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] > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > 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]> > Subject: [Rdkit-discuss] SetFormalCharge and AddHs > To: RDKit Discuss <[email protected]> > Message-ID: > <[email protected]> > 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 -------------- > An HTML attachment was scrubbed... > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: bnz.mol > Type: application/octet-stream > Size: 1130 bytes > Desc: not available > -------------- next part -------------- > An embedded and charset-unspecified text was scrubbed... > Name: why.py > > ------------------------------ > > Message: 2 > Date: Wed, 6 May 2015 07:36:46 +0200 > From: Greg Landrum <[email protected]> > Subject: [Rdkit-discuss] 2015.03 (Q1 2015) RDKit Release > To: RDKit Discuss <[email protected]>, > [email protected], RDKit Developers List > <[email protected]> > Message-ID: > <CAD4fdRRhgwJL0jzGNYSjf7166CobtMAW=v4uhd0jxd4dsco...@mail.gmail.com> > 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] > 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 _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
