Skip to main content

Python package for preparing small molecule for docking

Project description

Meeko

License PyPI version fury.io

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)

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for meeko, version 0.1.dev3
Filename, size File type Python version Upload date Hashes
Filename, size meeko-0.1.dev3-py2.py3-none-any.whl (45.4 kB) File type Wheel Python version py2.py3 Upload date Hashes View
Filename, size meeko-0.1.dev3.tar.gz (30.9 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page