Running Linux ubuntu in windows 11 using WSL
I have anaconda3 installed
I'm running the covalent docking tutorial for autodock vina available from:
https://autodock.scripps.edu/resources/covalent-docking/
When i run the prepareCovalent.py script I get the following:
Input:
(vina) gorrie06@DMGLaptop:~/docking/covalent$ python ~/docking/covalent/adcovalent/prepareCovalent.py --ligand /3upo_test/ligand.mol2 --ligindices 1,2 --receptor /3upo_test/3upo_protein.pdb --residue B:SER222 --outputfile ligcov.pdb
Output:
Traceback (most recent call last):
File "/home/gorrie06/docking/covalent/adcovalent/prepareCovalent.py", line 36, in
import pybel
File "/home/gorrie06/anaconda3/envs/vina/lib/python2.7/site-packages/pybel.py", line 89, in
informats = _formatstodict(_obconv.GetSupportedInputFormat())
File "/home/gorrie06/anaconda3/envs/vina/lib/python2.7/site-packages/pybel.py", line 68, in _formatstodict
broken = [(x, y.strip()) for x, y in broken]
ValueError: need more than 1 value to unpack
This is the function that is being referred to by the output (from pybel.py):
def _formatstodict(list):
if sys.platform[:4] == "java":
list = [list.get(i) for i in range(list.size())]
broken = [x.replace("[Read-only]", "").replace("[Write-only]", "").split(
" -- ") for x in list]
broken = [(x, y.strip()) for x, y in broken]
return dict(broken)
I have been able to modify pybel.py to prevent error but then the script prepareCovalent.py fails to read the pdb file.
Any help is greatly appreciated!
Thank you!
The error suggests an issue with the `broken` list in the `_formatstodict` function of `pybel.py`.
Try updating the `pybel` package to a compatible version by running the following command in your terminal:
```bash
(vina) gorrie06@DMGLaptop:~/docking/covalent$ pip install --upgrade pybel
```
This command will upgrade the `pybel` package to the latest version available. After upgrading, try running the `prepareCovalent.py` script again to see if the issue is resolved.
If the issue persists or upgrading `pybel` doesn't work, you can try using an alternative approach to run the covalent docking tutorial. Instead of using the `pybel` package, you can use the `rdkit` package, which is a powerful cheminformatics library that can handle various file formats, including PDB files.
To use `rdkit` in your script, you will need to install it by running the following command:
```bash
(vina) gorrie06@DMGLaptop:~/docking/covalent$ pip install rdkit
```
Once `rdkit` is installed, you can modify the `prepareCovalent.py` script to replace the `pybel` import and related code with the corresponding `rdkit` code for reading PDB files. Here's an example of how you can modify the script:
1. Open the `prepareCovalent.py` script in a text editor.
2. Remove the line `import pybel`.
3. Replace the line `ligand = pybel.readfile("mol2", ligandfile).next()` with the following code:
```python
from rdkit import Chem
ligand = Chem.MolFromMol2File(ligandfile)
```
4. Replace the line `receptor = pybel.readfile("pdb", receptorfile).next()` with the following code:
```python
receptor = Chem.MolFromPDBFile(receptorfile)
```
5. Save the modified script.
With these modifications, the script should now use `rdkit` instead of `pybel` for reading the ligand and receptor files. This should resolve the issue you encountered with `pybel` and allow the script to read the PDB file correctly. Make sure you have the `rdkit` package installed in your Anaconda environment (`vina`) before running the modified script.
Good luck: partial credit AI