I can reproduce this with an older version, but the problem is that you
have RemoveHs instead of removeHs.
On Mon, Oct 2, 2017 at 7:20 AM, Guillaume GODIN <
guillaume.go...@firmenich.com> wrote:
> Dear Greg,
>
>
> I don't know if it's related but I have this issue on my mac version since
> this morning:
>
>
> ---------------------------------------------------------------------------ArgumentError
> Traceback (most recent call
> last)<ipython-input-32-0a8ef72c2eb1> in <module>()----> 1 suppl =
> Chem.SDMolSupplier("/Users/GVALMTGG/Github/neemp/examples/set01.sdf",RemoveHs=False)
> 2 for mol in suppl: 3 for atom in mol.GetAtoms(): 4
> print str(atom.GetSymbol())+ ":" +str(Atomtype(atom,mol)) 5
> ArgumentError: Python argument types in
> SDMolSupplier.__init__(SDMolSupplier, str)
> did not match C++ signature:
> __init__(_object*, std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > fileName, bool
> sanitize=True, bool removeHs=True, bool strictParsing=True)
> __init__(_object*)
>
>
>
> Best regards,
>
>
> *Dr. Guillaume GODIN*
> Principal Scientist
> Chemoinformatic & Datamining
> Innovation
> CORPORATE R&D DIVISION
> DIRECT LINE +41 (0)22 780 3645 <+41%2022%20780%2036%2045>
> MOBILE +41 (0)79 536 1039 <+41%2079%20536%2010%2039>
> Firmenich SA
> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>
> ------------------------------
> *De :* Greg Landrum <greg.land...@gmail.com>
> *Envoyé :* vendredi 29 septembre 2017 09:30
> *À :* RDKit Discuss; RDKit Developers List
> *Objet :* [Rdkit-discuss] Beta of the 2017.09 release available
>
> Dear all,
>
> This morning I tagged the beta of the 2017.09 RDKit release in github:
> https://github.com/rdkit/rdkit/releases/tag/Release_2017_09_1b1
>
> I will try to get some conda builds up over the next day or so. These will
> 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 python=3.6
>
> 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).
>
> You can check to see if a build is available for your platform/python
> version here:
> https://anaconda.org/rdkit/rdkit/files?version=2017.09.1.b1
>
> Note that I've done the conda linux builds using a Centos7 system - in the
> past I've used Centos6 - if this causes compatibility problems or if you
> think that this is a bad idea please let me know and I will switch back to
> Centos6 for the builds.
>
> The relevant section of the release notes is below.
>
> 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 a week
> from today.
>
> Best,
> -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
>
> ## Acknowledgements:
> Brian Cole, Peter Gedeck, Guillaume Godin, 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, 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 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)
> - - 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)
>
>
>
> **********************************************************************
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> **********************************************************************
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