vina · PyPI

2023-09-11 15:16| 来源: 网络整理| 查看: 265

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 $ git checkout boost-python $ cd 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.

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vina · PyPI

vina · PyPI

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