Hi Greg, > > 5. Downloaded the INCHI src as described in the wiki and set the > > RDK_BUILD_INCHI_SUPPORT option later in cmake. Incidentally, the > > location for the downloads from IUPAC have changed (ie the info in the > > README is out of date): > > http://www.iupac.org/home/publications/e-resources/inchi/download.html > > The link that is in the README, which is to a more recent version (1.04 > instead of 1.03), does still work for me. Did you have problems with that?
I realised that in my first attempts I had mistakenly linked to the RDKit repo on SourceForge (following the wiki). The README there points to http://www.iupac.org/inchi/download/version1.03/INCHI-1-API.zip which no longer exists. I am now using the INCHI download link from the current README - thanks! > > 7. Re-ran configure, then generate, then followed the rest of the > > wiki instructions to build and test - all tests passed except the > > dbCli one. > > > What was the DbCLI test failure? I just see " 76/82 Test #76: pythonTestDbCLI ..................***Failed 50.66 sec" > > I thought I did everything right for adding INCHI support. However, I > > see the following: > > > > In [1]: from rdkit import Chem > > In [2]: Chem.inchi.INCHI_AVAILABLE > > Out[2]: False > > > > Do I also need to download the InChi binary and set these two > > variables appropriately in CMake? > > > No; that should not be necessary. > If you have the source in the right place (and that cmake message makes it > look like you do) and have RDK_BUILD_INCHI_SUPPORT set, run "generate", > and then do a build and an install, it should produce the binaries you need > and update that file so that Chem.inchi.INCHI_AVAILABLE is True. Did you > re-run "generate" after installing the INCHI source? I thought I had re-run 'generate'... Perhaps it was an issue with using older INCHI source? > > Also, I am struggling to build with Avalon support... > > 1) download the beta source distribution from sf.net; > http://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.1_beta/AvalonToolkit_1.1_beta.source.tar/download > 2) extract that tar file somewhere. It's going to create SourceDistribution > and a StandardFiles directories > 3) set the cmake variable AVALONTOOLS_DIR to point to the SourceDistribution > directory > 3) set RDK_BUILD_AVALON_SUPPORT=ON in cmake > 4) run a build and install. > > Note: one or two of the avalontools tests may fail on windows. This is > currently expected. I have now included the INCHI 1.04 source, and followed your Avalon steps above. The AVALONTOOLS_DIR currently needs to be added manually in CMake (but that's ok). I should also say that, just in case, I deleted the build folder and cleared the CMake cache before this build attempt. I also *definitely* re-ran the 'generate' command (a few times!) before 'configure'. Anyway, I now see more tests when running 'ctest' - which I think is due to the addition of testInchi, testAvalonLib1, and pyAvalonTools - all of which pass! I can also confirm that Chem.inchi.INCHI_AVAILABLE now returns "True". (pythonTestDbCLI still fails as before.) Thanks very much for the help! Kind regards James ______________________________________________________________________ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or [email protected]. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 0000 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. ______________________________________________________________________ ------------------------------------------------------------------------------ WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
