meeko

library0.7.1pypypiunverified

Meeko is a Python package for preparing small molecules for docking with AutoDock Vina and other docking programs. It converts RDKit mol objects to PDBQT format, handling protonation, tautomers, and flexible rotatable bonds. Current version is 0.7.1, with irregular release cadence.

ai-ml

pip install meeko

github ↗package ↗

INSTALL

IMPORT

SIG · MEEKO

meeko

ai-mlpythonv0.7.1

Install

1.6s avg

Import

—

Disk

19MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v0.7.1 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

installs and imports cleanly · install 0.0s · import 0.000s · 20.4MB

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 1.6s · import 0.000s · 21MB

19MB installed

● package 19MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

MoleculePreparation

✓ from meeko import MoleculePreparation

✗ from meeko import MoleculePreparation

Prepare a small molecule and output PDBQT string.

from rdkit import Chem from meeko import MoleculePreparation, RDKitMoleculeCreate mol = Chem.MolFromSmiles('Cc1ccccc1') preparator = MoleculePreparation() setup_list = preparator.prepare(mol) pdbqt_string = setup_list[0].write_pdbqt_string() print(pdbqt_string[:200])

Debug

Known issues

breakingIn v0.6.0, class LinkedRDKitChorizo was renamed to Polymer, and ChorizoResidue to Monomer. Old imports will break.

fix

Use from meeko import Polymer, Monomer

affects: >=0.6.0

deprecatedOpenBabel support was dropped in v0.6.0. Templates based on OpenBabel no longer work.

fix

Switch to RDKit-based methods. Remove openbabel dependency.

affects: >=0.6.0

gotchaThe MoleculePreparation.prepare() method returns a list of MoleculeSetup objects, not a single object. Iterate or index the list.

fix

setup = preparator.prepare(mol)[0]

affects: all

deprecatedThe mk_export.py script from older versions is removed. Use the Python API or CLI meeko_prepare.py.

fix

Use meeko_prepare or the Python API directly.

affects: >=0.6.0

Upgrade

Version history

0.7.1latest on PyPI · released Oct 23, 2025

Audit

Dependencies

rdkitrequiredCore dependency for molecule handling

numpyrequiredNumerical operations

openbabeloptionalOnly if using legacy openbabel templates (deprecated)

Agent activity

23 hits · last 30 days

node

Resources

githubhttps://github.com/forlilab/meeko ↗

packagehttps://pypi.org/project/meeko/ ↗