Python package for preparing small molecule for docking
Project description
Meeko: preparation of small molecules for AutoDock
Meeko reads an RDKit molecule object and writes a PDBQT string (or file) for AutoDock-Vina and AutoDock-GPU. Additionally, it has tools for post-processing of docking results which are not yet fully developed. Meeko supports the following features:
- Docking with explicit water molecules attached to the ligand (paper)
- Sampling of macrocyclic conformations during docking (paper)
- Creation of RDKit molecules with docked coordinates from PDBQT or DLG files without loss of bond orders.
Meeko is developed by the Forli lab at the Center for Computational Structural Biology (CCSB) at Scripps Research.
Dependencies
- Python (>=3.5)
- Numpy
- Scipy
- RDKit
Conda or Miniconda can install the dependencies:
conda install -c conda-forge numpy scipy rdkit
Installation (from PyPI)
$ pip install meeko
If using conda, pip
installs the package in the active environment.
Installation (from source)
$ git clone https://github.com/forlilab/Meeko
$ cd Meeko
$ pip install .
Optionally include --editable
. Changes in the original package location
take effect immediately without the need to run pip install .
again.
$ pip install --editable .
Examples using the command line scripts
mk_prepare_ligand.py -i molecule.sdf -o molecule.pdbqt
mk_prepare_ligand.py -i multi_mol.sdf --multimol_outdir folder_for_pdbqt_files
mk_copy_coords.py vina_results.pdbqt -o vina_results.sdf
mk_copy_coords.py adgpu_results.dlg -o adgpu_results.sdf
Quick Python tutorial
1. flexible macrocycle with attached waters
from meeko import MoleculePreparation
from rdkit import Chem
input_molecule_file = 'example/BACE_macrocycle/BACE_4.mol2'
mol = Chem.MolFromMol2File(input_molecule_file)
preparator = MoleculePreparation(macrocycle=True, hydrate=True)
preparator.prepare(mol)
preparator.show_setup()
output_pdbqt_file = "test_macrocycle_hydrate.pdbqt"
preparator.write_pdbqt_file(output_pdbqt_file)
2. RDKit molecule from docking results
Assuming that 'docked.dlg' was written by AutoDock-GPU and that Meeko prepared the input ligands.
from meeko import PDBQTMolecule
with open("docked.dlg") as f:
dlg_string = f.read()
pdbqt_mol = PDBQTMolecule(dlg_string, is_dlg=True, skip_typing=True)
# alternatively, read the .dlg file directly
pdbqt_mol = PDBQTMolecule.from_file("docked.dlg", is_dlg=True, skip_typing=True)
for pose in pdbqt_mol:
rdkit_mol = pose.export_rdkit_mol()
For Vina's output PDBQT files, omit is_dlg=True
.
pdbqt_mol = PDBQTMolecule.from_file("docking_results_from_vina.pdbqt", skip_typing=True)
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