meeko 0.1.dev2

Python package for preparing small molecule for docking

Meeko

The Python package meeko is a new type of package developped in 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

$ 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, amide_rigid=True)
preparator.prepare(mol)
preparator.show_setup()

output_pdbqt_file = "test_macrocycle_hydrate.pdbqt"
preparator.write_pdbqt_file(output_pdbqt_file)