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Docking_py is a python library allowing a simplified use of the Smina, vina, qvina2 and qvinaw docking software. Docking_py can be easily automatize and scripted.

Home Page: https://docking-py.readthedocs.io/en/latest

License: GNU General Public License v2.0

Makefile 2.70% Python 96.52% Shell 0.08% Dockerfile 0.70%

docking_py's Introduction

Docking Python

https://travis-ci.org/samuelmurail/docking_py.svg?branch=master

Docking_py is a python library allowing a simplified use of the Smina, vina, qvina2 and qvinaw docking software. Docking_py can be easily automatize and scripted.

Free software: GNU General Public License v2 (GPLv2)
Documentation: https://docking-py.readthedocs.io.

Features

Prepare receptors and ligands.
Launch docking using:
- Autodock with or without GPU acceleration
- Vina
- Smina
- Qvina2
- Qvinaw

Citing this work

If you use the code or data in this package, please cite:

@Article{SeamDock2021,
  title = {SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking},
  shorttitle = {SeamDock},
  author = {Murail, Samuel and de Vries, Sjoerd J. and Rey, Julien and Moroy, Gautier and Tuff{\'e}ry, Pierre},
  year = {2021},
  journal = {Frontiers in Molecular Biosciences},
  volume = {8},
  pages = {762},
  issn = {2296-889X},
  doi = {10.3389/fmolb.2021.716466},
}

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

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docking_py's Issues

Problems about Jupyter notebook when installing 0.3.0 version

Hello~
When I finish the installation of docking-py 0.3.0 version and try to input "from pdb_manip_py import pdb_manip" in Jupyter notebook under the docking-py virtual enviroment, it shows that " ModuleNotFoundError: No module named 'pdb_manip_py' ". But it is okay when I try the examples in the command line mode.
How to fix it? Thank you very much~

Problems about installing GPU version

Hello! When I try the examples in "Extract Receptor coordinates with pdb_manip_py" in usage, it appears that “AttributeError: module 'pdb_manip_py.pdb_manip' has no attribute 'PROTEIN_AA'”. How to fix it?

Problems about input of docking_py

Hello~ I have a problem of input of docking_py. Does the input need to be a binding complex of ligand and receptor? Can the ligand and the receptor be from different files and be of random initial coordinates rather than given positions in the binding complex?
Thank you for your patience and explanations!

Problems about trying examples in documentation

Hello! When I try to extract affinity and RMSD to crystal structure in examples "rmsd_list = test_dock.compute_dock_rmsd(test_dock.lig_pdbqt)", it appears that "File name doesn't finish with .pdb read it as .pdb anyway".
And then I try "rmsd_list = test_dock.compute_dock_rmsd(test_dock.lig_pdb)", value errors appear:
"
Traceback (most recent call last):
File "", line 1, in
File "/home/xxx/.conda/envs/docking/lib/python3.6/site-packages/docking_py-0.2.3-py3.6.egg/docking_py/docking.py", line 1382, in compute_dock_rmsd
rmsd = dock_coor.compute_rmsd_to(cryst_coor, selec_dict=selec_dict)
File "/home/xxx/.conda/envs/docking/lib/python3.6/site-packages/pdb_manip_py/pdb_manip.py", line 3932, in compute_rmsd_to
rmsd = atom_coor.compute_rmsd_to(atom_sel_2, selec_dict=selec_dict)
File "/home/xxx/.conda/envs/docking/lib/python3.6/site-packages/pdb_manip_py/pdb_manip.py", line 2545, in compute_rmsd_to
diff = coor_array_1 - coor_array_2
ValueError: operands could not be broadcast together with shapes (50,3) (45,3)
"
And the computed rmsd_list is also very different from the one shown in examples.

How to fix it? Thank you!