!pip install vina failed in Google Colab, with a Linux Python 3 Google Compute Engine backend

[rwxayheee]

The installation was attempted from Google Colaboratory, following a similar procedure to this.

!pip install vina gives

Collecting vina
  Downloading vina-1.2.5.tar.gz (89 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 89.5/89.5 kB 2.0 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting numpy>=1.18 (from vina)
  Downloading numpy-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.9/60.9 kB 3.2 MB/s eta 0:00:00
Downloading numpy-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.3 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 19.3/19.3 MB 53.6 MB/s eta 0:00:00
Building wheels for collected packages: vina
  error: subprocess-exited-with-error
  
  × Building wheel for vina (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> See above for output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  Building wheel for vina (pyproject.toml) ... error
  ERROR: Failed building wheel for vina
Failed to build vina
ERROR: Could not build wheels for vina, which is required to install pyproject.toml-based projects

The connected Python 3 Google Compute Engine backend is Linux.

On the other hand, conda install worked ^^

!conda install vina

after installing condacolab

!pip install -q condacolab
import condacolab
condacolab.install()

Hope the information is helpful anyone who run Jupyter Notebook with Google Colab

[Jameel9]

I had the same error on Colab and on conda env (Ubuntu PC). On my PC, I ran these commands

conda create -n vina
conda activate vina
conda config --env --add channels conda-forge
conda install -c conda-forge numpy swig boost-cpp sphinx sphinx_rtd_theme
pip install vina

the long msg error is attached
vina_error.txt

[rwxayheee]

Hi @Jameel9
Thanks for reporting this. conda install vina works for me. Please see this example Colab notebook from me ^^
https://colab.research.google.com/drive/1527GlrL-AHn4irrg19129PH4YvvabqNW?usp=sharing
I'm not sure why pip kept failing.. but we have had multiple reports on different platforms and we should look into that in the near future

[Jameel9]

pip

thank you!

[Jameel9]

Hi all,

I would be deeply grateful to receive help for this code issue (not vina itself). I have been trying to run virtual screening using the following code, but I couldn't capture the output for each molecule into a .log file.

import os
import glob
from vina import Vina
import gc


Directory = "/home/shirehorse/Desktop/VS"
ligand_files = glob.glob(f'{Directory}/ligands/*.pdbqt')
receptor_file = f"{Directory}/receptor_0.pdbqt"

for ligand_file in ligand_files:
    ligand_name = os.path.basename(ligand_file).replace('.pdbqt', '')
    result_file = f'{Directory}/results/{ligand_name}_out.pdbqt'
    
    if os.path.exists(result_file):
        print(f"Result file already exists: {result_file}. Skipping.")
        continue
    
    try:
        print(f"Starting docking for {ligand_file}...")
        
        # Initialize Vina
        vina = Vina(sf_name="vina", seed=4)
        vina.set_receptor(receptor_file)
        
        # Compute docking maps 
        vina.compute_vina_maps(Center=[5.84, 3.44, 2.09], box=[26, 38, 30] )
        
        # Set ligand and perform docking
        vina.set_ligand_from_file(ligand_file)
        vina.randomize()
        vina.dock(exhaustiveness=8, n_poses=9)
        
        # Write docking results
        vina.write_poses(
            result_file,
            energy_range=10000.0,
            overwrite=True,
            n_poses=9
        )
        
        print(f"Finished docking for {ligand_file}. Results saved to {result_file}.")
    
    except Exception as e:
        print(f"Exception occurred for {ligand_file}: {e}")
    
    finally:
        gc.collect() 

[rwxayheee]

Hi @Jameel9
vina.compute_vina_maps(Center=[5.84, 3.44, 2.09], box=[26, 38, 30] )
should be
vina.compute_vina_maps(center=[5.84, 3.44, 2.09], box_size=[26, 38, 30] )

Have you tried running this interactively? Doing this on a certain pair of receptor and ligand might be helpful for troubleshooting your own codes.

[Jameel9]

Thank you so much @rwxayheee for your response.
Sorry about this. I actually defined those parameters as individual variables.
BOX_SIZE = [26, 38, 30]
CENTER = [5.84, 3.44, 2.09]

and
vina.compute_vina_maps(center=CENTER, box_size=BOX_SIZE)

But when I copied the code to GitHub, I thought I would make it shorter and less messy but i successfully missed up with arguments wording :).

I did ran it interactively before and I kept getting something like this on the terminal as in the image below. The issue here is that I can't capture the affinities of each molecule into an independent log file.

[rwxayheee]

Hi @Jameel9
I see :) a quick way to redirect standard output and error is:
python virtual_screen.py &> virtual_screen.log
virtual_screen.log will have the contents that are printed to terminal

[Jameel9]

Ok. Thank you so much.