Metadata-Version: 2.4
Name: meeko
Version: 0.7.1
Summary: Python package for preparing small molecule for docking
Home-page: https://github.com/forlilab/meeko
Author: Forli Lab
Author-email: forli@scripps.edu
License: LGPL-2.1
Keywords: molecular modeling,drug design,docking,autodock
Classifier: Environment :: Console
Classifier: Environment :: Other Environment
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: OS Independent
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: C++
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Software Development :: Libraries
Description-Content-Type: text/markdown
License-File: LICENSE
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: keywords
Dynamic: license
Dynamic: license-file
Dynamic: summary

# 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=release)](https://meeko.readthedocs.io/en/release/?badge=release)

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/).


## Documentation

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


## 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 meeko
```

or from PyPI:

```bash
pip install 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/en/release) 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
```
