• RE: Jupyter notebook for CSD-python-API

    Hi Richard,

    Sorry for keeping bugging you for a week. 

    The csd_licence.data is located at /Applications/CCDC/CSD_2018/CSD_539/csd_licencw.dat.

    what I did is shown on the screen shot. I exported the PATH, but it doesn't work.

    And plus, this time export CSDHOME=/path/to/CCDC/CSD_2018 doesn't work either, I keep getting error msg even though I export it, it says can't find CSDHOME/

    Thanks for your help all the time.

  • RE: Jupyter notebook for CSD-python-API

    Hi Richard,

    The CSDHOME not found error is solved. However, I keep getting the error as I show here.

    Thanks,

    Frank

  • RE: Jupyter notebook for CSD-python-API

    And I got the wrong msg here too 

  • RE: Jupyter notebook for CSD-python-API

    Hi Richard,

    Thanks for all of the info. I installed the jupyter notebook to Miniconda environment.

    However, I got the wrong msg when I tried to import ccdc. Here is the screen shot. I already installed the whole CCDC package on the local, I don't understand why it still says I don't have the permission.

  • RE: Jupyter notebook for CSD-python-API

    Hi Richard,

    Thanks for your help.

    Just wanna make sure if I understand correctly, in your code,

    source /path/to/miniconda

    do I need to replace the /path/to/ with the directory where Miniconda is at on my computer?

    Best,

    Frank

  • RE: SMILES code of MOF sub-database

    Hi Richard,

    In your code:

    for b in deloc:
        m.add_bond('Aromatic', *b)
    print m.smiles

    The second line, could you explain the function of the "*" in front of b. I know that in deloc, it returns a nested list, with two atoms in each element. Here b is actually two atoms, why there is a asterisk in front of b?

    Thank you,

    Frank

  • RE: Jupyter notebook for CSD-python-API

    Hi Richard,

    I'm not sure if I understand correctly, I typed the code you gave me in terminal. There is no Jupyter notebook installed to Miniconda in CCDC package. (Here is what I did, I switched to "bin" directory and installed Jupyter, and I did Jupyter-console)

    Just FYI,  in Mac, I already installed anaconda and have Jupyte notebook with python 3.6.

     

  • RE: SMILES code of MOF sub-database

    Hi Richard,

    Sure, I tested two MOFs, they are ABACUF, and ABEMIF.

    Thanks,

    Frank

     

     

  • Jupyter notebook for CSD-python-API

    Hi,

    I'm new to csd-python-api, I installed from the csd 2018 release, the ~9GB package, it comes with csd-python-api already. However, I prefer to use Jupyter notebook to program stuff, easy editing. Is there anyway to run csd-python-api in Jupyter notebook? In the csd-python-api folder, it has Miniconda environment.

    Thank you very much!

    Frank

  • SMILES code of MOF sub-database

    Hi,

    Just wondering is there anyway to convert MOF structure into SMILES coding? I tried to assign the bond type to MOF molecules, however when I print the component.bond and component.smiles, it returns all of the bonds for components, but for SMILES ,it returns NONE.

    Thanks for your help!

    Frank