg Landrum <greg.land...@gmail.com> wrote:
> 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` >> >>
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