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leandroradusky / pyfoldx

pyFoldX: python bindings for FoldX.
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currently not running correctly? #1

Closed miangoar closed 3 years ago

miangoar commented 3 years ago

Hi Leandro. Thanks for the implementation of pyFoldX.

I want to use it but I have problems running the notebook "Working with PDB Structures". Can you help me please?

I have a PC with windows10 and enabled windows susbsystem from linux to use any program in github by using the bash terminal. I get an academic license for FoldX (v5; Executable Foldx5 - Linux 64bits) and dowloaded the file to set the path to binary file into my my .bashrc. Next, i create a conda enviroment with pyton 3.8 called "foldX" and then run "pip install pyfoldx". Then, run a jupyter notebook following the tutorial "Working with PDB Structures" exactly with the same code and get this issue in the cell that contains the code "st.getTotalEnergy ()"

image

what is the problem?

miangoar commented 3 years ago

Im so sorry! ... rookie mistake. I solved my problem ! I'll put my mistake if it is useful for anyone.

When i downloaded the binary exec. of foldX, i got a file "foldx5Linux64.tar.gz". Then i uncompress it using windows rar app and i thougth that the output file was the actuall binary. But not. I get confused by the extension ".tar.gz" ,so, i renamed this file as "foldx5Linux64.tar" and the uncompress it and the outputs files include the real binary.

leandroradusky commented 3 years ago

Thanks for using pyFoldx and sharing :)

miangoar commented 3 years ago

Thank you too Leandro!

Indeed i have a question. Can you help me please?

Is there an example of how to build an ensemeble from local PDB files? I have ~ 100 PDBs in my PC and yet not reached a way to build an esemble from my local files to compute it's energies.

The documentations shows how to build from Uniprot, but i want to do from my local files. To my undestand, first i have to build a Structure obj. per each one of my PDB files and then, add them to a Ensemble obj. Or there is another easy way to do that?