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Meeko

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Interface for AutoDock, molecule parameterization

// repository documentation

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# Meeko: interface for AutoDock

[![API stability](https://img.shields.io/badge/stable%20API-no-orange)](https://shields.io/)
[![PyPI version fury.io](https://img.shields.io/badge/version-0.7.1-green.svg)](https://pypi.python.org/pypi/meeko/)
[![Documentation Status](https://readthedocs.org/projects/meeko/badge/?version=develop)](https://meeko.readthedocs.io)

Meeko prepares the input for AutoDock and processes its output.
It is developed alongside AutoDock-GPU and AutoDock-Vina.
Meeko parameterizes both small organic molecules (ligands) and proteins
and nucleic acids (receptors).

Meeko is developed by the [Forli lab](https://forlilab.org/) at the
[Center for Computational Structural Biology (CCSB)](https://ccsb.scripps.edu)
at [Scripps Research](https://www.scripps.edu/).

If you use this, please cite: ["Meeko: molecule parameterization and software interoperability for docking and beyond"](https://pubs.acs.org/doi/full/10.1021/acs.jcim.5c02271)

## Documentation

The docs are hosted on [meeko.readthedocs.io](https://meeko.readthedocs.io)

## Reporting bugs

Please check if a similar bug has been reported and, if not, [open an issue](https://github.com/forlilab/Meeko/issues).

## Installation

Visit the docs for a more complete description. One option is conda or mamba:

```bash
micromamba install -c conda-forge meeko
```

or from PyPI:

```bash
pip install meeko
```

to install the latest version (`develop` branch), which is likely newer than latest release:

```bash
pip install git+https://github.com/forlilab/meeko
```

## Usage

Meeko exposes a Python API to enable scripting. Here we share very minimal examples
using the command line scripts just to give context.
Please visit the [meeko.readthedocs.io](https://meeko.readthedocs.io) for more information.

Parameterizing a ligand and writing a PDBQT file:
```bash
mk_prepare_ligand.py -i molecule.sdf -o molecule.pdbqt
```

Parameterizing a receptor with a flexible sidechain and writing a PDBQT file
as well as a JSON file that stores the entire receptor datastructure. In this
example, the `-o` option sets the output base name, `-j` triggers writing the
.json file, `-p` triggers writting the .pdbqt file, and `-f` makes residue
42 in chain A flexible.

```bash
mk_prepare_receptor.py -i nucleic_acid.cif -o my_receptor -j -p -f A:42
```

Finally, converting docking results to SDF for the ligand, and PDB for the
receptor with updated sidechain positions:

```bash
mk_export.py vina_results.pdbqt -j my_receptor.json -s lig_docked.sdf -p rec_docked.pdb
```

Meeko

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