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

Hi Frank,

it should be possible to install Jupyter notebook into the CSD's miniconda:

/path/to/csd/miniconda/bin/conda install jupyter

then you can run:

/path/to/csd/miniconda/bin/jupyter-console

Best wishes

Richard

 

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.

 

Hi Frank,

I've just done a clean install of the latest CSD system on a Mac, and installed jupyter on it with no problems:

source /path/to/miniconda/bin/activate
conda install jupyter
jupyter-console
In [1]: from ccdc import io
In [2]: csd = io.EntryReader('csd')
In [3]: len(csd)
Out[3]: 961466

So I'm really not sure what's happening when you try it.  Is it possibly an instance of this issue?
https://downloads.ccdc.cam.ac.uk/documentation/API/trouble_shooting.html#un-installing-in-csds-conda-environment

If not, are there any other details you can give me, like how you installed jupyter, and what error messages you have seen?

Best wishes

Richard

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

Hi Frank,

yes, that should be the full path to the miniconda under your CSD installation.  So on my network it was:

source CCDC_MAC/Python_API_2018/miniconda/bin/activate

This sets your path to include the miniconda bin directory at the front, so things like python and conda will be those in that directory.  You can call these directly from this bin directory without activating the miniconda, but it's usually easier to activate and make sure that you are using a consistent set of programs.
You can deactivate, i.e. return to your normal path settings by:

source deactivate

Best wishes

Richard

 

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.

And I got the wrong msg here too 

Hi Frank,

I think you need to set the environment variable, CSDHOME so the API can find where the CSD is located:

export CSDHOME=/path/to/CCDC/CSD_2018

Try this, and see if that works, please.

Best wishes

Richard

Hi Richard,

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

Thanks,

Frank

 HI Frank,

can you run mercury successfully?  If so, the Help->About mercury should say where it found the licence.  If the licence is in a non-standard place, i.e. not in CSD_2018/CSD_539/csd_licence.dat or /home/.../csd_licence.dat then you may need to set the environment variable CCDC_CSD_LICENCE_FILE to point to its location.

 

Let me know if this works.

 

Best wishes

Richard

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.

 Hi Frank,

It looks as if you've spelled csd_licence.dat as csd_licencw.dat, so that may be the source of the problem.

Incidentally, you're a brave man to be running these things as root!

Best wishes

Richard

Hello, I have trouble with installing csd-python-api 

by following the instruction in https://downloads.ccdc.cam.ac.uk/documentation/API/installation_notes.html

 

my machine is Mac OSX with python Python 3.6.8

after

export CSDHOME=/Applications/CCDC/CSD_2019
export DYLD_LIBRARY_PATH=$PYTHONHOME/lib/python2.7/site-packages/ccdc/_lib
export DYLD_FRAMEWORK_PATH=$PYTHONHOME/lib/python2.7/site-packages/ccdc/_lib

 

with conda install -c /Applications/CCDC/CSD_2019 csd-python-api

i got this error

{

Solving environment: failed

 

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

 

  - csd-python-api

 

Current channels:

 

  - file:///Applications/CCDC/CSD_2019/osx-64

  - file:///Applications/CCDC/CSD_2019/noarch

  - 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

 

To search for alternate channels that may provide the conda package you're

looking for, navigate to

 

    https://anaconda.org

 

and use the search bar at the top of the page.

}

 

if i try 

conda install -c /Applications/CCDC/Python_API_2019/ccdc_conda_channel csd-python-api

This error occure 

{

Solving environment: failed

 

UnsatisfiableError: The following specifications were found to be in conflict:

  - csd-python-api

  - fpsim2

Use "conda info <package>" to see the dependencies for each package.

 

(QSAR) Naravuts-MacBook-Pro:~ zeromtmu$ conda install -c /Applications/CCDC/Python_API_2019/ccdc_conda_channel csd-python-api

Solving environment: failed

 

UnsatisfiableError: The following specifications were found to be in conflict:

  - csd-python-api

  - matplotlib-base

Use "conda info <package>" to see the dependencies for each package.

}

 

What should i do?

 

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