Problems with pyFoldX in jupyter notebook using WSL

[EmilioKolo]

I'm trying to run pyFoldX using Windows Subsystem for Linux, and have encountered two different problems that may or may not have to do with running it on WSL. I made sure to include the path to foldx in the .bashrc file. I wasn't sure if I needed to put the path to the folder or to the file, but I tried both and it didn't change any of the error messages.

The code I'm running is getting a structure from PDB and trying to run getTotalEnergy() on it, and I get two different error messages, one on the command line and a different one in jupyter.

Using the Ubuntu command line, it throws back an index out of range error.

>>> from pyfoldx.structure import Structure
>>> st=Structure("3rkq");
>>> st.getTotalEnergy();
Computing total energy for structure...
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/emilio/.local/lib/python3.8/site-packages/pyfoldx/structure/structure.py", line 215, in getTotalEnergy
    foldxHandler.getTotalEnergy(self, consider_waters=consider_waters)[terms].loc[self.code]
  File "/home/emilio/.local/lib/python3.8/site-packages/pyfoldx/foldx/foldxHandler.py", line 101, in getTotalEnergy
    dfData = st_lines[0].split("\t")[1:-1]
IndexError: list index out of range

Using jupyter, the code is a bit longer but it seems to not get the FOLDX_LOCATION variable, which ends up being None.

Computing total energy for structure...
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[3], line 4
      1 ### Pruebas de pyfoldx
      3 st=Structure("3rkq"); 
----> 4 st.getTotalEnergy(); 
      6 print('fin')

File ~/.local/lib/python3.8/site-packages/pyfoldx/structure/structure.py:215, in Structure.getTotalEnergy(self, terms, consider_waters)
    212     self.totalEnergy = pd.DataFrame(columns=foldxHandler.ENERGY_TERMS)
    213     terms=foldxHandler.ENERGY_TERMS
--> 215 foldxHandler.getTotalEnergy(self, consider_waters=consider_waters)[terms].loc[self.code]
    218 print( "Energy computed." )
    219 return self.totalEnergy

File ~/.local/lib/python3.8/site-packages/pyfoldx/foldx/foldxHandler.py:87, in getTotalEnergy(st, consider_waters, other_parameters)
     84 st.toPdbFile(TMP_FOLDER+"tmp.pdb")
     86 # Run FoldX
---> 87 runFoldX(command          = "Stability", 
     88          working_folder   = TMP_FOLDER, 
     89          pdb              = "tmp.pdb",
     90          other_parameters = other_parameters,
     91          consider_waters  = consider_waters )
     93 # Read files
     94 st_lines = FileHandler.getLines(TMP_FOLDER+"tmp_0_ST.fxout")

File ~/.local/lib/python3.8/site-packages/pyfoldx/foldx/foldxHandler.py:47, in runFoldX(command, working_folder, pdb, other_parameters, working_with_rna, silent, consider_waters)
     44     out = open(working_folder+"./tmp.pdb","r")
     46 with out: 
---> 47     checkFoldx()
     50     c="cd "+working_folder+"; "
     51     c+=FOLDX_LOCATION+" --command="+command+" --pdb="+pdb

File ~/.local/lib/python3.8/site-packages/pyfoldx/foldx/foldxHandler.py:31, in checkFoldx()
     30 def checkFoldx():
---> 31     if not FileHandler.fileExists(FOLDX_LOCATION):
     32         print("FoldX executable not found, please set the variable FOLDX_LOCATION")
     33         exit(0)

File ~/.local/lib/python3.8/site-packages/pyfoldx/handlers/fileHandler.py:30, in FileHandler.fileExists(path)
     23 '''
     24 Check if a file exists.
     25 
     26 :param path: The file or folder to check if exists.
     27 :return: True if the file or folder exists. 
     28 '''
     29 try:
---> 30     with open(path): return True
     31 except IOError:
     32     return False

TypeError: expected str, bytes or os.PathLike object, not NoneType

I'm not sure if I set up something wrong or if this is a WSL problem.

Thanks in advance.

[ascusf]

Download FoldX Suite 5.0 fixed the problem so far. I downloaded FoldX Suite 4.0 first and ran into those issues. I have to type: source ~/.bashrc each time before entering spyder to run pyfoldx.

and I used

Load a protein PDB file from the internet

st = Structure("2ci2","/to_path/2ci2.pdb")

Append and turn horizontal both dataframes

combinedDf = seqEnergyOriginal.T._append(seqRepaired.T)

[leandroradusky]

As said above, this problem is due to the inability of pyFoldx to run with Foldx4.

Closing this issue.