Hi,
That's a clear indication that your PYTHONPATH is not set correctly
On Friday, May 8, 2015, [email protected] <[email protected]> wrote:
> Hi,
>
> kindly advise on this error I got while using ipython notebook to run
> Rdkit:
>
> from rdkit import Chem
>
> ImportError: No module named rdkit
>
> I can run Rdkit on my local python editor.
>
> Thank you
>
> Samuel
>
>
>
> > Send Rdkit-discuss mailing list submissions to
> > [email protected] <javascript:;>
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
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> > or, via email, send a message with subject or body 'help' to
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> >
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> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Rdkit-discuss digest..."
> >
> >
> > Today's Topics:
> >
> > 1. SetFormalCharge and AddHs (S.L. Chan)
> > 2. 2015.03 (Q1 2015) RDKit Release (Greg Landrum)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Tue, 5 May 2015 07:22:21 +0000 (UTC)
> > From: "S.L. Chan" <[email protected] <javascript:;>>
> > Subject: [Rdkit-discuss] SetFormalCharge and AddHs
> > To: RDKit Discuss <[email protected] <javascript:;>>
> > Message-ID:
> > <[email protected]
> <javascript:;>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear colleagues,
> > I am trying to fix a molecule (originally in PDB format - what can you
> > expect?) which is a fluro-chloro-benzene with a hydrogen missing. I have
> > somehow already converted it into MDL MOL format (see attached). The
> > carbon atom with the missing hydrogen was set to have a formal charge of
> > -1. I loaded it into RDKit, looked for the atom with a formal charge of
> -1
> > and reset its formal charge to 0. Then I used the AddHs() function to add
> > the missing hydrogen. I also inquired the partial charges of all atoms
> > using the GetMMFFPartialCharge() function. However, nothing seems to have
> > changed after the fix.
> > I got two questions.
> > (1) why is it that no hydrogen atom was added by AddHs() ?
> > (2) in any case, even if the hydrogen was not added, why is it that the
> > sum of all MMFFPartialCharges does not equal the net formal charge of the
> > molecule?
> > My python script is attached.
> > Thank you for your insight.
> > Ling
> > -------------- next part --------------
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> > Name: why.py
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Wed, 6 May 2015 07:36:46 +0200
> > From: Greg Landrum <[email protected] <javascript:;>>
> > Subject: [Rdkit-discuss] 2015.03 (Q1 2015) RDKit Release
> > To: RDKit Discuss <[email protected] <javascript:;>>,
> > [email protected] <javascript:;>, RDKit
> Developers List
> > <[email protected] <javascript:;>>
> > Message-ID:
> > <CAD4fdRRhgwJL0jzGNYSjf7166CobtMAW=
> [email protected] <javascript:;>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear all,
> >
> > I'm pleased to announce that the next version of the RDKit -- 2015.03
> > (a.k.a. Q1 2015) -- is released. Better late than never. :-)
> >
> > The release notes are below.
> >
> > The release and binary files are on the github release page:
> > https://github.com/rdkit/rdkit/releases/tag/Release_2015_03_1
> > and will be uploaded to the sourceforge downloads page in the next few
> > days:
> > http://sourceforge.net/projects/rdkit/files/rdkit/Q1_2015/
> >
> > I have uploaded 32-bit and 64-bit Windows binaries for Python 2.7 and, in
> > response to a couple of requests, 32-bit and 64-bit Windows binaries for
> > Java.
> >
> > Gianluca's binary RPMs for Fedora 20, 21 and RHEL/Centos 6, 7 are
> > available
> > from
> > this repository:
> > https://copr.fedoraproject.org/coprs/giallu/rdkit/
> >
> > We have updated the homebrew recipe and conda build script (thanks
> > Riccardo!) to reflect the new version.
> >
> > The online version of the documentation at rdkit.org will be updated in
> > the
> > next week.
> >
> > Thanks to the 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 September 2015.
> >
> > Best Regards,
> > -greg
> >
> >
> > ****** Release_2015.03.1 *******
> > (Changes relative to Release_2014.09.2)
> >
> > !!!!!! IMPORTANT !!!!!!
> >
> > - This release has a new algorithm for canonical atom ordering. This
> > means that canonical SMILES generated with the new version will be
> > different from those generated with previous versions.
> >
> > Acknowledgements:
> > David Cosgrove, Andrew Dalke, JP Ebejer, Niko Fechner, Igor Filippov,
> > Patrick Fuller, David Hall, J Bach Hardie, Jan Holst Jensen, Brian
> > Kelley, Rich Lewis, John May, Michael Reutlinger, Sereina Riniker,
> > Alexander Savelyev, Roger Sayle, Nadine Schneider, Gianluca Sforna,
> > Paolo Tosco, Samo Turk, JL Varjo, Riccardo Vianello
> >
> > Highlights:
> >
> > - A new algorithm for generating canonical atom orders. The new
> > algorithm is faster and more robust than the old one.
> > - C++-based molecule drawing code, allows consistent molecule
> > renderings from C++, Java, and Python. This will become the
> > default renderer in the next release.
> > - General performance improvements and reduction of memory usage.
> > - Torsion Fingerprints for comparing 3D conformations to each other
> > - MCS code now available from the PostgreSQL cartridge
> >
> > Bug Fixes:
> >
> > - fmcs: use the zero bond type instead of other
> > (github issue #368 from AlexanderSavelyev)
> > - bug fixed in TorsionFingerprints.GetTFDMatrix
> > (github issue #376 from sriniker)
> > - rdkit.Chem.MolDb.Loader_sa does not work with python3.4
> > (github issue #390)
> > - ChemReactions: Bugfix/Memleak-fix in runReactants
> > (github issue #394 from NadineSchneider)
> > - TorsionConstraint bug fix
> > (github issue #395 from ptosco)
> > - Fixed LoadSDF to keep 3D info
> > (github pull #401 from samoturk)
> > - Incorrect expected absolute stereochemistries in a test
> > (github issue #407)
> > - GetSubstructMatches() consumes all available memory
> > (github issue #409)
> > - Bugfix in the chirality handling of chemical reactions
> > (github pull #410 from NadineSchneider)
> > - fixed two minor bugs in MMFF code
> > (github issue #416 from ptosco)
> > - Varied sanitise rejection with hydrogen representation
> > (github issue #418)
> > - Fixed two trivial bugs
> > (github issue #419 from ptosco)
> > - RDKit learns how to roundtrip MOLFile values.
> > (github issue #420 from bp-kelley)
> > - cairoCanvas.py python3 compatibility
> > (github issue #426 from bach-hardie)
> > - Chem.FragmentOnSomeBonds() should update implicit H count on aromatic
> > heteroatoms when addDummies is False
> > (github issue #429)
> > - Chem.FragmentOnSomeBonds() crashes if the bond list is empty
> > (github issue #430)
> > - Increase limit for smallest ring size
> > (github issue #431 from cowsandmilk)
> > - Problems caused by heteroatoms with radicals in aromatic rings.
> > (github issue #432)
> > - Conversion from mol to InChI getting ring stereo wrong
> > (github issue #437)
> > - Metals in mol2 blocks handled incorrectly
> > (github issue #438)
> > - Fixed a few tests failing when the Windows git client is used
> > (github pull #439 from ptosco)
> > - Fixed tests failing on Windows when retrieving sources through the
> > Windows git client
> > (github pull #440 from ptosco)
> > - Conformers not copied correctly in renumberAtoms
> > (github issue #441)
> > - Radicals are not correctly assigned when reading from SMILES
> > (github issue #447)
> > - moving RDBoost/Exceptions.h to RDGeneral
> > (github pull #458 from rvianello)
> > - Add code to accept blank SMILES input.
> > (github issue #468 from janholstjensen)
> > - Accept empty SMILES and SMARTS
> > (github issue #470)
> > - Fix MolFile Atom Line List Writer
> > (github issue #471 from bp-kelley)
> > - Moved 3D ipython renderer to dependency
> > (github pull #472 from patrickfuller)
> > - Windows build/test failure fixes
> > (github issue #473 from ptosco)
> > - install missing FMCS/Graph.h header file
> > (github pull #478 from rvianello)
> > - added const qualifiers to some methods of Atom/Bond iterator classes
> > (github pull #479 from rvianello)
> > - Bugfix in SmilesWrite and some additional tests for getMolFrags
> > function
> > (github issue #482 from NadineSchneider)
> > - Removed a while(1) {} in BFGSOpt.h which might result in an infinite
> > loop
> > (github issue #484 from ptosco)
> > - Gasteiger charge calculation fails with hexavalent sulfur #485
> > (github issue #485)
> > - SmilesWriter not creating automatic name values for molecules read
> > from
> > CTABs
> > (github issue #488)
> > - Fix StringType access, remove unused imports
> > (github issue #494 from bp-kelley)
> >
> > New Features:
> >
> > - Isomeric fix in PandasTools
> > (github issue #369 from samoturk)
> > - added SaveXlsxFromFrame - first version
> > (github issue #371 from samoturk)
> > - New feature: Torsion fingerprints
> > (github issue #372 from sriniker)
> > - Add function to extract a molecule with a single (particular)
> > conformer
> > from a multiconf mol
> > (github issue #384)
> > - Added C++ and Python helpers to retrieve force-field parameters
> > (github issue #387 from ptosco)
> > - Support providing all options to SWIG-wrapped FMCS
> > (github issue #397)
> > - Add function to request if calling UpdatePropertyCache is necessary
> > (github issue #399)
> > - Add function to test if UpdatePropertyCache is necessary
> > (github issue #400 from NadineSchneider)
> > - Substructure highlighting in pandas dataframe (fixes #362)
> > (github issue #403 from nhfechner)
> > - Added SDF Export to PandasTools and adjusted SDF Import
> > (github issue #404 from nhfechner)
> > - support count-based avalon fingerprint
> > (github issue #408)
> > - New C++ drawing code
> > (github issue #412 from greglandrum)
> > - RDKit learns how to compute code coverage for tests
> > (github issue #413 from bp-kelley)
> > - Dictionary access is saniztized and optimized.
> > (github issue #414 from bp-kelley)
> > - expose MolOps::rankAtoms() and MolOps::rankAtomsInFragment() to
> python
> > (github issue #421)
> > - Dev/expose rank atoms to python
> > (github issue #422 from bp-kelley)
> > - rdkit learns how to wrap a proper RWMol in python
> > (github issue #423 from bp-kelley)
> > - Docs: document "magic" property values that are used throughout the
> > code
> > (github issue #425)
> > - MolDraw2D: expose class to Python
> > (github issue #433)
> > - RDKit learns how to query properties on Atoms
> > (github issue #442 from bp-kelley)
> > - Issue445: provide helper functions for multithreaded evaluation of
> > some
> > expensive functions
> > (github issue #448 from greglandrum)
> > - RDKit learns how to release the GIL in python
> > (github pull #449 from bp-kelley)
> > - Dev/property queries
> > (github pull #450 from bp-kelley)
> > - Support a confId argument to the atom pair fingerprinting code
> > (github issue #453)
> > - Save the atom bookmarks so we can deconvolute reaction products.
> > (github pull #454 from bp-kelley)
> > - Cartridge: Support converting no structs to InChI
> > (github issue #455)
> > - RDKit learns how to expose ChemicalReaction copy constructor to
> python
> > (github pull #456 from bp-kelley)
> > - chirality flag was implemented for fmcs() function
> > (github pull #466 from AlexanderSavelyev)
> > - Support copy and deepcopy properly for at least Mol and RWMol
> > (github issue #467)
> > - Cartridge: add qmol_from_smiles() and qmol_from_ctab()
> > (github issue #469)
> > - restore java and python wrappers. New parameter (matchChiralTag)
> > (github issue #477 from AlexanderSavelyev)
> > - Added a Python wrapper for getShortestPath()
> > (github issue #487 from ptosco)
> > - Dev/merge query hs no unmapped atoms
> > (github issue #490 from bp-kelley)
> >
> > New Database Cartridge Features:
> >
> > - The MCS code is now available within the cartridge
> > - The functions qmol_from_smiles() and qmol_from_ctab()
> >
> > New Java Wrapper Features:
> >
> > - The new molecule rendering code is accessible from the SWIG wrappers.
> >
> > Deprecated code (to be removed in next release):
> >
> > - C++: The functionality in $RDBASE/Code/GraphMol/MolDrawing has been
> > superseded by the new drawing code in $RDBASE/Code/GraphMol and will
> > be removed in the next release.
> > - Python:
> > - rdkit/Dbase/Pubmed
> > - rdkit/Chem/fmcs (this has been superseded by the C++
> > implementation)
> > - Cartridge: support for v8.x of PostgreSQL (v8.4 is no longer
> > supported by the PostgreSQL project team as of July 2014)
> >
> > Removed code:
> >
> > - the method Atom::setMass() has been removed. Please use setIsotope()
> > instead.
> > - the methods involving an atom's dativeFlag have been removed.
> >
> > Contrib updates:
> >
> > Other:
> > - Python 2.6 support is deprecated. Starting with the next RDKit
> > release, we will only support python 2.7 and python 3.4 and
> > higher. Python 2.6 has not been supported since October 2013. If you
> > believe that you are stuck with python 2.6 because of the version of
> > RHEL you are running, please read this post to learn about your
> > options:
> >
> http://www.curiousefficiency.org/posts/2015/04/stop-supporting-python26.html
> > - The RDKit molecule objects (ROMol and RWMol) now require about 15%
> > less memory to store
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> >
> > ------------------------------
> >
> >
> ------------------------------------------------------------------------------
> > One dashboard for servers and applications across Physical-Virtual-Cloud
> > Widest out-of-the-box monitoring support with 50+ applications
> > Performance metrics, stats and reports that give you Actionable Insights
> > Deep dive visibility with transaction tracing using APM Insight.
> > http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> >
> > ------------------------------
> >
> > _______________________________________________
> > Rdkit-discuss mailing list
> > [email protected] <javascript:;>
> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >
> >
> > End of Rdkit-discuss Digest, Vol 91, Issue 4
> > ********************************************
> >
>
>
> --
> Samuel Ayodele Egieyeh
> South African National Bioinformatics Institute
> University of the Western Cape
> Bellville
> 7535
> Cape Town
> South Africa.
> Mobile Number: +27843477250
> Work Telephone Number: +270219592987
>
>
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> _______________________________________________
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>
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Performance metrics, stats and reports that give you Actionable Insights
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