• RE: Writing crystals

    That worked perfectly! Thanks a lot.

  • Writing crystals

    Hello, 

     

    I am trying to do something reasonably simple but I'm a bit confused by the documentation for the io.CrystalWriter module. I'm trying to feed in a list of refcodes for which to output the corresponding crystal structures as pdb files into a new folder. 

     

    Would you be able to help?
    Thanks a lot 

    Puck 

  • RE: Installing rdkit fails due to csd python api installation

    Hi Stewart,

     

    Sorry, I temporarily gave up on this. Yes, it's listed in the installed environments so it's definitely installed. Before the ccdc package is installed in the environment it imports fine, but once the ccdc package is installed in the same environment it won't import anymore. I've tried both in ipython and from a python file. I've just been resorting to using rdkit and ccdc in separate environments but it would make my life a lot easier if I could use them in the same environment! 

    Puck 

  • RE: Installing rdkit fails due to csd python api installation

    Hi, 

     

    I just tried this and now it seems to install the rdkit package but when I try to import it in ipython it says "ImportError: No module named rdkit". The ccdc package works fine.

    Any ideas?

    Puck 

  • Installing rdkit fails due to csd python api installation

    Hi,

     

    I'm trying to install rdkit (I have tried both through conda and pip) and it fails with the following error message:

     

    PackagesNotFoundError: The following packages are not available from current channels:

     

      - csd-python-api-1.5.1-mac-64

     

    Current channels:

     

      - https://repo.anaconda.com/pkgs/main/osx-64

      - https://repo.anaconda.com/pkgs/main/noarch

      - https://repo.anaconda.com/pkgs/free/osx-64

      - https://repo.anaconda.com/pkgs/free/noarch

      - https://repo.anaconda.com/pkgs/r/osx-64

      - https://repo.anaconda.com/pkgs/r/noarch

      - https://repo.anaconda.com/pkgs/pro/osx-64

      - https://repo.anaconda.com/pkgs/pro/noarch

      - https://conda.anaconda.org/conda-forge/osx-64

      - https://conda.anaconda.org/conda-forge/noarch

     

    Am I missing something? I need rdkit and the csd python api working on the same environment, so any help would be appreciated..

     

    Thanks

    Puck 

  • RE: Filtering CSD for molecules with no disorder

    Dear Richard, 

     

    That has fixed it. Thanks a lot!

     

    Puck 

  • Filtering CSD for molecules with no disorder

     Hi, 

     

    I am new to using the Python API for the CSD and am trying to filter the CSD for organic crystals with no disorder or errors, and one distinct molecule / component . I am trying to use the search.Search.Setttings() and specifying:

    settings.only_organic= True 
    settings.no_metals= True
    settings.has_3d_coordinates= True
    settings.no_disorder= True
    settings.no_errors= True

     

    Then applying:

    for crystal in csd_crystals:
         if (len(crystal.molecule.components) == 1 and settings.test(crystal)):
              refcodes.append(crystal.identifier)

     

    However some crystals that don't meet these criteria are being selected - such as refcode AARBOX and ABABUB. What am I doing wrong?