rdkit-announce — Low-traffic list for project-related announcements.

[Rdkit-announce] Save the date for the 2025 RDKit UGM

[Greg L. <gre...@gm...>]

Dear all,

I'm happy to announce that we have set the dates and location for next
year's UGM.

The 2025 RDKit UGM will take place in Prague, Czechia from 10-12 September.
The organizers are Martin Šícho and Daniel Svozil from the Department of
Informatics and Chemistry at the University of Chemistry and Technology in
Prague.

Many thanks to Martin and Daniel for volunteering, I don't think we've ever
had dates and a location figured out so early!

Registration details and more information will follow early next year.

Best regards,
-greg

[Rdkit-announce] Registration for the 2024 RDKit UGM is now open

[Greg L. <gre...@gm...>]

Dear all,

The (free) registration for the 2024 RDKit UGM, being held from 11-13
September at the ETH in Zurich, Switzerland, is now open:
https://www.eventbrite.com/e/860637719587

You can submit proposals to do talks, tutorials, lightning talks, and
posters here:
https://forms.gle/5GK5ej7hCdPguwKz8

As in the past couple of years, we will stream the talks for people who
cannot attend in person.

Best regards,
-greg

[Rdkit-announce] Save the Date! 2024 RDKit UGM

[Greg L. <gre...@gm...>]

Dear all,

The 2024 RDKit UGM will take place from 11-13 September in Zurich
Switzerland.

We'll post more information and open registration in Q1 of next year.

Best regards,
-greg

[Rdkit-announce] 2023 RDKit UGM registration open

[Greg L. <gre...@gm...>]

Dear all,

This year's RDKit UGM will take place in Mainz, Germany from 20-22
September. Paul Czodrowski is this year's organizer.

As last year, we're planning the UGM as an in-person event with a live
stream of the sessions for people who can't make it in person.

Free registration for both in-person and virtual attendance is open here:
https://www.eventbrite.com/e/12th-rdkit-ugm-2023-tickets-566636253287
<https://www.eventbrite.com/e/11th-rdkit-ugm-2022-tickets-289161448677>

If you're interested in contributing a talk, poster, lightning talk,
tutorial, etc. to the UGM, please submit your ideas here:
https://forms.gle/P2Xt7ag9fQMSkAJt5

We're really looking forward to another great UGM and to getting to see
some of you in Mainz!

Best regards,
Greg and Paul

[Rdkit-announce] 2022 RDKit UGM registration open

[Greg L. <gre...@gm...>]

Dear all,

This year's RDKit UGM will take place in Berlin, Germany from 12-14
October. The organizers are the Machine Learning Research group from Bayer
Pharma.

We're planning the UGM as an in-person event, but we will, assuming the
technology works, also live stream the sessions.

Free registration for both in-person and virtual attendance is open here:
https://www.eventbrite.com/e/11th-rdkit-ugm-2022-tickets-289161448677

If you're interested in contributing a talk, poster, lightning talk,
tutorial, etc. to the UGM, please submit your ideas here:
https://forms.gle/J2eHVkNjh4ngg1e76

We're really looking forward to another great UGM and to getting to see
some of you in Berlin!

Best regards,
Greg and the rest of the organizers

[Rdkit-announce] [RDKit UGM2021] Save the date: Oct 14 and 15

[Greg L. <gre...@gm...>]

Hi,

This year's RDKit UGM is going to take place October 14 and 15. It will,
unfortunately, once again be a purely virtual event. Hopefully next year we
will be able to travel again and all get together in one physical location,
but this year it's not possible to really plan an in-person meeting.

Since it seemed to work well last time, we'll do a combination of zoom and
either discord or some other text-based chat functionality and will have
two sessions per meeting day: one earlier in the day which is easier for
people in Asia to attend and one later in the day which is easier for
people in the Americas.

I'll send around more info and a link to the registration in the next week
or so.

I'd also like to try a virtual hackathon of some type, but will schedule
that for a different time, probably sometime this summer. Again, more
details on that soon.

Best,
-greg

Re: [Rdkit-announce] 2021.03.1 RDKit Release

[Greg L. <gre...@gm...>]

Apologies, I forgot to remove the beta tag in a file in the release, so
I've deleted that tag and done a new one.
The new DOI is:
https://zenodo.org/record/4639764

Everything else remains the same.

sorry for the noise,
-greg
p.s. hopefully there are no other silly mistakes/oversights...

On Fri, Mar 26, 2021 at 4:13 PM Greg Landrum <gre...@gm...> wrote:

> Dear all,
>
> I'm pleased to announce that the 2021.03 version of the RDKit is released.
> We actually managed to get the .03 release done during March. Shocking! ;-)
> The release notes are below.[1]
>
> The release files are on the github release page:
> https://github.com/rdkit/rdkit/releases/tag/Release_2021_03_1
> The DOI for this release is:
> https://doi.org/10.5281/zenodo.4639022
>
> I do not plan to do conda builds for the Python wrappers in the rdkit
> channel for this release. The builds done as part of the conda-forge
> project are automated and cover more Python versions and operating systems
> than I could ever hope to do manually.
> Please install the rdkit using conda-forge:
> conda install -c conda-forge rdkit
> I believe that the conda-forge builds of the new version should appear
> over the next couple of days.
>
> I hope to finish the conda builds of the PostgreSQL cartridge for linux
> and the mac and have them available in the rdkit channel by later today
> or tomorrow.
>
> The online version of the documentation at rdkit.org (
> http://rdkit.org/docs/index.html) has been updated.
>
> 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 September/October 2021.
>
> Best Regards,
> -greg
> [1] We probably should figure out some way to make the release notes a bit
> less verbose. ;-)
>
>
> # Release_2021.03.1
> (Changes relative to Release_2020.09.1)
>
> ## Backwards incompatible changes
> - The distance-geometry based conformer generation now by defaults
> generates
>   trans(oid) conformations for amides, esters, and related structures.
> This can
>   be toggled off with the `forceTransAmides` flag in EmbedParameters. Note
> that
>   this change does not impact conformers created using one of the ET
> versions.
>   (#3794)
> - The conformer generator now uses symmetry by default when doing RMS
> pruning.
>   This can be disabled using the `useSymmetryForPruning` flag in
>   EmbedParameters. (#3813)
> - Double bonds with unspecified stereochemistry in the products of chemical
>   reactions now have their stereo set to STEREONONE instead of STEREOANY
> (#3078)
> - The MolToSVG() function has been moved from rdkit.Chem to rdkit.Chem.Draw
>   (#3696)
> - There have been numerous changes to the RGroup Decomposition code which
> change
>   the results. (#3767)
> - In RGroup Decomposition, when onlyMatchAtRGroups is set to false, each
> molecule
>   is now decomposed based on the first matching scaffold which adds/uses
> the
>   least number of non-user-provided R labels, rather than simply the first
>   matching scaffold.
>   Among other things, this allows the code to provide the same results for
> both
>   onlyMatchAtRGroups=true and onlyMatchAtRGroups=false when suitable
> scaffolds
>   are provided without requiring the user to get overly concerned about the
>   input ordering of the scaffolds. (#3969)
> - There have been numerous changes to
> `GenerateDepictionMatching2DStructure()` (#3811)
> - Setting the kekuleSmiles argument (doKekule in C++) to MolToSmiles will
> now
>   cause the molecule to be kekulized before SMILES generation. Note that
> this
>   can lead to an exception being thrown. Previously this argument would
> only
>   write kekulized SMILES if the molecule had already been kekulized (#2788)
> - Using the kekulize argument in the MHFP code will now cause the molecule
> to be
>   kekulized before the fingerprint is generated. Note that becaues
> kekulization
>   is not canonical, using this argument currently causes the results to
> depend
>   on the input atom numbering. Note that this can lead to an exception
> being
>   thrown. (#3942)
> - Gradients for angle and torsional restraints in both UFF and MMFF were
> computed
>   incorrectly, which could give rise to potential instability during
> minimization.
>   As part of fixing this problem, force constants have been switched to
> using
>   kcal/degree^2 units instead of kcal/rad^2 units, consistently with the
> fact that
>   angle and dihedral restraints are specified in degrees. (#3975)
>
> ## Highlights
> - MolDraw2D now does a much better job of handling query features like
> common
>   query bond types, atom lists, variable attachment points, and link
> nodes. It
>   also supports adding annotations at the molecule level, displaying
> brackets
>   for Sgroups, rendering the ABS flag for stereochemistry, and a new
> "comic"
>   mode.
> - There are two new Contrib packages: NIBRStructureFilters and CalcLigRMSD
> - There have been a number of improvements made to the R-Group
> Decomposition
>   code which make it both more flexible and considerably faster
>
> ## Acknowledgements
> Michael Banck, Christopher Von Bargen, Jason Biggs, Patrick Buder, Ivan
> Chernyshov, Andrew Dalke, Xiaorui Dong, Carmen Esposito, Nicholas Firth,
> Enrico
> Gandini, James Gayvert, Gareth Jones, Eisuke Kawashima, Steven Kearnes,
> Brian
> Kelley, Mark Mackey, Niels Kristian Kjærgård Madsen, Luca Naef, Dan
> Nealschneider, Jin Pan, Daniel Paoliello, António JM Ribeiro, Sereina
> Riniker,
> Braxton Robbason, Jaime Rodríguez-Guerra, Ricardo Rodriguez-Schmidt, Steve
> Roughley, Vincent F. Scalfani, Nadine Schneider, Philippe Schwaller, Dan
> Skatov,
> Pascal Soveaux, Paolo Tosco, Kazuya Ujihara, Riccardo Vianello, Shuzhe
> Wang,
> Piotr Wawrzyniak, Maciej Wójcikowski, Zhijiang Yang, Yutong Zhao
> 'driesvr', 'GintasKam', 'SPKorhonen', 'pkubaj', 'AnPallo', 'darintay',
> 'slchan3', 'Robins', 'sirbiscuit', 'amateurcat', 'noncomputable',
> 'yurivict',
> 'magattaca'
>
> ## Contrib updates:
>   - Added NIBRStructureFilters: a set of substructure filters for hit-list
> triaging together with python code for applying them. The filters are
> described in the publication
> https://dx.doi.org/10.1021/acs.jmedchem.0c01332
>    (github pull #3516 from NadineSchneider)
>   - Added CalcLigRMSD: flexible python code for calculating RMSD between
> pre-aligned molecules
>    (github pull #3812 from cespos)
>
> ## Bug Fixes:
>   - Casting int to uint in MorganFingerprintHelper leads to unexpected
> behaviour.
>  (github issue #1761 from SiPa13)
>   - MolChemicalFeature.GetPos() returns value for molecule's default
> conformer
>  (github issue #2530 from greglandrum)
>   - Unable to catch RDKit exceptions in linked library when compiling with
> fvisibility=hidden
>  (github issue #2753 from cdvonbargen)
>   - Reaction rendering always shows molecules in aromatic form
>  (github issue #2976 from greglandrum)
>   - Reactions setting unspecified double-bond stereo to STEREOANY
>  (github issue #3078 from ricrogz)
>   - PDB output flavor&2 documentation change
>  (github issue #3089 from adalke)
>   - WedgeMolBonds() should prefer degree-1 atoms
>  (github issue #3216 from greglandrum)
>   - Error in ChemAxon SMILES "parsing"
>  (github issue #3320 from IvanChernyshov)
>   - Incorrect number of radical electrons calculated for metals
>  (github issue #3330 from greglandrum)
>   - Problem with lifetime linkage of mols and conformers
>  (github issue #3492 from amateurcat)
>   - Traceback when pickling ROMol after BCUT descriptors are calculated
>  (github issue #3511 from d-b-w)
>   - Fix AUTOCORR2D descriptors
>  (github pull #3512 from ricrogz)
>   - SDMolSupplier requires several attempts to load a SDF file in Python
> 3.6/3.7
>  (github issue #3517 from jaimergp)
>   - Remove accidentally included boost header
>  (github pull #3518 from ricrogz)
>   - legend_height_ should be preserved after drawing the molecule
>  (github pull #3520 from greglandrum)
>   - remove the include directive for unused <access/tuptoaster.h> header
>  (github pull #3525 from rvianello)
>   - C++ build fails when configured with RDKIT_USE_BOOST_SERIALIZATION=OFF
>  (github issue #3529 from rvianello)
>   - Newest RDKIT version allowing chemically invalid smiles
>  (github issue #3531 from GintasKam)
>   - Behaviour of generate_aligned_coords for erroneous inputs
>  (github issue #3539 from dskatov)
>   - Drawing artifacts in draw_to_canvas_with_offset
>  (github issue #3540 from dskatov)
>   - Error adding PNG metadata when kekulize=False
>  (github issue #3543 from gayverjr)
>   - Add missing methods to remove SubstanceGroup attributes
>  (github pull #3547 from greglandrum)
>   - Error writing SDF data containing UTF-8 to a StringIO object
>  (github issue #3553 from greglandrum)
>   - correct handling of amide distances for macrocycles
>  (github pull #3559 from hjuinj)
>   - rdMolDraw2D, problems during generation of pictures from SMARTS,
> differences between Cairo and SVG
>  (github issue #3572 from wopozka)
>   - Fix example of SmilesToMol
>  (github pull #3575 from kazuyaujihara)
>   - atom/bond notes handle capital letters incorrectly
>  (github issue #3577 from greglandrum)
>   - Get MolDraw2DQt working again
>  (github pull #3592 from greglandrum)
>   - Scientific notation in SDF V3000 files
>  (github issue #3597 from mark-cresset)
>   - Fix: add missing python wrappers for MolDraw2DQt
>  (github pull #3613 from greglandrum)
>   - V3K mol block parser not saving the chiral flag
>  (github issue #3620 from greglandrum)
>   - Inconsistent metal disconnectors
>  (github issue #3625 from pschwllr)
>   - Ring stereochemistry not properly removed from N atoms
>  (github issue #3631 from greglandrum)
>   - moldraw2djs should not close all polygonal paths
>  (github pull #3634 from greglandrum)
>   - Unidentifiable C++ Exception with FMCS
>  (github issue #3635 from proteneer)
>   - Bump catch2 version to allow builds on Apple M1
>  (github pull #3641 from naefl)
>   - Segmentation fault when parsing InChI
>  (github issue #3645 from AnPallo)
>   - RDK_BUILD_THREADSAFE_SSS does not work as expected
>  (github issue #3646 from pascal-soveaux)
>   - Disabling MaeParser and CoordGen Support Breaks the Build
>  (github issue #3648 from proteneer)
>   - BondStereo info lost in FragmentOnBonds()
>  (github pull #3649 from bp-kelley)
>   - memory leak when sanitization fails in InChIToMol()
>  (github issue #3655 from greglandrum)
>   - Qt GUI libraries being linked into rdmolops.so when Qt support is
> enabled
>  (github issue #3658 from ricrogz)
>   - Documentation of Chem.rdmolops.GetMolFrags's frag argument is wrong
>  (github issue #3670 from noncomputable)
>   - fmcs() + bogus input causes engine crash
>  (github issue #3687 from robins)
>   - qmol_from_ctab() with NULL crashes engine
>  (github issue #3688 from robins)
>   - qmol_from_smiles() + bogus input causes engine crash
>  (github issue #3689 from robins)
>   - Check PIL support for tostring and fromstring
>  (github pull #3690 from sirbiscuit)
>   - Move MolToSVG() to rdkit.Chem.Draw (Addresses #3694)
>  (github pull #3696 from ricrogz)
>   - Pandas AttributeError when rendering Molecule in DataFrame
>  (github issue #3701 from enricogandini)
>   - Memory leak in EnumerateLibrary
>  (github issue #3702 from jose-mr)
>   - Fix to add ZLIB_INCLUDE_DIRS for Windows build
>  (github pull #3714 from kazuyaujihara)
>   - Docs/Book: Unexpected unicode character makes pdflatex build fail
>  (github issue #3738 from mbanck)
>   - Test suite failures if eigen3 is not available
>  (github issue #3740 from mbanck)
>   - Regression in depiction of double bonds in aromatic rings
>  (github issue #3744 from ptosco)
>   - RGD with RGroupMatching.GA leaks memory and takes too long
>  (github issue #3746 from ptosco)
>   - Fix comment to match the code in RemoveHsParameters
>  (github pull #3747 from jasondbiggs)
>   - Inconsistent canonical tautomer on repeated application
>  (github issue #3755 from darintay)
>   - bonds no longer highlighted in substruct matches in jupyter
>  (github issue #3762 from greglandrum)
>   - SubstanceGroup output doesn't correctly quote " symbols
>  (github issue #3768 from greglandrum)
>   - MolToSmarts inverts direction of dative bond
>  (github issue #3774 from IvanChernyshov)
>   - Regression in dihedral constraints
>  (github issue #3781 from ptosco)
>   - Fix pillow error in IPythonConsole.py
>  (github pull #3783 from skearnes)
>   - lock swig version in MacOS CI builds
>  (github pull #3789 from greglandrum)
>   - DrawMorganBit errors when useSVG is False
>  (github issue #3796 from ncfirth)
>   - SubstructLibrary Cached Smiles Holders have bad behavior with bad
> smiles
>  (github issue #3797 from bp-kelley)
>   - MolFromSmiles('[He]') produces a diradical helium atom
>  (github issue #3805 from jasondbiggs)
>   - NaNs from AUTOCORR2D descriptor
>  (github issue #3806 from greglandrum)
>   - MaeMolSupplier throws an invariant exception on parsing an "undefined"
> chirality label
>  (github issue #3815 from ricrogz)
>   - Sanitize molecules when SMILES needs to be produced in PandasTools
>  (github pull #3818 from mwojcikowski)
>   - Tautomer Query copy constructor is shallow not deep causing segfaults
> in destructor
>  (github issue #3821 from bp-kelley)
>   - OptimizeMolecule and OptimizeMoleculeConfs Argument Bug
>  (github issue #3824 from xiaoruiDong)
>   - rdMolEnumerator.Enumerate() fragile w.r.t. atom ordering
>  (github issue #3844 from greglandrum)
>   - MinimalLib: Bonds are parallel in SVG but not on an HTML5 Canvas
>  (github issue #3852 from dskatov)
>   - AddHs creates H atom with nan coordinates on edge case 2D structure
>  (github issue #3854 from ricrogz)
>   - Build error with static boost libraries (v1.73)
>  (github issue #3865 from nielskm)
>   - Make sure that added R-groups have non-zero coordinates
>  (github pull #3877 from ptosco)
>   - Bad H coordinates on fused ring
>  (github issue #3879 from greglandrum)
>   - SubstructLibrary needs to check bond ring queries as well
>  (github issue #3881 from bp-kelley)
>   - Fixes Amine.Tertiary.Aromatic definition
>  (github pull #3883 from bp-kelley)
>   - inconsistency in seedSmarts in FMCS between and GetSubstructureMatches
>  (github issue #3886 from proteneer)
>   - PandasTools.RGroupDecomposition throws an error when redraw_sidechains
> is set to True.
>  (github pull #3888 from greglandrum)
>   - Dev/update glare to py3
>  (github pull #3892 from bp-kelley)
>   - ConfGen: Macrocycle torsion terms not being used with fused macrocycles
>  (github pull #3894 from greglandrum)
>   - Broken KNIME link in README
>  (github issue #3897 from yurivict)
>   - Change class to struct for forward declaration
>  (github pull #3906 from bp-kelley)
>   - Fixes issues with unlabelled groups on aromatic nitrogens
>  (github pull #3908 from ptosco)
>   - Fix #3659 regression introduced in #3832
>  (github pull #3909 from ricrogz)
>   - Error rendering SMARTS queries with atom OR lists
>  (github issue #3912 from greglandrum)
>   - MoDraw2D: Get tests working without freetype
>  (github pull #3923 from greglandrum)
>   - RGD default scoring function does not always work as expected
>  (github issue #3924 from jones-gareth)
>   - MolDraw2D: relative font size changes with bond lengths in molecule
>  (github issue #3929 from greglandrum)
>   - MolDraw2D: coordinates for reactions not being used
>  (github issue #3931 from greglandrum)
>   - Follow-on patch for changes in #3899
>  (github issue #3932 from greglandrum)
>   - Fix MolDraw2DQt exports
>  (github pull #3935 from ricrogz)
>   - Fix building JavaWrappers on Windows, dynamic linking
>  (github pull #3936 from ricrogz)
>   - Boost header warnings when compiling
>  (github issue #3956 from jasondbiggs)
>   - Adds removeAllHydrogenRGroupsAndLabels and fixes kekulization issues
>  (github pull #3944 from ptosco)
>   - MolToJSONData fails when mol has a property that can't be stringified
>  (github issue #3956 from jasondbiggs)
>   - RWMol should reset(), not release(), dp_delAtoms and dp_delBonds
>  (github pull #3970 from greglandrum)
>
>
> ## New Features and Enhancements:
>   - add context managers for writers
>  (github issue #2217 from greglandrum)
>   - MolToSmiles(kekuleSmiles=True) gives SMILES with aromatic bonds
>  (github issue #2788 from adalke)
>   - allow specification of color map when drawing similarity maps
>  (github issue #2904 from greglandrum)
>   - Clean up CMake files
>  (github pull #3417 from e-kwsm)
>   - Speed up GraphMol/Chirality.cpp/iterateCIPRanks
>  (github pull #3482 from jinpan)
>   - Removes function which is an exact duplicate of another function
>  (github pull #3524 from ptosco)
>   - A couple of minor improvements to FindCairo
>  (github pull #3535 from ptosco)
>   - Give a bit more time to RGD test in debug builds
>  (github pull #3536 from ptosco)
>   - A couple of fixes to the build system
>  (github pull #3538 from ptosco)
>   - Modularized WASM module
>  (github issue #3561 from dskatov)
>   - A couple changes to speedup bulk similarity calculations from Python
>  (github pull #3574 from greglandrum)
>   - add documentation for the JS wrappers
>  (github pull #3583 from greglandrum)
>   - add a "comic mode" to MolDraw2D
>  (github pull #3584 from greglandrum)
>   - Add rendering of SGroup brackets to MolDraw2D
>  (github pull #3586 from greglandrum)
>   - Update Install.md
>  (github pull #3589 from slchan3)
>   - Add explicit support for remaining CTAB query bond types
>  (github issue #3599 from greglandrum)
>   - update Cookbook stereochemistry examples
>  (github pull #3604 from vfscalfani)
>   - Add support for rendering SGroup data fields to MolDraw2D
>  (github pull #3619 from greglandrum)
>   - Support rendering the "ABS" flag in MolDraw2D
>  (github issue #3623 from greglandrum)
>   - Support drawing some query bonds
>  (github pull #3624 from greglandrum)
>   - Support rendering variable attachment points
>  (github pull #3626 from greglandrum)
>   - add configuration option to disable atom symbols in the rendering
>  (github pull #3630 from greglandrum)
>   - Render link nodes in MolDraw2D
>  (github issue #3637 from greglandrum)
>   - First pass at MolZip (now with bond stereo!)
>  (github pull #3644 from bp-kelley)
>   - Add molecule annotations/notes to MolDraw2D
>  (github pull #3651 from greglandrum)
>   - support setting MolDraw2DOptions using JSON from Python
>  (github pull #3660 from greglandrum)
>   - Make the scope control for Qt more idiomatic
>  (github pull #3663 from d-b-w)
>   - Expanded MolEnumerator functionality
>  (github pull #3664 from greglandrum)
>   - add support for generating pattern fps for MolBundles
>  (github pull #3665 from greglandrum)
>   - Add a callback function to EmbedParameters struct
>  (github issue #3667 from jasondbiggs)
>   - update SequenceParsers.cpp
>  (github pull #3683 from magattaca)
>   - MCS: extend completeRingsOnly to cover atoms as well
>  (github issue #3693 from driesvr)
>   - Add Molbundle search to SWIG
>  (github pull #3698 from jones-gareth)
>   - Added getMessage method to exceptions
>  (github pull #3700 from sroughley)
>   - add context manager for MolSuppliers
>  (github issue #3703 from greglandrum)
>   - Make better use of strictParsing for SGroups
>  (github pull #3705 from ptosco)
>   - Allow using  POPCNT on big-endian ppc64
>  (github pull #3727 from pkubaj)
>   - Cleanup: remove fromstring and tostring from functions working with
> pillow
>  (github issue #3730 from greglandrum)
>   - Set strictParsing to false in MinimalLib
>  (github pull #3737 from ptosco)
>   - 3D MCS - Minimal version, no refactoring
>  (github pull #3749 from robbason)
>   - Include Winsock2.h instead of Windows.h in DebugTrace.h
>  (github pull #3756 from dpaoliello)
>   - R group match any issue
>  (github pull #3767 from jones-gareth)
>   - Support new coordgen option to not always make bonds to metals
> zero-order
>  (github pull #3769 from greglandrum)
>   - DistanceGeometry: add flag to enforce trans amides
>  (github pull #3794 from greglandrum)
>   - MolDraw2D: first pass at rendering atom lists
>  (github pull #3804 from greglandrum)
>   - Issue a warning when embedding a molecule with no Hs
>  (github pull #3807 from greglandrum)
>   - Add tautomer query to the substructlibrary
>  (github pull #3808 from bp-kelley)
>   - Enhanced generateDepictionMatching2DStructure functionality
>  (github pull #3811 from ptosco)
>   - Confgen: add option to use symmetry when doing RMS pruning
>  (github pull #3813 from greglandrum)
>   - Remove boost::foreach from public headers
>  (github pull #3820 from ricrogz)
>   - Adds isotopeLabels and dummyIsotopeLabels MolDrawOptions
>  (github pull #3825 from ptosco)
>   - Added 2 Cookbook examples
>  (github pull #3831 from vfscalfani)
>   - Separate MolDraw2DQt into its own library
>  (github pull #3832 from d-b-w)
>   - Facilities for interactive modification of molecule drawing
>  (github pull #3833 from SPKorhonen)
>   - cleanup a bunch of compiler warnings
>  (github pull #3849 from greglandrum)
>   - add a new mol draw option to draw wedge bonds with a single color
>  (github pull #3860 from jasondbiggs)
>   - Add Kier Phi descriptor
>  (github pull #3864 from greglandrum)
>   - Add basic support for hydrogen bonds
>  (github pull #3871 from greglandrum)
>   - Allow batch editing of molecules: removal only
>  (github pull #3875 from greglandrum)
>   - Allow retrieving the _ErGAtomTypes property from Python
>  (github pull #3878 from ptosco)
>   - Exposes InsertMol to python RWMol
>  (github pull #3907 from bp-kelley)
>   - Use https for Avalon and Inchi downloads
>  (github pull #3915 from ptosco)
>   - support empty/missing SDT lines for SGroup data
>  (github pull #3916 from greglandrum)
>   - Cookbook entries should be updated
>  (github issue #3917 from greglandrum)
>   - MolDraw2D: support changing annotation colours
>  (github pull #3919 from greglandrum)
>   - include context managers for the multithreaded suppliers too
>  (github pull #3920 from greglandrum)
>   - Documentation cleanup and update
>  (github pull #3922 from greglandrum)
>   - remove an MSVC++ warning caused by #3849
>  (github pull #3927 from greglandrum)
>   - Adds removeAllHydrogenRGroupsAndLabels and fixes kekulization issues
>  (github pull #3944 from ptosco)
>   - Remove temporary labels from RGD results
>  (github pull #3947 from ptosco)
>   - appended a new project depend on RDKit
>  (github pull #3955 from kotori-y)
>   - Do not add unnecessary R-labels (and an optimization)
>  (github pull #3969 from ptosco)
>   - Add return codes and make RGroupDecomp less verbose
>  (github pull #3971 from bp-kelley)
>   - update to coordgen 2.0.0
>  (github pull #3974 from greglandrum)
>
>
> ## Deprecated code (to be removed in a future release):
> - The "minimizeOnly" option for coordgen will be removed in the next RDKit
> release
>
>

[Rdkit-announce] 2021.03.1 RDKit Release

[Greg L. <gre...@gm...>]

Dear all,

I'm pleased to announce that the 2021.03 version of the RDKit is released.
We actually managed to get the .03 release done during March. Shocking! ;-)
The release notes are below.[1]

The release files are on the github release page:
https://github.com/rdkit/rdkit/releases/tag/Release_2021_03_1
The DOI for this release is:
https://doi.org/10.5281/zenodo.4639022

I do not plan to do conda builds for the Python wrappers in the rdkit
channel for this release. The builds done as part of the conda-forge
project are automated and cover more Python versions and operating systems
than I could ever hope to do manually.
Please install the rdkit using conda-forge:
conda install -c conda-forge rdkit
I believe that the conda-forge builds of the new version should appear over
the next couple of days.

I hope to finish the conda builds of the PostgreSQL cartridge for linux and
the mac and have them available in the rdkit channel by later today
or tomorrow.

The online version of the documentation at rdkit.org (
http://rdkit.org/docs/index.html) has been updated.

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 September/October 2021.

Best Regards,
-greg
[1] We probably should figure out some way to make the release notes a bit
less verbose. ;-)


# Release_2021.03.1
(Changes relative to Release_2020.09.1)

## Backwards incompatible changes
- The distance-geometry based conformer generation now by defaults generates
  trans(oid) conformations for amides, esters, and related structures. This
can
  be toggled off with the `forceTransAmides` flag in EmbedParameters. Note
that
  this change does not impact conformers created using one of the ET
versions.
  (#3794)
- The conformer generator now uses symmetry by default when doing RMS
pruning.
  This can be disabled using the `useSymmetryForPruning` flag in
  EmbedParameters. (#3813)
- Double bonds with unspecified stereochemistry in the products of chemical
  reactions now have their stereo set to STEREONONE instead of STEREOANY
(#3078)
- The MolToSVG() function has been moved from rdkit.Chem to rdkit.Chem.Draw
  (#3696)
- There have been numerous changes to the RGroup Decomposition code which
change
  the results. (#3767)
- In RGroup Decomposition, when onlyMatchAtRGroups is set to false, each
molecule
  is now decomposed based on the first matching scaffold which adds/uses the
  least number of non-user-provided R labels, rather than simply the first
  matching scaffold.
  Among other things, this allows the code to provide the same results for
both
  onlyMatchAtRGroups=true and onlyMatchAtRGroups=false when suitable
scaffolds
  are provided without requiring the user to get overly concerned about the
  input ordering of the scaffolds. (#3969)
- There have been numerous changes to
`GenerateDepictionMatching2DStructure()` (#3811)
- Setting the kekuleSmiles argument (doKekule in C++) to MolToSmiles will
now
  cause the molecule to be kekulized before SMILES generation. Note that
this
  can lead to an exception being thrown. Previously this argument would only
  write kekulized SMILES if the molecule had already been kekulized (#2788)
- Using the kekulize argument in the MHFP code will now cause the molecule
to be
  kekulized before the fingerprint is generated. Note that becaues
kekulization
  is not canonical, using this argument currently causes the results to
depend
  on the input atom numbering. Note that this can lead to an exception being
  thrown. (#3942)
- Gradients for angle and torsional restraints in both UFF and MMFF were
computed
  incorrectly, which could give rise to potential instability during
minimization.
  As part of fixing this problem, force constants have been switched to
using
  kcal/degree^2 units instead of kcal/rad^2 units, consistently with the
fact that
  angle and dihedral restraints are specified in degrees. (#3975)

## Highlights
- MolDraw2D now does a much better job of handling query features like
common
  query bond types, atom lists, variable attachment points, and link nodes.
It
  also supports adding annotations at the molecule level, displaying
brackets
  for Sgroups, rendering the ABS flag for stereochemistry, and a new "comic"
  mode.
- There are two new Contrib packages: NIBRStructureFilters and CalcLigRMSD
- There have been a number of improvements made to the R-Group Decomposition
  code which make it both more flexible and considerably faster

## Acknowledgements
Michael Banck, Christopher Von Bargen, Jason Biggs, Patrick Buder, Ivan
Chernyshov, Andrew Dalke, Xiaorui Dong, Carmen Esposito, Nicholas Firth,
Enrico
Gandini, James Gayvert, Gareth Jones, Eisuke Kawashima, Steven Kearnes,
Brian
Kelley, Mark Mackey, Niels Kristian Kjærgård Madsen, Luca Naef, Dan
Nealschneider, Jin Pan, Daniel Paoliello, António JM Ribeiro, Sereina
Riniker,
Braxton Robbason, Jaime Rodríguez-Guerra, Ricardo Rodriguez-Schmidt, Steve
Roughley, Vincent F. Scalfani, Nadine Schneider, Philippe Schwaller, Dan
Skatov,
Pascal Soveaux, Paolo Tosco, Kazuya Ujihara, Riccardo Vianello, Shuzhe Wang,
Piotr Wawrzyniak, Maciej Wójcikowski, Zhijiang Yang, Yutong Zhao
'driesvr', 'GintasKam', 'SPKorhonen', 'pkubaj', 'AnPallo', 'darintay',
'slchan3', 'Robins', 'sirbiscuit', 'amateurcat', 'noncomputable',
'yurivict',
'magattaca'

## Contrib updates:
  - Added NIBRStructureFilters: a set of substructure filters for hit-list
triaging together with python code for applying them. The filters are
described in the publication https://dx.doi.org/10.1021/acs.jmedchem.0c01332
   (github pull #3516 from NadineSchneider)
  - Added CalcLigRMSD: flexible python code for calculating RMSD between
pre-aligned molecules
   (github pull #3812 from cespos)

## Bug Fixes:
  - Casting int to uint in MorganFingerprintHelper leads to unexpected
behaviour.
 (github issue #1761 from SiPa13)
  - MolChemicalFeature.GetPos() returns value for molecule's default
conformer
 (github issue #2530 from greglandrum)
  - Unable to catch RDKit exceptions in linked library when compiling with
fvisibility=hidden
 (github issue #2753 from cdvonbargen)
  - Reaction rendering always shows molecules in aromatic form
 (github issue #2976 from greglandrum)
  - Reactions setting unspecified double-bond stereo to STEREOANY
 (github issue #3078 from ricrogz)
  - PDB output flavor&2 documentation change
 (github issue #3089 from adalke)
  - WedgeMolBonds() should prefer degree-1 atoms
 (github issue #3216 from greglandrum)
  - Error in ChemAxon SMILES "parsing"
 (github issue #3320 from IvanChernyshov)
  - Incorrect number of radical electrons calculated for metals
 (github issue #3330 from greglandrum)
  - Problem with lifetime linkage of mols and conformers
 (github issue #3492 from amateurcat)
  - Traceback when pickling ROMol after BCUT descriptors are calculated
 (github issue #3511 from d-b-w)
  - Fix AUTOCORR2D descriptors
 (github pull #3512 from ricrogz)
  - SDMolSupplier requires several attempts to load a SDF file in Python
3.6/3.7
 (github issue #3517 from jaimergp)
  - Remove accidentally included boost header
 (github pull #3518 from ricrogz)
  - legend_height_ should be preserved after drawing the molecule
 (github pull #3520 from greglandrum)
  - remove the include directive for unused <access/tuptoaster.h> header
 (github pull #3525 from rvianello)
  - C++ build fails when configured with RDKIT_USE_BOOST_SERIALIZATION=OFF
 (github issue #3529 from rvianello)
  - Newest RDKIT version allowing chemically invalid smiles
 (github issue #3531 from GintasKam)
  - Behaviour of generate_aligned_coords for erroneous inputs
 (github issue #3539 from dskatov)
  - Drawing artifacts in draw_to_canvas_with_offset
 (github issue #3540 from dskatov)
  - Error adding PNG metadata when kekulize=False
 (github issue #3543 from gayverjr)
  - Add missing methods to remove SubstanceGroup attributes
 (github pull #3547 from greglandrum)
  - Error writing SDF data containing UTF-8 to a StringIO object
 (github issue #3553 from greglandrum)
  - correct handling of amide distances for macrocycles
 (github pull #3559 from hjuinj)
  - rdMolDraw2D, problems during generation of pictures from SMARTS,
differences between Cairo and SVG
 (github issue #3572 from wopozka)
  - Fix example of SmilesToMol
 (github pull #3575 from kazuyaujihara)
  - atom/bond notes handle capital letters incorrectly
 (github issue #3577 from greglandrum)
  - Get MolDraw2DQt working again
 (github pull #3592 from greglandrum)
  - Scientific notation in SDF V3000 files
 (github issue #3597 from mark-cresset)
  - Fix: add missing python wrappers for MolDraw2DQt
 (github pull #3613 from greglandrum)
  - V3K mol block parser not saving the chiral flag
 (github issue #3620 from greglandrum)
  - Inconsistent metal disconnectors
 (github issue #3625 from pschwllr)
  - Ring stereochemistry not properly removed from N atoms
 (github issue #3631 from greglandrum)
  - moldraw2djs should not close all polygonal paths
 (github pull #3634 from greglandrum)
  - Unidentifiable C++ Exception with FMCS
 (github issue #3635 from proteneer)
  - Bump catch2 version to allow builds on Apple M1
 (github pull #3641 from naefl)
  - Segmentation fault when parsing InChI
 (github issue #3645 from AnPallo)
  - RDK_BUILD_THREADSAFE_SSS does not work as expected
 (github issue #3646 from pascal-soveaux)
  - Disabling MaeParser and CoordGen Support Breaks the Build
 (github issue #3648 from proteneer)
  - BondStereo info lost in FragmentOnBonds()
 (github pull #3649 from bp-kelley)
  - memory leak when sanitization fails in InChIToMol()
 (github issue #3655 from greglandrum)
  - Qt GUI libraries being linked into rdmolops.so when Qt support is
enabled
 (github issue #3658 from ricrogz)
  - Documentation of Chem.rdmolops.GetMolFrags's frag argument is wrong
 (github issue #3670 from noncomputable)
  - fmcs() + bogus input causes engine crash
 (github issue #3687 from robins)
  - qmol_from_ctab() with NULL crashes engine
 (github issue #3688 from robins)
  - qmol_from_smiles() + bogus input causes engine crash
 (github issue #3689 from robins)
  - Check PIL support for tostring and fromstring
 (github pull #3690 from sirbiscuit)
  - Move MolToSVG() to rdkit.Chem.Draw (Addresses #3694)
 (github pull #3696 from ricrogz)
  - Pandas AttributeError when rendering Molecule in DataFrame
 (github issue #3701 from enricogandini)
  - Memory leak in EnumerateLibrary
 (github issue #3702 from jose-mr)
  - Fix to add ZLIB_INCLUDE_DIRS for Windows build
 (github pull #3714 from kazuyaujihara)
  - Docs/Book: Unexpected unicode character makes pdflatex build fail
 (github issue #3738 from mbanck)
  - Test suite failures if eigen3 is not available
 (github issue #3740 from mbanck)
  - Regression in depiction of double bonds in aromatic rings
 (github issue #3744 from ptosco)
  - RGD with RGroupMatching.GA leaks memory and takes too long
 (github issue #3746 from ptosco)
  - Fix comment to match the code in RemoveHsParameters
 (github pull #3747 from jasondbiggs)
  - Inconsistent canonical tautomer on repeated application
 (github issue #3755 from darintay)
  - bonds no longer highlighted in substruct matches in jupyter
 (github issue #3762 from greglandrum)
  - SubstanceGroup output doesn't correctly quote " symbols
 (github issue #3768 from greglandrum)
  - MolToSmarts inverts direction of dative bond
 (github issue #3774 from IvanChernyshov)
  - Regression in dihedral constraints
 (github issue #3781 from ptosco)
  - Fix pillow error in IPythonConsole.py
 (github pull #3783 from skearnes)
  - lock swig version in MacOS CI builds
 (github pull #3789 from greglandrum)
  - DrawMorganBit errors when useSVG is False
 (github issue #3796 from ncfirth)
  - SubstructLibrary Cached Smiles Holders have bad behavior with bad smiles
 (github issue #3797 from bp-kelley)
  - MolFromSmiles('[He]') produces a diradical helium atom
 (github issue #3805 from jasondbiggs)
  - NaNs from AUTOCORR2D descriptor
 (github issue #3806 from greglandrum)
  - MaeMolSupplier throws an invariant exception on parsing an "undefined"
chirality label
 (github issue #3815 from ricrogz)
  - Sanitize molecules when SMILES needs to be produced in PandasTools
 (github pull #3818 from mwojcikowski)
  - Tautomer Query copy constructor is shallow not deep causing segfaults
in destructor
 (github issue #3821 from bp-kelley)
  - OptimizeMolecule and OptimizeMoleculeConfs Argument Bug
 (github issue #3824 from xiaoruiDong)
  - rdMolEnumerator.Enumerate() fragile w.r.t. atom ordering
 (github issue #3844 from greglandrum)
  - MinimalLib: Bonds are parallel in SVG but not on an HTML5 Canvas
 (github issue #3852 from dskatov)
  - AddHs creates H atom with nan coordinates on edge case 2D structure
 (github issue #3854 from ricrogz)
  - Build error with static boost libraries (v1.73)
 (github issue #3865 from nielskm)
  - Make sure that added R-groups have non-zero coordinates
 (github pull #3877 from ptosco)
  - Bad H coordinates on fused ring
 (github issue #3879 from greglandrum)
  - SubstructLibrary needs to check bond ring queries as well
 (github issue #3881 from bp-kelley)
  - Fixes Amine.Tertiary.Aromatic definition
 (github pull #3883 from bp-kelley)
  - inconsistency in seedSmarts in FMCS between and GetSubstructureMatches
 (github issue #3886 from proteneer)
  - PandasTools.RGroupDecomposition throws an error when redraw_sidechains
is set to True.
 (github pull #3888 from greglandrum)
  - Dev/update glare to py3
 (github pull #3892 from bp-kelley)
  - ConfGen: Macrocycle torsion terms not being used with fused macrocycles
 (github pull #3894 from greglandrum)
  - Broken KNIME link in README
 (github issue #3897 from yurivict)
  - Change class to struct for forward declaration
 (github pull #3906 from bp-kelley)
  - Fixes issues with unlabelled groups on aromatic nitrogens
 (github pull #3908 from ptosco)
  - Fix #3659 regression introduced in #3832
 (github pull #3909 from ricrogz)
  - Error rendering SMARTS queries with atom OR lists
 (github issue #3912 from greglandrum)
  - MoDraw2D: Get tests working without freetype
 (github pull #3923 from greglandrum)
  - RGD default scoring function does not always work as expected
 (github issue #3924 from jones-gareth)
  - MolDraw2D: relative font size changes with bond lengths in molecule
 (github issue #3929 from greglandrum)
  - MolDraw2D: coordinates for reactions not being used
 (github issue #3931 from greglandrum)
  - Follow-on patch for changes in #3899
 (github issue #3932 from greglandrum)
  - Fix MolDraw2DQt exports
 (github pull #3935 from ricrogz)
  - Fix building JavaWrappers on Windows, dynamic linking
 (github pull #3936 from ricrogz)
  - Boost header warnings when compiling
 (github issue #3956 from jasondbiggs)
  - Adds removeAllHydrogenRGroupsAndLabels and fixes kekulization issues
 (github pull #3944 from ptosco)
  - MolToJSONData fails when mol has a property that can't be stringified
 (github issue #3956 from jasondbiggs)
  - RWMol should reset(), not release(), dp_delAtoms and dp_delBonds
 (github pull #3970 from greglandrum)


## New Features and Enhancements:
  - add context managers for writers
 (github issue #2217 from greglandrum)
  - MolToSmiles(kekuleSmiles=True) gives SMILES with aromatic bonds
 (github issue #2788 from adalke)
  - allow specification of color map when drawing similarity maps
 (github issue #2904 from greglandrum)
  - Clean up CMake files
 (github pull #3417 from e-kwsm)
  - Speed up GraphMol/Chirality.cpp/iterateCIPRanks
 (github pull #3482 from jinpan)
  - Removes function which is an exact duplicate of another function
 (github pull #3524 from ptosco)
  - A couple of minor improvements to FindCairo
 (github pull #3535 from ptosco)
  - Give a bit more time to RGD test in debug builds
 (github pull #3536 from ptosco)
  - A couple of fixes to the build system
 (github pull #3538 from ptosco)
  - Modularized WASM module
 (github issue #3561 from dskatov)
  - A couple changes to speedup bulk similarity calculations from Python
 (github pull #3574 from greglandrum)
  - add documentation for the JS wrappers
 (github pull #3583 from greglandrum)
  - add a "comic mode" to MolDraw2D
 (github pull #3584 from greglandrum)
  - Add rendering of SGroup brackets to MolDraw2D
 (github pull #3586 from greglandrum)
  - Update Install.md
 (github pull #3589 from slchan3)
  - Add explicit support for remaining CTAB query bond types
 (github issue #3599 from greglandrum)
  - update Cookbook stereochemistry examples
 (github pull #3604 from vfscalfani)
  - Add support for rendering SGroup data fields to MolDraw2D
 (github pull #3619 from greglandrum)
  - Support rendering the "ABS" flag in MolDraw2D
 (github issue #3623 from greglandrum)
  - Support drawing some query bonds
 (github pull #3624 from greglandrum)
  - Support rendering variable attachment points
 (github pull #3626 from greglandrum)
  - add configuration option to disable atom symbols in the rendering
 (github pull #3630 from greglandrum)
  - Render link nodes in MolDraw2D
 (github issue #3637 from greglandrum)
  - First pass at MolZip (now with bond stereo!)
 (github pull #3644 from bp-kelley)
  - Add molecule annotations/notes to MolDraw2D
 (github pull #3651 from greglandrum)
  - support setting MolDraw2DOptions using JSON from Python
 (github pull #3660 from greglandrum)
  - Make the scope control for Qt more idiomatic
 (github pull #3663 from d-b-w)
  - Expanded MolEnumerator functionality
 (github pull #3664 from greglandrum)
  - add support for generating pattern fps for MolBundles
 (github pull #3665 from greglandrum)
  - Add a callback function to EmbedParameters struct
 (github issue #3667 from jasondbiggs)
  - update SequenceParsers.cpp
 (github pull #3683 from magattaca)
  - MCS: extend completeRingsOnly to cover atoms as well
 (github issue #3693 from driesvr)
  - Add Molbundle search to SWIG
 (github pull #3698 from jones-gareth)
  - Added getMessage method to exceptions
 (github pull #3700 from sroughley)
  - add context manager for MolSuppliers
 (github issue #3703 from greglandrum)
  - Make better use of strictParsing for SGroups
 (github pull #3705 from ptosco)
  - Allow using  POPCNT on big-endian ppc64
 (github pull #3727 from pkubaj)
  - Cleanup: remove fromstring and tostring from functions working with
pillow
 (github issue #3730 from greglandrum)
  - Set strictParsing to false in MinimalLib
 (github pull #3737 from ptosco)
  - 3D MCS - Minimal version, no refactoring
 (github pull #3749 from robbason)
  - Include Winsock2.h instead of Windows.h in DebugTrace.h
 (github pull #3756 from dpaoliello)
  - R group match any issue
 (github pull #3767 from jones-gareth)
  - Support new coordgen option to not always make bonds to metals
zero-order
 (github pull #3769 from greglandrum)
  - DistanceGeometry: add flag to enforce trans amides
 (github pull #3794 from greglandrum)
  - MolDraw2D: first pass at rendering atom lists
 (github pull #3804 from greglandrum)
  - Issue a warning when embedding a molecule with no Hs
 (github pull #3807 from greglandrum)
  - Add tautomer query to the substructlibrary
 (github pull #3808 from bp-kelley)
  - Enhanced generateDepictionMatching2DStructure functionality
 (github pull #3811 from ptosco)
  - Confgen: add option to use symmetry when doing RMS pruning
 (github pull #3813 from greglandrum)
  - Remove boost::foreach from public headers
 (github pull #3820 from ricrogz)
  - Adds isotopeLabels and dummyIsotopeLabels MolDrawOptions
 (github pull #3825 from ptosco)
  - Added 2 Cookbook examples
 (github pull #3831 from vfscalfani)
  - Separate MolDraw2DQt into its own library
 (github pull #3832 from d-b-w)
  - Facilities for interactive modification of molecule drawing
 (github pull #3833 from SPKorhonen)
  - cleanup a bunch of compiler warnings
 (github pull #3849 from greglandrum)
  - add a new mol draw option to draw wedge bonds with a single color
 (github pull #3860 from jasondbiggs)
  - Add Kier Phi descriptor
 (github pull #3864 from greglandrum)
  - Add basic support for hydrogen bonds
 (github pull #3871 from greglandrum)
  - Allow batch editing of molecules: removal only
 (github pull #3875 from greglandrum)
  - Allow retrieving the _ErGAtomTypes property from Python
 (github pull #3878 from ptosco)
  - Exposes InsertMol to python RWMol
 (github pull #3907 from bp-kelley)
  - Use https for Avalon and Inchi downloads
 (github pull #3915 from ptosco)
  - support empty/missing SDT lines for SGroup data
 (github pull #3916 from greglandrum)
  - Cookbook entries should be updated
 (github issue #3917 from greglandrum)
  - MolDraw2D: support changing annotation colours
 (github pull #3919 from greglandrum)
  - include context managers for the multithreaded suppliers too
 (github pull #3920 from greglandrum)
  - Documentation cleanup and update
 (github pull #3922 from greglandrum)
  - remove an MSVC++ warning caused by #3849
 (github pull #3927 from greglandrum)
  - Adds removeAllHydrogenRGroupsAndLabels and fixes kekulization issues
 (github pull #3944 from ptosco)
  - Remove temporary labels from RGD results
 (github pull #3947 from ptosco)
  - appended a new project depend on RDKit
 (github pull #3955 from kotori-y)
  - Do not add unnecessary R-labels (and an optimization)
 (github pull #3969 from ptosco)
  - Add return codes and make RGroupDecomp less verbose
 (github pull #3971 from bp-kelley)
  - update to coordgen 2.0.0
 (github pull #3974 from greglandrum)


## Deprecated code (to be removed in a future release):
- The "minimizeOnly" option for coordgen will be removed in the next RDKit
release

[Rdkit-announce] 2020.09.1 RDKit Release

[Greg L. <gre...@gm...>]

Dear all,

I'm pleased to announce that the 2020.09 version of the RDKit is released.
The release notes are below.

The release files are on the github release page:
https://github.com/rdkit/rdkit/releases/tag/Release_2020_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

I hope to finish the conda builds of the PostgreSQL cartridge and do the PR
to update conda-forge this weekend.

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 2021.

Best Regards,
-greg

# Release_2020.09.1
(Changes relative to Release_2020.03.1)


## Backwards incompatible changes
- We've added additional allowed valences for Cl (now 1, 3, 5), Br (now 1,
3,
  5), I (now 1, 3, 5), At (now 1, 3, 5), Xe (now 0, 2, 4, 6), and Po (now
2, 4,
  6). Molecules with atoms in the new valence states will no longer generate
  sanitization errors. Note that this has an impact on the chemistry of
  molecules containing 3-valent I and at least one implict H (present 24
times
  in ChEMBL 27): previously this was incorrectly assigned two implicit Hs,
now
  it has no implicit Hs.
- Aromaticity perception of molecules like `Cc1nnc2n1c1ccccc1n1c(C)nnc12`
now
  correctly recognizes the full outer envelope, i.e. the bonds joining the
rings
  are now also aromatic.
- FindMCS() may return single atom MCSs, whereas previously it returned an
empty
  MCS unless there was at least one commond bond across the input
structures.
  So the MCS between molecules `CC` and `CO` is now `[#6]` rather than
being null.
- The fontSize()/setFontSize() (FontSize()/SetFontSize()) methods in
MolDraw2D
  now work in units of pixels (more or less) instead of the molecule units.
- The Open3DAlign functionality is now in its own separate library -
`O3AAlign`
  in cmake. If you are working in C++ and using O3A functionality, you'll
need
  to link against this library as well now.
- Due to improvements in the tautomer enumeration code, the method
  `TautomerEnumerator::enumerate` now returns a `TautomerEnumeratorResult`
  object instead of a vector of molecules. Note that if you are iterating
over
  the results of a call to `enumerate()` you shouldn't need to change your
code.
  If you want to invoke the old (and deprecated, see below) form from C++,
call
  `TautomerNumerator::enumerate(mol, nullptr)` or explicitly pass a
  `boost::dynamic_bitset*` to capture the modified atoms.
- The default precision setting for coordgen has been changed. The new
default
  was selected to greatly reduce the number of molecules for which it takes
a
  very long time to generate coordinates while still producing nice looking
  structures. We may continue to tweak this default value if/when problems
  with it are reported. If you would like to go back to the previous
setting, set
  CoordgenParams.minimizerPrecision to
CoordgenParams.sketcherStandardPrecision
  when you invoke rdCoordGen.AddCoords()
- Uncharger::uncharge() will now neutralize `[Cl,Br,I][O-],
[Cl,Br,I](=O)[O-],
  [Cl,Br,I](=O)(=O)[O-], [Cl,Br,I](=O)(=O)(=O)[O-], [O-]N=N[O-],
[N,P](=O)[O-],
  [N+](=O)([O-])[O-], P(=O)([O-])[O-], P(=O)([O-])([O-])[O-], S([O-])[O-],
  S(=O)([O-])[O-], S(=O)(=O)([O-])[O-], S(=O)(=O)([O-])OOS(=O)(=O)[O-]`.
  Previously not all of these inorganic acid counterions were consistently
  neutralized.
- The `None` value in the `RGroupCoreAlignment` enum was renamed to
`NoAlignment`
  in both C++ and Python, in order to avoid issues when attempting to
access it
  from Python.

## Highlights
- There's been another big improvement in the quality of molecule drawings:
  character and font handling is greatly improved thanks to the use of the
  FreeType library
- A new feature has been added to efficiently allow tautomer-insensitive
  substructure search.
- A new, much more accurate, algorithm is available for calculating CIP
labels
  on atoms and bonds.
- There's a new rdDeprotect module to allow automatically deprotecting
molecules
  before putting them into reactions
- Molecule and reaction metadata can now be added to PNG files generated by
  MolDraw2DCairo

## Acknowledgements
Shrey Aryan, Jinserk Baik, Francois Berenger, Cédric Bouysset, David
Cosgrove,
Ivan Chernyshov, Guillaume Godin, Manan Goel, Jan H. Jensen, Gareth Jones,
Maria
Kadukova, Eisuke Kawashima, Steven Kearnes, Brian Kelley, Joos Kiener,
Kenneth
Lum, Joshua Meyers, Rocco Moretti, Paul R Moses, Dan Nealschneider, Jin Pan,
Joann Prescott-Roy, Matthew Robinson, Jaime Rodríguez-Guerra, Ricardo
Rodriguez-Schmidt, Jeff van Santen, Roger Sayle Vincent F. Scalfani Eric
Taw,
Ansgar Schuffenhauer, Paolo Tosco, Ivan Tubert-Brohman, Riccardo Vianello,
Rachel Walker, Maciej Wójcikowski, Christopher Zou, daverona, hjuinj,
intrigus-lgtm, autodataming, paconius, sailfish009

## Bug Fixes:
  - Python tests fail when RDK_BUILD_COMPRESSED_SUPPLIERS is enabled
 (github issue #1888 from greglandrum)
  - ResonanceMolSupplier potentially stuck in infinite loop
 (github issue #2597 from tawe141)
  - ctest pythonTestDirChem failed
 (github issue #2757 from jinserk)
  - Issue with inversion/retention of stereochemistry
 (github issue #2891 from mc-robinson)
  - cannot parse reaction SMILES/SMARTS with dative bonds
 (github issue #2954 from greglandrum)
  - ResonanceMolSupplier can fail with small maxStructs values
 (github issue #3041 from greglandrum)
  - seg fault in ResonanceMolSupplier()
 (github issue #3048 from greglandrum)
  - Bug in image rendering of dative bonds
 (github issue #3056 from IvanChernyshov)
  - Coordinates from coordgen are not centered around the origin
 (github pull #3058 from DavidACosgrove)
  - fix a typo in ScaffoldNetwork/CMakeLists.txt
 (github pull #3060 from greglandrum)
  - Bad double bond placement in polycyclic aromatics
 (github issue #3061 from DavidACosgrove)
  - SGroups with more than one attachment point are now properly parsed
 (github pull #3072 from greglandrum)
  - Reactions should not use strict implicit valence calculations
 (github issue #3097 from mwojcikowski)
  - partial reacting atom detection
 (github issue #3119 from thegodone)
  - DrawMolecules does not center molecules
 (github issue #3126 from JoshuaMeyers)
  - results from coordgen are sometimes not centered
 (github issue #3131 from greglandrum)
  - GCC 10.0.1 compile error
 (github issue #3135 from rvianello)
  - Memory leak when parsing bad SMILES
 (github issue #3139 from intrigus-lgtm)
  - Error breaking StereoBonds in reactions
 (github issue #3147 from mc-robinson)
  - MolOps::removeHs() removes hydrides
 (github issue #3150 from jhjensen2)
  - Kekulization error from CreateScaffoldNetwork
 (github issue #3153 from greglandrum)
  - Fix drawing of N plus
 (github pull #3165 from DavidACosgrove)
  - RWMol::clear() does not explicitly clean up SubstanceGroups or
StereoGroups
 (github issue #3167 from greglandrum)
  - Modifying a molecule should not automatically clear SubstanceGroups
 (github issue #3168 from greglandrum)
  - removeHs() should not remove atoms in SubstanceGroups
 (github issue #3169 from greglandrum)
  - fix a memory problem detected in malformed SMILES
 (github pull #3171 from greglandrum)
  - Python wrapper: SetQuery and ExpandQuery for bonds
 (github pull #3172 from i-tub)
  - S-groups: PARENT field should reference index
 (github issue #3175 from greglandrum)
  - rdScaffoldNetwork causes segmenation fault upon None molecule
 (github issue #3177 from AnsgarSchuffenhauer)
  - fix a small inconsistency in the name of the inchi package
 (github pull #3182 from rvianello)
  - Molecule constructed from CXSMILES cannot be translated to SMARTS
 (github issue #3197 from greglandrum)
  - Formatting fix of CalcRMS
 (github pull #3203 from chmnk)
  - fix the CompressedSDMolSupplier python iterator interface
 (github pull #3204 from rvianello)
  - Queries generated from PreprocessReaction cannot be translated to SMARTS
 (github issue #3206 from greglandrum)
  - Attachment point info not being read from V2000 mol blocks
 (github issue #3207 from greglandrum)
  - Memory Sanitizer fails on molFromPickle on empty file
 (github issue #3211 from intrigus-lgtm)
  - Throw exception when reading from stream fails.
 (github pull #3212 from intrigus-lgtm)
  - fix molstogridimage on certain fragments/smarts patterns
 (github pull #3217 from bp-kelley)
  - Lines in wedge bonds being drawn too closely together
 (github issue #3226 from paconius)
  - EnumerateStereochemistry should clear CIP labels
 (github issue #3231 from greglandrum)
  - lock CI cairo version to force an install from the rdkit repo
 (github pull #3240 from greglandrum)
  - XBCORR and XBHEAD in Sgroups no longer cause parse failures
 (github pull #3242 from greglandrum)
  - LINKNODEs are ignored by the CTAB parsers
 (github pull #3247 from greglandrum)
  - add GetStringVectProp() to SubstanceGroup class
 (github pull #3251 from greglandrum)
  - Envelope aromaticity not detected in complex fused system
 (github issue #3256 from greglandrum)
  - Draw.MolsToGridImage repeating atom indices
 (github issue #3258 from greglandrum)
  - Atom indices clash with atom symbols in small pictures.
 (github issue #3262 from DavidACosgrove)
  - MinimalLib Dockerfile is broken at HEAD
 (github issue #3267 from skearnes)
  - Fixes #2757
 (github pull #3268 from greglandrum)
  - RGroupDecomposition restructuring
 (github pull #3270 from bp-kelley)
  - Get PPC builds working
 (github pull #3285 from greglandrum)
  - ScaffoldNetwork not in C# wrappers
 (github pull #3289 from jones-gareth)
  - bonds with "either' stereo cannot be read from JSON
 (github pull #3290 from greglandrum)
  - Small bug fixes and cleanups from fuzz testing
 (github pull #3299 from greglandrum)
  - DrawOptions: bondLineWidth behaving differently since 2020 versions
 (github issue #3305 from kienerj)
  - Not possible to copy SubstanceGroups in Python
 (github issue #3312 from greglandrum)
  - Stereochemistry perception getting confused by a bad drawing.
 (github issue #3314 from greglandrum)
  - SubstanceGroups should not be written with quotes around missing fields
 (github issue #3315 from greglandrum)
  - SetDoubleBondNeighborDirections() not overwriting existing bond
directions
 (github issue #3322 from greglandrum)
  - AdjustQueryParameters.adjustSingleBondsBetweenAromaticAtoms does not
modify ring bonds
 (github issue #3325 from greglandrum)
  - Fixes for aromatic bond fuzzy queries
 (github pull #3328 from jones-gareth)
  - lock sphinx version in CI due to problem with v3.2.0
 (github pull #3332 from greglandrum)
  - Remove deprecated Sphinx options
 (github pull #3335 from greglandrum)
  - more bug fixes and cleanups from fuzz testing
 (github pull #3339 from greglandrum)
  - unspecified branch bonds in SMARTS don't have aromaticity set
 (github issue #3342 from greglandrum)
  - Incorrect resonance structures in presence of dative bonds
 (github issue #3349 from IvanChernyshov)
  - Converting atoms with high radical counts to InChI generates incorrect
results
 (github issue #3365 from greglandrum)
  - Replace fill-opacity= with fill-opacity: in MolDraw2DSVG and tests
 (github pull #3368 from lummyk)
  - Fixes a bug in AddHs() involving sp2 centers with degree 1
 (github pull #3383 from ptosco)
  - Information about charges and isotopes lost when calling
AdjustQueryProperties
 (github issue #3388 from greglandrum)
  - prepareMolForDrawing() incorrectly adds chiral Hs if no ring info is
present
 (github issue #3392 from greglandrum)
  - CXSMILES parser should not set atom maps for attachment points
 (github issue #3393 from greglandrum)
  - Fixes a couple of query-related bugs
 (github pull #3398 from ptosco)
  - Doing a match of a recursive smarts leaves traces of the previous match
 (github issue #3403 from bp-kelley)
  - Recursive smarts cannot be used in the core for rgroup decomposition
 (github pull #3404 from bp-kelley)
  - Improvements to reaction chirality handling
 (github pull #3412 from greglandrum)
  - V3K mol blocks with no atoms fail to parse
 (github issue #3413 from greglandrum)
  - Problem parsing SGroup data comtaining `""`
 (github issue #3415 from greglandrum)
  - MolEnumerator::enumerate() should call updatePropertyCache()
 (github pull #3420 from greglandrum)
 - Fixed bad draw scale in drawMolecules. Github3391.  Take 2.
 (github pull #3424 from DavidACosgrove)
  - Replace fill-opacity= to fill-opacity: in reaction.out
 (github pull #3426 from daverona)
  - set the ChiralityPossible tag when using the new code with
FindMolChiralCenters
 (github pull #3434 from greglandrum)
  - Silence deprecation warning
 (github pull #3439 from ptosco)
  - update minimallib python requirements to python3
 (github pull #3449 from greglandrum)
  - Fix dead links to inchi-trust
 (github pull #3451 from jvansan)
  - ringMatchesRingOnly=True produces a SMARTS query that return no
substructure matches
 (github issue #3458 from jaimergp)
  - Normalization rule incorrectly matches sulfones
 (github issue #3460 from greglandrum)
  - BlockLogs was reenabling all logs, not just the ones that were disabled
 (github pull #3466 from bp-kelley)
  - Hydrogen is incorrectly identified as an "early" atom
 (github issue #3470 from greglandrum)
  - Fixes typo that causes the build to fail
 (github pull #3477 from ptosco)
  - Fix a crashing bug with None in rdMolStandardize
 (github pull #3481 from greglandrum)
  - zlib.h not found if not in system directories
 (github issue #3493 from ricrogz)
  - fix paths in ConformerParser tests
 (github pull #3504 from ricrogz)

## New Features and Enhancements:
  - Add GetBestRMS function
 (github issue #1820 from chmnk)
  - Add reorder tautomers function and accompanying tests
 (github pull #3043 from chriswzou)
  - Set RDK_BOOST_VERSION to pass minimum required version to FindBoost
 (github pull #3074 from e-kwsm)
  - bug: the MCS of the molecules CH4 and CH3OH is empty. how to return C?
 (github issue #3095 from autodataming)
  - start using boost:stacktrace
 (github pull #3124 from greglandrum)
  - Add Fuzzing, fixes #2857
 (github pull #3128 from intrigus-lgtm)
  - Cookbook entry for ETKDG with rings
 (github pull #3129 from hjuinj)
  - Fixes #2795
 (github pull #3134 from manangoel99)
  - Bump Catch2 to v2.12.1
 (github pull #3136 from e-kwsm)
  - Modernize how legacy C headers are included
 (github pull #3137 from e-kwsm)
  - Avoid C preprocessor macros
 (github pull #3138 from e-kwsm)
  - Modernization: use nullptr
 (github pull #3143 from e-kwsm)
  - Update fuzzer dict
 (github pull #3162 from intrigus-lgtm)
  - Add BCUT2D and AUTOCORR2D to desclist
 (github pull #3178 from bp-kelley)
  - Remove usage of the deprecated random_shuffle() function
 (github pull #3187 from greglandrum)
  - clang-tidy modernize-use-default-member-init and modernize-use-emplace
 (github pull #3190 from greglandrum)
  - Tautomer search
 (github pull #3205 from jones-gareth)
  - Add optional timeout to RGroupDecomposition
 (github pull #3223 from greglandrum)
  - Allow symmetrization to be completely disabled in RGD code
 (github issue #3224 from greglandrum)
  - gitignore source and build files from the RingFamilies external lib
 (github pull #3228 from d-b-w)
  - Add new CIP labelling algorithm
 (github pull #3234 from ricrogz)
  - Adds more options to adjustQueryProperties
 (github pull #3235 from greglandrum)
  - Improve SSSR performance for large molecules
 (github pull #3236 from d-b-w)
  - Support using FreeType for text rendering
 (github pull #3237 from DavidACosgrove)
  - Cleanup warnings from clang-10
 (github pull #3238 from greglandrum)
  - DEB packaging: cairo support is needed to generate PNGs
 (github pull #3250 from UnixJunkie)
  - Added call to test legends.
 (github pull #3252 from DavidACosgrove)
  - Improve performance of aromaticity detection for large molecules
 (github pull #3253 from d-b-w)
  - Speed up ring finding by skipping nodes not in rings
 (github pull #3254 from d-b-w)
  - Support enumerating some mol file features into `MolBundles`
 (github pull #3257 from greglandrum)
  - Add cxsmiles query atoms to CTAB parsers and writers
 (github pull #3261 from greglandrum)
  - Update to Coordgen v1.4.1
 (github pull #3265 from ricrogz)
  - ScaffoldNetwork: add feature to count the number of molecules a
scaffold originates from
 (github pull #3275 from greglandrum)
  - rgroup speedup
 (github pull #3279 from bp-kelley)
  - Stop trying to assign hybridization to actinides
 (github pull #3281 from greglandrum)
  - Decouple coordgen and maeparser integrations
 (github pull #3286 from greglandrum)
  - Avoid really slow Windows conda builds
 (github pull #3287 from ptosco)
  - Embed default truetype font
 (github pull #3288 from greglandrum)
  - Expanded support for CXSMILES features
 (github pull #3292 from greglandrum)
  - Deprotection Library
 (github pull #3294 from bp-kelley)
  - Use operator() and __call__() consistently across RDKit
 (github pull #3295 from ptosco)
  - Molecule metadata in PNGs
 (github pull #3316 from greglandrum)
  - Cleanup alignment dependencies
 (github pull #3317 from greglandrum)
  - Add the option to minimize structures with coordgen
 (github pull #3319 from greglandrum)
  - Updated code for chirality perception
 (github pull #3324 from greglandrum)
  - Some work on TautomerEnumerator
 (github pull #3327 from ptosco)
  - Add fragmentOnBonds to SWIG wrappers
 (github issue #3329 from greglandrum)
  - Sped up SSSR by not storing every path back to root
 (github pull #3333 from rachelnwalker)
  - Fix Cookbook formatting and added 4 new examples
 (github pull #3345 from vfscalfani)
  - switch to using target_compile_definitions instead of add_definitions
 (github pull #3350 from greglandrum)
  - [GSoC-2020] Generalized and Multithreaded File Reader
 (github pull #3363 from shrey183)
  - support new CIP code and StereoGroups in
MolDraw2D_detail::addStereoAnnotation()
 (github issue #3369 from greglandrum)
  - expose additional SubstanceGroup data members to Python
 (github pull #3375 from greglandrum)
  - Add MolDraw2DJS
 (github pull #3376 from greglandrum)
  - Add APK package link for Alpine Linux distribution
 (github pull #3379 from daverona)
  - Add SubstanceGroups to the SWIG Wrappers
 (github pull #3390 from jones-gareth)
  - Add better support for isotopic Hs to removeHs() and addHs()
 (github pull #3396 from ptosco)
  - Add support for abbreviations
 (github pull #3406 from greglandrum)
  - Allow passing explicit removeHs, sanitize and strict flags to the MDL
rxn parser
 (github pull #3411 from ptosco)
  - Improvements to reaction chirality handling
 (github pull #3412 from greglandrum)
  - RGD cleanup, optimization and a better fix for #1705
 (github pull #3428 from ptosco)
  - Tautomers with endocyclic double bonds should be preferred over
exocyclic ones
 (github issue #3430 from ptosco)
  - RGD: Code modernization and an optimization
 (github pull #3437 from ptosco)
  - expose PNG metadata functions to python
 (github pull #3440 from greglandrum)
  - Replace basestring
 (github pull #3441 from iammosespaulr)
  - Get the Uncharger to deal with a larger set of acids correctly
 (github pull #3448 from ptosco)
  - expose templated coordinate generation to the JS Wrapper
 (github pull #3450 from greglandrum)
  - change default precision for coordgen
 (github pull #3452 from greglandrum)
  - add coordgen support to demo.html
 (github pull #3453 from greglandrum)
  - Two simple MolStandardizer code cleanups
 (github pull #3454 from ptosco)
  - A few improvements to MolStandardize::Normalizer
 (github pull #3455 from ptosco)
  - Add Cookbook entries 30-32
 (github pull #3459 from vfscalfani)
  - A few small tweaks to the drawing code
 (github pull #3464 from greglandrum)
  - Make MetalDisconnector more robust against metallorganics
 (github pull #3465 from greglandrum)
  - Add nocharge algorithm example to cookbook
 (github pull #3467 from vfscalfani)
  - ROMol: add inline impl for common getNumAtoms call
 (github pull #3469 from jinpan)
  - Improve sphinx formatting in rdSubstructLibrary
 (github issue #3471 from cbouy)
  - Cmake config improvements
 (github pull #3478 from rvianello)
  - allow fillColour to be changed from python
 (github pull #3480 from greglandrum)
  - Fix undefined behavior in testCoordGen test
 (github pull #3495 from roccomoretti)
  - Add a version for the pattern fingerprint
 (github pull #3496 from greglandrum)
  - Fixes a number of issues flagged by clang
 (github pull #3498 from ptosco)
  - Update to maeparser v1.2.4
 (github pull #3506 from sailfish009)
  - Fix python invalid escape sequences
 (github pull #3508 from ricrogz)

## Code removed in this release:
- To improve API consistency of the exceptions in RDKit with the default
ones in
  the STL, the several `message()` methods and `Invariant::getMessage()` in
RDKit's
  exceptions have been removed in favor of `what()`.
- The old MolHash code has been removed from the C++ code, all wrappers,
and the
  PostgreSQL cartridge.

## Deprecated code (to be removed in a future release):
- The function `FileParserUtils::replaceAtomWithQueryAtom()` has been moved
to
  the namespace QueryOps. Please use `QueryOps::replaceAtomWithQueryAtom()`
  instead. The version in the `FileParserUtils` namespace will be removed
in the
  next release.
- The method `std::vector<ROMOL_SPTR> TautomerEnumerator::enumerate(const
ROMol &mol, boost::dynamic_bitset<> *modifiedAtoms, boost::dynamic_bitset<>
*modifiedBonds = nullptr)`
  is deprecated and will be removed in a future release.
  Please use `TautomerEnumeratorResult TautomerEnumerator::enumerate(const
ROMol &mol,bool reassignStereo = true)`
  instead.
- The `MolDraw2DQt` class is no longer supported since we don't think
anyone is
  using it. It will be removed in the 2021.03 release unless we learn
otherwise.

[Rdkit-announce] Registration for the 2020 virtual RDKit UGM

[Greg L. <gre...@gm...>]

[apologies to those of you who are seeing this multiple times, I'm trying
to be sure to distribute this information as broadly as possible]

Dear RDKit community,

The Covid19 situation has caused us to have to cancel the physical RDKit
UGM for 2020, but we *are* going to do a virtual version of the event.

We're still working out the exact details for the technology and agenda,
but please go ahead and register for the virtual event here:
https://www.eventbrite.com/e/virtual-9th-rdkit-ugm-2020-tickets-116854100761


We are looking for speakers (both regular and lightning talks), so please
get in touch with a title/topic if you're interested in talking.

Best Regards,
-greg

[Rdkit-announce] 2020 RDKit UGM Registration open

[Greg L. <gre...@gm...>]

Dear all

This year's RDKit User Group Meeting will take place from 6-8 October in
Berlin, Germany and is being hosted by Djork-Arné Clevert and Floriane
Montanari at Bayer AG,  Digital Technologies.

Registration for the RDKit UGM is free:
https://www.eventbrite.com/e/9th-rdkit-ugm-2020-tickets-103907616478

We will once again stick to what has become a tried and true format:
Days 1 and 2: Talks, lightning talks, roundtable(s), discussion, poster
sessions, and talktorials. For those who haven’t attended before,
talktorials are somewhere between a talk and a tutorial, they cover
something interesting done with the RDKit and include the code used to do
the work. During the presentation you'll give an overview of what you did
and also show the pieces of the code that are central to the work. The idea
is to mix the science up with the tutorial aspects.

Day 3 will be a hackathon and training sessions: those who choose to stay
will spend an intense day working in small groups to produce useful
artifacts: new bits of code, KNIME nodes, KNIME workflows, tutorials,
documentation, Jupyter notebooks, etc. As usual we will try to structure
this a bit by collecting a bunch of ideas for things to work on in advance.
We will also try and organize a couple of training/tutorial sessions for
people who are interested in that.

There will also be, of course, social activities. We will be announcing
more details about these later.

A more detailed announcement with additional information about place,
hotels and logistics will follow soon.

We are looking for people who are willing to do presentations, talktorials
or posters on the first two days. If you're interested in contributing,
please send the three of us an email.
Lighting talks don't need to be arranged too far in advance; we will start
collecting the list of people interested in doing those shortly before the
event.

*COVID-19 note*: At the time we're planning this (in late April), it's not
at all certain that we'll be able to actually hold the UGM. Since we think
it's super valuable (and fun!) to get people together in one place for
these events, we've decided to try. At the moment it looks like things
should be back to normal enough in Germany that we will be able to actually
do the UGM, but we realize that this could easily change and will also make
preparations for a purely virtual version of the UGM, just in case.

We know that this isn't just our decision, some people may not be able to
travel to Berlin due to government- or employer-imposed travel restrictions
or may just feel uncomfortable arranging a trip at this point, since having
a UGM without attendees doesn't make sense, we want to hear from the
community before making any final decisions. So... please take a minute and
answer the four multiple choice questions here:
https://forms.gle/YMtqKRgv1vVwqM1J8

Best Regards,
Greg, Okko, and Floriane

[Rdkit-announce] 2020.03.1 RDKit Release

[Greg L. <gre...@gm...>]

Dear all,

I'm pleased to announce that the next version of the RDKit - 2020.03 - is
released. This time we even managed to get it out during the correct month!
:-) The release notes are below.

The release files are on the github release page:
https://github.com/rdkit/rdkit/releases/tag/Release_2020_03_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

The PR is in to switch conda-forge to the new version as well. There are
currently some non-RDKit-related build problems with conda-forge, but
hopefully that will be updated soon as well.

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 September/October 2020.

Best Regards,
-greg

# Release_2020.03.1
(Changes relative to Release_2019.09.1)

## Backwards incompatible changes
- Searches for equal molecules (i.e. `mol1 @= mol2`) in the PostgreSQL
cartridge
  now use the `do_chiral_sss` option. So if `do_chiral_sss` is false (the
  default), the molecules `CC(F)Cl` and `C[C@H](F)Cl` will be considered to
be equal.
  Previously these molecules were always considered to be different.
- Attempting to create a MolSupplier from a filename pointing to an empty
file,
  a file that does not exist or sometihing that is not a standard file (i.e.
  something like a directory) now generates an exception.
- The cmake option `RDK_OPTIMIZE_NATIVE` has been renamed to
`RDK_OPTIMIZE_POPCNT`

# Highlights:
- The drawings generated by the MolDraw2D objects are now significantly
improved
  and can include simple atom and bond annotations (#2931 and #3010)
- An initial implementation of a modified scaffold network algorithm is now
  available (#2911)
- A few new descriptor/fingerprint types are available - BCUTs (#2957),
Morse
  atom fingerprints (#1773), Coulomb matrices (#2993), and MHFP and SECFP
  fingerprints (#2643)
- There is a new, and greatly improved, version of the RDKit Cookbook
(#2884)
- There is a new version (v3) of the ETKDG conformer generator along with
  optional new terms for handling small rings and macrocyles (
http://doi.org/dqnh) (#2999)


## Acknowledgements:
Marcel Baltruschat, Jason Biggs, Eliane Briand, Ben Cornett, David Cosgrove,
Andrew Dalke, Tim Dudgeon, Zhenting Gao, Guillaume Godin, Manan Goel, Gareth
Jones, Zachary Kaplan, Eisuke Kawashima, Steven Kearnes, Brian Kelley, Maxim
Koltsov, Franziska Kruger, Mieszko Manijak, Dan Nealschneider, Daniil
Polykovskiy, Daniel Probst, Sereina Riniker, Matthew Robinson, Steve
Roughley,
Kevin Ryan, Vincent F. Scalfani, Ricardo Rodriguez Schmidt, Rim
Shayakhmetov,
Aryan Shrey, Nik Stiefl, Matt Swain, Paolo Tosco, Wiep van der Toorn,
Riccardo
Vianello, Shuzhe Wang, Piotr Wawrzyniak, Hsiao Yi, 'jasad1',
'luancarvalhomartins'


## Bug Fixes:
  - Mol rendering within DataFrames in a Jupyter Notebook is broken with
Pandas 0.25.1
 (github issue #2673 from mrcblt)
  - Removed RDKIT_SIMDIVPICKERS_EXPORT
 (github pull #2740 from ptosco)
  - - enable building RDKitRingDecomposerLib.dll under Windows
 (github pull #2742 from ptosco)
  - Do a windows DLL build as part of the Azure DevOps setup
 (github pull #2743 from greglandrum)
  - Fix data race in sascorer.py
 (github pull #2744 from skearnes)
  - Uncharger not properly setting explicit/implicit H count
 (github issue #2749 from greglandrum)
  - MSVC compile error: MolHash scoped enum cannot be redeclared as unscoped
 (github issue #2752 from mcs07)
  - Molecules whose Y size is very small won't display as SVG
 (github issue #2762 from ptosco)
  - Make the cartridge tests work with PostgreSQL 12
 (github pull #2767 from greglandrum)
  - Salt stripper should consider bond matches as well as atom matches
 (github pull #2768 from greglandrum)
  - Bismuth should count as an early element
 (github issue #2775 from greglandrum)
  - addHs() fails on atoms with "bad" valences
 (github issue #2782 from greglandrum)
  - Element symbol lookup for some transuranics returns incorrect results
 (github issue #2784 from LeanAndMean)
  - [cartridge] molecular equality should use do_chiral_sss setting
 (github issue #2790 from greglandrum)
  - uncharger removes Hs from carbocations instead of adding them
 (github issue #2792 from greglandrum)
  - Fix build without boost serialization library
 (github pull #2796 from maksbotan)
  - Using `SetBoundsMat` significantly slows down conformer generation
process.
 (github issue #2800 from hjuinj)
  - rdkit.Ched.rdFMCS.FindMCS generates invalid smarts
 (github issue #2801 from luancarvalhomartins)
  - Remove confId from *FFOptimizeMoleculeConfs Python docs
 (github issue #2805 from ptosco)
  - Hybridization queries on dummy atoms not written properly to SMARTS
 (github issue #2814 from greglandrum)
  - Charge range queries not properly written to SMARTS
 (github issue #2815 from greglandrum)
  - RDKit segfaults in MMFFOptimizeMoleculeConfs()
 (github issue #2820 from ptosco)
  - Trusted Smiles holder doesn't handle ring queries
 (github issue #2830 from bp-kelley)
  - Fix windows substructure crash
 (github pull #2836 from greglandrum)
  - Fix YAeHMOP build
 (github pull #2838 from ptosco)
  - testGithub2245 in testPickers.cpp occasionally fails
 (github issue #2839 from ptosco)
  - add define for RDK_USE_BOOST_SERIALIZATION
 (github pull #2859 from greglandrum)
  - fix start/end atoms when wedging bonds
 (github pull #2861 from greglandrum)
  - Fixes the size of the reduced charge matrix from eHT calculations
 (github pull #2864 from greglandrum)
  - Dev/pvs studio cleanups2
 (github pull #2877 from greglandrum)
  - segfault in MaeMolSupplier
 (github issue #2881 from greglandrum)
  - update maven url in build system
 (github pull #2889 from greglandrum)
  - EnumerateStereoisomers cannot handle STEREOANY bonds
 (github issue #2890 from ricrogz)
  - Update one of the cartridge tests that got missed
 (github pull #2894 from greglandrum)
  - acepentalene aromaticity perception
 (github issue #2895 from adalke)
  - New Similarity Maps drawing code Java Wrappers non-functional
 (github issue #2896 from sroughley)
  - Fix to allow multistructure images in Java/C# and use MCS for c# wrapper
 (github pull #2898 from jones-gareth)
  - Remove bogus URFLib library
 (github pull #2900 from greglandrum)
  - java wrapper build cleanups
 (github pull #2901 from greglandrum)
  - SMARTS parser fails on high-numbered ring closures in branches
 (github issue #2909 from greglandrum)
  - patch to make PandasTools tests pass with pandas v0.22
 (github pull #2913 from greglandrum)
  - fix doctest problem with Pandas v1.0
 (github pull #2918 from greglandrum)
  - Build with -D RDK_BUILD_COORDGEN_SUPPORT=OFF includes a test case that
depends on MaeMolSupplier
 (github issue #2929 from rvianello)
  - MinimalLib: get_stereo_tags() should also return unspecified centers
 (github issue #2936 from greglandrum)
  - Fix regression introduced by e245349c
 (github pull #2945 from cornett)
  - Avoid data race warning in SmilesParse.cpp
 (github pull #2946 from skearnes)
  - Empty molecule has non-zero LabuteASA
 (github issue #2948 from jasondbiggs)
  - Fix a problem with aromatic heteroatom tautomer enumeration
 (github pull #2952 from greglandrum)
  - Molecule properties not retained with
MolStandardize.rdMolStandardize.Cleanup()
 (github issue #2965 from ZacharyKaplan)
  - Fix build without boost serialization.
 (github pull #2972 from ricrogz)
  - RDKFuncs.chargeParent() core dumps when standardization is skipped
 (bithub issue #2970 from tdudgeon)
  - fix a typo in the scaffold network wrappers and add some tests
 (github pull #2982 from greglandrum)
  - Tautomer enumeration should remove stereo in all tautomers
 (github issue #2990 from greglandrum)
  - Segmentation fault on EmbedMolecule
 (github issue #3019 from shayakhmetov)
  - Removed dllexport from a function that lives in the anonymous namespace
 (github pull #3027 from ptosco)


## New Features and Enhancements:
  - Morse atom fingerprint
 (github pull #1773 from thegodone)
  - Allow serializing coordinates as doubles
 (github issue #2510 from danpol)
  - Rework MaeMolSupplier, fix #2617
 (github pull #2620 from ricrogz)
  - Implementation of MHFP and SECFP Fingerprints
 (github pull #2643 from daenuprobst)
  - MatchFusedRings does not imply CompleteRingsOnly anymore
 (github pull #2748 from ptosco)
  - Improvements to JS wrappers
 (github pull #2751 from greglandrum)
  - Fix installed header directory structure
 (github pull #2754 from ricrogz)
  - Add doRandom to the header docs
 (github pull #2756 from bp-kelley)
  - Add queryMol data member to MCSResult
 (github pull #2759 from ptosco)
  - Add functions to enable/disable the substructure matching monkey
patching in IPythonConsole.py
 (github issue #2786 from greglandrum)
  - Add a function to assign chiral tags from sss atom parity
 (github issue #2823 from ptosco)
  - Support MRV_IMPLICIT_H S groups when reading Mol blocks
 (github issue #2829 from greglandrum)
  - Unset executable flag
 (github pull #2833 from e-kwsm)
  - Remove O(N) behavior of getNumBonds
 (github pull #2847 from bp-kelley)
  - Feature proposal: add remove_stereochemistry=False flag for RemoveHs()
 (github issue #2848 from shayakhmetov)
  - Expose SubstructLibrary serialization stream
 (github pull #2853 from bp-kelley)
  - Fix typo
 (github pull #2862 from e-kwsm)
  - Rename RDK_OPTIMIZE_NATIVE to RDK_OPTIMIZE_POPCNT
 (github pull #2865 from ElianeBriand)
  - Update Draw.MolToImage() and Draw.MolToFile() to use the new drawing
code
 (github pull #2866 from greglandrum)
  - Improve PostgreSQL cartridge install documentation
 (github pull #2870 from yellowBirdy)
  - Fixes #2858
 (github pull #2871 from greglandrum)
  - Add a cartridge test to the azure devops config
 (github pull #2873 from greglandrum)
  - Add a new Cookbook v2 to the RDKit docs
 (github pull #2884 from vfscalfani)
  - Add MolVS tautomer canonicalization
 (github pull #2886 from greglandrum)
  - add a convenience function for RGD--Pandas integration
 (github pull #2887 from greglandrum)
  - run clang-tidy with readability-braces-around-statements
 (github pull #2899 from greglandrum)
  - Allow RDProps::clearProp to succeed even if the prop doesn't exist
 (github issue #2910 from greglandrum)
  - Add a scaffold network implementation
 (github pull #2911 from greglandrum)
  - cleanup of the SMILES/SMARTS parsing and writing code
 (github pull #2912 from greglandrum)
  - Add _ctab, _mol2, _pdb to allow direct mol construction from strings
 (github issue #2916 from greglandrum)
  - Parse and handle the stereoCare or STBOX flags in CTABs
 (github pull #2917 from greglandrum)
  - RDKit exceptions do not override the default `what()` method
 (github issue #2920 from ricrogz)
  - Allow custom post-match filters for substructure matching
 (github pull #2927 from greglandrum)
  - Proposed improvements to 2D Drawing Code
 (github issue #2931 from DavidACosgrove)
  - Include running the documentation tests as part of the CI runs
 (github pull #2932 from greglandrum)
  - Add support for phosphine and arsine chirality
 (github issue #2949 from wopozka)
  - A couple additions to the extended Hueckel integration
 (github pull #2955 from greglandrum)
  - Add BCUT 2D descriptors
 (github pull #2957 from bp-kelley)
  - Add multithreaded pattern/fp generator
 (github pull #2973 from bp-kelley)
  - Description for the data files.
 (github pull #2975 from zhentg)
  - Enable larger ring matches in SMARTS expressions
 (github pull #2981 from d-b-w)
  - ScaffoldNetwork rearrangements
 (github pull #2985 from greglandrum)
  - add add_hs() and remove_hs() to JS wrappers
 (github pull #2986 from greglandrum)
  - Add Atom Feature Vectors
 (github pull #2988 from thegodone)
  - Add CoulombMat calculator
 (github pull #2993 from thegodone)
  - Update azure-pipelines.yml
 (github pull #2997 from greglandrum)
  - Improve Conformational Sampling of Small and Large Ring Molecules
 (github pull #2999 from hjuinj)
  - Fix atom highlighting in notebook PNGs
 (github pull #3000 from greglandrum)
  - adds a one-liner for getting a vector of random smiles for a molecule
 (github pull #3002 from greglandrum)
  - Allow enhanced stereo to be used in substructure search
 (github pull #3003 from d-b-w)
  - Add support for the rest of the v3000 atom properties
 (github pull #3007 from greglandrum)
  - Move jupyter extension logging to the python logger
 (github pull #3008 from bp-kelley)
  - Commit of 2D draw annotation.
 (github pull #3010 from DavidACosgrove)
  - Update Maeparser & Coordgen Dependencies
 (github pull #3011 from ricrogz)
  - Remove unnecessary files
 (github pull #3012 from e-kwsm)
  - allow retrieval of the atoms/bonds modified by the tautomerization
 (github pull #3013 from greglandrum)
  - Add 5 new recipes to Cookbook
 (github pull #3014 from vfscalfani)
  - Turns on cairo support (and testing) in the Azure DevOps CI builds
 (github pull #3022 from greglandrum)
  - Added support for Python FMCS functors
 (github pull #3023 from ptosco)
  - add random seed to docs to get reproducible conformations
 (github pull #3026 from greglandrum)
  - update docs for 2020.03
 (github pull #3028 from greglandrum)
  - update Getting Started in C++ document
 (github pull #3039 from DavidACosgrove)



## Deprecated code (to be removed in a future release):
- To improve API consistency of the exceptions in RDKit with the default
ones in
  the STL, the several `message()` methods and `Invariant::getMessage()` in
RDKit's
  exceptions are from now on deprecated in favor of `what()`. Both
`message()` and
  `Invariant::getMessage()` will be removed in the next release.
- The old MolHash code should be considered deprecated. This release
introduces
  a more flexible alternative. Specifically the following pieces will be
removed in the next release:
  - The python functionality
`rdkit.Chem.rdMolHash.GenerateMoleculeHashString()`
  - The C++ functionality directly present in the header file
`GraphMol/MolHash/MolHash.h`

[Rdkit-announce] (no subject)

[Greg L. <gre...@gm...>]

Dear all,

The beta of the 2020.03 RDKit release has been tagged in github:
https://github.com/rdkit/rdkit/releases/tag/Release_2020_03_1b1

I've done conda builds for Python 3.6 and 3.7 for Mac, and Linux and I'm
working on the Windows builds now. These all use the beta label so that
they do not install by default; you'll need to run "conda install" as
follows:

conda install -c rdkit/label/beta rdkit

Be sure to confirm that it's installing the right version when you are
prompted (if there's no build available, it will pick the current
production release instead).

The relevant section of the release notes (which still may need a highlight
or two added) is below, or you can see a nicely formatted version here:
https://github.com/rdkit/rdkit/releases/tag/Release_2020_03_1b1

As usual, if you have time to try out the new release I would love
feedback. If nothing major comes up, I plan to do the actual release next
Monday.

Best,
-greg

# Release_2020.03.1
(Changes relative to Release_2019.09.1)

## Backwards incompatible changes
- Searches for equal molecules (i.e. `mol1 @= mol2`) in the PostgreSQL
cartridge
  now use the `do_chiral_sss` option. So if `do_chiral_sss` is false (the
  default), the molecules `CC(F)Cl` and `C[C@H](F)Cl` will be considered to
be equal.
  Previously these molecules were always considered to be different.
- Attempting to create a MolSupplier from a filename pointing to an empty
file,
  a file that does not exist or sometihing that is not a standard file (i.e.
  something like a directory) now generates an exception.
- The cmake option `RDK_OPTIMIZE_NATIVE` has been renamed to
`RDK_OPTIMIZE_POPCNT`

# Highlights:
- The drawings generated by the MolDraw2D objects are now significantly
improved
  and can include simple atom and bond annotations (#2931 and #3010)
- An initial implementation of a modified scaffold network algorithm is now
  available (#2911)
- A few new descriptor/fingerprint types are available - BCUTs (#2957),
Morse
  atom fingerprints (#1773), Coulomb matrices (#2993), and MHFP and SECFP
  fingerprints (#2643)


## Acknowledgements:
Marcel Baltruschat, Jason Biggs, Eliane Briand, Ben Cornett, David Cosgrove,
Zhenting Gao, Guillaume Godin, Gareth Jones, Zachary Kaplan, Eisuke
Kawashima,
Steven Kearnes, Brian Kelley, Maxim Koltsov, Mieszko Manijak, Dan
Nealschneider,
Daniil Polykovskiy, Daniel Probst, Steve Roughley, Kevin Ryan, Vincent F.
Scalfani, Ricardo Rodriguez Schmidt, Rim Shayakhmetov, Aryan Shrey, Matt
Swain,
Paolo Tosco, Wiep van der Toorn, Riccardo Vianello, Shuzhe Wang, Piotr
Wawrzyniak, Hsiao Yi, 'luancarvalhomartins'


## Bug Fixes:
  - Mol rendering within DataFrames in a Jupyter Notebook is broken with
Pandas 0.25.1
 (github issue #2673 from mrcblt)
  - Removed RDKIT_SIMDIVPICKERS_EXPORT
 (github pull #2740 from ptosco)
  - - enable building RDKitRingDecomposerLib.dll under Windows
 (github pull #2742 from ptosco)
  - Do a windows DLL build as part of the Azure DevOps setup
 (github pull #2743 from greglandrum)
  - Fix data race in sascorer.py
 (github pull #2744 from skearnes)
  - Uncharger not properly setting explicit/implicit H count
 (github issue #2749 from greglandrum)
  - MSVC compile error: MolHash scoped enum cannot be redeclared as unscoped
 (github issue #2752 from mcs07)
  - Molecules whose Y size is very small won't display as SVG
 (github issue #2762 from ptosco)
  - Make the cartridge tests work with PostgreSQL 12
 (github pull #2767 from greglandrum)
  - Salt stripper should consider bond matches as well as atom matches
 (github pull #2768 from greglandrum)
  - Bismuth should count as an early element
 (github issue #2775 from greglandrum)
  - addHs() fails on atoms with "bad" valences
 (github issue #2782 from greglandrum)
  - Element symbol lookup for some transuranics returns incorrect results
 (github issue #2784 from LeanAndMean)
  - [cartridge] molecular equality should use do_chiral_sss setting
 (github issue #2790 from greglandrum)
  - uncharger removes Hs from carbocations instead of adding them
 (github issue #2792 from greglandrum)
  - Fix build without boost serialization library
 (github pull #2796 from maksbotan)
  - Using `SetBoundsMat` significantly slows down conformer generation
process.
 (github issue #2800 from hjuinj)
  - rdkit.Ched.rdFMCS.FindMCS generates invalid smarts
 (github issue #2801 from luancarvalhomartins)
  - Remove confId from *FFOptimizeMoleculeConfs Python docs
 (github issue #2805 from ptosco)
  - Hybridization queries on dummy atoms not written properly to SMARTS
 (github issue #2814 from greglandrum)
  - Charge range queries not properly written to SMARTS
 (github issue #2815 from greglandrum)
  - RDKit segfaults in MMFFOptimizeMoleculeConfs()
 (github issue #2820 from ptosco)
  - Trusted Smiles holder doesn't handle ring queries
 (github issue #2830 from bp-kelley)
  - Fix windows substructure crash
 (github pull #2836 from greglandrum)
  - Fix YAeHMOP build
 (github pull #2838 from ptosco)
  - testGithub2245 in testPickers.cpp occasionally fails
 (github issue #2839 from ptosco)
  - add define for RDK_USE_BOOST_SERIALIZATION
 (github pull #2859 from greglandrum)
  - fix start/end atoms when wedging bonds
 (github pull #2861 from greglandrum)
  - Fixes the size of the reduced charge matrix from eHT calculations
 (github pull #2864 from greglandrum)
  - Dev/pvs studio cleanups2
 (github pull #2877 from greglandrum)
  - segfault in MaeMolSupplier
 (github issue #2881 from greglandrum)
  - update maven url in build system
 (github pull #2889 from greglandrum)
  - EnumerateStereoisomers cannot handle STEREOANY bonds
 (github issue #2890 from ricrogz)
  - Update one of the cartridge tests that got missed
 (github pull #2894 from greglandrum)
  - New Similarity Maps drawing code Java Wrappers non-functional
 (github issue #2896 from sroughley)
  - Fix to allow multistructure images in Java/C# and use MCS for c# wrapper
 (github pull #2898 from jones-gareth)
  - Remove bogus URFLib library
 (github pull #2900 from greglandrum)
  - java wrapper build cleanups
 (github pull #2901 from greglandrum)
  - SMARTS parser fails on high-numbered ring closures in branches
 (github issue #2909 from greglandrum)
  - patch to make PandasTools tests pass with pandas v0.22
 (github pull #2913 from greglandrum)
  - fix doctest problem with Pandas v1.0
 (github pull #2918 from greglandrum)
  - Build with -D RDK_BUILD_COORDGEN_SUPPORT=OFF includes a test case that
depends on MaeMolSupplier
 (github issue #2929 from rvianello)
  - MinimalLib: get_stereo_tags() should also return unspecified centers
 (github issue #2936 from greglandrum)
  - Fix regression introduced by e245349c
 (github pull #2945 from cornett)
  - Avoid data race warning in SmilesParse.cpp
 (github pull #2946 from skearnes)
  - Empty molecule has non-zero LabuteASA
 (github issue #2948 from jasondbiggs)
  - Fix a problem with aromatic heteroatom tautomer enumeration
 (github pull #2952 from greglandrum)
  - Molecule properties not retained with
MolStandardize.rdMolStandardize.Cleanup()
 (github issue #2965 from ZacharyKaplan)
  - Fix build without boost serialization.
 (github pull #2972 from ricrogz)
  - fix a typo in the scaffold network wrappers and add some tests
 (github pull #2982 from greglandrum)
  - Tautomer enumeration should remove stereo in all tautomers
 (github issue #2990 from greglandrum)
  - Removed dllexport from a function that lives in the anonymous namespace
 (github pull #3027 from ptosco)


## New Features and Enhancements:
  - Morse atom fingerprint
 (github pull #1773 from thegodone)
  - Allow serializing coordinates as doubles
 (github issue #2510 from danpol)
  - Rework MaeMolSupplier, fix #2617
 (github pull #2620 from ricrogz)
  - Implementation of MHFP and SECFP Fingerprints
 (github pull #2643 from daenuprobst)
  - MatchFusedRings does not imply CompleteRingsOnly anymore
 (github pull #2748 from ptosco)
  - Improvements to JS wrappers
 (github pull #2751 from greglandrum)
  - Fix installed header directory structure
 (github pull #2754 from ricrogz)
  - Add doRandom to the header docs
 (github pull #2756 from bp-kelley)
  - Add queryMol data member to MCSResult
 (github pull #2759 from ptosco)
  - Add functions to enable/disable the substructure matching monkey
patching in IPythonConsole.py
 (github issue #2786 from greglandrum)
  - Add a function to assign chiral tags from sss atom parity
 (github issue #2823 from ptosco)
  - Support MRV_IMPLICIT_H S groups when reading Mol blocks
 (github issue #2829 from greglandrum)
  - Unset executable flag
 (github pull #2833 from e-kwsm)
  - Remove O(N) behavior of getNumBonds
 (github pull #2847 from bp-kelley)
  - Feature proposal: add remove_stereochemistry=False flag for RemoveHs()
 (github issue #2848 from shayakhmetov)
  - Expose SubstructLibrary serialization stream
 (github pull #2853 from bp-kelley)
  - Fix typo
 (github pull #2862 from e-kwsm)
  - Rename RDK_OPTIMIZE_NATIVE to RDK_OPTIMIZE_POPCNT
 (github pull #2865 from ElianeBriand)
  - Update Draw.MolToImage() and Draw.MolToFile() to use the new drawing
code
 (github pull #2866 from greglandrum)
  - Improve PostgreSQL cartridge install documentation
 (github pull #2870 from yellowBirdy)
  - Fixes #2858
 (github pull #2871 from greglandrum)
  - Add a cartridge test to the azure devops config
 (github pull #2873 from greglandrum)
  - Add a new Cookbook v2 to the RDKit docs
 (github pull #2884 from vfscalfani)
  - Add MolVS tautomer canonicalization
 (github pull #2886 from greglandrum)
  - add a convenience function for RGD--Pandas integration
 (github pull #2887 from greglandrum)
  - run clang-tidy with readability-braces-around-statements
 (github pull #2899 from greglandrum)
  - Allow RDProps::clearProp to succeed even if the prop doesn't exist
 (github issue #2910 from greglandrum)
  - Add a scaffold network implementation
 (github pull #2911 from greglandrum)
  - cleanup of the SMILES/SMARTS parsing and writing code
 (github pull #2912 from greglandrum)
  - Add _ctab, _mol2, _pdb to allow direct mol construction from strings
 (github issue #2916 from greglandrum)
  - Parse and handle the stereoCare or STBOX flags in CTABs
 (github pull #2917 from greglandrum)
  - RDKit exceptions do not override the default `what()` method
 (github issue #2920 from ricrogz)
  - Allow custom post-match filters for substructure matching
 (github pull #2927 from greglandrum)
  - Proposed improvements to 2D Drawing Code
 (github issue #2931 from DavidACosgrove)
  - Include running the documentation tests as part of the CI runs
 (github pull #2932 from greglandrum)
  - Add support for phosphine and arsine chirality
 (github issue #2949 from wopozka)
  - A couple additions to the extended Hueckel integration
 (github pull #2955 from greglandrum)
  - Add BCUT 2D descriptors
 (github pull #2957 from bp-kelley)
  - Add multithreaded pattern/fp generator
 (github pull #2973 from bp-kelley)
  - Description for the data files.
 (github pull #2975 from zhentg)
  - Enable larger ring matches in SMARTS expressions
 (github pull #2981 from d-b-w)
  - ScaffoldNetwork rearrangements
 (github pull #2985 from greglandrum)
  - add add_hs() and remove_hs() to JS wrappers
 (github pull #2986 from greglandrum)
  - Add Atom Feature Vectors
 (github pull #2988 from thegodone)
  - Improve Conformational Sampling of Small and Large Ring Molecules
 (github pull #2731 from ptosco)
  - Add CoulombMat calculator
 (github pull #2993 from thegodone)
  - Update azure-pipelines.yml
 (github pull #2999 from hjuinj)
  - Fix atom highlighting in notebook PNGs
 (github pull #3000 from greglandrum)
  - adds a one-liner for getting a vector of random smiles for a molecule
 (github pull #3002 from greglandrum)
  - Allow enhanced stereo to be used in substructure search
 (github pull #3003 from d-b-w)
  - Add support for the rest of the v3000 atom properties
 (github pull #3007 from greglandrum)
  - Move jupyter extension logging to the python logger
 (github pull #3008 from bp-kelley)
  - Commit of 2D draw annotation.
 (github pull #3010 from DavidACosgrove)
  - Update Maeparser & Coordgen Dependencies
 (github pull #3011 from ricrogz)
  - Remove unnecessary files
 (github pull #3012 from e-kwsm)
  - allow retrieval of the atoms/bonds modified by the tautomerization
 (github pull #3013 from greglandrum)
  - Add 5 new recipes to Cookbook
 (github pull #3014 from vfscalfani)
  - Turns on cairo support (and testing) in the Azure DevOps CI builds
 (github pull #3022 from greglandrum)
  - Added support for Python FMCS functors
 (github pull #3023 from ptosco)
  - add random seed to docs to get reproducible conformations
 (github pull #3026 from greglandrum)
  - update docs for 2020.03
 (github pull #3028 from greglandrum)



## Deprecated code (to be removed in a future release):
- To improve API consistency of the exceptions in RDKit with the default
ones in
  the STL, the several `message()` methods and `Invariant::getMessage()` in
RDKit's
  exceptions are from now on deprecated in favor of `what()`. Both
`message()` and
  `Invariant::getMessage()` will be removed in the next release.
- The old MolHash code should be considered deprecated. This release
introduces
  a more flexible alternative. Specifically the following pieces will be
removed in the next release:
  - The python functionality
`rdkit.Chem.rdMolHash.GenerateMoleculeHashString()`
  - The C++ functionality directly present in the header file
`GraphMol/MolHash/MolHash.h`

[Rdkit-announce] 2019.09.1 RDKit Release

[Greg L. <gre...@gm...>]

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-announce] 2019.03.1 RDKit Release

[Greg L. <gre...@gm...>]

Dear all,

I'm pleased to announce that the next version of the RDKit - 2019.03 - 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_03_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

I believe that conda-forge will also switch to the new version in the near
future.

Please note that the RDKit no longer supports Python 2.7. More details on
this here:
https://www.mail-archive.com/rdk...@li.../msg08354.html

I plan to put conda builds of the PostgreSQL cartridge up 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 October 2019.

Best Regards,
-greg

# Release_2019.03.1
(Changes relative to Release_2018.09.1)

## REALLY IMPORTANT ANNOUNCEMENT
- As of this realease (2019.03.1) the RDKit no longer supports Python 2.
Please
  read this rdkit-discuss post to learn what your options are if you need to
  keep using Python 2:

https://www.mail-archive.com/rdk...@li.../msg08354.html

## Backwards incompatible changes
- The fix for github #2245 means that the default behavior of the
MaxMinPicker
  is now truly random. If you would like to reproduce the previous behavior,
  provide a seed value of 42.
- The uncharging method in the MolStandardizer now attempts to generate
  canonical results for a given molecule. This may result in different
output
  for some molecules.

## Highlights:
- There's now a Japanese translation of large parts of the RDKit
documentation
- SGroup data can now be read from and written to Mol/SDF files
- The enhanced stereo handling has been improved: the information is now
  accessible from Python, EnumerateStereoisomers takes advantage of it, and
it
  can be read from and written to CXSmiles

## Acknowledgements:
Michael Banck, Francois Berenger, Thomas Blaschke, Brian Cole, Andrew Dalke,
Bakary N'tji Diallo, Guillaume Godin, Anne Hersey, Jan Holst Jensen,
Sunhwan Jo,
Brian Kelley, Petr Kubat, Karl Leswing, Susan Leung, John Mayfield, Adam
Moyer,
Dan Nealschneider, Noel O'Boyle, Stephen Roughley, Takayuki Serizawa,
Gianluca
Sforna, Ricardo Rodriguez Schmidt, Gianluca Sforna, Matt Swain, Paolo
Tosco,
Ricardo Vianello, 'John-Videogames', 'magattaca', 'msteijaert', 'paconius',
'sirbiscuit'

## Bug Fixes:
  - PgSQL: fix boolean definitions for Postgresql 11
 (github pull #2129 from pkubatrh)
  - update fingerprint tutorial notebook
 (github pull #2130 from greglandrum)
  - Fix typo in RecapHierarchyNode destructor
 (github pull #2137 from iwatobipen)
  - SMARTS roundtrip failure
 (github issue #2142 from mcs07)
  - Error thrown in rdMolStandardize.ChargeParent
 (github issue #2144 from paconius)
  - SMILES parsing inconsistency based on input order
 (github issue #2148 from coleb)
  - MolDraw2D: line width not in python wrapper
 (github issue #2149 from greglandrum)
  - Missing Python API Documentation
 (github issue #2158 from greglandrum)
  - PgSQL: mol_to_svg() changes input molecule.
 (github issue #2174 from janholstjensen)
  - Remove Unicode From AcidBasePair Name
 (github pull #2185 from lilleswing)
  - Inconsistent treatment of `[as]` in SMILES and SMARTS
 (github issue #2197 from greglandrum)
  - RGroupDecomposition fixes, keep userLabels more robust
onlyMatchAtRGroups
 (github pull #2202 from bp-kelley)
  - Fix TautomerTransform in operator=
 (github pull #2203 from bp-kelley)
  - testEnumeration hangs/takes where long on 32bit architectures
 (github issue #2209 from mbanck)
  - Silencing some Python 3 warning messages
 (github pull #2223 from coleb)
  - removeHs shouldn't remove atom lists
 (github issue #2224 from rvianello)
  - failure round-tripping mol block with Q atom
 (github issue #2225 from rvianello)
  - problem round-tripping mol files that include bond topology info
 (github issue #2229 from rvianello)
  - aromatic main-group atoms written to SMARTS incorrectly
 (github issue #2237 from greglandrum)
  - findPotentialStereoBonds() stopping too early
 (github issue #2244 from greglandrum)
  - MinMax Diversity picker seeding shows deterministic / non-random
behaviour
 (github issue #2245 from sroughley)
  - Fix to serialize binary strings
 (github pull #2264 from bp-kelley)
  - Recognize N in three-membered rings as potentially chiral
 (github issue #2268 from greglandrum)
  - Failure when parsing mol block with M  PXA
 (github issue #2277 from greglandrum)
  - query-query matching failing for atoms constructed from SMARTS
 (github issue #2299 from greglandrum)
  - SMILES parsing fails for dative ring closures
 (github issue #2303 from greglandrum)
  - Missing Dict.h overload: std::string Dict::getVal<std::string>
 (github issue #2308 from greglandrum)
  - fix a problem with the random pickers test
 (github pull #2310 from greglandrum)
  - Some tests still failing on less common platforms.
 (github issue #2311 from giallu)
  - AddHs() using 3D coordinates with 2D conformations
 (github pull #2328 from greglandrum)
  - change to make the SWIG builds work on windows
 (github pull #2340 from greglandrum)
  - uncharger behaves differently on molecules constructed from mol blocks
and SMILES
 (github issue #2346 from greglandrum)
  - Memory Error When Writing ToBinary With "AllProps"
 (github issue #2352 from atom-moyer)
  - Seg fault on init if RDBASE is not set
 (github issue #2368 from greglandrum)
  - PandasTools.FrameToGridImage() fails with SVG output
 (github issue #2380 from greglandrum)
  - ClusterMols.GetDistanceMatrix throws a type error in Python 3
 (github issue #2387 from John-Videogames)
  - Uncharging logic reversed: protonate non-acids first
 (github issue #2392 from Anne Hersey)

## New Features and Enhancements:
  - Allow access to Enhanced Stereochemistry information from Python
 (github issue #2108 from d-b-w)
  - Adopt EnumerateStereoisomers to use extended stereo
 (github issue #2109 from greglandrum)
  - Enable ctest -T memcheck
 (github pull #2113 from ricrogz)
  - Support for parsing/writing SGroups in SD Mol files
 (github pull #2138 from ricrogz)
   - Rename the #define _DEBUG to MMPA_DEBUG in mmpa.cpp
 (github pull #2140 from baoilleach)
  - MolDraw2D: line width should be controlled by MolDrawOptions
 (github issue #2151 from greglandrum)
  - Some refactoring of the distance geometry code
 (github pull #2153 from greglandrum)
  - Less warnings
 (github pull #2155 from UnixJunkie)
  - ShapeTverskyIndex python function
 (github pull #2156 from susanhleung)
  - Skip compound if smiles conversion fails
 (github pull #2168 from msteijaert)
  - Fix #2176: InChI functions should return NULL on un-InChI-able input
molecules.
 (github pull #2177 from janholstjensen)
  - Update installation instructions for Linux
 (github pull #2181 from sirbiscuit)
  - Update CMake rules to find external coorgen & maeparser libs
 (github pull #2184 from ricrogz)
  - Update to use the travis Xenial environment
 (github pull #2200 from greglandrum)
  - Do not allow PandasTools to overwrite pandas settings
 (github pull #2206 from sirbiscuit)
  - re-enable (and update) the file parser tests
 (github pull #2208 from greglandrum)
  - Added documentation files written in Japanese into Book directory
 (github pull #2210 from magattaca)
  - Add C++ convenience function for drawing ROMols
 (github issue #2220 from greglandrum)
  - Change boost int types to std types
 (github pull #2233 from bp-kelley)
  - Added exports for SGroup functions
 (github pull #2242 from ricrogz)
  - Use coordMap when starting embedding from random coords
 (github issue #2246 from greglandrum)
  - Improve interactivity of output SVG
 (github pull #2253 from greglandrum)
  - Add options for substructure searching
 (github pull #2254 from greglandrum)
  - keep extra information about bonds from Mol files
 (github pull #2260 from greglandrum)
  - Allow converting mol blocks directly to InChI
 (github pull #2262 from greglandrum)
  - Patch/pains updates
 (github pull #2272 from johnmay)
  - add warning for 2D conformations flagged as 3D
 (github pull #2273 from greglandrum)
  - Store extra CXSMILES data as a property
 (github pull #2281 from ricrogz)
  - Parse enhanced stereo information from CXSMILES
 (github pull #2282 from ricrogz)
  - Robustify parsing of CTABs and SGROUPs
 (github pull #2283 from greglandrum)
  - Write enhanced stereo to cxsmiles
 (github pull #2290 from greglandrum)
  - Allow custom type-handlers in the RDProps interface
 (github pull #2293 from bp-kelley)
  - Add serialization to SubstructLibrary
 (github pull #2295 from bp-kelley)
  - support reading/writing atom props from SD files
 (github pull #2297 from greglandrum)
  - Add test for issue #2285, fix molbundle test
 (github pull #2301 from bp-kelley)
  - Update maeparser & coordgen libraries
 (github pull #2302 from ricrogz)
  - Mem errors clean up
 (github pull #2305 from ricrogz)
  - Add definition of MolFragmentToCXSmiles
 (github pull #2307 from greglandrum)
  - Doc update
 (github pull #2312 from greglandrum)
  - Adds gzstream stream, exposes to swig
 (github pull #2314 from bp-kelley)
  - Remove a bunch of Python2-related warts
 (github pull #2315 from greglandrum)
  - some much-needed optimization work on the new property lists
 (github pull #2317 from greglandrum)
  - Build warnings revisited
 (github pull #2318 from ricrogz)
  - change bogus "3D" to "2D" in a test file
 (github pull #2319 from greglandrum)
  - Allow copying atoms in Python
 (github pull #2322 from d-b-w)
  - fixes an r-group symmetrization problem
 (github pull #2324 from greglandrum)
  - simple docstring fix
 (github pull #2326 from sunhwan)
  - allow using system's catch2 for tests
 (github pull #2327 from giallu)
  - Python wrap DetectAtomStereoChemistry from MolFileStereochem.h
 (github issue #2329 from d-b-w)
  - switch to using cmake to handle the C++ spec
 (github pull #2334 from greglandrum)
  - WIP: optional integration with YAeHMOP
 (github pull #2335 from greglandrum)
  - Exposes substructlibrary to swig
 (github pull #2337 from bp-kelley)
  - Add a skip_all_if_match option to the FragmentRemover
 (github pull #2338 from greglandrum)
  - Dev/general csharp fixes
 (github pull #2341 from bp-kelley)
  - Add a read-only Python wrapper for SGroups
 (github pull #2343 from greglandrum)
  - Expose RGroupDecomposition to SWIG
 (github pull #2345 from greglandrum)
  - update debian build script to python3
 (github pull #2350 from UnixJunkie)
  - add GetStereoIsomerCount() function to EnumerateStereoisomers
 (github pull #2354 from greglandrum)
  - Update coordgenlibs to v1.2.2
 (github pull #2355 from ricrogz)
  - Small fixes to get DLLs to build on Windows
 (github pull #2356 from ptosco)
  - Boost deprecation warning
 (github pull #2357 from d-b-w)
  - Removes an extra debugging cerr statment
 (github pull #2360 from d-b-w)
  - Preserve enhanced stereo in reactions
 (github pull #2366 from d-b-w)
  - improvements to the Uncharge functionality
 (github pull #2374 from greglandrum)
  - Add ExplicitBitVect prop and query
 (github pull #2384 from bp-kelley)
  - Allow components of the MolStandardize code to be initialized from
streams
 (github pull #2385 from greglandrum)

[Rdkit-announce] [Announcement] 8th RDKit UGM in Hamburg, Germany

[Greg L. <gre...@gm...>]

Dear all,

This year's RDKit User Group Meeting will take place from 25-27 September
in Hamburg, Germany and is being hosted by Emanuel Ehmki at the University
of Hamburg.

Registration for the RDKit UGM is free:
https://www.eventbrite.com/e/8th-rdkit-ugm-2019-tickets-58836131453

We will once again mostly stick to what has become a tried and true format:
Days 1 and 2: Talks, lightning talks, roundtable(s), discussion, poster
sessions, and talktorials. For those who haven’t attended before,
talktorials are somewhere between a talk and a tutorial, they cover
something interesting done with the RDKit and include the code used to do
the work. During the presentation you'll give an overview of what you did
and also show the pieces of the code that are central to the work. The idea
is to mix the science up with the tutorial aspects.

Day 3 will be a hackathon: those who choose to stay will spend an intense
day working in small groups to produce useful artifacts: new bits of code,
KNIME nodes, KNIME workflows, tutorials, documentation, Jupyter notebooks,
etc. We will once again try to structure this a bit by collecting a bunch
of ideas for things to work on in advance. In the past we have also done
extended tutorials on Day 3; if there are volunteers to do tutorials and
people interested in attending them, we'll repeat that this year as well.

Like last year there will be an optional training day on Tuesday (the
24th). Daria Goldmann (KNIME) will offer a course on KNIME and the RDKit.
We hope to also be able to offer an RDKit and Python course, but we're
still finalizing the details on that. Space for both of these is limited,
so we'll do separate registrations for them. We will send around
registration links once we've got the logistics figured out.

There will also be, of course, social activities. We will be announcing
more details about these later.

A more detailed announcement with additional information about place,
hotels and logistics will follow soon.

We are looking for people who are willing to do presentations, talktorials
or posters on the first two days. If you're interested in contributing,
please send Greg and Emanuel an email.
Lighting talks don't need to be arranged too far in advance; we will start
collecting the list of people interested in doing those shortly before the
event.

Best Regards,
Greg and Emanuel

[Rdkit-announce] Some info on this year's RDKit UGM

[Greg L. <gre...@gm...>]

Dear all,

We're currently planning that this year's RDKit UGM will take place in
Hamburg Germany. It's being organized by Emanuel Ehmki. Emanuel is still
working on finalizing the lecture room reservations (it's the 100th year
anniversary of the Uni Hamburg, making this is much more complicated than
it otherwise would be), so we don't yet have a final date but we're
targeting the end of September.

We'll do a real announcement once we finalize the rooms and date, but I
wanted to let everyone know that there *will* be a UGM this year so that
you can start planning for it.

Best,
-greg

[Rdkit-announce] 2018.09.1 RDKit Release

[Greg L. <gre...@gm...>]

I'm pleased to announce that the next version of the RDKit - 2018.09 - is
released. The release notes are below.

The release files are on the github release page:
https://github.com/rdkit/rdkit/releases/tag/Release_2018_09_1

Binaries have been uploaded to anaconda.org (https://anaconda.org/rdkit).
The available conda binaries for this release are:
Linux 64bit: python 2.7, 3.6
Mac OS 64bit: python 2.7, 3.6
Windows 64bit: python 3.6

I hope to be able to do python 3.7 binaries sometime in the not-too-distant
future.

The missing binary for python 2.7 on windows is explained here:
https://www.mail-archive.com/rdk...@li.../msg07850.html

Please note that this is the last feature release of the RDKit which will
support Python 2.7. More details on this here:
https://www.mail-archive.com/rdk...@li.../msg08354.html

I've also put conda builds of the PostgreSQL cartridge up for Linux and the
Mac.

The online version of the documentation at rdkit.org (
http://rdkit.org/docs/index.html) has been updated. Note that because of
the move away from epydoc, the structure of the documentation has changed a
bit and old URLs may not work.

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 April 2019.

Best Regards,
-greg


# Release_2018.09.1
(Changes relative to Release_2018.03.1)

## 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.

## 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.

## 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)

[Rdkit-announce] RDKit 2018.03.2 release

[Greg L. <gre...@gm...>]

Hi,

The 2018.03.2 release of the RDKit is now available. This is a patch
release, so it just contains bug fixes.

I've uploaded conda builds for Linux, the Mac, and Windows (I'm still
working on the python 3.5 build, but 3.6 is up), as well as Linux and Mac
builds of the cartridge. NOTE that this is now called: rdkit-postgresql.
There should be builds available that work with the conda postgresql
packages for v9.5, 9.6, and 10.0. If you give the cartridge builds a try, I
would love to hear feedback on how it goes.

The release notes are here:
https://github.com/rdkit/rdkit/releases/tag/Release_2018_03_2

Best,
-greg

[Rdkit-announce] 2018.03.1 RDKit release

[Greg L. <gre...@gm...>]

 I'm pleased to announce that the next version of the RDKit - 2018.03 - is
released. The release notes are below.

The release files are on the github release page:
https://github.com/rdkit/rdkit/releases/tag/Release_2018_03_1

Binaries have been uploaded to anaconda.org (https://anaconda.org/rdkit).
The available conda binaries for this release are:
Linux 64bit: python 2.7, 3.5, 3.6
Mac OS 64bit: python 2.7, 3.5, 3.6
Windows 64bit: python 3.5, 3.6

The missing binary for python 2.7 on windows is explained here:
https://www.mail-archive.com/rdk...@li.../msg07850.html

Some things that will be finished over the next couple of days:
- The conda build scripts will be updated to reflect the new version and
new conda builds will be available in the RDKit channel at anaconda.org (
https://anaconda.org/rdkit).
- The homebrew script
- The online version of the documentation at rdkit.org (I'm traveling this
week, so this is unlikely to be done before next weekend).

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 Octobera 2018.

Best Regards,
-greg

# Release_2018.03.1
(Changes relative to Release_2017.09.1)

## C++11 notes

Starting with this release, the RDKit core C++ code is written in modern
C++;
for this release that means C++11. This means that the compilers used to
build
it cannot be completely ancient. Here are the minimum tested versions:
- g++ v4.8: though note that the SLN parser code cannot be built with v4.8.
It
  will automatically be disabled when this older compiler is used.
- clang v3.9: it may be that older versions of the compiler also work, but
we
  haven't tested them.
- Visual Studio 2015: it may be that older versions of the compiler also
work,
  but we haven't tested them.

## Backwards incompatible changes

This release includes a set of changes to make the default arguments to
common
functions less error prone (github #1679).
- MolToSmiles() now generates isomeric SMILES by default.
- The embedding code now uses the ETKDG method by default.
- MolToMolBlock() will now by default generate a set of 2D coordinates for
  molecules when the includeStereo option is set to True. The changes are
made
  to a copy of the molecule; the molecule itself will not be modified.
- The Mol file (and SDF) parser now determines atomic stereochemisty based
on
  the 3D coordinates provided (if 3D coordinates are provided).
- The SMILES parser now supports CXSMILES by default (assuming that
additional
  text that looks like CXSMILES extensions is there).

In every case the old behavior can be obtained by providing an optional
argument
to the function(s) mentioned.

## Acknowledgements:
Boran Adas, José Emilio Sánchez Aparicio, Patrick Avery, Jason Biggs, Brian
Cole, Andrew Dalke, JW Feng, Peter Gedeck, Guillaume Godin, Richard Hall,
Thomas
Heavy, Gareth Jones, Brian Kelley, Karl Leswing, Susan Leung, Chris Morris,
Dan
Nealschneider, Noel O'Boyle, Axel Pahl, Pavel Polishchuk, Sereina Riniker,
Jeff
van Santen, Roger Sayle, Martin Šícho, Matt Swain, Paolo Tosco, Sam Webb,
Maciej
Wójcikowski, Nicola Zonta, 'clinntt', 'hjuinj', 'iwatobipen',

## Highlights:
  - An initial version of an integration with Schrodinger's coordgen
library is
    included. This produces much better 2D coordinates for complex
molecules.
  - Thanks to the move to modern C++ the RDKit is now faster and uses less
    memory
  - A number of improvements were made to the PDB reader
  - v2 of the ETKDG torsions and potentials is now available

## Contrib updates:
  - Implementation of Peter Ertl's IFG method for identifying functional
groups
    from Guillaume Godin and Richard Hall
  (github pull #1813 from thegodone)

## New Features and Enhancements:
  - Support InChi 1.05
 (github issue #1533 from greglandrum)
  - Update CPack to create .deb files correctly
 (github pull #1580 from psavery)
  - Initial commit of EnumerateHeterocycles
 (github pull #1588 from coleb)
  - Version 2 of ETKDG
 (github pull #1597 from sriniker)
  - GetMolFrags now optionally returns atom indices along with mols
 (github pull #1602 from ptosco)
  - NP Likeness with confidence value
 (github pull #1608 from apahl)
  - Adding an option to EnumerateStereoisomers to only return unique isomers
 (github pull #1612 from coleb)
  - Add function wedgeBond()
  (github issue #1615 from greglandrum)
  - Dev/substructlibrary docs
 (github pull #1620 from bp-kelley)
  - Turns off exception throwing for certain classes Rlabel sanitization.
 (github pull #1621 from bp-kelley)
  - Add an "MDL" aromaticity model
 (github issue #1622 from hjuinj)
  - Add support for %(NNN) notation for ring closures
 (github pull #1624 from baoilleach)
  - Enable windows build that uses cairo
 (github pull #1628 from greglandrum)
  - [MRG] Fix PDB reader + add argument to toggle proximity bonding
 (github pull #1629 from mwojcikowski)
  - Improve AddHs for molecules read from PDB
 (github pull #1647 from mwojcikowski)
  - Improved regression test for ETKDG version 2
 (github pull #1640 from sriniker)
  - RDKit interpretation of atom stereo SMILES is different from 4 other
toolkits
 (github issue #1652 from coleb)
  - Treat bonds in PDB CONECT records explicitly, but make blacklisted ones
zero-order.
 (github pull #1658 from mwojcikowski)
  - There is no need to enforce that (i, j) and (k, l) be bonded when
setting a i, j, k, l dihedral
 (github pull #1673 from ptosco)
  - Make default arguments to common functions less error prone
 (github issue #1679 from greglandrum)
  - Add Fast cluster script
 (github pull #1683 from iwatobipen)
  - Update embedded InChI to v1.05
 (github pull #1684 from mcs07)
  - Add `AllChem.MMFFGetMoleculeForceField().CalcGradient()` to Python
wrappers
 (github issue #1688 from theavey)
  - Play nice with naughty MOL blocks
 (github issue #1689 from jw-feng)
  - Make the defaults for some functions less error prone.
 (github pull #1690 from greglandrum)
  - implemented Python wrappers for computing PMI axes and moments
 (github pull #1700 from ptosco)
  - Enable range-based for loops for molecules
 (github pull #1701 from bp-kelley)
  - Support some cactvs extensions to SMARTS
 (github pull #1704 from greglandrum)
  - Integrate Coordgen
 (github pull #1708 from greglandrum)
  - Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
 (github pull #1713 from greglandrum)
  - Set atomic properties from SMARTS
 (github pull #1716 from greglandrum)
  - Allow installation of Python tests to facilitate testing installations
 (github pull #1724 from greglandrum)
  - setAromaticity() should work even if there are aromatic atoms present
 (github issue #1730 from greglandrum)
  - Use uint32 atom and bond indices
 (github pull #1742 from greglandrum)
  - Switch from boost::thread to std::thread
 (github pull #1745 from greglandrum)
  - switch to using std::regex in the SLN parser
 (github pull #1746 from greglandrum)
  - replace the usage of rdk_auto_ptr with std::unique_ptr
 (github pull #1752 from greglandrum)
  - getMolBoundsMatrix() should do triangle bound smoothing by default
 (github issue #1763 from greglandrum)
  - Added Morgan feature fingerprints to Java API
 (github pull #1764 from jones-gareth)
  - Reaction fingerprints not exposed in Java wrapper
 (github issue #1776 from webbres)
  - add Tversky index calculation for shapes
 (github pull #1777 from susanhleung)
  - Add MolToInchiKey function()
 (github pull #1784 from greglandrum)
  - speedup the NumBitsInCommon operation
 (github pull #1785 from greglandrum)
  - Stop putting brackets around * atoms in SMILES
 (github pull #1788 from greglandrum)
  - Support for a JSON-based molecule interchange format
 (github pull #1798 from greglandrum)

## Bug Fixes:
  - Fixes Java wrapper build error with Boost 1.64
 (github pull #1613 from ptosco)
  - AssignStereochemistry cleanIt=True incorrectly removing new CIS/TRANS
bond stereo
 (github issue #1614 from coleb)
  - switch to using a specific freesasa version
 (github pull #1619 from greglandrum)
  - Add support for %(NNN) notation for ring closures
 (github pull #1624 from baoilleach)
  - Draw._moltoSVG() raises an exception
 (github issue #1625 from greglandrum)
  - MolDrawCairo2D does not build on windows
 (github issue #1627 from greglandrum)
  - Enable windows build that uses cairo
 (github pull #1628 from greglandrum)
  - don't always download the FreeSASA source
 (github issue #1630 from greglandrum)
  - Make sure EmbedMultipleConfs is deterministic for very large seeds and
a seed of 0
 (github pull #1635 from coleb)
  - from rdkit.Chem import AllChem has grown a six dependency
 (github issue #1637 from bp-kelley)
  - Fixing bug in IPythonConsole SVG rendering introduced in
1027d4469545653180fff9a38dc8224bd50e8b0d
 (github pull #1641 from coleb)
  - changes required to allow replacing the obsolete __conda_version__ in
conda-rdkit
 (github pull #1644 from ptosco)
  - GetConformerRMSMatrix does not work if some conformers were removed
 (github issue #1650 from DrrDom)
  - EnumerateLibrary with initFromString called twice doesn't clear the
reaction
 (github issue #1657 from bp-kelley)
  - Missed symmetrization in R-Group decomposition
 (github issue #1659 from greglandrum)
  - Use numpy not numeric for boost 1.65+ - fixes #1581
 (github pull #1664 from mcs07)
  - Support valence 7 for As, Sb, and Bi
 (github issue #1668 from greglandrum)
  - Fix: GetDonor2FeatVects heavy atoms confusion
 (github pull #1676 from josan82)
  - Acetylenic hydrogens not given appropriate 2D coordinates
 (github issue #1691 from jasondbiggs)
  - Warning on import of rgroup decomposition package
 (github issue #1695 from greglandrum)
  - AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is
required
 (github issue #1702 from baoilleach)
  - Dative bonds interfere with kekulization and the perception of
aromaticity
 (github issue #1703 from greglandrum)
  - Fix/rgroup prefer matching nonhs over hs
 (github pull #1707 from bp-kelley)
  - bonds that are STEREOCIS or STEREOTRANS cannot be depickled
 (github issue #1710 from greglandrum)
  - Get queries from the new cactvs SMARTS extensions to pickle correctly
 (github pull #1712 from greglandrum)
  - fix an irritating cmake problem
 (github pull #1715 from greglandrum)
  - Added dependency from Boost headers to PgSQL CMakeLists.txt
 (github pull #1717 from ptosco)
  - Updates python test runner to always use sys.executable
 (github pull #1721 from bp-kelley)
  - - make bond stereo detection in rings consistent
 (github pull #1727 from ptosco)
  - xlocale.h not needed to compile with clang
 (github issue #1728 from adalke)
 - BreakBRICSBonds() not preserving stereochemistry
 (github issue #1734 from greglandrum)
  - rdmolfiles.CanonicalRankAtoms segfaults on 0 atom molecules
 (github issue #1735 from lilleswing)
  - deprecated apply() function causes GetRDKFingerprint to fail in Python 3
 (github issue #1747 from clinntt)
  - Stop dereferencing end() iterators
 (github pull #1748 from greglandrum)
  - out of range fromAtom causes GetMorganFingerprintAsBitVect to segfault
 (github issue #1749 from adalke)
  - Generated SMARTS does not contain atomic chiral tags
 (github issue #1756 from greglandrum)
  - make the build work even if boost::serialization is disabled
 (github pull #1767 from greglandrum)
  - Fix typo in GetBoolProp documentation
 (github pull #1770 from jvansan)
  - Fingerprint segfaults with branchedPaths=False and useHs=False
 (github issue #1793 from chrishmorris)
  - Fix python linkage (primarily for conda builds)
 (github pull #1808 from greglandrum)
  - removeHs() should not remove H atoms that are contributing to the
definition of a stereo bond
 (github pull #1810 from d-b-w)
  - global EmbedParameters objects should not be writeable in SWIG wrappers
 (github issue #1826 from greglandrum)
  - RDKit crashes when MolsToGridImage function is called with an empty
iterable.
 (github issue #1829 from martin-sicho)

[Rdkit-announce] [Announcement] 7th RDKit UGM in Cambridge UK

[Greg L. <gre...@gm...>]

Dear all,

This year's RDKit User Group Meeting will take place from 19-21 September
in Cambridge, UK and is being hosted by Andreas Bender at Cambridge
University.

Registration for the RDKit UGM is free:
https://www.eventbrite.com/e/7th-rdkit-ugm-2018-tickets-44883066460

We will once again mostly stick to what has become a tried and true format:
Days 1 and 2: Talks, lightning talks, roundtable(s), discussion, poster
sessions, and talktorials. For those who haven’t attended before,
talktorials are somewhere between a talk and a tutorial, they cover
something interesting done with the RDKit and include the code used to do
the work. During the presentation you'll give an overview of what you did
and also show the pieces of the code that are central to the work. The idea
is to mix the science up with the tutorial aspects.

Day 3 will be a hackathon: those who choose to stay will spend an intense
day working in small groups to produce useful artifacts: new bits of code,
KNIME nodes, KNIME workflows, tutorials, documentation, IPython notebooks,
etc. We will once again try to structure this a bit by collecting a bunch
of ideas for things to work on in advance. Two years ago we also did
extended tutorials on Day 3; if there are volunteers to do tutorials and
people interested in attending them, we'll repeat that this year as well.

As an experiment this year there will be an optional training day on
Tuesday the 18th. Andrew Dalke (Dalke Scientific) will offer a course on
Python and the RDKit and Daria Goldmann (KNIME) will offer a course on
KNIME and the RDKit. Space for both of these is limited, so we'll do
separate registrations for them (links will be included on the main UGM
registration page). Many thanks to Andrew for coming up with the idea to do
this!

There will also be, of course, social activities. This year we have the
special opportunity to have the dinner on the 19th in the Old Library of
Pembroke College. I can't wait for that. :-)

A more detailed announcement with additional information about place,
hotels and logistics will follow soon.

We are looking for people who are willing to do presentations, talktorials
or posters on the first two days. If you're interested in contributing,
please send Greg and Andreas an email.

Lightning talks don't need to be arranged too far in advance; we will start
collecting the list of people interested in doing those shortly before the
event.

Best Regards,
Greg and Andreas

[Rdkit-announce] Save the date: 2018 RDKit UGM

[Greg L. <gre...@gm...>]

Dear all,

This year's RDKit UGM will take place in Cambridge England from the 19-21
September. The event will take place in the Department of Chemistry at the
University of Cambridge and our host/organizer will be Andreas Bender.

A formal announcement with more details and a registration link will come
in the next month or so, but please go ahead and mark your calendars so
that you can attend!

Best,
-greg

[Rdkit-announce] 2017.09.1 RDKit release

[Greg L. <gre...@gm...>]

I'm pleased to announce that the next version of the RDKit -- 2017.09 -- is
released. The release notes are below.

The release files are on the github release page:
https://github.com/rdkit/rdkit/releases/tag/Release_2017_09_1

Binaries have been uploaded to anaconda.org (https://anaconda.org/rdkit).
The available conda binaries for this release are:
Linux 64bit: python 2.7, 3.5, 3.6
Mac OS 64bit: python 2.7, 3.5, 3.6
Windows 64bit: python 2.7, 3.5, 3.6

I left out the Win32 python2.7 build this time. If that's important to
someone, let me know and I'll see if I can get it working again.

Some notes on the conda builds:
- These builds are tested with conda v4.3.25 and, as of the release date,
are very unlikely to work with anything newer than that. This thread has
more information on that: https://www.mail-archive.com/rdkit-discuss@lists.
sourceforge.net/msg07315.html
- The conda builds now depend on numpy 1.13 instead of 1.11.
- The Mac and Linux builds now use v1.63 of boost. The rdkit conda channel
has the appropriate binaries.

Some things that will be finished over the next couple of days:
- The conda build scripts will be updated to reflect the new version and
new conda builds will be available in the RDKit channel at anaconda.org (
https://anaconda.org/rdkit).
- The homebrew script
- The online version of the documentation at rdkit.org

Thanks to everyone who submitted 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 2018.

Best Regards,
-greg

# Release_2017.09.1
(Changes relative to Release_2017.03.1)

## Important
- The fix for bug #1567 changes the way fragment SMILES are canonicalized.
  MolFragmentToSmiles() and canonicalizeFragment() will now often return
  different results
- The fix for bug #1604 changes the behavior of QueryAtom::setQuery(), which
  now deletes the current query before setting the new value. If you are
using
  QueryAtom::setQuery() from C++ (or possibly Java), be sure that you are
not
  also deleting that memory.

## Acknowledgements:
Brian Cole, Peter Gedeck, Guillaume Godin, Jan Halborg Jensen, Malitha
Kabir,
Tuomo Kalliokoski, Brian Kelley, Noel O'Boyle, Matthew O'Meara, Pavel
Polishchuk, Cameron Pye, Christian Ribeaud, Stephen Roughley, Patrick
Savery,
Roger Sayle, Nadine Schneider, Gregor Simm, Matt Swain, Paolo Tosco, Alain
Vaucher, Sam Webb, 'phenethyl', 'xiaotaw'

## Highlights:
- The new R-Group decomposition code provides a flexible and powerful tool
for
  building R-group tables or datasets look in $RDBASE/Docs/Notebooks for
  example notebooks showing how to use this.
- Drawing of chemical reactions has been greatly improved and is now done
using
  the C++ rendering code.
- The MaxMinPicker is dramatically faster.
- New descriptors: the QED descriptor has been added as have a large
collection
  of new 3D descriptors and implementations of the USR and USRCAT
fingerprints.

## New Features and Enhancements:
  - Bring back USR and USRCAT descriptors
 (github pull #1417 from greglandrum)
  - Generate a warning for conflicting bond directions
 (github issue #1423 from greglandrum)
  - expose and test GetDrawCoords()
 (github pull #1427 from greglandrum)
  - Improvement suggestions for SaltRemover
 (github issue #1431 from ribeaud)
  - Remove obsolete scripts from Scripts dir
 (github pull #1440 from greglandrum)
  - Support drawing reactions from C++
 (github pull #1444 from greglandrum)
  - QED code with unit test file
 (github pull #1445 from gedeck)
  - Add support for other datatypes to  ConvertToNumpyArray
 (github issue #1447 from pyeguy)
  - - updated FindCairo.cmake
 (github pull #1455 from ptosco)
  - - fixes PgSQL CMakeLists.txt to enable conda build on Windows
 (github pull #1457 from ptosco)
  - Some cleanups to make Travis builds faster
 (github pull #1464 from greglandrum)
  - ExplainPairScore does not support includeChirality=True
 (github issue #1466 from xiaotaw)
  - Add a collection of new 3D descriptors
 (github pull #1467 from greglandrum)
  - Update cartridge documentation to use ChEMBL 23
 (github issue #1491 from greglandrum)
  - First entry of the SubstructLibrary module
 (github pull #1493 from bp-kelley)
  - assorted fixes to get the current master branch to build on Windows
 (github pull #1495 from ptosco)
  - Support assignment of stereochemistry tags to bonds from 3D structure
 (github issue #1497 from gncs)
  - Support black and white molecule drawing
 (github issue #1510 from greglandrum)
  - Missing def_readwrite for backgroundColour in rdMolDraw2D.cpp
 (github issue #1519 from goraj)
  - Adds canonicalization of atom maps
 (github pull #1521 from bp-kelley)
  - Implement stereoisomer enumeration
 (github pull #1531 from greglandrum)
  - Add a MolBundle class
 (github pull #1537 from greglandrum)
  - Provide support for color palettes in MolDraw2D
 (github pull #1546 from greglandrum)
  - A few reaction drawing tweaks
 (github pull #1549 from greglandrum)
  - R group improvements
 (github pull #1552 from greglandrum)
  - Add a canned Atom query for heavy atom degree
 (github issue #1563 from greglandrum)
  - Adds FreeSASA adapter
 (github pull #1565 from bp-kelley)
  - Added C++ version of getBestRMS()
 (github pull #1568 from psavery)
  - SMILES lexer optimization/enhancement
 (github pull #1575 from greglandrum)
  - Update IPythonConsole and PandasTools to use new drawing code
 (github pull #1577 from greglandrum)
  - Squashes warnings on cygwin
 (github pull #1578 from bp-kelley)
  - Support continuous highlighting in drawMolecules().
 (github pull #1579 from greglandrum)
  - Enhanced Similarity Maps depiction
 (github pull #1594 from gerebtzoff)

## Bug Fixes:
  - RDKit gets stuck on PubChem CID 102128817
 (github issue #1281 from TuomoKalliokoski)
  - MMP code not including molecules with no cuts
 (github issue #1406 from greglandrum)
  - Fixes PandasTools to also work with pandas 0.20
 (github pull #1410 from bp-kelley)
  - csharp input files out of date
 (github issue #1413 from greglandrum)
  - Fix cxsmiles parse on VS2008
 (github pull #1415 from mcs07)
  - MaxMinPicker picking non-existent element
 (github issue #1421 from greglandrum)
  - _isCallable clashes with Celery
 (github issue #1434 from momeara)
  - Impossible to build the RDKit from source without Python installed
 (github issue #1435 from greglandrum)
  - RemoveHs() removes H atom attached to dummy if it came from AddHs()
 (github issue #1439 from DrrDom)
  - fix a couple failing windows tests related to temp file removal
 (github pull #1446 from greglandrum)
  - SanitizeRxn fails with a runtime exception when unused Rlabels are in
product
 (github issue #1448 from bp-kelley)
  - String module conversion bug
 (github pull #1452 from coleb)
  - GetConformerRMS() documentation is misleading
 (github pull #1459 from greglandrum)
  - URANGE_CHECK not doing its job in RWMol::addBond
 (github issue #1461 from baoilleach)
  - ExplainPairScore does not support includeChirality=True
 (github issue #1466 from xiaotaw)
  - MolToSmarts does not include atom-map or isotope info for molecules
built from SMILES
 (github issue #1472 from greglandrum)
  - AdjustQueryProperties() removing properties from dummy atoms
 (github issue #1474 from greglandrum)
  - Fixes lookup for HELM Monomer 'D'
 (github pull #1477 from bp-kelley)
  - Aromatic rings composed solely of dummy atoms should not be kekulized
 (github issue #1478 from bp-kelley)
  - Directly specify rotor model used in QED.
 (github pull #1483 from bp-kelley)
  - Unicode problem with pidPS tests on Mac
 (github issue #1490 from greglandrum)
  - Pattern fingerprint setting bad bits with degree zero atoms
 (github issue #1496 from greglandrum)
  - Remove xlocale header
 (github pull #1501 from greglandrum)
  - Fixes atom documentation
 (github pull #1505 from bp-kelley)
  - TypeError from PandasTools.SaveXlsxFromFrame
 (github issue #1507 from pyeguy)
  - Removes trailing spaces after \ to fix windows compilation errors
 (github pull #1516 from bp-kelley)
  - prepareMolForDrawing() not in SWIG wrappers
 (github issue #1522 from greglandrum)
  - Bond is missing IsInRing methods in Java wrapper
 (github issue #1535 from sroughley)
  - Fixes blanking of non-query atom data when QueryAtomData was being pi…
 (github pull #1541 from bp-kelley)
  - ChemicalReaction code not calling setNoImplicit() when H counts are set.
 (github issue #1544 from greglandrum)
  -  Fixes failing build with MSVC
 (github pull #1547 from ptosco)
  - Kekulization error with cores from R-Group Decomposition
 (github issue #1550 from greglandrum)
  - Fixes double free for Dict::update
 (github pull #1571 from bp-kelley)
  - QueryAtom::setQuery() should delete the old query first
 (github pull #1604 from greglandrum)

Re: [Rdkit-announce] RDKit Patch Release: 2017.03.3

[Greg L. <gre...@gm...>]

[Apologies for that incomplete email. Outlook freaked out on me. Let's try that again]

This morning I tagged the next RDKit patch release: v2017.03.3. The release itself, along with release notes, is here:
https://github.com/rdkit/rdkit/releases/tag/Release_2017_03_3

I have uploaded the usual collection of binaries to the anaconda repo as well. Note: the windows build for Python v3.5 didn't finish before I needed to leave this morning; I will finish that build and upload it on Monday.

The next patch release will be in early August. Thanks to everyone who contributed to this one!

Extra special thanks to Paolo for his changes to the way the conda builds work on Windows. It is sooooo much faster to have the builds run in parallel.

-greg

[Rdkit-announce] RDKit Patch Release: 2017.03.3

[Greg L. <gre...@gm...>]

Dear all,

This morning I tagged the next RDKit patch release: v2017.03.3.
The release itself, along with release notes, is here:https://github.com/rdkit/rdkit/releases/tag/Release_2017_03_3