• Compare Molecule Similarity Pseudocode


    I have used the CSD for my third year project. One of the sections requires us to explain what algorithms we have used. I was wondering if there was a formal pseudocode for the similarity search when comparing two molecules. I have looked at the source code but it's a bit complex.

    Is there any pseudocode for the methods in the documentation?

    Cheers, Alex

  • OS X Conda issue

    When trying to install, update, or remove anything using either command line or anaconda an error (see attached file). This occurs despite not trying to modify the csd files in the slightest. Has anyone else encountered this issue?

    I have come across it in the past and I realised that I had installed a package using a python3 build. My solution to that was to uninstall the package from the environment however I get the error: "ResolvePackageNotFound:- csd-python-api-1.3.0-mac-64" so now I'm unsure how to proceed.




  • RE: SQLite breaks when running similarity search

    Hi Stewart,

    This has solved my issue. Thank you for all the help it has improved the programs memory use as well as running to completion.


  • RE: SQLite breaks when running similarity search

    Hi Steward,

    Thanks for getting back to me

    I'm currently storing a list of entry names, would I need to make read them into the molecule reader before trying this?


  • SQLite breaks when running similarity search

    I have a program which measures the similarity of all items of a set against every other item in the set. However, after 81 loops I get this error: RuntimeError: open failed (code 14) - unable to open database file - /Applications/CCDC/CSD_2017/DATA/CSD_538/Nov16_ASER.sqlite

    My guess is that there is no room in the temporary files folder to store the data but the source code gives the impression that it deletes temporary databases once they have been used. I've tried to use garbage collector and only the readers when I run the function to make the search (I'm assuming they close once the function finishes) but this has only slightly increased the number of loops before the error occurs. I have ran the program on just the entries that it breaks on to see if there are some corrupted filed however they worked fine.


    Is this a common issue? Currently it breaks after 81 similarity searches