Python package for preparing small molecule for docking
Project description
Meeko
The Python package meeko is a new type of package developped and maintained by the Forli lab also at the Center for Computational Structural Biology (CCSB). It provides tools covering other docking aspects not handled by the ADFR software suite. This package provides addtionnal tools for the following docking protocols:
- Hydrated docking
- Macrocycles
Prerequisites
You need, at a minimum (requirements):
- Python (>=3.5)
- Numpy
- Openbabel (>=3)
Installation (from source)
$ git clone https://github.com/ccsb-scripps/Meeko
$ cd Meeko
$ python setup.py build install
Quick tutorial
from meeko import MoleculePreparation
from meeko import obutils
input_molecule_file = 'example/BACE_macrocycle/BACE_4.mol2'
mol = obutils.load_molecule_from_file(input_molecule_file)
preparator = MoleculePreparation(merge_hydrogens=True, macrocycle=True, hydrate=True)
preparator.prepare(mol)
preparator.show_setup()
output_pdbqt_file = "test_macrocycle_hydrate.pdbqt"
preparator.write_pdbqt_file(output_pdbqt_file)
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