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Becksteinlab / propkatraj

pKa estimates for proteins using an ensemble approach
https://becksteinlab.github.io/propkatraj/
GNU General Public License v2.0
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AttributeError: module 'propkatraj' has no attribute 'get_propka' #64

Closed evelyne-deplazes closed 11 months ago

evelyne-deplazes commented 1 year ago

Hi

I am having issues running propkatraj and I think it's related to my local propkatraj or Propka installation because the error I get is

AttributeError: module 'propkatraj' has no attribute 'get_propka'

(I get no error about the module not being found)

I have MDAnalysis 2.5 installed (on a MacOS 10.15) and that works fine. I have install propka and propkatraj using

pip install propka==3.1
pip install propkatraj

No error messages during the installation

I tried a very stripped-back test script (see attached) but I can't even call the function help(propkatraj.get_propka)

Any help would be much appreciated.

thanks from Australia Evelyne

I came across this older issue https://github.com/Becksteinlab/propkatraj/issues/18

I checked the lib.py in /Users/evelyne/opt/anaconda3/lib/python3.9/site-packages/propka/lib.py and as far as I can tell the required code for the function open_file_for_reading is there pka_test.txt

IAlibay commented 1 year ago

Hi @evelyne-deplazes,

The get_propka method was replaced in the last release of propkatraj. Instead you must now use the PropakTraj class. We have some example usage here which should help translate any code you currently rely on: https://becksteinlab.github.io/propkatraj/usage/examples.html

orbeckst commented 11 months ago

I hope that using the new API solved your problem. I am going to close but please feel free to ask again/reopen if necessary.