AutoDock Vina - Python API
Requirements
You need, at a minimum (requirements):
- Python (>=3.5)
- Numpy
- SWIG
- Boost-cpp
- Sphinx (documentation)
- Sphinx_rtd_theme (documentation)
Installation (from source)
I highly recommand you to install the Anaconda distribution (https://www.continuum.io/downloads) if you want a clean python environnment with nearly all the prerequisites already installed. To install everything properly, you just have to do this:
$ conda create -n vina python=3
$ conda activate vina
$ conda install -c conda-forge numpy swig boost-cpp sphinx sphinx_rtd_theme
Finally, we can install the Vina package
$ git clone https://github.com/ccsb-scripps/AutoDock-Vina
$ cd AutoDock-Vina/build/python
$ python setup.py build install
Quick tutorial
#!/usr/bin/env python
from vina import Vina
v = Vina()
v.set_receptor(rigid_pdbqt_filename="protein.pdbqt")
v.set_ligand_from_file('ligand.pdbqt')
v.compute_vina_maps(center=[0., 0., 0.], box_size=[30, 30, 30])
print(v.score())
print(v.optimize())
v.dock(exhaustiveness=32)
v.write_poses(pdbqt_filename="docking_results.pdbqt")
Full documentation
The installation instructions, documentation and tutorials can be found on readthedocs.org.
Citations
- Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry, 31(2), 455-461.
3 maintainers
Release files for vina 1.2.7
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| vina-1.2.7.tar.gz | 89.2 kB | Details |
Built distributions (wheels)
Total release size: 69.2 MB
Release files / vina-1.2.7.tar.gz
| Download URL | vina-1.2.7.tar.gz |
|---|---|
| Size | 89.2 kB |
| Tags | Source |
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No |
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Release files / vina-1.2.7-cp312-cp312-musllinux_1_2_x86_64.whl
| Download URL | vina-1.2.7-cp312-cp312-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 7.0 MB |
| Tags | CPython 3.12 Linux musl 1.2+ x86-64 |
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No |
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Release files / vina-1.2.7-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | vina-1.2.7-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 6.9 MB |
| Tags | CPython 3.12 Linux glibc 2.17+ x86-64 |
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No |
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twine/6.1.0 CPython/3.13.2
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Release files / vina-1.2.7-cp311-cp311-musllinux_1_2_x86_64.whl
| Download URL | vina-1.2.7-cp311-cp311-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 7.0 MB |
| Tags | CPython 3.11 Linux musl 1.2+ x86-64 |
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Release files / vina-1.2.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | vina-1.2.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 6.8 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 |
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Release files / vina-1.2.7-cp310-cp310-musllinux_1_2_x86_64.whl
| Download URL | vina-1.2.7-cp310-cp310-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 7.0 MB |
| Tags | CPython 3.10 Linux musl 1.2+ x86-64 |
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Release files / vina-1.2.7-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | vina-1.2.7-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 6.8 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 |
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Release files / vina-1.2.7-cp39-cp39-musllinux_1_2_x86_64.whl
| Download URL | vina-1.2.7-cp39-cp39-musllinux_1_2_x86_64.whl |
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| Tags | CPython 3.9 Linux musl 1.2+ x86-64 |
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Release files / vina-1.2.7-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | vina-1.2.7-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 6.8 MB |
| Tags | CPython 3.9 Linux glibc 2.17+ x86-64 |
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Release files / vina-1.2.7-cp38-cp38-musllinux_1_2_x86_64.whl
| Download URL | vina-1.2.7-cp38-cp38-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 7.0 MB |
| Tags | CPython 3.8 Linux musl 1.2+ x86-64 |
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Release files / vina-1.2.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | vina-1.2.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 6.8 MB |
| Tags | CPython 3.8 Linux glibc 2.17+ x86-64 |
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